Population Genetic Structure of Transcaucasian Mole Vole (<Emphasis Type="Italic">Ellobius lutescens</Emphasis>) Along Zagros Mountains,Iran

The Zagros and Alborz mountainous ridges can be regarded as one of the most interesting and known physical barriers responsible for the vicariance event. Based on the probable effect of Zagros Mountains on the rodent population vicariance, a research on Caucasian mole vole phylogeography, population genetic structure and diversity was designed along the mentioned mountainous areas. To this end, a total of 38 tissue samples were collected from the northern parts of the study area to the southern parts. Obtained mitochondrial cytb (1041 bp) sequences were used in this phylogenetic analysis. The phylogenetic analysis was based on the TRN+I evolutionary model and gaining Bayesian phylogenetic tree with maximum verification. By using median joining logic, the relationships between different acquired haplotypes were analyzed. It was shown that the Caucasian mole vole population had been disjointed (based on posterior probability of 1 and 100 bootstraps) along the Zagros mountainous ridges, especially in both geographical extremes located in the northern and southern parts of the mountainous ridges. Meanwhile from the 38 analyzed sequences, 17 haplotypes were obtained, of which 10 haplotypes were unique. The mutational steps between haplotypes were assessed by generating statistical parsimony haplotype networks, which yielded 36 mutational steps between the northern and southern populations. Based on neutrality tests and analyzing their power under sudden population expansions, it was found that this event happened around the northern and southern populations. Genetic distance of two percent between the northern and southern populations indicated the existence of local adaptations by these two groups, which can be regarded as evolutionary units.     

Postglacial colonization of Europe by the barbastelle bat: agreement between molecular data and past predictive modelling

The barbastelle (Barbastella barbastellus) is a rare forest bat with a wide distribution in Europe. Here, we combine results from the analysis of two mtDNA fragments with species distribution modelling to determine glacial refugia and postglacial colonization routes. We also investigated whether niche conservatism occurs in this species. Glacial refugia were identified in the three southern European peninsulas: Iberia, Italy and the Balkans. These latter two refugia played a major role in the postglacial colonization process, with their populations expanding to England and central Europe, respectively. Palaeo‐distribution models predicted that suitable climatic conditions existed in the inferred refugia during the last glacial maximum (LGM). Nevertheless, the overlap between the current and the LGM distributions was almost inexistent in Italy and in the Balkans, meaning that B. barbastellus populations were forced to shift range between glacial and interglacial periods, a process that probably caused some local extinctions. In contrast, Iberian populations showed a ‘refugia within refugium’ pattern, with two unconnected areas containing stable populations (populations that subsisted during both glacial and interglacial phases). Moreover, the match between LGM models and the refugial areas determined by molecular analysis supported the hypothesis of niche conservatism in B. barbastellus. We argue that geographic patterns of genetic structuring, altogether with the modelling results, indicate the existence of four management units for conservation: Morocco, Iberia, Italy and UK, and Balkans and central Europe. In addition, all countries sampled possessed unique gene pools, thus stressing the need for the conservation of local populations.     

Genetic evidence for the persistence of the critically endangered Sierra Nevada red fox in California

California is home to both the native state-threatened Sierra Nevada red fox (Vulpes vulpes necator), which historically inhabited high elevations of the Sierra Nevada and Cascade mountains, and to multiple low-elevation red fox populations thought to be of exotic origin. During the past few decades the lowland populations have dramatically expanded their distribution, and possibly moved into the historic range of the native high-elevation fox. To determine whether the native red fox persists in its historic range in California, we compared mitochondrial cytochrome-b haplotypes of the only currently-known high-elevation population (n = 9 individuals) to samples from 3 modern lowland populations (n = 35) and historic (1911–1941) high-elevation (n = 22) and lowland (n = 7) populations. We found no significant population differentiation among the modern and historic high-elevation populations (average pairwise F _ST = 0.06), but these populations differed substantially from all modern and historic lowland populations (average pairwise F _ST = 0.52). Among lowland populations, the historic and modern Sacramento Valley populations were not significantly differentiated from one another (F _ST = −0.06), but differed significantly from recently founded populations in the San Francisco Bay region and in southern California (average pairwise F _ST = 0.42). Analysis of molecular variance indicated that 3 population groupings (mountain, Sacramento Valley, and other lowland regions) explained 45% of molecular variance (F _CT = 0.45) whereas only 4.5% of the variance was partitioned among populations within these groupings (F _SC = 0.08). These findings provide strong evidence that the native Sierra Nevada red fox has persisted in northern California. However, all nine samples from this population had the same haplotype, suggesting that several historic haplotypes may have become lost. Unidentified barriers have apparently prevented gene flow from the Sacramento Valley population to other eastern or southern populations in California. Future studies involving nuclear markers are needed to assess the origin of the Sierra Nevada red fox and to quantify levels of nuclear gene flow.     

Phylogeography and conservation genetics of the hellbender salamander (Cryptobranchus alleganiensis)

We investigated hellbender phylogeography through phylogenetic analyses of individuals sampled from 16 locations throughout their range in the eastern United States. Analyses were conducted on concatenated cytochrome-oxidase I (COI), cytochrome-b (Cytb) and NADH dehydrogenase subunit 4 (ND4) mtDNA sequence, totaling 2160 nucleotides. Hellbender haplotypes differed by 0.1 to 5.8% maximum likelihood (ML) corrected sequence divergence. Phylogenetic analyses reveal that hellbenders are separated into 8 reciprocally monophyletic populations or clades differentiated by a minimum of 0.7 to 5.4% sequence divergence, each of which constitutes a separate Management Unit (MU). High among population divergence and reciprocal monophyly suggest that female-mediated gene flow is severely restricted or non-existent among each MU. Hellbenders are currently divided into two subspecies, Cryptobranchus alleganiensis alleganiensis and C. a. bishopi based on morphological characters. The phylogenetic analyses presented here strongly indicate that these subspecies are paraphyletic. Management priorities for the hellbender should be reconsidered in light of these new molecular data. Results from Bayesian rooting indicate the root of the hellbender mtDNA tree lies on the branch leading to hellbender haplotypes from the Current, Eleven Point and New Rivers. The rooted tree suggests that a common ancestor in the southern Ozarks and/or southern Appalachians gave rise to northern hellbender populations, consistent with a Pleistocene refuge hypothesis.     

Mitochondrial evidence for distinct phylogeographic units in the endangered Malagasy poison frog Mantella bernhardi

Mantella bernhardi is an endemic species of Malagasy poison frog threatened by loss and fragmentation of its natural habitat and collection for the pet trade. It is classified as threatened according to the International Union for Conservation of Nature and Natural Resources (IUCN) categories and included in Appendix II of the Convention on the International Trade of Endangered Species (CITES). A recent survey has increased the known distributional range of the species from one to eight populations across southeastern Madagascar, but little is known about its biology and genetic diversity. Here we estimate inter- and intrapopulation mitochondrial genetic variation of four populations. Populations from the northern and southern parts of the distributional range showed a high degree of divergence (maximum of 11.35% in cytochrome b) and were recovered as reciprocally monophyletic groups. Nine haplotypes were detected in the northern and 12 in the southern populations. The population from Ranomafana National Park showed the lowest number of haplotypes and nucleotide diversity, and shared its most common haplotype with the second northern population from Tolongoina. All the other detected haplotypes were unique to each of the four populations. This suggests the existence of important barriers to gene flow, pre-dating human colonization of Madagascar at about 2000 years ago, in distinct contrast to other Mantella species that show a high degree of haplotype sharing throughout their range. The continued habitat fragmentation within the distribution range of M. bernhardi prevents any connection between its populations. Our data indicate the existence of at least two different management units for conservation in this species, corresponding to the North and South of its distribution range, and highlight the existence of strong regional endemism in southeastern Madagascar.     

Genetic diversity and population structure in the rare Algodones sunflower (Helianthus niveus ssp. tephrodes)

Assessing levels and patterns of population genetic variation is an important step for evaluating rare or endangered species and determining appropriate conservation strategies. This is particularly important for ensuring the preservation of novel genetic variation in wild relatives of crops, which could provide beneficial alleles for plant breeding and improvement. In this study, we evaluate the population genetics of Helianthus niveus ssp. tephrodes (the Algodones sunflower), which is an endangered, wild relative of cultivated sunflower (H. annuus L.). This rare sunflower species is native to the sand dunes of the Sonoran Desert in southern California, southwestern Arizona, and northern Mexico and is thought to harbor beneficial alleles for traits related to drought tolerance. We genotyped nine populations of this species with a set of simple-sequence repeat markers derived from expressed sequence tags (EST-SSRs) and investigated levels of genetic diversity and population structure, in H. niveus ssp. tephrodes. We also compared our results to findings from five related sunflower species that have been analyzed with these same markers, including annuals and perennials that range from rare to widespread. The Algodones sunflower harbors lower levels of standing genetic variation, but similar levels of population structure as compared to other sunflower species. We also discovered that a disjunct population from northern Mexico was genetically distinct from populations elsewhere in the range. Given the occurrence of such a genetically unique population, our recommendations include population surveys of the southern portion of the range in hopes of bolstering the existing germplasm collection.     

Phylogeography and genetic structure of the endemic cyprinid fish Microphysogobio brevirostris in northern Taiwan

This study used the mitochondrial DNA cytochrome b and control region sequences to examine the population genetic structure of Microphysogobio brevirostris, an endemic cyprinid species in northern Taiwan. In total, 90 specimens were collected from six populations belonging to four major rivers. All haplotypes were identified as two major clades (Clades N and S), exhibiting a southern and a northern distribution. The results of statistical dispersal-vicariance analysis (S-DIVA) revealed that two vicariance events and one dispersal event shaped the phylogeographic pattern of M. brevirostris. These results suggest that the ancestral populations of M. brevirostris are widely distributed throughout northern Taiwan, north of the Miaoli Plateau. The ancestral populations then diverged into two clades (N and S) by the raising of the Taoyuan Plateau. Finally, two major rivers of the S clade diverged and dispersed into adjacent rivers. Besides, our results revealed that Microphysogobio alticorpus and M. brevirostris colonized Taiwan during the same ice age through different colonization routes.     

Genetic perspectives on “Lion Conservation Units” in Eastern and Southern Africa

Current understanding of genetic variation in lions (Panthera leo) is inadequate to guide many management decisions necessary for conservation of the species. We studied sequence variation in the mitochondrial cytochrome-b (cyt-b) gene of 75 lions and nuclear variation at 11 microsatellite loci of 480 lions across 8 range states (Cameroon, Uganda, Kenya, Zambia, Zimbabwe, South Africa, Botswana, and Namibia) and 13 Lion Conservation Units (LCUs) plus two other unassigned sites (Cameroon and Zimbabwe). A total of 11 cyt-b haplotypes were found, whose variation follows an isolation-by-distance model. In combination with previously known sequences, the haplotypes document the close relationship, derived position, and limited variability of Asian and West and Central African lions relative to other extant lions. Both phylogenetic analyses and substitution networks identify two clades in Eastern and Southern Africa—one restricted to Namibia and South Africa and the other more widespread across the region. However, these analyses are equivocal on which of these is closest to the ancestor of modern lions. Microsatellite analyses showed high levels of variation within and among populations, subdivision among most LCUs, and evidence of isolation by distance. While rates of gene flow are generally low, admixture among lions in northern Botswana, Caprivi Strip (Namibia) and Zambia is apparent from STRUCTURE analyses. Conservation management plans should incorporate information on genetic variability and gene flow in delimiting management units and in guiding translocations of lions to minimize inbreeding and to control problem animals.     

Genetic diversity and structure of the endangered lady's slipper orchid Cypripedium japonicum Thunb. (Orchidaceae) in Japan

Cypripedium japonicum Thunb. (Orchidaceae), once a common perennial herb, is now designated as endangered throughout most of its distribution due to habitat destruction and fragmentation, and the impacts of horticultural collection. We investigated the genetic characteristics of this species for conservation purposes, using microsatellite markers to examine the genetic diversity and structure of 15 native and 5 ex situ populations in Japan. The results imply that although allelic variation is low in Japanese C. japonicum, sexual reproduction by seed, as well as clonal propagation, may occur in some populations. Both native and ex situ populations were found to be genetically differentiated, indicating that some populations may have experienced recent population declines, genetic fragmentation, or bottlenecks. The degree of genetic drift from the putative ancestral population, inferred through STRUCTURE analysis, was more pronounced in northern populations than in southern populations. Some of the ex situ conserved populations exhibited a low degree of differentiation from ancestral native populations. Our results imply that conservation of C. japonicum in Japan is best supported by maintaining individual populations and their unique genetic characteristics.     

Geographic independence and phylogenetic diversity of red shiner introductions

Identifying areas at risk of invasion can be difficult when the distribution of a non-native species encompasses geographically disjunct regions. Understanding genealogical relationships among native and non-native populations can clarify the origins of fragmented distributions, which in turn can clarify how fast and far a non-native species may spread. We evaluated genetic variation across the native and invasive ranges of red shiner (Cyprinella lutrensis), a minnow known to displace and hybridize with native species, to reconstruct invasion pathways across the United States (USA). Examination of mitochondrial cytochrome-b variation found that native range populations of red shiner fall into four highly divergent lineages that likely warrant species recognition. Introduced red shiner populations in the eastern and western USA are derived from only two of these lineages. Western USA populations originate from the mid-western and western genetic lineages, whereas eastern introductions derive only from the mid-western lineage. Western USA invasive populations exhibit fewer, but more diverse haplotypes compared to eastern USA invasive populations. We also recovered an undescribed, divergent lineage of Cyprinella that has been cryptically introduced into the western USA, which raises the possibility that hybridization has proceeded following secondary contact between previously allopatric lineages. Approximate Bayesian Computation modeling suggests that the disjunct distribution of red shiner across North America is an agglomeration of independent regional invasions with distinct origins, rather than stepwise advance of an invasion front or secondary introductions across regions. Thus localized control may be effective in managing non-native red shiner, including further spread to areas of conservation concern.     

Genetic structure of Salsola junatovii (Chenopodiaceae) in the northern edge of the Taklimakan desert and conservational implications

Salsola junatovii Botsch. (Chenopodiaceae), a desert shrub endemic to the northern edge of the Taklimakan desert in China, is listed as an endangered species because of its narrow habitat requirements and a decline in numbers of individuals. In order to provide information on conservation strategies, we investigated the genetic patterns and evolutionary history of this species. Two cpDNA spacers, (psbA-trnH and psbK-psbI), and the nrITS sequence were employed in 116 individuals from 15 populations across the whole range of the species. A total of 7 haplotypes and 12 ribotypes were detected. Based on separate BEAST analyses, we suggest that intraspecific differentiation of S. junatovii occurred at 2.284–0.264 Ma for cpDNA haplotypes, and 1.304–0.1 Ma for nrITS ribotypes, both in the Pleistocene. Only mismatch analysis and neutrality tests for nrITS sequences over all populations were indicative of demographic expansion. Inconsistency between results from chloroplast and nuclear sequences was detected, apparently due to a stronger seed-mediated gene flow among populations than pollen-mediated flow under the severe desert conditions. Based on genetic structure results, one population, KMS, with the highest number of unique genotypes, should be a conservation priority; another nine populations containing unique genotypes were suggested for ex situ conservation.     

Genetic and morphological differentiation in the clam Coelomactra antiquata (Bivalvia: Veneroida) along the coast of China

Coelomactra antiquata is a commercially exploited bivalve, and its populations have been severely declining in the coast of China during the last two decades. In order to provide guidelines for conservation strategies and management programs, four populations of C. antiquata, representing the most important populations in China, were analysed morphologically and genetically to reveal the genetic structure by using 7 polymorphic allozyme loci and 12 morphological variables. The mean allele richness ranged from 2.79 to 3.53, while the mean heterozygosity ranged from 0.326 to 0.519. All genetic distance metrics revealed high level of genetic differentiation between the three northern populations and one southern population. The marked genetic differentiation can be explained by the freshwater outflow of Yangtze River and upwelling of Zhejiang province. The morphological analyses were in accordance with the allozyme data, which also disclosed a high degree of differentiation between the northern and southern populations. The results obtained in this study indicate that the northern and southern populations in C. antiquata should be treated as separate units for conservation management.     

Subspecies and units for conservation and management of the northern bobwhite in the eastern United States

The northern bobwhite (Colinus virginianus) is a small game bird with sedentary lifestyle and has experienced population declines throughout most of its native distribution in the eastern United States. We investigated intraspecific genetic relationships among 14 local populations covering four putative subspecies (C. v. marilandicus, C. v. virginianus, C. v. mexicanus, and C. v. floridanus) in the United States. Analysis of mitochondrial DNA sequences revealed a small, but significant, genetic structure of northern bobwhite populations or subspecies in the eastern US. However, our results did not support current subspecies limits as distinct evolutionarily significant units, based on the amount of population genetic divergences and insufficient lineage sorting of mtDNA haplotypes among subspecies. Instead, our results suggest that C. v. virginianus, C. v. marilandicus, and C. v. mexicanus be merged into a single management unit, and C. v. floridanus be considered as another distinct unit for conservation and management.     

Microsatellite Markers Reveal Strong Genetic Structure in the Endemic Chilean Dolphin

Understanding genetic differentiation and speciation processes in marine species with high dispersal capabilities is challenging. The Chilean dolphin, Cephalorhynchus eutropia, is the only endemic cetacean of Chile and is found in two different coastal habitats: a northern habitat with exposed coastlines, bays and estuaries from Valparaíso (33°02′S) to Chiloé (42°00′S), and a southern habitat with highly fragmented inshore coastline, channels and fjords between Chiloé and Navarino Island (55°14′S). With the aim of evaluating the potential existence of conservation units for this species, we analyzed the genetic diversity and population structure of the Chilean dolphin along its entire range. We genotyped 21 dinucleotide microsatellites for 53 skin samples collected between 1998 and 2012 (swab: n = 8, biopsy: n = 38, entanglement n = 7). Bayesian clustering and spatial model analyses identified two genetically distinct populations corresponding to the northern and southern habitats. Genetic diversity levels were similar in the two populations (He: 0.42 v/s 0.45 for southern and northern populations, respectively), while effective size population was higher in the southern area (Ne: 101 v/s 39). Genetic differentiation between these two populations was high and significant (F_ST = 0.15 and R_ST = 0.19), indicating little or no current gene flow. Because of the absence of evident geographical barriers between the northern and southern populations, we propose that genetic differentiation may reflect ecological adaptation to the different habitat conditions and resource uses. Therefore, the two genetic populations of this endemic and Near Threatened species should be considered as different conservation units with independent management strategies.     

Genetic diversity and population history of a critically endangered primate, the northern muriqui (Brachyteles hypoxanthus)

Social, ecological, and historical processes affect the genetic structure of primate populations, and therefore have key implications for the conservation of endangered species. The northern muriqui (Brachyteles hypoxanthus) is a critically endangered New World monkey and a flagship species for the conservation of the Atlantic Forest hotspot. Yet, like other neotropical primates, little is known about its population history and the genetic structure of remnant populations. We analyzed the mitochondrial DNA control region of 152 northern muriquis, or 17.6% of the 864 northern muriquis from 8 of the 12 known extant populations and found no evidence of phylogeographic partitions or past population shrinkage/expansion. Bayesian and classic analyses show that this finding may be attributed to the joint contribution of female-biased dispersal, demographic stability, and a relatively large historic population size. Past population stability is consistent with a central Atlantic Forest Pleistocene refuge. In addition, the best scenario supported by an Approximate Bayesian Computation analysis, significant fixation indices (Φ_ST = 0.49, Φ_CT = 0.24), and population-specific haplotypes, coupled with the extirpation of intermediate populations, are indicative of a recent geographic structuring of genetic diversity during the Holocene. Genetic diversity is higher in populations living in larger areas (>2,000 hectares), but it is remarkably low in the species overall (θ = 0.018). Three populations occurring in protected reserves and one fragmented population inhabiting private lands harbor 22 out of 23 haplotypes, most of which are population-exclusive, and therefore represent patchy repositories of the species'' genetic diversity. We suggest that these populations be treated as discrete units for conservation management purposes.     

Mitochondrial DNA analysis reveals hidden genetic diversity in captive populations of the threatened American crocodile (Crocodylus acutus) in Colombia

Identification of units within species worthy of separate management consideration is an important area within conservation. Mitochondrial DNA (mtDNA) surveys can potentially contribute to this by identifying phylogenetic and population structure below the species level. The American crocodile (Crocodylus acutus) is broadly distributed throughout the Neotropics. Its numbers have been reduced severely with the species threatened throughout much of its distribution. In Colombia, the release of individuals from commercial captive populations has emerged as a possible conservation strategy that could contribute to species recovery. However, no studies have addressed levels of genetic differentiation or diversity within C. acutus in Colombia, thus complicating conservation and management decisions. Here, sequence variation was studied in mtDNA cytochrome b and cytochrome oxidase I gene sequences in three Colombian captive populations of C. acutus. Two distinct lineages were identified: C. acutus‐I, corresponding to haplotypes from Colombia and closely related Central American haplotypes; and C. acutus‐II, corresponding to all remaining haplotypes from Colombia. Comparison with findings from other studies indicates the presence of a single “northern” lineage (corresponding to C. acutus‐I) distributed from North America (southern Florida), through Central America and into northern South America. The absence of C. acutus‐II haplotypes from North and Central America indicates that the C. acutus‐II lineage probably represents a separate South American lineage. There appears to be sufficient divergence between lineages to suggest that they could represent two distinct evolutionary units. We suggest that this differentiation needs to be recognized for conservation purposes because it clearly contributes to the overall genetic diversity of the species. All Colombian captive populations included in this study contained a mixture of representatives of both lineages. As such, we recommend against the use of captive‐bred individuals for conservation strategies until further genetic information is available.     

Wild Gazelles of the Southern Levant: Genetic Profiling Defines New Conservation Priorities

The mountain gazelle (Gazella gazelle), Dorcas gazelle (Gazella Dorcas) and acacia gazelle (Gazella arabica acacia) were historically abundant in the southern Levant, and more specifically in Israel. Anthropogenic and natural changes have caused a rapid decline in gazelle populations, raising concerns about their conservation status and future survival. The genetic profile of 111 wild gazelles from Israel was determined based on three regions of mitochondrial DNA (control region, Cytochrome b and 12S ribosomal RNA) and nine nuclear microsatellite markers. Genetic analysis of the mountain gazelle population, the largest known population of this rare species, revealed adequate diversity levels and gene flow between subpopulations. Nevertheless, ongoing habitat degradation and other human effects, such as poaching, suggest the need for drastic measures to prevent species extinction. Dorcas gazelles in Israel displayed inbreeding within subpopulations while still maintaining considerable genetic diversity overall. This stable population, represented by a distinctive genetic profile, is fragmented and isolated from its relatives in neighboring localities. Based on the genetic profile of a newly sampled subpopulation in Israel, we provide an alternative hypothesis for the historic dispersal of Dorcas gazelle, from the Southern Levant to northern Africa. The small acacia gazelle population was closest to gazelles from the Farasan Islands of Saudi Arabia, based on mitochondrial markers. The two populations did not share haplotypes, suggesting that these two populations may be the last remnant wild gazelles of this species worldwide. Only a dozen acacia gazelles survive in Israel, and urgent steps are needed to ensure the survival of this genetically distinctive lineage. The genetic assessments of our study recognize new conservation priorities for each gazelle species in the Southern Levant.     

Pathways of introduction of the invasive aquatic plant Cabomba caroliniana

The pathway and frequency of species' introductions can affect the extent, impact, and management of biological invasions. Here, we examine the pathway of introduction of the aquatic plant Cabomba caroliniana (fanwort) into Canada and the northern United States using plastid DNA sequence (intergenic spacers atpF‐atpH, trnH‐psbA, and trnL‐trnF) and DNA content analyses. We test the hypothesis that the spread of fanwort is a result of commercial trade by comparing a Canadian population (Kasshabog Lake, ON) to native populations from southern U.S., introduced populations in northern U.S., and plants from commercial retailers. Thirteen plastid haplotypes were identified throughout North America, including one dominant haplotype, which was present in all C. caroliniana populations. Several rare haplotypes were used to infer shared colonization history. In particular, the Canadian population shared two rare alleles with a population from Massachusetts, suggesting range expansion of C. caroliniana from the northern U.S. However, the possibility of a commercial introduction cannot be excluded, as common alleles were shared between the Canadian population and both commercial and southern U.S. sources. Variation in C. caroliniana genome size was bimodal and populations were classified into “high” and “low” categories. The Canadian population had DNA contents similar to several northern U.S. populations (low DNA content). This may provide additional support for range expansion from these introduced populations rather than from commercial sources or populations in the southern U.S., which had high DNA content.     

Phylogeography of an Italian endemic salamander (genus Salamandrina): glacial refugia,postglacial expansions,and secondary contact

The Italian endemic genus Salamandrina has been historically regarded as monotypic but, recently, studies based on both mitochondrial and nuclear markers have indicated the existence of two distinct species of spectacled salamanders: Salamandrina perspicillata, in central and northern Italy, and Salamandrina terdigitata, in southern Italy. We analyzed nucleotide variation at mitochondrial and nuclear genes [cytochrome b, 12S and 16S rRNA, recombination activating gene (RAG 1)] in 223 individuals from 56 locations, aiming to investigate their genetic structure and recent evolutionary histories. Phylogenetic and phylogeographical analyses revealed the existence of three and two genetically distinct groups of populations in northern and southern salamander, respectively. Historical demographic analyses led to the inference of range expansion for both species in the late Pleistocene. During the last glacial stage, each salamander survived in a single refugium, namely the southern in Calabria and the northern in central Italy. At the end of this period, both lineages expanded northward and established secondary contact. Spatial distribution of RAG 1 haplotype variation revealed two differentiated population groups corresponding to the major mitochondrial (mt)DNA clades. Nuclear pattern of introgressive hybridization was more extensive than the highly limited introgression of mtDNA markers. From a conservation standpoint, southern Latium and Calabria proved to be the major genetic diversity reservoirs, thus deserving particular conservation efforts. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 903–922.     

Phylogeography and ecological niche modelling in Eugenia uniflora (Myrtaceae) suggest distinct vegetational responses to climate change between the southern and the northern Atlantic Forest

In this study, we evaluate phylogeographic patterns and predictions of ecological niche modelling (ENM) for Eugenia uniflora (Myrtaceae), a widely distributed taxon in the Atlantic forest domain, to understand the effect of past climatic oscillations on the demographic history of this species. An analysis of phylogeographic population structure and demography was conducted on E. uniflora from 46 localities in natural environments across the distribution range of the species based on three plastid markers. ENM was also performed to predict suitable environments and areas of dramatic decrease in future suitability for the species under distinct representative concentration pathways (RCPs). Eugenia uniflora exhibited higher haplotype and nucleotide diversity in the southern part of its distribution than in the northern part. Two divergent lineages were revealed in the phylogenetic analysis of haplotypes, with an estimated divergence at c. 4.9 Mya. The populations in the northern and central regions of the range probably experienced population growth, whereas populations in the southern region are marked by historical demographic stability. ENM results indicate that the distribution of E. uniflora was fragmented in cool periods and was broader and more connected during warm periods during Pleistocene. The results suggest distinct evolutionary histories in southern to northern populations, indicating region‐specific responses to changes.