Pleistocene glaciation is implicated in the phylogeographical structure of Potamopyrgus antipodarum, a New Zealand snail

Pleistocene glaciation has been identified as an important factor shaping present-day patterns of phylogeographical structure in a diverse array of taxa. The purpose of this study was to use mitochondrial sequence data to address whether Pleistocene glaciation is also a major determinant of phylogeographical patterns in Potamopyrgus antipodarum, a freshwater snail native to New Zealand. We found that haplotypes were separated by no more than 3.7% sequence divergence, and major genetic divisions tended to occur on a north-south axis. These data fit the predictions of the hypothesis that isolation of P. antipodarum in glacial refugia at the northern and southern tip of the South Island of New Zealand during the Pleistocene glaciation underlies the present-day phylogeographical structure. Because sexual P. antipodarum occasionally produce asexual offspring, we also used these data to show that the appearance of asexuality is not phylogeographically constrained. This means that the maintenance of sex in P. antipodarum cannot be wholly due to limited contact between sexual and asexual lineages and must instead be linked to a selective advantage of sexual reproduction.     

Phylogeography of the barbel (Barbus barbus) assessed by mitochondrial DNA variation

Using the phylogeographic framework, we assessed the DNA sequence variation at the mitochondrial cytochrome b gene across the distribution range of the barbel Barbus barbus, a widely distributed European cyprinid. Reciprocal monophyly of non-Mediterranean European and Balkan/Anatolian populations is taken as evidence for a long-term barrier to gene flow, and interpreted as a consequence of survival of the species in two separate refugia during several later glacial cycles. Lack of profound genealogical divergence across Europe from western France to the northwestern Black Sea basin is consistent with recent colonization of this area from a single glacial refuge, which was probably located in the Danube River basin. This may have occurred in two steps: into the Western European river basins during the last interglacial, and throughout the Central European river basins after the last glacial. The populations from the Balkans and Anatolia apparently did not contribute mitochondrial DNA to the post-Pleistocene colonization of non-Mediterranean Europe. Lack of detectable variation within the Balkans/Anatolia is attributed mainly to recent expansion throughout these regions, facilitated by the freshwater conditions and seashore regression in the Black Sea during the Late Pleistocene and Early Holocene.     

Ploidy race distributions since the Last Glacial Maximum in the North American desert shrub, Larrea tridentata

• 1 A classic biogeographic pattern is the alignment of diploid, tetraploid and hexaploid races of creosote bush (Larrea tridentata) across the Chihuahuan, Sonoran and Mohave Deserts of western North America. We used statistically robust differences in guard cell size of modern plants and fossil leaves from packrat middens to map current and past distributions of these ploidy races since the Last Glacial Maximum (LGM).
• 2 Glacial/early Holocene (26–10 ¹⁴C kyr bp or thousands of radiocarbon years before present) populations included diploids along the lower Rio Grande of west Texas, 650 km removed from sympatric diploids and tetraploids in the lower Colorado River Basin of south‐eastern California/south‐western Arizona. Diploids migrated slowly from lower Rio Grande refugia with expansion into the northern Chihuahuan Desert sites forestalled until after ~4.0 ¹⁴C kyr bp . Tetraploids expanded from the lower Colorado River Basin into the northern limits of the Sonoran Desert in central Arizona by 6.4 ¹⁴C kyr bp . Hexaploids appeared by 8.5 ¹⁴C kyr bp in the lower Colorado River Basin, reaching their northernmost limits (~37°N) in the Mohave Desert between 5.6 and 3.9 ¹⁴C kyr bp .
• 3 Modern diploid isolates may have resulted from both vicariant and dispersal events. In central Baja California and the lower Colorado River Basin, modern diploids probably originated from relict populations near glacial refugia. Founder events in the middle and late Holocene established diploid outposts on isolated limestone outcrops in areas of central and southern Arizona dominated by tetraploid populations.
• 4 Geographic alignment of the three ploidy races along the modern gradient of increasingly drier and hotter summers is clearly a postglacial phenomenon, but evolution of both higher ploidy races must have happened before the Holocene. The exact timing and mechanism of polyploidy evolution in creosote bush remains a matter of conjecture.

     

Late glacial history of the cold-adapted freshwater fish Cottus gobio,revealed by microsatellites

The distribution of genetic diversity at 10 highly polymorphic microsatellite loci within the European freshwater fish, Cottus gobio, L. was examined. The sampling range comprised a large geographical scale including lineages known to be highly divergent at both mitochondrial DNA (mtDNA) and allozymes. An analysis of genetic variability within populations showed that expected heterozygosity and allelic richness could be explained largely by current effective population sizes. Evidence was found, however, that historical processes predating the last major glaciation affected allelic richness. In addition to confirming the large-scale patterns from earlier studies, the microsatellite data revealed new insights into recent processes by analysing genetic structure within ancient lineages defined by mtDNA data. Stepwise mutation model (SMM) and nonSMM-based methods demonstrated a clear genetic structuring within the Northwestern European lineage comprising populations from Britain and Belgium, and within the Central European lineage populations from the rivers Danube, Elbe and Main. Supported by an analysis of genetic variability within populations these results showed that the bullhead populations most probably persisted throughout the last major glaciation within the British Isles and within the drainages of the rivers Elbe and Main. Such observations provide the first genetic evidence for a glacial refugium in such close proximity to the European glacial margins.     

Comparative phylogeography of the two pink salmon broodlines: an analysis based on a mitochondrial DNA genealogy

Over most of their natural northern Pacific Ocean range, pink salmon (Oncorhynchus gorbuscha) spawn in a habitat that was repeatedly and profoundly affected by Pleistocene glacial advances. A strictly two-year life cycle of pink salmon has resulted in two reproductively isolated broodlines, which spawn in alternating years and evolved as temporal replicates of the same species. To study the influence of historical events on phylogeographical and population genetic structure of the two broodlines, we first reconstructed a fine-scale mtDNA haplotype genealogy from a sample of 80 individuals and then determined the geographical distribution of the major genealogical assemblages for 718 individuals sampled from nine Alaskan and eastern Asian even- and nine odd-year pink salmon populations. Analysis of restriction site states in seven polymerase chain reaction (PCR)-amplified mtDNA regions (comprising 97% of the mitochondrial genome) using 13 endonucleases resolved 38 haplotypes, which clustered into five genealogical lineages that differed from 0.065 to 0.225% in net sequence divergence. The lineage sorting between broodlines was incomplete, which suggests a recent common ancestry. Within each lineage, haplotypes exhibited star-like genealogies indicating recent population growth. The depth of the haplotype genealogy is shallow ( approximately 0.5% of nucleotide sequence divergence) and probably reflects repeated decreases in population size due to Pleistocene glacial advances. Nested clade analysis (NCA) of geographical distances showed that the geographical distribution observed for mitochondrial DNA (mtDNA) haplotypes resulted from alternating influences of historical range expansions and episodes of restricted dispersal. Analyses of molecular variance showed weak geographical structuring of mtDNA variation, except for the strong subdivision between Asian and Alaskan populations within the even-year broodline. The genetic similarities observed among and within geographical regions probably originated from postglacial recolonizations from common sources rather than extensive gene flow. The phylogeographical and population genetic structures differ substantally between broodlines. This can be explained by stochastic lineage sorting in glacial refugia and perhaps different recolonization routes in even- and odd-year broodlines.     

Palaeoecology of Upper Pleistocene-Holocene bryozoan and foraminiferal assemblages from Ku?dili (Kadiköy, Istanbul, Turkey)

Bryozoan and foraminiferal assemblages from a core drilled in the Kusdili (Kadiköy, Istanbul) Upper Pleistocene-Holocene sequence were studied. Assemblages are absent from the very basal and top parts but they are well represented all along the middle part of the sequence. All the species found presently live in the Mediterranean. In the area sedimentation seemingly started about 13?000 years ago in very shallow near-shore environments with the deposition of pebbly sediments rapidly evolving to mud. Near the base, the presence of erosional surface allows to recognize three successive sedimentary cycles. Bryozoan and foraminiferal assemblages found in the middle part of the sequence testify to a shallow water, estuarine or lagoonal paleo-environment, in which effects of low salinity waters, more obvious toward the top, could be related to the reestablishment of a connection between the Marmara Sea and the Black Sea through the Bosphorus, about 7000 years BP.     

Non-occlusal dental microwear variability in a sample of Middle and Late Pleistocene human populations from Europe and the Near East

Non-occlusal, buccal tooth microwear variability has been studied in 68 fossil humans from Europe and the Near East. The microwear patterns observed suggest that a major shift in human dietary habits and food processing techniques might have taken place in the transition from the Middle to the Late Pleistocene populations. Differences in microwear density, average length, and orientation of striations indicate that Middle Pleistocene humans had more abrasive dietary habits than Late Pleistocene populations. Both dietary and cultural factors might be responsible for the differences observed. In addition, the Middle Paleolithic Neanderthal specimens studied show a highly heterogeneous pattern of microwear when compared to the other samples considered, which is inconsistent with a hypothesis of all Neanderthals having a strictly carnivorous diet. The high density of striations observed in the buccal surfaces of several Neanderthal teeth might be indicative of the inclusion of plant foods in their diet. The buccal microwear variability observed in the Neanderthals is compatible with an overall exploitation of both plant and meat foods on the basis of food availability. A preliminary analysis of the relationship between buccal microwear density and climatic conditions prevailing in Europe during the Late Pleistocene has been attempted. Cold climatic conditions, as indicated by oxygen isotope stage data, seem to be responsible for higher densities of microwear features, whereas warmer periods could correspond to a reduced pattern of scratch density. Such a relationship would be indicative of less abrasive dietary habits, perhaps more meat dependent, during warmer periods.     

Phylogeographical pattern correlates with pliocene mountain building in the alpine scree weta (Orthoptera, anostostomatidae)

Most research on the biological effects of Pleistocene glaciation and refugia has been undertaken in the northern hemisphere and focuses on lowland taxa. Using single-strand conformation polymorphism (SSCP) analysis and sequencing of mitochondrial cytochrome oxidase I, we explored the intraspecific phylogeography of a flightless orthopteran (the alpine scree weta, Deinacrida connectens) that is adapted to the alpine zone of South Island, New Zealand. We found that several mountain ranges and regions had their own reciprocally monophyletic, deeply differentiated lineages. Corrected genetic distance among lineages was 8.4% (Kimura 2-parameter [K2P]) / 13% (GTR + I + Gamma), whereas within-lineage distances were only 2.8% (K2P) / 3.2% (GTR + I + Gamma). We propose a model to explain this phylogeographical structure, which links the radiation of D. connectens to Pliocene mountain building, and maintenance of this structure through the combined effects of mountain-top isolation during Pleistocene interglacials and ice barriers to dispersal during glacials.