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Advances from empirical studies in phylogeography, systematics and species delimitation highlight the importance of integrative approaches for quantifying taxonomic diversity. Genomic data have greatly improved our ability to discern both systematic diversity and evolutionary history. Here we combine analyses of mitochondrial DNA sequences, thousands of genome-wide SNPs and linear and geometric morphometrics on Antaresia, a clade of four currently recognised dwarf pythons from Australia and New Guinea (Antaresia childreni, A. stimsoni, A. maculosa and A. perthensis). Our integrative analyses of phylogenetics, population structure, species delimitation, historical demography and morphometrics revealed that the true evolutionary diversity is not well reflected in the current appraisal of the diversity of the group. We find that Antaresia childreni and A. stimsoni comprise a widespread network of populations connected by gene flow and without evidence of species-level divergence among them. However, A. maculosa shows considerable genetic structuring which leads us to recognise two subspecies in northeastern Australia and a new species in Torres Strait and New Guinea. These two contrasting cases of over and under estimation of diversity, respectively, illustrate the power of thorough integrative approaches into understanding evolution of biodiversity. Furthermore, our analyses of historical demographic patterns highlight the importance of the Kimberley, Pilbara and Cape York as origins of biodiversity in Australia., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Cercospora zeina is a causal pathogen of gray leaf spot (GLS) disease of maize in Africa. This fungal pathogen exhibits a high genetic diversity in South Africa. However, little is known about the pathogen's population structure in the rest of Africa. In this study, we aimed to assess the diversity and gene flow of the pathogen between major maize producing countries in East and Southern Africa (Kenya, Uganda, Zambia, Zimbabwe, and South Africa). A total of 964 single-spore isolates were made from GLS lesions and confirmed as C.zeina using PCR diagnostics. The other causal agent of GLS, Cercospora zeae-maydis, was absent. Genotyping all the C.zeina isolates with 11 microsatellite markers and a mating-type gene diagnostic revealed (i) high genetic diversity with some population structure between the five African countries, (ii) cryptic sexual recombination, (iii) that South Africa and Kenya were the greatest donors of migrants, and (iv) that Zambia had a distinct population. We noted evidence of human-mediated long-distance dispersal, since four haplotypes from one South African site were also present at five sites in Kenya and Uganda. There was no evidence for a single-entry point of the pathogen into Africa. South Africa was the most probable origin of the populations in Kenya, Uganda, and Zimbabwe. Continuous annual maize production in the tropics (Kenya and Uganda) did not result in greater genetic diversity than a single maize season (Southern Africa). Our results will underpin future management of GLS in Africa through effective monitoring of virulent C.zeina strains., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Genomic data has opened new possibilities to understand how organisms change over time, and could enable the discovery of previously undescribed species. Although taxonomy used to be based on phenotypes, molecular data has frequently revealed that morphological traits are insufficient to describe biodiversity. Genomics holds the promise of revealing even more genetic discontinuities, but the parameters on how to describe species from genomic data remain unclear. Fungi have been a successful case in which the use of molecular markers has uncovered the existence of genetic boundaries where no crosses are possible. In this minireview, we highlight recent advances, propose a set of standards to use genomic sequences to uncover species boundaries, point out potential pitfalls, and present possible future research directions., (Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.)

Maladapted individuals can only colonise a new habitat if they can evolve a positive growth rate fast enough to avoid extinction, a process known as evolutionary rescue. We treat log fitness at low density in the new habitat as a single polygenic trait and use the infinitesimal model to follow the evolution of the growth rate; this assumes that the trait values of offspring of a sexual union are normally distributed around the mean of the parents' trait values, with variance that depends only on the parents' relatedness. The probability that a single migrant can establish depends on just two parameters: the mean and genetic variance of the trait in the source population. The chance of success becomes small if migrants come from a population with mean growth rate in the new habitat more than a few standard deviations below zero; this chance depends roughly equally on the probability that the initial founder is unusually fit, and on the subsequent increase in growth rate of its offspring as a result of selection. The loss of genetic variation during the founding event is substantial, but highly variable. With continued migration at rate M, establishment is inevitable; when migration is rare, the expected time to establishment decreases inversely with M. However, above a threshold migration rate, the population may be trapped in a 'sink' state, in which adaptation is held back by gene flow; above this threshold, the expected time to establishment increases exponentially with M. This threshold behaviour is captured by a deterministic approximation, which assumes a Gaussian distribution of the trait in the founder population with mean and variance evolving deterministically. By assuming a constant genetic variance, we also develop a diffusion approximation for the joint distribution of population size and trait mean, which extends to include stabilising selection and density regulation. Divergence of the population from its ancestors causes partial reproductive isolation, which we measure through the reproductive value of migrants into the newly established population., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Major gaps remain in our understanding of the ecology, evolution, biodiversity, biogeography, extinction risk, and adaptive potential of reef building corals. One of the central challenges remains that there are few informative genetic markers for studying boundaries between species, and variation within species. Reduced representation sequencing approaches, such as RADseq (Restriction site Associated DNA sequencing) have great potential for resolving such relationships. However, it is necessary to identify loci in order to make inferences for endosymbiotic organisms such as corals. Here, we examined twenty-one coral holobiont ezRAD libraries from Hawai'i, focusing on P. lobata and P. compressa, two species with contrasting morphology and habitat preference that previous studies have not resolved. We used a combination of de novo assembly and reference mapping approaches to identify and compare loci: we used reference mapping to extract and compare nearly complete mitochondrial genomes, ribosomal arrays, and histone genes. We used de novo clustering and phylogenomic methods to compare the complete holobiont data set with coral and symbiont subsets that map to transcriptomic data. In addition, we used reference assemblies to examine genetic structure from SNPs (Single Nucleotide Polymorphisms). All approaches resolved outgroup taxa but failed to resolve P. lobata and P. compressa as distinct, with mito-nuclear discordance and shared mitochondrial haplotypes within the species complex. The holobiont and 'coral transcriptomic' datasets were highly concordant, revealing stronger genetic structure between sites than between coral morphospecies. These results suggest that either branching morphology is a polymorphic trait, or that these species frequently hybridize. This study provides examples of several approaches to acquire, identify, and compare loci across metagenomic samples such as the coral holobiont while providing insights into the nature of coral variability., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Across the animal tree of life, the prevalence and evolutionary role(s) of hybridization remain incompletely understood. Rapidly radiating clades can serve as important systems for investigating these issues; however, such groups are often characterized by additional, widespread sources of gene tree discordance (e.g., incomplete lineage sorting). In this paper, we employed a multilocus dataset, Bayesian gene tree inference, and multiple species tree reconstruction methods to infer phylogeny of Holarctic ground squirrels (Urocitellus). We tested phylogenetic hypotheses based on previous morphological, cytological and single-locus datasets, and began to parse the causes of pervasive gene tree discordance that was observed. There is widespread incomplete lineage sorting in Urocitellus, consistent with rapid diversification embedded within the larger radiation of marmotine ground squirrels. We also recovered strong support for 2 instances of mitonuclear discord due to ancient hybridization among members of the high-latitude parryii-richardsonii-elegans clade. These results add to a growing number of documented hybridization events in ground squirrels, suggesting their radiation is a fertile system for understanding the interplay of diversification and hybridization in animal evolution., (Copyright © 2016 Elsevier Inc. All rights reserved.)

The distylous genus Pulmonaria contains approximately 18 species that are widely distributed across Eurasia. Previous studies have shown that species delimitation in the genus is problematic, but have not yet explored the evolutionary history of the genus. Premating reproductive barriers between European species appear to be weak, as several species have strongly overlapping distribution areas, flower at the same time and share the same pollinators, suggesting that hybridization may have contributed to the evolutionary history of Pulmonaria. To test this hypothesis, phylogenetic analyses of nuclear ITS and plastid data (rps16, trnH-psbA, rpl16) from 48 allopatric and four sympatric populations were performed to (1) provide a molecular phylogeny for nine of the most common Pulmonaria species in Europe, (2) detect current and ancient hybridization events, and (3) assess the contribution of hybridization versus incomplete lineage sorting to the inferred phylogenetic patterns. Our results showed that gene trees displayed widespread, strongly supported incongruence associated with the conflicting position of hybrid samples rather than incomplete lineage sorting. Evidence was found of different degrees of hybridization, ranging from current interspecific gene flow at secondary contact zones to introgression at the population level and at least one event of hybrid speciation. Overall, these results suggest that hybridization and introgression were - and could still be - important processes affecting speciation in the genus Pulmonaria., (Copyright © 2015 Elsevier Inc. All rights reserved.)

The evolutionary mechanisms underlying the geographic distribution of gene lineages in the marine environment are not as well understood as those affecting terrestrial groups. The continuous nature of the pelagic marine environment may limit opportunities for divergence to occur and lineages to spatially segregate, particularly in highly mobile species. Here, we studied the phylogeography and historical demography of two tropically distributed, pelagic seabirds, the Madeiran Storm-petrel Oceanodroma castro, sampled in the Azores, Madeira, Galapagos and Japan, and its sister species Monteiro's Storm-petrel O. monteiroi (endemic to the Azores), using a multi-locus dataset consisting of 12 anonymous nuclear loci and the mitochondrial locus control region. Both marker types support the existence of four significantly differentiated genetic clusters, including the sampled O. monteiroi population and three populations within O. castro, although only the mitochondrial locus suggests complete lineage sorting. Multi-locus coalescent analyses suggest that most divergence events occurred within the last 200,000years. The proximity in divergence times precluded robust inferences of the species tree, in particular of the evolutionary relationships of the Pacific populations. Despite the great potential for dispersal, divergence among populations apparently proceeded in the absence of gene flow, emphasizing the effect of non-physical barriers, such as those driven by the paleo-oceanographical environments, philopatry and local adaptation, as important mechanisms of population divergence and speciation in highly mobile marine species. In view of the predicted climate change impacts, future changes in the demography and evolutionary dynamics of marine populations might be expected., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Genetic subdivision within populations can ultimately lead to the evolution of new species, and in populations of broadcast-spawners a potential facilitator of genetic subdivision is asynchronous reproduction. However, the factors that shape genetic variation in marine systems are complex and ambiguous, and ecological genetic structure may be influenced by the overriding signature of past demographic events. Here, the relative roles of the timing of reproduction and historical geography on the partitioning of genetic variation were examined in seven populations of the broadcast-spawning coral Acropora tenuis over 12° of latitude. The analysis of multiple loci (mitochondrial control region, two nuclear introns and six microsatellites) revealed significant genetic division between the most northern reef and all other reefs, suggesting that WA reefs were re-colonized from two different sources after the Pleistocene glaciation. Accompanying this pattern was significant genetic differentiation associated with different breeding seasons (spring and autumn), which was greatest in PaxC, in which there were two divergent lineages (ΦST=0.98). This is the second study to find divergent clades of PaxC associated with spring and autumn spawners, strengthening the suggestion of some selective connection to timing of reproduction in corals. This study reiterates the need to incorporate reproductive timing into population genetic studies of corals because it facilitates genetic differentiation; however, careful analysis of population genetic data is required to separate ecological and evolutionary processes., (Copyright © 2016 Elsevier Inc. All rights reserved.)

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., (Copyright © 2016 Elsevier Inc. All rights reserved.)

The sweet potato whitefly, Bemisia tabaci, is a highly differentiated species complex. Despite consisting of several morphologically indistinguishable entities and frequent invasions on all continents with important associated economic losses, the phylogenetic relationships, species status, and evolutionary history of this species complex is still debated. We sequenced and analyzed one mitochondrial and three single-copy nuclear genes from 9 of the 12 genetic groups of B. tabaci and 5 closely related species. Bayesian species delimitation was applied to investigate the speciation events of B. tabaci. The species statuses of the different genetic groups were strongly supported under different prior settings and phylogenetic scenarios. Divergence histories were estimated by a multispecies coalescence approach implemented in (*)BEAST. Based on mitochondrial locus, B. tabaci was originated 6.47 million years ago (MYA). Nevertheless, the time was 1.25MYA based on nuclear loci. According to the method of approximate Bayesian computation, this difference is probably due to different degrees of migration among loci; i.e., although the mitochondrial locus had differentiated, gene flow at nuclear loci was still possible, a scenario similar to parapatric mode of speciation. This is the first study in whiteflies using multilocus data and incorporating Bayesian coalescence approaches, both of which provide a more biologically realistic framework for delimiting species status and delineating the divergence history of B. tabaci. Our study illustrates that gene flow during species divergence should not be overlooked and has a great impact on divergence time estimation., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Phylogeographic analysis brings organism phylogeny, regional geological/climatic history, and population demography together, and provides insights into species history and speciation. Using DNA sequence data from a mitochondrial marker (cytochrome b) and a nuclear marker (cmyc intron 2), we examined phylogeography of the Amolops mantzorum species group. We first constructed Bayesian and maximum-likelihood gene trees and medium-joint networks for the recovered haplotypes, and estimated divergence time for each major lineage. Species boundaries were then delineated using the general mixed Yule-coalescent model (GMYC) and a Bayesian species-delimitation method (BP&P). Potential gene flow between putative species was also estimated using the isolation-with-migration model. Furthermore, species-distribution modeling was used to probe linkage between climatic changes and speciation. Lastly, extended Bayesian skyline plotting was employed to reveal historical demography for each putative species. Our analyses clearly delimit nine species in the group, including four well-recognized species and five putative species, of which three are often listed as synonyms of A. mantzorum. The nominal species A. mantzorum may in fact include two cryptic species. Divergence-time estimates align the speciation events with the recent intense uplift of the Tibetan Plateau in the last 3.6 million years. The species-distribution modeling also reveals different habitat preferences among species that are potentially linked to climatic changes associated with the uplift. Furthermore, three species sustained continuous population growth through the last glaciation, while others expanded only after the last glaciation. The eastern escarpment of Tibet is a biodiversity hotspot; its rich species diversity, unique topography, and well-established geological history provide an excellent system for evolutionary studies., (Copyright © 2014 Elsevier Inc. All rights reserved.)

We study sexual populations structured by a phenotypic trait and a space variable, in a non-homogeneous environment. Departing from an infinitesimal model, we perform an asymptotic limit to derive the system introduced in Kirkpatrick and Barton (1997). We then perform a further simplification to obtain a simple model. Thanks to this simpler equation, we can describe rigorously the dynamics of the population. In particular, we provide an explicit estimate of the invasion speed, or extinction speed of the species. Numerical computations show that this simple model provides a good approximation of the original infinitesimal model, and in particular describes quite well the evolution of the species' range., (Copyright © 2013 Elsevier Inc. All rights reserved.)

Manta rays have been taxonomically revised as two species, Manta alfredi and M. birostris, on the basis of morphological and meristic data, yet the two species occur in extensive mosaic sympatry. We analysed the genetic signatures of the species boundary using a portion of the nuclear RAG1 (681 base pairs), mitochondrial CO1 (574 bp) and ND5 genes (1188 bp). The assay with CO1 sequences, widely used in DNA barcoding, failed to distinguish the two species. The two species were clearly distinguishable, however, with no shared RAG1 or ND5 haplotypes. The species were reciprocally monophyletic for RAG1, but paraphyletic for ND5 sequences. Qualitative evidence and statistical inferences using the 'Isolation-with-Migration models' indicated that these results were better explained with post-divergence gene flow in the recent past rather than incomplete lineage sorting with zero gene flow since speciation. An estimate of divergence time was less than 0.5 Ma with an upper confidence limit of within 1 Ma. Recent speciation of highly mobile species in the marine environment is of great interest, as it suggests that speciation may have occurred in the absence of long-term physical barriers to gene flow. We propose that the ecologically driven forces such as habitat choice played a significant role in speciation in manta rays., (Copyright © 2012 Elsevier Inc. All rights reserved.)

In response to climate changes that have occurred during Pleistocene glacial cycles, taxa associated to steppe vegetation might have followed a pattern of historical evolution in which isolation and fragmentation of populations occurred during the short interglacials and expansion events occurred during the long glacial periods, in contrast to the pattern described for temperate species. Here, we use molecular genetic data to evaluate this idea in a steppe bird with Palaearctic distribution, the little bustard (Tetrax tetrax). Overall, extremely low genetic diversity and differentiation was observed among eight little bustard populations distributed in Spain and France. Mismatch distribution analyses showed that most little bustard populations expanded during cooling periods previous to, and just after, the last interglacial period (127,000-111,000 years before present), when steppe habitats were widespread across Europe. Coalescent-based methods suggested that glacial expansions have resulted in substantial admixture in Western Europe due to the existence of different interglacial refugia. Our results are consistent with a model of evolution and genetic consequences of Pleistocene cycles with low between-population genetic differentiation as a result of short-term isolation periods during interglacials and long-term exchange during glacial periods., (Copyright © 2011 Elsevier Inc. All rights reserved.)

The origin of the terrestrial biota of Madagascar and, especially, the smaller island chains of the western Indian Ocean is relatively poorly understood. Madagascar represents a mixture of Gondwanan vicariant lineages and more recent colonizers arriving via Cenozoic dispersal, mostly from Africa. Dispersal must explain the biota of the smaller islands such as the Comoros and the chain of Mascarene islands, but relatively few studies have pinpointed the source of colonizers, which may include mainland Africa, Asia, Australasia, and Madagascar. The pantropical hermit spiders (genus Nephilengys) seem to have colonized the Indian Ocean island arc stretching from Comoros through Madagascar and onto Mascarenes, and thus offer one opportunity to reveal biogeographical patterns in the Indian Ocean. We test alternative hypotheses on the colonization route of Nephilengys spiders in the Indian Ocean and simultaneously test the current taxonomical hypothesis using genetic and morphological data. We used mitochondrial (COI) and nuclear (ITS2) markers to examine Nephilengys phylogenetic structure with samples from Africa, southeast Asia, and the Indian Ocean islands of Madagascar, Mayotte, Réunion and Mauritius. We used Bayesian and parsimony methods to reconstruct phylogenies and haplotype networks, and calculated genetic distances and fixation indices. Our results suggest an African origin of Madagascar Nephilengys via Cenozoic dispersal, and subsequent colonization of the Mascarene islands from Madagascar. We find strong evidence of gene flow across Madagascar and through the neighboring islands north of it, while phylogenetic trees, haplotype networks, and fixation indices all reveal genetically isolated and divergent lineages on Mauritius and Réunion, consistent with female color morphs. These results, and the discovery of the first males from Réunion and Mauritius, in turn falsify the existing taxonomic hypothesis of a single widespread species, Nephilengys borbonica, throughout the archipelago. Instead, we diagnose three Nephilengys species: Nephilengys livida (Vinson, 1863) from Madagascar and Comoros, N. borbonica (Vinson, 1863) from Réunion, and Nephilengys dodo new species from Mauritius. Nephilengys followed a colonization route to Madagascar from Africa, and on through to the Mascarenes, where it speciated on isolated islands. The related golden orb-weaving spiders, genus Nephila, have followed the same colonization route, but Nephila shows shallower divergencies, implying recent colonization, or a moderate level of gene flow across the archipelago preventing speciation. Unlike their synanthropic congeners, N. borbonica and N. dodo are confined to pristine island forests and their discovery calls for evaluation of their conservation status., (Copyright © 2011 Elsevier Inc. All rights reserved.)

Spatial and temporal heterogeneity in environmental factors can have profound effects on diversification in species that are tightly linked to their environments. The Caddo Mountain Salamander (Plethodon caddoensis) inhabits a unique physiographic section of the Ouachita Mountains in central North America, a region in which Pleistocene climatic fluctuations have been implicated in driving lineage diversification in two other closely related salamanders. We examined P. caddoensis to determine whether it was similarly impacted by historic climatic changes and test whether physiographic features unique to the area also contributed to its diversification. We found that P. caddoensis is composed of four highly divergent, geographically distinct lineages that abut one another along an east-west axis. Phylogeographic structure was significantly related to both geographic distance and stream drainages, indicating that connectivity of streams and stream-associated habitats (e.g., talus) influence patterns of interpopulation gene flow. Lineages originated during the Middle Miocene and population size decreased in all lineages during the Pleistocene. Surface Geology and precipitation were the most important variables predicting the species distribution. Our results show that the unique physiographic features of the area coupled with species response to climatic factors have driven lineage diversification and phylogeographic structure in P. caddoensis. Variation in responses to historic climatic fluctuations among salamander species in this region underscore the importance of integrating species ecology with other factors such as geology and hydrology in order to better understand the effects of climate change on species with close associations to their environments., (Copyright © 2011 Elsevier Inc. All rights reserved.)

We present a statistical model for incorporating the extra variability in allelic counts due to subpopulation structures. In forensic genetics, this effect is modelled by the identical-by-descent parameter θ, which measures the relationship between pairs of alleles within a population relative to the relationship of alleles between populations (Weir, 2007). In our statistical approach, we demonstrate that θ may be defined as an overdispersion parameter capturing the subpopulation effects. This formulation allows derivation of maximum likelihood estimates of the allele probabilities and θ together with computation of the profile log-likelihood, confidence intervals and hypothesis testing. In order to compare our method with existing methods, we reanalysed FBI data from Budowle and Moretti (1999) with allele counts in six US subpopulations. Furthermore, we investigate properties of our methodology from simulation studies., (Copyright © 2010 Elsevier Inc. All rights reserved.)

Ocean currents, prevailing winds, and the hierarchical structures of river networks are known to create asymmetries in re-colonization between habitat patches. The impacts of such asymmetries on metapopulation persistence are seldom considered, especially rarely in theoretical studies. Considering three classical models (the island, the stepping stone and the distance-dependent model), we explore how metapopulation persistence is affected by (i) asymmetry in dispersal strength, in which the colonization rate between two patches differs in direction, and (ii) asymmetry in connectivity, in which the overall colonization pattern displays asymmetry (circulating or dendritic networks). Viability can be drastically reduced when directional bias in dispersal strength is higher than 25%. Re-colonization patterns that allow for strong local connectivity provide the highest persistence compared to systems that allow circulation. Finally, asymmetry has relatively weak effects when metapopulations maintain strong general connectivity., (Copyright © 2010 Elsevier Inc. All rights reserved.)

Species delimitation is a fundamental biological concept which is frequently discussed and altered to integrate new insights. These revealed that speciation is not a one step phenomenon but an ongoing process and morphological characters alone are not sufficient anymore to properly describe the results of this process. Here we want to assess the degree of speciation in two closely related lianescent taxa from the tropical African genus Haumania which display distinct vegetative traits despite a high similarity in reproductive traits and a partial overlap in distribution area which might facilitate gene flow. To this end, we combined phylogenetic and phylogeographic analyses using nuclear (nr) and chloroplast (cp) DNA sequences in comparison to morphological species descriptions. The nuclear dataset unambiguously supports the morphological species concept in Haumania. However, the main chloroplastic haplotypes are shared between species and, although a geographic analysis of cpDNA diversity confirms that individuals from the same taxon are more related than individuals from distinct taxa, cp-haplotypes display correlated geographic distributions between species. Hybridization is the most plausible reason for this pattern. A scenario involving speciation in geographic isolation followed by range expansion is outlined. The study highlights the gain of information on the speciation process in Haumania by adding georeferenced molecular data to the morphological characteristics. It also shows that nr and cp sequence data might provide different but complementary information, questioning the reliability of the unique use of chloroplast data for species recognition by DNA barcoding., (Copyright © 2010 Elsevier Inc. All rights reserved.)

The impact of barriers to dispersal and gene flow is often inferred to be the primary cause of lineage divergence and phylogeographic structure in terrestrial organisms. In particular, the Mississippi River has been implicated as a barrier to gene flow in many species, including aquatic taxa. However, if barriers are permeable to organisms, then phylogeographic structure may be difficult to detect due to gene flow between lineages. Using time-calibrated Bayesian phylogenetic analyses of mtDNA, and phylogeographic coalescent simulations, we determine if the Mississippi River operates as a barrier to gene flow in the aquatic diamond-backed watersnake (Nerodia rhombifer). The phylogenetic analyses support a basal division within N. rhombifer mtDNA lineages that coincides with populations generally east and west of the Mississippi River. These results, and that of the divergence dating analyses, therefore suggest that the river was a significant barrier to gene flow in the Pleistocene ∼ 1.4 million years ago, presumably during an interglacial period when the river was much wider. However, we also detect western haplotypes in the eastern clade, and vice versa, thereby indicating that this barrier has not been complete. Nonetheless, the coalescent simulations that account for limited migration suggest that the Mississippi River was an important feature that shaped the phylogeographic history of this aquatic snake in the USA despite limited gene flow., (Copyright © 2010 Elsevier Inc. All rights reserved.)

The European spiny lobster (Palinurus elephas) is a suitable model organism to study the effects of past history and current oceanographic processes on the genetic diversity and population structure of marine species with a long-lived larval phase. A portion of the COI gene was sequenced in 227 individuals from 11 localities, covering most of the present distribution of the species. Divergence was found between Atlantic and Mediterranean regions, which could be explained by restricted gene flow between populations. Moreover, a principal component analysis detected differences within basins. The existence of genetic differentiation between Brittany and Ireland-Scotland populations could be accounted for by the large effect of the Gulf Stream, while mesoscale processes suffered by the incoming Atlantic waters could be responsible of genetic differentiation within the Mediterranean. Furthermore, historical processes could be responsible for a reduction on the overall genetic variability of P. elephas. The haplotypic distribution found in P. elephas, with the presence of one abundant haplotype and a large number of closely related haplotypes, is typical of species experiencing reduction in variability and subsequent expansions. Climatic fluctuations related to glacial cycles could explain the present level of variability and nucleotide diversity found. Interestingly, these glacial events do not seem to have the same impact in other species of the same genus. Our results indicate that recent glacial events could have had a lower impact on Palinurus mauritanicus, a congeneric species that presents an overlapping distribution area but is found in cooler waters than P. elephas.

Male-killing (MK) and cytoplasmic incompatibility (CI) inducing bacteria are among the most common endosymbionts of arthropods. Previous theoretical research has demonstrated that these two types of endosymbionts cannot stably coexist within a single unstructured host population if no doubly infected host individuals occur. Here, we analyse a model of two host subpopulations connected by migration. We demonstrate that coexistence of MK- and CI-inducing endosymbionts is possible if migration rates are sufficiently low. In particular, our results suggest that for coexistence to be possible, migration rates into the subpopulation infected predominantly with MK-inducing endosymbionts must be considerably low, while migration rates from the MK- to the CI-infected subpopulation can be very high. We also analyse how the presence of MK- and CI-inducing endosymbionts affects host gene flow between the two subpopulations. Employing the concept of the 'effective migration rate', we demonstrate that compared with an uninfected subdivided population, gene flow is increased towards the MK-infected island, but decreased towards the CI-infected island. We discuss our results with respect to the butterfly Hypolimnas bolina, in which infection polymorphism of CI- and MK-inducing Wolbachia has been reported across South-Pacific island populations.