Evolutionary history of Gymnocarpos (Caryophyllaceae) in the arid regions from North Africa to Central Asia

Gymnocarpos has only about ten species distributed in the arid regions of Asia and Africa, but it exhibits a geographical disjunction between eastern Central Asia and western North Africa and Minor Asia. We sampled eight species of the genus and sequenced two chloroplast regions (rps16 and psbB–psbH), and the nuclear rDNA (ITS) to study the phylogeny and biogeography. The results of the phylogenetic analyses corroborated that Gymnocarpos is monophyletic, in the phylogenetic tree two well supported clades are recognized: clade 1 includes Gymnocarpos sclerocephalus and G. decandrus, mainly the North African group, whereas clade 2 comprises the remaining species, mainly in the Southern Arabian Peninsula. Molecular dating analysis revealed that the divergence age of Gymnocarpos was c. 31.33 Mya near the Eocene and Oligocene transition boundary, the initial diversification within Gymnocarpos dated to c. 6.69 Mya in the late Miocene, and the intraspecific diversification mostly occurred during the Quaternary climate oscillations. Ancestral area reconstruction suggested that the Southern Arabian Peninsula was the ancestral area for Gymnocarpos. Our conclusions revealed that the aridification since mid‐late Miocene significantly affected the diversification of the genus in these areas.     

The Phylogeny and Biogeographic History of Ashes (Fraxinus,Oleaceae) Highlight the Roles of Migration and Vicariance in the Diversification of Temperate Trees

The cosmopolitan genus Fraxinus, which comprises about 40 species of temperate trees and shrubs occupying various habitats in the Northern Hemisphere, represents a useful model to study speciation in long-lived angiosperms. We used nuclear external transcribed spacers (nETS), phantastica gene sequences, and two chloroplast loci (trnH-psbA and rpl32-trnL) in combination with previously published and newly obtained nITS sequences to produce a time-calibrated multi-locus phylogeny of the genus. We then inferred the biogeographic history and evolution of floral morphology. An early dispersal event could be inferred from North America to Asia during the Oligocene, leading to the diversification of the section Melioides sensus lato. Another intercontinental dispersal originating from the Eurasian section of Fraxinus could be dated from the Miocene and resulted in the speciation of F. nigra in North America. In addition, vicariance was inferred to account for the distribution of the other Old World species (sections Sciadanthus, Fraxinus and Ornus). Geographic speciation likely involving dispersal and vicariance could also be inferred from the phylogenetic grouping of geographically close taxa. Molecular dating suggested that the initial divergence of the taxonomical sections occurred during the middle and late Eocene and Oligocene periods, whereas diversification within sections occurred mostly during the late Oligocene and Miocene, which is consistent with the climate warming and accompanying large distributional changes observed during these periods. These various results underline the importance of dispersal and vicariance in promoting geographic speciation and diversification in Fraxinus. Similarities in life history, reproductive and demographic attributes as well as geographical distribution patterns suggest that many other temperate trees should exhibit similar speciation patterns. On the other hand, the observed parallel evolution and reversions in floral morphology would imply a major influence of environmental pressure. The phylogeny obtained and its biogeographical implications should facilitate future studies on the evolution of complex adaptive characters, such as habitat preference, and their possible roles in promoting divergent evolution in trees.     

An expanded phylogeny of Cuphea (Lythraceae) and a North American monophyly

A phylogenetic analysis of the New World genus Cuphea was conducted employing sequences from the nuclear rDNA internal transcribed spacer (ITS) and chloroplast trnL-trnF spacer and rpl16 intron. The analysis expands the number of Cuphea species from 53 in an earlier ITS study to 70 and adds two chloroplast data sets in order to generate a more complete and robust phylogeny and to test a previous result that suggested the presence of a large North American clade. Results reaffirm the monophyly of Cuphea with Pleurophora as the sister genus and recover a basal divergence event that mirrors the two subgenera of the current classification. Phylogenies of the two chloroplast regions are largely unresolved beyond the initial dichotomy and some resolution at the terminal and subterminal nodes. Based on the ITS phylogeny, five major clades are recognized. Subgenus Cuphea (Clade 1), defined morphologically by the synapomorphic loss of bracteoles, is sister to the much larger subg. Bracteolatae (Clades 2–5). Clades 2–4, comprising the South American and Caribbean species, grade successively to Clade 5, an exclusively North American lineage of 29 species. Among the 12 sections included in the study, only section Trispermum, a subclade of Clade 4, is monophyletic. Section Pseudocircaea is nested within Clade 3, which is largely equivalent to section Euandra. The North American endemic clade includes four sections, of which none are recovered as monophyletic in this study.     

Genetic relationships among American species of the genus Prosopis (Mimosoideae, Leguminosae) inferred from ITS sequences: evidence for long-distance dispersal

Aim  The genus Prosopis includes 44 species and has a pseudoamphitropical, disjunct distribution. We aimed to determine whether American Prosopis sections arose in North or South America, and to explain the current distribution of their species on the basis of their genetic relationships.
Location  South-western USA, Mexico, Caribbean Antilles, Peru–Ecuador, central and northern Argentina, south-western Argentina (Patagonia) and Cuyo, south-western Asia and northern Africa.
Methods  Internal transcribed spacer fragments from 21 species of Prosopis were sequenced and the data were used to analyse the phylogenetic relationships using Microlobius and Mimosa as outgroups. Genetic distances were calculated to estimate the degree of divergence. Dispersal–vicariance (DIVA) analysis was conducted to help understand the biogeographical history of the genus.
Main conclusions  The sections Strombocarpa and Algarobia are not monophyletic. Prosopis argentina (section Monilicarpa ) and the species of Algarobia are included in single clade. The phylogeny, DIVA analysis, and the pattern of genetic distances indicate that the ancestral area for the American species was wide, from south-western USA to Central and northern Argentina. Successive vicariance events split this area, and long-distance dispersal episodes (perhaps mediated by birds) led to recolonizations from North to South America, and vice versa .     

Phylogeny and biogeography of wild roses with specific attention to polyploids

Background and Aims The genus Rosa (150–200 species) is widely distributed throughout temperate and sub-tropical habitats from the northern hemisphere to tropical Asia, with only one tropical African species. In order to better understand the evolution of roses, this study examines infrageneric relationships with respect to conventional taxonomy, considers the extent of allopolyploidization and infers macroevolutionary processes that have led to the current distribution of the genus.Methods Phylogenetic relationships among 101 species of the genus Rosa were reconstructed using sequences from the plastid psbA-trnH spacer, trnL intron, trnL-F spacer, trnS-G spacer and trnG intron, as well as from nuclear glyceraldehyde 3-phosphate dehydrogenase (GAPDH), which was used to identify putative allopolyploids and infer their possible origins. Chloroplast phylogeny was used to estimate divergence times and reconstruct ancestral areas.Key Results Most subgenera and sections defined by traditional taxonomy are not monophyletic. However, several clades are partly consistent with currently recognized sections. Allopolyploidy seems to have played an important role in stabilizing intersectional hybrids. Biogeographic analyses suggest that Asia played a central role as a genetic reservoir in the evolution of the genus Rosa.Conclusions The ancestral area reconstruction suggests that despite an early presence on the American continent, most extant American species are the results of a later re-colonization from Asia, probably through the Bering Land Bridge. The results suggest more recent exchanges between Asia and western North America than with eastern North America. The current distribution of roses from the Synstylae lineage in Europe is probably the result of a migration from Asia approx. 30 million years ago, after the closure of the Turgai strait. Directions for a new sectional classification of the genus Rosa are proposed, and the analyses provide an evolutionary framework for future studies on this notoriously difficult genus.     

Against all odds: reconstructing the evolutionary history of <Emphasis Type="Italic">Scrophularia</Emphasis> (Scrophulariaceae) despite high levels of incongruence and reticulate evolution

The figwort genus Scrophularia (Scrophulariaceae), widespread across the temperate zone of the Northern Hemisphere, comprises about 250 species and is a taxonomically challenging lineage displaying large morphological and chromosomal diversity. Scrophularia has never been examined in a large-scale phylogenetic and biogeographic context and represents a useful model for studying evolutionary history in the context of reticulation. A comprehensively sampled phylogeny of Scrophularia was constructed, based on nuclear ribosomal (ITS) and plastid DNA sequences (trnQ-rps16 intergenic spacer, trnL-trnF region) of 147 species, using Bayesian inference and maximum likelihood approaches. Selected individuals were cloned. A combination of coding plastid indels and ITS intra-individual site polymorphisms, and applying Neighbor-Net and consensus network methods for adequate examination of within-dataset uncertainty as well as among-dataset incongruence, was used to disentangle phylogenetic relationships. Furthermore, divergence time estimation and ancestral area reconstruction were performed to infer the biogeographic history of the genus. The analyses reveal significant plastid-nuclear marker incongruence and considerable amounts of intra-individual nucleotide polymorphism in the ITS dataset. This is due to a combination of processes including reticulation and incomplete lineage sorting, possibly complicated by inter-array heterogeneity and pseudogenization in ITS in the presence of incomplete concerted evolution. Divergence time estimates indicate that Scrophularia originated during the Miocene in Southwestern Asia, its primary center of diversity. From there, the genus spread to Eastern Asia, the New World, Europe, Northern Africa, and other regions. Hybridization and polyploidy played a key role in the diversification history of Scrophularia, which was shaped by allopatric speciation in mountainous habitats during different climatic periods.     

Molecular phylogeny and historical biogeography of the genus Tuber, the 'true truffles'

Aim Various data sets and methods of analysis were combined to produce the first comprehensive molecular phylogeny of the genus Tuber and to analyse its biogeography. Location Europe, North Africa, China, Asia, North America. Methods Phylogenetic relationships among Tuber species were reconstructed based on a data set of internal‐transcribed spacer (ITS) sequences and various phylogenetic inference methods, specifically maximum parsimony, Bayesian analysis and neighbour joining. Tajima’s relative rate test showed that Tuber 18S rRNA, 5.8S rRNA, 5.8S‐ITS2 rRNA and β‐tubulin sequences evolved in a clock‐like manner. These genes, combined or not, were employed for molecular clock estimates after construction of linearized trees using mega 3.1. We reconstructed ancestral areas in the Northern Hemisphere by means of a dispersal–vicariance analysis (diva 1.1) based on current distribution patterns of the genus Tuber determined from the literature. Results The resulting molecular phylogeny divided the genus Tuber into five distinct clades, in agreement with our previously published studies. The Puberulum, Melanosporum and Rufum groups were diversified in terms of species and geographical distribution. In contrast, the Aestivum and Excavatum groups were less diversified and were located only in Europe or North Africa. Using a global molecular clock analysis, we estimated the divergence times for the origin of the genus and for the origin of several groups. diva inferred nine dispersal events and suggested that the ancestor of Tuber was originally present in Europe or was widespread in Eurasia. Equally optimal distributions were obtained for several nodes, suggesting different possible biogeographical patterns. Main conclusions Our analyses identified several discrepancies with the classical taxonomy of the genus, and we propose a new phylogenetic classification. According to molecular clocks, the radiation of the genus Tuber could have started between 271 and 140 Ma. Used in combination with the results obtained from time divergence estimates, this allows us to propose two equally probable scenarios of intra‐ and inter‐continental diversification of the genus according to the geographic distribution of the most recent common ancestor in Europe or Eurasia. The biogeographical patterns imply intra‐continental dispersal events between Europe and Asia and inter‐continental dispersal events between North America and Europe or Asia, which are compatible with land connections during the Tertiary.     

Evolutionary history of spiny‐tailed lizards (Agamidae: Uromastyx) from the Saharo‐Arabian region

The subfamily Uromastycinae within the Agamidae is comprised of 18 species: three within the genus Saara and 15 within Uromastyx. Uromastyx is distributed in the desert areas of North Africa and across the Arabian Peninsula towards Iran. The systematics of this genus has been previously revised, although incomplete taxonomic sampling or weakly supported topologies resulted in inconclusive relationships. Biogeographic assessments of Uromastycinae mostly agree on the direction of dispersal from Asia to Africa, although the timeframe of the cladogenesis events has never been fully explored. In this study, we analysed 129 Uromastyx specimens from across the entire distribution range of the genus. We included all but one of the recognized taxa of the genus and sequenced them for three mitochondrial and three nuclear markers. This enabled us to obtain a comprehensive multilocus time‐calibrated phylogeny of the genus, using the concatenated data and species trees. We also applied coalescent‐based species delimitation methods, phylogenetic network analyses and model‐testing approaches to biogeographic inferences. Our results revealed Uromastyx as a monophyletic genus comprised of five groups and 14 independently evolving lineages, corresponding to the 14 currently recognized species sampled. The onset of Uromastyx diversification is estimated to have occurred in south‐west Asia during the Middle Miocene with a later radiation in North Africa. During its Saharo‐Arabian colonization, Uromastyx underwent multiple vicariance and dispersal events, hypothesized to be derived from tectonic movements and habitat fragmentation due to the active continental separation of Arabia from Africa and the expansion and contraction of arid areas in the region.     

Molecular phylogeny and historical biogeography of the Holarctic wetland leaf beetle of the genus Plateumaris

Leaf beetles of the genus Plateumaris inhabit wetlands across the temperate zone of the Holarctic region. To explore the phylogeographic relationships among North American, East Asian, and European members of this genus and the origin of the species endemic to Japan, we studied the molecular phylogeny of 20 of the 27 species in this genus using partial sequences of mitochondrial cytochrome oxidase subunit I (COI) and the 16S and nuclear 28S rRNA genes. The molecular phylogeny revealed that three species endemic to Europe are monophyletic and sister to the remaining 11 North American and six Asian species. Within the latter clade, North American and Asian species did not show reciprocal monophyly. Dispersal-vicariance analysis and divergence time estimation revealed that the European and North America-Asian lineages diverged during the Eocene. Moreover, subsequent differentiation occurred repeatedly between North American and Asian species, which was facilitated by three dispersal events from North America to Asia and one in the opposite direction during the late Eocene through the late Miocene. Two Japanese endemics originated from different divergence events; one differentiated from the mainland lineage after differentiation from the North American lineage, whereas the other showed a deep coalescence from the North American lineage with no present-day sister species on the East Asian mainland. This study of extant insects provides molecular phylogenetic evidence for ancient vicariance between Europe and East Asia-North America, and for more recent (but pre-Pleistocene) faunal exchanges between East Asia and North America.     

A tale of worldwide success: Behind the scenes of Carex (Cyperaceae) biogeography and diversification

The megadiverse genus Carex (c. 2000 species, Cyperaceae) has a nearly cosmopolitan distribution, displaying an inverted latitudinal richness gradient with higher species diversity in cold‐temperate areas of the Northern Hemisphere. Despite great expansion in our knowledge of the phylogenetic history of the genus and many molecular studies focusing on the biogeography of particular groups during the last few decades, a global analysis of Carex biogeography and diversification is still lacking. For this purpose, we built the hitherto most comprehensive Carex‐dated phylogeny based on three markers (ETS–ITS–matK), using a previous phylogenomic Hyb‐Seq framework, and a sampling of two‐thirds of its species and all recognized sections. Ancestral area reconstruction, biogeographic stochastic mapping, and diversification rate analyses were conducted to elucidate macroevolutionary biogeographic and diversification patterns. Our results reveal that Carex originated in the late Eocene in E Asia, where it probably remained until the synchronous diversification of its main subgeneric lineages during the late Oligocene. E Asia is supported as the cradle of Carex diversification, as well as a “museum” of extant species diversity. Subsequent “out‐of‐Asia” colonization patterns feature multiple asymmetric dispersals clustered toward present times among the Northern Hemisphere regions, with major regions acting both as source and sink (especially Asia and North America), as well as several independent colonization events of the Southern Hemisphere. We detected 13 notable diversification rate shifts during the last 10 My, including remarkable radiations in North America and New Zealand, which occurred concurrently with the late Neogene global cooling, which suggests that diversification involved the colonization of new areas and expansion into novel areas of niche space.     

Molecular systematics and global phylogeography of angel sharks (genus Squatina)

Angel sharks of the genus Squatina represent a group comprising 22 extant benthic species inhabiting continental shelves and upper slopes. In the present study, a comprehensive phylogenetic reconstruction of 17 Squatina species based on two mitochondrial markers (COI and 16S rRNA) is provided. The phylogenetic reconstructions are used to test biogeographic patterns. In addition, a molecular clock analysis is conducted to estimate divergence times of the emerged clades. All analyses show Squatina to be monophyletic. Four geographic clades are recognized, of which the Europe–North Africa–Asia clade is probably a result of the Tethys Sea closure. A second sister group relationship emerged in the analyses, including S. californica (eastern North Pacific) and S. dumeril (western North Atlantic), probably related to the rise of the Panamanian isthmus. The molecular clock analysis show that both lineage divergences coincide with the estimated time of these two geological events.     

Integrated Fossil and Molecular Data Reveal the Biogeographic Diversification of the Eastern Asian-Eastern North American Disjunct Hickory Genus (Carya Nutt.)

The hickory genus (Carya) contains ca. 17 species distributed in subtropical and tropical regions of eastern Asia and subtropical to temperate regions of eastern North America. Previously, the phylogenetic relationships between eastern Asian and eastern North American species of Carya were not fully confirmed even with an extensive sampling, biogeographic and diversification patterns had thus never been investigated in a phylogenetic context. We sampled 17 species of Carya and 15 species representing all other genera of the Juglandaceae as outgroups, with eight nuclear and plastid loci to reconstruct the phylogeny of Carya. The phylogenetic positions of seven extinct genera of the Juglandaceae were inferred using morphological characters and the molecular phylogeny as a backbone constraint. Divergence times within Carya were estimated with relaxed Bayesian dating. Biogeographic analyses were performed in DIVA and LAGRANGE. Diversification rates were inferred by LASER and APE packages. Our results support two major clades within Carya, corresponding to the lineages of eastern Asia and eastern North America. The split between the two disjunct clades is estimated to be 21.58 (95% HPD 11.07-35.51) Ma. Genus-level DIVA and LAGRANGE analyses incorporating both extant and extinct genera of the Juglandaceae suggested that Carya originated in North America, and migrated to Eurasia during the early Tertiary via the North Atlantic land bridge. Fragmentation of the distribution caused by global cooling in the late Tertiary resulted in the current disjunction. The diversification rate of hickories in eastern North America appeared to be higher than that in eastern Asia, which is ascribed to greater ecological opportunities, key morphological innovations, and polyploidy.     

Using multilocus approach to uncover cryptic diversity within Pseudotrapelus lizards from Saudi Arabia

The agamid Pseudotrapelus lizards inhabit the mountainous areas of the Arabian Peninsula and eastern North Africa. Currently six Pseudotrapelus species are recognised, though diagnostic morphological characters are still lacking, creating great difficulty in describing new species. Recently, two specimens of Pseudotrapelus were collected from the vicinity of Riyadh in central Saudi Arabia, an area that was not sampled in previous phylogenetic studies. In here we used both mitochondrial and nuclear data to investigate the phylogenetic position of the new samples, and assess their phylogenetic relationships with the other recognised species of Pseudotrapelus from across the distribution range of the genus. We used a multilocus approach of haplotype networks, concatenated datasets and species trees, performed mitochondrial and nuclear species delimitation analyses, and estimated divergence times. In general, our results support previous molecular studies and uncover the presence of cryptic diversity within Pseudotrapelus. The phylogenetic structure of the genus is of two major clades and within them seven distinct, delimited phylogenetic groups belonging to the six recognised species and the seventh to the individuals from Riyadh. The Riyadh specimens were distinct in all analyses performed. We suggest that the new specimens from the Riyadh area are a distinct lineage, forming a clade with their phylogenetic relatives, P. sinaitus and P. chlodnickii. The clade formed by these three species diverged during the Late Miocene around 6.4 Ma, with cladogenesis possibly facilitated by vicariance and isolation caused due to climatic fluctuations and the progression of sandy areas. Our results suggest further morphological research is necessary to revise the taxonomic status of this lineage and of the entire genus.     

African origin and global distribution patterns: Evidence inferred from phylogenetic and biogeographical analyses of ectomycorrhizal fungal genus Strobilomyces

Aim

The ectomycorrhizal genus Strobilomyces is widely distributed throughout many parts of the world, but its origin, divergence and distribution patterns remain largely unresolved. In this study, we aim to explore the species diversity, distribution and evolutionary patterns of Strobilomyces on a global scale by establishing a general phylogenetic framework with extensive sampling.

Location

Africa, Australasia, East Asia, Europe, North America, Central America and Southeast Asia.

Methods

The genealogical concordance phylogenetic species recognition method was used to delimit phylogenetic species. Divergence times were estimated using a Bayesian uncorrelated lognormal relaxed molecular clock. The ancestral area and host of Strobilomyces were inferred via the programs rasp and mesquite . The change of diversification rate over time was estimated using Ape, Laser and Bammtools software packages.

Results

We recognize a novel African clade and 49 phylogenetic species with morphological evidence, including 18 new phylogenetic species and 23 previously described ones. Strobilomyces probably originated in Africa, in association with Detarioideae/Phyllanthaceae/Monotoideae during the early Eocene. The dispersal to Southeast Asia can be explained by Wolfe's “Boreotropical migration” hypothesis. East Asia, Australasia, Europe and North/Central America are primarily the recipients of immigrant taxa during the Oligocene or later. A rapid radiation implied by one diversification shift was inferred within Strobilomyces during the Miocene.

Main conclusions

An unexpected phylogenetic species diversity within Strobilomyces was uncovered. The highest diversity, resulting probably from a rapid radiation, was found in East Asia. Dispersal played an important role in the current distribution pattern of Strobilomyces. The Palaeotropical disjunction is explained by species dispersal from Africa to Southeast Asia through boreotropical forests during the early Eocene. Species from the Northern Hemisphere and Australasia are largely derived from immigrant ancestors from Southeast Asia.     

A New Fishfly Species (Megaloptera: Corydalidae: Neohermes Banks) Discovered from North America by a Systematic Revision,with Phylogenetic and Biogeographic Implications

The taxonomy of Megaloptera from the Nearctic region is fairly well known and their faunal diversity has been largely surveyed, even in relatively remote regions. However, the evolutionary history of Nearctic Megaloptera is still poorly known with phylogenetic and biogeographic studies lacking. In this paper, we report a new fishfly species of the endemic North American genus Neohermes Banks, 1908, increasing the total number known of species to six. This new species (Neohermes inexpectatus sp. nov.) is currently known to occur only in California (USA) and is apparently confined to the Northern Coastal Range. The new species resembles the three Neohermes species from eastern North America based on the relatively small body size and the presence of female gonostyli 9. However, our phylogenetic analysis using adult morphological data recovered the new species as the sister species to the remaining Neohermes, which includes two species from western North America and three from eastern North America. According to the present interspecific phylogeny of Neohermes, with reconstructed ancestral areas, the initial divergence within the genus was found to take place in western North America, with a subsequent eastward dispersal. This likely lead to the modern distribution of Neohermes in eastern North America with the closure of the Mid-Continental Seaway, which separated western and eastern North America in the Mid-Late Cretaceous (100–80 MYA) and finally disappeared at the end of the Cretaceous (70 MYA). The uplift of the Cordilleran System probably accounted for the divergence between the eastern and two western Neohermes species.     

Dynamic colonization exchanges between continents and islands drive diversification in paradise‐flycatchers (Terpsiphone,Monarchidae)

Aim We use parametric biogeographical reconstruction based on an extensive DNA sequence dataset to characterize the spatio‐temporal pattern of colonization of the Old World monarch flycatchers (Monarchidae). We then use this framework to examine the role of dispersal and colonization in their evolutionary diversification and to compare plumages between island and continental Terpsiphone species. Location Africa, Asia and the Indian Ocean. Methods We generate a DNA sequence dataset of 2300 bp comprising one nuclear and three mitochondrial markers for 89% (17/19) of the Old World Monarchidae species and 70% of the Terpsiphone subspecies. By applying maximum likelihood and Bayesian phylogenetic methods and implementing a Bayesian molecular clock to provide a temporal framework, we reveal the evolutionary history of the group. Furthermore, we employ both Lagrange and Bayes‐ Lagrange analyses to assess ancestral areas at each node of the phylogeny. By combining the ancestral area reconstruction with information on plumage traits we are able to compare patterns of plumage evolution on islands and continents. Results We provide the first comprehensive molecular phylogenetic reconstruction for the Old World Monarchidae. Our phylogenetic results reveal a relatively recent diversification associated with several dispersal events within this group. Moreover, ancestral area analyses reveal an Asian origin of the Indian Ocean and African clades. Ancestral state reconstruction analyses of plumage characters provide an interpretation of the plumage differentiation on islands and continents. Ancestral plumage traits are inferred to be close to those of the Asian paradise‐flycatcher (Terpsiphone paradisi), and island species display a high degree of plumage autapomorphy compared with continental species. Main conclusions Terpsiphone paradisi is polyphyletic and comprises populations that have retained the ancestral plumage of the widespread Terpsiphone genus. The genus appears to have colonized south‐west Asia, the Indian Ocean and Africa from eastern Asia. The phylogeny and divergence time estimates indicate multiple simultaneous colonizations of the western Old World by Terpsiphone. These results reinforce a hypothesis of range expansions of a Terpsiphone paradisi‐like ancestor into eastern Asia and the western Old World.     

Molecular Phylogeny and Biogeography of Petaurista Inferred from the Cytochrome b Gene,with Implications for the Taxonomic Status of P. caniceps,P. marica and P. sybilla

The polymorphic genus Petaurista includes a group of diverse species and subspecies that are adapted for gliding and arboreal life. This morphological diversity has resulted in taxonomic discrepancies, and molecular phylogenetic studies have been limited by taxon sampling. To clarify this controversial taxonomy, we used the cytochrome b gene to reconstruct the phylogeny to obtain a more accurate picture of the evolutionary relationships, species differentiation and divergence pattern of Petaurista. The results revealed a significant inconsistency between taxonomic designations, phylogeny and genetic distances. When 6 recognized species were included, species delimitation revealed 15 putative species, a finding that warrants a comprehensive morphological diagnosis and a re-assessment of the species status. The validity of P. caniceps and P. marica was discussed. An estimation of the molecular divergence time demonstrated that the diversification and speciation of Petaurista began during the later Miocene and may have been affected by the uplifting of the Qinghai-Tibet plateau and subsequent climate change.     

Chloroplast genomic diversity in Bulbophyllum section Macrocaulia (Orchidaceae,Epidendroideae, Malaxideae): Insights into species divergence and adaptive evolution

Bulbophyllum is the largest genus in Orchidaceae with a pantropical distribution. Due to highly significant diversifications, it is considered to be one of the most taxonomically and phylogenetically complex taxa. The diversification pattern and evolutionary adaptation of chloroplast genomes are poorly understood in this species-rich genus, and suitable molecular markers are necessary for species determination and phylogenetic analysis. A natural Asian section Macrocaulia was selected to estimate the interspecific divergence of chloroplast genomes in this study. Here, we sequenced the complete chloroplast genome of four Bulbophyllum species, including three species from section Macrocaulia. The four chloroplast genomes had a typical quadripartite structure with a genome size ranged from 156,182 to 158,524 bp. The chloroplast genomes included 113 unique genes encoding 79 proteins, 30 tRNAs and 4 rRNAs. Comparison of the four chloroplast genomes showed that the three species from section Macrocaulia had similar structure and gene contents, and shared a number of indels, which mainly contribute to its monophyly. In addition, interspecific divergence level was also great. Several exclusive indels and polymorphism SSR loci might be used for taxonomical identification and determining interspecific polymorphisms. A total of 20 intergenic regions and three coding genes of the most variable hotspot regions were proposed as candidate effective molecular markers for future phylogenetic relationships at different taxonomical levels and species divergence in Bulbophyllum. All of chloroplast genes in four Bulbophyllum species were under purifying selection, while 13 sites within six genes exhibited site-specific selection. A whole chloroplast genome phylogenetic analysis based on Maximum Likelihood, Bayesian and Parsimony methods all supported the monophyly of section Macrocaulia and the genus of Bulbophyllum. Our findings provide valuable molecular markers to use in accurately identifying species, clarifying taxonomy, and resolving the phylogeny and evolution of the genus Bulbophyllum. The molecular markers developed in this study will also contribute to further research of conservation of Bulbophyllum species.     

Biogeographical history of cuckoo‐shrikes (Aves: Passeriformes): transoceanic colonization of Africa from Australo‐Papua

Aim Cuckoo‐shrikes and allies (Campephagidae) form a radiation of birds widely distributed in the Indo‐Pacific and Africa. Recent studies on the group have been hampered by poor taxon sampling, causing inferences about systematics and biogeography to be rather speculative. With improved taxon sampling and analyses within an explicit spatiotemporal framework, we elucidate biogeographical patterns of dispersal and diversification within this diverse clade of passerine birds. Location Africa, Asia, Australo‐Papua, the Pacific, the Philippines and Wallacea. Methods We use model‐based phylogenetic methods (Mr Bayes and garli ) to construct a phylogenetic hypothesis of the core Campephagidae (Campephagidae with the exclusion of Pericrocotus). The phylogeny is used to assess the biogeographical history of the group with a newly developed Bayesian approach to dispersal–vicariance analysis (Bayes‐diva) . We also made use of a partitioned beast analysis, with several calibration points taken from island ages, passerine mitochondrial substitution rates and secondary calibration points for passerine birds, to assess the timing of diversification and dispersal. Results We present a robust molecular phylogeny that includes all genera and 84% of the species within the core Campephagidae. Furthermore, we estimate divergence dates and ancestral area relationships. We demonstrate that Campephagidae originated in Australo‐Papua with a single lineage (Pericrocotus) dispersing to Asia early. Later, there was further extensive transoceanic dispersal from Australo‐Papua to Africa involving lineages within the core Campephagidae radiation. Main conclusions The phylogenetic relationships, along with the results of the ancestral area analysis and the timing of dispersal events, support a transoceanic dispersal scenario from Australo‐Papua to Africa by the core Campephagidae. The sister group to core Campephagidae, Pericrocotus, dispersed to mainland Asia in the late Oligocene. Asia remained uncolonized by the core Campephagidae until the Pliocene. Transoceanic dispersal is by no means an unknown phenomenon, but our results represent a convincing case of colonization over a significant water gap of thousands of kilometres from Australo‐Papua to Africa.     

Species, genomes, and section relationships in the genus Arachis (Fabaceae): a molecular phylogeny

The economically important genus Arachis (Fabaceae) comprises 80 species restricted to South America. One monograph on the genus divided it into nine sections and included an intuitive assessment of evolutionary relationships. There is no comprehensive phylogenetic study of the genus. To test the current systematic treatment of the genus, we reconstructed a phylogeny for Arachis using nuclear ITS and plastid trnT–trnF sequences from 46 species representing all nine sections. ITS cloning of the allotetraploid species of section Arachis indicated the presence of A and B genome alleles and chimeric sequences. Our study revealed that species from section Extranervosae were the first emerging lineage in the genus, followed by sections Triseminatae and Caulorrhizae, and two terminal major lineages, which we refer to as erectoides and arachis. The lineage erectoides comprises members of sections Erectoides, Heteranthae, Procumbentes, Rhizomatosae, and Trierectoides. Species in the arachis lineage form two major clades, arachis I (B and D genomes species and the aneuploids) and arachis II (A genome species). Our results substantiated the sectional treatment of Caulorrhizae, Extranervosae, and Triseminatae, but demonstrated that sections Erectoides, Procumbentes, and Trierectoides are not monophyletic. A detailed study of the genus Arachis with denser taxon sampling, additional genomic regions, plus information from morphology and cytogenetics is needed for comprehensive assessment of its systematics.