Tempo and mode of speciation in the Baja California disjunct fish species Anisotremus davidsonii

The Baja California region provides a natural setting for studying the early mechanisms of allopatric speciation in marine systems. Disjunct fish populations from several species that occur in the northern Gulf of California and northern Pacific coast of Baja California, but are absent from its southern shores, were previously shown to be genetically isolated, making them excellent candidates for studying allopatry. In addition, one of these species, the sargo Anisotremus davidsonii, has two pairs of congeneric Panamic trans-isthmian geminate species that allow for internal molecular clock calibration. Phylogeographic and demographic approaches based on mitochondrial (cytochrome b) and nuclear (S7 ribosomal protein) sequences showed that A. davidsonii entered the gulf from the south, and later colonized the Pacific coast, approximately 0.6-0.16 million years ago. Pacific coast colonization may have used a route either around the southern cape of Baja California or across the peninsula through a natural seaway. However, while several seaways have been described from different geological times, none matches the dates of population disjunction, yet much geological work remains to be done in that area. At the present time, there is no evidence for dispersal around the southern tip of the Baja California Peninsula. Signatures of incipient allopatric speciation were observed, such as the reciprocal monophyly of disjunct populations for the mitochondrial marker. However, other characteristics were lacking, such as a strong difference in divergence and coalescence times. Taken together, these results suggest that disjunct populations of A. davidsonii may be consistent with the earliest stages of allopatric speciation.     

Population genetic structure of annual and perennial populations of Zostera marina L. along the Pacific coast of Baja California and the Gulf of California

The Baja California peninsula represents a biogeographical boundary contributing to regional differentiation among populations of marine animals. We investigated the genetic characteristics of perennial and annual populations of the marine angiosperm, Zostera marina, along the Pacific coast of Baja California and in the Gulf of California, respectively. Populations of Z. marina from five coastal lagoons along the Pacific coast and four sites in the Gulf of California were studied using nine microsatellite loci. Analyses of variance revealed significant interregional differentiation, but no subregional differentiation. Significant spatial differentiation, assessed using θ_ST values, was observed among all populations within the two regions. Z. marina populations along the Pacific coast are separated by more than 220 km and had the greatest θ_ST (0.13–0.28) values, suggesting restricted gene flow. In contrast, lower but still significant genetic differentiation was observed among populations within the Gulf of California (θ_ST = 0.04–0.18), even though populations are separated by more than 250 km. This suggests higher levels of gene flow among Gulf of California populations relative to Pacific coast populations. Direction of gene flow was predominantly southward among Pacific coast populations, whereas no dominant polarity in the Gulf of California populations was observed. The test for isolation by distance (IBD) showed a significant correlation between genetic and geographical distances in Gulf of California populations, but not in Pacific coast populations, perhaps because of shifts in currents during El Niño Southern Oscillation (ENSO) events along the Pacific coast.     

Phylogenetic structure among pocket gopher populations,genus Thomomys (Rodentia: Geomyidae), on the Baja California Peninsula

We determined the phylogenetic relationships, population history, and hierarchical structure of genetic variation in pocket gophers distributed on the Baja California Peninsula (BCP), based on extensive geographic sampling. Using a fragment of the mitochondrial gene cytochrome b (cyt b), we found three latitudinal structured geographic clades (northern, central, and southern). The northern clade occurs in the border area of the USA and the north of BCP, the central clade occurs from the peninsular highlands through the Central Desert of Baja California, and the southern clade is distributed south of the San Ignacio Lagoon. AMOVA showed that genetic variation is higher among clades (64%) than within populations (18.1%). The deepest divergence among clades is very shallow (～300 000 years), which suggests that climatic changes during the Pleistocene or some inhospitable habitats have affected the structure of this group, rather than influences from older marine transgressions. Phylogenetic groups disclosed by our results do not coincide with the current infraspecific classification; therefore, we propose a change of epithet for BCP gophers (Thomomys nigricans) and a new subspecific taxonomic arrangement with four subspecies: Thomomys nigricans anitae, Thomomys nigricans martirensis, Thomomys nigricans nigricans, and Thomomys nigricans russeolus. © 2013 The Linnean Society of London     

Effects of Pleistocene climatic fluctuations on the phylogeographic and demographic histories of Pacific herring (Clupea pallasii)

We gathered mitochondrial DNA sequences (557 bp from the control region in 935 specimens and 668 bp of the cytochrome b gene in 139 specimens) of Pacific herring collected from 20 nearshore localities spanning the species' extensive range along the North Pacific coastlines of Asia and North America. Haplotype diversity and nucleotide diversity were high, and three major phylogeographic lineages (sequence divergences ca. 1.5%) were detected. Using a variety of phylogenetic methods, coalescent reasoning, and molecular dating interpreted in conjunction with paleoclimatic and physiographic evidence, we infer that the genetic make-up of extant populations of C. pallasii was shaped by Pleistocene environmental impacts on the historical demography of this species. A deep genealogical split that cleanly distinguishes populations in the western vs. eastern North Pacific probably originated as a vicariant separation associated with a glacial cycle that drove the species southward and isolated two ancestral populations in Asia and North America. Another deep genealogical split may have involved either a vicariant isolation of a third herring lineage (perhaps originally in the Gulf of California) or it may have resulted simply from the long coalescent times that are possible in large populations. Coalescent analyses showed that all the three evolutionary lineages of C. pallasii experienced major expansions in their most recent histories after having remained more stable in the preceding periods. Independent of the molecular calibration chosen, populations of C. pallasii appear to have remained stable or grown throughout the periods that covered at least two major glaciations, and probably more.     

Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island South‐East Asian Sus species during the Plio‐Pleistocene climatic fluctuations

In many temperate regions, ice ages promoted range contractions into refugia resulting in divergence (and potentially speciation), while warmer periods led to range expansions and hybridization. However, the impact these climatic oscillations had in many parts of the tropics remains elusive. Here, we investigate this issue using genome sequences of three pig (Sus) species, two of which are found on islands of the Sunda‐shelf shallow seas in Island South‐East Asia (ISEA). A previous study revealed signatures of interspecific admixture between these Sus species (Genome biology, 14 , 2013, R107). However, the timing, directionality and extent of this admixture remain unknown. Here, we use a likelihood‐based model comparison to more finely resolve this admixture history and test whether it was mediated by humans or occurred naturally. Our analyses suggest that interspecific admixture between Sunda‐shelf species was most likely asymmetric and occurred long before the arrival of humans in the region. More precisely, we show that these species diverged during the late Pliocene but around 23% of their genomes have been affected by admixture during the later Pleistocene climatic transition. In addition, we show that our method provides a significant improvement over D‐statistics which are uninformative about the direction of admixture.     

Biogeography and endemism of ants (Hymenoptera: Formicidae) in Baja California, Mexico: afirst overview

Abstract Aims Ants (Hymenoptera: Formicidae) of the Baja California peninsula are poorly known, with information based largely on scattered museum and literature records. We provide the first comprehensive account of ant species occurring on the peninsula, we examine distribution patterns, and we assess the ‘peninsular effect’ which predicts that species richness declines from the base to the tip of a peninsula. Location Peninsula of Baja California, Mexico. Methods Data collection involved examining, identifying and recording label data from c. 2350 series of ants. These records provide a provisional, if incomplete, species list. We applied the incidence‐based estimator, Chao‐2, to our data base of specimen records to estimate the total number of ant species on the peninsula. We assessed endemism by comparing our peninsular species list to those from adjacent states. The peninsular effect was tested by comparing genus and species level richness between the two states of Baja California, and across five latitudinal blocks. Results We document 170 native ant species in thirty‐three genera, plus six non‐native species, in Baja California. It seems likely that additional species remain to be discovered: the Chao‐2 estimator of species richness, at 206.0 species, is about 20% higher than our observed species richness. About 30% of the species and 20% of the genera are restricted within Baja California to the relatively mesic California Floristic Province of north‐western Baja California. Nearly all of these species also occur in California. Forty‐seven species (27.6%) are peninsula endemics. Using our entire data set, the peninsular effect appears to be strong, with about twice as many species in the northern state of Baja California than are recorded from the southern state of Baja California Sur; the ratio of genera is 33 to 24. However, this effect becomes weak at the species level and absent at the genus level when minimizing habitat effects by omitting species restricted to the California Floristic Province. At a finer scale, across latitudinal blocks of about 1.9°, the number of species declines towards central portions of the peninsula and then increases in the Cape Region. Nine ant species display strongly disjunct distributions, and these occur in two general patterns: peninsula disjuncts and peninsula–mainland disjuncts. Main conclusions The Baja California peninsula supports a diverse and distinctive ant fauna, with the proportion of endemic species similar to that displayed by plants. Patterns of species and genus richness across the five latitudinal blocks provide poor support for the peninsular effect. Moreover, habitat diversity, especially that related to topographic relief, appears to be the most important factor affecting the gradient of ant species richness in Baja California. Additional collections are needed to develop a more complete species list and to determine the boundaries and status of many species. Nevertheless, the present data base provides a useful starting point for understanding the evolution of ant assemblages in Baja California and for comparison with peninsular patterns in other taxa.     

Refugial isolation and secondary contact in the dyeing poison frog Dendrobates tinctorius

Recent palaeoclimactic research suggests that fluctuating environmental conditions throughout the Pleistocene of Amazonia occurred with previously unrecognized frequency. This has resulted in a theoretical shift from glacially influenced fluctuations to those driven by precessional rhythms. This theoretical revolution has a profound impact on expectations of biotic diversity within biogeographical regions that have long been based on the idea of large-scale landscape fragmentation associated with increased aridity and glacial cycles. Generally speaking, this shifts phylogeographical expectations from that of (i) large areas of sympatry of closely related (but not sister) species whose origins lie in separate refugia, and current distributions are the results of cyclic connectivity of those two refugia (refuge hypothesis), to that of (ii) fine scale genetic structure, often associated with elevation, and divergence well below expected speciation levels [disturbance-vicariance (DV) hypothesis]. To date there have been few tests of the expectations of the DV hypothesis based on empirical studies of Neotropical floral and faunal communities. Herein we examine phylogeographical structure of Dendrobates tinctorius, an amphibian species endemic to the uplands of the eastern Guiana Shield, based on sampling of 114 individuals from 24 localities. Phylogenetic, nested clade, and dispersal-vicariance (DIVA) analyses of cytochrome b sequence data reveal the presence of two mitochondrial lineages that are associated with previously identified western and eastern uplands of this area. The geographical distribution of mitochondrial haplotypes and the results of DIVA and coalescent analyses suggest that there has been extensive secondary contact between these lineages indicating a complex history of connectivity between these western and eastern highlands, supporting the predictions of the DV hypothesis.     

Pleistocene climatic cycling drives intra‐specific diversification in the intermediate horseshoe bat (Rhinolophus affinis) in Southern China

The repeated formation and loss of land‐bridges during the Pleistocene have had lasting impacts on population genetic structure. In the tropics, where island populations persisted through multiple glacial cycles, alternating periods of isolation and contact are expected to have driven population and taxonomic divergence. Here, we combine mitochondrial and nuclear sequence data with microsatellites to dissect the impact of Pleistocene climate change on intra‐specific diversification in the horseshoe bat Rhinolophus affinis. This taxon shows considerable morphological and acoustic variation: two parapatric subspecies (himalayanus and macrurus) occur on mainland China and a third (hainanus) on Hainan Island. Our phylogeographic reconstruction and coalescent analyses suggest the island subspecies formed from an ancestral population of himalayanus via two colonization events c. 800 000 years before present. R. a. hainanus then recolonized the mainland, forming macrurus and thus a secondary contact zone with himalayanus. Finally, macrurus recolonized Hainan following the LGM. We found that all three biological events corresponded to known periods of land‐bridge formation. Evidence of introgression was detected between macrurus and both its sister taxa, with geographical proximity rather than length of separation appearing to be the biggest determinant of subsequent genetic exchange. Our study highlights the important role of climate‐mediated sea level changes have had in shaping current processes and patterns of population structure and taxonomic diversification.     

Novel patterns of historical isolation, dispersal, and secondary contact across Baja California in the Rosy Boa (Lichanura trivirgata)

Mitochondrial DNA (mtDNA) sequence variation was examined in 131 individuals of the Rosy Boa (Lichanura trivirgata) from across the species range in southwestern North America. Bayesian inference and nested clade phylogeographic analyses (NCPA) were used to estimate relationships and infer evolutionary processes. These patterns were evaluated as they relate to previously hypothesized vicariant events and new insights are provided into the biogeographic and evolutionary processes important in Baja California and surrounding North American deserts. Three major lineages (Lineages A, B, and C) are revealed with very little overlap. Lineage A and B are predominately separated along the Colorado River and are found primarily within California and Arizona (respectively), while Lineage C consists of disjunct groups distributed along the Baja California peninsula as well as south-central Arizona, southward along the coastal regions of Sonora, Mexico. Estimated divergence time points (using a Bayesian relaxed molecular clock) and geographic congruence with postulated vicariant events suggest early extensions of the Gulf of California and subsequent development of the Colorado River during the Late Miocene-Pliocene led to the formation of these mtDNA lineages. Our results also suggest that vicariance hypotheses alone do not fully explain patterns of genetic variation. Therefore, we highlight the importance of dispersal to explain these patterns and current distribution of populations. We also compare the mtDNA lineages with those based on morphological variation and evaluate their implications for taxonomy.     

Genomic patterns in the widespread Eurasian lynx shaped by Late Quaternary climatic fluctuations and anthropogenic impacts

Disentangling the contribution of long‐term evolutionary processes and recent anthropogenic impacts to current genetic patterns of wildlife species is key to assessing genetic risks and designing conservation strategies. Here, we used 80 whole nuclear genomes and 96 mitogenomes from populations of the Eurasian lynx covering a range of conservation statuses, climatic zones and subspecies across Eurasia to infer the demographic history, reconstruct genetic patterns, and discuss the influence of long‐term isolation and/or more recent human‐driven changes. Our results show that Eurasian lynx populations shared a common history until 100,000 years ago, when Asian and European populations started to diverge and both entered a period of continuous and widespread decline, with western populations, except Kirov, maintaining lower effective sizes than eastern populations. Population declines and increased isolation in more recent times probably drove the genetic differentiation between geographically and ecologically close westernmost European populations. By contrast, and despite the wide range of habitats covered, populations are quite homogeneous genetically across the Asian range, showing a pattern of isolation by distance and providing little genetic support for the several proposed subspecies. Mitogenomic and nuclear divergences and population declines starting during the Late Pleistocene can be mostly attributed to climatic fluctuations and early human influence, but the widespread and sustained decline since the Holocene is more probably the consequence of anthropogenic impacts which intensified in recent centuries, especially in western Europe. Genetic erosion in isolated European populations and lack of evidence for long‐term isolation argue for the restoration of lost population connectivity.     

Genomic diversity,population structure,and migration following rapid range expansion in the Balsam Poplar,Populus balsamifera

Rapid range expansions can cause pervasive changes in the genetic diversity and structure of populations. The postglacial history of the Balsam Poplar, Populus balsamifera, involved the colonization of most of northern North America, an area largely covered by continental ice sheets during the last glacial maximum. To characterize how this expansion shaped genomic diversity within and among populations, we developed 412 SNP markers that we assayed for a range‐wide sample of 474 individuals sampled from 34 populations. We complemented the SNP data set with DNA sequence data from 11 nuclear loci from 94 individuals, and used coalescent analyses to estimate historical population size, demographic growth, and patterns of migration. Bayesian clustering identified three geographically separated demes found in the Northern, Central, and Eastern portions of the species’ range. These demes varied significantly in nucleotide diversity, the abundance of private polymorphisms, and population substructure. Most measures supported the Central deme as descended from the primary refuge of diversity. Both SNPs and sequence data suggested recent population growth, and coalescent analyses of historical migration suggested a massive expansion from the Centre to the North and East. Collectively, these data demonstrate the strong influence that range expansions exert on genomic diversity, both within local populations and across the range. Our results suggest that an in‐depth knowledge of nucleotide diversity following expansion requires sampling within multiple populations, and highlight the utility of combining insights from different data types in population genomic studies.     

Biogeographic barriers,Pleistocene refugia,and climatic gradients in the southeastern Nearctic drive diversification in cornsnakes (Pantherophis guttatus complex)

The southeastern Nearctic is a biodiversity hotspot that is also rich in cryptic species. Numerous hypotheses (e.g., vicariance, local adaptation, and Pleistocene speciation in glacial refugia) have been tested in an attempt to explain diversification and the observed pattern of extant biodiversity. However, previous phylogeographic studies have both supported and refuted these hypotheses. Therefore, while data support one or more of these diversification hypotheses, it is likely that taxa are forming within this region in species‐specific ways. Here, we generate a genomic data set for the cornsnakes (Pantherophis guttatus complex), which are widespread across this region, spanning both biogeographic barriers and climatic gradients. We use phylogeographic model selection combined with hindcast ecological niche models to determine regions of habitat stability through time. This combined approach suggests that numerous drivers of population differentiation explain the current diversity of this group of snakes. The Mississippi River caused initial speciation in this species complex, with more recent divergence events linked to adaptations to ecological heterogeneity and allopatric Pleistocene refugia. Lastly, we discuss the taxonomy of this group and suggest there may be additional cryptic species in need of formal recognition.     

Geological barriers and restricted gene flow in the holarctic skipper Hesperia comma (Hesperiidae)

Patterns of genetic variation within a species may be a consequence of historical factors, such as past fragmentation, as well as current barriers to gene flow. Using sequence data from the mitochondrial cytochrome oxidase subunit II region (COII) and the nuclear gene wingless, we conducted a phylogeographical study of the holarctic skipper Hesperia comma to elucidate patterns of genetic diversity and to infer historical and contemporary processes maintaining genetic variation. One hundred and fifty-one individuals were sampled from throughout North America and Eurasia, focusing on California and adjacent regions in the western United States where morphological diversity is highest compared to the rest of the range. Analyses of sequence data obtained from both genes revealed a well-supported division between the Old and New World. Within western North America, wingless shows little geographical structure, while a hierarchical analysis of genetic diversity of COII sequences indicates three major clades: a western clade in Oregon and Northern California, an eastern clade including the Great Basin, Rocky Mountains and British Columbia, and a third clade in southern California. The Sierra Nevada and the Transverse Ranges appear to be the major barriers to gene flow for H. comma in the western United States. Relatively reduced haplotype diversity in Eurasia compared to North America suggests that populations on the two continents have been affected by different historical processes.     

Multilocus genealogies reveal multiple cryptic species and biogeographical complexity in the California turret spider Antrodiaetus riversi (Mygalomorphae, Antrodiaetidae)

Antrodiaetus riversi (Araneae, Antrodiaetidae) is a dispersal-limited, habitat specialized mygalomorph spider species endemic to mesic woodlands of northern and central California. This species occupies a disjunct distribution, with populations in the Sierra Nevada and Coast Ranges, separated by the inhospitable Central Valley. Previous studies of morphological and allozyme variation have suggested that these populations may constitute cryptic species. We investigated the phylogeography of A. riversi using both nuclear and mitochondrial DNA sequences, collected for a comprehensive population sample. These data reveal the presence of at least five species in the A. riversi complex - these species are deeply diverged, and genealogically exclusive in both nuclear and mitochondrial genomes. Each of these species is characterized by extreme population subdivision and deep phylogeographical structuring, consistent with minimal gene flow across the dissected Californian landscape. Three species are restricted to the Coast Ranges, one to high altitudes of the central Sierran Nevada, and one species is found in both ranges. These species have allopatric distributions, although species parapatry is hypothesized to occur in several areas. Species diversification appears to have pulsed in the Late Miocene/Early Pliocene, a timing consistent with biogeographical reconstructions for many Californian taxa, and a time of turbulent geological activity in the region.     

Evolution of rattlesnakes (Viperidae; Crotalus) in the warm deserts of western North America shaped by Neogene vicariance and Quaternary climate change

During Pleistocene, the Laurentide ice sheet rearranged and diversified biotic distributions in eastern North America, yet had minimal physical impact in western North America where lineage diversification is instead hypothesized to result from climatic changes. If Pleistocene climatic fluctuations impacted desert species, the latter would reflect patterns of restricted gene flow concomitant with indications of demographic bottlenecks. Accordingly, molecular evidence for refugia should be present within these distributions and for subsequent range expansions as conditions improved. We sought answers to these questions by evaluating mitochondrial DNA (mtDNA) sequences from four species of rattlesnakes [Crotalus mitchellii (speckled rattlesnake), Crotalus cerastes (sidewinder), Crotalus tigris (tiger rattlesnake), Crotalus ruber (red diamond rattlesnake)] with distributions restricted to desert regions of southwestern North America. We inferred relationships using parsimony and maximum likelihood, tested intraspecific clades for population expansions, applied an isolation-with-migration model to determine bi-directional migration rates (m) among regions, and inferred divergence times for species and clades by applying a semiparametric penalized likelihood approach to our molecular data. Evidence for significant range expansion was present in two of eight regions in two species (Crotalus mitchellii pyrrhus, C. tigris region north). Two species (C. cerastes, C. mitchellii) showed a distribution concomitant with northward displacement of Baja California from mainland México, followed by vicariant separation into subclades. Effects of Pleistocene climate fluctuations were found in the distributions of all four species. Three regional diversification patterns were identified: (i) shallow genetic diversity that resulted from Pleistocene climatic events (C. tigris, C. ruber); (ii) deep Pleistocene divisions indicating allopatric segregation of subclades within refugia (C. mitchellii, C. cerastes); and (iii) lineage diversifications that extended to Pliocene or Late Miocene (C. mitchellii, C. cerastes). Clade-diversifying and clade-constraining effects impacted the four species of rattlesnakes unequally. We found relatively high levels of molecular diversification in the two most broadly distributed species (C. mitchellii, C. cerastes), and lower levels of genetic diversification in the two species (C. tigris, C. ruber) whose ranges are relatively more restricted. Furthermore, in several cases, the distributions of subspecies were not congruent with our molecular information. We suggest regional conservation perspectives for southwestern deserts cannot rely upon subspecies as biodiversity surrogates, but must instead employ a molecular and deep historical perspective as a primary mechanism to frame biodiversity reserves within this region.     

Phylogeography of the Alpine salamander, Salamandra atra (Salamandridae) and the influence of the Pleistocene climatic oscillations on population divergence

Fifty individuals of the endemic Alpine salamander, Salamandra atra, representing 13 populations throughout the range of the two currently recognized subspecies, atra and aurorae, were examined for sequence variation in a large portion (1050 bp) of the mitochondrial cytochrome b gene. We revealed a large number of mitochondrial DNA (mtDNA) haplotypes (10). Interpopulation sequence divergence was very low, ranging from 0 to 3.1%. The relationships among haplotypes were poorly resolved. The divergence time estimate between several mtDNA haplotypes suggested a pre-Pleistocene differentiation approximately 3 million years ago. Moreover, the impact of the Pleistocene glaciations on the phylogeographical patterns appears to have been secondary, although a somewhat reduced genetic variability was found in populations living in areas that were directly affected by the glaciation.     

Geological events play a larger role than Pleistocene climatic fluctuations in driving the genetic structure of Quasipaa boulengeri (Anura: Dicroglossidae)

Paleoclimatic and paleogeological events have been identified as being the two main drivers of genetic structuring in extant organisms. We used a montane stream‐dwelling frog, Quasipaa boulengeri, to explore the relative roles played by these drivers on species in southern China, a region needing thorough studies. We detected four major matrilines, and no broadly distributed haplotypes occurred. The complex orogenesis of south‐western China drove matrilineal divergence in Q. boulengeri into highly structured geographical units. These matrilines subsequently persisted in situ with stable populations rather than undergoing expansions during glacial cycling. The unification of the upper and middle Yangtze River in the Three Gorges mountain region mediated downstream colonization of this frog. Analyses identified geological events as playing a larger role than climatic fluctuations in driving the population history of Q. boulengeri. Nuclear allele analyses indicated gene flow; this maintained genetic cohesion of the species. South‐eastern Sichuan Basin was identified as the area of secondary contact for several matrilines, and this area deserves further study and special protection.     

Limited phylogeographical structure across Eurasia in two red wood ant species Formica pratensis and F. lugubris (Hymenoptera, Formicidae)

The phylogeography and demographic history of two closely related species of the red wood ant (Formica pratensis and F. lugubris) were examined across Eurasia. The phylogeny based on a 1.5-kilobase mitochondrial DNA fragment, including the cytochrome b gene and part of the ND6 gene, showed one phylogeographical division in F. pratensis. This division (0.7% of nucleotide divergence) suggests postglacial colonization of western Europe and of a wide area ranging from Sweden on the west to Lake Baikal on the east from separate forest refugia. In two localities, mitochondrial DNA has been transferred from F. lugubris to F. pratensis and all the individuals of F. pratensis sampled from the Pyrenees had haplotypes clustering in the lugubris clade. No phylogeographical divisions were detected in F. lugubris. Comparison of species-wide phylogeography between the two sympatrically distributed species of ant demonstrates a difference in phylogeographical structure that implies different vicariant histories. However, over most of the species' distribution ranges, similar signs of demographic expansion predating the last glaciation and the lack of phylogeographical structure were found in both the eastern phylogroup of F. pratensis and F. lugubris. This finding is highly consistent with the results reported for all other boreal forest animal species studied to date in Eurasia. Contraction of the distribution range of each species to a single refugial area at different times during the late Pleistocene and a subsequent population expansion seem to be an explanation for the lack of phylogeographical structure across most of Eurasia in species that are ecologically associated with the boreal forest.     

Testing the ‘Pleistocene species pump’ in alpine habitats: lineage diversification of flightless ground beetles (Coleoptera: Carabidae: Nebria) in relation to altitudinal zonation

Alpine species often have similar demographic responses to Pleistocene climate changes, but exhibit different spatial patterns of genetic diversity. Using a comparative phylogeographical approach, we examined the factors influencing lineage formation in three alpine carabid beetles of the genus Nebria Latreille inhabiting the California Sierra Nevada. These flightless beetles differ in altitudinal zonation and habitat preferences, but overlap spatially, have limited dispersal capacities and share life history characteristics. Species distribution modelling predicted decreasing population connectivity in relation to increasing altitudinal preferences. Diversity patterns at the cytochrome oxidase subunit I gene revealed north–south genetic structure and recent population growth in all three species. The high‐elevation‐restricted species, Nebria ingens Horn, exhibited a deep phylogeographical split, morphological divergence and evidence of limited, unidirectional gene flow towards the south. This was supported by additional data from three nuclear genes and isolation with migration analysis. Nebria spatulata Van Dyke, inhabiting an intermediate altitudinal range, exhibited fixed morphological differences between northern and southern populations, but showed limited structure. The broadly distributed Nebria ovipennis LeConte showed less structure and lacked morphological variation. Diversification of these Nebria species supports the role of altitudinal zonation in lineage formation and is consistent with the Pleistocene species pump model. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Recency, range expansion, and unsorted lineages: implications for interpreting neutral genetic variation in the sharp-tailed grouse (Tympanuchus phasianellus)

Both current and historical patterns of variation are relevant to understanding and managing ecological diversity. Recently derived species present a challenge to the reconstruction of historical patterns because neutral molecular data for these taxa are more likely to exhibit effects of recent and ongoing demographic processes. We studied geographical patterns of neutral molecular variation in a species thought to be of relatively recent origin, Tympanuchus phasianellus (sharp-tailed grouse), using mitochondrial control region sequences (CR-I), amplified fragment length polymorphisms (AFLP), and microsatellites. For historical context, we also analysed CR-I in all species of Tympanuchus. Within T. phasianellus, we found evidence for restricted gene flow between eastern and western portions of the species range, generally corresponding with the range boundary of T. p. columbianus and T. p. jamesi. The mismatch distribution and molecular clock estimates from the CR-I data suggested that all Tympanuchus underwent a range expansion prior to sorting of mitotypes among the species, and that sorting may have been delayed as a result of mutation-drift disequilibrium. This study illustrates the challenge of using genetic data to detect historical divergence in groups that are of relatively recent origin, or that have a history dominated by nonequilibrium conditions. We suggest that in such cases, morphological, ecological, and behavioural data may be particularly important adjuncts to molecular data for the recognition of historically or adaptively divergent groups.