Biochemistry, Genetics and Molecular Biology › Molecular Biology

Plant and Fungal Species Descriptions

Works Count: 43503

Wikipedia

Description

This cluster of papers focuses on the molecular systematics, phylogenetic reconstruction, and species diversification within the Gesneriaceae family and its allies. It includes studies on karst flora, conservation priorities, endemic flora, taxonomic treatments, biogeography, and plant evolution.

Keywords

Gesneriaceae; phylogenetic reconstruction; molecular systematics; species diversification; karst flora; conservation priorities; endemic flora; taxonomic treatments; biogeography; plant evolution

Plastid Genomes of Seed Plants

2012-01-01

Robert K. Jansen , Tracey A. Ruhlman

A new subfamilial and tribal classification of the pantropical flowering plant family Annonaceae informed by molecular phylogenetics

2012-04-18

Lars W. Chatrou , Michael D. Pirie , Roy H.J. Erkens +7 more

The pantropical flowering plant family Annonaceae is the most species-rich family of Magnoliales. Despite long-standing interest in the systematics of Annonaceae, no authoritative classification has yet been published in the … The pantropical flowering plant family Annonaceae is the most species-rich family of Magnoliales. Despite long-standing interest in the systematics of Annonaceae, no authoritative classification has yet been published in the light of recent molecular phylogenetic analyses. Here, using the largest, most representative, molecular dataset compiled on Annonaceae to date, we present, for the first time, a robust family-wide phylogenetic tree and subsequent classification. We used a supermatrix of up to eight plastid markers sequenced from 193 ingroup and seven outgroup species. Some of the relationships at lower taxonomic levels are poorly resolved, but deeper nodes generally receive high support. Annonaceae comprises four major clades, which are here given the taxonomic rank of subfamily. The description of Annonoideae is amended, and three new subfamilies are described: Anaxagoreoideae, Ambavioideae and Malmeoideae. In Annonoideae, seven tribes are recognized, one of which, Duguetieae, is described as new. In Malmeoideae, seven tribes are recognized, six of which are newly described: Dendrokingstonieae, Fenerivieae, Maasieae, Malmeeae, Monocarpieae and Piptostigmateae. This new subfamilial and tribal classification is discussed against the background of previous classifications and characters to recognize subfamilies are reviewed.

View PDF Chat

Flora of Java (spermatophytes only)

1963-01-01

C. A. Backer , R. C. Bakhuizen van den Brink

The Morphology of the Tunicata, and its bearings on the Phylogeny of the Chordata

1928-08-01

Walter Garstang

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

2015-08-03

Stephen A. Smith , Michael J. Moore , Joseph W. Brown +1 more

The use of transcriptomic and genomic datasets for phylogenetic reconstruction has become increasingly common as researchers attempt to resolve recalcitrant nodes with increasing amounts of data. The large size and … The use of transcriptomic and genomic datasets for phylogenetic reconstruction has become increasingly common as researchers attempt to resolve recalcitrant nodes with increasing amounts of data. The large size and complexity of these datasets introduce significant phylogenetic noise and conflict into subsequent analyses. The sources of conflict may include hybridization, incomplete lineage sorting, or horizontal gene transfer, and may vary across the phylogeny. For phylogenetic analysis, this noise and conflict has been accommodated in one of several ways: by binning gene regions into subsets to isolate consistent phylogenetic signal; by using gene-tree methods for reconstruction, where conflict is presumed to be explained by incomplete lineage sorting (ILS); or through concatenation, where noise is presumed to be the dominant source of conflict. The results provided herein emphasize that analysis of individual homologous gene regions can greatly improve our understanding of the underlying conflict within these datasets. Here we examined two published transcriptomic datasets, the angiosperm group Caryophyllales and the aculeate Hymenoptera, for the presence of conflict, concordance, and gene duplications in individual homologs across the phylogeny. We found significant conflict throughout the phylogeny in both datasets and in particular along the backbone. While some nodes in each phylogeny showed patterns of conflict similar to what might be expected with ILS alone, the backbone nodes also exhibited low levels of phylogenetic signal. In addition, certain nodes, especially in the Caryophyllales, had highly elevated levels of strongly supported conflict that cannot be explained by ILS alone. This study demonstrates that phylogenetic signal is highly variable in phylogenomic data sampled across related species and poses challenges when conducting species tree analyses on large genomic and transcriptomic datasets. Further insight into the conflict and processes underlying these complex datasets is necessary to improve and develop adequate models for sequence analysis and downstream applications. To aid this effort, we developed the open source software phyparts ( https://bitbucket.org/blackrim/phyparts ), which calculates unique, conflicting, and concordant bipartitions, maps gene duplications, and outputs summary statistics such as internode certainy (ICA) scores and node-specific counts of gene duplications.

View PDF Chat

A subfamilial classification for the expanded asparagalean families Amaryllidaceae, Asparagaceae and Xanthorrhoeaceae

2009-10-01

Mark W. Chase , James L. Reveal , Michael F. Fay

We provide here a subfamilial scheme for the expanded asparagalean families Amaryllidaceae, Asparagaceae and Xanthorrhoeaceae. Our recommendation is that the first family has three subfamilies (Agapanthoideae, Allioideae and Amaryllidoideae), the … We provide here a subfamilial scheme for the expanded asparagalean families Amaryllidaceae, Asparagaceae and Xanthorrhoeaceae. Our recommendation is that the first family has three subfamilies (Agapanthoideae, Allioideae and Amaryllidoideae), the second has seven (Agavoideae, Aphyllanthoideae, Asparagoideae, Brodiaeoideae, Lomandroideae, Nolinoideae and Scilloideae) and the last has three (Asphodeloideae, Hemerocallidoideae and Xanthorrhoeoideae). Tribal names are provided for the large subfamilies Allioideae, Amaryllidoideae and Scilloideae. The use of these subfamily names permits easier descriptions of characters by specialists for these well-supported subclades, but the use of the broader family limits greatly simplifies the taxonomy of Asparagales and thus makes the teaching of these families much easier. A new subfamilial name, Xanthorrhoeoideae, and a new tribal name, Oziroëeae, are proposed.

View PDF Chat

The largest eukaryotic genome of them all?

2010-09-15

Jaume Pellicer , Michael F. Fay , Ilia J. Leitch

We report the largest eukaryotic genome to date in the monocot Paris japonica (Melanthiaceae, 1C = 152.23 pg), measured using flow cytometry. This value is 15% larger than any previous … We report the largest eukaryotic genome to date in the monocot Paris japonica (Melanthiaceae, 1C = 152.23 pg), measured using flow cytometry. This value is 15% larger than any previous estimate and extends the range of genome sizes to c. 2400-fold across angiosperms and c. 66 000-fold across eukaryotes. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 164, 10–15.

Barcoding the kingdom Plantae: new <scp>PCR</scp> primers for <scp>ITS</scp> regions of plants with improved universality and specificity

2015-06-18

Tao Cheng , Chao Xu , Lei Li +3 more

The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended … The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. Despite this popularity, the universality and specificity of PCR primers for the ITS region are not satisfactory, resulting in amplification and sequencing difficulties. By thoroughly surveying and analysing the 18S, 5.8S and 26S sequences of Plantae and Fungi from GenBank, we designed new universal and plant-specific PCR primers for amplifying the whole ITS region and a part of it (ITS1 or ITS2) of plants. In silico analyses of the new and the existing ITS primers based on these highly representative data sets indicated that (i) the newly designed universal primers are suitable for over 95% of plants in most groups; and (ii) the plant-specific primers are suitable for over 85% of plants in most groups without amplification of fungi. A total of 335 samples from 219 angiosperm families, 11 gymnosperm families, 24 fern and lycophyte families, 16 moss families and 17 fungus families were used to test the performances of these primers. In vitro PCR produced similar results to those from the in silico analyses. Our new primer pairs gave PCR improvements up to 30% compared with common-used ones. The new universal ITS primers will find wide application in both plant and fungal biology, and the new plant-specific ITS primers will, by eliminating PCR amplification of nonplant templates, significantly improve the quality of ITS sequence information collections in plant molecular systematics and DNA barcoding.

Relevance of the Equilibrium Theory of Island Biogeography and Species-Area Relations to Conservation with a Case from Amazonia

1986-03-01

Barbara L. Zimmerman , Richard O. Bierregaard

Stable URL:http://links.jstor.org/sici?sici=0305-0270%28198603%2913%3A2%3C133%3AROTETO%3E2.0.CO%3B2-YJournal of Biogeography is currently published by Blackwell Publishing.Your use of the JSTOR archive indicates your acceptance of JSTOR's Terms and Conditions of Use, available athttp://www.jstor.org/about/terms.html. JSTOR's Terms and … Stable URL:http://links.jstor.org/sici?sici=0305-0270%28198603%2913%3A2%3C133%3AROTETO%3E2.0.CO%3B2-YJournal of Biogeography is currently published by Blackwell Publishing.Your use of the JSTOR archive indicates your acceptance of JSTOR's Terms and Conditions of Use, available athttp://www.jstor.org/about/terms.html. JSTOR's Terms and Conditions of Use provides, in part, that unless you have obtainedprior permission, you may not download an entire issue of a journal or multiple copies of articles, and you may use content inthe JSTOR archive only for your personal, non-commercial use.Please contact the publisher regarding any further use of this work. Publisher contact information may be obtained athttp://www.jstor.org/journals/black.html.Each copy of any part of a JSTOR transmission must contain the same copyright notice that appears on the screen or printedpage of such transmission.JSTOR is an independent not-for-profit organization dedicated to and preserving a digital archive of scholarly journals. Formore information regarding JSTOR, please contact [email protected]://www.jstor.orgMon May 7 11:39:03 2007

Vicariance and dispersal in the alpine perennial Bupleurum stellatum L. (Apiaceae)

2005-08-01

Peter Schönswetter , Andreas Tribsch

Abstract Using Amplified Fragment Length Polymorphism (AFLP), we explored the intraspecific phylogeography of the alpine vascular plant Bupleurum stellatum (Apiaceae), disjunctly distributed in the Alps and Corsica. Within the Alps, … Abstract Using Amplified Fragment Length Polymorphism (AFLP), we explored the intraspecific phylogeography of the alpine vascular plant Bupleurum stellatum (Apiaceae), disjunctly distributed in the Alps and Corsica. Within the Alps, the species' distribution area is also not contiguous, spatially isolated groups of populations occuring in the Dolomites (Italy) and the Montafon (Austria). A main goal of our study was to explore the degree of differentiation of the isolated populations in Corsica, the Dolomites and the Montafon from the populations in the main distributional area and to test for hypotheses of vicariance or dispersal. We also sought a better general knowledge of glacial refugia of low alpine silicicolous plants. Phenetic as well as cladistic analyses of the AFLP multilocus phenotypes reveal a substantial north‐south split through the contiguous distribution area of B . stellatum in the Alps. The resulting phylogeographic groups can be related to glacial refugia in peripheral areas of the Alps that were recognised in previous studies. The disjunct populations in Corsica, the Dolomites and the Montafon, however, are less strongly differentiated. For example, the Corsican population clustered with high bootstrap support with populations from the Eastern Alps, suggesting immigration to Corsica from that region. Our study shows that deep phylogeographic splits resulting from old vicariance events can be concealed by presently contiguous distribution areas. In contrast, disjunctions, if they are due to dispersal events, need not be accompanied by genetic divergence.

Thirteen Camelliachloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships

2014-07-07

Hui Huang , Chao Shi , Yuan Liu +2 more

Camellia is an economically and phylogenetically important genus in the family Theaceae. Owing to numerous hybridization and polyploidization, it is taxonomically and phylogenetically ranked as one of the most challengingly … Camellia is an economically and phylogenetically important genus in the family Theaceae. Owing to numerous hybridization and polyploidization, it is taxonomically and phylogenetically ranked as one of the most challengingly difficult taxa in plants. Sequence comparisons of chloroplast (cp) genomes are of great interest to provide a robust evidence for taxonomic studies, species identification and understanding mechanisms that underlie the evolution of the Camellia species. The eight complete cp genomes and five draft cp genome sequences of Camellia species were determined using Illumina sequencing technology via a combined strategy of de novo and reference-guided assembly. The Camellia cp genomes exhibited typical circular structure that was rather conserved in genomic structure and the synteny of gene order. Differences of repeat sequences, simple sequence repeats, indels and substitutions were further examined among five complete cp genomes, representing a wide phylogenetic diversity in the genus. A total of fifteen molecular markers were identified with more than 1.5% sequence divergence that may be useful for further phylogenetic analysis and species identification of Camellia. Our results showed that, rather than functional constrains, it is the regional constraints that strongly affect sequence evolution of the cp genomes. In a substantial improvement over prior studies, evolutionary relationships of the section Thea were determined on basis of phylogenomic analyses of cp genome sequences. Despite a high degree of conservation between the Camellia cp genomes, sequence variation among species could still be detected, representing a wide phylogenetic diversity in the genus. Furthermore, phylogenomic analysis was conducted using 18 complete cp genomes and 5 draft cp genome sequences of Camellia species. Our results support Chang's taxonomical treatment that C. pubicosta may be classified into sect. Thea, and indicate that taxonomical value of the number of ovaries should be reconsidered when classifying the Camellia species. The availability of these cp genomes provides valuable genetic information for accurately identifying species, clarifying taxonomy and reconstructing the phylogeny of the genus Camellia.

View PDF Chat

Land plants and DNA barcodes: short-term and long-term goals

2005-09-12

Mark W. Chase , Nicolas Salamin , M. J. Wilkinson +4 more

Land plants have had the reputation of being problematic for DNA barcoding for two general reasons: (i) the standard DNA regions used in algae, animals and fungi have exceedingly low … Land plants have had the reputation of being problematic for DNA barcoding for two general reasons: (i) the standard DNA regions used in algae, animals and fungi have exceedingly low levels of variability and (ii) the typically used land plant plastid phylogenetic markers (e.g. rbcL , trnL-F , etc.) appear to have too little variation. However, no one has assessed how well current phylogenetic resources might work in the context of identification (versus phylogeny reconstruction). In this paper, we make such an assessment, particularly with two of the markers commonly sequenced in land plant phylogenetic studies, plastid rbcL and internal transcribed spacers of the large subunits of nuclear ribosomal DNA (ITS), and find that both of these DNA regions perform well even though the data currently available in GenBank/EBI were not produced to be used as barcodes and BLAST searches are not an ideal tool for this purpose. These results bode well for the use of even more variable regions of plastid DNA (such as, for example, psbA-trnH ) as barcodes, once they have been widely sequenced. In the short term, efforts to bring land plant barcoding up to the standards being used now in other organisms should make swift progress. There are two categories of DNA barcode users, scientists in fields other than taxonomy and taxonomists. For the former, the use of mitochondrial and plastid DNA, the two most easily assessed genomes, is at least in the short term a useful tool that permits them to get on with their studies, which depend on knowing roughly which species or species groups they are dealing with, but these same DNA regions have important drawbacks for use in taxonomic studies (i.e. studies designed to elucidate species limits). For these purposes, DNA markers from uniparentally (usually maternally) inherited genomes can only provide half of the story required to improve taxonomic standards being used in DNA barcoding. In the long term, we will need to develop more sophisticated barcoding tools, which would be multiple, low-copy nuclear markers with sufficient genetic variability and PCR-reliability; these would permit the detection of hybrids and permit researchers to identify the ‘genetic gaps’ that are useful in assessing species limits.

View PDF Chat

Phylogenetics of asterids based on 3 coding and 3 non-coding chloroplast DNA markers and the utility of non-coding DNA at higher taxonomic levels

2002-08-01

Birgitta Bremer , Kåre Bremer , Nahid Heidari +5 more

Phylogeny and classification of Ranunculales: Evidence from four molecular loci and morphological data

2009-01-01

Wei Wang , An‐Ming Lu , Yi Ren +2 more

ycf1, the most promising plastid DNA barcode of land plants

2015-02-12

Wenpan Dong , Chao Xu , Changhao Li +6 more

Abstract A DNA barcode is a DNA fragment used to identify species. For land plants, DNA fragments of plastid genome could be the primary consideration. Unfortunately, most of the plastid … Abstract A DNA barcode is a DNA fragment used to identify species. For land plants, DNA fragments of plastid genome could be the primary consideration. Unfortunately, most of the plastid candidate barcodes lack species-level resolution. The identification of DNA barcodes of high resolution at species level is critical to the success of DNA barcoding in plants. We searched the available plastid genomes for the most variable regions and tested the best candidates using both a large number of tree species and seven well-sampled plant groups. Two regions of the plastid gene ycf1 , ycf1 a and ycf1 b, were the most variable loci that were better than existing plastid candidate barcodes and can serve as a barcode of land plants. Primers were designed for the amplification of these regions and the PCR success of these primers ranged from 82.80% to 98.17%. Of 420 tree species, 357 species could be distinguished using ycf1 b, which was slightly better than the combination of matK and rbcL . For the well-sampled representative plant groups, ycf1 b generally performed better than any of the matK , rbcL and trnH-psbA . We concluded that ycf1 a or ycf1 b is the most variable plastid genome region and can serve as a core barcode of land plants.

View PDF Chat

Phylogenetic Inference in Saxifragaceae Sensu Stricto and Gilia (Polemoniaceae) Using matK Sequences

1995-01-01

Leigh A. Johnson , Pamela S. Soltis

matK SEQUENCES'the [iast decade.These approaches have pro-, en extremely useful in addressing a broad range of -\stematic and e\ olntionarv questions at all levels ill laxuniimic hierarchy.Of these approaches, comparative … matK SEQUENCES'the [iast decade.These approaches have pro-, en extremely useful in addressing a broad range of -\stematic and e\ olntionarv questions at all levels ill laxuniimic hierarchy.Of these approaches, comparative sequencing of chloroplast, as well as nu clear, genes has become particularly popular in recent years, due in large part to the relative ease of generating sequences and the unamhigml\ <>l the data.The large number ul recent systematic -indies employing sequencing "I the chlompla-t gene rbcL attests to the enormous phylogenetic potential of comparative sequem ing (e.

Molecular evolution and phylogenetic implications of internal transcribed spacer sequences of Ribosomal DNA in Winteraceae

1993-09-01

Youngbae Suh , Leonard B. Thien , Helena E. Reeve +1 more

The internal transcribed spacers and the 5.8S coding region of nuclear ribosomal DNA were sequenced and analyzed to address questions of generic relationships in Winteraceae. The molecular data generated a … The internal transcribed spacers and the 5.8S coding region of nuclear ribosomal DNA were sequenced and analyzed to address questions of generic relationships in Winteraceae. The molecular data generated a single tree that is congruent with one based on morphological data. The sequences of ITS 1 in the family range from 235 to 252 bases in size and of ITS 2 from 213 to 226 bases. The size of the 5.8S coding region is 164 bases. The range of ITS 1 and ITS 2 sequence divergence between pairs of genera within Winteraceae is relatively low in comparison to other plant families. Two types of ITS 1 and ITS 2 sequences were observed in the same individual for some taxa. Sequence variations between the two arrays are 4.7%–6.3% for ITS 1 and 5.1%–7.0% for ITS 2. Both arrays of sequences, however, generate the same phylogenetic relationships. Rates of nucleotide substitutions for the internal transcribed spacers are 3.2–5.2 × 10 ‐10 substitution per site per year estimated in ITS 1 and 3.6–5.7 × 10 ‐10 in ITS 2.

Noncoding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms

2003-06-18

Thomas Borsch , Khidir W. Hilu , Dietmar Quandt +3 more

Abstract Recent contributions from DNA sequences have revolutionized our concept of systematic relationships in angiosperms. However, parts of the angiosperm tree remain unclear. Previous studies have been based on coding … Abstract Recent contributions from DNA sequences have revolutionized our concept of systematic relationships in angiosperms. However, parts of the angiosperm tree remain unclear. Previous studies have been based on coding or rDNA regions of relatively conserved genes. A phylogeny for basal angiosperms based on noncoding, fast-evolving sequences of the chloroplast genome region trnT-trnF is presented. The recognition of simple direct repeats allowed a robust alignment. Mutational hot spots appear to be confined to certain sectors, as in two stem-loop regions of the trnL intron secondary structure. Our highly resolved and well-supported phylogeny depicts the New Caledonian Amborella as the sister to all other angiosperms, followed by Nymphaeaceae and an Austrobaileya–Illicium–Schisandra clade. Ceratophyllum is substantiated as a close relative of monocots, as is a monophyletic eumagnoliid clade consisting of Piperales plus Winterales sister to Laurales plus Magnoliales. Possible reasons for the striking congruence between the trnT-trnF based phylogeny and phylogenies generated from combined multi-gene, multi-genome data are discussed.

View PDF Chat

matK DNA Sequences and Phylogenetic Reconstruction in Saxifragaceae s. str.

1994-01-01

Leigh A. Johnson , Pamela S. Soltis

Comparative DNA sequencing of matK, a maturase coding gene located within the intron of the chloroplast gene trnK, was evaluated for phylogenetic utility using genera of Saxi- fragaceae s. str. … Comparative DNA sequencing of matK, a maturase coding gene located within the intron of the chloroplast gene trnK, was evaluated for phylogenetic utility using genera of Saxi- fragaceae s. str. The entire matK gene was sequenced for two members of the family, Sullivantia sullivantii and Saxifraga integrifolia. Comparison of base substitution rates between these two species indicated that matK evolves approximately three-fold faster than rbcL. Comparative sequencing of 754 base pairs within matK was subsequently conducted using 25 genera in Saxifragaceae s. str. and two outgroup taxa. Summed over the 31 taxa sequenced for this 754 base pair region, 40% of the base positions were variable and 15.6% were potentially informative. Five insertion/deletion events of three or six base pairs were also detected. Skewness and randomization tests both suggest that significant non-random structure is present in the matK data set. Parsimony analyses provided 72 most parsimonious trees of 223 steps (excluding autapomorphies) with a consistency index of 0.565. Several well-supported groups of genera are highly concordant with relationships suggested by two other chloroplast DNA data sets: chloroplast DNA restriction sites and rbcL sequences.

Phylogenetic Analyses of Polemoniaceae Using Nucleotide Sequences of the Plastid Gene matK

1994-01-01

Kelly P. Steele , Rytas Vilgalys

Nucleotide sequences of the plastid encoded gene matK were examined for their potential utility in phylogenetic analyses within angiosperm families. Sequences 661 bases in length were obtained from twenty species … Nucleotide sequences of the plastid encoded gene matK were examined for their potential utility in phylogenetic analyses within angiosperm families. Sequences 661 bases in length were obtained from twenty species of Polemoniaceae. Phylogenetic analyses resulted in four equally parsimonious trees with a consistency index of 0.70. Several well supported groups allowed us to test hypotheses of relationship within Polemoniaceae. The segregation of Ipomopsis and Allophyllum from Gilia was supported by the placement of each in distinct groups separate from a group of four species of Gilia. Several strongly supported groups include genera now placed in different tribes. There was no support for the current separation of temperate Polemoniaceae into two tribes. The tropical genera were resolved as basal and paraphyletic within the family. The family as a whole was monophyletic with no support for the segregate family Cobaeaceae. Sequences of matK, a gene that had not been used previously for phylogenetic analyses, provided a sufficient number of reliable characters for phylogenetic analysis within Polemoniaceae. Pairwise comparisons of matK and rbcL sequences of the same taxa were performed. Sequences of matK varied at an overall rate twice that of rbcL sequences. Substitutions at the third codon position predominated in rbcL sequences, while in matK substitutions were more evenly distributed across codon positions.

a molecular phylogeny of apiaceae subfamily Apioideae: evidence from nuclear ribosomal DNA internal transcribed spacer sequences

1996-02-01

Stephen R. Downie , Deborah S. Katz‐Downie

Phylogenetic relationships among 40 New World and Old World members of Apiaceae subfamily Apioideae, representing seven of the eight tribes and eight of the ten subtribes commonly recognized in the … Phylogenetic relationships among 40 New World and Old World members of Apiaceae subfamily Apioideae, representing seven of the eight tribes and eight of the ten subtribes commonly recognized in the subfamily, were inferred from nucleotide sequence variation in the internal transcribed spacer (ITS) regions of 18‐26S nuclear ribosomal DNA. Although the sequences are alignable, with only 11% of sites excluded from the analyses because of alignment ambiguity, divergence values in pairwise comparisons of unambiguous positions among all taxa were high and ranged from 0.5 to 33.2% of nucleotides in ITS 1 and from 0 to 33.2% of nucleotides in ITS 2. Average sequence divergence across both spacer regions was 18.4% of nucleotides. Phylogenies derived from ITS sequences estimated using neighbor‐joining analysis of substitution rates, and maximum likelihood and parsimony methods give trees of essentially similar topology and indicate that: (1) there is little support for any existing system of classification of the subfamily that is based largely on morphological and anatomical features of the mericarp; (2) there is a major phylogenetic division within the subfamily, with one clade comprising the genus Smyrnium and those taxa belonging to Drude's tribes Dauceae, Scandiceae, and Laserpitieae and the other clade comprising all other examined taxa; and (3) the genera Arracacia, Coaxana, Coulterophytum, Enantiophylla, Myrrhidendron, Prionosciadium , and Rhodosciadium , all endemic to Mexico and Central America, comprise a clade but their relationships to other New World taxa are equivocal. A phylogeny derived from parsimony analysis of chloroplast DNA rpo C1 intron sequences is consistent with, but considerably less resolved than, relationships derived from these ITS regions. This study affirms that ITS sequences are useful for phylogenetic inference among closely related members of Apioideae but, owing to high rates of nucleotide substitution, are less useful in resolving relationships among the more ancestral nodes of the phylogeny.

Borneo and Indochina are Major Evolutionary Hotspots for Southeast Asian Biodiversity

2014-07-28

Mark de Bruyn , Björn Stelbrink , Robert J. Morley +7 more

Tropical Southeast (SE) Asia harbors extraordinary species richness and in its entirety comprises four of the Earth's 34 biodiversity hotspots. Here, we examine the assembly of the SE Asian biota … Tropical Southeast (SE) Asia harbors extraordinary species richness and in its entirety comprises four of the Earth's 34 biodiversity hotspots. Here, we examine the assembly of the SE Asian biota through time and space. We conduct meta-analyses of geological, climatic, and biological (including 61 phylogenetic) data sets to test which areas have been the sources of long-term biological diversity in SE Asia, particularly in the pre-Miocene, Miocene, and Plio-Pleistocene, and whether the respective biota have been dominated by in situ diversification, immigration and/or emigration, or equilibrium dynamics. We identify Borneo and Indochina, in particular, as major "evolutionary hotspots" for a diverse range of fauna and flora. Although most of the region's biodiversity is a result of both the accumulation of immigrants and in situ diversification, within-area diversification and subsequent emigration have been the predominant signals characterizing Indochina and Borneo's biota since at least the early Miocene. In contrast, colonization events are comparatively rare from younger volcanically active emergent islands such as Java, which show increased levels of immigration events. Few dispersal events were observed across the major biogeographic barrier of Wallace's Line. Accelerated efforts to conserve Borneo's flora and fauna in particular, currently housing the highest levels of SE Asian plant and mammal species richness, are critically required.

View PDF Chat

A review of long‐branch attraction

2005-04-01

Johannes Bergsten

Abstract The history of long‐branch attraction, and in particular methods suggested to detect and avoid the artifact to date, is reviewed. Methods suggested to avoid LBA‐artifacts include excluding long‐branch taxa, … Abstract The history of long‐branch attraction, and in particular methods suggested to detect and avoid the artifact to date, is reviewed. Methods suggested to avoid LBA‐artifacts include excluding long‐branch taxa, excluding faster evolving third codon positions, using inference methods less sensitive to LBA such as likelihood, the Aguinaldo et al. approach, sampling more taxa to break up long branches and sampling more characters especially of another kind, and the pros and cons of these are discussed. Methods suggested to detect LBA are numerous and include methodological disconcordance, RASA, separate partition analyses, parametric simulation, random outgroup sequences, long‐branch extraction, split decomposition and spectral analysis. Less than 10 years ago it was doubted if LBA occurred in real datasets. Today, examples are numerous in the literature and it is argued that the development of methods to deal with the problem is warranted. A 16 kbp dataset of placental mammals and a morphological and molecular combined dataset of gall waSPS are used to illustrate the particularly common problem of LBA of problematic ingroup taxa to outgroups. The preferred methods of separate partition analysis, methodological disconcordance, and long branch extraction are used to demonstrate detection methods. It is argued that since outgroup taxa almost always represent long branches and are as such a hazard towards misplacing long branched ingroup taxa, phylogenetic analyses should always be run with and without the outgroups included. This will detect whether only the outgroup roots the ingroup or if it simultaneously alters the ingroup topology, in which case previous studies have shown that the latter is most often the worse. Apart from that LBA to outgroups is the major and most common problem; scanning the literature also detected the ill advised comfort of high support values from thousands of characters, but very few taxa, in the age of genomics. Taxon sampling is crucial for an accurate phylogenetic estimate and trust cannot be put on whole mitochondrial or chloroplast genome studies with only a few taxa, despite their high support values. The placental mammal example demonstrates that parsimony analysis will be prone to LBA by the attraction of the tenrec to the distant marsupial outgroups. In addition, the murid rodents, creating the classic “the guinea‐pig is not a rodent” hypothesis in 1996, are also shown to be attracted to the outgroup by nuclear genes, although including the morphological evidence for rodents and Glires overcomes the artifact. The gall wasp example illustrates that Bayesian analyses with a partition‐specific GTR + Γ + I model give a conflicting resolution of clades, with a posterior probability of 1.0 when comparing ingroup alone versus outgroup rooted topologies, and this is due to long‐branch attraction to the outgroup. © The Willi Hennig Society 2005.

Testing candidate plant barcode regions in the Myristicaceae

2007-10-03

Steven G. Newmaster , Aron J. Fazekas , Royce Steeves +1 more

The concept and practice of DNA barcoding have been designed as a system to facilitate species identification and recognition. The primary challenge for barcoding plants has been to identify a … The concept and practice of DNA barcoding have been designed as a system to facilitate species identification and recognition. The primary challenge for barcoding plants has been to identify a suitable region on which to focus the effort. The slow relative nucleotide substitution rates of plant mitochondria and the technical issues with the use of nuclear regions have focused attention on several proposed regions in the plastid genome. One of the challenges for barcoding is to discriminate closely related or recently evolved species. The Myristicaceae, or nutmeg family, is an older group within the angiosperms that contains some recently evolved species providing a challenging test for barcoding plants. The goal of this study is to determine the relative utility of six coding (Universal Plastid Amplicon - UPA, rpoB, rpoc1, accD, rbcL, matK) and one noncoding (trnH-psbA) chloroplast loci for barcoding in the genus Compsoneura using both single region and multiregion approaches. Five of the regions we tested were predominantly invariant across species (UPA, rpoB, rpoC1, accD, rbcL). Two of the regions (matK and trnH-psbA) had significant variation and show promise for barcoding in nutmegs. We demonstrate that a two-gene approach utilizing a moderately variable region (matK) and a more variable region (trnH-psbA) provides resolution among all the Compsonuera species we sampled including the recently evolved C. sprucei and C. mexicana. Our classification analyses based on nonmetric multidimensional scaling ordination, suggest that the use of two regions results in a decreased range of intraspecific variation relative to the distribution of interspecific divergence with 95% of the samples correctly identified in a sequence identification analysis.

Taxon sampling effects in molecular clock dating: An example from the African Restionaceae

2005-01-26

H. P. Linder , Christopher R. Hardy , Frank Rutschmann

Radiation and diversification within the Ligularia–Cremanthodium–Parasenecio complex (Asteraceae) triggered by uplift of the Qinghai-Tibetan Plateau

2005-11-15

Jianquan Liu , Yujing Wang , Ai‐Lan Wang +2 more

Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms

2000-11-01

Sean W. Graham , Richard G. Olmstead

Sequences from 14 slowly evolving chloroplast genes (including three highly conserved introns) were obtained for representative basal angiosperm and seed-plant taxa, using novel primers described here. These data were combined … Sequences from 14 slowly evolving chloroplast genes (including three highly conserved introns) were obtained for representative basal angiosperm and seed-plant taxa, using novel primers described here. These data were combined with published sequences from atpB, rbcL, and newly obtained sequences from ndhF. Combined data from these 17 genes permit sturdy, well-resolved inference of major aspects of basal angiosperm relationships, demonstrating that the new primers are valuable tools for sorting out the deepest events in flowering plant phylogeny. Sequences from the inverted repeat (IR) proved to be particularly reliable (low homoplasy, high retention index). Representatives of Cabomba and Illicium were the first two successive branches of the angiosperms in an initial sampling of 19 exemplar taxa. This result was strongly supported by bootstrap analysis and by two small insertion/deletion events in the slowly evolving introns. Several paleoherb groups (representatives of Piperales) formed a strongly supported clade with taxa representing core woody magnoliids (Laurales, Magnoliales, and Winteraceae). The monophyly of the sampled eudicots and monocots was also well supported. Analyses of three major partitions of the data showed many of the same clades and supported the rooting seen with all the data combined. While Amborella trichopoda was supported as the sister group of the remaining angiosperms when we added Amborella and Nymphaea odorata to the analysis, a strongly conflicting rooting was observed when Amborella alone was added.

Malpighiales phylogenetics: Gaining ground on one of the most recalcitrant clades in the angiosperm tree of life

2009-08-01

Kenneth J. Wurdack , Charles C. Davis

The eudicot order Malpighiales contains ∼16000 species and is the most poorly resolved large rosid clade. To clarify phylogenetic relationships in the order, we used maximum likelihood, Bayesian, and parsimony … The eudicot order Malpighiales contains ∼16000 species and is the most poorly resolved large rosid clade. To clarify phylogenetic relationships in the order, we used maximum likelihood, Bayesian, and parsimony analyses of DNA sequence data from 13 gene regions, totaling 15604 bp, and representing all three genomic compartments (i.e., plastid: atpB, matK, ndhF, and rbcL; mitochondrial: ccmB, cob, matR, nad1B-C, nad6, and rps3; and nuclear: 18S rDNA, PHYC, and newly developed low-copy EMB2765). Our sampling of 190 taxa includes representatives from all families of Malpighiales. These data provide greatly increased support for the recent additions of Aneulophus, Bhesa, Centroplacus, Ploiarium, and Rafflesiaceae to Malpighiales; sister relations of Phyllanthaceae + Picrodendraceae, monophyly of Hypericaceae, and polyphyly of Clusiaceae. Oxalidales + Huaceae, followed by Celastrales are successive sisters to Malpighiales. Parasitic Rafflesiaceae, which produce the world's largest flowers, are confirmed as embedded within a paraphyletic Euphorbiaceae. Novel findings show a well-supported placement of Ctenolophonaceae with Erythroxylaceae + Rhizophoraceae, sister-group relationships of Bhesa + Centroplacus, and the exclusion of Medusandra from Malpighiales. New taxonomic circumscriptions include the addition of Bhesa to Centroplacaceae, Medusandra to Peridiscaceae (Saxifragales), Calophyllaceae applied to Clusiaceae subfamily Kielmeyeroideae, Peraceae applied to Euphorbiaceae subfamily Peroideae, and Huaceae included in Oxalidales.

Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae)

1997-08-01

Tao Sang , Daniel J. Crawford , Tod F. Stuessy

The coding region of the matK gene and two intergenic spacers, psb A‐ trn H and trn L(UAA)‐ trn F(GAA), of cpDNA were sequenced to study phylogenetic relationships of 32 … The coding region of the matK gene and two intergenic spacers, psb A‐ trn H and trn L(UAA)‐ trn F(GAA), of cpDNA were sequenced to study phylogenetic relationships of 32 Paeonia species. In the psbA‐ trn H intergenic spacer, short sequences bordered by long inverted repeats have undergone inversions that are often homoplasious mutations. Insertions/deletions found in the two intergenic spacers, mostly resulting from slipped‐strand mispairing, provided relatively reliable phylogenetic information. The matK coding region, evolving more rapidly than the trn L‐ trn F spacer and more slowly than the psbA‐trnH spacer, produced the best resolved phylogenetic tree. The matK phylogeny was compared with the phylogeny obtained from sequences of internal transcribed spacers (ITS) of nuclear ribosomal DNA. A refined hypothesis of species phylogeny of section Paeonia was proposed by considering the discordance between the nuclear and cpDNA phylogenies to be results of hybrid speciation followed by inheritance of cpDNA of one parent and fixation of ITS sequences of another parent. The Eurasian and western North American disjunct distribution of the genus may have resulted from interrruption of the continuous distribution of ancestral populations of extant peony species across the Bering land bridge during the Miocene. Pleistocene glaciation may have played an important role in triggering extensive reticulate evolution within section Paeonia and shifting distributional ranges of both parental and hybrid species.

Phylogenetic analyses of Begonia sect. Coelocentrum and allied limestone species of China shed light on the evolution of Sino-Vietnamese karst flora

2014-01-07

Kuo‐Fang Chung , Wai Yie Leong , Rosario Rivera Rubite +4 more

Abstract Background The picturesque limestone karsts across the Sino-Vietnamese border are renowned biodiversity hotspot, distinguished for extremely high endemism of calciphilous plants restricted to caves and cave-like microhabitats that have … Abstract Background The picturesque limestone karsts across the Sino-Vietnamese border are renowned biodiversity hotspot, distinguished for extremely high endemism of calciphilous plants restricted to caves and cave-like microhabitats that have functioned as biological refugia on the otherwise harsh habitats. To understand evolutionary mechanisms underlying the splendid limestone flora, dated phylogeny is reconstructed for Asian Begonia , a species-rich genus on limestone substrates represented by no less than 60 species in southern China, using DNA sequences of nrITS and chloroplast rpL16 intron. The sampling includes 94 Begonia species encompassing most major Asian clades with a special emphasized on Chinese species. Results Except for two tuberous deciduous species and a species with upright stems, a majority of Sino-Vietnamese limestone Begonia ( SVLB ), including sect. Coelocentrum (19 species sampled) and five species of sect. Diploclinium , Leprosae , and Petermannia , are rhizomatous and grouped in a strongly supported and yet internally poorly resolved clade (Clade SVLB ), suggesting a single evolutionary origin of the adaptation to limestone substrates by rhizomatous species, subsequent species radiation, and a strong tendency to retain their ancestral niche. Divergence-time estimates indicate a late Miocene diversification of Clade SVLB , coinciding with the onset of the East Asian monsoon and the period of extensive karstification in the area. Conclusions Based on our phylogenetic study, Begonia sect. Coelocentrum is recircumscribed and expanded to include other members of the Clade SVLB (sect. Diploclinium : B. cavaleriei , B. pulvinifera , and B. wangii ; sect. Leprosae : B. cylindrica and B. leprosa ; sect. Petermannia : B. sinofloribunda ). Because species of Clade SVLB have strong niche conservatism to retain in their ancestral habitats in cave-like microhabitats and Begonia are generally poor dispersers prone to diversify allopatrically, we propose that extensive and continuous karstification of the Sino-Vietnamese limestone region facilitated by the onset of East Asian monsoon since the late Miocene has been the major driving force for species accumulation via geographic isolation in Clade SVLB . Morphologically species of Clade SVLB differ mainly in vegetative traits without apparent adaptive value, suggesting that limestone Begonia radiation is better characterized as non-adaptive, an underappreciated speciation mode crucial for rapid species accumulations in organisms of low vagility and strong niche conservatism.

View PDF Chat

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function

2011-03-21

Susann Wicke , Gerald M. Schneeweiss , Claude W. dePamphilis +2 more

This review bridges functional and evolutionary aspects of plastid chromosome architecture in land plants and their putative ancestors. We provide an overview on the structure and composition of the plastid … This review bridges functional and evolutionary aspects of plastid chromosome architecture in land plants and their putative ancestors. We provide an overview on the structure and composition of the plastid genome of land plants as well as the functions of its genes in an explicit phylogenetic and evolutionary context. We will discuss the architecture of land plant plastid chromosomes, including gene content and synteny across land plants. Moreover, we will explore the functions and roles of plastid encoded genes in metabolism and their evolutionary importance regarding gene retention and conservation. We suggest that the slow mode at which the plastome typically evolves is likely to be influenced by a combination of different molecular mechanisms. These include the organization of plastid genes in operons, the usually uniparental mode of plastid inheritance, the activity of highly effective repair mechanisms as well as the rarity of plastid fusion. Nevertheless, structurally rearranged plastomes can be found in several unrelated lineages (e.g. ferns, Pinaceae, multiple angiosperm families). Rearrangements and gene losses seem to correlate with an unusual mode of plastid transmission, abundance of repeats, or a heterotrophic lifestyle (parasites or myco-heterotrophs). While only a few functional gene gains and more frequent gene losses have been inferred for land plants, the plastid Ndh complex is one example of multiple independent gene losses and will be discussed in detail. Patterns of ndh-gene loss and functional analyses indicate that these losses are usually found in plant groups with a certain degree of heterotrophy, might rendering plastid encoded Ndh1 subunits dispensable.

View PDF Chat

Age and rate of diversification of the Hawaiian silversword alliance (Compositae)

1998-08-04

Bruce G. Baldwin , Michael J. Sanderson

Comparisons between insular and continental radiations have been hindered by a lack of reliable estimates of absolute diversification rates in island lineages. We took advantage of rate-constant rDNA sequence evolution … Comparisons between insular and continental radiations have been hindered by a lack of reliable estimates of absolute diversification rates in island lineages. We took advantage of rate-constant rDNA sequence evolution and an "external" calibration using paleoclimatic and fossil data to determine the maximum age and minimum diversification rate of the Hawaiian silversword alliance (Compositae), a textbook example of insular adaptive radiation in plants. Our maximum-age estimate of 5.2 +/- 0.8 million years ago for the most recent common ancestor of the silversword alliance is much younger than ages calculated by other means for the Hawaiian drosophilids, lobelioids, and honeycreepers and falls approximately within the history of the modern high islands (</=5.1 +/- 0.2 million years ago). By using a statistically efficient estimator that reduces error variance by incorporating clock-based estimates of divergence times, a minimum diversification rate for the silversword alliance was estimated to be 0.56 +/- 0.17 species per million years. This exceeds average rates of more ancient continental radiations and is comparable to peak rates in taxa with sufficiently rich fossil records that changes in diversification rate can be reconstructed.

View PDF Chat

Disintegration of the Scrophulariaceae

2001-02-01

Richard G. Olmstead , Claude W. de Pamphilis , Andrea D. Wolfe +3 more

A molecular systematic study of Scrophulariaceae sensu lato using DNA sequences of three plastid genes (rbcL, ndhF, and rps2) revealed at least five distinct monophyletic groups. Thirty-nine genera representing 24 … A molecular systematic study of Scrophulariaceae sensu lato using DNA sequences of three plastid genes (rbcL, ndhF, and rps2) revealed at least five distinct monophyletic groups. Thirty-nine genera representing 24 tribes of the Scrophulariaceae s.l. (sensu lato) were analyzed along with representatives of 15 other families of Lamiales. The Scrophulariaceae s.s. (sensu stricto) include part or all of tribes Aptosimeae, Hemimerideae, Leucophylleae, Manuleae, Selagineae, and Verbasceae (= Scrophularieae) and the conventional families Buddlejaceae and Myoporaceae. Veronicaceae includes all or part of tribes Angelonieae, Antirrhineae, Cheloneae, Digitaleae, and Gratioleae and the conventional families Callitrichaceae, Globulariaceae, Hippuridaceae, and Plantaginaceae. The Orobanchaceae include tribes Buchnereae, Rhinantheae, and the conventional Orobanchaceae. All sampled members of Orobanchaceae are parasitic, except Lindenbergia, which is sister to the rest of the family. Family Calceolariaceae Olmstead is newly erected herein to recognize the phylogenetic distinctiveness of tribe Calceolarieae. The Calceolariaceae are close to the base of the Lamiales. The Stilbaceae are expanded by the inclusion of Halleria. Mimulus does not belong in any of these five groups.

Phylogeny of Basal Angiosperms: Analyses of Five Genes from Three Genomes

2000-11-01

Yin‐Long Qiu , Jung-Ho Lee , Fabiana Bernasconi‐Quadroni +6 more

DNA sequences of five mitochondrial, plastid, and nuclear genes from 105 species (103 genera and 63 families) representing all major lineages of gymnosperms and basal angiosperms were analyzed using parsimony … DNA sequences of five mitochondrial, plastid, and nuclear genes from 105 species (103 genera and 63 families) representing all major lineages of gymnosperms and basal angiosperms were analyzed using parsimony methods to reconstruct the phylogeny of basal angiosperms. The standard most parsimonious trees search, taxon deletion analyses, and constraint analyses in combination with Kishino‐Hasegawa tests provided a rigorous analytical perspective for identifying Amborella, Nymphaeales, and Illiciales‐Trimeniaceae‐Austrobaileya (ANITA) as the basalmost lineages of extant angiosperms. The parsimony criterion (equal weighting) favored the trees in which Amborella was sister to all other angiosperms, whereas the likelihood measure favored the trees in which the Amborella‐Nymphaeales clade represented the first diverging lineage of angiosperms. However, the Kishino‐Hasegawa test showed that these trees, as well as those in which Nymphaeales were sister to all other angiosperms, were not significantly different from each other. The clade of eumagnoliids, consisting of Winterales, Piperales, Magnoliales, and Laurales, was also consistently recovered in all of the analyses, albeit with low bootstrap support. Two genera of Gnetales, Gnetum and Welwitschia, did not form a sister group to angiosperms but fell into conifers with strong support. This result refutes the anthophyte hypothesis.

A Three-Gene Phylogeny of the Genus Solanum (Solanaceae)

2007-04-01

Terri L. Weese , Lynn Bohs

Solanum, with approximately 1,500 species, is the largest genus in the Solanaceae and includes economically important species such as the tomato, potato, and eggplant. In part due to its large … Solanum, with approximately 1,500 species, is the largest genus in the Solanaceae and includes economically important species such as the tomato, potato, and eggplant. In part due to its large size and tropical center of diversity, resolving evolutionary relationships across Solanum as a whole has been challenging. In order to identify major clades within Solanum and to gain insight into phylogenetic relationships among these clades, we sampled 102 Solanum species and seven outgroup taxa for three DNA sequence regions (chloroplast ndhF and trnT- F, and nuclear waxy) and analyzed the data using parsimony and Bayesian methods. The same major Solanum clades were identified by each data partition, and the combined analysis provided the best resolved hypothesis of relationships within the genus. Our data suggest that most traditionally recognized Solanum subgenera are not monophyletic. The Thelopodium clade is sister to the rest of Solanum, which is split into two large clades. These two large clades are further divided into at least 10 subclades, for which informal names are provided and morphological synapomorphies are proposed. The identification of these subclades provides a framework for directed sampling in further phylogenetic studies, and identifies natural groups for focused revisionary work.

Plant Recolonization and Vegetation Succession on the Krakatau Islands, Indonesia

1989-06-01

Robert J. Whittaker , Mark B. Bush , Karen Richards

The development of the vegetation and floras of the Krakatau Islands in the Sunda Straits, Indonesia, since their "sterilization" in 1883 is described. Key features of the post—1883 environment, such … The development of the vegetation and floras of the Krakatau Islands in the Sunda Straits, Indonesia, since their "sterilization" in 1883 is described. Key features of the post—1883 environment, such as pedogenesis, geomorphology (coastal change), human influence, and recent volcanic activity are detailed, and their possible influence on spatial and temporal patterns in both vegetation and flora is discussed. Field work conducted in 1979, 1983, and 1984 has enabled an assessment of the present state of vegetation development, aided by plot—based sampling and analysis of the arboreal component, employing numerical classification (by TWINSPAN) and ordination (by DCA). The coastal communities were established early and have remained little changed, although the distribution of the various components has changed according to the influence of a dynamic coastal geomorphology. Fifty years after forest closure, the forest of the interiors remain species—poor and composed of typical early—seral species. Rakata was dominated inland by Neonauclea calycina and Ficus pubinervis up to ≈550 m altitude, above which a mossy forest of Ficus spp. and Schefflera polybotrya scrub was recorded. The main inland forest types on Rakata Kecil and Sertung were of young, evenaged stands of Timonius compressicaulis (extensive) and older stands of Dysoxylum gaudichaudianum (often with a T. compressicaulis understory). The principal axes of variation within the data were found to be between extremes of the Rakata forest types, with Sertung and R. Kecil stands remaining undifferentiated until lower levels of the analyses. These patterns were ascribed to a mix of environmental variation (coastal and altitudinal factors), chance variations in colonization, and to volcanic action following the emergence of Anak Krakatau in 1927. Disturbance by volcanism (e.g., in 1930, 1934—1936, 1939, 1952—1953, 1961) has resulted in the deflection of vegetation succession on R. Kecil and Sertung into a different pathway from that followed on Rakata, which has remained unaffected by the activity. On Anak Krakatau, volcanic action has prevented successful colonization away from accreting coastal deposits, and has several times eliminated the entire flora. In addition, the major source of propagules for Anak Krakatau is from within the group, and for these several reasons the new island is shown to be a poor analogue for the early recovery phases of the other islands. Complete floral lists are given for each recorded survey for each island in the group, including data from surveys in 1979, 1982, and 1983. These data have been revised from previous publications on the basis of recent herbarium work and literature searches. The data are analyzed according to several different models: cumulative species totals, species totals for particular combinations of surveys, and totals calculated on the assumption of minimum turnover. The early beach spermatophyte assemblages of Rakata have undergone relatively few losses in comparison to the assemblages of the interior, while within the latter there has been a relatively high proportion of losses among the pioneering pteridophytes. The possession of major habitat types has been identified as critical in determining the shape of the overall colonization curve, through the passive sampling of different source pools. The diversity of the floras of the group as a whole and of Rakata and Anak Krakatau has continued to increase. The curves of species present on Sertung and R. Kecil have levelled and fallen respectively, as a result of the volcanic activity of Anak Krakatau. It is shown that the number of animal—transported species on the Krakatau group has continued to increase over the last 50 yr, and that this accounts for the majority of the increase in the size of the spermatophyte flora. The animal—transported species and the early sea—dispersed species appear to be species—stable groups. Later sea—dispersed species included ephemerals and species of temporary habitats, and have experienced a relatively high proportion of losses. Few beach species that have established on all of the three main islands have subsequently become extinct from the group. The number of pteridophytes on the islands has increased over the last 50 yr, mainly through the addition of forest species. A large proportion of plant species has been found only on Rakata, which samples an upland source pool not represented on the other islands. It is argued that the assumptions of "classical" island biogeography are inappropriate to these data and that the pattern in floral recolonization can best be understood as a successional process involving broad habitat and dispersal mechanism determinants. The implication of these findings is that community dynamics are highly significant in determining rates of immigration, colonization (i.e., successful immigration), and extinction, and that the probabilities of each vary among different groups of species and through time.

Ecological Studies of Lianas in Lambir National Park, Sarawak, Malaysia

1987-06-01

Francis E. Putz , Paul P. K. Chai

(1) Liana (climber or woody vine) abundance and climbing habitats were studied in primary dipterocarp forest in Lambir National Park, Sarawak. (2) Sample plots of 01 ha were established on … (1) Liana (climber or woody vine) abundance and climbing habitats were studied in primary dipterocarp forest in Lambir National Park, Sarawak. (2) Sample plots of 01 ha were established on the upper slopes of a broad ridge at altitudes of about 100-140 m and in an adjacent valley at an altitude of approximately 50 m. Five plots were selected at random in each area. The diameters of all lianas > 1 cm dbh and trees > 10 cm dbh were measured and the proportion of trees infested with lianas was recorded. In a 0 04 ha area in each plot we identified all lianas > 1 cm dbh, recorded on which trees the lianas were growing, and noted how the lianas attached to their host trees. Vines 2 cm ha-' in the valley and on the hilltop, respectively. Upright (self-supporting) liana seedlings were also approximately twice as abundant in the valley. (4) A total of seventy-nine woody liana species representing twenty-four familes were recorded, with thirty-nine species in the ridge plots and fifty-three species in the valley plots. Only fourteen species were common to both areas. (5) Approximately half of the trees > 20 cm dbh were liana-infested in both the valley and hilltop plots. Trees supporting more than one liana were more numerous in the valley. The average canopy liana connected the crowns of 1 4 trees > 20 cm dbh in both areas. (6) The influences of soil fertility and frequency of forest disturbance on the abundance of lianas are discussed with reference to data from other tropical forests.

Fern genomes elucidate land plant evolution and cyanobacterial symbioses

2018-06-29

Fay‐Wei Li , Paul Brouwer , Lorenzo Carretero‐Paulet +7 more

Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes … Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns-one at the base of 'core leptosporangiates' and one specific to Azolla. One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N2-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla-cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.

View PDF Chat

Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family

2019-02-19

Ilias Lagkouvardos , Till Robin Lesker , Thomas C. A. Hitch +7 more

Bacteria within family S24-7 (phylum Bacteroidetes) are dominant in the mouse gut microbiota and detected in the intestine of other animals. Because they had not been cultured until recently and … Bacteria within family S24-7 (phylum Bacteroidetes) are dominant in the mouse gut microbiota and detected in the intestine of other animals. Because they had not been cultured until recently and the family classification is still ambiguous, interaction with their host was difficult to study and confusion still exists regarding sequence data annotation.We investigated family S24-7 by combining data from large-scale 16S rRNA gene analysis and from functional and taxonomic studies of metagenomic and cultured species.A total of 685 species was inferred by full-length 16S rRNA gene sequence clustering. While many species could not be assigned ecological habitats (93,045 samples analyzed), the mouse was the most commonly identified host (average of 20% relative abundance and nine co-occurring species). Shotgun metagenomics allowed reconstruction of 59 molecular species, of which 34 were representative of the 16S rRNA gene-derived species clusters. In addition, cultivation efforts allowed isolating five strains representing three species, including two novel taxa. Genome analysis revealed that S24-7 spp. are functionally distinct from neighboring families and versatile with respect to complex carbohydrate degradation.We provide novel data on the diversity, ecology, and description of bacterial family S24-7, for which the name Muribaculaceae is proposed.

View PDF Chat

IRGAN

2017-07-28

Jun Wang , Lantao Yu , Weinan Zhang +5 more

This paper provides a unified account of two schools of thinking in information retrieval modelling: the generative retrieval focusing on predicting relevant documents given a query, and the discriminative retrieval … This paper provides a unified account of two schools of thinking in information retrieval modelling: the generative retrieval focusing on predicting relevant documents given a query, and the discriminative retrieval focusing on predicting relevancy given a query-document pair. We propose a game theoretical minimax game to iteratively optimise both models. On one hand, the discriminative model, aiming to mine signals from labelled and unlabelled data, provides guidance to train the generative model towards fitting the underlying relevance distribution over documents given the query. On the other hand, the generative model, acting as an attacker to the current discriminative model, generates difficult examples for the discriminative model in an adversarial way by minimising its discrimination objective. With the competition between these two models, we show that the unified framework takes advantage of both schools of thinking: (i) the generative model learns to fit the relevance distribution over documents via the signals from the discriminative model, and (ii) the discriminative model is able to exploit the unlabelled data selected by the generative model to achieve a better estimation for document ranking. Our experimental results have demonstrated significant performance gains as much as 23.96% on [email protected] and 15.50% on MAP over strong baselines in a variety of applications including web search, item recommendation, and question answering.

View PDF Chat

CSIC-Real Jardín Botánico-Colección de Hongos Histórica (MA-Funhist)

2023-01-01

Margarita Dueñas

English: The historical collection of the Royal Botanic Gardens fungi includes all the fungi that were deposited in the Herbarium MA before 1976, date in which separated collections of Cryptogams … English: The historical collection of the Royal Botanic Gardens fungi includes all the fungi that were deposited in the Herbarium MA before 1976, date in which separated collections of Cryptogams of the Phanerogams and ferns. It consists of more than 10,000 species and 15,000 taxa, whose information is collected on more than 20,000 records. It includes some collections such as that of Fragoso Gonzalez or Jordan Urriés, of phytopathogenic fungi which meant the start of Mycology in the current concept in Spain. The specimens come, mostly from Spain, but also in other countries of Europe, America, and to a lesser extent in Africa and Asia. Español: La colección histórica de los hongos del Real Jardín Botánico incluye todos los hongos que se depositaron en el Herbario MA antes de 1976, fecha en la que se separaron las colecciones de criptógamas de las fanerógamas y helechos. Se compone de más de 10.000 especies y 15.000 taxa, cuya información se recoge en más de 20.000 registros. Incluye algunas colecciones de hongos fitopatógenos como la de Fragoso González o Jordan Urriés, que significaron el inicio del concepto actual de la Micología en España. Los especímenes provienen, sobre todo de España, pero también de otros países de Europa, América y, en menor medida, de África y Asia.

Flora Sumatra: Digitizing and data basing specimens of the Sumatran Flora deposited at Herbarium Universitas Andalas (ANDA)-Part 2

2022-01-01

Nurainas Nurainas , Ahmad Taufiq , Heru Handika +2 more

Herbarium of Andalas University (ANDA) is one of the active herbaria in Sumatra, Indonesia. Our herbarium host specimens mainly from Sumatra and adjacent islands, but limited numbers of collections also … Herbarium of Andalas University (ANDA) is one of the active herbaria in Sumatra, Indonesia. Our herbarium host specimens mainly from Sumatra and adjacent islands, but limited numbers of collections also available from elsewhere. Since its establishment in 1983, the herbarium collections have grown with over 65,000 sheets of specimens. Although the collections are actively being used for research and education by locals and internationals, the lack of a database system has made the collections hard to access. Since 2018, we have worked with the Global Biodiversity Information Facility (GBIF) to catalog and digitize our collections. Here we reviewed our cataloged specimens. Until now, we have cataloged more than 31,000 of sheet specimens from 1700 species in 340 genera and 29 families of vascular plants. Those are reported in several datasets. This dataset elucidated the geo-referenced data from 676 species in 255 genera within 14 families of vascular plants. Among all of the families we have cataloged here are Acanthaceae, Anacardiaceae, Annonaceae, Apocynaceae, Compositae, Convolvulaceae, Cucurbitaceae, Ebenaceae, Lauraceae, Leguminosae, Melastomataceae, Primulaceae, Rutaceae, Ulmaceae. Among them are 3 species that are endemic to Sumatra, Endangered (1 species) , Near Threatened (1 species), Vulnerable (8 species), Least concern (79 species) and 1 species protected under Indonesian government regulation. This data mobilazation program is our first step to improve research and education for plant species in Sumatra.

Begonia tesselata (Begoniaceae) a new species from the Colombian eastern Cordillera

2025-06-25

Orlando Adolfo Jara-Muñoz , Heidy Caterine Caro-Ayala , Susana María Arango-Carvajal +1 more | Brittonia

Updated checklist of Araceae in Vietnam

2025-06-25

Van Tien Tran , Van Du Nguyen , Xuan Thanh Trinh | Ministry of Science and Technology Vietnam

Silver nanoparticles enhanced shoot regeneration from Begonia × tuberhybrida Voss petal explants via carbohydrate synthesis pathway

2025-06-25

Dac Khai Hoang , Viet Hung Nguyen , Thanh Tung Hoang +7 more | Ministry of Science and Technology Vietnam

АЗОЛЛА ВО ФЛОРЕ КЫРГЫЗСТАНА: РАСПРОСТРАНЕНИЕ, ЭКОЛОГИЯ И ПРАКТИЧЕСКОЕ ЗНАЧЕНИЕ

2025-06-25

Zh. Abdyrakhmanova , Гулбарчин Исраилова , Байгелди Жусупов +1 more | Bulletin of Osh State University

В данной статье представлены результаты исследования нового для флоры Кыргызстана вида водного папоротника – азоллы каролинской (Azolla caroliniana Willd.). Растение было обнаружено в коллекторно-дренажных сетях южного региона, что открывает перспективы … В данной статье представлены результаты исследования нового для флоры Кыргызстана вида водного папоротника – азоллы каролинской (Azolla caroliniana Willd.). Растение было обнаружено в коллекторно-дренажных сетях южного региона, что открывает перспективы для изучения его адаптационных способностей и потенциального использования в сельском хозяйстве. Проведен анализ физико-химических параметров воды в местах произрастания азоллы, выявлены особенности ее распространения и экологическая значимость. Прозрачность воды устанавливали диском Секки. Содержание растворенного кислорода определяли по методу Винклера. Величину рН определяли набором индикаторов по Михаэлису и универсальным индикатором, портативным рН-метром. В качестве стандартного раствора использовали кобальт-хромовую шкалу. Отмечено, что азолла каролинская, обладая способностью фиксировать азот, представляет интерес как зеленое удобрение и кормовая культура. Обсуждаются вопросы сохранения вида и возможности его интродукции. Статья вносит вклад в изучение биоразнообразия Кыргызстана и подчеркивает необходимость дальнейших исследований в области водной флоры. Выяснение роли данного растения в водных экосистемах поможет в разработке мер по их сохранению и устойчивому использованию.

Cytological study of the genus Aspidistra Ker-Gawl. from Guangxi, China I

2025-06-24

Maigeng Zhou , Li-Zhen Luo , Junwen Zhu +3 more | CYTOLOGIA

Comparative karyotype analysis of Indian Dipcadi (Asparagaceae): insights on chromosome evolution and biogeography

2025-06-24

Priya E. Shelke , Siddharthan Surveswaran , Asif S. Tamboli +2 more | Systematics and Biodiversity

Columnea flammeostoma, a new species of Gesneriaceae from the Cordillera del Cóndor in southern Ecuador

2025-06-23

John L. Clark | Journal of the Botanical Research Institute of Texas

Ongoing research on the systematics of Columnea (Gesneriaceae) has resulted in the discovery of a new species, Columnea flammeostoma J.L. Clark of the Gesneriaceae (tribe: Gesnerieae, subtribe: Columneinae). The new … Ongoing research on the systematics of Columnea (Gesneriaceae) has resulted in the discovery of a new species, Columnea flammeostoma J.L. Clark of the Gesneriaceae (tribe: Gesnerieae, subtribe: Columneinae). The new species is distinguished by the combination of isophyllous leaf pairs, fimbriate calyx lobe margins, and a deeply bilabiate corolla that is dark purple with yellow corolla lobe margins. The new species is endemic to the Cordillera del Cóndor in southern Ecuador where it was collected from the wild in 2005 and brought into cultivation by Ecuagenera and has since been distributed by horticulturists throughout several countries.

A new species of Aureonarius (Cortinariaceae, Agaricales) from Southwestern China

2025-06-23

YUAN FANG , Yingtong Feng , J Li +6 more | Phytotaxa

The genus Aureonarius belongs to the family Cortinariaceae. In this study, phylogenetic inferences of Aureonarius were conducted based on sequences from a multi-locus dataset (ITS, nrLSU, RPB1, RPB2). A new … The genus Aureonarius belongs to the family Cortinariaceae. In this study, phylogenetic inferences of Aureonarius were conducted based on sequences from a multi-locus dataset (ITS, nrLSU, RPB1, RPB2). A new species of Aureonarius discovered in Yunnan province of China was described based on morphological and molecular evidence. Aureonarius baimaensis is characterized by its medium-sized basidiomata; brownish-orange to reddish-brown tinge pileus and a pastel yellow tinge in the context; smooth central surface, with yellowish white to butter yellow finely fibrils near the edge; it typically has sterile lamella edges composed of smaller clavate cells. Morphological description, illustrations, and phylogenetic result of the new species are provided, as well as their comparisons to related taxa.

Synonymization of the name Cathetus roeperianus (Phyllanthaceae) with an emended description and lectotypification of Cathetus fasciculata from the collections of India

2025-06-23

Kapil Kumar Kemprai , KSHIPRATIV BASUMATARY , Souravjyoti Borah | Phytotaxa

The Indian species Cathetus roeperianus is synonymized under Cathetus fasciculata. The species is reported in this communication as an addition to the Flora of Assam, India. Nomenclatural treatment, taxonomic enumeration … The Indian species Cathetus roeperianus is synonymized under Cathetus fasciculata. The species is reported in this communication as an addition to the Flora of Assam, India. Nomenclatural treatment, taxonomic enumeration and an emended description of the species are provided along with colored images and SEM images of the seeds for aid in identification and further studies. Lectotype for the name Cathetus fasciculata is designated here as the name was published without mentioning the type.

Schimperella subcompressa, a New Combination and an Earlier Name for S. bellointricata (Brachytheciaceae)

2025-06-23

John J. Atwood , John C. Brinda | Novon A Journal for Botanical Nomenclature

Hypnum subcompressum Müll. Hal. from Ethiopia is transferred to Schimperella Thér. (Brachytheciaceae) based on its evenly foliate habit with ovate-lanceolate to ovate, acuminate leaves and twisted apices; serrate to serrulate … Hypnum subcompressum Müll. Hal. from Ethiopia is transferred to Schimperella Thér. (Brachytheciaceae) based on its evenly foliate habit with ovate-lanceolate to ovate, acuminate leaves and twisted apices; serrate to serrulate leaf margins with teeth extending nearly to the insertion; leaf bases with numerous subquadrate to short-rectangular alar cells; autoicous sexuality; blackish, cylindrical, and erect to suberect capsules; and peristome with a slightly reduced endostome. The new combination, S. subcompressa (Müll. Hal.) J. J. Atwood & Brinda, is an earlier name for S. bellointricata (Müll. Hal. ex Broth.) W. R. Buck (≡ H. bellointricatum Müll. Hal. ex Broth.), which we consider to be conspecific. Lectotypes are designated for both H. subcompressum and H. bellointricatum.

Begonia nyishiorum (Begoniaceae), a New Species from Arunachal Pradesh, Northeast India

2025-06-23

Ashish K. Soni , Akshath Shenoy , Abhinav Kumar +3 more | Novon A Journal for Botanical Nomenclature

A new species, Begonia nyishiorum A. Shenoy, A. K. Soni & Ab. Kumar, classified within Begonia L. sect. Platycentrum (Klotzsch) A. DC., is described from East Kameng, Arunachal Pradesh, Northeast … A new species, Begonia nyishiorum A. Shenoy, A. K. Soni & Ab. Kumar, classified within Begonia L. sect. Platycentrum (Klotzsch) A. DC., is described from East Kameng, Arunachal Pradesh, Northeast India. It is allied with B. kekarmonyingensis Taram, D. Borah & M. Hughes. The morphological similarities and differences between the two species are discussed. Notably, the striking petiole indument of B. nyishiorum is highly distinctive within section Platycentrum. The species is assessed as Data Deficient according to the IUCN Red List criteria.

Evaluation of Antimicrobial Activity of Methanol and Aqueous Extracts of Begonia cucullata against Selected Human Pathogenic Bacteria

2025-06-19

Ramesh Londonkar , Hemalatha S.A. | Journal of Advances in Microbiology

Background: Plants are a significant source of bioactive compounds with potential therapeutic properties. Due to the growing concern of antibiotic-resistant pathogens, exploring plant-based antimicrobials has become increasingly essential. This study … Background: Plants are a significant source of bioactive compounds with potential therapeutic properties. Due to the growing concern of antibiotic-resistant pathogens, exploring plant-based antimicrobials has become increasingly essential. This study evaluated the antimicrobial activity of methanol and aqueous extracts of Begonia cucullata against 12 bacterial strains to validate its traditional use and identify its potential bioactivity. Methods: Petroleum ether, Chloroform, Methanol and aqueous extracts of Begonia cucullata were prepared and tested for antimicrobial activity using the agar well diffusion method on Muller Hinton agar media. The diameter of the inhibition zones was measured after 48 hours of incubation at 37°C. Minimum Inhibitory Concentrations (MICs) were determined using the broth microdilution method. Results: The methanol extract exhibited significant antibacterial activity against Escherichia coli, Klebsiella pneumoniae, and Proteus vulgaris with inhibition zones ranging from 13 to 18 mm. The aqueous extract also demonstrated activity against Klebsiella pneumoniae, Escherichia coli, Bacillus cereus and Pseudomonas aeruginosa with inhibition zones ranging from 8 to 18 mm. The MIC values for Bacillus cereus and Escherichia coli were 125 µg/mL, while Klebsiella pneumoniae showed inhibition at 62.5 µg/mL. Petroleum ether and chloroform extracts showed no antibacterial activity. Conclusion: The study confirms that the methanol and aqueous extracts of Begonia cucullata possess potent antibacterial properties against several pathogenic bacteria, highlighting their potential as natural antimicrobial agents. These findings suggest that Begonia cucullata could serve as a valuable source for developing plant-based therapeutics to combat antibiotic-resistant infections, warranting further investigation into its bioactive constituents.

THE HALOPHYTE PLANT RESOURCES OF THE FOREDUNES ON THE SOUTH-CENTRAL COAST OF VIETNAM

2025-06-19

Ba Bien Le , Van Binh Nguyen , Truong Thi Lan Anh +7 more | Dalat University Journal of Science

Halophytic plant resources play a vital role in meeting the needs of local people, and they have potential applications in nutrition and sustainable agriculture. Ethnobotanical surveys were conducted on foredunes … Halophytic plant resources play a vital role in meeting the needs of local people, and they have potential applications in nutrition and sustainable agriculture. Ethnobotanical surveys were conducted on foredunes at 41 study sites in 8 provinces of the south-central coastal region of Vietnam. The findings show that the majority of halophytic plants fall into the following resource groups: traditional medicine (45.13%, 88 species), food, (13.85%, 27 species), woody plants (4.62%, 9 species), and ornamentals (4.10%, 8 species). In comparison, 26.67% (54 species) have not been documented for specific uses. Halophytic resources account for 73.34% of the surveyed species, highlighting their significant ethnobotanical value. Cultivating these natural resources can benefit coastal communities by supporting local socio-economic development while promoting the environmental sustainability of the coastal soils and climate.

Unraveling the taxonomy of Asian Buddleja: Species discovery and delimitation through morphological comparison, ploidy analysis and phylogenomic insights

2025-06-18

Fengmao Yang , En-De Liu , Yongjie Guo +7 more | Taxon

Abstract Hybridization and polyploidization have given rise to complex cytonuclear conflicts and morphological continuity within the Asian Buddleja group, posing challenges in species delimitation and the assignment of conservation efforts. … Abstract Hybridization and polyploidization have given rise to complex cytonuclear conflicts and morphological continuity within the Asian Buddleja group, posing challenges in species delimitation and the assignment of conservation efforts. This study employed an integrative approach, utilizing morphological comparisons, ploidy estimations and phylogenomic insights to investigate the taxonomy of B. purdomii , previously treated as a synonym of B. brachystachya , and to describe two new species, B. atropurpurea and B. calostachya . A comprehensive phylogenetic analysis was conducted using whole plastid genomes and a large number of low‐copy nuclear genes assembled from genome skimming data from 61 samples, covering all the known Asian Buddleja species. Additionally, a population genetic analysis of B. lindleyana and B. atropurpurea was performed to further confirm whether B. atropurpurea is a distinct taxon from B. lindleyana . The ploidy level of each of the three species studied in depth was determined through chromosome counts, and morphological comparisons were made between the two putative new species with their sister relatives. The time of divergence of each species was estimated by dating of the maternally inherited plastomes. Phylogenetic reconstruction combined with morphological measurements confirmed the distinct taxonomic status of B. purdomii , B. atropurpurea , and B. calostachya. The times of divergence between these putative species and their sister taxa are estimated to be 10.7 Ma, 3.6 Ma, and 2.1 Ma, which may correspond to the intensification of the East Asian Summer Monsoon (EASM), the Qingzang movement and the Quaternary climate upheaval, respectively. This study sheds new light on species delimitation and the speciation process in Asian Buddleja , and also provides a robust taxonomic framework for the conservation and utilization of these species.

Ipomoea laxiflora HJ Chowdhery & Debta (Convolvulaceae): A new distribution record for Madhya Pradesh, India

2025-06-18

Ajay Gangurde , TARUN R. NAYI , Mayur Bhagwat +4 more | Phytomorphology Phytomorphology An International Journal of Plant Sciences

Rhizophora stylosa (Rhizophoraceae) newly recorded from Thailand: lectotypification, leaf anatomy, and pollen morphology

2025-06-17

Chatchai Ngernsaengsaruay , Nittaya Mianmit , Supol Kamsanor +6 more | PhytoKeys

Rhizophora stylosa (Rhizophoraceae), previously known from India (Andaman and Nicobar Islands), China to Indo-China, and the Pacific Island, is reported here as a new record from coastal areas with muddy-sandy, … Rhizophora stylosa (Rhizophoraceae), previously known from India (Andaman and Nicobar Islands), China to Indo-China, and the Pacific Island, is reported here as a new record from coastal areas with muddy-sandy, sandy or sandy-rocky substrates at Ko Lidi and Ko Bulon Le, within Mu Ko Phetra National Park, La-ngu District, and at Ao Talo Wao, Ko Tarutao, Tarutao National Park, Mueang Satun District, Satun Province, Peninsular Thailand. A detailed morphological description, illustrations and a distribution map of the species are provided, along with notes on distribution, habitat and ecology, phenology, a preliminary conservation assessment, etymology and specimens examined. In addition, Rhizophora stylosa is lectotypified, the Thai vernacular name “Kongkang phetra” is herein proposed for this species, and an updated identification key to the species of Rhizophora in Thailand is presented. The species is currently assessed as Least Concern [LC] under the IUCN conservation status. Furthermore, detailed descriptions of leaf anatomical features and pollen morphology are provided. The thick cuticles, sunken stomata, large hypodermal cells, and cork warts are adaptive anatomical features of leaves in Rhizophora that live in the mangrove environments. The pollen grains of Rhizophora stylosa are tricolporate, prolate spheroidal or oblate spheroidal shapes, small-sized, and reticulate exine sculpturing.

Taxonomic note on Iphigenia magnifica (Colchicaceae) an endemic and vulnerable species from Maharashtra, India

2025-06-16

Pravin P Sangale , A. K. Chaudhari , Shailendra M Kamble +2 more | Species

Revisiting taxonomy of Litsea lancifolia var. alternifolia (Lauraceae), a neglected element of the East Himalayas in India

2025-06-16

Anand Kumar , Tapas Chakrabarty | Species

Camellia yangii (Theaceae), a new species of tea plants (Camellia section Thea)

2025-06-13

Dongwei Zhao | PhytoKeys

Camellia sect. Thea contains plants of beverage sources with huge profits. Their natural germplasm resources have yet to be fully explored. Here, morphological, phenological and phylogenetic analyses were undertaken to … Camellia sect. Thea contains plants of beverage sources with huge profits. Their natural germplasm resources have yet to be fully explored. Here, morphological, phenological and phylogenetic analyses were undertaken to reveal a new species of tea plants, C. yangii D.Wei Zhao. It is described with an illustration and photos of fresh characters provided. The new species is similar to C. fangchengensis and C. ptilophylla by the densely pubescent new branchlets, abaxial surface of leaves and pedicel, but differs from them in bearing a larger flower, fewer (3 vs. 5) but larger sepals, and the indumentum of the sepals. Molecular phylogenetic analysis using RPB2 introns 11–15 and 23 and waxy suggests that it is a member of C. sect. Thea and its phylogenetically closely related species are C. longissima and C. taliensis . Camellia yangii has a later flowering phase compared with other taxa of C. sect. Thea that occurred or were planted nearby, so it cannot naturally hybridize with other tea plants. The new species bears a red or purplish red and densely pubescent terminal bud, which suggests it is a rare germplasm resource of tea plants. Camellia yangii is only known from a single extremely vulnerable population and strict conservation and asexual propagations are urgently needed to avoid extinction.

Taxonomy, Lectotypification, and Conservation of the Genus Phyllodium (Fabaceae: Desmodieae) in Cambodia, Laos, and Vietnam

2025-06-13

WITSANU SAISORN , Jiratthi Satthaphorn , Shuichiro Tagane | Plants

A taxonomy of the genus Phyllodium Desv. in Cambodia, Laos, and Vietnam is presented. The plant specimens collected from the fields and herbarium specimens kept at Asian and European herbaria … A taxonomy of the genus Phyllodium Desv. in Cambodia, Laos, and Vietnam is presented. The plant specimens collected from the fields and herbarium specimens kept at Asian and European herbaria are examined. The IUCN conservation status of each species at regional and national levels is assessed. Five species are enumerated, viz., Phyllodium elegans (Lour.) Desv., P. kurzianum (Kuntze) H.Ohashi, P. longipes (Craib) Schindl., P. pulchellum (L.) Desv., and P. vestitum Benth. Lectotypification of two names, Desmodium longipes Craib and D. tonkinense Schindl., is performed. A key to the species, description, distribution, ecology, phenology, vernacular names, full list of specimens examined, and photographs are provided. The conservation status of five Phyllodium species varies across Cambodia, Laos, Vietnam, and Indochina. Phyllodium elegans and P. pulchellum are consistently Least Concern (LC) in all regions. Phyllodium kurzianum is Data Deficient (DD) in Laos, Near Threatened (NT) in Vietnam, and LC in Indochina. Phyllodium longipes is EN in Cambodia but LC elsewhere. Phyllodium vestitum is NT in Cambodia, Vulnerable (VU) in Laos and Vietnam, and LC in Indochina. The taxonomic information provided in this work will contribute to the advancement of the Flora of Cambodia, Laos, and Vietnam and the conservation status of each species proposed in this paper can be used for future conservation planning.

Earliest fossil record of Cryptocarya R. Br. (Lauraceae) from Asia and its biogeographic and palaeoenvironmental implications

2025-06-13

Harshita Bhatia , Gaurav Srivastava | Palaeobiodiversity and Palaeoenvironments

New Records of Species of Phlebotominae from Durango, Mexico

2025-06-13

Jorge J. Rodríguez‐Rojas , Jesús Guillermo Armijo-Nájera , Aldo I. Ortega‐Morales | Southwestern Entomologist

Synopsis of Croton section Barhamia subsection Barhamia (Euphorbiaceae)

2025-06-12

Nicolas Giovanny Burilli , Amanda da Paixão Noronha Pereira , Maria Beatriz Rossi Caruzo | Phytotaxa

Croton section Barhamia is one of the largest sections of the genus, with about 80 species found in the West Indies, Central and South America, with its greatest diversity in … Croton section Barhamia is one of the largest sections of the genus, with about 80 species found in the West Indies, Central and South America, with its greatest diversity in Brazil. Section Barhamia is subdivided into five subsections, including subsection Barhamia. During taxonomic studies of subsection Barhamia in Brazil, we came across some nomenclatural issues and delimitation inconsistencies for species belonging to the group. To establish better boundaries for the subsection, a checklist was compiled from a review of herbarium specimens, bibliographic databases and fieldwork, focusing on the most important known localities of occurrence for some species. We recognize fourteen species for the subsection: Croton adenocalyx, C. aemulus, C. betulaster, C. essequiboensis, C. glandulosodentatus, C. glutinosus, C. graomogolensis, C. guianensis, C. hircinus, C. longibracteatus, C. muscicapa, C. rhexiifolius, C. rudolphianus and C. urticifolius. Therefore, we here provide an updated list of species, including data of habitat and distribution.

Ficha de Paragoniates alburnus

2025-06-12

André Luiz Henriques Esguícero , André Luiz Netto Ferreira , Bruno Francelino de Melo +7 more | Datasets - Sistema SALVE - ICMBio

Anacacumisporium thailandicum ( Chaetosphaeriaceae, Sordariomycetes ), a new species from Heynea trijuga ( Meliaceae ) in Northern Thailand

2025-06-12

Ashani D. Madagammana , Chitrabhanu S. Bhunjun , Chayanard Phukhamsakda +3 more | New Zealand Journal of Botany

Begonia species: a review on its ethnobotany, phytochemicals, and biological activities

2025-06-10

Dipankar Borah , Rohit Dutta , Sibani Majumdar +1 more | Discover Plants.

Effect of PGPB on leaf nutrient status and growth of Begonia semperflorens

2025-06-05

Merve Şenol Kotan | International Journal of Agriculture Environment and Food Sciences

Bacteria are increasingly used in agriculture as eco-friendly alternatives to promote plant growth through mechanisms such as nitrogen fixation, phosphate solubilization, hormone production, and improved nutrient uptake. This study aims … Bacteria are increasingly used in agriculture as eco-friendly alternatives to promote plant growth through mechanisms such as nitrogen fixation, phosphate solubilization, hormone production, and improved nutrient uptake. This study aims to examine the effects of plant growth-promoting bacteria on the growth, quality, and nutrient content of Begonia semperflorens, a commercially valuable ornamental plant known for its long flowering period and vibrant blooms. In this study, one-month-old Begonia semperflorens seedlings were dipped into bacterial suspensions (10⁸ CFU ml⁻¹) of Pseudomonas chlororaphis MF-1, Bacillus megaterium M-3, and Agrobacterium radiobacter A-16 for 20 minutes prior to planting. After planting, the seedlings were irrigated with bacterial suspensions as watering solution at twice at 15-day intervals. At the end of one month, plant growth and quality parameters (plant height, number of leaves, leaf area, plant fresh weight, plant dry weight, stem diameter, flower stem, plant crown width, number of blooming flowers). were evaluated, along with macro- and microelement contents (total N, P, K, Ca, Mn, Mg, and Fe) in both plant leaves and the growing medium. All bacterial treatments significantly improved plant growth and quality compared to the control group, with M-3 exhibiting the most pronounced effects, increasing plant height by 40%, leaf number by 133%, leaf area by 348%, and flower number by 61%. A-16 enhanced crown width (45%) and flower stem length (26%), while MF-1 improved plant height (43%) and flower production (51%). Additionally, M-3 increased total nitrogen in leaves by 43%, while bacterial treatments enhanced various elements in plant leaves. The results show that these bacterial isolates improve begonia plant characteristics, providing high-quality plants and offering a sustainable alternative as microbial fertilizers in ornamental plant cultivation.

Revisiting the Taxonomy of Myanmar Endemics Cinnamomum lucens and C. tavoyanum (Lauraceae)

2025-06-03

Tapas Chakrabarty , Anand Kumar | Annales Botanici Fennici

Resolving taxonomic complexities in medicinal Aralia: genome-scale phylogeny and super-barcoding advance species identification and conservation

2025-06-01

Yanan Cao , Menghao Wang , Jiamei Li +5 more | Journal of Applied Research on Medicinal and Aromatic Plants

Correction to: A single dominant GLOBOSA allele accounts for repeated origins of hose-in-hose flowers in Sinningia (Gesneriaceae)

2025-06-01

| PubMed

Comparative Genomics and Phylogenetic Analyses of Aquarius macrophyllus and Related Genera in Alismataceae Based on Plastome Data

2025-06-01

Jie Li , Shengnan Wei , Jianming Ying +1 more | Ecology and Evolution

ABSTRACT Aquarius macrophyllus , an aquatic species native to South America, has been widely utilized as an ornamental plant. Although the plastome data have been commonly used in plant evolution … ABSTRACT Aquarius macrophyllus , an aquatic species native to South America, has been widely utilized as an ornamental plant. Although the plastome data have been commonly used in plant evolution and phylogenetics, research on the plastome of A. macrophyllus remains scarce. In this study, we sequenced the plastome of A. macrophyllus and conducted a comparative analysis incorporating eight species from related genera of Caldesia , Sagittaria , Alisma , and Luronium . The assembled plastome was 180,860 bp in size, with 133 genes annotated, including 88 protein‐coding genes, 8 rRNA, and 37 tRNA. Comparative analyses showed that the genome lengths of the nine plastomes ranged from 159,063 to 180,860 bp, including a large single copy (LSC, 89,203–99,125 bp), a small single copy (SSC, 10,131–19,753 bp), and a pair of inverted repeat sequences (IR, 25,124–39,664 bp). The nine plastomes were similar in GC content, codon usage, and gene distribution but contained variations, including IR expansion in A. macrophyllus , loss of trnV‐UAC introns, and gene inversion in Caldesia and Sagittaria species. Two sequence inversions of 5.6 and 6.4 kb were detected in Sagittaria and Caldesia , respectively. A total of 532 simple sequence repeats (SSRs) and 667 dispersed repeats were detected in the nine plastomes. Selection pressure analysis using A. macrophyllus as a reference to compare with other species revealed that three ribosomal protein genes rps2 , rps18 , and rps7 were positively selected, which showed intergeneric specificity, especially displaying higher selection pressure in Sagittaria species than that in Caldesia species. Phylogenetic analysis of Alismataceae elucidated that Alisma , Luronium , and Burnatia species were early diverged, followed by Hydrocleys and Limnocharis . The monophyly of Aquarius and its sister relationship with Echinodorus were revealed, supporting the classification of the new genus Aquarius . Our study enriches the genomic resources of Aquarius and provides new insights into plastome structure and evolution in Alismataceae.

The Natural History of My Begonia

2025-06-01

Barbara Sjoholm | Michigan State University Press eBooks

Unfolding the Complete Chloroplast Genome of Myrica esculenta Buch.‐Ham. ex D.Don (1825): Advancing Phylogenetic Insights Within Fagales and Pioneering <scp>DNA</scp> Barcodes for Precise Species Identification

2025-06-01

Raju Balaji , S. Easwaran , Krishnamoorthy Devanathan +4 more | Ecology and Evolution

ABSTRACT This study aims to delineate the chloroplast (cp) genome of Myrica esculenta Buch.‐Ham. ex D.Don (1825), a traditional medicinal plant from the Myricaceae family, to elucidate its phylogenetic relationships … ABSTRACT This study aims to delineate the chloroplast (cp) genome of Myrica esculenta Buch.‐Ham. ex D.Don (1825), a traditional medicinal plant from the Myricaceae family, to elucidate its phylogenetic relationships within the Fagales order. The objective was to assemble the complete cp genome and assess its utility as a molecular marker for species identification and evolutionary analysis. The methodology involved assemby of the cp genome of M. esculenta , which was found to be 159,538 base pairs (bp) in length and exhibited a typical quadripartite structure. This included an 88,830 bp large single‐copy (LSC) region, an 18,810 bp small single‐copy (SSC) region, and two inverted repeats each of 25,949 bp. Phylogenetic analysis utilized the ycf1 gene sequences from 13 Fagales species. Results indicated that M. esculenta and other Myrica species form a monophyletic clade, with the ycf1 gene showing substantial divergence, suggesting its potential as a novel DNA barcode marker. This marker could significantly improve the resolution of species identification beyond traditional morphological methods. Future perspectives include expanding the genomic datasets across the Myrica genus to enhance the phylogenetic framework and further refine the utility of the ycf1 gene as a DNA barcode for broader applications in plant breeding, herbal drug authentication, and evolutionary studies.

Exploring karst biodiversity: ecological, evolutionary, and conservation perspectives

2025-05-31

Meng Li | Nordic Journal of Botany