Ancestral Area Estimation Research Articles

Multilocus phylogeny of the Asian Lance-headed pitvipers (Squamata, Viperidae, Protobothrops)

Despite the public health significance and potential applications to medical research, the evolutionary history of the Asian Lance-headed pitvipers (genus Protobothrops) remains inadequately studied. Previous research generally focused on a few selected species with no comprehensive molecular study of Protobothrops. Here, we conduct the first study to infer the phylogenetic relationships of all currently recognized species in this genus based on four mitochondrial DNA fragments and four nuclear genes. Bayesian Inference and Maximum Likelihood analyses show that within Protobothrops there are four strongly supported clades forming distinct subgroups. The first subgroup, which is sister to the other three, consists of three species, P. himalayanus, P. kaulbacki, and P. sieversorum. The second subgroup contains only P. mangshanensis. The final two subgroups, which are sister groups, include the other four and six Protobothrops species. Although our findings provide additional information on the phylogenetic relationships of the genus Protobothrops, the placement of P. dabieshanensis and P. elegans remains problematic. In addition, our molecular results indicate that P. trungkhanhensis, currently considered endemic to Vietnam, should be added to the species known from China. Our ancestral area estimation indicated that Protobothrops likely originated in southwestern China. This study improves our understanding of the evolutionary relationships among species of Asian Lance-headed pitvipers, providing a greater framework for future studies.

Ancient islands acted as refugia and pumps for conifer diversity.

Island species are thought to be extinction-prone because of small population sizes, restricted geographical distribution and limited dispersal ability. However, the topographical and environmental heterogeneity, geographical isolation and stability of islands over long timescales could create refugia for taxa whose source area is threatened by environmental changes. We address this possibility by inferring the evolution of the New Caledonia (NC) and New Zealand (NZ) conifer diversity, which represents over 10% of the world's diversity for this group. We estimate speciation and extinction rates in relation to the presence/absence on these islands, and dispersal rates between the islands and surrounding areas. We also test the Eocene submersion of NC and the Oligocene drowning of NZ by comparing the fit of biogeographical scenarios using ancestral area estimations. We find that extinction rates were significantly lower for island species, and dispersal "out of islands" was higher. A model including a diversification shift when NC emerged better explains the diversification dynamics. Biogeographical analyses corroborate that conifers experienced high continental extinctions, but survived on islands. NC and NZ have thus contributed to the world's conifer diversity as "island refugia", by maintaining early-diverging lineages from continents during environmental changes on continents. These ancient islands also acted as "species pumps", providing species into adjacent areas. Our study highlights the important but neglected role of islands in promoting the evolution and conservation of biodiversity.

Molecular phylogeography of white‐lipped tree viper (Trimeresurus; Viperidae)

The white‐lipped tree viper (Trimeresurus albolabris) is one of the most common venomous snakes with medicine importance in South East Asia. To explore the genetic diversity, population structure and evolutionary history of Trimeresurus albolabris, we collected 98 samples from 27 localities covering its entire distribution. Two mitochondrial gene fragments (cyt‐b and ND‐4) and two nuclear genes (RAG‐1 and NT‐3) were sequenced and analysed. Bayesian inference and maximum‐likelihood methods were employed to reconstruct the phylogenetic relationships among populations based on the two mitochondrial fragments, and the median‐joining networks were depicted using nuclear genes. Divergence date and ancestral area were estimated, and the population demographic history was inferred. Both phylogenetic analyses consistently uncovered that Trimeresurus albolabris was monophyletics, with five geographically structured lineages. Divergence date and ancestral area estimation indicated that T. albolabris originated in northern Thailand and eastern Myanmar at c. 7.15 Ma. Population dynamics analyses showed the southern China lineage has experienced population expansion and contraction, but the others have not. Both the interglacial expansion and the highly heterogeneous habitats resulting from the uplift of the Plateau played a joint role in shaping the present distribution and population structure. The evolutionary history of T. albolabris can be explained by a pattern of two direction dispersal: first from North to South, and then from West to East.

Is the sword moss (Bryoxiphium) a preglacial Tertiary relict?

The disjunction of floras between East Asia, Southeast North America, West North America, and Southwest Eurasia has been interpreted in terms of the fragmentation of a once continuous mixed mesophytic forest that occurred throughout the Northern Hemisphere due to the climatic and geological changes during the late Tertiary. The sword moss, Bryoxiphium, exhibits a distribution that strikingly resembles that of the mesophytic forest elements such as Liriodendron and is considered as the only living member of an early Tertiary flora in Iceland. These hypotheses are tested here using molecular dating analyses and ancestral area estimations. The results suggest that the extant range of Bryoxiphium results from the fragmentation of a formerly wider range encompassing North America and Southeast Asia about 10 million years ago. The split of continental ancestral populations is too recent to match with a continental drift scenario but is spatially and temporally remarkably congruent with that observed in Tertiary angiosperm relict species. The timing of the colonization of Iceland from Macaronesian ancestors, about two million years ago, is, however, incompatible with the hypothesis that Bryoxiphium is the only living member of an early Tertiary flora of the island. Alaska was recurrently colonized from East Asia. The ability of Bryoxiphium to overcome large oceanic barriers is further evidenced by its occurrence on remote oceanic archipelagos. In particular, Madeira was colonized twice independently from American and East Asian ancestors, respectively. The striking range disjunction of Bryoxiphium is interpreted in terms of its mating system, as the taxon exhibits a very singular pattern of spatial segregation of the sexes.

Coordinated Dispersal and Pre-Isthmian Assembly of the Central American Ichthyofauna.

We document patterns of coordinated dispersal over evolutionary time frames in heroine cichlids and poeciliine live-bearers, the two most species-rich clades of freshwater fishes in the Caribbean basin. Observed dispersal rate ( values were estimated from time-calibrated molecular phylogenies in Lagrange+, a modified version of the ML-based parametric biogeographic program Lagrange. is measured in units of “wallaces” (wa) as the number of biogeographic range-expansion events per million years. estimates were generated on a dynamic paleogeographic landscape of five areas over three time intervals from Upper Cretaceous to Recent. Expected dispersal rate ( values were generated from alternative paleogeographic models, with dispersal rates proportional to target area and source-river discharge volume, and inversely proportional to paleogeographic distance. Correlations between and were used to assess the relative contributions of these three biogeographic parameters. estimates imply a persistent dispersal corridor across the Eastern (Antillean) margin of the Caribbean plate, under the influence of prevailing and perennial riverine discharge vectors such as the Proto–Orinoco–Amazon river. Ancestral area estimation places the earliest colonizations of the Greater Antilles and Central America during the Paleocene–Eocene (ca. 58–45 Ma), potentially during the existence of an incomplete Paleogene Arc (∼59 Ma) or Lesser Antilles Arc (∼45 Ma), but predating the GAARlandia land bridge (∼34–33 Ma). Paleogeographic distance is the single best predictor of . The Western (Central American) plate margin did not serve as a dispersal corridor until the Late Neogene (12–0 Ma), and contributed relatively little to the formation of modern distributions.

Multilocus Phylogeny of the Afrotropical Freshwater Crab Fauna Reveals Historical Drainage Connectivity and Transoceanic Dispersal Since the Eocene.

Phylogenetic reconstruction, divergence time estimations and ancestral range estimation were undertaken for 66% of the Afrotropical freshwater crab fauna (Potamonautidae) based on four partial DNA loci (12S rRNA, 16S rRNA, cytochrome oxidase one [COI], and histone 3). The present study represents the most comprehensive taxonomic sampling of any freshwater crab family globally, and explores the impact of paleodrainage interconnectivity on cladogenesis among freshwater crabs. Phylogenetic analyses of the total evidence data using maximum-likelihood (ML), maximum parsimony (MP), and Bayesian inference (BI) produced a robust statistically well-supported tree topology that reaffirmed the monophyly of the Afrotropical freshwater crab fauna. The estimated divergence times suggest that the Afrotropical Potamonautidae diverged during the Eocene. Cladogenesis within and among several genera occurred predominantly during the Miocene, which was associated with major tectonic and climatic ameliorations throughout the region. Paleodrainage connectivity was observed with specimens from the Nilo-Sudan and East African coast proving to be sister to specimens from the Upper Guinea Forests in West Africa. In addition, we observed strong sister taxon affinity between specimens from East Africa and the Congo basin, including specimens from Lake Tanganyika, while the southern African fauna was retrieved as sister to the Angolan taxa. Within the East African clade we observed two independent transoceanic dispersal events, one to the Seychelles Archipelago and a second to Madagascar, while we observe a single transoceanic dispersal event from West Africa to São Tomé. The ancestral area estimation suggested a West African/East African ancestral range for the family with multiple dispersal events between southern Africa and East Africa, and between East Africa and Central Africa The taxonomic implications of our results are discussed in light of the widespread paraphyly evident among a number of genera.

Molecular phylogeny and biogeographic history of the armored neotropical catfish subfamilies hypoptopomatinae, neoplecostominae and otothyrinae (siluriformes: loricariidae).

The main objectives of this study are estimate a species-dense, time-calibrated molecular phylogeny of Hypoptopomatinae, Neoplecostominae, and Otothyrinae, which together comprise a group of armoured catfishes that is widely distributed across South America, to place the origin of major clades in time and space, and to demonstrate the role of river capture on patterns of diversification in these taxa. We used maximum likelihood and Bayesian methods to estimate a time-calibrated phylogeny of 115 loricariid species, using three mitochondrial and one nuclear genes to generate a matrix of 4,500 base pairs, and used parametric biogeographic analyses to estimate ancestral geographic ranges and to infer the effects of river capture events on the geographic distributions of these taxa. Our analysis recovered Hypoptopomatinae, Neoplecostominae, and Otothyrinae as monophyletic with strong statistical support, and Neoplecostominae as more closely related to Otothyrinae than to Hypoptopomatinae. Our time-calibrated phylogeny and ancestral-area estimations indicate an origin of Hypoptopomatinae, Neoplecostominae, and Otothyrinae during the Lower Eocene in the Atlantic Coastal Drainages, from which it is possible to infer several dispersal events to adjacent river basins during the Neogene. In conclusion we infer a strong influence of river capture in: (1) the accumulation of modern clade species-richness values; (2) the formation of the modern basin-wide species assemblages, and (3) the presence of many low-diversity, early-branching lineages restricted to the Atlantic Coastal Drainages. We further infer the importance of headwater stream capture and marine transgressions in shaping patterns in the distributions of Hypoptopomatinae, Neoplecostominae and Otothyrinae throughout South America.

Evolution and diversification related to rainfall regimes: diversification patterns in the South African genus Metalasia (Asteraceae–Gnaphalieae)

AbstractAimThe Cape region is known for its exceptional species richness, although much remains unknown regarding the appearance of the modern Cape flora. One explanation is that floral diversification was influenced by the establishment of winter rainfall/summer arid conditions hypothesized to have occurred towards the end of the Miocene. We studied the evolution and diversification of the plant genus Metalasia (Asteraceae–Gnaphalieae), with the aim of testing whether radiation patterns may have been influenced by the climatic changes.LocationSouth Africa, with emphasis on the south‐west.MethodsThe radiation of Metalasia was investigated using two approaches: a species diffusion approach, which estimated the ancestral areas by means of a relaxed random walk while sampling from extant distributions; and a discrete approach, in which distributions were defined according to the phytogeographical centres of the Cape region. Secondarily derived clock rates from an earlier Gnaphalieae study were used for calibration purposes.ResultsOur analyses date Metalasia to approximately 6.9 Ma, after the Miocene–Pliocene boundary and the establishment of the winter rainfall/summer arid conditions. Metalasia consists of two sister clades: Clade A and Clade B. Clade B, which is endemic to the winter rainfall area, is estimated to have diversified c. 6.4 Ma, whereas Clade A, with a main distribution in the all‐year rainfall area, is considerably younger, with a crown group age estimated to 3.3 Ma. Diversification rates suggest an early rapid speciation, with rates decreasing through time both for Metalasia and for clades A and B separately. Ancestral area estimations show a possible scenario for the radiation of Metalasia to its current diversity and distribution, with no conflict between results inferred from diffusion or discrete methods.Main conclusionsThe diversification of Metalasia is estimated to have begun after the establishment of the winter rainfall/summer arid conditions, consistent with its radiation having been influenced by changes in the climatic regime.

Out of Asia: Natricine snakes support the Cenozoic Beringian Dispersal Hypothesis

Based on a combination of six mitochondrial gene fragments (12S RNA, cyt b, ND1, ND2, ND4 and CO1) and one nuclear gene (c-mos) from 22 genera we infer phylogenetic relationships among natricine snakes and examine the date and area of origin of these snakes. Our phylogenetic results indicate: (1) the subfamily Natricinae is strongly supported as monophyletic including a majority of extant genera, and a poorly known and previously unassigned species Trachischium monticola, (2) two main clades are inferred within Natricinae, one containing solely taxa from the Old World (OW) and the other comprising taxa from a monophyletic New World (NW) group with a small number of OW relatives. Within the first clade, the genera Xenochrophis and Amphiesma are apparently not monophyletic. Divergence dating and ancestral area estimation indicate that the natricines originated in tropical Asia during the later Eocene or the Oligocene. We recover two major dispersals events out of Asia, the first to Africa in the Oligocene (28Ma) and the second to the Western Palearctic and the New World at 27Ma. This date is consistent with the dispersal of numerous other OW groups into the NW.

Phylogeography of the Coccus scale insects inhabiting myrmecophytic Macaranga plants in Southeast Asia

AbstractComparative historical biogeography of multiple symbionts occurring on a common host taxa can shed light on the processes of symbiont diversification. Myrmecophytic Macaranga plants are associated with the obligate mutualistic symbionts: Crematogaster (subgenus Decacrema) ants and Coccus scale insects. We conduct phylogeographic analyses based on mitochondrial cytochrome oxidase I (COI) from 253 scale insects collected from 15 locations in Borneo, Malaya and Sumatra, to investigate the historical biogeography of the scales, and then to draw comparisons with that of the symbiotic, but independently dispersing, Decacrema ants which are not specific to different Coccus lineages. Despite the different mode of ancient diversification, reconstruction of ancestral area and age estimation on the Coccus phylogeny showed that the scales repeatedly migrated between Borneo and Malaya from Pliocene to Pleistocene, which is consistent with the Decacrema ants. Just as with the ants, the highest number of lineages in the scale insects was found in northern northwest Borneo, suggesting that these regions were rainforest refugia during cool dry phases of the Pleistocene. Overall, general congruence between the Plio–Pleistocene diversification histories of the symbiotic scales and ants suggests that they experienced a common history of extinction/migration despite their independent mode of dispersal and host‐colonization.