Phylogeography of the pallid kangaroo mouse,Microdipodops pallidus: a sand‐obligate endemic of the Great Basin,western North America

Aim Kangaroo mice, genus Microdipodops Merriam, are endemic to the Great Basin and include two species: M. pallidus Merriam and M. megacephalus Merriam. The pallid kangaroo mouse, M. pallidus, is a sand‐obligate desert rodent. Our principal intent is to identify its current geographical distribution and to formulate a phylogeographical hypothesis for this taxon. In addition, we test for orientation patterns in haplotype sharing for evidence of past episodes of movement and gene flow. Location The Great Basin Desert region of western North America, especially the sandy habitats of the Lahontan Trough and those in south‐central Nevada. Methods Mitochondrial DNA sequence data from portions of three genes (16S ribosomal RNA, cytochrome b, and transfer RNA for glutamic acid) were obtained from 98 individuals of M. pallidus representing 27 general localities sampled throughout its geographical range. Molecular sequence data were analysed using neighbour‐joining, maximum‐parsimony, maximum‐likelihood and Bayesian methods of phylogenetic inference. Directional analysis of phylogeographical patterns, a novel method, was used to examine angular measurements of haplotype sharing between pairs of localities to detect and quantify historical events pertaining to movement patterns and gene flow. Results Collecting activities showed that M. pallidus is a rather rare rodent (mean trapping success was 2.88%), and its distribution has changed little from that determined three‐quarters of a century ago. Two principal phylogroups, distributed as eastern and western moieties, are evident from the phylogenetic analyses (mean sequence divergence for cytochrome b is c. 8%). The western clade shows little phylogenetic structure and seems to represent a large polytomy. In the eastern clade, however, three subgroups are recognized. Nine of the 42 unique composite haplotypes are present at two or more localities and are used for the orientation analyses. Axial data from haplotype sharing between pairwise localities show significant, non‐random angular patterns: a north‐west to south‐east orientation in the western clade, and a north‐east to south‐west directional pattern in the eastern clade. Main conclusions The geographical range of M. pallidus seems to be remarkably stable in historical times and does not show a northward (or elevationally upward) movement trend, as has been reported for some other kinds of organism in response to global climate change. The eastern and western clades are likely to represent morphologically cryptic species. Estimated times of divergence of the principal clades of M. pallidus (4.38 Ma) and between M. pallidus and M. megacephalus (8.1 Ma; data from a related study) indicate that kangaroo mice diverged much earlier than thought previously. The phylogeographical patterns described here may serve as a model for other sand‐obligate members of the Great Basin Desert biota.     

Populations at risk: conservation genetics of kangaroo mice (Microdipodops) of the Great Basin Desert

The Great Basin Desert of western North America has experienced frequent habitat alterations due to a complex biogeographic history and recent anthropogenic impacts, with the more recent alterations likely resulting in the decline of native fauna and flora. Dark (Microdipodops megacephalus) and pallid (M. pallidus) kangaroo mice are ecological specialists found within the Great Basin Desert and are potentially ideal organisms for assessing ecosystem health and inferring the biogeographic history of this vulnerable region. Herein, newly acquired nuclear‐encoded microsatellite loci were utilized to assess patterns of variation within and among spatially discrete groups of kangaroo mice and to evaluate gene flow, demographic trends, and genetic integrity. Results confirm that there are at least three genetically distinct units within M. megacephalus and two such units within M. pallidus. The three units of M. megacephalus appear to have different demographic histories, with effectively no gene flow among them since their divergence. Similarly, the two units of M. pallidus also appear to have experienced different demographic histories, with effectively no gene exchange. Contemporary effective population sizes of all groups within Microdipodops appear to be low (<500), suggesting that each genetic lineage may have difficulty coping with changing environmental pressures and hence may be at risk of extirpation. Results of this study indicate that each Microdipodops group should be recognized, and therefore managed, as a separate unit in an effort to conserve these highly specialized taxa that contribute to the diversity of the Great Basin Desert ecosystem.     

The distribution of divergent mitochondrial DNA lineages of threespine stickleback (Gasterosteus aculeatus) in the northeastern Pacific Basin: post-glacial dispersal and lake accessibility

Aim This study furthers the documentation of the geographical distribution of two divergent (c. 3%) mitochondrial DNA clades in the threespine stickleback (Gasterosteus aculeatus) and tests the hypotheses that the northeastern Pacific distribution has been influenced by post‐glacial colonization and lake elevation and that clade identity is associated with certain morphological attributes such as reduction in body armour. Location Lakes and nearshore marine environments of the eastern Pacific Basin from southcentral Alaska to southeastern British Columbia, (BC) Canada. Methods Restriction enzyme analysis of polymerase chain reaction‐amplified mitochondrial DNA fragments (cytochrome b) from a total of 45 new populations combined with existing data for a further 45 populations. Lake elevation data were collected for 78 localities and tested for an association with mtDNA clade by contingency table analyses. Morphological data were collected on sticklebacks from eight samples representing four lake‐stream systems and tested for differentiation among populations with different mtDNA clade identities using analyses of variance. Results We extend the known distribution of the haplotypes diagnostic of the Trans‐North Pacific Clade (TNPC) southward to mid‐Vancouver Island and, for the first time, on mainland BC, in other island populations far from putative refugia, and in nearby anadromous populations. A morphological analysis indicated that the mainland population with the TNPC was not characterized by reduced spine or lateral plate (‘armour’) traits that characterize some putative relict populations on the Queen Charlotte Islands. We found a significant association between lake elevation and the presence of the TNPC; the TNPC was present more often in lakes located at or lower than 42 m than in higher elevation lakes. Main conclusions Our data support the hypothesis that post‐glacial colonization by TNPC‐bearing marine sticklebacks and aspects of lake ‘accessibility’ were important in determining the distribution of mtDNA clades in the eastern Pacific Ocean basin. More generally, our study demonstrates how processes acting both across immense geographic scales (e.g. pan‐Pacific dispersal) and local scales (lake accessibility contingent on timing and extent of isostatic rebound) may interact to explain biogeographical patterns.     

Ecological niche modelling of montane mammals in the Great Basin, North America: examining past and present connectivity of species across basins and ranges

Aim The goal of this study was to determine the extent of suitable habitats across the basins and ranges of the Great Basin for 13 montane mammals in the present and during the Last Glacial Maximum (LGM). For all these mammal species, we test whether: (1) more suitable habitat was available in basin areas during the LGM; (2) suitable habitat shifted upwards in elevation between the LGM and the present; (3) more ranges have suitable habitat than are currently occupied; and (4) these species are currently restricted to suitable habitats at higher‐elevation range areas. We also examine whether and how much distributional response varies among these montane mammal species. Location The Great Basin of western North America. Methods We re‐examine the past and present distributions of 13 Great Basin montane mammals using ecological niche modelling techniques that utilize now widely available species occurrence data and new, fine‐scale past climatological GIS layers in the present and at the LGM. These methods provide an objective, repeatable means for visual comparison of past and present modelled distributions for species examined in previous biogeographical studies. Results Our results indicate greater areal and lower elevational suitable habitat in the LGM than at present for nearly all montane mammals, and that there is more suitable habitat at present than is currently occupied. Our results also show that lowland areas provide suitable dispersal routes between ranges for most of the montane mammals both at the LGM and at present. However, three of the 13 species have little to no predicted suitable habitat in the LGM near currently occupied ranges, in contrast to the pattern for the other 10. For these species, the model results support more recent long‐distance colonization. Main conclusions Our finding of suitable lowland dispersal routes in the present for most species supports and greatly extends similar findings from single‐species studies. Our results also provide a visually striking confirmation that changes in species distribution and colonization histories of Great Basin montane mammals vary in a fashion related to the tolerances and requirements of each of these species; this has previously been hypothesized but not rigorously tested for multiple montane mammals in the region.     

Phylogeography of the Rhabditis (Pellioditis) marina species complex: evidence for long-distance dispersal, and for range expansions and restricted gene flow in the northeast Atlantic

Pinpointing processes that structure the geographical distribution of genetic diversity of marine species and lead to speciation is challenging because of the lack of obvious dispersal barriers and the likelihood of substantial (passive) dispersal in oceans. In addition, cryptic radiations with sympatric distributions abound in marine species, challenging the allopatric speciation mechanism. Here, we present a phylogeographical study of the marine nematode species complex Rhabditis ( Pellioditis ) marina to investigate processes shaping genetic structure and speciation. Rhabditis ( P .) marina lives on decaying macroalgae in the intertidal, and may therefore disperse over considerable distances. Rhabditis ( P .) marina consists of several cryptic species sympatrically distributed at a local scale. Genetic variation in the COI gene was screened in 1362 specimens from 45 locations around the world. Two nuclear DNA genes (ITS and D2D3) were sequenced to infer phylogenetic species. We found evidence for ten sympatrically distributed cryptic species, seven of which show a strong genetic structuring. A historical signature showed evidence for restricted gene flow with occasional long-distance dispersal and range expansions pre-dating the last glacial maximum. Our data also point to a genetic break around the British Isles and a contact zone in the Southern Bight of the North Sea. We provide evidence for the transoceanic distribution of at least one cryptic species (PmIII) and discuss the dispersal capacity of marine nematodes. The allopatric distribution of some intraspecific phylogroups and of closely related cryptic species points to the potential for allopatric speciation in R. ( P .) marina .     

Molecular phylogeography of Troglophilus cave crickets (Orthoptera,Rhaphidophoridae): A combination of vicariance and dispersal drove diversification in the East Mediterranean region

In this study, we investigated the molecular phylogenetic divergence and historical biogeography of cave crickets belonging to the genus Troglophilus (Orthoptera, Rhaphidophoridae) from caves in eastern Mediterranean and Anatolia regions. Three mitochondrial DNA genes (COI, 12S rDNA, and 16S rDNA) and two nuclear ones (18S rDNA and 28S rDNA) were amplified and partially sequenced to reconstruct phylogenetic relationships among most of the known Troglophilus species. Results showed a well‐resolved phylogeny with three main clades representing the Balkan, the Anatolian, and the Cycladian–Cretan lineages. Based on Bayesian analyses, we applied a relaxed molecular clock model to estimate the divergence times between these three lineages. Dating estimates indicate that radiation of the ingroup might have been triggered by the opening of the Mid‐Aegean trench, while the uplift of the Anatolian Plateau in Turkey and the changes of relief, emergence, and disappearance of orographic and hydrographical barriers in the Balkan Peninsula are potential paleogeographic events responsible for the initial diversification of the genus Troglophilus. A possible biogeographic scenario, reconstructed using S‐DIVA with RASP software, suggested that the current distribution of Troglophilus species can be explained by a combination of both dispersal and vicariance events that occurred in particular in the ancestral populations. The radiation of Troglophilus species likely started from the Aegean and proceeded eastward to Anatolia and westward to the Balkan region. Results are additionally compared to those available for Dolichopoda, the only other representative genus of Rhaphidophoridae present in the Mediterranean area.