Microsatellite loci for Euglossa annectans (Hymenoptera: Apidae) and their variability in other orchid bees

Orchid or euglossine bees are conspicuous Hymenoptera of the Neotropics, where they pollinate numerous plants, including orchids. Allozyme-based analyses have suggested that their populations suffer from inbreeding, as evidenced by so-called diploid male production. We have developed nine polymorphic microsatellite loci for the widespread Euglossa annectans, with observed heterozygosities ranging from 0.143 to 0.952 and between 2 and 9 alleles per species. These loci will be useful for analysis of relatedness, population genetic structure and diploid male production in this and related species.

Characterization of 14 polymorphic microsatellite loci for the facultatively eusocial sweat bee Halictus rubicundus (Hymenoptera, Halictidae) and their variability in related species

Sweat bees display considerable variation in social organization and a few species, such as Halictus rubicundus, are even facultatively eusocial. Fourteen polymorphic, unlinked microsatellite loci were isolated from H. rubicundus and characterized in 45 females. The number of alleles per locus ranged from two to 18 (mean 10.1), observed heterozygosity ranged from 0.24 to 0.98 (mean 0.71) and expected heterozygosity ranged from 0.24 to 0.98 (mean 0.70). Six or more loci cross-amplified in four other sweat bees. These loci will be useful for the study of social evolution and population genetic structure in H. rubicundus and many other sweat bees.

Larval Transport Modeling of Deep-Sea Invertebrates Can Aid the Search for Undiscovered Populations

Background: Many deep-sea benthic animals occur in patchy distributions separated by thousands of kilometres, yet because deep-sea habitats are remote, little is known about their larval dispersal. Our novel method simulates dispersal by combining data from the Argo array of autonomous oceanographic probes, deep-sea ecological surveys, and comparative invertebrate physiology. The predicted particle tracks allow quantitative, testable predictions about the dispersal of benthic invertebrate larvae in the south-west Pacific. Principal Findings: In a test case presented here, using non-feeding, non-swimming (lecithotrophic trochophore) larvae of polyplacophoran molluscs (chitons), we show that the likely dispersal pathways in a single generation are significantly shorter than the distances between the three known population centres in our study region. The large-scale density of chiton populations throughout our study region is potentially much greater than present survey data suggest, with intermediate ‘stepping stone’ populations yet to be discovered. Conclusions/Significance: We present a new method that is broadly applicable to studies of the dispersal of deep-sea organisms. This test case demonstrates the power and potential applications of our new method, in generating quantitative, testable hypotheses at multiple levels to solve the mismatch between observed and expected distributions: probabilistic predictions of locations of intermediate populations, potential alternative dispersal mechanisms, and expected population genetic structure. The global Argo data have never previously been used to address benthic biology, and our method can be applied to any non-swimming larvae of the deep-sea, giving information upon dispersal corridors and population densities in habitats that remain intrinsically difficult to assess.

Isolation and characterization of eight polymorphic microsatellite loci for Natterer's bat, Myotis nattereri (Vespertilionidae, Chiroptera)

Eight new microsatellite loci were isolated and characterized for the Natterer's bat Myotis nattereri from a microsatellite-enriched genomic library. The usefulness of these markers was assessed by screening a sample comprising 100 specimens collected from throughout the species range in Europe. Both moderately and highly polymorphic loci were identified with 3-17 alleles segregating per locus (mean 8.1 SE +/- A 0.048). No evidence for departure from HWE or linkage disequilibrium among loci was observed. These markers will provide a valuable addition to the molecular toolbox currently available for studies of population genetic structure, parentage and social organisation of M. nattereri and related species.

Isolation and characterization of thirty microsatellite loci for Atlantic mackerel (Scomber scombrus L.)

Atlantic mackerel (Scomber scombrus L.) is a widely distributed commercially important pelagic species. Little is known about the stock structure of this species, but it is thought to be undergoing a range extension due to environmental changes. Knowledge of the stock structure under these changing conditions is fundamental for effective management. In this paper, 30 highly polymorphic microsatellite loci developed with next generation sequencing are described. The number of alleles per locus ranged from 4 to 39 in two geographically distant populations, observed and expected heterozygosities ranged between 0. 370-0. 978 and 0. 426-0. 962, respectively. These loci are an important resource that will allow assessment of the current population genetic structure of this species, and enable monitoring of climate related changes in the species range and distribution. 

Twenty-two novel microsatellite loci for lumpfish (Cyclopterus lumpus)

Lumpfish (Cyclopterus lumpus L. 1758) are widely distributed on both sides of the North Atlantic. They are a commercially important species, but stock size estimates have declined since the mid-1980s in Canada, Norway and Iceland. Little is known about the biology of this species, in particular the breeding migrations and population structure which are fundamental for effective management. This paper describes the development and characterization of twenty-two polymorphic microsatellite loci using next generation sequencing. The number of alleles per locus ranged from 3 to 27 in two geographically distant North Atlantic populations, with observed and expected heterozygosities ranging between 0. 0625-0. 979 and 0. 0618-0. 946, respectively. These loci are an important resource that will allow assessment of the population genetic structure of this species, and contribute to its appropriate management.

New microsatellite loci for the longnose velvet dogfish Centroselachus crepidater (Squaliformes: Somniosidae) and other deep sea sharks

The continuing over-exploitation of traditional coastal stocks has resulted in the shift of commercial fishing towards deep-sea ecosystems in many parts of the world. The effects on target and non-target species have been dramatic; particularly for the deep-sea sharks. With the aim of providing tools that will allow the assessment of population genetic structure of Centroselachus crepidater, novel microsatellite loci have been developed for this deep-sea elasmobranch. Seven of these markers showed between 3 and 7 alleles per locus in two North Atlantic populations, with observed and expected heterozygosities between 0.18-0.95 and 0.25-0.82, respectively. Additionally, ten loci cross-amplify in other Elasmobranch species.

Novel microsatellite loci for a deep sea fish (Macrourus berglax) and their amplification in other grenadiers (Gadiformes: Macrouridae)

Over-exploitation of traditional coastal stocks and a rising demand for seafood have resulted in the shift of commercial fishing towards less-known, deep-sea species in many parts of the world. Yet, the lack of knowledge of the biology, ecology and life-history of these species represents a serious impediment for establishing sound stock management plans. With the aim of providing tools that will allow assessment of the population genetic structure of Macrourus berglax, we have isolated and characterised a suite of novel microsatellite loci for this deep sea grenadier. Eight of these markers showed between 4 and 11 alleles per locus in two distant North Atlantic populations, with observed and expected heterozygosities between 0.17-0.83 and 0.35-0.87, respectively. Importantly, eight of these loci also cross-amplify in other Macrourid species. 

Demographics and landscape features determine intrariver population structure in Atlantic salmon (Salmo salar L.): the case of the River Moy in Ireland

Contemporary genetic structure of Atlantic salmon (Salmo salar L.) in the River Moy in Ireland is shown here to be strongly related to landscape features and population demographics, with populations being defined largely by their degree of physical isolation and their size. Samples of juvenile salmon were collected from the 17 major spawning areas on the river Moy and from one spawning area in each of five smaller nearby rivers. No temporal allele frequency differences were observed within locations for 12 microsatellite loci, whereas nearly all spatial samples differed significantly, suggesting that each was a separate population. Bayesian clustering and landscape genetic analyses suggest that these populations can be combined hierarchically into five genetically informative larger groupings. Lakes were found to be the single most important determinant of the observed population structure. Spawning area size was also an important factor. The salmon population of the closest nearby river resembled genetically the largest Moy population grouping. In addition, we showed that anthropogenic influences on spawning habitats, in this case arterial drainage, can affect relationships between populations. Our results show that Atlantic salmon biodiversity can be largely defined by geography, and thus, knowledge of landscape features (for example, as characterized within Geographical Information Systems) has the potential to predict population structure in other rivers without an intensive genetic survey, or at least to help direct sampling. This approach of combining genetics and geography, for sampling and in subsequent statistical analyses, has wider application to the investigation of population structure in other freshwater/anadromous fish species and possibly in marine fish and other organisms.

High levels of genetic structuring as a result of population fragmentation in the tropical tree species Caesalpinia echinata Lam.

We have investigated levels of genetic diversity within and among seven remnant populations of Caesalpinia echinata Lam., an endangered species found as fragmented populations in three major areas around the coastal regions of Brazil. Using amplified fragment length polymorphism (AFLP) genetic markers, we detected levels of within-population genetic diversity ranging from 0.092 to 0.163, with the lowest values generally being found in the smallest populations. Estimates of between-population genetic differentiation were strongly correlated with geographical distance ( r = 0.884, p <0.001), which, along with a neighbour-joining phylogenetic analysis, strongly suggested high levels of genetic isolation by distance. Over half (62%) of the total genetic diversity was partitioned between populations, further highlighting the genetic distinctness of individual populations. Taken together, these results suggest that fragmentation has led to an increase in population differentiation between fragments of C. echinata. These formations will be of great value in the development of conservation plans for species exhibiting high levels of genetic differentiation due to fragmentation, such as indication of conservation unit size, which populations should be chosen as priority in conservation plans and which samples should be introduced in areas with a low number of individuals of brazilwood.

Using ancestry-informative markers to identify fine structure across 15 populations of European origin

The Wellcome Trust Case Control Consortium 3 anorexia nervosa genome-wide association scan includes 2907 cases from 15 different populations of European origin genotyped on the Illumina 670K chip. We compared methods for identifying population stratification, and suggest list of markers that may help to counter this problem. It is usual to identify population structure in such studies using only common variants with minor allele frequency (MAF) >5%; we find that this may result in highly informative SNPs being discarded, and suggest that instead all SNPs with MAF >1% may be used. We established informative axes of variation identified via principal component analysis and highlight important features of the genetic structure of diverse European-descent populations, some studied for the first time at this scale. Finally, we investigated the substructure within each of these 15 populations and identified SNPs that help capture hidden stratification. This work can provide information regarding the designing and interpretation of association results in the International Consortia. 

Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture

Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.

Myeloperoxidase G-463A polymorphism and Alzheimer's disease in the ApoEurope study

Alzheimer's disease (AD) is the most common cause of dementia in the elderly. Epidemiological and molecular genetic studies have shown the existence of several genes associated with increased risk of AD, the major genetic susceptibility locus coding for apolipoprotein E (apoE). A polymorphism in the myeloperoxidase gene (MPO) has previously been associated with AD susceptibility. However, results in the literature are controversial and seem to be dependent on several factors such as gender, apoE polymorphism or the genetic structure of the population. We investigated MPO G-463A and apoE polymorphism in 265 cases and 246 controls from the ApoEurope Study. In females, we found a significant association between MPO genotype and AD (P=0.034), GG genotype frequency being lower in cases (52.4%) as compared to controls (64.2%). In men, there was no significant effect of MPO polymorphism. No interaction was found between MPO polymorphism and apoE epsilon 4 allele. In conclusion, the G-463A polymorphism of MPO was statistically associated with AD in a gender-specific manner. However, given the low significance of P value we suggest no causal effect of the MPO gene in AD, as also evidenced in a recent meta-analysis. Our results support the hypothesis of a possible linkage disequilibrium between the MPO G-463A gene polymorphism and another functional variant involved in AD.

Impacts of climate change on species, populations and communities: palaeobiogeographical insights and frontiers

Understanding climate change and its potential impact on species, populations and communities is one of the most pressing questions of twenty-fi rst-century conservation planning. Palaeobiogeographers working on Cenozoic fossil records and other lines of evidence are producing important insights into the dynamic nature of climate and the equally dynamic response of species, populations and communities. Climatic variations ranging in length from multimillennia to decades run throughout the palaeo-records of the Quaternary and earlier Cenozoic and have been shown to have had impacts ranging from changes in the genetic structure and morphology of individual species, population sizes and distributions, community composition to large-scale bio-diversity gradients. The biogeographical impacts of climate change may be due directly to the effects of alterations in temperature and moisture on species, or they may arise due to changes in factors such as disturbance regimes. Much of the recent progress in the application of palaeobiogegraphy to issues of climate change and its impacts can be attributed to developments along a number of still advancing methodological frontiers. These include increasingly finely resolved chronological resolution, more refi ned atmosphere-biosphere modelling, new biological and chemical techniques in reconstructing past species distributions and past climates, the development of large and readily accessible geo-referenced databases of biogeographical and climatic information, and new approaches in fossil morphological analysis and new molecular DNA techniques.

Tracing early stages of species differentiation: Ecological, morphological and genetic divergence of Galapagos sea lion populations

Background: Oceans are high gene flow environments that are traditionally believed to hamper the build-up of genetic divergence. Despite this, divergence appears to occur occasionally at surprisingly small scales. The Galápagos archipelago provides an ideal opportunity to examine the evolutionary processes of local divergence in an isolated marine environment. Galápagos sea lions (Zalophus wollebaeki) are top predators in this unique setting and have an essentially unlimited dispersal capacity across the entire species range. In theory, this should oppose any genetic differentiation.
Results: We find significant ecological, morphological and genetic divergence between the western colonies and colonies from the central region of the archipelago that are exposed to different ecological conditions. Stable isotope analyses indicate that western animals use different food sources than those from the central area. This is likely due to niche partitioning with the second Galápagos eared seal species, the Galápagos fur seal (Arctocephalus galapagoensis) that exclusively dwells in the west. Stable isotope patterns correlate with significant differences in foraging-related skull morphology. Analyses of mitochondrial sequences as well as microsatellites reveal signs of initial genetic differentiation.
Conclusion: Our results suggest a key role of intra- as well as inter-specific niche segregation in the evolution of genetic structure among populations of a highly mobile species under conditions of free movement. Given the monophyletic arrival of the sea lions on the archipelago, our study challenges the view that geographical barriers are strictly needed for the build-up of genetic divergence. The study further raises the interesting prospect that in social, colonially breeding mammals additional forces, such as social structure or feeding traditions, might bear on the genetic partitioning of populations.