Origin and in situ diversification in Hemidactylus geckos of the Socotra Archipelago

The Socotra Archipelago is an ancient continental fragment of Gondwanan origin and one of the most isolated landforms on Earth and a biodiversity hot spot. Yet, the biogeography and evolutionary history of its endemic fauna still remain largely overlooked. We investigate the origin, tempo and mode of diversification in the Hemidactylus geckos of the Socotra Archipelago. Concatenated and multilocus species coalescent analyses of Hemidactylus from Arabia and North Africa indicate that the Hemidactylus from Socotra do not form a monophyletic group and branch as three independent and well-supported clades instead. Both the chronogram inferred using the gene tree approach of BEAST and the age-calibrated multilocus species tree obtained using *BEAST suggest that the origin of Hemidactylus from Socotra may have involved a first vicariance event that occurred in the Early Miocene, followed by two independent transoceanic dispersal events that occurred more recently, during the Pliocene. Within Socotra, we analysed patterns of genetic diversity, the phylogeography and the demographic history in all seven nonintroduced species of Hemidactylus. Results based on two mitochondrial and two nuclear loci from 144 individuals revealed complex patterns of within-island diversification and high levels of intra-species genetic divergence. The interplay of both historical and ecological factors seems to have a role in the speciation process of this group of geckos. Interestingly, the case of H. forbesii and H. oxyrhinus, which inhabit the island of Abd al Kuri with an area of 133 km(2), may represent one of the most extreme cases of intra-island speciation in reptiles ever reported.     

Not an ancient relic: the endemic Livistona palms of arid central Australia could have been introduced by humans

Livistona mariae is an endemic palm localized in arid central Australia. This species is separated by about 1000 km from its congener L. rigida, which grows distantly in the Roper River and Nicholson-Gregory River catchments in northern Australia. Such an isolated distribution of L. mariae has been assumed to have resulted from contraction of ancestral populations as Australia aridified from the Mid-Miocene (ca 15 Ma). To test this hypothesis at the population level, we examined the genetic relationships among 14 populations of L. mariae and L. rigida using eight nuclear microsatellite loci. Our population tree and Bayesian clustering revealed that these populations comprised two genetically distinct groups that did not correspond to the current classification at species rank, and L. mariae showed closest affinity with L. rigida from Roper River. Furthermore, coalescent divergence-time estimations suggested that the disjunction between the northern populations (within L. rigida) could have originated by intermittent colonization along an ancient river that has been drowned repeatedly by marine transgression. During that time, L. mariae populations could have been established by opportunistic immigrants from Roper River about 15 000 years ago, concurrently with the settlement of indigenous Australians in central Australia, who are thus plausible vectors. Thus, our results rule out the ancient relic hypothesis for the origin of L. mariae.     

A coalescent framework for comparing alternative models of population structure with genetic data: evolution of Celebes toads

Isolation of populations eventually leads to divergence by genetic drift, but if connectivity varies over time, its impact on diversification may be difficult to discern. Even when the habitat patches of multiple species overlap, differences in their demographic parameters, molecular evolution and stochastic events contribute to differences in the magnitude and distribution of their genetic variation. The Indonesian island of Sulawesi, for example, harbours a suite of endemic species whose intraspecific differentiation or interspecific divergence may have been catalysed by habitat fragmentation. To further test this hypothesis, we have performed phylogenetic and coalescent-based analyses on molecular variation in mitochondrial and nuclear DNA of the Celebes toad (Bufo celebensis). Results support a role for habitat fragmentation that led to a population structure in these toads that closely matches distributions of Sulawesi macaque monkeys. Habitat fragmentation, therefore, may also have affected other groups on this island.     

Phylogeography and postglacial expansion of Mus musculus domesticus inferred from mitochondrial DNA coalescent, from Iran to Europe

Few genetic data document the postglacial history of the western house mouse, Mus musculus domesticus. We address this by studying a sample from the southeastern tip of the Fertile Crescent in the Iranian province of Ahvaz. Including other published and unpublished data from France, Germany, Italy, Bulgaria, Turkey and other places in Iran, altogether 321 mitochondrial D-loop sequences are simultaneously analysed. The patterns of coalescence obtained corroborate the classical proposal according to which the Fertile Crescent is where commensalism with humans has started in the Western Hemisphere, and from where the subspecies has expanded further west. Our data also clearly show that despite multiple colonisations and long-range transportation, there is still a rather high PhiST of 0.39. The original expansion signal is still recognisable, with two well-separated derived clades, allowing us to propose a hypothetical scenario in which expansion toward Europe and Asia Minor took at least two routes, tentatively termed the Mediterranean and the Bosphorus/Black Sea routes. This scenario resembles that of another domesticated species, the goat, and fits with the known progression of Neolithic culture. Given the concomitance of both phenomena around 12,000 years ago, we propose a recalibration of the D-loop mutation rate to a much faster tick of approximately 40% per site per million years (Myr). This value should be used for intrasubspecific polymorphism, while the interspecific rate in Mus is presently estimated at 6-10%/site/Myr. This is in keeping with the now well recognised fact that only a subfraction of segregating mutations go to fixation.     

Speciation and DNA barcodes: testing the effects of dispersal on the formation of discrete sequence clusters

Large-scale sequencing of short mtDNA fragments for biodiversity inventories ('DNA barcoding') indicates that sequence variation in animal mtDNA is highly structured and partitioned into discrete genetic clusters that correspond broadly to species-level entities. Here we explore how the migration rate, an important demographic parameter that is directly related to population isolation, might affect variation in the strength of mtDNA clustering among taxa. Patterns of mtDNA variation were investigated in two groups of beetles that both contain lineages occupying habitats predicted to select for different dispersal abilities: predacious diving beetles (Dytiscidae) in the genus Bidessus from lotic and lentic habitats across Europe and darkling beetles (Tenebrionidae) in the genus Eutagenia from sand and other soil types in the Aegean Islands. The degree of genetic clustering was determined using the recently developed 'mixed Yule coalescent' (MYC) model that detects the transition from between-species to within-population branching patterns. Lineages from presumed stable habitats, and therefore displaying lower dispersal ability and migration rates, showed greater levels of mtDNA clustering and geographical subdivision than their close relatives inhabiting ephemeral habitats. Simulations of expected patterns of mtDNA variation under island models showed that MYC clusters are only detected when the migration rates are much lower than the value of Nm=1 typically used to define the threshold for neutral genetic divergence. Therefore, discrete mtDNA clusters provide strong evidence for independently evolving populations or species, but their formation is suppressed even under very low levels of dispersal.     

A comparison of two popular statistical methods for estimating the time to most recent common ancestor (TMRCA) from a sample of DNA sequences

We have compared two statistical methods of estimating the time to most recent common ancestor (TMRCA) from a sample of DNA sequences, which have been proposed by Templeton (1993) and Bandeltet al. (1995). Monte-Carlo simulations were used for generating DNA sequence data. Different evolutionary scenarios were simulated and the estimation procedures were evaluated. We have found that for both methods (i) the estimates are insensitive to demographic parameters and (ii) the standard deviations of the estimates are too high for these methods to be reliably used in practice.     

Inferring the mode of origin of polyploid species from next‐generation sequence data

Many eukaryote organisms are polyploid. However, despite their importance, evolutionary inference of polyploid origins and modes of inheritance has been limited by a need for analyses of allele segregation at multiple loci using crosses. The increasing availability of sequence data for nonmodel species now allows the application of established approaches for the analysis of genomic data in polyploids. Here, we ask whether approximate Bayesian computation (ABC), applied to realistic traditional and next‐generation sequence data, allows correct inference of the evolutionary and demographic history of polyploids. Using simulations, we evaluate the robustness of evolutionary inference by ABC for tetraploid species as a function of the number of individuals and loci sampled, and the presence or absence of an outgroup. We find that ABC adequately retrieves the recent evolutionary history of polyploid species on the basis of both old and new sequencing technologies. The application of ABC to sequence data from diploid and polyploid species of the plant genus Capsella confirms its utility. Our analysis strongly supports an allopolyploid origin of C. bursa‐pastoris about 80 000 years ago. This conclusion runs contrary to previous findings based on the same data set but using an alternative approach and is in agreement with recent findings based on whole‐genome sequencing. Our results indicate that ABC is a promising and powerful method for revealing the evolution of polyploid species, without the need to attribute alleles to a homeologous chromosome pair. The approach can readily be extended to more complex scenarios involving higher ploidy levels.     

Understanding the mechanisms of antitropical divergence in the seabird White‐faced Storm‐petrel (Procellariiformes: Pelagodroma marina) using a multilocus approach

Analytical methods that apply coalescent theory to multilocus data have improved inferences of demographic parameters that are critical to understanding population divergence and speciation. In particular, at the early stages of speciation, it is important to implement models that accommodate conflicting gene trees, and benefit from the presence of shared polymorphisms. Here, we employ eleven nuclear loci and the mitochondrial control region to investigate the phylogeography and historical demography of the pelagic seabird White‐faced Storm‐petrel (Pelagodroma marina) by sampling subspecies across its antitropical distribution. Groups are all highly differentiated: global mitochondrial Φ_ST = 0.89 (P < 0.01) and global nuclear Φ_ST varies between 0.22 and 0.83 (all P < 0.01). The complete lineage sorting of the mitochondrial locus between hemispheres is corroborated by approximately half of the nuclear genealogies, suggesting a long‐term antitropical divergence in isolation. Coalescent‐based estimates of demographic parameters suggest that hemispheric divergence of P. marina occurred approximately 840 000 ya (95% HPD 582 000–1 170 000), in the absence of gene flow, and divergence within the Southern Hemisphere occurred 190 000 ya (95% HPD 96 000–600 000), both probably associated with the profound palaeo‐oceanographic changes of the Pleistocene. A fledgling sampled in St Helena (tropical South Atlantic) suggests recent colonization from the Northern Hemisphere. Despite the great potential for long‐distance dispersal, P. marina antitropical groups have been evolving as independent, allopatric lineages, and divergence is probably maintained by philopatry coupled with asynchronous reproductive phenology and local adaptation.