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Within the southwestern Australian biodiversity hotspot, the Shark Bay region displays high levels of plant and animal endemism, particularly in the herpetofauna. The region has been subjected to dramatic climatic fluctuations and has been geologically active from the Late Miocene to the present. The myobatrachid frog Arenophryne rotunda, a Shark Bay endemic, provides an ideal opportunity to examine the relative effects of fluctuating climates and geological activity on the biota of Shark Bay. A comprehensive phylogeographic analysis of A. rotunda, based on data comprising 1154 bp of the mitochondrial gene ND2, is presented. My results demonstrate a major genetic break that divides this species at the northern edge of the Victorian Plateau into northern and southern species lineages, dating to the Late Miocene, with a further division of the southern species lineage across the Murchison Gorge dating to the Plio-Pleistocene border. Both of these periods are related to prominent geological activity and climatic shifts in the Shark Bay region. Interpretation of phylogeographic results point to the prominent role of fluctuating Pleistocene climates and associated coastal landscape evolution in the generation of phylogeographic structure within the distinct A. rotunda species lineages. Similar processes have been invoked to explain the diversity of other Shark Bay biota.

We investigated the endangered status and taxonomic status of the freshwater crayfish Procambarus ferrugineus, a crayfish species considered for the candidate list of the Endangered Species Act. This species has a narrow distribution from central Arkansas, USA and is codistributed with its presumed sister species, Procambarus liberorum. We sampled extensively throughout the ranges of both primary burrowing species and collected mitochondrial DNA from a hypervariable fragment of the 16S gene from 109 individuals across 22 sites. We also collected data from a variable region of the 12S gene from a subset of the resulting 16S haplotypes. Due to our inability to sample what we considered P. ferrugineus in the field, we included museum specimens from the United States Natural History Museum of both P. ferrugineus and P. liberorum. Analyses of the resulting data suggested that these two species are indeed the same and we therefore synonymize them under the name of priority—P. liberorum. Additionally, our sampling discovered three new cryptic species from southwestern Arkansas all from the genus Procambarus. Nested clade phylogeographic analysis coupled with population genetic analyses suggested that P. liberorum has had three rounds of range expansion throughout the inferred evolutionary history. Using IUCN Red List criteria for conservation assessment, we conclude that the species P. liberorum should be considered stable, but with special concern because of habitat fragmentation and urbanization, small restricted range, and a moderate level of genetic diversity. Procambarus reimeri should be considered endangered due to its limited geographic range and the potential for a decline in suitable habitat. The three potentially newly discovered species should be considered data deficient until more information is obtained on their distributional limits and habitat requirements. Our study highlights the importance of thorough geographic and taxonomic sampling coupled with the utility of collecting data from museum specimens to reach robust taxonomic and conservation conclusions for endangered species. [ABSTRACT FROM AUTHOR]

Abstract: Dendroctonus mexicanus is polyphagous within the Pinus genus and has a wide geographical distribution in Mexico and Guatemala. We examined the pattern of genetic variation across the range of this species to explore its demographic history and its phylogeographic pattern. Analysis of the mtDNA sequences of 173 individuals from 25 Mexican populations allowed to us identify 53 geographically structured haplotypes. High haplotype and low nucleotide diversities and Tajima’s D indicate that D. mexicanus experienced rapid population expansion during its dispersal across mountain systems within its current range. The nested clade phylogeographic analysis indicates that the phylogeographic pattern of D. mexicanus is explained by continuous dispersion among lineages from the Sierra Madre Occidental, the Sierra Madre Oriental and the Trans-Mexican Volcanic Belt. However, we also observed isolation events among haplotypes from the Cofre de Perote/Trans-Mexican Volcanic Belt/Sierra Madre Oriental and the Trans-Mexican Volcanic Belt/Sierra Madre del Sur, which is consistent with the present conformation of mountain systems in Mexico and the emergence of geographical barriers during the Pleistocene. [Copyright &y& Elsevier]

Abstract: Whilst we have now a good understanding how past glaciation influenced species at the northern hemisphere, our knowledge of patterns and modes of speciation is far more limited for the southern hemisphere. We provide mtDNA based data on the phylogeography of a circumpolar distributed southern hemisphere seabird group—the southern skua complex (Catharacta spp.). Diversification of southern skuas dates between 210,000yBP and 150,000yBP and coincides with a glacial spanning 230,000–140,000yBP. Skuas most likely first inhabited the Antarctic continent, in the course of global cooling and increasing glaciation spread to the sub-antarctic islands and Tristan da Cunha and finally colonized Patagonia and the Falkland Islands at the glacial maximum. Despite significant differences between taxa most populations still exchange genes with neighboring populations of other taxa and speciation is incomplete. [Copyright &y& Elsevier]

Abstract: An intraspecific study on Phlebotomus papatasi, the main proven vector of Leishmania major among the members of the subgenus Phlebotomus, was performed. The internal transcribed spacer 2 (ITS 2) of rDNA and the ND4 gene of mt DNA were sequenced from 26 populations from 18 countries (Albania, Algeria, Cyprus, Egypt, Greece, India, Iran, Israel, Italy, Lebanon, Morocco, Saudi Arabia, Spain, Syria, Tunisia, Turkey, Yugoslavia and Yemen), and compared. Samples also included three other species belonging to the subgenus Phlebotomus: P. duboscqi, a proven vector of L. major in the south of Sahara (three populations from Burkina Faso, Kenya and Senegal), P. bergeroti, a suspected vector of L. major (three populations from Oman Sultanate, Iran and Egypt), and one population of P. salehi from Iran. A phylogenetic study was carried out on the subgenus Phlebotomus. Our results confirm the validity of the morphologically characterized taxa. The position of P. salehi is doubtful. Variability in P. papatasi contrasts with that observed within other species having a wide distribution like P. (Paraphlebotomus) sergenti in the Old World or Lutzomyia (Lutzomyia) longipalpis in the New World. Consequently, it could be hypothesized that all populations of P. papatasi over its distribution area have similar vectorial capacities. The limits of the distribution area of L. major are correlated with the distribution of common rodents acting as hosts of the parasites. [Copyright &y& Elsevier]

Nested clade phylogeographic analysis (NCPA) is a popular method for reconstructing the demographic history of spatially distributed populations from genetic data. Although some parts of the analysis are automated, there is no unique and widely followed algorithm for doing this in its entirety, beginning with the data, and ending with the inferences drawn from the data. This article describes a method that automates NCPA, thereby providing a framework for replicating analyses in an objective way. To do so, a number of decisions need to be made so that the automated implementation is representative of previous analyses. We review how the NCPA procedure has evolved since its inception and conclude that there is scope for some variability in the manual application of NCPA. We apply the automated software to three published datasets previously analyzed manually and replicate many details of the manual analyses, suggesting that the current algorithm is representative of how a typical user will perform NCPA. We simulate a large number of replicate datasets for geographically distributed, but entirely random-mating, populations. These are then analyzed using the automated NCPA algorithm. Results indicate that NCPA tends to give a high frequency of false positives. In our simulations we observe that 14% of the clades give a conclusive inference that a demographic event has occurred, and that 75% of the datasets have at least one clade that gives such an inference. This is mainly due to the generation of multiple statistics per clade, of which only one is required to be significant to apply the inference key. We survey the inferences that have been made in recent publications and show that the most commonly inferred processes (restricted gene flow with isolation by distance and contiguous range expansion) are those that are commonly inferred in our simulations. However, published datasets typically yield a richer set of inferences with NCPA than obtained in our random-mating simulations, and further testing of NCPA with models of structured populations is necessary to examine its accuracy. [ABSTRACT FROM AUTHOR]

Cnemidophorus longicauda is a poorly-studied species of whiptail lizard distributed in the Monte Desert region of Argentina. Some variation in dorsal color pattern has been observed between northern and southern populations along the latitudinal range of the species. Recently, a new species of Cnemidophorus (C. tergolaevigatus) previously considered as C. longicauda has been described, although no comparative morphological study has been conducted. In this study we use the mitochondrial ND4 gene region to examine the phylogeography and genetic structure of this species complex. Phylogenetic reconstruction, Nested Clade Phylogeographic Analysis, and AMOVA reveal deep genetic divergence between northern and southern populations that are geographically separated by the Famatina-Sañogasta Mountains. Because most of the localities of C. tergolaevigatus are from the general region of the "northern group" recovered in this study, there is general concordance between geographic patterns of mtDNA and morphological (color pattern) variation, and thus Support for the recognition of this species. We discuss this genetic break and the phylogenetic/phylogeographic history of the Cnemidophorus in the context of other lizard species with similar distributions, and the implications for understanding the evolutionary history temperate South American biota. [ABSTRACT FROM AUTHOR]

Abstract: Sequence data from a 200bp fragment of the Cytochrome Oxidase I mitochondrial gene was derived from endemic populations of the darkling beetle Pimelia laevigata (Coleoptera, Tenebrionidae) from the volcanic islands of La Gomera, La Palma and El Hierro and from three related congeneric species of Tenerife (Canary Islands). Statistical phylogeographic methods and estimates of demographic parameters suggest that there is a higher genetic variation and geographical structure in two of the Tenerife nominal species than in populations of P. laevigata in the western islands. In La Gomera, La Palma and El Hierro, the patterns are consistent with relatively recent colonizations, followed by range expansions. The results show that hypotheses based on coalescent theory can be useful to reconstruct historic biogeographical events of oceanic islands in a range of different organisms provided that the sample design is adequate and enough genetic resolution is present. However, some specific problems arise when interpreting the inference key applied to the volcanic islands populations. [Copyright &y& Elsevier]

This study uses mitochondrial DNA (mtDNA) to examine the phylogeography of the White-headed Woodpecker (Picoides albolarvatus), one of the least-studied woodpeckers in North America. A mismatch distribution and calculation of Tajima's D indicate that the overall phylogeographic history of the species is characterized by a recent range expansion that probably occurred after the start of the Pleistocene. In addition, a nested clade phylogeographic analysis indicates that additional processes such as allopatric fragmentation and restricted gene flow have influenced the evolutionary history of this species. Traditionally, the White-headed Woodpecker has been split into two subspecies whose distributions meet in the northern part of the Transverse Ranges in California. The two subspecies differ morphologically, with the southern subspecies having a larger bill in proportion to its body size than the northern subspecies. Geographical variation in mtDNA is concordant with a division at the Transverse Ranges that corresponds to the morphological variation seen between the two subspecies. An analysis of molecular variance indicates that 27% of the genetic variation results from differences between the northern and southern subspecies. Furthermore, birds in the northern part of the range differ from those in the southern part of the range by at least one base substitution. These results agree with the hypothesis that the larger bill of the southern subspecies is the result of recent local adaptation to feeding on the large cones of Coulter pines (Pinus coulteri). [ABSTRACT FROM AUTHOR]

Populations of the European Spadefoot toad (Pelobates fuscus) have experienced recent declines all over Europe, but these appear to be more intense in north and western Europe. Due to the toad's fossorial nature and specific habitat requirements, environmental conditions have played a major role in structuring current populations. We examined the phylogeographic structure in P. fuscus from 16 localities throughout Europe using mitochondrial cytochrome b gene sequence analysis. Sequence divergence among haplotypes was low (0.54 ± 0. 15%). Three very closely related haplotypes occupy northern and western parts of Europe whereas 12 others were observed among samples from south-eastern Europe, including the Balkans. Our results suggest that toads only recently colonized the northern and western parts of Europe following glacial retreat. This expansion probably took place in steppic-like areas during the younger Dryas cold interval, about 12,900-11,500 years ago. Restricted gene flow with an isolation-by-distance population structure characterises a major part of its distribution range. Based on our results we suggest that the northern and western lineages should be considered as distinct conservation units, while the south-eastern populations from the refugial areas, where nearly all genetic polymorphism occurs and populations appear less vulnerable, should receive special attention. [ABSTRACT FROM AUTHOR]

Mitochondrial cytochrome-b (Cytb) and control region (CR) sequence data were used to investigate the phylogeography of the disjunct population of southern flying squirrels (Glaucomys volans) from Nova Scotia. Consistent with previous studies, there is little differentiation in Cytb sequences (0-1.3% sequence divergence) across the entire range of G. volans in North America. Nested clade phylogeographic analysis of CR sequences (which exhibited 0.5-5.7% sequence divergence) provided a finer scale of differentiation and allowed for inferences to be made regarding the phylogeographic history of the population from Nova Scotia. We propose that G. volans rapidly expanded its range from a southern refugium after the Wisconsin glaciation (∼12,000 years ago) and was then isolated in southwestern Nova Scotia during subsequent climactic fluctuations. More specifically, the population from Nova Scotia was isolated from extant populations in Ontario by the loss of intermediate populations. Although the population of G. volans in Nova Scotia would not be considered an evolutionarily significant unit under some definitions, examination of CR sequence data suggests that this population may nevertheless be diverging from other populations. [ABSTRACT FROM AUTHOR]

Volcanic islands with well-characterized geological histories can provide ideal templates for generating and testing phylogeographic predictions. Many studies have sought to utilize these to investigate patterns of colonization and speciation within groups of closely related species across a number of islands. Here we focus attention within a single volcanic island with a well-characterized geological history to develop and test phylogeographic predictions. We develop phylogeographic predictions within the island of La Palma of the Canary Islands and test these using 69 haplotypes from 570 base pairs of mitochondrial DNA cytochrome oxidase II sequence data for 138 individuals of Brachyderes rugatus rugatus, a local endemic subspecies of curculionid beetle occurring throughout the island in the forests of Pinus canariensis. Although geological data do provide some explanatory power for the phylogeographic patterns found, our network-based analyses reveal a more complicated phylogeographic history than initial predictions generated from data on the geological history of the island. Reciprocal illumination of geological and phylogeographic history is also demonstrated with previous geological speculation gaining phylogeographic corroboration from our analyses. [ABSTRACT FROM AUTHOR]