Evaluating environmental and geometrical constraints on endemic vertebrates of the semiarid Caatinga (Brazil)

Most hypotheses explaining species diversity are related to the current and/or past environment, but explanations that rely on geometrical constraints, such as the mid-domain effect, have been recently proposed. Under this type of model, more species are expected in the centre of a domain due to the extent of occurrence of the species being constrained by the domain's geometry. Here we evaluated the proportion of the explanatory power of space, the current environment, historical vicariance events and geometric constraints on the richness of the Caatinga's terrestrial endemic vertebrates using a partial regression approach. The current environment had the highest proportion of explanatory power for the variance of the Caatinga's endemic species, in its shared effect, explaining approximately 47%. On the other hand the geometric constraints model (GCM) had the highest proportion in its single explanatory power with 15% of explanatory power. The amount of explanation by GCM changes when analyzing richness of endemics calculated from species with different range sizes. Despite the fact that GCM is the main driver of the Caatinga's endemic species, in its single effect, this does not necessarily indicate that geometric constraints and random dispersal within species ranges drive richness. The GCM model underestimates richness in the centre of the Caatinga, suggesting that other ecological and evolutionary processes may help explain the overall pattern of decreasing richness towards the borders of the biome.     

Does organismal pedigree impact the magnitude of topological congruence among gene trees for unlinked loci?

One of the fundamental assumptions in the multi-locus approach to phylogeographic studies is that unlinked loci have independent genealogies. For this reason, congruence among gene trees from unlinked loci is normally interpreted as support for the existence of external forces that may have concordantly shaped the topology of multiple gene trees. However, it is also important to address and quantify the possibility that gene trees within a given species are all inherently constrained to some degree by their shared organismal pedigree, and thus in this strict sense are not entirely independent. Here we demonstrate by computer simulations that gene trees from a shared pedigree tend to display higher topological concordance than do gene trees from independent pedigrees with the same demographic parameters, but we also show that these constraining effects are normally minor in comparison to the much higher degree of topological concordance that can routinely emerge from external phylogeographic shaping forces. The topology-constraining effect of a shared pedigree decreases as effective population size increases, and becomes almost negligible in a random mating population of more than 1,000 individuals. Moreover, statistical detection of the pedigree effect requires a relatively large number of unlinked loci that far exceed what is typically used in current phylogeographic studies. Thus, with the possible exception of extremely small populations, multiple unlinked genes within a pedigree can indeed be assumed, for most practical purposes, to have independent genealogical histories.     

Population genetic structure in the endemic cyprinid fish Microphysogobio alticorpus in Taiwan: Evidence for a new phylogeographical area

The Formosa Bank is a significant zoogeographical barrier for the freshwater fish in Southern Taiwan. Here, we present population genetic structure analyses on Microphysogobio alticorpus populations in Taiwan, and biogeographic pattern to infer the relationship between historic dispersal geological dynamics. A total of 24 haplotypes were genotyped for mitochondrial CR + cyt b region in 134 specimens collected from 9 populations. Relatively high levels of haplotype diversity (h = 0.896) and low levels of nucleotide diversity (π = 0.005) were detected in M. alticorpus. Two major phylogenetic haplotype groups, Clade N1+N2 and S, were revealed and estimated to diverge about 0.121 myr (million years) ago. Haplotype network and population genetic analyses indicated significant genetic structure (F_ST = 0.876), largely concordant with the geographical location of the populations. According to SAMOVA analysis, M. alticorpus populations were divided into five units that can be explained by episodes of dispersal and population expansion followed by population fragmentation and restricted gene flow. The results of the topological pattern and network suggested that the Kaoping River was the first habitat colonized by the ancestor of M. alticorpus, before the northward dispersal.     

Cracking the nut: geographical adjacency of sister taxa supports vicariance in a polytomic salamander clade in the absence of node support

The urodelan genus Lyciasalamandra, which inhabits a relatively small area along the southern Turkish coast and some Aegean islands, provides an outstanding example of a diverse but phylogenetically unresolved taxon. Molecular trees contain a single basal polytomy that could be either soft or hard. We here use the information of nuclear (allozymes) and mitochondrial (fractions of the 16S rRNA and ATPase genes) datasets in combination with area relationships of lineages to resolve the phylogenetic relationships among Lyciasalamandra species in the absence of sufficient node support. We can show that neither random processes nor introgressive hybridization can be invoked to explain that the majority of pairs of sister taxa form geographically adjacent units and interpret that this pattern has been shaped by vicariant events. Topology discordance between mitochondrial and nuclear trees mainly refers to an affiliation of L. helverseni, a taxon restricted to the Karpathos archipelago, to the western-most and geographically proximate mainland taxon in the nuclear tree, while in the organelle tree it turns out to be the sister lineage to the geographically most distant eastern clade. As this discordance cannot be explained by long-branch attraction in either dataset we suppose that oversea dispersal may have accounted for a second colonization of the Karpathos archipelago. It may have initiated introgression and selection driven manifestation of alien eastern mitochondrial genomes on a western nuclear background. Our approach of testing for area relationships of sister taxa against the null hypothesis of random distribution of these taxa seems to be especially helpful in phylogenetic studies where traditional measures of phylogenetic branch support fail to reject the null hypothesis of a hard polytomy.     

Biogeography of the chaetodontidae: an analysis of allopatry among closely related species

Synopsis A recent survey of chaetodontid osteology has produced a hypothesis of relationships among 22 osteologically distinct genera and subgenera. Fourteen supra-specific taxa have distributions that are Indo-Pacific or larger. Most sister taxa inferred by osteology are broadly sympatric. The basal dichotomy within the large genusChaetodon contrasts monophyletic groups centered in the Atlantic and Indo-Pacific with little overlap. Divergence of Atlantic and Indo-Pacific distributions is correlated with the closing of the Tethys seaway 18–13 million years ago. Distributional data of Burgess (1978) and Allen (1980) are reevaluated in the context of putative species pairs and complexes. Species in nearly two thirds of these complexes (18 of 31) are distributed allopatrically. Eight complexes are examined in more detail. Five of these eight contain at least one peripherically isolated species. Distributions of species in four complexes indicate that previously wide-spread species were cleaved more symmetrically. Sympatric distributions within two species pairs indicate that the more narrowly distributed species in each pair arose through central isolation within a broadly distributed ancestor. The area of central isolation corresponds to the classical center of origin. A new hypothesis of vicariance followed by dispersal may partially explain the diversity gradient so prominently featured in dispersal-oriented tropical marine biogeography.     

Diversification and vicariance of desert plants: Evidence inferred from chloroplast DNA sequence variation of Lagochilus ilicifolius (Lamiaceae)

To document arid Northern China as a diversification center for desert plants, and to better understand the mechanisms of desert taxa diversification, we used five cpDNA spacers (trnL-trnF, rps16, psbA-trnH, psbK-psbI and trnS-trnG) to investigate Lagochilus ilicifolius in all distribution areas, including Northern China, Mongolia and Russia. Phylogenetic analyses showed that L. ilicifolius comprises two distinctive lineages, one distributed in China, and another in Mongolia–Russia. Our data confirmed that arid Northern China, is a distinctive area with many endemic genera. Biogeographic inferences, based on a Bayesian uncorrelated lognormal model together with molecular dating, suggested that the main diversification within the species occurred in the Pleistocene (ca. 1.38–0.3 Ma), resulting from the transition of the climate of Eurasia to a dry-cold pattern as well as the desertification caused the vicariance of desert plants.     

Spiny Norman in the Garden of Eden? Dispersal and early biogeography of Placentalia

The persistent finding of clades endemic to the southern continents (Afrotheria and Xenarthra) near the base of the placental mammal tree has led molecular phylogeneticists to suggest an origin of Placentalia, the crown group of Eutheria, somewhere in the southern continents. Basal splits within the Placentalia have then been associated with vicariance due to the breakup of Gondwana. Southern-origin scenarios suffer from several problems. First, the place of origin of Placentalia cannot be reconstructed using phylogenetic reasoning without reference to outgroups. When available outgroups are considered, a Laurasian origin is most parsimonious. Second, a model of pure vicariance would require that basal placental splits occurred not with the breakup of Gondwana, but of Pangea in the Late Triassic—Early Jurassic. This event long preceded even the oldest molecular divergence estimates for the Placentalia and was coeval only with the earliest mammals in the fossil record. Third, a problem with the number of dispersal events that would be required emerges under different southern-origin scenarios. In considering the geographic distribution of the major placental clades at their first appearance (mostly Early Cenozoic), it becomes clear that a Laurasian center of origin would require fewer dispersal events. Southern-origin models would require at least twice the number of dispersal events in comparison with a model of Laurasian origins. This number of required dispersal events increases if extinct groups of placental mammals are also considered. Results are similar assuming a morphology-based phylogeny. These facts, along with earlier findings speaking against a major placental radiation deep in the Cretaceous without leaving fossil evidence, suggest an origin of Placentalia somewhere in Laurasia with few supraordinal splits occurring before the last 5–10 million years of the Cretaceous.     

Ecomorphological diversification among South American spiny rats (Rodentia; Echimyidae): a phylogenetic and chronological approach

The phylogeny of South American spiny rats (Rodentia; Echimyidae) was studied using the exon 28 of the von Willebrand Factor nuclear gene (vWF). Sequences were analysed separately and in combination with a mitochondrial dataset (cyt b, 12S and 16S rRNAs) used in previous publications. The basal polytomy of echimyids was partially resolved and unexpected intergeneric clades were recovered. Thus, the intimate nested position of Myocastor within echimyids is evidenced. A well-supported clade is identified, including all the arboreal genera, and a group formed by Myocastor, Thrichomys, and Proechimys+Hoplomys. The clustering of Euryzygomatomys+Clyomys with Trinomys is also suggested. On the opposite, the phylogenetic position of Capromys as well as the relationships among arboreal genera remain unclear. Molecular divergence times were estimated using a Bayesian relaxed molecular clock and suggest a Middle Miocene origin for most of modern genera. The ecomorphological diversification of echimyids is discussed in the light of these new results and past environmental modifications in South America.     

The phylogeography of the gecko Cyrtopodion kotschyi (Reptilia: Gekkonidae) in the Aegean archipelago

Cyrtopodion kotschyi is a small gecko, widely distributed on the islands of the Aegean archipelago and the adjacent mainland. We unveiled the phylogeography of the species by using a portion of the cytochrome oxidase I mitochondrial DNA gene from 35 insular and mainland populations. The distinct geographic distribution of the major clades of the phylogenetic tree and its topology suggest a spatial and temporal sequence of phylogenetic separations that coincide with some major paleogeographical separations during the geological history of the Aegean and support a mainly vicariant pattern of differentiation. The separation times and 95% confidence limits among the different clades were estimated according to two different paleogeographical scenarios. The very high interpopulation genetic divergence (up to 20% uncorrected pairwise distances) and the better concordance between paleogeographical and phylogenetic separations for one of the scenarios suggest that species differentiation started during Miocene (about 10 Mya) due to the fragmentation of the united landmass of "Agais" that was Aegean at that time.     

The genus Chaerilus Simon, 1877 in Vietnam (Scorpiones; Chaerilidae): A possible case of a vicariant species

A new species of the genus Chaerilus Simon, 1877 is described from a cave in Dien Bien District, West of Dien Bien Phu city in northern Vietnam. The new species is morphologically similar to other Chaerilus species distributed only in the south of Vietnam and Cambodia and suggests a case of a vicariant species between northern and southern populations in the Southeast Asian peninsula.