Statistical Dispersal-vicariance Analysis Research Articles

The Neotropical endemic liverwort subfamily Micropterygioideae had circum-Antarctic links to the rest of the Lepidoziaceae during the early Cretaceous.

Lepidoziaceae are the third-largest family of liverworts, with about 860 species distributed on all continents. The evolutionary history of this family has not been satisfactorily resolved, with taxa such as Micropterygioideae yet to be included in phylogenetic analyses. We inferred a dated phylogeny of Lepidoziaceae using a data set consisting of 13 genetic markers, sampled from 147 species. Based on our phylogenetic estimate, we used statistical dispersal-vicariance analysis to reconstruct the biogeographic history of the family. We inferred a crown age of 197 Ma (95% credible interval 157-240 Ma) for the family in the Australian region, with most major lineages also originating in the same region. Micropterygioideae are placed as the sister group to Lembidioideae, with these two lineages diverging from each other about 132 Ma in the South American-Australian region. With South America and Australia being connected through Antarctica at the time, our results suggest a circum-Antarctic link between Micropterygioideae and the rest of the family. Crown Micropterygioideae were inferred to have arisen 45 Ma in South America before the continent separated from Antarctica. Extinction from southern temperate regions might explain the present-day restriction of Micropterygioideae to the Neotropics. Our study reveals the influence of past geological events, such as continental drift, on the evolution and distribution of a widespread and diverse family of liverworts.

Supporting a young age for the North American deserts: Historical biogeography of Grusonia (Cylindropuntieae) in a Plio‐Pleistocene temporal framework

AbstractGrusonia is an opuntioid genus in the Cylindropuntieae, Cactaceae, endemic to the North American deserts in Mexico and the United States. The monophyletic status of the genus and the degrees of endemicity of its species make Grusonia a suitable study group in order to test biogeographic hypotheses such as vicariant or dispersal events, biogeographic barriers and time‐calibrated phylogenies in order to propose speciation events in the group. The statistical dispersal‐vicariance analysis (S‐DIVA) and a statistical dispersal‐local extinction‐cladogenesis (S‐DEC) analyses show general congruence postulating ancestral ranges for the species of Grusonia. They disagree, however, in a clade with four species from the Sonoran Desert, the Baja California Peninsula and one species endemic to the central portion of the Chihuahuan Desert Region. The time‐calibrated phylogeny here proposed shows an average age of 3.7 Ma for the genus. Grusonia has two internal clades comprising species most likely generated by allopatric speciation under a vicariant scenario. The results of this study support a young age for the North American deserts and identify the end of the Pliocene and mainly the Plio‐Pleistocene boundary as the starting point of the cladogenetic events that gave rise to the two main clades of Grusonia.

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.

Vicariance and dispersal events inferred from mitochondrial genomes and nuclear genes (18S, 28S) shaped global Cryptocercus distributions

Cryptocercus Scudder, a genus of wingless, subsocial cockroaches, has low vagility but exhibits a disjunct distribution in eastern and western North America, and in China, South Korea and the Russian Far East. This distribution provides an ideal model for testing hypotheses of vicariance through plate tectonics or other natural barriers versus dispersal across oceans or other natural barriers. We sequenced 45 samples of Cryptocercus to resolve phylogenetic relationships among members of the genus worldwide. We identified four types of tRNA rearrangements among samples from the Qin-Daba Mountains. Our maximum-likelihood and Bayesian phylogenetic trees, based on mitochondrial genomes and nuclear genes (18S, 28S), strongly supported six major lineages of Cryptocercus, which displayed a clear geographical distribution pattern. We used Bayesian molecular dating to estimate the evolutionary timescale of the genus, and reconstructed Cryptocercus ancestral ranges using statistical dispersal-vicariance analysis (S-DIVA) in RASP. Two dispersal events and six vicariance events for Cryptocercus were inferred with high support. The initial vicariance event occurred between American and Asian lineages at 80.5 Ma (95% credibility interval: 60.0–104.7 Ma), followed by one vicariance event within the American lineage 43.8 Ma (95% CI: 32.0–57.5 Ma), and two dispersal 31.9 Ma (95% CI: 25.8–39.5 Ma), 21.7 Ma (95% CI: 17.3–27.1 Ma) plus four vicariance events c. 29.3 Ma, 27.2 Ma, 24.8 Ma and 16.7 Ma within the Asian lineage. Our analyses provide evidence that both vicariance and dispersal have played important roles in shaping the distribution and diversity of these woodroaches.

A closer look at the migration and diversification of the false foxgloves (genus: Agalinis; family: Orobanchaceae) in temperate North America

The genus Agalinis (commonly known as the “false foxgloves”) belonging to the family Orobanchaceae, is native to the Western Hemisphere. Approximately 40 species are distributed across temperate North America, and a large group is native to Missouri and the Midwestern United States. Twenty-one species of this genus warrant conservation measures. Our main aims were to understand the migration and diversification of temperate North American Agalinis, as well as focusing on the six species native to the state of Missouri. This study is the first to investigate the evolutionary diversification of this genus in temperate North America. Computer applications including BEAST (Bayesian evolutionary analysis sampling trees) and SDIVA (statistical dispersal vicariance analysis), and secondary calibrations from previous studies were implemented to understand the diversification timings and ancestral areas of this group. Our study points to southeastern United States as the center of diversity and place of origin of the Agalinis in temperate North America, from which they spread to the rest of the United States and even migrated to Canada, around the mid-late Miocene period. We were also able to trace the biogeography of the Missouri natives which diversified between the late Miocene and the Pleistocene period. It may be hypothesized that climatic shifts and increase in seasonality during the mid-late Miocene period was one of the primary causes leading to the migration and diversification of this genus throughout temperate North America.

Genetic diversity of Rhinogobius delicatus (Perciformes: Gobiidae): origins of the freshwater fish in East Taiwan

Mitochondrial DNA cytochrome b and d-loop sequences (1,984 bp) from 92 specimens of the freshwater goby Rhinogobius delicatus from seven drainages in East Taiwan were identified as two major lineages exhibiting a southern or northern distribution. The existence of low genetic diversity, a pattern of population decline and high population differentiation (F ST=0.711) support the need for the development of management strategies for the conservation of localized populations. The results of a statistical dispersal-vicariance analysis suggested that the ancestral populations of R. delicatus were widely distributed in East Taiwan. Compared with the phylogeographic patterns of the other endemic eastern Taiwan freshwater fishes, Onychostoma alticorpus, Aphyocypris kikuckii and Hemimyzon taitungensis, our study suggests that the freshwater fishes colonized East Taiwan through northeastern and southwestern Taiwan, although the ancestral populations colonized the island before it reached its present shape.

Genetic diversity and structure of the Chinese lake gudgeon (Sarcocheilichthys sinensis)

Mitochondrial DNA cytochrome b and d-loop sequences (2,137 bp) in 65 specimens of Sarcocheilichthys sinensis from five populations were identified as two lineages (I and II). The pairwise genetic distance between lineages I and II was 1.94%. SAMOVA analyses suggested that the best grouping occurred at three groups, Yangtze, Qiantang and Minjiang Rivers. High haplotype diversity (0.949) and low nucleotide diversity (θ π = 1.067%) were detected. The results of the neutrality tests, mismatch distribution and approximate Bayesian computation (ABC) did not support demographic expansions. The results of phylogenetic analysis, statistical dispersal-vicariance analysis (S-DIVA), ABC, MIGRATE-N and the time to the most recent common ancestor (TMRCA) indicated two colonization routes. First, before the Wuyi Mountains lifted, S. sinensis dispersed from the Yangtze River to the Minjiang River. Second, during glaciation, the continental shelf was exposed, which contributed to the dispersion of populations from the Yangtze River.

Historical biogeography of Trigonostemon and Dimorphocalyx (Euphorbiaceae)

AbstractTrigonostemon and Dimorphocalyx are two morphologically similar genera in tropical Asia. We estimated their divergence times through a Bayesian clock analysis and reconstructed the historical biogeography using a likelihood analysis under the dispersal-extinction-cladogenesis (DEC) model and a statistical dispersal-vicariance analysis (S-DIVA). We have found that the two genera differ in their historical biogeography: Trigonostemon originated on the South-East Asian mainland, but one section dispersed to the Malay Peninsula and Borneo, where rapid speciation events occurred during the Pleistocene, whereas Dimorphocalyx originated on and extended to its current distribution from Borneo. The dispersal routes of both genera are well supported by the tectonic history and are comparable to the conclusions in previous case studies. Long-distance dispersals across Wallace’s line are of particular interest in biogeography. We compared the patterns of historical distribution and dispersal of our taxa and other comparable taxa in this area. Our data support the hypothesis that the Philippines is the most common stepping stone for crossing Wallace’s line. Furthermore, we consider that the frequent change of sea levels during the Pleistocene propelled the diversification of Trigonostemon section Trigonostemon in Borneo and the Malay Peninsula.

Population structure of Aphyocypris normalis: phylogeography and systematics.

Aphyocypris normalis (Teleostei: Cyprinidae) is an endemic species in South China, but little is known about its genetic structure. This study examined the population structure of A. normalis using sequences of the mitochondrial DNA control region and cytochrome b gene (2,086 bp). In total, 107 specimens were collected from nine populations. All 105 mtDNA haplotypes were identified as belonging to two allopatric phylogroups. The results of a statistical dispersal-vicariance analysis (S-DIVA) suggested that the ancestral populations of A. normalis were distributed widely on Hainan Island and east of the Leizhou Peninsula. A comparison of the fixation indices NST (0.532) and GST (0.004) revealed that the phylogeny and geography had a significant relationship. Our study found that (1) the Wuzhishan and Yinggeling Mountain Range was an important barrier limiting gene exchange between populations on both sides; (2) cyclic climate changes may have shaped migrations and population differentiations; and (3) different colonization times caused different population diversities between codistributed species. In addition, the inter- and intraspecific diversities of the genus Aphyocypris were estimated.

Biogeography and phylogenetic relationships of Hyrcanian wild apple using cpDNA and ITS noncoding sequences

The Hyrcanian forest of northern Iran is considered one of the potential centres for the evolution and domestication of the genus Malus (Rosaceae). However, the biogeography, phylogenetic position, and taxonomic status of the Hyrcanian wild apples have never been evaluated. In our study, the nucleotide sequences of the internal transcribed spacer (ITS) and the trnH-psbA intergenic spacer region from 14 natural populations were analysed. Phylogenetic analysis based on the ITS and the Maximum-likelihood (ML) tree showed that all Hyrcanian samples were closely related to M. orientalis and M. asiatica and can be placed within section Malus and series Malus. Furthermore, based on a comparison of ITS2 secondary structures, the Hyrcanian samples were identical to M. orientalis and M. sieversii. Biogeographic scenarios constructed using Statistical Dispersal-Vicariance Analysis (S-DIVA) and the Bayesian Binary Method (BBM) indicated that the ancestor of Malus originated during the Eocene, ∼53 million years ago (Ma), and that China played a vital role in the expansion of the range of the genus. The members of Malus colonized the Hyrcanian region from China during the Miocene, ∼22-10 Ma.

Relationships between Tertiary relict and circumboreal woodland floras: a case study in Chimaphila (Ericaceae).

Tertiary relict and Arctic/circumboreal distributions are two major patterns of Northern Hemisphere intercontinental disjunctions with very different histories. Each has been well researched, but members of one biome have generally not been incorporated in the biogeographical analyses of the other, and links or transitions between these two biomes have rarely been addressed. Phylogenies of Chimaphila were generated based on cpDNA and nuclear ITS, using Bayesian and maximum likelihood methods. A time-calibrated phylogeny was generated using BEAST. Ancestral area reconstruction was inferred using both statistical dispersal-vicariance analysis and a dispersal-extinction-cladogenesis model. The Chimaphila crown group was estimated to have originated in the early Miocene. The lineages of C. umbellata diverged early, but its present circumboreal distribution was not achieved until around the middle Pliocene or later. Sister to this is a clade of four species with Tertiary relict distribution. Among these, two expansions occurred from North America to Asia, probably via the Bering Land Bridge, generating its current disjunctions. Our data concur with a few other studies, indicating that the circumboreal woodland biome has an older origin than most true Arctic-alpine taxa, having gradually recruited taxa since the early Oligocene. For the origin of Asia-North America disjunctions in Chimaphila, an 'out-of-America' migration was supported. It is not clear in which direction Pyroloideae lineages moved between Tertiary relict disjunctions and Arctic/circumboreal distributions; each biome might have recruited species from the other.

Genetic diversity and biogeography of T. officinale inferred from multi locus sequence typing approach.

Taraxacum officinale (Asteraceae) is widely distributed weedy plant used as a traditional medicinal herb. The population genetics and historical biogeography of this plant have remained relatively unexplored. This study explores phylogeny, population genetics and ancestral reconstructions adopting multi locus sequence typing (MLST) approach. MLST sequences dataset was generated from genomics and chloroplast DNA sequences obtained from 31 T. officinale haplotypes located in 16 different countries. Phylogenetic analysis distributed these haplotypes in well differentiated geographic clades. The study suggested a close relationship between Europe and adjacent Asian countries. Populations of these regions predominantly formed common haplogroups, showed considerable level of gene flow and evidence for recombination events across European and Asian population. Biogeographical inferences obtained by applying statistical dispersal-vicariance analysis (S-DIVA) and Bayesian binary MCMC (BBM) analysis showed that T. officinale was putatively originated in Europe. Molecular clock analysis based on ITS dataset suggested that the divergence between Europe and East Asian populations can be dated to 1.07 Mya with subsequent dispersal and vicariance events. Among different spatial process long distance seed dispersal mediated by wind had potentially assisted the population expansion of T. officinale.

But they move! Vicariance and dispersal in southern South America: Using two methods to reconstruct the biogeography of a clade of lizards endemic to South America.

This study aims to identify events that modeled the historical biogeography of Phymaturus, using three methodologies: Spatial Analysis of Vicariance (VIP), Statistical Dispersal-Vicariance Analysis (S-DIVA), and Bayesian Binary Method MCMC (BBM). In order to assign areas for the Dispersal-Vicariance and the BBM analyses, we preferred not to use predefined areas, but to identify areas defined via an endemism analysis of Phymaturus species. The analyses were conducted using the same basic topology, which we obtained by constructing a metatree with two recent phylogenies, both morphology and molecular-based. This topology was also used to obtain time divergence estimates in BEAST, using more outgroups than for the metatree in order to get more accurate estimates. The S-DIVA analysis based on the metatree found 25 vicariance events, 20 dispersals and two extinctions; the S-DIVA analysis based on the BEAST tree yielded 30 vicariance events, 42 dispersal events and five extinctions, and the BBM analysis yielded 63 dispersal events, 28 vicariance events and 1 extinction event. According to the metatree analysis, the ancestral area for Phymaturus covers northern Payunia and southern Central Monte. A vicariant event fragmented the ancestral distribution of the genus, resulting in northern Payunia and southern Central Monte as ancestral area for the P. palluma group, and southern Payunia for the P. patagonicus group. The analysis based on the BEAST tree showed a more complex reconstruction, with several dispersal and extinction events in the ancestral node. The Spatial Analysis of Vicariance identified 41 disjunct sister nodes and removed 10 nodes. The barrier that separates the P. palluma group from the P. patagonicus group is roughly congruent with the southern limit of the P. palluma group. The ancestral range for the genus occupies a central position relative to the distribution of the group, which implies that the species must have migrated to the north (P. palluma group) and to the south (P. patagonicus group). To answer questions related to the specific timing of the events, a molecular clock for Phymaturus was obtained, using a Liolaemus fossil for calibration. The present contribution provides a hypothetical framework for the events that modeled the distribution of Phymaturus.

Igdabatis marmii sp. nov. (Myliobatiformes) from the lower Maastrichtian (Upper Cretaceous) of north-eastern Spain: an Ibero-Armorican origin for a Gondwanan batoid

Microvertebrate fossil assemblages (chondrichthyans, osteichthyans, lissamphibians and squamates) from the Campanian and Maastrichtian of south-western Europe include taxa with very different palaeobiogeographical affinities. However, most of these biogeographical histories remain unclear. As inhabitants of shallow marine waters, batoids are considered good palaeobiogeographical indicators that could reveal connections between continental platforms. Igdabatis is a stingray (Myliobatiformes) with an abundant Gondwanan fossil record, whereas its occurrence in the Ibero-Armorican landmass is intriguing. In this paper, a new species of Igdabatis – Igdabatis marmii sp. nov. – is reported from the lower Maastrichtian of Spain. Based on this new record, the phylogenetic relationships of Myliobatiformes are assessed, including Igdabatis taxa for first time. In addition, three new morphological characters are proposed based on the diagnoses of the different species and added to the dataset. The palaeobiogeographical events that these stingrays underwent during their speciation were explored through a Statistical Dispersal-Vicariance Analysis (S-DIVA) performed in RASP 2.1. The phylogenetic analysis suggests a highly nested position within Myliobatidae for the genus Igdabatis; and the new species was recovered as the most basal taxon in the clade. The S-DIVA results point to an Ibero-Armorican ancestral area for Igdabatis, from where its species diverged by a combination of vicariant and dispersal events. Both phylogenetic and palaeobiogeographical analyses were congruent with occurrences in the fossil record. Results and fossil evidence allow the proposal of a dispersal route between European and Gondwanan landmasses for these stingrays. The dispersal of Igdabatis between Ibero-Armorica and India during the Late Cretaceous was promoted by the proximity of the European and African continental platforms and then by the Kohistan-Ladakh island arc.http://zoobank.org/urn:lsid:zoobank.org:pub:F5C51029-2E26-48C6-8A87-A2D4310887EF

A large-sized basal ankylopollexian from East Asia, shedding light on early biogeographic history of Iguanodontia

A presumably mostly quadrupedal ankylopollexian iguanodontian, Bayannurosaurus perfectus gen. et sp. nov., is reported here, and is represented by an excellently well-preserved skeleton from the Lower Cretaceous Bayingebi Formation of Inner Mongolia, China. The diagnosis of the taxon includes several autapomorphies, notably a dorsally directed, strap-like posterodorsal process of the jugal and a horizontally oriented preacetabular process of the ilium. The nearly complete caudal series retains eight posterior-most caudals with procoelous, trapezoidal centra in dorsal view, and the last three caudals are fully fused. The discovery of B. perfectus opens a critical new window on the early evolution and intercontinental dispersal of Iguanodontia. The skeleton displays a transitional morphology between non-hadrosauriform ankylopollexians and Hadrosauriformes. A phylogenetic analysis indicates that Bayannurosaurus is positioned higher on the tree than Hypselospinus, but below Ouranosaurus just outside of Hadrosauriformes. The tree topology of Iguanodontia with temporal and spatial constraints reveals a possible biogeographic scenario supported by the statistical dispersal-vicariance analysis: around the J/K boundary, non-hadrosauriform ankylopollexians experienced multiple dispersal events from Europe to Asia, accompanying the coeval fall of the global sea level.

Cold-blooded in the Ice Age: “refugia within refugia”, inter-and intraspecific biogeographic diversification of European whipsnakes (Squamata, Colubridae, Hierophis)

In this work, we performed a biogeographic analysis with Bayesian binary MCMC (BBM) statistical dispersal-vicariance analysis (S-DIVA) and species distribution models (SDM) on three phylogenetically closely related Mediterranean whipsnakes (Hierophis gemonensis, H. carbonarius, H. viridiflavus), to investigate the pathways of their geographical diversification and locate putative refugial areas in the last glacial maximum (LGM). Our analysis suggests that the diversification processes between the studied species overall followed an east-west route, from eastern Greece to the Iberian Peninsula and continental France, highlighting a significant role of dispersal and vicariance processes at both inter- and intraspecific levels. In particular, the main lineage-splitting events between H. gemonensis, H. carbonarius and H. viridiflavus coincide with two events of vicariance, involving respectively eastern Greece and eastern Italy, and eastern Italy and western Italy, Iberian Peninsula and continental France. SDM analyses highlight the occurrence of multiple putative glacial refugia in the Balkans, Italy and southern France, which represent well the occurrence of distinct “refugia within refugia” in the main Mediterranean peninsulas. Furthermore, our results suggest how these refugia may have played an important role during the Quaternary climatic oscillations in shaping the current haplotype distribution of European whipsnakes.

Mitochondrial diversity and phylogeography of Acrossocheilus paradoxus (Teleostei: Cyprinidae)

Mitochondrial DNA cytochrome b sequences (1141 bp) in 229 specimens of Acrossocheilus paradoxus from 26 populations were identified as four lineages. The pairwise genetic distances among these four lineages ranged from 1.57 to 2.37% (mean= 2.00%). Statistical dispersal-vicariance analysis suggests that the ancestral populations were distributed over mainland China and Northern and Western Taiwan. Approximate Bayesian computation approaches show that the three lineages in Taiwan originated from the lineage in mainland China through three colonization routes during two glaciations. The results indicated that during the glaciation and inter-glacial periods, the Taiwan Strait was exposed and sank, which contributed to the dispersion and differentiation of populations. Furthermore, the populations of A. paradoxus colonized Taiwan through a land bridge to the north of the Formosa Bank, and the Miaoli Plateau in Taiwan was an important barrier that limited gene exchange between populations on both the sides.

Phylogeny and biogeography of East Asian evergreen oaks (Quercus section Cyclobalanopsis; Fagaceae): Insights into the Cenozoic history of evergreen broad-leaved forests in subtropical Asia

The evolutionary history of Quercus section Cyclobalanopsis, a dominant lineage in East Asian evergreen broadleaved forests (EBLFs), has not been comprehensively studied using molecular tools. In this study, we reconstruct the first comprehensive phylogeny of this lineage using a genomic approach (restriction-site associated DNA sequencing, RAD-seq), sampling 35 of the ca. 90 species currently recognized, representing all main morphological groups of section Cyclobalanopsis. In addition, 10 other species of Quercus and two outgroups were also sampled. Divergence times were estimated using a relaxed clock model and two fossil calibrations. Ancestral areas and dispersal routes were inferred using statistical dispersal-vicariance analysis and the dispersal-extinction-cladogenesis (DEC) model. The phylogeny of Quercus section Cyclobalanopsis demonstrates the section to be monophyletic, comprising two main lineages and six subclades that are well supported by anatomical traits. Biogeographical reconstructions indicate that the wide northern hemisphere distribution of Quercus was disrupted in the Late Eocene, leading to the main extant groups at about 33 Ma. The earliest divergences in section Cyclobalanopsis correspond to the phased uplift of the Himalayas and lateral extrusion of Indochina at the transition of the Oligocene and Miocene, where the highest rate of diversification occurred in the late Miocene. Dispersal from Sino-Himalaya and the Palaeotropics to Sino-Japan in the Miocene was facilitated by the increased intensity of East Asian summer monsoons and by the Middle Miocene Climatic Optimum. Our results highlight the importance of climatic changes and Indo-Eurasian collision-induced tectonic activities from the Neogene onward to the spatial-temporal diversification patterns of Asian EBLF lineages.

Differential diversifications of South American and Eastern Asian disjunct genera Bocconia and Macleaya (Papaveraceae)

AbstractBocconia (10 species) and Macleaya (2 species) are two disjunct genera between South America and eastern Asia (EAS) in the Papaveraceae offering an opportunity to compare its biogeographic history with that of the well‐known disjunction between EAS and eastern North American (ENA). Our phylogenetic analyses of the chloroplast matK and rbcL gene sequences of Ranunculales including two species of Macleaya and six species of Bocconia supported the monophyly of Bocconia, Macleaya, and Chelidonioideae to which Bocconia and Macleaya belong. Nucleotide sequences of matK, rbcL, and nrDNA ITS supported the sister relationship of Bocconia and Macleaya. Biogeographic analyses of Chelidonioideae using S‐DIVA (statistical dispersal vicariance analysis) and DEC (dispersal extinction cladogenesis) methods inferred Eurasia as the most likely ancestral area of Bocconia and Macleaya and suggested no extinction events in either Bocconia or Macleaya. This agrees with the “Out‐of‐Asia” pattern of the EAS‐ENA disjunction. Molecular dating of Ranunculales with fossil‐based calibrations showed that Bocconia and Macleaya diverged in the late Eocene and early Oligocene, which is much earlier than most EAS‐ENA disjunct taxa. The disjunction may have formed via long distance dispersal or boreotropical connections via the North Atlantic and Bering land bridges. Both Bocconia and Macleaya diversified in the late mid‐Miocene, but Bocconia has apparently experienced a greater diversification probably aided by the evolution of the bird dispersal syndrome in fruit and seed after migration to South America. The greater diversification of Bocconia is also evidenced by the diverse leaf morphology and growth habit in response to colonization in various local habitats in South America.

Contrasting evolutionary processes during Quaternary climatic changes and historical orogenies: a case study of the Japanese endemic primroses Primula sect. Reinii.

Recent biogeographic studies have illustrated that Quaternary climatic changes and historical orogenies have driven the development of high levels of biodiversity. In this context, phylogenetic niche conservatism may play a role as a major precursor of allopatric speciation. However, the effects of niche evolution on the diversification patterns of plant species under rapid habitat changes are still unknown. Here, Primula section Reinii, one of the few primroses endemic to the Japanese Archipelago, was investigated. This study aimed to clarify the phylogenetic position and relationships of section Reinii, interpret the biogeographic and diversification patterns of this group and gain a better understanding of the role of climatic niche evolution in the Japanese endemic primroses. Dated phylogeny for Primula section Reinii is presented based on the sequences of six chloroplast genes and one nuclear gene. Biogeographic history was reconstructed using statistical dispersal-vicariance analysis. Macro-evolutionary modelling of the climatic niche was combined with biogeographic inferences. Section Reinii was shown to be monophyletic based on chloroplast and nuclear sequences. Fossil-calibrated dating analysis estimated that this section diverged from its sister taxon, sect. Cortusoides, around 1.82 million years ago, and intraspecific diversification occurred within the last million years. This time frame was characterized by Quaternary climatic oscillations and uplift of high mountains in Japan. Biogeographic inference suggested that this section originated at the northern end of the Japanese Archipelago and then dispersed southward to other islands. Models of climatic niche evolution indicated that the closely related species P. reinii and P. tosanensis have contrasting niche optima and rates of niche evolution. Our results highlight that spatiotemporal heterogeneity in the Japanese islands may play a significant role in the biogeographic history of Japanese endemic primroses. Contrasting evolutionary processes found in closely related species illustrate the effects of climatic niche evolution on species' diversification patterns.