Population genetic structure of turbot (Scophthalmus maximus L., 1758) in the Black Sea

Turbot, Scophthalmus maximus, is a commercially important demersal flatfish species distributed throughout the Black Sea. Several studies performed locally with a limited number of specimens using both mitochondrial DNA (mtDNA) and microsatellite markers evidenced notable genetic variation among populations. However, comprehensive population genetic studies are required to help management of the species in the Black Sea. In the present study eight microsatellite loci were used to resolve the population structure of 414 turbot samples collected from 12 sites across the Black Sea. Moreover, two mtDNA genes, COI and Cyt-b, were used for taxonomic identification. Microsatellite markers of Smax-04 and B12-I GT14 were excluded from analysis due to scoring issues. Data analysis was performed with the remaining six loci. Loci were highly polymorphic (average of 17.8 alleles per locus), indicating high genetic variability. Locus 3/20CA17, with high null allele frequency (>30%), significantly deviated from HW equilibrium. Pairwise comparison of the F_ST index showed significant differences between most of the surveyed sampling sites (P < 0.01). Cluster analysis evidenced the presence of three genetic groups among sampling sites. Significant genetic differentiation between Northern (Sea of Azov and Crimea) and Southern (Turkish Black Sea Coast) Black Sea sampling sites were detected. The Mantel test supported an isolation by distance model of population structure. These findings are vital for long-term sustainable management of the species and development of conservation programs. Moreover, generated mtDNA sequences would be useful for the establishment of a database for S. maximus.     

Genetic surfing,not allopatric divergence,explains spatial sorting of mitochondrial haplotypes in venomous coralsnakes

Strong spatial sorting of genetic variation in contiguous populations is often explained by local adaptation or secondary contact following allopatric divergence. A third explanation, spatial sorting by stochastic effects of range expansion, has been considered less often though theoretical models suggest it should be widespread, if ephemeral. In a study designed to delimit species within a clade of venomous coralsnakes, we identified an unusual pattern within the Texas coral snake (Micrurus tener): strong spatial sorting of divergent mitochondrial (mtDNA) lineages over a portion of its range, but weak sorting of these lineages elsewhere. We tested three alternative hypotheses to explain this pattern—local adaptation, secondary contact following allopatric divergence, and range expansion. Collectively, near panmixia of nuclear DNA, the signal of range expansion associated sampling drift, expansion origins in the Gulf Coast of Mexico, and species distribution modeling suggest that the spatial sorting of divergent mtDNA lineages within M. tener has resulted from genetic surfing of standing mtDNA variation—not local adaptation or allopatric divergence. Our findings highlight the potential for the stochastic effects of recent range expansion to mislead estimations of population divergence made from mtDNA, which may be exacerbated in systems with low vagility, ancestral mtDNA polymorphism, and male‐biased dispersal.     

PHYLOGEOGRAPHY OF THE SPOTTED SAND BASS, PARALABRAX MACULATOFASCIATUS: DIVERGENCE OF GULF OF CALIFORNIA AND PACIFIC COAST POPULATIONS

Abstract Have the warm tropical waters and currents of the southern Gulf of California, Mexico (also known as the Sea of Cortez), formed a barrier to gene flow, resulting in disjunct populations in the upper gulf that are isolated from the outer Pacific Coast? Phylogeographic and genetic divergences of the spotted sand bass, Paralabrax maculatofasciatus, from three Gulf of California and two outer Pacific coastal locations were tested using mitochondrial DNA (mtDNA) control region sequences. Sequence data from two congeners that are sympatrically distributed along the outer Pacific Coast, the barred sand bass, P. nebulifer, and the kelp bass, P. clathratus, were used to gauge the levels of genetic divergences. Differences among the three species and between the northern gulf and outer Pacific coastal populations of P. maculatofasciatus also were analyzed using 40 allozymic presumptive gene loci. Allozyme and mtDNA analyses each revealed many fixed differences among the species. Three significant allozymic frequency differences and two fixed mtDNA substitutions differentiated the gulf and outer Pacific coastal populations of P. maculatofasciatus. Three unique mtDNA haplotypes and three unique allozyme alleles were identified from the outer Pacific coastal population. The gulf sites contained four unique mtDNA haplotypes and six unique allozyme alleles. Partitioning of the mtDNA variation revealed that 72% of the variance occurred between the gulf and outer Pacific Coast, 20% between sampling sites in the two regions, and 8% within the sites. There appears to be little gene flow across the waters of the southern Baja Penninsula, producing divergence estimated as 120,000 to 600,000 years between the outer Pacific coastal and the Gulf of California populations. This separation level may date to a hypothesized seaway closure near La Paz, Mexico, during the mid‐Pleistocene, and characterizes other fish populations. A second pattern of deeper allopatric species‐level divergences in some other fishes may date to a Pliocene closure of a mid‐Baja Penninsular seaway. Significant differences also were discerned in P. maculatofasciatus between the San Diego and central Baja California coastal sites and between the upper/central and the lower gulf locations. Variation between locations in the two regions may be indicative of larval retention and low adult migration, which needs to be tested further.     

A biogeographical profile of the sand cockroach Arenivaga floridensis and its bearing on origin hypotheses for Florida scrub biota

Florida scrub is a xeric ecosystem associated with the peninsula's sand ridges, whose intermittent Pliocene–Pleistocene isolation is considered key to scrub endemism. One scrub origin hypothesis posits endemics were sourced by the Pliocene dispersal of arid‐adapted taxa from southwestern North America; a second invokes Pleistocene migration within eastern North America. Only one study to date has explicitly tested these competing hypotheses, supporting an eastern origin for certain scrub angiosperms. For further perspective, we conducted a genetic analysis of an endemic arthropod, the Florida sand cockroach (Arenivaga floridensis), with two aims: (1) to reconstruct the peninsular colonization and residence history of A. floridensis and (2) determine whether its biogeographic profile favors either origin hypothesis. We sequenced the cox2 mitochondrial gene for 237 specimens (65 populations) as well as additional loci (cox1, nuclear H3) for a subset of Florida roaches and congeners. Using Network and Bayesian inference methods, we identified three major lineages whose genetic differentiation and phylogeographical structure correspond with late Pliocene peninsula insularization, indicating Arenivaga was present and broadly distributed in Florida at that time. Stem and crown divergence estimates (6.36 Ma; 2.78 Ma) between A. floridensis and western sister taxa span a period of extensive dispersal by western biota along an arid Gulf Coast corridor. These phylogeographical and phylogenetic results yield a biogeographic profile consistent with the western origin hypothesis. Moreover, age estimates for the roach's peninsular residence complement those of several other endemics, favoring a Pliocene (or earlier) inception of the scrub ecosystem. We argue that eastern versus western hypotheses are not mutually exclusive; rather, a composite history of colonization involving disparate biotas better explains the diverse endemism of Florida scrub.     

Phylogeography of Douglas‐fir based on mitochondrial and chloroplast DNA sequences: testing hypotheses from the fossil record

The integration of fossil and molecular data can provide a synthetic understanding of the ecological and evolutionary history of an organism. We analysed range‐wide maternally inherited mitochondrial DNA and paternally inherited chloroplast DNA sequence data with coalescent simulations and traditional population genetic methods to test hypotheses of population divergence generated from the fossil record of Douglas‐fir (Pseudotsuga menziesii), an ecologically and economically important western North American conifer. Specifically, we tested (i) the hypothesis that the Pliocene orogeny of the Cascades and Sierra Nevada caused the divergence of coastal and Rocky Mountain Douglas‐fir varieties; and (ii) the hypothesis that multiple glacial refugia existed on the coast and in the Rocky Mountains. We found that Douglas‐fir varieties diverged about 2.11 Ma (4.37 Ma–755 ka), which could be consistent with a Pliocene divergence. Rocky Mountain Douglas‐fir probably resided in three or more glacial refugia. More variable molecular markers would be required to detect the two coastal refugia suggested in the fossil record. Comparison of mitochondrial DNA and chloroplast DNA variation revealed that gene flow via pollen linked populations isolated from seed exchange. Postglacial colonization of Canada from coastal and Rocky Mountain refugia near the ice margin at the Last Glacial Maximum produced a wide hybrid zone among varieties that formed almost exclusively by pollen exchange and chloroplast DNA introgression, not seed exchange. Postglacial migration rates were 50–165 m/year, insufficient to track projected 21st century warming in some regions. Although fossil and genetic data largely agree, each provides unique insights.     

Range instability leads to cytonuclear discordance in a morphologically cryptic ground squirrel species complex

The processes responsible for cytonuclear discordance frequently remain unclear. Here, we employed an exon capture data set and demographic methods to test hypotheses generated by species distribution models to examine how contrasting histories of range stability vs. fluctuation have caused cytonuclear concordance and discordance in ground squirrel lineages from the Otospermophilus beecheyi species complex. Previous studies in O. beecheyi revealed three morphologically cryptic and highly divergent mitochondrial DNA lineages (named the Northern, Central and Southern lineages based on geography) with only the Northern lineage exhibiting concordant divergence for nuclear genes. Here, we showed that these mtDNA lineages likely formed in allopatry during the Pleistocene, but responded differentially to climatic changes that occurred since the last interglacial (~120,000 years ago). We find that the Northern lineage maintained a stable range throughout this period, correlating with genetic distinctiveness among all genetic markers and low migration rates with the other lineages. In contrast, our results suggested that the Southern lineage expanded from Baja California Sur during the Late Pleistocene to overlap and potentially swamp a contracting Central lineage. High rates of intraspecific gene flow between Southern lineage individuals among expansion origin and expansion edge populations largely eroded Central ancestry from autosomal markers. However, male‐biased dispersal in this system preserved signals of this past hybridization and introgression event in matrilineal‐biased X‐chromosome and mtDNA markers. Our results highlight the importance of range stability in maintaining the persistence of phylogeographic lineages, whereas unstable range dynamics can increase the tendency for lineages to merge upon secondary contact.     

Historic speciation and recent colonization of Eurasian monkey gobies (Neogobius fluviatilis and N. pallasi) revealed by DNA sequences,microsatellites, and morphology

Aim Hidden diversity within an invasive ‘species’ can mask both invasion pathways and confound management goals. We assessed taxonomic status and population structure of the monkey goby Neogobius fluviatilis across Eurasia, comparing genetic variation across its native and invasive ranges. Location Native populations were analysed within the Black and Caspian Sea basins, including major river drainages (Dnieper, Dniester, Danube, Don and Volga rivers), along with introduced locations within the upper Danube and Vistula river systems. Methods DNA sequences and 10 nuclear microsatellite loci were analysed to test genetic diversity and divergence patterns of native and introduced populations; phylogenetic analysis of mtDNA cytochrome b and nuclear RAG‐1 sequences assessed taxonomic status of Black and Caspian Sea lineages. Multivariate analysis of morphology was used to corroborate phylogenetic patterns. Population genetic structure within each basin was evaluated with mtDNA and microsatellite data using F_ST analogues and Bayesian assignment tests. Results Phylogenetic analysis of mitochondrial and nuclear sequences discerned a pronounced genetic break between monkey gobies in the Black and Caspian Seas, indicating a long‐term species‐level separation dating to c. 3 million years. This pronounced separation further was confirmed from morphological and population genetic divergence. Bayesian inference showed congruent patterns of population structure within the Black Sea basin. Introduced populations in the Danube and Vistula River basins traced to north‐west Black Sea origins, a genetic expansion pattern matching that of other introduced Ponto‐Caspian gobiids. Main conclusions Both genetic and morphological data strongly supported two species of monkey gobies that were formerly identified as subspecies: N. fluviatilis in the Black Sea basin, Don and Volga Rivers, and the Kumo‐Manych Depression, and Neogobius pallasi in the Caspian Sea and Volga River delta. Genetic origins of introduced N. fluviatilis populations indicated a common invasion pathway shared with other introduced Ponto‐Caspian fishes and invertebrates.     

Climatic fluctuations shape the phylogeography of a mesic direct‐developing frog from the south‐western Australian biodiversity hotspot

Aim To assess phylogeographic pattern throughout the range of Metacrinia nichollsi in order to develop specific biogeographical hypotheses for the wet forests of south‐western Australia. This was carried out by contrasting a direct‐developing frog species, M. nichollsi, that breeds independently of free surface water with conventional, aquatic breeders and highly specialized direct developers. Location Wet forests of the south‐western Australian biodiversity hotspot – an area of high species richness and endemism for myobatrachid frogs and many other faunal groups. Methods We compiled an extensive phylogeographic data set from field‐collected samples based on mitochondrial ND2 sequences. Phylogenetic analyses combined with estimates of divergence times were used to build a model of major biogeographical events affecting the species. Phylogeographic analyses were used to provide insights into smaller‐scale processes acting within each major lineage. Results Phylogenetic analysis recovered three major lineages, with divergence dates coincident with late Miocene–early Pliocene arid cycles. One lineage was confined to geographically isolated populations in the Stirling Ranges (Stirling Ranges Lineage, SRL). The continuous range of M. nichollsi was split into two: the Main Range Lineage (MRL) and the Southern Coastal Lineage (SCL). The SCL displays a strong drainage‐based population structure, whereas the MRL displays a strong signature of recent expansion, suggesting that these two lineages have had very different biogeographical histories. Main conclusions Late Miocene–Pliocene aridity appears to have isolated populations in the Stirling Ranges and resulted in the formation of two additional lineages on a north–south gradient that are independent of southward‐flowing drainage systems. Our results demonstrate that climatic fluctuations are likely to have generated fine‐scale phylogeographic structure within M. nichollsi and that catchment regions are important refugia during arid cycles.     

Genetic signs of multiple colonization events in Baltic ciscoes with radiation into sympatric spring‐ and autumn‐spawners confined to early postglacial arrival

Presence of sympatric populations may reflect local diversification or secondary contact of already distinct forms. The Baltic cisco (Coregonus albula) normally spawns in late autumn, but in a few lakes in Northern Europe sympatric autumn and spring‐ or winter‐spawners have been described. So far, the evolutionary relationships and taxonomic status of these main life history forms have remained largely unclear. With microsatellites and mtDNA sequences, we analyzed extant and extinct spring‐ and autumn‐spawners from a total of 23 Swedish localities, including sympatric populations. Published sequences from Baltic ciscoes in Germany and Finland, and Coregonus sardinella from North America were also included together with novel mtDNA sequences from Siberian C. sardinella. A clear genetic structure within Sweden was found that included two population assemblages markedly differentiated at microsatellites and apparently fixed for mtDNA haplotypes from two distinct clades. All sympatric Swedish populations belonged to the same assemblage, suggesting parallel evolution of spring‐spawning rather than secondary contact. The pattern observed further suggests that postglacial immigration to Northern Europe occurred from at least two different refugia. Previous results showing that mtDNA in Baltic cisco is paraphyletic with respect to North American C. sardinella were confirmed. However, the inclusion of Siberian C. sardinella revealed a more complicated pattern, as these novel haplotypes were found within one of the two main C. albula clades and were clearly distinct from those in North American C. sardinella. The evolutionary history of Northern Hemisphere ciscoes thus seems to be more complex than previously recognized.     

Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera acutorostrata

How do populations of highly mobile species inhabiting open environments become reproductively isolated and evolve into new species? We test the hypothesis that elevated ocean‐surface temperatures can facilitate allopatry among pelagic populations and thus promote speciation. Oceanographic modelling has shown that increasing surface temperatures cause localization and reduction of upwelling, leading to fragmentation of feeding areas critical to pelagic species. We test our hypothesis by genetic analyses of populations of two closely related baleen whales, the Antarctic minke whale (Balaenoptera bonaerensis) and common minke whale (Balaenoptera acutorostrata) whose current distributions and migration patterns extent are largely determined by areas of consistent upwelling with high primary production. Phylogeographic and population genetic analyses of mitochondrial DNA control‐region nucleotide sequences collected from 467 whales sampled in four different ocean basins were employed to infer the evolutionary relationship among populations of B. acutorostrata by rooting an intraspecific phylogeny with a population of B. bonaerensis. Our findings suggest that the two species diverged in the Southern Hemisphere less than 5 million years ago (Ma). This estimate places the speciation event during a period of extended global warming in the Pliocene. We propose that elevated ocean temperatures in the period facilitated allopatric speciation by disrupting the continuous belt of upwelling maintained by the Antarctic Circumpolar Current. Our analyses revealed that the current populations of B. acutorostrata likely diverged after the Pliocene some 1.5 Ma when global temperatures had decreased and presumably coinciding with the re‐establishment of the polar–equatorial temperature gradient that ultimately drives upwelling. In most population samples, we detected genetic signatures of exponential population expansions, consistent with the notion of increasing carrying capacity after the Pliocene. Our hypothesis that prolonged periods of global warming facilitate speciation in pelagic marine species that depend on upwelling should be tested by comparative analyses in other pelagic species.     

Phylogeography of the Temminck’s Stint (Calidris temminckii): historical vicariance but little present genetic structure in a regionally endangered Palearctic wader

Aim We study the population differentiation and phylogeography of the Temminck’s Stint (Calidris temminckii). Specifically, we seek signs of past and present population size changes and dispersal events and evaluate management and conservation unit status of the populations. We also study the possibility of introgression as the origin of two mitochondrial DNA (mtDNA) lineages found and estimate the divergence time of the lineages. Location Northern Eurasia. Methods We analysed 583 bp of mtDNA control region domains I and II and 11 microsatellite loci from 13 localities throughout the breeding range. In addition, we used mitochondrial cytochrome c oxidase subunit I (COI), a barcoding gene, to search for signs of introgression. Results More population differentiation was found from microsatellites than from mtDNA, although differentiation was weak in both markers. Signs of past population growth were observed, in addition to more recent decline in some areas. Both control region and COI sequences revealed two maternal lineages coexisting in Fennoscandia and in north‐west Siberia. No signs of introgression were detected. Lineage divergence time was estimated to have occurred during the glacial periods of Pleistocene. Main conclusions Slight differences in mtDNA and microsatellite differentiation and diversity may reflect different features – such as the mutation rate and effective population size – of the markers used, or female‐biased dispersal pattern and high male site‐fidelity of the species. The coexistence of the two mitochondrial lineages is most likely a consequence of post‐glacial mixing of two refugial Pleistocene populations. Based on genetic information alone, global conservation concerns are not imminent. However, fast decline of a marginal Bothnian Bay population and the smallness and remoteness of a Central Yakutian population warrant conservation actions.     

Genetic isolation within the malaria mosquito Anopheles melas

Anopheles melas is a brackish water–breeding member of the Anopheles gambiae complex that is distributed along the coast of West Africa and is a major malaria vector within its range. Because little is known about the population structure of this species, we analysed 15 microsatellite markers and 1161 bp of mtDNA in 11 A. melas populations collected throughout its range. Compared with its sibling species A. gambiae, A. melas populations have a high level of genetic differentiation between them, representing its patchy distribution due to its fragmented larval habitat that is associated with mangroves and salt marsh grass. Populations clustered into three distinct groups representing Western Africa, Southern Africa and Bioko Island populations that appear to be mostly isolated. Fixed differences in the mtDNA are present between all three clusters, and a Bayesian clustering analysis of the microsatellite data found no evidence for migration from mainland to Bioko Island populations, and little migration was evident between the Southern to the Western cluster. Surprisingly, mtDNA divergence between the three A. melas clusters is on par with levels of divergence between other species of the A. gambiae complex, and no support for monophyly was observed in a maximum‐likelihood phylogenetic analysis. Finally, an approximate Bayesian analysis of microsatellite data indicates that Bioko Island A. melas populations were connected to the mainland populations in the past, but became isolated, presumably when sea levels rose after the last glaciation period (≥10 000–11 000 bp ). This study has exposed species‐level genetic divergence within A. melas and also has implications for control of this malaria vector.     

SEX-BIASED GENE FLOW IN SPECTACLED EIDERS (ANATIDAE): INFERENCES FROM MOLECULAR MARKERS WITH CONTRASTING MODES OF INHERITANCE

Abstract Genetic markers that differ in mode of inheritance and rate of evolution (a sex‐linked Z‐specific micro‐satellite locus, five biparentally inherited microsatellite loci, and maternally inherited mitochondrial [mtDNA] sequences) were used to evaluate the degree of spatial genetic structuring at macro‐ and microgeographic scales, among breeding regions and local nesting populations within each region, respectively, for a migratory sea duck species, the spectacled eider (Somateria fisheri). Disjunct and declining breeding populations coupled with sex‐specific differences in seasonal migratory patterns and life history provide a series of hypotheses regarding rates and directionality of gene flow among breeding populations from the Indigirka River Delta, Russia, and the North Slope and Yukon‐Kuskokwim Delta, Alaska. The degree of differentiation in mtDNA haplotype frequency among breeding regions and populations within regions was high (φ_CT= 0.189, P < 0.01; φ_SC= 0.059, P < 0.01, respectively). Eleven of 17 mtDNA haplotypes were restricted to a single breeding region. Genetic differences among regions were considerably lower for nuclear DNA loci (sex‐linked: φ_ST= 0.001, P > 0.05; biparentally inherited microsatellites: mean θ= 0.001, P > 0.05) than was observed for mtDNA. Using models explicitly designed for uniparental and biparentally inherited genes, estimates of spatial divergence based on nuclear and mtDNA data together with elements of the species' breeding ecology were used to estimate effective population size and degree of male and female gene flow. Differences in the magnitude and spatial patterns of gene correlations for maternally inherited and nuclear genes revealed that females exhibit greater natal philopatry than do males. Estimates of generational female and male rates of gene flow among breeding regions differed markedly (3.67 × 10^‐4 and 1.28 × 10^‐2, respectively). Effective population size for mtDNA was estimated to be at least three times lower than that for biparental genes (30,671 and 101,528, respectively). Large disparities in population sizes among breeding areas greatly reduces the proportion of total genetic variance captured by dispersal, which may accelerate rates of inbreeding (i.e., promote higher coancestries) within populations due to nonrandom pairing of males with females from the same breeding population.     

The hidden history of the snowshoe hare,Lepus americanus: extensive mitochondrial DNA introgression inferred from multilocus genetic variation

Hybridization drives the evolutionary trajectory of many species or local populations, and assessing the geographic extent and genetic impact of interspecific gene flow may provide invaluable clues to understand population divergence or the adaptive relevance of admixture. In North America, hares (Lepus spp.) are key species for ecosystem dynamics and their evolutionary history may have been affected by hybridization. Here we reconstructed the speciation history of the three most widespread hares in North America – the snowshoe hare (Lepus americanus), the white‐tailed jackrabbit (L. townsendii) and the black‐tailed jackrabbit (L. californicus) – by analysing sequence variation at eight nuclear markers and one mitochondrial DNA (mtDNA) locus (6240 bp; 94 specimens). A multilocus–multispecies coalescent‐based phylogeny suggests that L. americanus diverged ~2.7 Ma and that L. californicus and L. townsendii split more recently (~1.2 Ma). Within L. americanus, a deep history of cryptic divergence (~2.0 Ma) was inferred, which coincides with major speciation events in other North American species. While the isolation‐with‐migration model suggested that nuclear gene flow was generally rare or absent among species or major genetic groups, coalescent simulations of mtDNA divergence revealed historical mtDNA introgression from L. californicus into the Pacific Northwest populations of L. americanus. This finding marks a history of past reticulation between these species, which may have affected other parts of the genome and influence the adaptive potential of hares during climate change.     

Migration and isolation during the turbulent Ponto‐Caspian Pleistocene create high diversity in the crustacean Paramysis lacustris

The Ponto‐Caspian brackish‐water fauna inhabits estuaries and rivers of the Black, Azov and Caspian seas and is fragmented by higher salinity waters and a major interbasin watershed. The fauna is known for the high levels of endemism, complex zoogeographic histories, and as a recent source of successful invasive species. It remains debated whether the Black and Azov Sea brackish‐water populations survived unfavourable Pleistocene conditions in multiple separate refugia or whether the two seas were (repeatedly) recolonized from the Caspian. Using microsatellite and mtDNA markers, we demonstrate deep among‐ and within‐basin subdivisions in a widespread Ponto‐Caspian mysid crustacean Paramysis lacustris. Five genetic clusters were identified, but their relationships did not reflect the geography of the region. The Azov cluster was the most distinct (4–5% COI divergence), despite its geographic position in the corridor between Black and Caspian seas, and may represent a new species. In the northern Black Sea area, the Dnieper cluster was closer to the Caspian cluster than to the neighbouring Danube–Dniester–Bug populations, suggesting separate colonizations of the Black Sea. Overall, the data implied a predominant gene flow from the east to the Black Sea and highlight the importance of Caspian Sea transgressions in facilitating dispersal. Yet, the presence of distinct lineages in the Black Sea points to the persistence of isolated refugial populations that have gained diagnostic differences under presumably high mutation rates and large population sizes. The unfavourable Pleistocene periods in the Black Sea therefore appear to have promoted diversification of the brackish‐water lineages, rather than extirpated them.     

Impact of Pleistocene aridity oscillations on the population history of a widespread,vagile Australian mammal,Macropus fuliginosus

Aim Climatic fluctuations during the Pleistocene have shaped the population structure of many extant taxa. However, few studies have examined widespread species inhabiting the Australian continent, where periods of increased aridity characterized the Pleistocene. Here we investigate the phylogeography and population history of a widespread and vagile southern Australian marsupial, the western grey kangaroo (Macropus fuliginosus). Location Southern Australia. Methods We examined the variation of the mitochondrial DNA (mtDNA) control region from 511 individuals of M. fuliginosus sampled throughout their transcontinental distribution. Maximum likelihood and Bayesian analyses were used to investigate the phylogeography and coalescence analyses were then used to test hypothesized biogeographical scenarios. Results The combined results of the phylogeographical and coalescence analyses revealed a complex evolutionary history. Macropus fuliginosus originated in the south‐west of the continent, with north‐western and south‐western populations subsequently diverging as a result of vicariance events during the mid‐Pleistocene. Subsequent arid phases affected these populations differently. In the north‐west, the expansion and contraction of the arid zone resulted in repeated vicariance events and multiple divergent north‐western mtDNA subclades. In contrast, the south‐western population was less impacted by climatic oscillations but gave rise to a major transcontinental eastward expansion. Main conclusions Macropus fuliginosus exhibits the genetic signature of divergence due to unidentified barriers in south‐western Western Australia, while previously identified barriers across southern Australia appear to have had little impact despite evidence of a broad‐scale range expansion prior to the Last Glacial Maximum (LGM). This pattern of localized expansion and contraction is comparable to unglaciated regions in both the Northern and Southern Hemispheres. Furthermore, this study indicates that despite the potential similarities between Northern Hemisphere glaciation and the activation of dune systems in the Australian arid zone, both of which rendered large areas inhospitable, the biotic responses and resultant phylogeographical signatures are dissimilar. Whereas a limited number of major geographically concordant refugia are observed in glaciated areas, the Southern Hemisphere arid zone appears to be associated with multiple species‐specific idiosyncratic refugia.     

Phylogeography of Podocarpus matudae (Podocarpaceae): pre‐Quaternary relicts in northern Mesoamerican cloud forests

Aim Cloud forests of northern Mesoamerica represent the northern and southern limit of the contact zone between species otherwise characteristic of North or South America. Several phylogeographic studies featuring temperate conifer species have improved our understanding of species responses to environmental changes. In contrast, conifer species that presumably colonized northern Mesoamerica from South America are far less studied. A phylogeographic study of Podocarpus matudae (Podocarpaceae) was conducted to identify any major evolutionary divergences or disjunctions across its range and to determine if its current distribution is associated with pre‐Quaternary climatic and/or long‐distance dispersal events. Location Northern Mesoamerica (Mexico and Guatemala). Methods Sixteen populations (157 individuals) of P. matudae were screened for variation at two plastid DNA markers. The intra‐specific phylogenetic relationships among haplotypes were reconstructed using Bayesian inference. Population genetic analyses were undertaken to gain insight into the evolutionary history of these populations. To test whether genetic divergence among populations occurred at different time‐scales plastid DNA sequence data and fossil‐ and coalescent‐based calibrations were integrated. Results The combination of plastid markers yielded 11 haplotypes. Differentiation among populations based on DNA variation (G_ST) (0.707, SE 0.0807) indicated a clear population structure in P. matudae. Differentiation for ordered alleles (N_ST) (0.811, SE 0.0732) was higher than that for G_ST, indicating phylogeographical structure in P. matudae. Most of the total variation (81.3%, P < 0.0001) was explained by differences among populations. The estimated divergence time between the unique haplotypes from a Guatemalan population and the two most common haplotypes from the Sierra Madre Oriental in Mexico was between 10 and 20 Ma, and further haplotype divergence in the poorly resolved clade of the Sierra Madre Oriental occurred between 3 and 0.5 Ma. Main conclusions Divergence estimations support the hypothesis that extant Podocarpus matudae populations are pre‐Quaternary relicts. This finding is consistent with fossil and pollen data that support a Miocene age for temperate floristic elements in Mesoamerican cloud forests, whereas further haplotype divergence within the Sierra Madre Oriental, Chiapas and Guatemala occurred more recently, coinciding with Pleistocene cloud forest refugia.     

Population genomic evidence for multiple Pliocene refugia in a montane‐restricted harvestman (Arachnida,Opiliones, Sclerobunus robustus) from the southwestern United States

The integration of ecological niche modelling into phylogeographic analyses has allowed for the identification and testing of potential refugia under a hypothesis‐based framework, where the expected patterns of higher genetic diversity in refugial populations and evidence of range expansion of nonrefugial populations are corroborated with empirical data. In this study, we focus on a montane‐restricted cryophilic harvestman, Sclerobunus robustus, distributed throughout the heterogeneous Southern Rocky Mountains and Intermontane Plateau of southwestern North America. We identified hypothetical refugia using ecological niche models (ENMs) across three time periods, corroborated these refugia with population genetic methods using double‐digest RAD‐seq data and conducted population‐level phylogenetic and divergence dating analyses. ENMs identify two large temporally persistent regions in the mid‐latitude highlands. Genetic patterns support these two hypothesized refugia with higher genetic diversity within refugial populations and evidence for range expansion in populations found outside hypothesized refugia. Phylogenetic analyses identify five to six genetically divergent, geographically cohesive clades of S. robustus. Divergence dating analyses suggest that these separate refugia date to the Pliocene and that divergence between clades pre‐dates the late Pleistocene glacial cycles, while diversification within clades was likely driven by these cycles. Population genetic analyses reveal effects of both isolation by distance (IBD) and isolation by environment (IBE), with IBD more important in the continuous mountainous portion of the distribution, while IBE was stronger in the populations inhabiting the isolated sky islands of the south. Using model‐based coalescent approaches, we find support for postdivergence migration between clades from separate refugia.     

Genetic divergence of three freshwater isopod species from southern New Zealand

Aim We examined the biogeography of three freshwater isopod species (Austridotea annectens, A. lacustris, A. benhami), and tested the hypotheses that genetic differences would: (1) exist between geographic locations; and (2) correspond to known geological events (e.g. appearance of islands leading to the availability of habitat). Location Southern New Zealand, including South Island, Stewart Island, Campbell Island and Chatham Islands. Methods We examined specimens throughout the known species range from 12 populations of A. lacustris, five populations of A. annectens, and three populations of A. benhami, using mitochondrial DNA (cytochrome c oxidase I) sequence analyses. Results We resolved three main clades corresponding to the three species, with 16% sequence divergence between A. annectens and A. benhami, and 31% divergence between these species and A. lacustris. Divergence within A. benhami was < 2.0%. However, divergence within A. lacustris reached up to 10% with four main groupings: (1) Chatham Islands; (2) Campbell Island; (3) Fiordland; and (4) east coast South Island and Stewart Island. Divergence within A. annectens reached up to 4.4%, with two main groupings: (1) Chatham Islands and (2) east coast South Island and Stewart Island. Patterns of genetic divergence were most likely the result of geographical isolation among A. lacustris and A. annectens populations. In particular, the divergence of A. lacustris and A. annectens on Chatham Islands may correspond to the availability of this habitat c. 4 Ma, whereas the divergence of A. lacustris on the much older Campbell Island and in Fiordland may indicate either a rare founder event or a change in ocean circulation that resulted in their isolation from a once more widespread gene pool. Main conclusions The three New Zealand species of Austridotea are genetically distinct, with up to 31% divergence between species. Genetic variability was highest between populations of the two most widely distributed species, and divergence was greatest on islands distant from mainland New Zealand and in the discrete Fiordland region. The magnitude of genetic divergence of isopods on the Auckland and Chatham Islands is consistent with these populations having been founded in the Pliocene via oceanic dispersal from mainland New Zealand.     

Biogeographical patterns of genetic differentiation in dung beetles of the genus Trypocopris (Coleoptera, Geotrupidae) inferred from mtDNA and AFLP analyses

Aim To examine the phylogeography and population structure of three dung beetle species of the genus Trypocopris (Coleoptera, Geotrupidae). We wanted to test whether genetic differences and genealogies among populations were in accordance with morphologically described subspecies and we aimed to establish times of divergence among subspecies to depict the appropriate temporal framework of their phylogeographical differentiation. We also wished to investigate the historical demographic events and the relative influences of gene flow and drift on the distribution of genetic variability of the different populations. Location Europe (mostly Italy). Methods We collected adult males from dung pats from 15 Italian localities over the period 2000–2002. For sequence analysis, some dried specimens from Albania, Croatia, Slovakia and Spain were also used. We applied cytochrome oxidase I mitochondrial DNA sequencing and the amplified fragment length polymorphism (AFLP) technique to determine whether phylogeographical patterns within the three species support the proposed hypotheses of subspecies designations, and to detect further structure among populations that might mediate diversification. Results and main conclusions The results show a high concordance between the distribution of mtDNA variation and the main morphological groups recognized as subspecies, which thus may represent independent evolutionary units. The degree of mitochondrial divergence suggests that speciation events occurred during the Pliocene, while diversification of the main subspecific lineages took place in the Pleistocene, from c. 0.3 to 1.5 Ma. Mitochondrial and nuclear data also reveal that there is phylogeographical structuring among populations within each of the main groups and that both contemporary and historical processes determined this pattern of genetic structure. Geographical populations form monophyletic clades in both phylogenetic and network reconstructions. Despite the high levels of intrapopulational diversity, F_ST values indicate moderate but significant genetic differentiation among populations, and a Bayesian clustering analysis of the AFLP data clearly separates the geographical populations. Nucleotide and gene diversity estimates reveal interspecific differences in the degree of diversification among populations that may be related to the different ecological requirements of the three species.