Ancestral Area Research Articles

Global phylogeography of the flood mosquito, Aedes vexans (Diptera: Culicidae), from mitochondrial DNA

This contribution endeavored to investigate the genetic structure and gene flow of the flood mosquito, Aedes vexans (Meigen, 1830). Using partial sequences of the mitochondrial COI gene, available from BOLD Systems and GenBank, the Haplotypic (Hd) and nucleotide (π) gene diversity, genetic structuring and gene flow of A. vexans at the global, continental, and country levels were calculated. In total, 1,184 sequences were obtained, distributed among America (88.60%; represented by EUA and Canada), Europe (7.35%), Asia (3.89%), and Africa (0.17%). From these, 395 haplotypes (H) without presence of pseudogenes (NUMTs) were detected. The cluster analyses grouped the haplotypes into six clades. Clade I includes haplotypes from countries in America and Europe, while clades II and III include haplotypes exclusively from Asia and Europe; clade IV grouped only one haplotype from Africa and clade V grouped haplotypes from America and Africa. The global Hd and π were 0.92 and 0.01, respectively. In addition, there is evidence of genetic structuring among continents (7.07%), countries (1.62%), and within countries (91.30%; FST = 0.08, p < 0.05) and no isolation by distance was detected (r = 0.003, p > 0.05). The genetic diversity of A. vexans was found to be greater in North America than in other continents. Although this provisional conclusion might be influenced by a sample bias, since 88.60% of the sequences are from America, is also plausible to consider that America corresponds to the ancestral distribution area of the flood mosquito. This hypothesis needs further testing, using a more comprehensive sample from other continents. Additionally, the six clusters found and their geographical distribution do not support previous proposals of splitting the genus into three subspecies confined to certain geographical areas.

PHYLOGENY AND EVOLUTIONARY HISTORY OF VIETNAMESE Arisaema (ARACEAE)

In the family Araceae, Arisaema Mart is one of the largest genera with 200 species in the world, and mainly distributed in the temperate and warm-temperate areas from the East to South-East of North America to northern Mexico, from tropical East and North-East Africa to the Arabian Penisula, and from temperate East Asia to South and South-East Asia and Malesia. Several species of Arisaema are used as food and local medicine in India, China and Vietnam. Exploring the relationship between plants and explaining where plants originated and how they migrated between regions in the world and Vietnam is still challenging. Construction of molecular phylogeny, estimations of the divergence time and ancestral area of lineages based on evidences of molecular data, fossils, geology have provided major insights into plant evolution. This study was conducted based on comprehensive taxon sampling and molecular data from four chloroplast DNA regions of Arisaema to determine the phylogeny and evolutionary history of Vietnamese Arisaema (Araceae). The phylogeny of Arisaema was studied by using ML and BI methods. Our results indicated that Arisaema originated in Southeast Asia at ca. 31 Ma during the Oligocene and that Vietnamese Arisaema was derived from the Southeast Asia Arisaema during climate optimum period of Mid-Miocene with the presence and development of the tropical rainforest. Whereas, Vietnamese Arisaema likely does not have any connection with Arisaema from India, North China, Japan and the Korean Peninsula regions

Phylogeny and phylogeography of Diestramima cave crickets (Orthoptera: Rhaphidophoridae): speciation driven by multiple dispersal and vicariance events

AbstractCave crickets (Orthoptera: Rhaphidophoridae) are an understudied family with poor dispersal abilities and broad distributions, which makes them ideal for investigations of historical biogeography. Within Rhaphidophoridae, Diestramima is the largest genus of the tribe Diestramimini, and most species are endemic to China. It was divided into three subgenera based only on morphological characteristics, and no molecular evidence has been previously reported. Here, we reconstruct the phylogeny and phylogeography of Diestramima based on three mitochondrial (COI, 12S rRNA and 16S rRNA) and two nuclear fragments (18S rRNA and 28S rRNA). A total of 114 samples representing 28 morphological species were sampled from China. Molecular phylogenies were reconstructed using Bayesian inference and maximum likelihood and four approaches (ABGD, jMOTU, GMYC and bPTP) were employed to delimit species. Phylogenetic analyses highly supported the monophyly of Diestramima, but did not support the classification system consisting of three subgenera. Species delimitation methods suggested 28 species, among which six new species were described: Diestramima furcata Zhu &amp; Shi sp. n., Diestramima spinata Zhu &amp; Shi sp. n., Diestramima qionglaiensis Zhu &amp; Shi sp. n., Diestramima taiwanensis Zhu &amp; Shi sp. n., Diestramima longifolia Zhu &amp; Shi sp. n., Diestramima sichuanensis Zhu &amp; Shi sp. n. Divergence time estimation and reconstruction of ancestral areas indicated that Diestramima may have originated from Southern Yunnan at 17.72 Ma (95% highest probability density: 14.71–21.05 Ma) in the early Miocene. The initial divergence within the genus was likely to be correlated with geographical isolation. Most speciation events have occurred since the Pliocene, possibly driven by multiple dispersal and vicariance events and influenced by the uplift of the Himalaya–Tibetan plateau and climate change.ZooBank URL: http://zoobank.org/urn:lsid:zoobank.org:pub:D461A536‐6728‐4547‐9EC4‐AF56D3BB9000. http://zoobank.org/urn:lsid:zoobank.org:act:5FA4075B‐4CD2‐43A5‐B109‐D32882CCF369. http://zoobank.org/urn:lsid:zoobank.org:act:C3D02B4E‐1442‐456F‐BD59‐C811716F0704. http://zoobank.org/urn:lsid:zoobank.org:act:E022BD2C‐8A69‐4C00‐B008‐129DE9ABB229. http://zoobank.org/urn:lsid:zoobank.org:act:4E5552E4‐78CB‐498F‐ABB6‐98D56BEC6FBC. http://zoobank.org/urn:lsid:zoobank.org:act:480E002C‐4B82‐4F0D‐B421‐2AFD9F333333. http://zoobank.org/urn:lsid:zoobank.org:act:220EE409‐293B‐4ACC‐B853‐090EF226123D.

World Travelers: Parthenogenesis and Ecological Tolerance Enable Multiple Colonization Events by the Widespread Short-Tailed Whipscorpion, Stenochrus portoricensis (Schizomida: Hubbardiidae)

Abstract Whereas morphology remains a powerful tool for the diagnosis and description of short-tailed whip scorpions, or schizomids (Order Schizomida Petrunkevitch, 1945), especially when adults of both sexes are available, the systematics of some schizomid taxa is difficult to resolve due to a lack of characters in these morphologically conserved arachnids. Stenochrus portoricensis Chamberlin, 1922, defined on a single character of the female spermathecae, is the most widespread schizomid in the New World. Numerous records in the Neotropics, from the southern United States to Brazil, throughout the Caribbean, and further afield, including the Galapagos Islands and Europe, raise the question as to whether S. portoricensis is indeed a single widespread species or a complex of multiple species with conserved morphology? The present study uses a multilocus dataset and the broadest geographical sample currently available to address the phylogeography of S. portoricensis with molecular divergence dating and ancestral area reconstruction of all currently known species of Stenochrus Chamberlin, 1922. Analyses recovered S. portoricensis as paraphyletic. Two species previously synonymized are revalidated and transferred to Stenochrus. Population structure analyses recovered the remaining samples of S. portoricensis as a single monophyletic species with low genetic divergence and comprising two subclades. Ancestral area reconstruction suggests a Mesoamerican origin for Stenochrus, which contains a widespread species, recently introduced to multiple localities. Introductions to Europe and the Caribbean occurred from a single clade in the Yucatán Peninsula, Mexico, within which genetic divergence is minimal, confirming the hypothesis of multiple independent introductions with successful colonization facilitated by parthenogenetic reproduction.

Palaeobiogeography of the family Nisusiidae (Cambrian rhynchonelliform brachiopods) using the ‘area‐transition count’ method and systematic revision of Korean species

AbstractNisusiidae is a rhynchonelliform brachiopod family that was widely distributed in low‐latitude regions during the middle Cambrian (Stage 3 of Series 2 to the Drumian Stage of the Miaolingian Series). Cladistic analysis of 24 nisusiid species including two species from South Korea (Nisusia paucicostellata and Nisusiidae gen. et sp. indet.) demonstrates that the nisusiids consist of two sister clades (Clade 1 and 2) whose common ancestor was derived from a paraphyletic ‘basal’ group. Non‐spinose taxa are all included in Clade 1, while spinose Nisusia species are found throughout the three groups including Clade 1, indicating paraphyly of Nisusia. The optimized ancestral area(s) are assigned to internal nodes of the taxon area cladogram using both the Fitch algorithm and the DIVALIKE+J model of BioGeoBEARS, and then the relationship between cladogenetic area transition types and palaeogeographical areas is examined using the ‘area‐transition count’ method. Of 10 possible cladogenetic area transitions, which are combinations of range contraction (C), expansion (E), switch (S) and no range change (N), six (CC, CE, CN, EN, NN and NS) are observed in the two optimization results. It is proposed that the nisusiids originated in Laurentia as a strongly spinose form and dispersed into high‐latitude peri‐Gondwana during Stage 3 and then strongly diversified into other areas during Stage 4, and that non‐spinose forms evolved later, mainly in Laurentia. The nisusiid palaeobiogeographical pattern is interpreted to reflect distributional range changes that were probably caused by palaeo‐oceanic currents with the aid of island arcs as stepping stones, and pumice, produced by volcanic activity, as the means of dispersal.

Reconstruction of the evolutionary biogeography reveals the origins of Alpinia Roxb. (Zingiberaceae): A case of “out-of-Asia” migration to the Southern Hemisphere

Alpinia is considered the largest genus of Zingiberaceae with ca. 250 species occurring in tropical and subtropical Asia, Australia, and Pacific Islands. The historical biogeography of Alpinia was conducted to explain where Alpinia originated and how it migrated to other regions. The phylogeny, divergence times and ancestral area reconstruction of Alpinia were performed by using the molecular data based on the comprehensive taxon sampling. Our results provide an objective approach to understand the historical biogeography of Alpinia. The genus originated in Asia during the Late Cretaceous ca. 69 Ma and started to diverge after the K-Pg boundary during the early Paleocene with the presence and development of the tropical rainforest and a warm, moist climate. Alpinia migrated to Malesia and then dispersed to Australasia. The molecular analyses supported the diversification of Alpinia in Asia and Malesia. Additionally, the Indian Alpinia has likely a common ancestor with Renealmia and Aframomum, and it is possible that after originating in Asia, Alpinia migrated from Asia to India then to Africa during the early period of collision between the Indian subcontinent and Eurasia to form the common ancestor of Indian Alpinia, Renealmia, and Aframomum. Our phylogeny provides a framework for studies in biogeography, comparative ecology, and evolution.

Systematics and biogeography of the whistlers (Aves: Pachycephalidae) inferred from ultraconserved elements and ancestral area reconstruction

The utility of islands as natural laboratories of evolution is exemplified in the patterns of differentiation in widespread, phenotypically variable lineages. The whistlers (Aves: Pachycephalidae) are one of the most complex avian radiations, with a combination of widespread and locally endemic taxa spanning the vast archipelagos of the Indo-Pacific, making them an ideal group to study patterns and processes of diversification on islands. Here, we present a robust, species-level phylogeny of all five genera and 85% of species within Pachycephalidae, based on thousands of ultraconserved elements (UCEs) generated with a target-capture approach and high-throughput sequencing. We clarify phylogenetic relationships within Pachycephala and report on divergence timing and ancestral range estimation. We explored multiple biogeographic coding schemes that incorporated geological uncertainty in this complex region. The biogeographic origin of this group was difficult to discern, likely owing to aspects of dynamic Earth history in the Indo-Pacific. The Australo-Papuan region was the likely origin of crown-group whistlers, but the specific ancestral area could not be identified more precisely than Australia or New Guinea, and Wallacea may have played a larger role than previously realized in the evolutionary history of whistlers. Multiple independent colonizations of island archipelagos across Melanesia, Wallacea, and the Philippines contributed to the relatively high species richness of extant whistlers. This work refines our understanding of one of the regions’ most celebrated bird lineages and adds to our growing knowledge about the patterns and processes of diversification in the Indo-Pacific.

Genetic diversity analysis of Moroccan saffron (Crocus sativus L.) of different origins based on intermicrosatellite markers

Saffron (Crocus sativus L.) is an autumnal herbaceous triploid plant; it is the source of saffron spice, recognized as the most expensive spice in the world. In this study, genetic diversity among 14 saffron accessions collected from different ancestral geographic areas in Morocco, Greece and France, has been assessed using inter-simple sequence repeats (ISSRs) markers system. Ten ISSR primers were amplified, a total of 143 fragments of which 44.05 % are polymorphic with an average of 6.3 polymorphic fragments per each primer and average of polymorphic information content (PIC) of 0.236. ISSR markers proved to be a powerful tool for assessment of genetic diversity among saffron accessions. Cluster analysis using unweighted pair group method with arithmetic mean (UPGMA), based on Jaccard’s similarity coefficient and supported by the principal coordinate analysis (PCoA), divided the studied accessions into three major groups, and showed that genetic distance is independent of geographical distance. In this paper, we report for the first time the level of genetic diversity among Moroccan saffron; this information allows an unequivocal development of a suitable approach for the conservation of C. sativus germplasm and reduce its genetic erosion.

Historical biogeography and comparative phylogeography of the Mexican genusBakerantha(Bromeliaceae): insights into evolution and diversification

AbstractWe studied the rupicolous and dioecious species of Bakerantha (Bromeliaceae) that grow as narrow endemics in central-eastern Mexico. We aimed to describe the spatio-temporal framework in which Bakerantha and its species originated using a phylogeographic and population genetics approach. We carried out population genetics analyses on 29 populations of the five Bakerantha spp., using plastid and nuclear DNA sequences. The data were used to analyse their diversity, genetic structure and demography, to carry out molecular dating and to reconstruction their ancestral area. Our analyses revealed that speciation in Bakerantha began in the Late Pliocene, associated with vicariance resulting from the rise of the Trans-Mexican Volcanic Belt, a barrier that isolated the Bakerantha spp. to its north and south, and subsequent dispersal events in the Sierra Madre Oriental. Genetic data suggest that the species have achieved a high degree of genetic differentiation and variation, but most of them lack intraspecific structure, even though species have remained stable over the time due their life history traits.

Biogeographic breaks in the Atlantic Forest: evidence for Oligocene/Miocene diversification inBertolonia(Melastomataceae)

AbstractThe distribution of major clades in Bertolonia (Melastomataceae) is congruent with subareas of the Atlantic Forest, providing an opportunity to estimate ages of historical breaks in the Atlantic Forest, from its major north/south split to more restricted local radiations. The role of niche conservatism in driving diversification of Bertolonia is also analysed and discussed in the light of its historical distribution. We estimated the age of the diversification events, gathered the climatic envelopes of species and clades, generated bioregions for the Atlantic Forest and reconstructed the ancestral areas of speciation for the genus. Our analysis subdivided the Atlantic Forest in five subareas, three of them in the northern and two in the southern Atlantic Forest. We also recovered a deep north/south divergence of the Atlantic Forest in the Oligocene (c. 30 Mya) followed by subsequent local radiations in both regions and a south-eastern/southern division in the Miocene. Later diversification happened mostly from the Mid-Miocene to Pliocene/Pleistocene with several dispersal events, mostly between neighbouring areas. We corroborated this assumption demonstrating that closely related lineages tend to occur in habitats with similar climatic conditions, mainly related to temperature. Our analyses on Bertolonia effectively captured relatively old historical events in the Atlantic Forest, such as the north/south division in the Oligocene and south/south-eastern split in the Miocene, but also recent ones, such as climatic fluctuations and forest fragmentation in the Quaternary. We indicate here for the first time that, for some organisms, the well-known north/south split of the Atlantic Forest could be older than expected. Recent radiation events occurred mainly on a regional basis after this deep division of the domain and the subclades that were recovered showed a significant climatic niche conservatism.

Phylogeographic pattern of a cryptoviviparous mangrove, Aegiceras corniculatum, in the Indo-West Pacific, provides insights for conservation actions.

This study identified the historical geoclimatic factors which caused low genetic diversity and strong phylogeographic structure in a cryptoviviparous mangrove. The phylogeographic pattern was used to suggest conservation actions. Phylogeographic studies are used to understand the spatial distribution and evolution of genetic diversity, and have major conservation implications, especially for threatened taxa like the mangroves. This study aimed to assess the phylogeographic pattern of Aegiceras corniculatum, a cryptoviviparous mangrove, across its distribution range in the Indo-West Pacific (IWP) region. We genotyped 398 samples, collected from 37 populations, at four chloroplast DNA (cpDNA) loci, and identified the influence of historical processes on the contemporary population structure of the species. Low genetic diversity at the population level was observed. The evolutionary relationship between 12 cpDNA haplotypes suggested a strong phylogeographic structure, which was further validated by the clustering algorithms and proportioning of maximum variation among hierarchical population groups. The magnitude and direction of historical gene flow indicated that the species attained its wide distribution from its likely ancestral area of the Malay Archipelago. The divergence time estimates of the haplotypes indicated that the geoclimatic changes during the Pleistocene, especially the glacial sea-level changes and emergence of landmasses, hindered genetic exchange and created genetic differentiation between the phylogenetic groups. The species overwintered the last glacial maxima in multiple refugia in the IWP, as identified by the environmental niche modelling. Overall, our findings indicated that ancient glacial vicariance had influenced the present genetic composition of A. corniculatum, which was maintained by the current demographic features of this region. We discussed how these findings can be used to prioritize areas for conservation actions, restore disturbed habitats and prevent further genetic erosion.

Molecular phylogeny and macroevolution of Chaitophorinae aphids (Insecta: Hemiptera: Aphididae)

AbstractChaitophorinae is a predominantly Northern Hemisphere aphid subfamily characterized by numerous setae on the body. Two constituent tribes are associated with different host plants, with Chaitophorini feeding on deciduous trees and shrubs and Siphini colonizing grasses. Based on data from multiple genes (COI, COII, Cytb and EF‐1α), geographical distribution and host association, this study investigated the phylogeny and macroevolution of Chaitophorinae using phylogenetic reconstruction, molecular dating, model‐based ancestral area and character estimations and diversification rate calculation. Our results support the monophyly of Chaitophorinae and two tribes, indicate that Sipha and the two largest genera Chaitophorus and Periphyllus are not monophyletic, and suggest a need for a change in the taxonomic status of Lambersaphis, which was nested within Chaitophorus in the phylogenetic tree. We recovered an origin of Chaitophorinae on Acer plants from eastern Asia during the Late Cretaceous to early Palaeocene, followed by multiple dispersals into other areas that were responsible for its contemporary distribution. The origins of Siphini and Chaitophorus + Lambersaphis coincided with colonizations of novel host plants. An increase in diversification rate occurred within Chaitophorus in the Miocene and was associated with range expansion and switching onto new host plants, highlighting the roles of dispersal and host shift in aphid diversification.

Phylogenomic analyses of the East Asian endemic Abelia (Caprifoliaceae) shed insights into the temporal and spatial diversification history with widespread hybridization.

Abelia (Caprifoliaceae) is a small genus with five species, including one artificial hybrid and several natural hybrids. The genus has a discontinuous distribution in Mainland China, Taiwan Island and the Ryukyu Islands, providing a model system to explore the mechanisms of species dispersal in the East Asian flora. However, the current phylogenetic relationships within Abelia remain uncertain. We reconstructed the phylogenetic relationships within Abelia using nuclear loci generated by target enrichment and plastomes from genome skimming. Divergence time estimation, ancestral area reconstruction and ecological niche modelling (ENM) were used to examine the diversification history of Abelia. We found extensive cytonuclear discordance across the genus. By integrating lines of evidence from molecular phylogenies, divergence times and morphology, we propose to merge Abelia macrotera var. zabelioides into A. uniflora. Network analyses suggested that there have been multiple widespread hybridization events among Abelia species. These hybridization events may have contributed to the speciation mechanism and resulted in the high observed morphological diversity. The diversification of Abelia began in the early Eocene, followed by A. chinensis var. ionandra colonizing Taiwan Island during the Middle Miocene. The ENM results suggested an expansion of climatically suitable areas during the Last Glacial Maximum and range contraction during the Last Interglacial. Disjunction between the Himalayan-Hengduan Mountain region and Taiwan Island is probably the consequence of topographical isolation and postglacial contraction. We used genomic data to reconstruct the phylogeny of Abelia and found a clear pattern of reticulate evolution in the group. In addition, our results suggest that shrinkage of postglacial range and the heterogeneity of the terrain have led to the disjunction between Mainland China and Taiwan Island. This study provides important new insights into the speciation process and taxonomy of Abelia.

Ancestral Area Reconstruction of SARS-CoV-2 Indicates Multiple Sources of Entry into Australia

Background: The ongoing COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). International travels to Australia during the early stages of the pandemic prior to border closure provided avenues for this virus to spread into Australia. Studies of SARS-CoV-2 biogeographical distribution can contribute to the understanding of the viral original sources to Australia. Objective: This study aimed to investigate the clonality and ancestral sources of Australian SARS-CoV-2 isolates using phylogenetic methods. Methods: We retrieved 1,346 complete genomes from Australia along with 153 genomes from other countries from the GISAID and NCBI nucleotide databases as of the 14th May 2020. A representative dataset of 270 Australian and international sequences were resulted from performance of nucleotide redundancy reduction by CD-HIT. We then constructed a median-joining network by Network 10.1.0.0, and phylogenies by IQ-Tree, BEAST and FastTree. The Bayesian statistical dispersal-vicariance analysis (S-DIVA) and Bayesian interference for discrete areas (BayArea) built in RASP were used to reconstruct ancestral ranges over the phylogenetic trees. Results: Two major clusters, from Europe and from Asia, were observed on the network of 183 haplotypes with distinct nucleotide variations. Analysis of ancestral area reconstruction over the phylogenies indicated most Australian SARS-CoV-2 sequences were disseminated from Europe and East Asia-Southeast Asia. Conclusion: The finding is genetic evidence for the geographic origins of the Australian SARS-CoV-2 sequences. Most Australian sequences were genetically similar to those from Europe and East Asia-Southeast Asia, which were also suggested as two main sources of introduction of SARS-CoV-2 to Australia.

Biogeography of curimatid fishes reveals multiple lowland-upland river transitions and differential diversification in the Neotropics (Teleostei, Curimatidae).

The Neotropics harbors a megadiverse ichthyofauna comprising over 6300 species with approximately 80% in just three taxonomic orders within the clade Characiphysi. This highly diverse group has evolved in tropical South America over tens to hundreds of millions of years influenced mostly by re‐arrangements of river drainages in lowland and upland systems. In this study, we investigate patterns of spatial diversification in Neotropical freshwater fishes in the family Curimatidae, a species‐rich clade of the order Characiformes. Specifically, we examined ancestral areas, dispersal events, and shifts in species richness using spatially explicit biogeographic and macroevolutionary models to determine whether lowlands–uplands serve as museums or cradles of diversification for curimatids. We used fossil information to estimate divergence times in BEAST, multiple time‐stratified models of geographic range evolution in BioGeoBEARS, and alternative models of geographic state‐dependent speciation and extinction in GeoHiSSE. Our results suggest that the most recent common ancestor of curimatids originated in the Late Cretaceous likely in lowland paleodrainages of northwestern South America. Dispersals from lowland to upland river basins of the Brazilian and Guiana shields occurred repeatedly across independently evolving lineages in the Cenozoic. Colonization of upland drainages was often coupled with increased rates of net diversification in species‐rich genera such as Cyphocharax and Steindachnerina. Our findings demonstrate that colonization of novel aquatic environments at higher elevations is associated with an increased rate of diversification, although this pattern is clade‐dependent and driven mostly by allopatric speciation. Curimatids reinforce an emerging perspective that Amazonian lowlands act as a museum by accumulating species along time, whereas the transitions to uplands stimulate higher net diversification rates and lineage diversification.

Center of origin and evolutionary history in the high Andean genus Oritrophium (Astereae, Asteraceae)

Páramo, the most species-rich tropical mountain ecosystem, is relatively well-researched in terms of the diversity and evolutionary sources of its flora, yet we know very little about the diversification within this environment. This study aims to unravel the evolutionary history of Oritrophium, an endemic genus of alpine habitats in North and South America, with a disjunct and bi-modal distribution of its species diversity. We aim to disentangle the center of origin and radiation of the genus, and mechanisms structuring its genetic diversity at inter- and intra-specific level. We sampled 19 species (85% from the total) and extended the sampling at population level for the two widely distributed species, O.limnophilum and O.peruvianum, comprising 19 and 24 populations, respectively. Using nuclear ribosomal internal transcribed spacer (ITS) and trnL-trnF chloroplast DNA region, we reconstructed dated phylogenies to test the monophyly of the genus and unravel possible historical forces underlying its diversification. We also performed an ancestral area estimation to reconstruct the biogeographic history of the genus. At the population level, we constructed haplotype networks and run spatial analyses of molecular variance to explore possible mechanisms that operate on structuring the diversity at intraspecific level. Oritrophium resulted polyphyletic, with two species being closely related to Erigeron and three other species ambiguously related to Erigeron, Diplostephium, Linochilus, and/or Hinterhubera. The remaining 14 species formed a clade, Oritrophiums.s., that likely originated during the Early Pliocene in the Andes of northwestern Bolivia to southern Ecuador, the center of the genus' diversity. The group likely diversified with the emergence of the Páramo during the Late Pliocene and further dispersed mainly from South-to-North in the Pleistocene. This migration involved both, long-distance dispersal from the Central Andes to Mexico and gradual migration of the species along the Andes. Accordingly, Oritrophium s.s. appears as the first record of a long-distance dispersal from the Páramo of South America to North America. The dispersal pattern within South America was mirrored by the intraspecific population diversity and structure of the investigated species.

Tracking the xeric biomes of South America: The spatiotemporal diversification of Mandacaru cactus

AbstractAimThe interconnectedness and biotic interchange among Neotropical biomes are thought to play an important role in driving adaptation and diversification. However, how these processes are in synteny to trait evolution in species of open and xeric areas is poorly studied. Here, we investigate the spatial and temporal dimensions of evolution and candidate traits associated with biome shifts in xeric vegetation, focusing on the family Cactaceae.LocationXeric and open areas of South America.TaxonGenus Cereus Mill. (Cactaceae, Cereeae).MethodsWe applied biogeographical reconstructions on a time‐calibrated phylogeny inferred from multilocus data (ddRAD‐Seq) using Bayesian analyses on BEAST2, species distribution modelling in Maxent, the reconstruction of biome affinities and niche shift analyses based on abiotic traits (climate and soil) using Mk‐model in BioGeoBEARS, and phenotypic trait‐based analysis in Mesquite.ResultsThe Cerrado domain is the ancestral area of Cereus, with most diversification events occurring in a time of intense orogenesis, climatic changes, and marine regressions within the last 5 Mya. Events of biome transition from the seasonally dry tropical forest (SDTF) were also associated with trait and niche shifts.Main conclusionsThe diversification of the xerophyte genus Cereus is associated with the climatic and geomorphological instabilities of the Pliocene and Pleistocene epochs. The Cerrado domain states an important region of dispersal for the genus. Some geographical range movements involved biome shifts associated with niche evolution while others were restricted to a simple biogeographical transition without niche change. Particular clades that experienced biome shifts displayed some phenotypic state changes, suggesting a role of biotic traits for environment transition. The results observed in Cereus may be a biogeographical pattern that should be tested with other cactus species, such as Pilosocereus spp., or species of xeric habitats, such as Annonaceae and Vochysiaceae.

A Natural Colonisation of Asia: Phylogenomic and Biogeographic History of Coin Spiders (Araneae: Nephilidae: Herennia)

Reconstructing biogeographic history is challenging when dispersal biology of studied species is poorly understood, and they have undergone a complex geological past. Here, we reconstruct the origin and subsequent dispersal of coin spiders (Nephilidae: Herennia Thorell), a clade of 14 species inhabiting tropical Asia and Australasia. Specifically, we test whether the all-Asian range of Herennia multipuncta is natural vs. anthropogenic. We combine Anchored Hybrid Enrichment phylogenomic and classical marker phylogenetic data to infer species and population phylogenies. Our biogeographical analyses follow two alternative dispersal models: ballooning vs. walking. Following these assumptions and considering measured distances between geographical areas through temporal intervals, these models infer ancestral areas based on varying dispersal probabilities through geological time. We recover a wide ancestral range of Herennia including Australia, mainland SE Asia and the Philippines. Both models agree that H. multipuncta internal splits are generally too old to be influenced by humans, thereby implying its natural colonisation of Asia, but suggest quite different colonisation routes of H. multipuncta populations. The results of the ballooning model are more parsimonious as they invoke fewer chance dispersals over large distances. We speculate that coin spiders’ ancestor may have lost the ability to balloon, but that H. multipuncta regained it, thereby colonising and maintaining larger areas.

Pleistocene origin and colonization history of Lobelia columnaris Hook. f. (Campanulaceae: Lobelioideae) across sky islands of West Central Africa.

We aimed to infer ancestral area and historical colonization of Lobelia columnaris in the sky islands of Bioko and Cameroon through dated phylogeny using chloroplast genomes. Specifically, we aim to answer the following questions: (1) What are the phylogenetic relationships among Bioko Island and Cameroon populations? (2) Are the older populations found in the older sky islands? We assembled novel plastomes from 20 individuals of L. columnaris from 5 mountain systems. The plastome data were explored with phylogenetic analyses using Maximum Likelihood and Bayesian Inference. The populations of L. columnaris have a monophyletic origin, subdivided into three plastomes‐geographic clades. The plastid phylogenomic results and age of the sky islands indicate that L. columnaris colonized first along with the Cameroon Volcanic Line's young sky islands of Bioko. The crown group (1.54 Ma) split the population in Bioko and mainland Cameroon. It is possible that Bioko was the ancestral area and likely isolated during cold and dry conditions in forest refugia. Presumably, the colonization history occurred during the middle‐late Pleistocene from South Bioko's young sky island to North Bioko and the northern old sky islands in Cameroon. Furthermore, the central depression with lowland forest between North and South Bioko is a current geographic barrier that keeps separating the populations of Bioko from each other. Also, the shallow sea channel keeps isolated the populations of Bioko and the mainland populations. The Pleistocene climatic oscillations led to the divergence of the Cameroon and Bioko populations into three clades. L. columnaris colonized the older sky islands in mainland Cameroon after establishment in Bioko's younger sky islands. Contrary to expectations, the biogeography history was an inverse progression with respect to the age of the Afromontane sky islands.

Cryptic diversity and phylogeography of the Rhabdophis nuchalis group (Squamata: Colubridae)

Previous studies, have found that the rapid uplift of the Tibetan plateau accelerated the diversification of species. However, there are few relevant biogeographic data for the Colubridae in this region. We conducted a comprehensive study of the Rhabdophis nuchalis Group, which presently contains four nominal species, R. nuchalis, R. pentasupralabialis, R. leonardi, and R. chiwen. Building upon previous studies with specimens we have recently examined, greater interspecific and intraspecific diversity has been revealed. Here we address three questions: (1) Do the intraspecific differences represent only geographic variation within lineages, or are there cryptic species? (2) What are the interspecific relationships among members of the R. nuchalis Group? (3) What has been the biogeographic history of this species group? To resolve these questions we used four mitochondrial gene sequences and one nuclear sequence to investigate the molecular phylogenetic and geographic relationships among populations. Our molecular analysis reveals cryptic species diversity within the R. nuchalis Group, and seven clades were identified in the analysis. Ancestral area estimation suggests that the R. nuchalis Group originated in the Hengduan Mountains approximately 6.24 Mya and expanded its range northward to the Qinling-Daba Mountains. The Sichuan Basin appears to have been a barrier to migration. Species divergence seems to have been related to the rapid uplift of the Qinghai-Tibet Plateau.