Showing papers in "Taxon in 2009"
TL;DR: The dating suggests that the radiation events correlate with an ancient genome duplication in the early history of the Brassicaceae family, which is evidenced by recent genomic studies.
Abstract: The Brassicaceae family is of great scientific interest because it contains the plant model organism Arabidopsis thaliana. Currently, contemporary plant research activities expand to other Brassicaceae taxa. Despite that, the phylogeny of this family is only partly understood. The present study deepens our understanding of a family-wide phylogeny by using two new approaches in phylogenetic family-wide research. We used a molecular marker from the mitochondrial genome and utilised a relaxed molecular dating method. Our data generally confirms a recent tribal alignment of Brassicaceae. We present for the first time a biogeographical scenario for the broad-scale Brassicaceae evolution. We suggest that Brassicaceae most likely evolved some 19 mya in or near the eastern Mediterranean region from a common ancestor of its sister family Cleomaceae. The early Brassicaceae formed a lineage adapted to more open/drier habitats than its capparoid progenitors. The early Brassicaceae evolution was very rapid and the radiation was most likely driven by climatic changes that created open habitats and the well-documented expansion of open grass-dominated ecosystems. Moreover, our dating suggests that the radiation events correlate with an ancient genome duplication in the early history of the family, which is evidenced by recent genomic studies.
108 citations
Duke University1, Centraalbureau voor Schimmelcultures2, Uppsala University3, American Museum of Natural History4, Swiss Federal Institute for Forest, Snow and Landscape Research5, King Juan Carlos University6, Naturhistorisches Museum7, Cardiff University8, University of Copenhagen9, University of Barcelona10, Polish Academy of Sciences11, Finnish Environment Institute12, University of Graz13
TL;DR: It is shown that it is necessary to revise the present morphology-based generic delineation of the lichen family Verrucariaceae in or in accordance with molecular phylogenetic analyses and morphological Studies.
Abstract: Recent molecular phylogenetic analyses and morphological Studies have shown that it is necessary to revise the present morphology-based generic delineation of the lichen family Verrucariaceae in or ...
105 citations
TL;DR: It is concluded that reaching an adequate knowledge of the Brazilian flora is a goal that can only be achieved through intensive investment in improving scientific collections and training human resources.
Abstract: This paper uses information from the 2,875 angiosperm species described from Brazil between the years 1990 and 2006 to provide insights into the present status of botanical collections and taxonomic research in this country. The analysis shows that approximately one new species is described every two days, mostly from the Atlantic rainforest and cerrado biomes. Most species described belong to Orchidaceae (297 species), Fabaceae (288), Bromeliaceae (280), Asteraceae (166) or Poaceae (126). The average number of collections per square kilometer in Brazil is 0.59, a number well below with the ideal index of three collections per square kilometer and indicates a need for more intensive collection efforts, especially in view of the land-use pressures causing loss of vegetational types before their floristic composition is known. We conclude that reaching an adequate knowledge of the Brazilian flora is a goal that can only be achieved through intensive investment in improving scientific collections and training human resources.
89 citations
TL;DR: The results do not reveal a significant role of past hybridisation, plastid lineage sorting or reticulation in the evolutionary diversification of the major lineages of the grass subfamily Pooideae and a largely well-supported pattern of divergence is results in.
Abstract: The grass subfamily Pooideae was studied using DNA sequence information from the chloroplast (cp) matK gene-3'trnK exon and the nuclear ribosomal (nr) ITS1-5.8S gene—ITS2 in a sample of 67 taxa covering all of its tribes. Branches with strong bootstrap support are consistently resolved in both datasets, whereas discrepancy is confined to low-support or unsupported nodes in one of the datasets. The results do not reveal a significant role of past hybridisation, plastid lineage sorting or reticulation in the evolutionary diversification of the major lineages of the subfamily. The combined analysis of the plastid and nuclear datasets results in a largely well-supported pattern of divergence for the major lineages of the subfamily. Some re-alignments of tribes and subtribes are proposed and discussed with reference to relevant morphological and structural characters. We propose the recognition of broader tribes Nardeae with subtribes Nardinae and Lygeinae, Meliceae with subtribes Brylkiniinae and Melicinae, Stipeae with subtribes Ampelodesminae and Stipinae, and Triticeae with subtribes Littledaleinae, Brominae and Hordeinae. For the tribe complex of Aveneae and Poeae, the clear-cut split into two major clades and further resolution into some high-support lineages depicted by cpDNA is not contradicted by nuclear ITS and their taxonomic treatment as separate tribes or a single tribe remains an unanswered question.
84 citations
TL;DR: A revised classification of Hyacinthaceae is presented, with necessary new combinations and complete listings of all currently accepted sub-Saharan species.
Abstract: The most recent classification of Hyacinthaceae subsumes all members of Ornithogaloideae into the single large genus Ornithogalum comprising 250―300 spp. A combined molecular phylogenetic analysis of matK, trnL intron, trnL-F spacer and rbcL plastid DNA sequence data was carried out to assess possible alternative treatments. The study includes 70 taxa, representing all segregate genera that have been recognised in the subfamily and over 20% of the species. The resulting phylogeny identifies three, well-supported primary clades. Clade A comprises a grade constituting the majority of species of Stellarioides plus the Madagascan Igidia, in which is nested a strongly supported clade comprising Albuca and Coilonox; Clade B comprises Dipcadi sister to Pseudogaltonia; and Clade C comprises Eliokarmos, Cathissa, Galtonia, Honorius, Loncomelos, Melomphis, Neopatersonia, Ornithogalum, Zahariadia and two species of Stellarioides. The Madagascan Avonsera convallarioides is weakly supported as sister to the rest of clade C. Several of the segregate genera of Ornithogalum are shown not to be monophyletic although many of the lineages identified by the analysis correspond to lower level taxa that have been recognised in the group. Each of the three primary clades has morphological integrity and could be recognised taxonomically, either at the level of tribe or genus. Within these clades, however, many lineages are poorly defined morphologically and thus their recognition at the level of genus is problematical. Alternative taxonomic treatments are assessed but considerations of nomenclatural stability and taxonomic utility predicate that these lineages are best recognised at infrageneric level. We accordingly prefer to define the genera more broadly. Clade A is recognised as genus Albuca, clade B as comprising the genera Dipcadi and Pseudogaltonia, and clade C as the genus Ornithogalum. Monophyletic, morphologically diagnosable lineages within the genera Albuca and Ornithogalum are treated as subgenera and sections. A revised classification is presented, with necessary new combinations and complete listings of all currently accepted sub-Saharan species.
83 citations
TL;DR: The Ranunculus auricomus complex is tried to elucidate the evolution of apomictic "cassubicus" morphotypes and a separate classification of the sexual species, R. notabilis and the closely related species pair R. cassubicifolius and R. carpaticola is proposed.
Abstract: The Ranunculus auricomus complex is an interesting model system for studying the evolution and diversity of apomictic polyploid complexes. It comprises hundreds of agamospecies, usually referred to two distinct morphotypes (traditionally named "R. auricomus" and "R. cassubicus") which are connected by several intermediate forms. Here we try to elucidate the evolution of apomictic "cassubicus" morphotypes and we test criteria for different classification concepts by combining the information of molecular phylogenetic, morphological, karyological and population genetic data (AFLPs, amplified fragment length polymorphism). Phylogenetic analysis based on sequences of the nrDNA ITS and plastid data (matK, trnk, psbJ-psbA) suggest a deep split between the diploid sexual species R. notabilis ("auricomus" morphotype) from the closely related allopatric taxa R. cassubicifolius and R. carpaticola ("cassubicus"). The apomictic "cassubicus" morphotypes are not monophyletic, as one, R. hungaricus, groups with R. notabilis, which may be due to hybrid origin. Morphometric studies and ploidy level determinations via Feulgen densitometry show a transition from 4x R. hungaricus to the 6x apomictic hybrid derivatives of R. cassubicifolius and R. carpaticola. In two accessions, AFLPs and flow cytometric data suggest local gene flow among different apomictic polyploid morphotypes. Frequent facultative sexuality of apomicts may increase genetic diversity by continuous formation of new cytotypes, local hybridization and introgression, which obstructs the fixation of distinct agamospecies. We conclude that "R. cassubicus" and "R. auricomus" cannot be regarded as species but should be treated as either informal groups, or as (notho)taxa at the sectional level. To reflect the different evolutionary processes involved, we propose a separate classification of the sexual species, R. notabilis and the closely related species pair R. cassubicifolius and R. carpaticola. Based on these well-defined biological species, the apomictic biotypes can be classified as nothotaxa.
78 citations
TL;DR: It is argued that conceptual change has a greater impact than changes in data do, since new data must be interpreted and translated into a classification and since conceptual changes may spur a search for new kinds of data.
Abstract: As a consequence of there being several ways in which observed patterns of variation in nature can be conveyed in a generic classification, long recognised genera have changed in size over time. The generic rank has its origins in folk taxonomy, where genera were homogenous units of relatively few kinds. In the era of Bentham there was a widespread preference for large genera, many of which were split during the 20th century. In a survey of contemporary (1998-2007) generic delimitation practice we found a significant dichotomy between studies that incorporate molecular data and those that rely exclusively on morphological data. The former lead to delimitation of larger genera whereas the latter in general do not. This finding spurred a broader investigation into what drives changes in overall generic sizes, new data sources or new concepts? Two new data types have been introduced during the course of history: detailed morphology (anatomy, cytology) and chemical data (amino acid and DNA sequence data). Conceptual development has seen several turns: from language and communication, through memory and stability, to evolution and monophyly. We argue that conceptual change has a greater impact than changes in data do, since new data must be interpreted and translated into a classification and since conceptual changes may spur a search for new kinds of data. We conclude that the current trend toward recognising larger genera is a result of a return to study on a broad scale, rather than of incorporation of molecular data.
76 citations
TL;DR: ITS sequences of 61 species of the Persea group (Lauraceae) and 30 other species of Lauraceae indicate that Persea, as currently circumscribed, is not monophyletic.
Abstract: The delimitation of genera within the Persea group (Lauraceae) has always been controversial. In an attempt to resolve the phylogenetic lines within this group, we analyzed ITS sequences of 61 species of the Persea group (Lauraceae) and 30 other species of Lauraceae. Several of the traditional genera or subgenera form well-supported groups, viz., Persea subg. Eriodaphne, Machilus, Persea subg. Persea, and Alseodaphne including Dehaasia. The included species of Phoebe form two clades that are unresolved with respect to Alseodaphne. However, Persea subg. Eriodaphne (together with the Macaronesian Apollonias barbujana) forms one of the clades of an unresolved basal trichotomy within the Persea group, whereas Persea subg. Persea is well supported as member of an otherwise Asian clade including Alseodaphne and Phoebe. This indicates that Persea, as currently circumscribed, is not monophyletic. The affinities of the Macaronesian Persea indica are clearly American rather than Asian.
72 citations
TL;DR: The ability to apply this phylogenetically-inspired approach and terminology to formal taxonomy has been increasingly compromised by modifications to successive editions of the International Code ofBotanical Nomenclature, culminating in the 2001 and 2006 Codes which reduced palaeobotanical provision to the fatally over-generalised 'morphotaxon' concept.
Abstract: A typical vascular land-plant consists often to twelve definable organs. Most plant fossils have been disarticulated into their component organs, which must therefore be correlated if the fossil plant is to be understood holistically and compared with its presumed descendants in the extant flora. The resulting conceptually reconstructed whole-plants are the crown jewels of palaeobotany, as they permit full morphological comparison with extant plants and provide templates that guide through reciprocal illumination further attempts at reconstruction. Each of the three lines of evidence facilitating whole-plant reconstruction (association/dissociation, morphological similarity and organic connection) yields only a probability statement that the organs in question have been successfully correlated. Disarticulation means (1) that phenotypic variation can be studied only at the level of individual organs, and (2) that in order to be distinguished from all other kinds of the same organ, an organ must bear a unique morphological character state (autapomorphy). In our terminology, each definable kind of organ is an organ-species. The few organ-species perceived as possessing autapomorphies (and thus as unique) are termed autapospecies, whereas the remaining organ-species characterise more than one whole-plant species and hence are termed form-species. The distinction between autapospecies and form-species is dependent on the range of taxa sampled and is wholly character-based; the age of the fossils under comparison is irrelevant, and the state of preservation is relevant only through its influence on the range of characters that can realistically be scored. None of the many other species concepts recognised by (palaeo)biologists is applicable to fossil plants. Our ability to apply this phylogenetically-inspired approach and terminology to formal taxonomy has been increasingly compromised by modifications to successive editions of the International Code ofBotanical Nomenclature, culminating in the 2001 and 2006 Codes which reduced palaeobotanical provision to the fatally over-generalised 'morphotaxon' concept. A more conceptually rigorous, palaeobotanically informed revision of the Code, placing nomenclature more clearly in the service of taxonomy, would strengthen the crucial roles of reconstructed plants within palaeobotany and of palaeobotany within 21st Century science.
70 citations
TL;DR: A database of 2,420 leaves from 151 species is used and a tight relationship between database size and accuracy is used in conjunction with results from probability theory to predict accuracy of species identification when dichotomous multiple-entry keys and combined Fourier and Procrustes analysis are used together.
Abstract: Species identification is a necessary component of most studies of biological diversity, and computational approaches are beginning to automate it. In particular, leaves of plants provide taxon-specific information that has successfully been applied to plant identification. Prior studies have not investigated the number of leaves or the resolution of the digitized leaf image required to represent a species' shape. Moreover, the relationship between accuracy and the size of the leaf shape database, and methods to integrate automated approaches with more traditional dichotomous keys have yet to be explored. Here, I use a database of 2,420 leaves from 151 species to address these issues. Using distance metrics derived from Fourier and Procrustes analyses, it is found that a minimum of 10 leaves of each species, 100 margin points, and 10 Fourier harmonics are required to accurately represent leaf shape of a species. These results are used to assess the success of species identification from images of leaves: 72% for all 151 species. The tight relationship between database size and accuracy is then used in conjunction with results from probability theory to predict accuracy of species identification when dichotomous multiple-entry keys and combined Fourier and Procrustes analysis are used together. Combining these two approaches to identification can greatly improve identification accuracy. Open-source software is available to implement the automated distance-based approach.
66 citations
TL;DR: This study implies that most previous taxonomic concepts of P. alpinum s.l. were highly artificial, and that either nearly all populations have to be raised to some taxonomic rank or that, preferably, no infraspecific taxa should be recognised at all.
Abstract: Papaver alpinum s.l. is an extraordinarily polymorphic taxon distributed throughout southern and central European mountain ranges. We tested previous hypotheses about relationships and taxonomical status of the numerous described taxa within this species or species group by applying different molecular approaches. In addition we re-evaluated morphological characters used in previous taxonomic treatments in the light of the molecular results. The ancestral sequence haplotypes were widespread and dominant throughout the Alps, whereas peripheral populations in other mountain ranges were often characterised by haplotypes directly derived from the central haplotypes involving one or two mutational steps. The AFLP data corroborated the pattern of a ‘centrifugal radiation’ and additionally showed that most populations were genetically distinct, presumably due to the effect of genetic drift in small and isolated populations. The morphological data did not reveal clear patterns of variation; only the Pyrenean and Sierra Nevada populations differed in two non-overlapping and presumably independent characters. Altogether, our study implies that most previous taxonomic concepts of P. alpinum s.l. were highly artificial, and that either nearly all populations have to be raised to some taxonomic rank or that, preferably, no infraspecific taxa should be recognised at all. The only segregate possibly deserving taxonomic rank, based on both morphology and genetics, is the Iberian P. alpinum subsp. lapeyrousianum.
TL;DR: This paper investigates the suitability of the psbA-trnH and atpF-H regions of the plastid genome for automated barcoding purposes and shows evidence of microsatellite-induced errors in electropherogram base calling.
Abstract: Plastid microsatellites are simple mono/dinucleotide repeats that can cause in-vitro taq Polymerase errors leading to 'stutter' peaks that reduce the clarity and reliability of electropherograms As an efficient and automated barcoding protocol requires high-quality raw data, this paper investigates the suitability of the psbA-trnH and atpF-H regions of the plastid genome for automated barcoding purposes Amplification of 92 individuals from species pairs and triplets was undertaken Of these, 59% of atpF-H species samples and 36% of psbA-trnH species samples showed evidence of microsatellite-induced errors in electropherogram base calling The downstream necessity of human intervention renders these non-coding regions sub-optimal for barcoding purposes
TL;DR: DNA sequences of the chloroplast genes atpB, matK, and rbcL are used to infer the phylogeny of 102 taxa in 41 genera plus four outgroup taxa of the Campanulaceae, providing strong evidence for two major clades in the family and evidence that the large, inclusive genera Wahlenbergia and Campanula are polyphyletic.
Abstract: Campanulaceae are a large, nearly cosmopolitan angiosperm family that are well-accepted as monophyletic but whose intrafamilial and intrageneric relationships are controversial. We used DNA sequences of the chloroplast genes atpB, matK, and rbcL to infer the phylogeny of 102 taxa in 41 genera plus four outgroup taxa. Our sampling represents a wide taxonomic and geographic diversity from within the family. Results from maximum parsimony and Bayesian analyses provide strong evidence for two major clades in the family, with the platycodonoids sister to the remaining members of the family, the wahlenbergioids and campanuloids. There are two clear divisions within the campanuloids that correspond well with the historical Campanula s.str. and Rapunculus groups ofBoissier and Fedorov. The phylogenetic positions of the Northern European species Wahlenbergia hederacea and the genus Jasione remain unresolved. Our results also provide evidence that the large, inclusive genera Wahlenbergia and Campanula are polyphyletic, and the smaller, segregate genera Symphyandra, Prismatocarpus, and Legousia are not monophyletic. Insights are provided into the different biogeographic origins of several oceanic island endemics. Heterochaenia, Nesocodon, and Berenice occur in a single clade, which suggests a single colonization of the Indian Ocean Mascarene Islands. Conversely, Wahlerrbergia linifolia and W. angustifolia of St. Helena Island in the mid-Atlantic are not sister taxa. The Macaronesian taxa, Canarina canariensis, and Musschia aurea, which display convergent bird-pollination adaptations and with Azorina vidalii of the Azores, woody growth form, fall into separate major lineages. The North American Campanulaceae also do not form a monophyletic group, providing evidence that these taxa are the descendents of multiple introductions onto the North American continent.
TL;DR: It is hypothesize that speciation in the Cousinioid clade was mainly allopatric, and poor phylogenetic resolution probably results from lack of characters and the high number of taxa in this species-rich and comparatively young lineage.
Abstract: The phylogeny and evolution of the Arctium-Cousinia complex, including Arctium, Cousinia as one of the largest genera of Asteraceae, Hypacanthium and Schmalhausenia, is investigated. This group of genera has its highest diversity in the Irano-Turanian region and the mountains of Central Asia. We generated ITS and rpS4-trnT-trnL sequences for altogether 138 species, including 129 (of ca. 600) species of Cousinia. As found in previous analyses, Cousinia is not monophyletic. Instead, Cousinia subgg. Cynaroides and Hypacanthodes with together ca. 30 species are more closely related to Arctium, Hypacanthium and Schmalhausenia (Arctioid clade) than to subg. Cousinia (Cousinioid clade). The Arctioid and Cousiniod clades are also supported by pollen morphology and chromosome number as reported earlier. In the Arctioid clade, the distribution of morphological characters important for generic delimitation, mainly leaf shape and armature and morphology of involucral bracts, are highly incongruent with phylogenetic relationships as implied by the molecular data. No taxonomic solution for this conflict can be offered, and the characters named are interpreted as homoplasious. Although phylogenetic resolution in the Cousinioid clade is poor, our ITS and rpS4-trnT-trnL sequences contain some phylogenetic information. For example, the six annual species of the Cousinioid clade fall into two groups. Poor phylogenetic resolution probably results from lack of characters and the high number of taxa in this species-rich and comparatively young (ca. 8.7 mya) lineage. We hypothesize that speciation in the Cousinioid clade was mainly allopatric.
TL;DR: Mapping the edaphic preferences of Lithospermeae onto molecular cladograms showed that serpentinophytism as an obligate condition originated separately in the clade of monotypic genera and in that of Onosma-Echium.
Abstract: Halacsya and Paramoltkia are monotypic and partially sympatric genera in the Balkans, with no clear relationships among extant Lithospermeae due to striking morphological autapomorphies and scarcity of phylogenetic analyses in this group. The two species H. sendtneri and P. doerfleri show a strict selectivity for serpentine soils, posing the question whether this edaphic specialization reflects a common ancestry or a parallel process of adaptive evolution in unrelated lineages. DNA sequences from the nuclear ITS and chloroplast matK regions were generated from multiple accessions of Halacsya and Paramoltkia, and from representatives of 16 other genera of Mediterranean Lithospermeae. SEM analyses of pollen morphology were also conducted to test relationships indicated by molecular phylogenies. Parsimony analyses retrieved a clade of morphologically well differentiated monotypic Lithospermeae including Halacsya and Paramoltkia. ITS provided a better resolution of relationships and showed the two genera to be sistergroups close to Mairetis and Moltkiopsis, and no affinity to Moltkia as supposed by past authors. Pollen characters corroborated the phylogenetic link between the two Balkan genera. Five further monophyletic clades were recognised: Onosma-Echium, Moltkia, Lithospermum s.I., Arnebia-Macrotomia, and Alkanna-Podonosma. Mapping the edaphic preferences of Lithospermeae onto molecular cladograms showed that serpentinophytism as an obligate condition originated separately in the clade of monotypic genera and in that of Onosma-Echium. In Halacsya and Paramoltkia it represents an early ecological synapomorphy which probably originated in situ from non-serpentine ancestors related to Moltkiopsis and Mairetis.
TL;DR: The complete nuclear ribosomal internal transcribed spacer region was sequenced for 31 species of Abies and its outgroup Keteleeria to reconstruct the phylogeny of the genus and suggest merging sect.
Abstract: Abies comprises ~48 species with a disjunct distribution in the Northern Hemisphere. Despite the economic and ecological importance of the genus, phylogenetic relationships among the species remain unclear. The complete nuclear ribosomal internal transcribed spacer (ITS) region was sequenced for 31 species of Abies and its outgroup Keteleeria to reconstruct the phylogeny of the genus. The results revealed three small subrepeats with a motif (5'-GGCCACCCTAGTC-3'), that is conserved across Pinaceae, and the 298 bp large subrepeats, specific to Abies occurring in all firs. Phylogenetic analysis of ITS recovered nine of the ten formerly recognized sections (sects. Abies, Amabilis, Balsamea, Bracteata, Grandis, Momi, Nobilis, Piceaster, Pseudopicea). The results suggest merging sect. Oiamel and Grandis. The monophyly of western North American species is suggested with robust support by ML and MP analysis. A close relationship between European and Asian species is also inferred, but with weak support.
TL;DR: These analyses suggest that the diversification patterns in Chamaecrista occurred through an initial shift from rainforest trees to a more diverse clade of savannah shrubs, more diverse in open grassland areas and includes many colonizers of waste ground.
Abstract: Chamaecrista Moench is a genus of caesalpinioid legumes with about 330 species mostly from the New World. The phylogeny of the genus was studied using sequence data from nuclear ITS and plastid trnL-F DNA spacers, representing all six sections of Chamaecrista. Separate and combined analyses recovered the same major clades with high bootstrap and posterior probabilities support, except for the subclades of representatives of sections Caliciopsis, Chamaecrista, and Xerocalyx. The monophyly of Chamaecrista was highly supported in all analyses. Sections Apoucouita and Xerocalyx were supported as monophyletic, sect. Absus was paraphyletic and subsect. Baseophyllum was resolved more closely related to species of sections Chamaecrista, Caliciopsis, and Xerocalyx than to subsect. Absus. The monotypic section Grimaldia was embedded within subsect. Absus. Section Chamaecrista was paraphyletic with respect to sections Caliciopsis and Xerocalyx. Our analyses suggest that the diversification patterns in Chamaecrista occurred through an initial shift from rainforest trees to a more diverse clade of savannah shrubs. Within the latter group, two main subclades were recovered: (1) a planaltine and high-mountain clade characterized by absence of extrafloral nectaries and the appearance of sticky glandular hairs; and (2) a mostly herbaceous clade with axillary fascicled inflorescences and reduced chromosome numbers. This last group is more diverse in open grassland areas and includes many colonizers of waste ground.
TL;DR: The results support that Aesculus originated as an element of the Paleogene mesophilic flora in the Beringian region with multiple eastward migrations characterizing the early spatial history of this genus, and supports Trans-Beringian migration of plants in the very early Paleogene.
Abstract: Conflicting phylogenies and biogeographic hypotheses for Aesculus L. were reevaluated using data integrating morphology, fossils, and DNA sequences. A more robust phylogeny of Aesculus was constructed by increasing taxon and character sampling to include 42 morphological characters and five DNA regions including rpsl6, trnHK, matK, ITS, and part of the LEAFY gene. Our analyses revealed three well-supported major lineages in Aesculus. These are sect. Calothyrsus excluding A. californica, sect. Macrothyrsus + A. californica, and sect. Aesculus + sect. Pavia + sect. Parryana. The relationship of sect. Aesculus to sect. Parryana + sect. Pavia is strongly supported and previously unreported. Relationships among the three major clades remained incompletely resolved. Biogeographic and divergence time analyses using DIVA and Multidivtime support a Paleocene origin of Aesculus in eastern Asia and western North America, and showed that the genus subsequently dispersed into eastern North America, Central America, and Europe. Our results support that Aesculus originated as an element of the Paleogene mesophilic flora in the Beringian region with multiple eastward migrations characterizing the early spatial history of this genus. This biogeographic history supports Trans-Beringian migration of plants in the very early Paleogene.
TL;DR: These results demonstrate the usefulness of geometric morphometrics to interrogate multiple independent phenotypic characters and detect individual traits affected by introgression and divergence in taxa with porous genomes.
Abstract: inter-individual component for symmetric aspects and an important intra-individual component for asymmetric aspects of variation in leaf outlines. Symmetric traits displayed a striking variety of phenotypes in hybrids compared to their parental species, consistent with the notion of the phenotypic mosaic. Linear discriminant analysis of these morphometric traits revealed (1) clear differentiation between parental species and (2) divergence between recombinant hybrids and their sympatric backcross parent P. alba, mediated primarily by two P. tremula–like and two transgressive traits. Our results demonstrate the usefulness of geometric morphometrics to interrogate multiple independent phenotypic characters and detect individual traits affected by introgression and divergence in taxa with porous genomes. Digital image-based morphometrics holds great promise for large-scale studies of relationships between DNA polymorphism and phenotypes in evolutionary biology.
TL;DR: The phylogenetic relationships between species within the Cruciata section confirmed the long-standing hypothesis that alpine plants in Central Asia and Europe originated from the QTP and/or West China and diversified extensively after the Pliocene when global temperatures decreased.
Abstract: Gentiana sect. Cruciata is mainly found on alpine mountains across Eurasia, with the greatest species diversity occurring on the Qinghai-Tibetan Plateau (QTP). In this study, we determined the phylogenetic relationships between species within the Cruciata section to further elucidate the biogeographical processes governing these relationships. Phylogenetic reconstructions, based on both parsimony and Bayesian methods, were applied to data from four cpDNA fragments (>3,000 bp) that were obtained for 39 accessions belonging to Cruciata and related sections or outgroups. Our results suggested that all the species sampled within this section comprise a monophyletic group, but rejected all previous hypotheses regarding intra-sectional classifications based on gross morphology. Five clades were identified. The basal clade comprised three species that were endemic to the QTP. The clade that diverged second comprised three Central Asian species. The European clade, containing only G. cruciata, was grouped with the remaining two clades containing species from the QTP and central Asia. The biogeographic analyses and divergence estimates Suggested that this section diversified initially on the QTP within four million years. Given the low genetic differentiation, most species/clades may be the result of more recent differentiation. These results together confirmed the long-standing hypothesis that alpine plants in Central Asia and Europe originated from the QTP and/or West China and diversified extensively after the Pliocene when global temperatures decreased.
TL;DR: Although Hypnea was found to be monophyletic, the distant relationship between H. asiatica and the other species raises questions about divergence pathways within the genus.
Abstract: Hypnea is an economically and ecologically important red alga including about 53 species worldwide. Here, we describe H. asiatica sp. nov. from Korea, Japan, and Taiwan. Specimens of this species from the northwestern Pacific have often been assigned to H. charoides. Hypnea asiatica is distinguished by percurrent main axes, branches with abruptly curved adaxial branchlets, and the presence of lenticular thickening in the walls of medullary cells. It is abundant in wave-exposed sites from summer through fall and produces tetrasporangial sori in fall. We analyzed three genes from three different genomes: nuclear SSU rDNA from 27 specimens, plastid rbcL from 51 specimens, and mitochondrial cox1 from 41 specimens, including putative relatives and H. charoides from Australia. All analyzed DNA datasets produced congruent trees in which H. asiatica was always separated from H. charoides. Network analysis of cox1 haplotypes indicated geographic structuring across the species distribution range. Although Hypnea was found to be monophyletic, the distant relationship between H. asiatica and the other species raises questions about divergence pathways within the genus.
TL;DR: A survey of chloroplast DNA sequence variation within and among twelve populations representing the overall distributional range of the Sino-Japanese floristic region endorsed the recognition of two 'evolutionarily significant units' within P. arguta, corresponding to var.
Abstract: Platycrater arguta (Hydrangeaceae) is a small deciduous shrub of the Sino-Japanese floristic region, where it occurs in montane sites mostly covered with warm-temperate deciduous forest. This sole representative of its genus contains two varieties disjunctly distributed between East China (var. sinensis) and South Japan (var. arguta). To illuminate the biogeographic and demographic history of this rare species, we conducted a survey of chloroplast DNA (cpDNA) sequence variation (trnD-trnE, trnH-psbA) within and among twelve populations (four from China, eight from Japan, 129 individuals in total) representing the overall distributional range of the species. Based on a total of 19 haplotypes identified, P. arguta was found to harbor surprisingly high levels of haplotype and nucleotide diversity (h T = 0.882; π T = 0.00475), possibly associated with its long evolutionary history. Spatial analysis of molecular variance found two regional phylogroups, corresponding to var. sinensis and var. arguta, and supported by genealogical (unrooted network) analysis of haplotypes. Using a coalescent-based model of 'divergence by isolation with migration', the likely vicariant origin of these varieties was dated to the mid-Pleistocene (ca. 0.89 mya). Very similar haplotype mismatch distributions indicate that var. sinensis and var. arguta underwent past demographic growth almost simultaneously (dated to ca. 0.43 and 0.45 mya, respectively), suggesting climate-induced expansion. However, var. sinensis likely experienced a mere demographic expansion in a narrowly circumscribed mountain range, while var. arguta underwent a spatial northward expansion that might have consisted of a series of bottlenecks, leading to genetically impoverished populations that most likely derived from initial population(s) in southern Kyushu. Our results endorse the recognition of two 'evolutionarily significant units' within P. arguta, corresponding to var. sinensis from East China and var. arguta from South Japan.
TL;DR: This is the first molecular study to assess Dipsacaceae phylogeny in detail, and includes representatives from all major subclades, and discusses the taxonomic implications of these results and their significance for understanding character evolution, particularly of the epicalyx in relation to seed dispersal.
Abstract: A phylogenetic study of Dipsacaceae, a Mediterranean-centered clade in the Dipsacales, was conducted using nuclear ITS and three chloroplast markers (atpB-rbcL, trnL-trnF, trnS UGA- trnG GCC ) This is the first molecular study to assess Dipsacaceae phylogeny in detail, and includes representatives from all major subclades Maximum parsimony, maximum likelihood, and Bayesian analyses were carried out on the ITS and plastid datasets separately and in combination For the most part, the ITS and plastid datasets resulted in similar topologies, and the combined data yielded a well-resolved estimate of Dipsacaceae phylogeny A small Asian clade composed of Bassecoia and Pterocephalodes hookeri is resolved as sister to the rest of Dipsacaceae Scabioseae sstr (Scabiosa, Sixalix, Pterocephalus sstr, Lomelosia, Pycnocomon) and a "Dipknautid" clade (Dipsacus, Cephalaria, Knautia, Pterocephalidum, Succisa, Succisella, Pseudoscabiosa) form the two major lineages within Dipsacaceae Most of the previously recognized genera are recovered as monophyletic, with the exception of Pycnocomon, which is nested within Lomelosia We discuss the taxonomic implications of these results and their significance for understanding character evolution, particularly of the epicalyx in relation to seed dispersal
TL;DR: It is shown for the first time that sexually and vegetatively dispersed entities in an anticipated "species pair" (Roccella galapagoensis/R. lirellina) actually form several distinct monophyletic genotypes, here interpreted as species in which sexual reproduction has been repeatedly evolved.
Abstract: The "species pair" concept obscures both intra- and interspecific relationships and should be abandoned, evolutionarily and taxonomically. Based on our molecular phylogenetic work on the genus Roccella we are able to show for the first time that sexually and vegetatively dispersed entities in an anticipated "species pair" (Roccella galapagoensis/R. lirellina) actually form several distinct monophyletic genotypes, here interpreted as species in which sexual reproduction has been repeatedly evolved. The species accepted here are based on a phylogenetic hypothesis supported by data from the ITS rDNA region and an unidentified locus possibly related to calmodulin. Altogether 89 sequences from both loci were newly produced and used in phylogenetic analyses. The Roccella galapagoensis aggregate was resolved as monophyletic. The sister group includes Roccella decipiens (sexual) and R. gracilis (asexual). Based on the present data it is equally parsimonious to suggest a sorediate or a fertile ancestor to the Roccella galapagoensis aggregate. The ancestor must have arrived in the Galapagos Islands through long distance dispersal and have included the ability to reproduce both sexually with ascospores and asexually with soredia. Taxonomy, nomenclature and phylogeny are provided for five American Roccella species in the Roccella galapagoensis aggregate with geographical focus on the Galapagos Islands. One species is obligatory sexual, one is obligatory asexual and three species are facultative sexual/asexual. Roccella albida Tehler is newly described. Roccella canariensis is united with R. tinctoria.
TL;DR: This paper will consider this historical process of biological classification through a series of upheavals, with emphasis on phylogenetic systematics (cladistics), and also consider where it might be heading in the future.
Abstract: Classification has been a centerpiece of biology ever since Linnaeus, providing a framework on which existing knowledge can be organized and predictions about unknown traits can be made. But the basis of biological classification has gone through a series of upheavals over the last three centuries, from being considered a plan in the mind of the creator, to a neutral assessment of overall similarity, to a reflection of evolutionary niches, and finally to a phylogenetic mapping of the tree of life. This paper will consider this historical process, with emphasis on phylogenetic systematics (cladistics), and also consider where we might be heading in the future. It is necessary first, however, to consider the purposes of classification itself, which have not changed much over time.
TL;DR: Although Charles Darwin's presentation of his theory in the Origin of Species, as well as descriptions of Darwinism after the Modern Synthesis of the 1940s, imply that establishing the causal role of natural selection was essential to proving that evolution has occurred, this is contradicted by Darwin's personal experience and by his own words.
Abstract: Darwin's belief in branching evolution was based upon his familiarity with the taxonomy of his day. Facts from biogeography, embryology, and paleontology acquired deep significance because biologists had come to believe that natural classification expressed real relationships. Although Charles Darwin's presentation of his theory in the Origin of Species, as well as descriptions of Darwinism after the Modern Synthesis of the 1940s, imply that establishing the causal role of natural selection was essential to proving that evolution has occurred, this is contradicted by Darwin's personal experience and by his own words. It is helpful to compare the history and logical structure of Darwin's revolutionary theory to the Copernican Revolution, for the moving Earth was recognized long before Newton identified causes to explain its motion. Copernicus saw that fixing the Sun as the center of planetary motion explained the appearance of the heavens better than the Ptolemaic system did, and Darwin saw that branching evolution explains the "truly wonderful fact" that a hierarchy of nested groups appears natural.
TL;DR: This work addresses evolutionary relationships in the Spermacoceae alliance (Rubioideae) with special emphasis on the Asian genera Mouretia and Neohymenopogon, here sequenced for the first time.
Abstract: Several recent phylogenetic studies of Rubiaceae have dealt with enigmatic taxa whose systematic positions have been previously unknown or controversial. We address evolutionary relationships in the Spermacoceae alliance (Rubioideae) with special emphasis on the Asian genera Mouretia and Neohymenopogon, here sequenced for the first time. Both genera belong in the tribe Argostemmateae and have persistent calyx lobes on the fruit in common with Argostemma and Mycetia. Other previous uncertainties are resolved with strong support; Saprosma is sister to Paederieae s. str. and Carpacoce is sister to remaining Anthospermeae. Our results further reveal some phylogenetic problems. Danaideae is sister to remaining taxa in the Spermacoceae alliance with high posterior probability, which contradicts results in a recent study. The uncertainty concerning evolutionary relationships of Dunnia and Theligonum is reinforced, despite a denser taxon sampling in the Spermacoceae alliance compared with earlier studies. We also demonstrate yet another example of the controversial correlation between molecular substitution rate and plant life history.
TL;DR: ITS, rpl16 and trnG sequences, together with morphological data, were used to circumscribe the European problematic taxa within the Sciuro-hypnum reflexum complex and several of the target taxa were sustained as distinct species.
Abstract: ITS, rpl16 and trnG sequences, together with morphological data, were used to circumscribe the European problematic taxa within the Sciuro-hypnum reflexum complex. Strongly supported monophyletic clades sustain several of the target taxa as distinct species (S. reflexum, S. starkii, S. tromsoeense, S. glaciale, S. dovrense, S. latifolium). The segregation of S. nelsonii and Brachythecium glaciale var. gelidum is found to be inconsistent with our results and the two taxa are therefore synonymized.
TL;DR: The resulting phylogeny is in agreement with other data such as phytochemistry and provides a framework for further investigation of character evolution in Lamiales.
Abstract: Phylogenetic placement of Triaenophora together with Rehmannia were explored with DNA sequence data from five regions (rbcL, ndhF, rps16, trnL-F, nr ITS) in two combined data matrices. One (rbcL, ndhF, rps16) represented a wide sampling across most families of Lamiales. The other data matrix represented two DNA regions partly unalignable across Lamiales (trnL-F, nr ITS) plus rps16, which proved to be variable enough to give resolution at a smaller taxonomic level in Lamiales. Triaenophora rupestris and Rehmannia are sister taxa, composing a strongly supported clade, which is sister to all representative genera of Orobanchaceae. Furthermore, Paulowniaceae and Phrymaceae are next to Orobanchaceae and Triaenophora-Rehmannia clade. All of the above taxa are only distantly related to Scrophulariaceae and/or Plantaginaceae (sensu APG II). Mazus and Lancea would be excluded from Phrymaceae. The resulting phylogeny is in agreement with other data such as phytochemistry and provides a framework for further investigation of character evolution in Lamiales.