Chloroplast DNA Sequence Data Research Articles

Updated Taxonomy of Iris scariosa (Iridaceae) Inferred from Morphological and Chloroplast DNA Sequence Data with Remarks on Classification of Iris subg. Iris.

Iris scariosa is a rhizomatous perennial whose taxonomy and distribution range still remain unclear. The results of our examination of literature, specimens, and wild plants have shown that I. glaucescens, described from Kazakhstan, and I. timofejewii, considered to be endemic to the Republic of Dagestan, Russia, are very closely related to I. scariosa. We have carried out molecular phylogenetic analyses for the first time to clarify the taxonomy of I. scariosa. For this, we sequenced six chloroplast DNA regions of an extended sampling that comprised the accepted species I. glaucescens and I. timofejewii, which has revealed their strong affinity to the accession of I. scariosa from the vicinity of Astrakhan, Russia. A thorough revision of the morphological characters has confirmed the lack of evident differences between I. scariosa and I. timofejewii. Thus, the analyses support a broad species circumscription of I. scariosa. We here reduce I. timofejewii, as well as I. curvifolia, considered to be endemic to Xinjiang, western China, to synonymy of I. scariosa. Color illustrations, updated nomenclature, and data on distribution of I. scariosa are provided. A lectotype for I. astrachanica and a neotype for I. timofejewii are designated here. Also, the phylogenetic relationships within I. subg. Iris are outlined, and an updated classification of the subgenus is proposed. We have recovered six major lineages within four major clades which we recognize as sections. Here, we propose two new nomenclatural combinations, a revised taxonomic treatment, and a new identification key to I. subg. Iris.

An overview of floral and vegetative evolution in the Asian clade of Bulbophyllum (Orchidaceae)

Background and aims – Bulbophyllum, the largest genus in Orchidaceae, exhibits a diverse morphology in both reproductive and vegetative characters. While trait diversity and evolution has been extensively studied in Malagasy species and within the Cirrhopetalum alliance clade, the evolution of reproductive and vegetative characters at the whole level of the Asian clade remains largely unexplored. Material and methods – We reconstructed the phylogeny of approximately 11% of all Asian Bulbophyllum species using Bayesian inference and maximum likelihood estimation based on nuclear (ITS) and chloroplast (matK, psbA-trnH) DNA sequence data. This phylogenetic framework allowed us to examine the evolution of two vegetative and four floral characters through ancestral state reconstruction. Key results and conclusion – The ancestral character states of the Asian clade of Bulbophyllum include a single leaf, distinct pseudobulbs, multiple-flowered inflorescences, and lateral and dorsal sepals similar in length. One-leaved pseudobulbs evolved into two-leaved pseudobulbs multiple times. Distinct pseudobulbs gave rise to indistinct pseudobulbs twice. Multiple-flowered inflorescences shifted to solitary flowers and 2–3-flowered inflorescences multiple times, with some instances of evolutionary reversal. Lateral sepal elongation also presents a convergent evolutionary scenario.

Silene fuscata'nın Anadolu'daki Varlığının Moleküler Açıdan Araştırılması

Silene fuscata is an annual species distributed to a wide geography including Eastern Mediterranean, Northern Africa, and Southern Europe. The native range of this species is known as the Mediterranean Region. Presence of S. fuscata in Anatolia is reported by several comprehensive botanical literatures; however, the actual situation has never been investigated thoroughly. This study focuses on the occurrence of S. fuscata in Anatolia. In order to determine the existence of this species in the aforementioned area, nuclear and chloroplast-DNA sequence data from a wide range of Silene samples were analyzed. DNA sequence analyses and other available evidence display no support for the presence of S. fuscata in Anatolia.

Artemisiaqingheensis (Asteraceae, Anthemideae), a new species from Xinjiang, China.

Artemisiaqingheensis (Asteraceae, Anthemideae), a new species from Qinghe County, Xinjiang, China, is described and illustrated. We investigated its phylogenetic position and relationships with 35 other species of Artemisia using whole chloroplast DNA sequence data. The molecular phylogenetic results and morphological evidence (multi-layered involucral bracts and homogamous capitula with bisexual flowers) showed that the new species belongs to ArtemisiasubgenusSeriphidium. A diagnostic table and discussion of morphological characters are provided to distinguish the new species from A.amoena, A.gracilescens, A.lessingiana and A.terrae-albae.

Phylogenetic Reconstruction of the Rainforest Lineage Fontainea Heckel (Euphorbiaceae) Based on Chloroplast DNA Sequences and Reduced-Representation SNP Markers

Fontainea is a plant genus with nine recognised species that occur across the tropical and subtropical rainforests of Australia, Papua New Guinea, New Caledonia, and Vanuatu. One of these species is cultivated commercially as the source of a cancer therapeutic, and several other species are under threat of extinction. Despite this, the phylogenetic relationships of the genus have not been explored. Our study assessed the phylogeny of seven Fontainea taxa from the Australian and Pacific Island complex using chloroplast DNA sequence data and reduced-representation genome sequencing. Maximum-likelihood and consensus network trees were used to infer the topology of phylogenetic relationships between species, which highlighted three distinct lineages and a number of sister species. Our results indicated that the geographically disjunct species Fontainea venosa and F. pancheri formed a sister group at the earliest position of divergence for the genus. The data also revealed that the vulnerable Fontainea australis and the critically endangered F. oraria form a sister subclade with evidence of some shared plastid genotypes. Generally, our phylogenetic reconstruction supports the modern taxonomical nomenclature. However, we suggest further accessions across several species may support improved genetic distinctions between the sister groups of Fontainea within the genus.

Molecular evidence for natural hybridization between Rumex crispus and R. obtusifolius (Polygonaceae) in Korea

Interspecific hybridization has been suggested to occur frequently in Rumex (Polygonaceae). Several hypothesized combinations of parental species of hybrids based on their intermediate morphology have been suggested in the genus, but few of them have been phylogenetically tested. We analyzed nuclear and chloroplast DNA sequence data of a putative natural hybrid between Rumex crispus and Rumex obtusifolius from Korea to confirm its hybrid status and to determine the maternal parent. Analysis of the nuclear DNA pgiC region revealed that R. crispus and R. obtusifolius have contributed to the nuclear genome of the putative hybrids. The haplotype distribution pattern inferred from the combined sequence data set of five chloroplast DNA regions (matK, rbcL-accD IGS, trnK-rps16 IGS, ycf6-psbM IGS and psbA-trnH IGS) indicated bidirectional hybridization events between R. crispus and R. obtusifolius. This paper provides the first molecular evidence for interspecific hybridization between R. crispus and R. obtusifolius. In addition, our findings strongly suggested that Korean populations of Rumex japonicus have a hybrid origin, and R. crispus may represent one of the parental taxa.

The evolutionary history of the Caribbean magnolias (Magnoliaceae): Testing species delimitations and biogeographical hypotheses using molecular data

The Caribbean islands provide an ideal setting for studying biodiversity, given their complex geological and environmental history, and their historical and current geographical proximity to the American mainland. Magnolia, a flagship tree genus that has 15 endemic and threatened taxa (12 species and 3 subspecies) on the Caribbean islands, offers an excellent case study to empirically test Caribbean biogeographical hypotheses. We constructed phylogenetic hypotheses to: (1) reveal their evolutionary history, (2) test the current largely morphology-based classification and assess species limits, and (3) investigate major biogeographic hypotheses proposed for the region. Nuclear and chloroplast DNA sequence data of all 15 Caribbean Magnolia taxa are included, supplemented by a selection of American mainland species, and species representing most major clades of the Magnoliaceae family. We constructed phylogenetic hypotheses in a time-calibrated Bayesian framework, supplemented with haplotype network analyses and ancestral range estimations. Genetic synapomorphies in the studied markers confirm the species limits of 14 out of 15 morphologically recognizable Caribbean Magnolia taxa. There is evidence for four colonization events of Magnolia into the Caribbean from the American mainland, which most likely occurred by overwater dispersal, given age estimates of maximum 16 mya for their presence on the Caribbean islands.

Phylogenetic relationship, biogeography, and conservation genetics of endangered Fraxinus chiisanensis (Oleaceae), endemic to South Korea

Endemic plants are important for understanding phylogenetic relationships, biogeographical history, and genetic variation because of their restricted distribution and their role in conserving biodiversity. Here, we investigated the phylogenetic relationships of the Korean endemic Fraxinus chiisanensis by reconstructing the molecular phylogeny of Fraxinus based on two nuclear DNA (nrITS and phantastica) and two chloroplast DNA (psbA-trnH and rpl32-trnL) regions. Within our fossil-calibrated phylogenetic framework, we also inferred the biogeographical history of F. chiisanensis. To provide a scientific basis for the conservation of F. chiisanensis, we determined the levels of genetic diversity and genetic differentiation in this species. Combining information from nuclear and chloroplast DNA sequence data, our molecular phylogenetic analyses identified F. chiisanensis as a genetically distinct unit from its sister group, Fraxinus platypoda from Japan. Our molecular dating analyses using nuclear and chloroplast DNA data sets show F. chiisanensis diverged from its sister F. platypoda in the Early or Middle Miocene and differentiated in the Late Miocene on the Korean Peninsula. Our results suggest that the divergence of F. chiisanensis was associated with the submergence of the East China Sea land bridge and enhanced monsoons in East Asia. When compared to F. platypoda, F. chiisanensis exhibits low genetic diversity within populations and high genetic differentiation among populations. These results help us to understand the evolutionary history of F. chiisanensis and to develop a conservation strategy for this species.

Identification of three independent fern gametophytes and Hymenophyllum wrightii f. serratum from Korea based on molecular data

Colonies of three independent gametophytes (one that is filamentous and two that are ribbon-like) without sporophytes occur in Gyeonggi-do, Gangwon-do, Gyeongsang-do, and Jeju-do, Korea. They have a moss-like appearance at first sight, with tiny plantlets and gemmae, and grow in cool, shaded, relatively deep dint places of large rocks, such as the small caves in high mountains, close to valleys. The gametophytes were identified based on morphological and molecular data by chloroplast DNA (cpDNA) sequence data (rbcL, rps4 gene and rps4-trnS intergenic spacer). Here, rbcL, rps4 gene and rps4-trnS intergenic spacer data of one independent gametophyte distributed in Korea have the same morphology, DNA sequence and monophyletic group as Crepidomanes intricatum from the eastern United States. They also share the same cpDNA data with Crepidomanes schmidtianum recently reported from Korea. The other independent gametophyte should be Hymenophyllum wrightii based on cpDNA data. The last one was presumed to be Pleurosoriopsis makinoi based on molecular data. The taxonomic status was confirmed to be the forma of Hymenophyllum wrightii through a revision of Hymenophyllum wrightii f. serratum based on molecular data.

Genetic diversity and population structure of the endangered orchid Pelatantheria scolopendrifolia (Orchidaceae) in Korea.

Due to substantial population decline, the Korean orchid P. scolopendrifolia is considered endangered and highly threatened. Like many endangered species, it is vulnerable to biological and anthropogenic threats that can lead to the loss of genetic diversity and, ultimately, extinction. Therefore, the assessment of genetic diversity and population genetic structure is imperative for conservation. In this study, we newly developed 15 polymorphic microsatellite markers. Analyses of genetic diversity and population genetic structure that included 182 samples from 11 populations were conducted using microsatellite markers and four noncoding regions of chloroplast DNA. Our study revealed a relatively low level of genetic diversity (Ho = 0.529, He = 0.356), albeit harboring with private alleles based on microsatellite genotyping data, and high haplotype diversities based on chloroplast DNA sequences data. The results of STRUCTURE and PCoA based on microsatellite genotyping data showed population differentiations. An AMOVA based on chloroplast DNA sequence data further corroborated these conclusions, indicating about 70% of variations found among populations. Low genetic diversity and divergence among the population might have been caused by factors, such as asexual reproduction, demographic events (bottleneck and population expansion), geographic isolation, and low gene flow. The development and implication of conservation strategies and management of P. scolopendrifolia are proposed based on these results.

Phylogenetic relationships in the southern African genus Drosanthemum (Ruschioideae, Aizoaceae).

BackgroundDrosanthemum, the only genus of the tribe Drosanthemeae, is widespread over the Greater Cape Floristic Region in southern Africa. With 114 recognized species, Drosanthemum, together with the highly succulent and species-rich tribe Ruschieae, constitute the ‘core ruschioids’ in Aizoaceae. Within Drosanthemum, nine subgenera have been described based on flower and fruit morphology. Their phylogenetic relationships, however, have not yet been investigated, hampering understanding of monophyletic entities and patterns of geographic distribution.MethodsUsing chloroplast and nuclear DNA sequence data, we performed network- and tree-based phylogenetic analyses of 73 species of Drosanthemum with multiple accessions for widespread species. A well-curated, geo-referenced occurrence dataset comprising the 134 genetically analysed and 863 further accessions was used to describe the distributional ranges of intrageneric lineages and the genus as a whole.ResultsPhylogenetic inference supports nine clades within Drosanthemum, seven of which group in two major clades, while the remaining two show ambiguous affinities. The nine clades are generally congruent to previously described subgenera within Drosanthemum, with exceptions such as cryptic species. In-depth analyses of sequence patterns in each gene region were used to reveal phylogenetic affinities inside the retrieved clades in more detail. We observe a complex distribution pattern including widespread, species-rich clades expanding into arid habitats of the interior (subgenera Drosanthemum p.p., Vespertina, Xamera) that are genetically and morphologically diverse. In contrast, less species-rich, genetically less divergent, and morphologically unique lineages are restricted to the central Cape region and more mesic conditions (Decidua, Necopina, Ossicula, Quastea, Quadrata, Speciosa). Our results suggest that the main lineages arose from an initial rapid radiation, with subsequent diversification in some clades.

Genetic differentiation among Psittacanthus rhynchanthus (Loranthaceae) populations: novel phylogeographic patterns in the Mesoamerican tropical lowlands

Historical geological events and climatic changes have played important roles in shaping population differentiation and distribution within species. In this study, we analysed the distribution, expansion and colonization patterns, and genetic differentiation among Psittacanthus rhynchanthus populations in Mesoamerica. Specifically, we determine the effects of major historical events and geographic barriers on population divergence using nuclear and chloroplast DNA sequence data and the impact of Pleistocene glacial cycles on the distribution dynamics of P. rhynchanthus using ecological niche modelling (ENM). Our results showed that P. rhynchanthus populations split into two lineages, one distributed on the Yucatan Peninsula and the second along the Pacific and Atlantic slopes and Honduras, approximately 1 million years ago. The two lineages were fragmented at the last interglacial according to ENM predictions and experienced postglacial range expansion during the Last Glacial Maximum. Analysis of climate differentiation and niche models showed that both lineages have different climatic preferences, where the climatic characteristics of the Yucatan populations are not fully represented in the rest of the distribution range of P. rhynchanthus. Additionally, our study suggests that Pleistocene expansion of suitable habitat, environmental segregation (ecological barrier between regions) and, perhaps host shifts, have acted as the isolation mechanisms between the two lineages. Our results provide new insight as to understanding the distribution and phylogeographic patterns and the possible mechanisms underlying intraspecific evolutionary relationships of plants in the Mesoamerican tropical lowlands.

An infrageneric classification of Thesium (Santalaceae) based on molecular phylogenetic data

AbstractRecent phylogenetic hypotheses reveal that Thesium (Santalaceae) is paraphyletic with respect to Austroamericium, Chrysothesium, Kunkeliella and Thesidium, suggesting the need for generic realignment. In addition, existing subgeneric and sectional classifications of this large genus lack a phylogenetic basis, thus compromising their predictive value. Using an expanded taxon sampling and a combination of nuclear (ITS) and chloroplast (matK, rpl32‐trnL, trnL‐F) DNA sequence data, we therefore re‐assessed the phylogenetic relationships of Thesium and used these as the basis of a new subgeneric classification of the genus. Our phylogeny confirms the need to sink the four segregate genera to render Thesium monophyletic. In addition, it resolves five well‐supported major clades within Thesium that we recognize as subgenera. Within Thesium, the South African endemic subgenus Hagnothesium is sister to the Eurasian subgenus Thesium (including Kunkeliella and Mauritanica). The subgenus Psilothesium, occurring in tropical South America (formerly genus Austroamericium) and tropical Africa, is sister to the rest of the subgenera, which are all confined to South Africa. Within the latter, the subgenus Discothesium consists of subtropical and temperate species, whereas subgenus Frisea, comprising the previously recognized sections Annulata, Barbata, Frisea, Imberbia and Penicillata, is entirely of the Greater Cape Floristic Region. To facilitate identification of subgenera, we identify morphological ancestral characters and present an identification key, brief diagnoses, species assigned, distribution and ecological data.

A review of the fern genus Pellaea (Pteridaceae) in Australasia

Five indigenous species of Pellaea in Australasia belong to section Platyloma. Their taxonomic history is outlined, morphological, cytological and genetic evidence for their recognition reviewed, and new morphological and chloroplast DNA-sequence data provided. Australian plants of P. falcata (R.Br.) Fée are diploid and have longer, narrower pinnae than do New Zealand plants previously referred to P. falcata, which are tetraploid. Evidence indicates that P. falcata does not occur in New Zealand, and that collections so-named are P. rotundifolia (G.Forst.) Hook. Chloroplast DNA sequences are uninformative in distinguishing Australian P. falcata from New Zealand P. rotundifolia, but show that Australian P. nana is distinct from both. Sequence data also show that Australian and New Zealand populations of P. calidirupium Brownsey & Lovis are closely related, and that Australian P. paradoxa (R.Br.) Hook. is distinct from other Australian species. Although P. falcata is diploid and P. rotundifolia tetraploid, P. calidirupium, P. nana (Hook.) Bostock and P. paradoxa each contain multiple ploidy levels. Diploid populations of Pellaea species are confined to Australia, and only tetraploids are known in New Zealand. Evolution of the group probably involved hybridisation, autoploidy, alloploidy, and possibly apomixis. Further investigation is required to resolve the status of populations from Mount Maroon, Queensland and the Kermadec Islands.

Morphological and genetic evidence for the separation of Phlegmariurus billardierei from P. varius (Lycopodiaceae)

ABSTRACTPhlegmariurus varius is an Australasian species of lycophyte that has long been recognised as morphologically and ecologically variable. A recent study reported incongruence between morphological and genetic variation within New Zealand samples. However, a reappraisal and repeat of the genetic analyses of chloroplast DNA sequence data, and a more detailed examination of morphological variation, strongly supports the recognition of two species that are sympatric in New Zealand. The combination Phlegmariurus billardierei (Spring) Brownsey & Perrie is made here for plants with distinct strobili. The other species, Phlegmariurus varius (R.Br.) A.R.Field & Bostock sensu stricto, has comparatively indistinct strobili, and remains morphologically and ecologically variable even after the segregation of P. billardierei. Phlegmariurus varius is indigenous to both Australia and New Zealand, while P. billardierei is the only species of Lycopodiaceae endemic to New Zealand.

New morphological and DNA evidence supports the existence of Calligonum jeminaicum Z. M. Mao (Calligoneae, Polygonaceae) in China.

Calligonum jeminaicum Z. M. Mao, a species regarded as endemic to China, was thought to be nonexistent owing to a lack of scientific records. The similarity of C. jeminaicum to C. mongolicum Turcz. warranted an investigation into the taxonomical relationship between these species. In this study, a naturally occurring population of C. jeminaicum was discovered and the taxonomical relationships of this species with C. mongolicum were resolved. Morphological traits, including fruit and flower characteristics, as well as nuclear (ETS, ITS) and chloroplast (psbA-trnH, ycf6-psbM, rpl32-trnL, rbcL, and trnL-F) DNA sequence data were studied to confirm the taxonomic status of C. jeminaicum. The nrDNA data (ITS1-2 and ETS) from C. jeminaicum reflected variability from the whole C. mongolicum complex, showing distinctive haplotypes in the Calligonum sect. Medusa Sosk. & Alexandr. The cpDNA data supplied similar evidence, showing unique branching in Bayesian and ML tree analyses. The specific status of C. jeminaicum is confirmed based on both morphological and molecular analyses. Here we present a revised description of C. jeminaicum along with its DNA barcode and discuss suggestions for the conservation of this species. Based on current evidence, this species was evaluated as Critically Endangered (CR) according to the IUCN criteria.

Phylogeographic Analysis and Genetic Structure of an Endemic Sino-Japanese Disjunctive Genus Diabelia (Caprifoliaceae).

The Sino-Japanese Floristic Region (SJFR) is a key area for plant phylogeographical research, due to its very high species diversity and disjunct distributions of a large number of species and genera. At present, the root cause and temporal origin of the discontinuous distribution of many plants in the Sino-Japanese flora are still unclear. Diabelia (Caprifoliaceae; Linnaeoideae) is a genus endemic to Asia, mostly in Japan, but two recent discoveries in China raised questions over the role of the East China Sea (ECS) in these species' disjunctions. Chloroplast DNA sequence data were generated from 402 population samples for two regions (rpl32-trnL, and trnH-psbA) and 11 nuclear microsatellite loci were screened for 549 individuals. Haplotype, population-level structure, combined analyses of ecological niche modeling, and reconstruction of ancestral state in phylogenies were also performed. During the Last Glacial Maximum (LGM) period after the Tertiary, Diabelia was potentially widely distributed in southeastern China, the continental shelf of the East China Sea and Japan (excluding Hokkaido). After LGM, all populations in China have disappeared except those in Zhejiang which may represent a Glacial refuge. Populations of Diabelia in Japan have not experienced significant bottleneck effects, and populations have maintained a relatively stable state. The observed discontinuous distribution of Diabelia species between China and Japan are interpreted as the result of relatively ancient divergence. The phylogenetic tree of chloroplast fragments shows the characteristics of multi-origin evolution (except for D. sanguinea). STRUCTURE analysis of nuclear Simple Sequence Repeat (nSSR) showed that the plants of the Diabelia were divided into five gene pools: D. serrata, D. spathulata, D. sanguinea, D. ionostachya (D. spathulata var. spathulata-Korea), and populations of D. ionostachya var. ionostachya in Yamagata prefecture, northern Japan. Molecular evidence provides new insights of Diabelia into biogeography, a potential glacial refuge, and population-level genetic structure within species. In the process of species differentiation, ECS acts as a corridor for two-way migration of animals and plants between China and Japan during glacial maxima, providing the possibility of secondary contact for discontinuously distributed species between China and Japan, or as a filter (creating isolation) during glacial minima. The influence of the ECS in speciation and biogeography of Diabelia in the Tertiary remains unresolved in this study. Understanding origins, evolutionary histories, and speciation will provide a framework for the conservation and cultivation of Diabelia.

Exploring natural hybridizations among <i>Asplenium ruprechtii</i> and related taxa in Korea

The purported four hybrid origins of Asplenium in Korea were tested based on morphological, cytological and DNA sequence data. Asplenium castaneo-viride, A. × uiryeongse, A. × montanus, and A. × kitazawae share several morphological characteristics with the Asian walking fern A. ruprechtii and related taxa as parents and show a sympatric distribution with the putative parents, raising the possibility of hybrid origins: A. castaneo-viride (A. ruprechtii and A. incisum), A. × uiryeongse (A. ruprechtii and A. pekinense), A. × montanus (A. ruprechtii, A. trichomanes, and A. incisum), and A. × kitazawae (A. ruprechtii and A. sarelii). We investigated flow cytometry and chloroplast DNA sequence data (rbcL, rps4-trnS, and rps4-trnS intergenic spacer) to clarify the hybridization and origin of each hybrid. In the flow cytometry analyses, A. ruprechtii shows diploid (2x) only, whereas A. castaneo-viride (3x, 4x), A. × uiryeongse (3x), A. × montanus (3x, 4x), and A. × kitazawae (2x, 4x) exhibit polyploidy, suggesting hybrid events along speciation. The rbcL and rps4-trnS and rps4-trnS intergenic spacer data suggest that A. ruprechtii is one the maternal ancestors of all four hybrids. In addition, the rps4-trnS and rps4-trnS intergenic spacer data indicate that A. incisum is also the maternal ancestor of A. × kitazawae and A. × montanus, proposing multiple hybridization events for these two hybrids. In A. × montanus, morphological features such as the leaf forms and sympatric distributions of the species also support the multimaternal hypothesis, but the morphological features of A. × kitazawae must be examined with consideration of hybrid events. To clarify the complex hybrid evolutionary lineages of the four Asplenium hybrids, further research with taxon sampling and molecular markers should be conducted.

Fern and lycophyte diversity in the Pacific Northwest: Patterns and predictors

AbstractRecent floristic efforts in the Pacific Northwest (PNW) have now made it possible to characterize the broad‐scale patterns of fern and lycophyte diversity across this large and geologically‐complex region of western North America. The physiography of the PNW has been developing for over 200 million years, but Pleistocene glaciation‐induced migrations and recolonizations have strongly influenced the assembly of the flora. With the high dispersal potential of fern and lycophyte spores, the distribution patterns of pteridophytes may be representative of habitat suitability more than dispersal constraints. Our objective was to describe the biodiversity of pteridophytes in the PNW, determine the spatial distribution of that biodiversity in terms of phylogenetic diversity, identify centers of regional endemism, explore the correlations between biodiversity and environmental variables, and infer possible influences of past glaciation on the pteridophyte flora. We obtained presence‐only distribution data from two online databases. A phylogenetic tree was constructed using chloroplast DNA sequence data from GenBank. We used the Biodiverse software package to estimate and map phylogenetic diversity and phylogenetic endemism across the PNW, and to identify those regions of the PNW where diversity was higher or lower than expected in comparison to randomization models. Environmental correlates of diversity were identified using principal components analysis with bioclimatic data from WorldClim.org, and we used Maxent to predict habitat suitability for species under past and future climate conditions. We found evidence for the influence of past glaciations and glacial refugia on the patterns of pteridophyte diversity, that moisture availability and cold temperatures are strongly correlated with patterns of genus richness, phylogenetic diversity, and phylogenetic endemism. We infer that the topographic complexity of the region may be driving the assembly of the pteridophyte flora indirectly by influencing climate and precipitation patterns.

Phylogenetics and dispersal patterns of Brassicaceae around the Qinghai–Tibet Plateau

AbstractBrassicaceae, one of the most diverse and economically valuable plant families, is distributed all over the world. Previous studies have suggested that Brassicaceae originated and diversified in the Old World. In this study, the phylogenetic relationships of 17 tribes of Brassicaceae from the Qinghai–Tibet Plateau (QTP) and adjacent areas were investigated using nuclear ribosomal internal transcribed spacer (nrITS) and chloroplast DNA sequence data (rbcL and petB‐petD) with maximum likelihood, maximum parsimony, and Bayesian methods. As suggested by both the nrITS and chloroplast DNA trees, Cardaria pubescens (C.A.Mey.) Jarm. (Lepidieae) and Draba lanceolata Royle (Arabideae) should be classified in the Eutremeae and Cardamineae, respectively. Based on over 700 newly sequenced and published nrITS sequences of Brassicaceae, an up‐to‐date comprehensive phylogeny of the family was reconstructed using the maximum likelihood method. In the phylogenetic tree, 10 monophyletic tribes were detected. They were used to clarify the lineage diversification and dispersal patterns of the 10 tribes. The results showed that most of the monophyletic tribes may have originated in different regions of the world, and then dispersed into other regions surrounding the QTP. Rapid lineage diversification rate shifts were detected in several tribes, such as Anastaticeae, which experienced a rapid shift event ∼1.38 Mya, corresponding to the rapid uplift of the QTP, indicating that the recent uplift of the QTP could have promoted diversification in Brassicaceae across and adjacent to the QTP.