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The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoena phocoena), in the Atlantic shelf waters follows a pattern of significant isolation-by-distance. The population structure of harbor porpoises from the Baltic Sea, which is connected with the North Sea through a series of basins separated by shallow underwater ridges, however, is more complex. Here, we investigated the population differentiation of harbor porpoises in European Seas with a special focus on the Baltic Sea and adjacent waters, using a population genomics approach. We used 2872 single nucleotide polymorphisms (SNPs), derived from double digest restriction-site associated DNA sequencing (ddRAD-seq), as well as 13 microsatellite loci and mitochondrial haplotypes for the same set of individuals. Spatial principal components analysis (sPCA), and Bayesian clustering on a subset of SNPs suggest three main groupings at the level of all studied regions: the Black Sea, the North Atlantic, and the Baltic Sea. Furthermore, we observed a distinct separation of the North Sea harbor porpoises from the Baltic Sea populations, and identified splits between porpoise populations within the Baltic Sea. We observed a notable distinction between the Belt Sea and the Inner Baltic Sea sub-regions. Improved delineation of harbor porpoise population assignments for the Baltic based on genomic evidence is important for conservation management of this endangered cetacean in threatened habitats, particularly in the Baltic Sea proper. In addition, we show that SNPs outperform microsatellite markers and demonstrate the utility of RAD-tags from a relatively small, opportunistically sampled cetacean sample set for population diversity and divergence analysis.
Unraveling the processes responsible for Earth's climate transition from an "El Nino-like state" during the warm early Pliocene into a modern-like "La Nina-dominated state" currently challenges the scientific community. Recently, the Pliocene climate switch has been linked to oceanic thermocline shoaling at similar to 3 million years ago along with Earth's final transition into a bipolar icehouse world. Here we present Pliocene proxy data and climate model results, which suggest an earlier timing of the Pliocene climate switch and a different chain of forcing mechanisms. We show that the increase in North Atlantic meridional overturning circulation between 4.8 and 4.0 million years ago, initiated by the progressive closure of the Central American Seaway, triggered overall shoaling of the tropical thermocline. This preconditioned the turnaround from a warm eastern equatorial Pacific to the modern equatorial cold tongue state about 1 million years earlier than previously assumed. Since similar to 3.6-3.5 million years ago, the intensification of Northern Hemisphere glaciation resulted in a strengthening of the trade winds, thereby amplifying upwelling and biogenic productivity at low latitudes.
In this study, we have used fragments of three mitochondrial genes (Control Region, CR; transfer RNA for methionine, tRNA-Met; NADH dehydrogenase subunit 2, ND2 for a total of 1066 bp) to reconstruct the phylogeographic history of the endemic Philippine bulbul (Hypsipetes philippinus) at the scale of the central area of the Philippine archipelago. The study includes two of the five recognized subspecies (guimarasensis and mindorensis), 7 populations and 58 individuals. Multiple phylogenetic and network analyses support the existence of two reciprocally monophyletic maternal lineages corresponding to the two named subspecies. Molecular clock estimates indicate that the split between the two subspecies is consistent with the Pleistocene geological history of the archipelago. Patterns of relationships within guimarasensis are biogeographically less clear. Here, a combination of vicariance and dispersal needs to be invoked to reconcile the molecular data with the geographical origin of samples. In particular, the two islands Boracay and Negros host mitochondrial lineages that do not form monophyletic clusters. Our genetic data suggest multiple independent colonization events for these locations.
We describe eight new microsatellite loci for the critically endangered fire-bellied toad, Bombina bombina. Seven of them are polymorphic with two to seven alleles per locus, an expected heterozygosity between 0.41 and 0.8, and an observed heterozygosity between 0.27 and 0.7. The yield of new loci was relatively low, presumably due to mildly repetitive sequence motifs in microsatellite flanking regions. As typical for anurans, cross-species amplification was limited (here, to congeners Bombina orientalis and Bombina variegata). Combining these new loci with those already available provides a reasonable number of loci for population studies and pedigree analysis in Bombina
Background: Mediterranean temporary water bodies are important reservoirs of biodiversity and host a unique assemblage of diapausing aquatic invertebrates. These environments are currently vanishing because of increasing human pressure. Chirocephalus kerkyrensis is a fairy shrimp typical of temporary water bodies in Mediterranean plain forests and has undergone a substantial decline in number of populations in recent years due to habitat loss. We assessed patterns of genetic connectivity and phylogeographic history in the seven extant populations of the species from Albania, Corfu Is. (Greece), Southern and Central Italy.
Methodology/Principal Findings: We analyzed sequence variation at two mitochondrial DNA genes (Cytochrome Oxidase I and 16s rRNA) in all the known populations of C. kerkyrensis. We used multiple phylogenetic, phylogeographic and coalescence-based approaches to assess connectivity and historical demography across the whole distribution range of the species. C. kerkyrensis is genetically subdivided into three main mitochondrial lineages; two of them are geographically localized (Corfu Is. and Central Italy) and one encompasses a wide geographic area (Albania and Southern Italy). Most of the detected genetic variation (approximate to 81%) is apportioned among the aforementioned lineages.
Conclusions/Significance: Multiple analyses of mismatch distributions consistently supported both past demographic and spatial expansions with the former predating the latter; demographic expansions were consistently placed during interglacial warm phases of the Pleistocene while spatial expansions were restricted to cold periods. Coalescence methods revealed a scenario of past isolation with low levels of gene flow in line with what is already known for other co-distributed fairy shrimps and suggest drift as the prevailing force in promoting local divergence. We recommend that these evolutionary trajectories should be taken in proper consideration in any effort aimed at protecting Mediterranean temporary water bodies.
In this study we used molecular markers to screen for the occurrence and prevalence of the three most common haemosporidian genera (Haemoproteus, Plasmodium, and Leucocytozoon) in blood samples of the Philippine Bulbul (Hypsipetes philippinus), a thrush-size passerine bird endemic to the Philippine Archipelago. We then used molecular data to ask whether the phylogeographic patterns in this insular host-parasite system might follow similar evolutionary trajectories or not. We took advantage of a previous study describing the pattern of genetic structuring in the Philippine Bulbul across the Central Philippine Archipelago (6 islands, 7 populations and 58 individuals; three mitochondrial DNA genes). The very same birds were here screened for the occurrence of parasites by species-specific PCR assays of the mitochondrial cytochrome b gene (471 base pairs). Twenty-eight out of the 58 analysed birds had Haemoproteus (48%) infections while just 2% of the birds were infected with either Leucocytozoon or Plasmodium. Sixteen of the 28 birds carrying Haemoproteus had multiple infections. The phylogeography of the Philippine Bulbul mostly reflects the geographical origin of samples and it is consistent with the occurrence of two different subspecies on (1) Semirara and (2) Carabao, Boracay, North Gigante, Panay, and Negros, respectively. Haemoproteus phylogeography shows very little geographical structure, suggesting extensive gene flow among locations. While movements of birds among islands seem very sporadic, we found co-occurring evolutionary divergent parasite lineages. We conclude that historical processes have played a major role in shaping the host phylogeography, while they have left no signature in that of the parasites. Here ongoing population processes, possibly multiple reinvasions mediated by other hosts, are predominant.
Hidden diversity in diatoms of Kenyan Lake Naivasha a genetic approach detects temporal variation
(2012)
This study provides insights into the morphological and genetic diversity in diatoms occurring in core sediments from tropical lakes in Kenya. We developed a genetic survey technique specific for diatoms utilizing a short region (7667 bp) of the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene as genetic barcode. Our analyses (i) validated the use of rbcL as a barcoding marker for diatoms, applied to sediment samples, (ii) showed a significant correlation between the results obtained by morphological and molecular data and (iii) indicated temporal variation in diatom assemblages on the inter- and intra-specific level. Diatom assemblages from a short core from Lake Naivasha show a drastic shift over the last 200 years, as littoral species (e.g. Navicula) are replaced by more planktonic ones (e.g. Aulacoseira). Within that same period, we detected periodic changes in the respective frequencies of distinct haplotype groups of Navicula, which coincide with wet and dry periods of Lake Naivasha between 1820 and 1938 AD. Our genetic analyses on historical lake sediments revealed inter- and intra-specific variation in diatoms, which is partially hidden behind single morphotypes. The occurrence of particular genetic lineages is probably correlated with environmental factors.
In this study, we report the genetic population structure of the Fire-bellied toad Bombina bombina in Brandenburg (East Germany) in the context of conservation. We analysed 298 samples originating from 11 populations in Brandenburg using mitochondrial control region sequences and six polymorphic microsatellite loci. For comparison, we included one population each from Poland and Ukraine into our analysis. Within Brandenburg, we detected a moderate variability in the mitochondrial control region (19 different haplotypes) and at microsatellite loci (9-12 alleles per locus). These polymorphisms revealed a clear population structure among toads in Brandenburg, despite a relatively high overall population density and the moderate size of single populations (100-2000 individuals). The overall genetic population structure is consistent with a postglacial colonization from South East-Europe and a subsequent population expansion. Based on genetic connectivity, we infer Management Units (MUs) as targets for conservation. Our genetic survey identified MUs, within which human infrastructure is currently preventing any genetic exchange. We also detect an unintentional translocation from South East to North West Brandenburg, presumably in the course of fish stocking activities. Provided suitable conservation measures are taken, Brandenburg should continue to harbor large populations of this critically endangered species.
Fourteen microsatellite markers were isolated and characterized for the endangered Visayan tarictic hornbill (Penelopides panini, Aves: Bucerotidae). In an analysis of 76 individuals, the number of alleles per locus varied from one to 12. Expected and observed heterozygosity ranged from 0.00 to 0.87 and from 0.00 to 0.89, respectively. All primers also amplify microsatellite loci in Luzon tarictic hornbill (Penelopides manillae), Mindanao tarictic hornbill (Penelopides affinis), the critically endangered Walden's hornbill (Aceros waldeni) and the near-threatened writhed hornbill (Aceros leucocephalus). Two loci which are monomorphic in P. panini were found polymorphic in at least one of the other species. These 14 new microsatellite markers specifically developed for two genera of Philippine hornbills, in combination with those already available for the hornbill genera Buceros and Bucorvus, comprise a reasonable number of loci to genetically analyse wild and captive populations of these and probably other related, often endangered hornbills.
Rates of multiple paternities were investigated in the sailfin molly (Poecilia latipinna), using eight microsatellite loci. Genotyping was performed for offspring and mothers in 40 broods from four allopatric populations from the south-eastern U.S.A. along a geographic stretch of 1200 km in west-east direction and approximately 200 km from north to south. No significant differences regarding rates of multiple paternities were found between populations despite sample populations stemming from ecologically divergent habitats. Even the most conservative statistical approach revealed a minimum of 70% of the broods being sired by at least two males, with an average of 1.80-2.95 putative fathers per brood. Within broods, one male typically sired far more offspring than would be expected under an assumed equal probability of all detected males siring offspring.