Ancestral Distribution Research Articles

Rafting spiders or drifting islands? Origins and diversification of the endemic trap‐door spiders from the Balearic Islands, Western Mediterranean

AbstractAimTo unravel the origins and to infer the processes of diversification in the low‐vagility nemesiid trap‐door spiders of the Balearic Islands. The specific goals were: (1) to determine whether nemesiid spiders colonized the islands by oversea dispersal, or whether they are the result of the fragmentation of a once continuous distribution by continental drift, and (2) to test whether the Balearic lineages have undergone local diversification processes.LocationsBalearic Islands, Iberian Peninsula, Western Mediterranean.MethodsMultilocus molecular phylogenetic inference using parsimony and model‐based methods, and divergence time estimation with relaxed clocks and informed substitution rate priors, and biogeographical ancestral reconstruction inferred in a Bayesian framework.ResultsPhylogenetic analyses revealed the monophyly of the genera Iberesia and Nemesia. Four independent clades were recovered for the Balearic fauna. One of the clades included a formerly unknown species from Minorca. The Balearic clades split from their continental relatives in the early Tortonian, except for Iberesia brauni, which dates to the Messinian‐Zanclean. The biogeographical reconstruction indicated that the Balearic fauna probably originated in the Betic region of the Iberian Peninsula.Main conclusionsThe presence of Nemesia on the Balearic Islands was explained by fragmentation of an ancestral distribution range that included the Betic region and the islands in the Early Tortonian. The arrival of Iberesia to the islands, however, was the result of a secondary range expansion that was facilitated by the emergence of land bridges with the continent during the Messinian salinity crisis (MSC). Similarly, the drops in the sea level that occurred during the MSC and subsequently in the Quaternary glacial cycles established land passages between Majorca and Minorca.

Phylogenetic analyses ofPilosocereus(Cactaceae) inferred from plastid and nuclear sequences

Pilosocereus is a large genus of Cactaceae with 42 species of columnar cacti distributed in the Americas. In this work we investigate the phylogenetics and evolutionary history of Pilosocereus based in plastid and nuclear DNA sequences. We use phylogenetic trees obtained as a basis to analyse infrageneric relationships and to study the evolution of selected morphological characters and geographical distribution in the group. Thirty-three species of the genus were sampled and five molecular regions were selected, four non-coding intergenic spacers of plastid DNA (trnS-trnG, psbD-trnT, trnL-trnT, petL-psbE) and one nuclear low-copy gene (phytochrome C). The phylogenetic analyses obtained point to a paraphyletic Pilosocereus, with P. bohlei and P. gounellei emerging nested in a clade of outgroup species (i.e. other genera of Cereinae). However, the majority of species of the genus form one well supported clade (excluding P. bohlei and P. gounellei) corresponding mostly to Pilosocereus subgenus Pilosocereus. Evidence indicates that the ancestor of Pilosocereus subgenus Pilosocereus clade was a shrub with a straight floral tube occurring in Brazil and the ancestor of Pilosocereus subgenus Gounellea was a shrub with a curved floral tube also occurring in Brazil. The ancestral distribution in central and eastern Brazil resulted in the diversification of most lineages in the same area, whereas the P. leucocephalus clade was able to disperse through the Amazonian areas and diversify further north and reach Central and North America.

Phylogeography of a freshwater crustacean species complex reflects a long‐gone archipelago

AbstractAimThe Carpathian Mountains are an important European biodiversity hotspot and are characterized by a dynamic geological history. Their freshwater amphipod fauna is ubiquitous and diverse, consisting of micro‐endemic lineages that apparently reflect historical geological events. In this study, we propose that the complementary distribution of two widespread morphotypes belonging to the Gammarus balcanicus species complex reflects two chronologically distinct uplift episodes of the Carpathian Archipelago during the Miocene.LocationSoutheastern Europe.MethodsWe sequenced two mitochondrial (COI and 16S) and three nuclear (28S, 18S and EF1α) markers from 68 localities (n = 171) across the Carpathian Arc. Distance and phylogenetic‐based methods were used to quantify cryptic diversity from the mitochondrial markers. We examined phylogenetic relationships, estimated divergence times and reconstructed ancestral geographical distributions of the Carpathian lineages within a wider geographical and phylogenetic context.ResultsOur results revealed that one morphotype, Gammarus cf. balcanicus, is a highly diverse and polyphyletic entity (consisting of at least 20 cryptic lineages), mostly inhabiting the areas corresponding to old Carpathian palaeo‐islands. We estimated that this morphotype originated and diversified on this archipelago throughout the Miocene. In contrast, a distinct morph, previously described as G. balcanicus dacicus (elevated here to species rank as G. dacicus [new status]), is monophyletic and comprises only two lineages that likely originated and diversified on younger landmasses at the onset of the Late Miocene. Furthermore, it appears that the Pleistocene glaciations did not have a significant effect on the observed distribution and diversity patterns. Each cryptic lineage detected by mitochondrial markers was also supported by at least one nuclear marker.Main conclusionsThe different timings of landmass uplifts of the Carpathian palaeo‐archipelago seem to have played a central role in the evolution and diversification of local lineages of the G. balcanicus species complex. This indicates that the genetic legacy of long‐gone archipelagos can persist for millions of years in contemporaneous continental biotas.

Historical biogeography of the fern genus Deparia (Athyriaceae) and its relation with polyploidy

The wide geographical distribution of many fern species is related to their high dispersal ability. However, very limited studies surveyed biological traits that could contribute to colonization success after dispersal. In this study, we applied phylogenetic approaches to infer historical biogeography of the fern genus Deparia (Athyriaceae, Eupolypods II). Because polyploids are suggested to have better colonization abilities and are abundant in Deparia, we also examined whether polyploidy could be correlated to long-distance dispersal events and whether polyploidy could play a role in these dispersals/establishment and range expansion. Maximum likelihood and Bayesian phylogenetic reconstructions were based on a four-region combined cpDNA dataset (rps16-matK IGS, trnL-L-F, matK and rbcL; a total of 4252 characters) generated from 50 ingroup (ca. 80% of the species diversity) and 13 outgroup taxa. Using the same sequence alignment and maximum likelihood trees, we carried out molecular dating analyses. The resulting chronogram was used to reconstruct ancestral distribution using the DEC model and ancestral ploidy level using ChromEvol. We found that Deparia originated around 27.7Ma in continental Asia/East Asia. A vicariant speciation might account for the disjunctive distribution of East Asia–northeast North America. There were multiple independent long-distance dispersals to Africa/Madagascar (at least once), Southeast Asia (at least once), south Pacific islands (at least twice), Australia/New Guinea/New Zealand (at least once), and the Hawaiian Islands (at least once). In particular, the long-distance dispersal to the Hawaiian Islands was associated with polyploidization, and the dispersal rate was slightly higher in the polyploids than in diploids. Moreover, we found five species showing recent infraspecific range expansions, all of which took place concurrently with polyploidization. In conclusion, our study provides the first investigation using phylogenetic and biogeographic analyses trying to explore the link between historical biogeography and ploidy evolution in a fern genus and our results imply that polyploids might be better colonizers than diploids.

A new Miocene vertebrate assemblage from the Río Yuca Formation (Venezuela) and the northernmost record of typical Miocene mammals of high latitude (Patagonian) affinities in South America

Geological explorations of the basal beds of the Río Yuca Formation (Tucupido region, Portuguesa State, western Venezuela) resulted in the recognition of a new vertebrate assemblage that includes eight taxa: the toxodont cf. Adinotherium, a Peltephilidae armadillo, the freshwaters fishes Platysilurus and Phractocephalus, the caiman Purussaurus, an indeterminate dolphin, turtles, and the previously recognized sloth Pseudoprepotherium venezuelanum. When compared with the higher latitudes faunas of Argentina and Chile, the presence of cf. Adinotherium and peltephilids in the Rio Yuca Formation is consistent, but not conclusive, with a Santacrucian to Frisian SALMA age. The associated fauna, as well recent apatite fission track analysis, indicates that the Río Yuca assemblage is more likely younger in age, specifically Middle to Late Miocene. So far, the Miocene localities of the northern part of South America have provided a less prolific fossil record compared to the southern part of the continent (e.g., Santacrucian and Friasian faunas of Patagonia), but the present work documents the surprising occurrence of two taxa (Peltephilidae and Nesodontinae) common in southern high latitude faunas of South America, implying the persistence of the Santacrucian-Friasian genus Adinotherium in younger strata from northern South America, and that peltephilids were much more widespread during the Miocene than previously recognized. The presence of these common Patagonian taxa (Peltephilidae and Nesodontinae) in Río Yuca also supports the hypothesis of prior researchers for the existence of biogeographical connections between the northern and southern portions of South America during the Late Oligocene or Early Miocene, which facilitated faunal interchange between the two regions. Finally, the biogeographical affinities of the freshwater fishes and the giant caiman (Purussaurus) indicate close relationships of the Tucupido region with the ancestral distribution of the Orinocoan–Amazonian drainage system.

Phylogeography of the Subgenus Drosophila (Diptera: Drosophilidae): Evolutionary History of Faunal Divergence between the Old and the New Worlds

The current subgenus Drosophila (the traditional immigrans-tripunctata radiation) includes major elements of temperate drosophilid faunas in the northern hemisphere. Despite previous molecular phylogenetic analyses, the phylogeny of the subgenus Drosophila has not fully been resolved: the resulting trees have more or less varied in topology. One possible factor for such ambiguous results is taxon-sampling that has been biased towards New World species in previous studies. In this study, taxon sampling was balanced between Old and New World species, and phylogenetic relationships among 45 ingroup species selected from ten core species groups of the subgenus Drosophila were analyzed using nucleotide sequences of three nuclear and two mitochondrial genes. Based on the resulting phylogenetic tree, ancestral distributions and divergence times were estimated for each clade to test Throckmorton’s hypothesis that there was a primary, early-Oligocene disjunction of tropical faunas and a subsequent mid-Miocene disjunction of temperate faunas between the Old and the New Worlds that occurred in parallel in separate lineages of the Drosophilidae. Our results substantially support Throckmorton’s hypothesis of ancestral migrations via the Bering Land Bridge mainly from the Old to the New World, and subsequent vicariant divergence of descendants between the two Worlds occurred in parallel among different lineages of the subgenus Drosophila. However, our results also indicate that these events took place multiple times over a wider time range than Throckmorton proposed, from the late Oligocene to the Pliocene.

A reinvestigation of phylogeny and divergence times of the Ablepharus kitaibelii species complex (Sauria, Scincidae) based on mtDNA and nuDNA genes

Morphological and DNA data support that the East Mediterranean snake-eyed skink Ablepharus kitaibelii represents a species complex that includes four species A. kitaibelii, A. budaki, A. chernovi, and A. rueppellii, highlighting the need of its taxonomic reevaluation. Here, we used Bayesian and Maximum Likelihood methods to estimate the phylogenetic relationships of all members of the complex based on two mitochondrial (cyt b, 16S rRNA) and two nuclear markers (MC1R, and NKTR) and using Chalcides, Eumeces, and Eutropis as outgroups. The biogeographic history of the complex was also investigated through the application of several phylogeographic (BEAST) and biogeographic (BBM) analyses. Paleogeographic and paleoclimatic data were used to support the inferred phylogeographic patterns. The A. kitaibelli species complex exhibits high genetic diversity, revealing cases of hidden diversity and cases of non-monophyletic species such as A. kitaibelii and A. budaki. Our results indicate that A. pannonicus branches off first and a group that comprises specimens of A. kitaibelli and A. budaki from Kastelorizo Island group (southeast Greece) and southwest Turkey, respectively is differentiated from the rest A. kitaibelli and A. budaki populations and may represent a new species. The estimated divergence times place the origin of the complex in the Middle Miocene (∼16Mya) and the divergence of most currently recognized species in the Late Miocene. The inferred ancestral distribution suggests that the complex originated in Anatolia, supposing that several vicariance and dispersal events that are related with the formation of the Mid-Aegean Trench, the Anatolian Diagonal and the orogenesis of the mountain chains in southern and eastern Anatolia have led to current distribution pattern of A. kitaibelii species complex in the Balkans and Middle East.

Molecular phylogeny, biogeography and chromosome evolution of Malagasy dwarf geckos of the genus Lygodactylus (Squamata, Gekkonidae)

We performed a phylogenetic analysis using nuclear (RAG‐1, RAG‐2) and mitochondrial (16S) markers, a statistical Bayesian reconstruction of ancestral distribution areas and a karyological analysis on most Malagasy species of the gekkonid genus Lygodactylus. The phylogenetic analysis largely confirms major basal branching pattern of previous molecular studies, but highlights significant differences concerning both the relationships between different species groups as well as those within groups. The biogeographic analysis supports a Malagasy origin of Lygodactylus, an oversea dispersal to continental Africa and a return to Madagascar. The L. madagascariensis group (also including a new candidate species identified herein) is the most basal clade in Lygodactylus, and the sister group of a clade with all the remaining species. The second most basal clade is the L. verticillatus group, placed as the sister group of a clade comprising African and Malagasy species. The sister lineage of the L. verticillatus group originated the African radiation through an oversea dispersal out of Madagascar. Eventually, the sister lineage of the L. capensis group originated secondary dispersals from Africa to Madagascar. In Madagascar, lineage diversification in different species groups mainly occurred from southern to northern and eastern regions. Dispersal, vicariance and paleoclimatic refugia probably played a relevant role in the evolutionary history of closely related taxa and in speciation mechanisms. The cytogenetic analysis evidenced a high karyotypic variability in Lygodactylus (from 2n = 34 to 2n = 40), which is at least partly consistent with the phylogenetic relationships and the composition of the various species group. Chromosome evolution occurred independently in different lineages, mainly through a reduction in the chromosome number and starting from a putative primitive karyotype of 2n = 40 with all telocentric elements.

Out of the Sichuan Basin: Rapid species diversification of the freshwater crabs in Sinopotamon (Decapoda: Brachyura: Potamidae) endemic to China

Sinopotamon Bott, 1967 is the most speciose and widely distributed freshwater crab genus in East Asia. Our extensive sampling includes about 76% of the known Sinopotamon taxa, and nearly covers its entire distribution area. Based on mitochondrial cytochrome oxidase I (COI) and 16S rRNA, as well as nuclear 28S rRNA and histone H3, we reconstructed the Sinopotamon phylogeny using maximum likelihood and Bayesian approaches. The divergence time was estimated and multiple methods were used to conduct diversification analyses. The ancestral geographic distribution and character state were reconstructed. Three main clades (Clades I, II and III) that roughly correspond to their main geographic distribution ranges were recovered. Our results challenge the current view of the four major species groups based on the morphological differences in the male first gonopod (G1). The most recent common ancestor of Sinopotamon most likely originated from the Sichuan Basin and surrounding mountains (SBSM) and subsequently dispersed throughout central and eastern China. The exceptionally rapid, recent diversification was detected in Clade II. The high incidence of species-level non-monophyly found in Clade II can be explained by recent rapid radiation. Climatic changes, morphological innovations, range expansion and geographical heterogeneity may all contribute to the diversification in Sinopotamon. This study contributes to our knowledge on diversification of freshwater benthic macro-invertebrates in the East Asian inland ecosystem.

Phylogeny and biogeography of Muusoctopus (Cephalopoda: Enteroctopodidae)

Deep‐sea octopuses of the genus Muusoctopus are thought to have originated in the Pacific Northern Hemisphere and then diversified throughout the Pacific and into the rest of the World Ocean. However, this hypothesis was inferred only from molecular divergence times. Here, the ancestral distribution and dispersal routes are estimated by Bayesian analysis based on a new phylogeny including 38 specimens from the south‐eastern Pacific Ocean. Morphological data and molecular sequences of three mitochondrial genes (16S rRNA, COI and COIII) are presented. The morphological data confirm that specimens newly acquired from off the coast of Chile comprise two species: Muusoctopus longibrachus and the poorly described species, Muusoctopus eicomar. The latter is here redescribed and is clearly distinguished from M. longibrachus and other closely related species in the region. A gene tree was built using Bayesian analysis to infer the phylogenetic position of these species within the species group, revealing that a large genetic distance separates the two sympatric Chilean species. M. longibrachus is confirmed as the sister species of Muusooctopus eureka from the Falkland Islands; while M. eicomar is a sister species of Muusoctopus yaquinae from the North Pacific, most closely related to the amphi‐Atlantic species Muusoctopus januarii. Molecular divergence times and ancestral distribution analyses suggest that genus Muusoctopus may have originated in the North Atlantic: one lineage dispersed directly southward to the Magellan region and another dispersed southward along the Eastern Pacific to the Southern Ocean and Antarctica. The Muusoctopus species in the Southern Hemisphere have different phylogenetic origins and represent independent invasions of this region.

A well-sampled phylogenetic analysis of the polystichoid ferns (Dryopteridaceae) suggests a complex biogeographical history involving both boreotropical migrations and recent transoceanic dispersals

Intercontinental disjunctions in ferns have often been considered as the result of long-distance dispersal (LDD) events rather than of vicariance. However, in many leptosporangiate groups, both processes appear to have played a major role in shaping current geographical distribution. In this study, we reconstructed the phylogenetic relationships and inferred the ancestral distribution areas of the polystichoid ferns (Cyrtomium, Phanerophlebia, and Polystichum), to evaluate the relative impact of vicariance and LDD on the biogeography of this group. We used a molecular dataset including 3346 characters from five plastid loci. With 190 accessions our taxon coverage was about three times as large as any previous worldwide sampling. Biogeographical analyses were performed using S-DIVA and S-DEC and divergence times were estimated by integrating fossil and secondary calibrations.The polystichoid ferns are a monophyletic clade that may have originated in East Asia during the Eocene, an age much younger than previously estimated. Three transoceanic disjunctions between East Asia and New World were identified in the Paleogene: one for Phanerophlebia during late Eocene (34Ma, 19–51Ma), and two in Polystichum at the Eocene–Oligocene boundary (30Ma, 18–43Ma; 28Ma, 19–39Ma respectively). During the Neogene, further range expansions took place from Asia to Africa, Hawaii, and the Southwestern Indian Ocean region.Our results indicate that early transfers between the Old and the New World are compatible with a boreotropical migration scenario. After evolving in Asia during the Eocene, the polystichoid ferns reached the New World in independent migrations at the Eocene–Oligocene boundary through the boreotropical belt. However, although less likely, the alternative hypothesis of independent transoceanic dispersals from the Old to the New World cannot be ruled out. Further range expansion during the Neogene was most likely the result of long-distance dispersal (LDD).

A global molecular phylogeny and timescale of evolution for Cryptocercus woodroaches

Cryptocercus is a genus of sub-social wood-feeding cockroaches that represents the sister group to the eusocial termites. We generated mitochondrial (12S+16S rRNA, COII), nuclear (28S rRNA) and Blattbacterium endosymbiont (16S+23S rRNA) sequence data for 8 new Chinese species, and combined these with previously available data to undertake the most extensive analysis of phylogenetic relationships within the genus to date. As expected, phylogenetic relationships among Blattabacterium strains were found to be congruent with those of their hosts. Three major clades were found to exist in Asian populations, one representing taxa from the Hengduan mountains in Southwestern China, a second including taxa from Russia, Korea, Northeastern China, and Yunnan in the Hengduan Mountains, and a third including taxa from the Qinling Mountains and Daba Mountains in Central China. A molecular dating analysis using 7 termite fossils to calibrate the molecular clock indicated that the divergence of American and Asian Cryptocercus occurred 55.09Ma (41.55–72.28Ma 95% CI), and that the radiations of American and Asian taxa occurred 28.48Ma (20.83–37.95Ma 95% CI) and 20.97Ma (15.78–27.21Ma 95% CI) respectively. Reconstruction of ancestral geographic distributions using S-DIVA suggested Cryptocercus was originally distributed across both continents, as opposed to ancestral migration of Cryptocercus from one continent to the other. The last common ancestor of Asian Cryptocercus was inferred to have existed in Central China. An examination of male chromosome numbers in Asian Cryptocercus showed that diploid numbers vary from 2n=15 to 2n=41, and indicates the presence of eight new species. Our study represents the most comprehensive phylogenetic and biogeographic study yet performed for this important group of cockroaches.

Spatiotemporal diversification of a low‐vagility Neotropical vertebrate clade (short‐tailed opossums, Didelphidae: Monodelphis)

AbstractAimTo infer historical‐biogeographical patterns and processes in South America based on estimated divergence times and ancestral distributions for a diverse clade of small marsupials (Monodelphis).LocationSouth America.MethodsWe estimated a time‐scaled phylogeny using sequence data from four nuclear genes and one mitochondrial gene for most currently recognized species, which we also scored for biome occupancy. We used maximum‐likelihood methods that explicitly model historical‐biogeographical processes to estimate ancestral distributions.ResultsThe earliest cladogenetic events in the genus occurred in the late Miocene, with subsequent diversification from the early Pliocene to the late Pleistocene. Model selection suggests an important role for founder‐event speciation, a process seldom accounted for in previous biogeographical analyses of continental clades. Two equivalently optimal models that incorporate this process each reconstruct the most recent common ancestor of Monodelphis as occurring in both Amazonia and the Atlantic Forest, from which the Andes, the Arid Diagonal (Caatinga, Cerrado, Chaco) and other neighbouring biomes were colonized during the Pliocene and Pleistocene.Main ConclusionsThe diversification of Monodelphis was not restricted to a narrow time interval, suggesting that speciation cannot be attributed to a single leading factor such as tectonism or Pleistocene climatic fluctuations. In particular, speciation within the Atlantic Forest biome appears to have occurred in the Neogene, whereas most Amazonian speciation events are substantially younger. Amazonia and/or the Atlantic Forest hosted most diversification events within Monodelphis and were the historical sources of lineages that subsequently colonized other areas. Founder‐event speciation, a concept traditionally associated with long‐distance dispersal among islands, must sustain other interpretations in historical‐biogeographical analyses of non‐vagile organisms in continental contexts. Possible mechanisms for founder‐event speciation in Monodelphis include historically transient connections between currently disjunct biomes and rapid reproductive isolation of populations colonizing adjacent but ecologically disparate biomes.

Cenozoic tectonic and climatic events in southern Iberian Peninsula: Implications for the evolutionary history of freshwater fish of the genus Squalius (Actinopterygii, Cyprinidae)

Southern Iberian freshwater ecosystems located at the border between the European and African plates represent a tectonically complex region spanning several geological ages, from the uplifting of the Betic Mountains in the Serravalian–Tortonian periods to the present. This area has also been subjected to the influence of changing climate conditions since the Middle–Upper Pliocene when seasonal weather patterns were established. Consequently, the ichthyofauna of southern Iberia is an interesting model system for analyzing the influence of Cenozoic tectonic and climatic events on its evolutionary history. The cyprinids Squalius malacitanus and Squalius pyrenaicus are allopatrically distributed in southern Iberia and their evolutionary history may have been defined by Cenozoic tectonic and climatic events. We analyzed MT-CYB (510 specimens) and RAG1 (140 specimens) genes of both species to reconstruct phylogenetic relationships and to estimate divergence times and ancestral distribution ranges of the species and their populations. We also assessed their levels of genetic structure and diversity as well as the amount of gene flow between populations. To investigate recent paleogeographical and climatic factors in southern Iberia, we modeled changes-through-time in sea level from the LGM to the present. Phylogenetic, geographic and population structure analyses revealed two well-supported species (S. malacitanus and S. pyrenaicus) in southern Iberia and two subclades (Atlantic and Mediterranean) within S. malacitanus. The origin of S. malacitanus and the separation of its Atlantic and Mediterranean populations occurred during the Serravalian–Tortonian and Miocene–Pliocene periods, respectively. These divergence events occurred in the Middle Pliocene and Pleistocene in S. pyrenaicus. In both species, Atlantic basins possessed populations with higher genetic diversity than Mediterranean, which may be explained by the Janda Lagoon. The isolation of S. malacitanus was earlier and related to the rising of the Betic Mountains. Divergence of its Atlantic and Mediterranean populations was associated with the creation of the freshwater systems of southern Iberia close to the Gibraltar Strait. The presence of S. pyrenaicus in southern Iberia may be the result of recent colonization associated with river capture, as demonstrated our biogeographic reconstruction.

Did a Miocene–Pliocene island isolation sequence structure diversification of funnel web spiders in the Taiwan‐Ryukyu Archipelago?

AbstractAimWe tested the competing hypotheses concerning the relative importance of Pleistocene versus Miocene–Pliocene geological events for the formation of endemism in an Asian archipelago using the Macrothele taiwanensis (Hexathelidae) species group.LocationTaiwan‐Ryukyu Archipelago.MethodsWe estimated phylogenetic trees from cytochrome oxidase I subunit (COI) and 16S rRNA (16S) gene regions and employed Bayesian ancestral range reconstructions to investigate previously debated models of lineage diversification in the Taiwan‐Ryukyu Archipelago. To evaluate alternative geological timeframes for their importance in shaping the genetic structure of funnel web spiders, we used five time calibration schemes to estimate timing of divergence, infer ancestral distributions, and to reconstruct historical demographic changes in each lineage. We tested taxonomic boundaries with two species delimitation procedures.ResultsOur results indicate a north‐to‐south isolation sequence of the M. taiwanensis group: the Amami lineage diverged first, then Yaeyama, and finally the Taiwanese lineages. Divergence time estimation and population demographic change analyses indicate that Pleistocene climate fluctuations minimally impacted the genetic structure of these spiders. Instead, estimated divergence events correspond to Miocene–Pliocene geological events, strongly supporting a much older timeframe for diversification. The results of species delimitation analyses coincide well with morphological differences observed among the island populations, reinforcing inferred species boundaries, and at least three potential cryptic species were statistically detected within Taiwan.Main conclusionsMiocene–Pliocene geological events appear to have contributed disproportionately to diversification in the M. taiwanensis species group. The clear association between geographical area, genetic structure and statistical species delimitation strongly supports an interpretation of allopatric speciation. We advocate comparing our results with those derived from additional study organisms with similar life histories to further explore the Miocene–Pliocene diversification hypothesis.

Biogeographic relationships between Macaronesia and the Americas

A vicariance model is presented for the origin of Macaronesian endemics and their allopatric American relatives. Trans-Atlantic relationships are identified for 21 taxa in which an endemicMacaronesian clade either has a sister group in the New World or is part of a larger monophyletic group that includes representatives in the New World. Historical implications of this pattern are discussed in relation to current tectonic and geological models for the Central Atlantic and theMacaronesian Islands. The proposed vicariance model identifies a local origin for theMacaronesian endemics from ancestral distributions that already encompassed ancestralMacaronesia and parts of the New and Old World before formation of the Atlantic. The present-day existence of Macaronesian endemics is attributed to sequential colonisation of newly formed islands within the Atlantic from Mesozoic time.

Phylogeny and Biogeographic History of <I>Astrophytum</I> (Cactaceae)

Abstract Despite efforts for a complete phylogeny of Cactaceae, generic circumscription and species level relationships remain unsolved. Within Astrophytum one species is assigned to a different genus (Digitostigma) and two are often treated as a single species (A. myriostigma and A. coahuilense). Astrophytum is endemic to the Chihuahuan Desert, but may also be found in adjacent regions. We reconstructed the phylogeny to date the origin of clades and infer the biogeographic patterns of Astrophytum in order to understand the relationships between group members. Three sequences of chloroplast DNA (rbcL gene, trnL-trnF intergenic spacer, and trnK-matK region) were used with Bayesian and Maximum likelihood methods to generate a phylogeny. Divergence times for each node were estimated using an uncorrelated lognormal clock (BEAST) and inferred ancestral distribution using RASP. Astrophytum is monophyletic, with six species grouped in two main clades. Astrophytum caput-medusae (recognized as Digitostigma) is der...

On the origin of mongrels: evolutionary history of free-breeding dogs in Eurasia.

Although a large part of the global domestic dog population is free-ranging and free-breeding, knowledge of genetic diversity in these free-breeding dogs (FBDs) and their ancestry relations to pure-breed dogs is limited, and the indigenous status of FBDs in Asia is still uncertain. We analyse genome-wide SNP variability of FBDs across Eurasia, and show that they display weak genetic structure and are genetically distinct from pure-breed dogs rather than constituting an admixture of breeds. Our results suggest that modern European breeds originated locally from European FBDs. East Asian and Arctic breeds show closest affinity to East Asian FBDs, and they both represent the earliest branching lineages in the phylogeny of extant Eurasian dogs. Our biogeographic reconstruction of ancestral distributions indicates a gradual westward expansion of East Asian indigenous dogs to the Middle East and Europe through Central and West Asia, providing evidence for a major expansion that shaped the patterns of genetic differentiation in modern dogs. This expansion was probably secondary and could have led to the replacement of earlier resident populations in Western Eurasia. This could explain why earlier studies based on modern DNA suggest East Asia as the region of dog origin, while ancient DNA and archaeological data point to Western Eurasia.

Ancient river systems and phylogeographical structure in the spring salamander, Gyrinophilus porphyriticus

AbstractAimThe river drainages of the Appalachian Mountains have experienced a dynamic history as glacial cycles, stream capture and other geological processes have led to the fragmentation and fusion of formerly isolated palaeodrainages. Some ancient rivers have gone extinct, including portions of the great Teays River. Here we investigate the contribution of contemporary and historical drainages to patterns of phylogeographical structure in the spring salamander complex, Gyrinophilus porphyriticus.LocationEastern North America, USA.MethodsSampling spanned the range of the G. porphyriticus complex, and included representative samples of the cave species of Gyrinophilus as well. Molecular sequence data included the mitochondrial DNA locus cytochrome b and the nuclear locus recombination‐activating gene 1 (RAG‐1). Time‐calibrated phylogenies were inferred, and Bayes‐LAGRANGE was used to reconstruct ancestral distributions. Contemporary and historical river influences on patterns of genetic diversity were tested using distance‐based redundancy analysis (db‐RDA).ResultsThe G. porphyriticus complex originated prior to the Pleistocene glacial cycles, and historical river systems explained more genetic variation than did contemporary drainages or geographical distance. Patterns of genetic variation suggest that extinct or remodelled palaeodrainages, including the Teays River, played an important role in structuring contemporary patterns of genetic variation.Main conclusionsThe hydrogeological history of eastern North American drainage basins has been instrumental in structuring patterns of regional biodiversity in freshwater species. Here we show that hydrological remodelling has also left its genetic signature in the semi‐aquatic spring salamander complex, G. porphyriticus. Historical drainages accounted for the largest fraction of phylogeographical structure, more so than did contemporary drainages or geographical distance, with spatial and temporal patterns of variation associated with the extinct Teays River.

Molecular phylogeography of four endemicSagittariaspecies (Alismataceae) in the Sino-Japanese Floristic Region of East Asia

To reveal the role of climate oscillations of the Quaternary in forming the contemporary plant diversity in the temperate Sino-Japanese Floristic Region of mainland China, we assess the phylogeographical patterns of four Sagittaria species in the region using sequence data from plastid DNA non-coding regions (psbA-trnH, the rpl16 intron and trnC-ycf6) and the internal transcribed spacers of nuclear ribosomal DNA (nrITS). Based on both datasets, the divergence time among the four studied species was estimated to fall in the Late Tertiary (plastid DNA: 7.1–13.7 Mya; ITS: 11.1–16.1 Mya). The ancestral distribution analyses revealed that regions with a great diversity in topography, climate and ecological conditions, e.g. the Hengduan Mountains, Central China and East China, were the areas where the endemics originated. Mismatch distribution analyses revealed that each species had experienced a range expansion in response to Quaternary climatic oscillations. Our findings contradict the hypothesis of Quaternary origins of the endemic Sagittaria spp.; we support the view that modern species in the Northern Hemisphere originated mostly during the Tertiary. Range expansion may have profoundly modified the current distribution ranges of Sagittaria species in the Sino-Japanese Floristic Region. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 00, 000–000.