Population Genetic Differences Research Articles

Ecological commonalities among pelagic fishes: comparison of freshwater ciscoes and marine herring and sprat

Systematic comparisons of the ecology between functionally similar fish species from freshwater and marine aquatic systems are surprisingly rare. Here, we discuss commonalities and differences in evolutionary history, population genetics, reproduction and life history, ecological interactions, behavioural ecology and physiological ecology of temperate and Arctic freshwater coregonids (vendace and ciscoes, Coregonus spp.) and marine clupeids (herring, Clupea harengus, and sprat, Sprattus sprattus). We further elucidate potential effects of climate warming on these groups of fish based on the ecological features of coregonids and clupeids documented in the previous parts of the review. These freshwater and marine fishes share a surprisingly high number of similarities. Both groups are relatively short-lived, pelagic planktivorous fishes. The genetic differentiation of local populations is weak and seems to be in part correlated to an astonishing variability of spawning times. The discrete thermal window of each species influences habitat use, diel vertical migrations and supposedly also life history variations. Complex life cycles and preference for cool or cold water make all species vulnerable to the effects of global warming. It is suggested that future research on the functional interdependence between spawning time, life history characteristics, thermal windows and genetic differentiation may profit from a systematic comparison of the patterns found in either coregonids or clupeids.

Identifying Highly Conserved and Highly Differentiated Gene Ontology Categories in Human Populations

Detecting and interpreting certain system-level characteristics associated with human population genetic differences is a challenge for human geneticists. In this study, we conducted a population genetic study using the HapMap genotype data to identify certain special Gene Ontology (GO) categories associated with high/low genetic difference among 11 Hapmap populations. Initially, the genetic differences in each gene region among these populations were measured using allele frequency, linkage disequilibrium (LD) pattern, and transferability of tagSNPs. The associations between each GO term and these genetic differences were then identified. The results showed that cellular process, catalytic activity, binding, and some of their sub-terms were associated with high levels of genetic difference, and genes involved in these functional categories displayed, on average, high genetic diversity among different populations. By contrast, multicellular organismal processes, molecular transducer activity, and some of their sub-terms were associated with low levels of genetic difference. In particular, the neurological system process under the multicellular organismal process category had low levels of genetic difference; the neurological function also showed high evolutionary conservation between species in some previous studies. These results may provide a new insight into the understanding of human evolutionary history at the system-level.

Coping with genetic diversity: the contribution of pathogen and human genomics to modern vaccinology

Vaccine development faces major difficulties partly because of genetic variation in both infectious organisms and humans. This causes antigenic variation in infectious agents and a high interindividual variability in the human response to the vaccine. The exponential growth of genome sequence information has induced a shift from conventional culture-based to genome-based vaccinology, and allows the tackling of challenges in vaccine development due to pathogen genetic variability. Additionally, recent advances in immunogenetics and genomics should help in the understanding of the influence of genetic factors on the interindividual and interpopulation variations in immune responses to vaccines, and could be useful for developing new vaccine strategies. Accumulating results provide evidence for the existence of a number of genes involved in protective immune responses that are induced either by natural infections or vaccines. Variation in immune responses could be viewed as the result of a perturbation of gene networks; this should help in understanding how a particular polymorphism or a combination thereof could affect protective immune responses. Here we will present: i) the first genome-based vaccines that served as proof of concept, and that provided new critical insights into vaccine development strategies; ii) an overview of genetic predisposition in infectious diseases and genetic control in responses to vaccines; iii) population genetic differences that are a rationale behind group-targeted vaccines; iv) an outlook for genetic control in infectious diseases, with special emphasis on the concept of molecular networks that will provide a structure to the huge amount of genomic data.

Reduced tree health and seedling production in fragmented Fagus sylvatica forest patches in the Montseny Mountains (NE Spain)

Habitat fragmentation results in smaller and more isolated populations that may be at higher risk of extirpation or further decline in comparison with their more continuously distributed progenitors. Risks to fragmented populations have frequently been considered from the perspective of population genetics, however, disruption of normal plant demography may be an equal or greater threat to population persistence. We compared demographic performance and tree health in continuous and fragmented forest plots with similar tree size structure and local climatic and physiographic conditions in order to determine if fragments are characterized by poor health and reproduction. We found that beech forest fragments showed lower seedling density, more tree crown damage and also higher percentage of dead trees. However, mortality of juveniles in the youngest age class was substantially lower in fragments such that long-term population structure remained similar between the two forest types. If reduced mortality compensates for reduced seedling establishment, as our data suggest, then fragmented populations should show greater long-term persistence than would be predicted based on comparison of young age cohorts alone. However, despite such demographic compensation, the decreased health of adult trees may pose an increasing future threat to the fragmented populations. Our results demonstrate the importance of integrating demographic patterns over long time periods and not relying on single year or cohort comparisons and may partly explain population genetic differences previously reported for the same populations.

Phylogeography of the Pacific Blueline Surgeonfish,Acanthurus nigroris, Reveals High Genetic Connectivity and a Cryptic Endemic Species in the Hawaiian Archipelago

Understanding genetic connectivity is fundamental to the design of marine protected areas in the service of ecosystem-scale management. Here we evaluate such trends for a Pacific surgeonfish (Acanthurus nigroris;N=544) at two spatial scales: (1) within the Hawaiian archipelago, and (2) across the entire species range from the central to southwest Pacific. The mtDNA cytochromebdata reveal genetic divergence (d=0.041) between Hawaii and the rest of the Pacific range indicating a cryptic species pair, with one taxon endemic to Hawaii. Johnston Atoll, 1400 km SW of Hawaii, also has the Hawaiian species but is distinct from most Hawaiian locations in population genetic comparisons, indicating the limits of gene flow for this widespread reef species. No consistent population genetic differences were observed among Hawaiian sites or among the other Pacific island sites. We also detected a modest bias in gene flow from the southeast towards the northwest islands of the Hawaiian Archipelago, indicating that the Papahānaumokuākea Marine National Monument may be a recipient, rather than a source of propagules to replenish reef resources.

Profound Differences in Virus Population Genetics Correspond to Protection from CD4 Decline Resulting from Feline Lentivirus Coinfection

CD4 decline is a hallmark of disease onset in individuals infected with Feline Immunodeficiency Virus (FIV) or Human Immunodeficiency Virus type 1 (HIV-1). Cats that are infected with a poorly replicating, apathogenic FIV (PLV) prior to exposure to a virulent FIV strain (FIVC) maintain CD4 numbers by mechanisms that are not correlated with a measurable adaptive immune response or reduction in circulating viral load. We employed population genetic approaches based on the 3′ portion of the viral genome to estimate the population structure of FIVC from single and dual infected cats. In dual infected cats, FIVC effective population size was decreased during the initial viral expansion phase, and after three weeks of infection, the population declined sharply. The FIVC population recovered to pre-bottleneck levels approximately seven weeks post-FIVC infection. However, the population emerging from the bottleneck in dual infected cats was distinct based on estimates of temporal population structure and substitution profiles. The transition to transversion rate ratio (κ) increased from early to late phases in dual infected cats due primarily to a decrease in transversions whereas in single infected cats, κ declined over time. Although one clone with extensive G to A substitutions, indicative of host cytidine deaminase editing, was recovered from a dual infected cat during the bottleneck, the post bottleneck population had an overall reduction in G to A substitutions. These data are consistent with a model of PLV-induced host restriction, putatively involving host DNA editing, that alters the dynamics of FIVC throughout the course of infection leading to disease attenuation.

Population genetic differences along a latitudinal cline between original and recently colonized habitat in a butterfly.

BackgroundPast and current range or spatial expansions have important consequences on population genetic structure. Habitat-use expansion, i.e. changing habitat associations, may also influence genetic population parameters, but has been less studied. Here we examined the genetic population structure of a Palaeartic woodland butterfly Pararge aegeria (Nymphalidae) which has recently colonized agricultural landscapes in NW-Europe. Butterflies from woodland and agricultural landscapes differ in several phenotypic traits (including morphology, behavior and life history). We investigated whether phenotypic divergence is accompanied by genetic divergence between populations of different landscapes along a 700 km latitudinal gradient.Methodology/Principal FindingsPopulations (23) along the latitudinal gradient in both landscape types were analyzed using microsatellite and allozyme markers. A general decrease in genetic diversity with latitude was detected, likely due to post-glacial colonization effects. Contrary to expectations, agricultural landscapes were not less diverse and no significant bottlenecks were detected. Nonetheless, a genetic signature of recent colonization is reflected in the absence of clinal genetic differentiation within the agricultural landscape, significantly lower gene flow between agricultural populations (3.494) than between woodland populations (4.183), and significantly higher genetic differentiation between agricultural (0.050) than woodland (0.034) pairwise comparisons, likely due to multiple founder events. Globally, the genetic data suggest multiple long distance dispersal/colonization events and subsequent high intra- and inter-landscape gene flow in this species. Phosphoglucomutase deviated from other enzymes and microsatellite markers, and hence may be under selection along the latitudinal gradient but not between landscape types. Phenotypic divergence was greater than genetic divergence, indicating directional selection on some flight morphology traits.Main Conclusions/SignificanceClinal differentiation characterizes the population structure within the original woodland habitat. Genetic signatures of recent habitat expansion remain, notwithstanding high gene flow. After differentiation through drift was excluded, both latitude and landscape were significant factors inducing spatially variable phenotypic variation.

Population structure on breeding grounds of Lake Malawi’s ‘twilight zone’ cichlid fishes

AbstractAim Free‐ranging benthopelagic fishes often have large population sizes and high rates of dispersal. These traits can act to homogenize population structure across the distributional range of a species and to reduce the likelihood of allopatric speciation. The apparent absence of any barriers to gene flow among populations, together with prior molecular evidence for panmixia across the ranges of three species, has resulted in Diplotaxodon, a genus of benthopelagic cichlid fishes of Lake Malawi, being proposed as a candidate case of sympatric speciation. Our aim was to further investigate this possibility by testing for intraspecific genetic subdivision among breeding populations, and intraspecific differences in breeding habitat.Location Lake Malawi, central‐east Africa.Methods We analysed eight microsatellite DNA loci to test for spatial genetic differences among populations on breeding grounds of eight Diplotaxodon species. We also tested for temporal population genetic differences within breeding grounds of three species. Records of ripe Diplotaxodon encountered during sampling were analysed to test if spatial variation in assemblage structure was linked to nearshore water depth and geographic proximity of sampling sites.Results Consistent with previous molecular evidence, within four of the eight species tested we found no evidence of spatial genetic structuring among breeding populations. However, within the other four species we found slight yet significant spatial genetic differences, indicating restricted gene flow among breeding grounds. There was no evidence of temporal genetic differences within sites. Analyses of the distributions of ripe Diplotaxodon revealed differences in assemblage structure linked to nearshore water depth.Main conclusions Together, these results demonstrate both the evolution of fidelity to deep‐water breeding locations in some Diplotaxodon species, and differences in breeding habitat among species. These findings are consistent with a role for divergence of breeding habitat in speciation of these cichlids, possibly promoted by dispersal limitation among geographically segregated spawning aggregations.

FLGmutations in ichthyosis vulgaris and atopic eczema: spectrum of mutations and population genetics

Filaggrin is a key protein involved in skin barrier function. Mutations in the gene encoding filaggrin (FLG) have been identified as the cause of ichthyosis vulgaris and have been shown to be major predisposing factors for atopic eczema (AE), initially in European populations. Subsequently, FLG mutations were identified in Japanese, Chinese, Taiwanese and Korean populations. It was demonstrated that FLG mutations are closely associated with AE in the Japanese population. Notably, the same FLG mutations identified in the European population were rarely found in Asians. These results exemplify differences in filaggrin population genetics between Europe and Asia. For mutation screening, background information needs to be obtained on prevalent FLG mutations for each geographical population. It is therefore important to establish the global population genetics maps for FLG mutations. Mutations at any site within FLG, even mutations in C-terminal imperfect filaggrin repeats, cause significant reductions in amounts of profilaggrin/filaggrin peptide in patient epidermis as the C-terminal region is essential for proper processing of profilaggrin into filaggrin. Thus, no genotype-phenotype correlation has been observed in patients with FLG mutations. A restoration of the barrier function seems a feasible and promising strategy for treatment and prevention in individuals with filaggrin deficiency.

Low diversity and high intra-island variation in prevalence of avianHaemoproteusparasites on Barbados, Lesser Antilles

Common bird species were screened during May and June 2007 on Barbados for haemosporidian parasites (Haemosporida) of the genera Haemoproteus and Plasmodium to determine whether the low parasite diversity reported in previous studies might have reflected limited sampling. PCR screening and DNA sequencing revealed a single predominant lineage of Haemoproteus identified as H. coatneyi. Sixty-two out of 257 birds were infected with Haemoproteus spp. on Barbados in 2007. Fifty-nine of the infections were identified as H. coatneyi (lineage HC), the only lineage recovered in the previous study in 1993. Two of the infections recovered from the bananaquit (Coereba flaveola) were identified as Haemoproteus spp. (lineage HD), which is the prevalent haemosporidian parasite in C. flaveola on Grenada. We discuss the possibility of infrequent colonization events and absence of vectors as explanations for Barbados's low avian haemosporidian diversity. In our study, the parasites were absent from the southeast of the island, whereas they were abundant in several host species in the northwest. Accordingly, environmental and host population genetic differences were also investigated between the areas with and without parasites. No host genetic differences were found between the parasite-free and the parasite-afflicted regions. However, the parasite-free region is slightly warmer and drier, and it supports less vegetation than the parasite-afflicted region. The influence that this harsher environment may have on vector survival is discussed.

Genetic Structure of Europeans: A View from the North–East

Using principal component (PC) analysis, we studied the genetic constitution of 3,112 individuals from Europe as portrayed by more than 270,000 single nucleotide polymorphisms (SNPs) genotyped with the Illumina Infinium platform. In cohorts where the sample size was >100, one hundred randomly chosen samples were used for analysis to minimize the sample size effect, resulting in a total of 1,564 samples. This analysis revealed that the genetic structure of the European population correlates closely with geography. The first two PCs highlight the genetic diversity corresponding to the northwest to southeast gradient and position the populations according to their approximate geographic origin. The resulting genetic map forms a triangular structure with a) Finland, b) the Baltic region, Poland and Western Russia, and c) Italy as its vertexes, and with d) Central- and Western Europe in its centre. Inter- and intra- population genetic differences were quantified by the inflation factor lambda (λ) (ranging from 1.00 to 4.21), fixation index (Fst) (ranging from 0.000 to 0.023), and by the number of markers exhibiting significant allele frequency differences in pair-wise population comparisons. The estimated lambda was used to assess the real diminishing impact to association statistics when two distinct populations are merged directly in an analysis. When the PC analysis was confined to the 1,019 Estonian individuals (0.1% of the Estonian population), a fine structure emerged that correlated with the geography of individual counties. With at least two cohorts available from several countries, genetic substructures were investigated in Czech, Finnish, German, Estonian and Italian populations. Together with previously published data, our results allow the creation of a comprehensive European genetic map that will greatly facilitate inter-population genetic studies including genome wide association studies (GWAS).

Population genetic study of the brain-derived neurotrophic factor (BDNF) gene

Genetic variants in the brain-derived neurotrophic factor (BDNF) gene, predominantly the functional Val66Met polymorphism, have been associated with risk of bipolar disorder and other psychiatric disorders. However, not all studies support these findings, and overall the evidence for BDNF association with disease risk is weak. As differences in population genetic structure between patient samples could cause discrepant or spurious association results, we investigated this possibility by carrying out population genetic analyses of the BDNF genomic region. Substantial variation was detected in BDNF coding region SNP allele and haplotype frequencies between 58 global populations, with the derived Met allele of Val66Met ranging from 0–72% frequency across populations. FST analyses to assess diversity in the HapMap populations determined that the Val66Met FST value was at the 99.8th percentile among all SNPs in the genome. As the BDNF population genetic differences may be due to local selection, we performed the long-range haplotype (LRH) test for selection using 68 SNPs spanning the BDNF genomic region in 12 European-derived pedigrees. Evidence for positive selection was found for a high frequency Val-carrying haplotype, with a relative extended haplotype homozygosity (REHH) value above the 99th percentile compared to HapMap data (P=4.6 ×10−4). In conclusion, we observed considerable BDNF allele and haplotype diversity among global populations and evidence for positive selection at the BDNF locus. These phenomena can have a profound impact on detection of disease susceptibility genes and must be considered in gene association studies of BDNF.

Genome-Wide Association Studies in an Isolated Founder Population from the Pacific Island of Kosrae

It has been argued that the limited genetic diversity and reduced allelic heterogeneity observed in isolated founder populations facilitates discovery of loci contributing to both Mendelian and complex disease. A strong founder effect, severe isolation, and substantial inbreeding have dramatically reduced genetic diversity in natives from the island of Kosrae, Federated States of Micronesia, who exhibit a high prevalence of obesity and other metabolic disorders. We hypothesized that genetic drift and possibly natural selection on Kosrae might have increased the frequency of previously rare genetic variants with relatively large effects, making these alleles readily detectable in genome-wide association analysis. However, mapping in large, inbred cohorts introduces analytic challenges, as extensive relatedness between subjects violates the assumptions of independence upon which traditional association test statistics are based. We performed genome-wide association analysis for 15 quantitative traits in 2,906 members of the Kosrae population, using novel approaches to manage the extreme relatedness in the sample. As positive controls, we observe association to known loci for plasma cholesterol, triglycerides, and C-reactive protein and to a compelling candidate loci for thyroid stimulating hormone and fasting plasma glucose. We show that our study is well powered to detect common alleles explaining ≥5% phenotypic variance. However, no such large effects were observed with genome-wide significance, arguing that even in such a severely inbred population, common alleles typically have modest effects. Finally, we show that a majority of common variants discovered in Caucasians have indistinguishable effect sizes on Kosrae, despite the major differences in population genetics and environment.

TRAVEL AND INFECTIOUS DISEASE

Travei facilitates the physicai transport of pathogens and vectors and increases the exposure of individuais and popuiation groups to disease. Reciprocaiiy, travei is affected by outbreak situations, particulariy those occurring in areas of heavy tourism. In the individual, specific i-isk factors associated with travel-induced iliness include the time of year traveled, travei destination and number of trips taken, age, predisposition to high risk behavior, pre-travel heaith, pre-trip counseling, and previous immunity. Whiie the speed and frequency of modern travei facilitate the introduction of infectious diseases into new environments, disease emergence is dependent on the complex interrelationship of population immunity and genetic differences, behaviorai patterns and cultural norms, environmefflai setting, the epidemioiogy of disease and the existing public heaith infrastructure. Travel-induced iilnesses have serious economic, politicai and medical consequences including costs to health care systems in both home and host country, iost revenue to decreased tourism, increased heaith insurance claims, lost working days, issues of nationai security and the spread of antibiotic resistance. To minimize the impact of travei on infectious disease emergence, travei-acquired illnesses must be prevented through safe, effective immunizations, pubiic and physician education programs, improved giobal sanitation and effective disease surveiliance.

A reanalysis of 409 European‐Ancestry and African American schizophrenia pedigrees reveals significant linkage to 8p23.3 with evidence of locus heterogeneity

The detection and replication of schizophrenia risk loci can require substantial sample sizes, which has prompted various collaborative efforts for combining multiple samples. However, pooled samples may comprise sub-samples with substantial population genetic differences, including allele frequency differences. We investigated the impact of population differences via linkage reanalysis of Molecular Genetics of Schizophrenia 1 (MGS1) affected sibling-pair data, comprising two samples of distinct ancestral origin: European (EA: 263 pedigrees) and African-American (AA: 146 pedigrees). To exploit the linkage information contained within these distinct continental samples, we performed separate analyses of the individual samples, allowing for within-sample locus heterogeneity, and the pooled sample, allowing for both within-sample and between-sample heterogeneity. Significance levels, corrected for the multiple tests, were determined empirically. For all suggestive peaks, stronger linkage evidence was obtained in either the EA or AA sample than the combined sample, regardless of how heterogeneity was modeled for the latter. Notably, we report genomewide significant linkage of schizophrenia to 8p23.3 and evidence for a second, independent susceptibility locus, reaching suggestive linkage, 29 cM away on 8p21.3. We also detected suggestive linkage on chromosomes 5p13.3 and 7q36.2. Many regions showed pronounced differences in the extent of linkage between the EA and AA samples. This reanalysis highlights the potential impact of population differences upon linkage evidence in pooled data and demonstrates a useful approach for the analysis of samples drawn from distinct continental groups.

Detecting natural selection in high-altitude human populations

High-altitude natives have distinctive biological characteristics that appear to offset the stress of hypoxia. Evolutionary theory reasons that they reflect genetic adaptations resulting from natural selection on traits with heritable variation. Furthermore, high-altitude natives of the Andean and Tibetan Plateaus differ from one another, perhaps resulting from different evolutionary histories. Three approaches have developed a case for the possibility of population genetic differences: comparing means of classical physiological traits measured in samples of natives and migrants between altitudes, estimating genetic variance using statistical genetics techniques, and comparing features of species with different evolutionary histories. Tibetans have an inferred autosomal dominant major gene for high oxygen saturation that is associated with higher offspring survival, a strong indicator of ongoing natural selection. New approaches use candidate gene and genomic analyses. Conclusive evidence about population genetic differences and associations with phenotypes remains to be discovered.

Population genetic aspects and phenotypic plasticity of ventilatory responses in high altitude natives

Highland natives show unique breathing patterns and ventilatory responses at altitude, both at rest and during exercise. For many ventilatory traits, there is also significant variation between highland native groups, including indigenous populations in the Andes and Himalaya, and more recent altitude arrivals in places like Colorado. This review summarizes the literature in this area with some focus on partitioning putative population genetic differences from differences acquired through lifelong exposure to hypoxia. Current studies suggest that Tibetans have high resting ventilation (V (E)), and a high hypoxic ventilatory response (HVR), similar to altitude acclimatized lowlanders. Andeans, in contrast, show low resting V (E) and a low or "blunted" HVR, with little evidence that these traits are acquired via lifelong exposure. Resting V (E) of non-indigenous altitude natives is not well documented, but lifelong hypoxic exposure almost certainly blunts HVR in these groups through decreased chemosensitivity to hypoxia in a process known as hypoxic desensitization (HD). Together, these studies suggest that the time course of ventilatory response, and in particular the origin or absence of HD, depends on population genetic background i.e., the allele or haplotype frequencies that characterize a particular population. During exercise, altitude natives have lower V (E) compared to acclimatized lowland controls. Altitude natives also have smaller alveolar-arterial partial pressure differences P(AO2) - P(aO2) during exercise suggesting differences in gas exchange efficiency. Small P(AO2) - P(aO2) in highland natives of Colorado underscores the likely importance of developmental adaptation to hypoxia affecting structural/functional aspects of gas exchange with resultant changes in breathing pattern. However, in Andeans, at least, there is also evidence that low exercise V (E) is determined by genetic background affecting ventilatory control independent of gas exchange. Additional studies are needed to elucidate the effects of gene, environment, and gene-environment interaction on these traits, and these effects are likely to differ widely between altitude native populations.

Sex differences in population genetics, home range size and habitat use of the parti-colored bat ( Vespertilio murinus, Linnaeus 1758) in Switzerland and their consequences for conservation

When habitats are declining, niche segregation by demographic groups, such as the two sexes, can have a profound impact on the extinction risk of a species as a whole. Thus, differences in the requirements of demographic groups are of importance in conservation. We combined behavioural and genetic data to investigate whether the sexually segregated parti-colored bat ( Vespertilio murinus) exhibits sex-specific niche partitioning. We use our data to evaluate implications for conservation of this potentially vulnerable species in Switzerland, the western boundary of its range. Using radio-telemetry, we found sex-specific differences in habitat use. Foraging females strongly relied on lakes while foraging males displayed more flexibility in their habitat use. Moreover, males covered significantly larger foraging areas than females. Sequencing 341 base pairs of the mitochondrial D-loop of 247 individuals revealed sex-specific differences in the genetic structure of colonies, but no such difference was observed for three nuclear micro-satellite markers. We found high mtDNA diversity in two Swiss male colonies and one German female colony, but low mtDNA diversity in two Swiss female colonies. Our genetic data suggest that considerable gene flow occurs via male dispersal and mating. At the same time immigration of females into the existing female colonies in Switzerland is rare compared to the immigration of new males into male colonies. Since we found the sexes in Vespertilio murinus to differ markedly in their ecology, population genetics, and behaviour, we conclude that sex-specific conservation plans are required to protect this species efficiently.

Geographical subdivision, demographic history and gene flow in two sympatric species of intertidal snails, Nerita scabricosta and Nerita funiculata, from the tropical eastern Pacific

The patchy distribution of rocky intertidal communities in the tropical eastern Pacific (TEP) may impose severe constraints on the genetic connectivity among populations of marine invertebrates associated with this habitat. In this study, we analyzed a portion of the mitochondrial cytochrome c oxidase subunit I (COI) gene in two sympatric species of marine snails, Nerita scabricosta and Nerita funiculata, common inhabitants of the rocky intertidal from the Gulf of California (Sea of Cortez) and outer Pacific coast of the southern Baja California (Baja) peninsula to northern South America, to assess genetic connectivity among populations of each species. One of our aims was to determine whether the morphological, behavioral, and ecological differences observed among populations of both species throughout their range in the TEP corresponded to population genetic differences. In addition, we were interested in elucidating the demographic history of both species. We found no evidence of genetic structure throughout the Gulf of California and outer coast of the Baja peninsula region for either species. Comparisons between Gulf of California/Baja and Panama populations, however, showed significant genetic differentiation for N. scabricosta, but not for N. funiculata. The genetic differences between Mexican and Panamanian populations of N. scabricosta were consistent with previously reported ecological and behavioral differences for this species between these two distant regions. However, previously reported size differences between northern and central/southern Gulf of California individuals of N. scabricosta do not correspond with our findings of genetic connectivity among these populations. Results from neutrality tests (Tajima’s D and Fu’s FS), the mismatch distribution, and Bayesian skyline analyses suggested that both species have experienced dramatic population expansions dating to the Pleistocene.

BARCSoySNP23: a panel of 23 selected SNPs for soybean cultivar identification

This report describes a set of 23 informative SNPs (BARCSoySNP23) distributed on 19 of the 20 soybean linkage groups that can be used for soybean cultivar identification. Selection of the SNPs to include in this set was made based upon the information provided by each SNP for distinguishing a diverse set of soybean genotypes as well as the linkage map position of each SNP. The genotypes included the ancestors of North American cultivars, modern North American cultivars and a group of Korean cultivars. The procedure used to identify this subset of highly informative SNP markers resulted in a significant increase in the power of identification versus any other randomly selected set of equal number. This conclusion was supported by a simulation which indicated that the 23-SNP panel can uniquely distinguish 2,200 soybean cultivars, whereas sets of randomly selected 23-SNP panels allowed the unique identification of only about 50 cultivars. The 23-SNP panel can efficiently distinguish each of the genotypes within four maturity group sets of additional cultivars/lines that have identical classical pigmentation and morphological traits. Comparatively, the 13 trinucleotide SSR set published earlier (BARCSoySSR13) has more power on a per locus basis because of the multi-allelic nature of SSRs. However, the assay of bi-allelic SNP loci can be multi-plexed using non-gel based techniques allowing for rapid determination of the SNP alleles present in soybean genotypes, thereby compensating for their relatively low information content. Both BARCSoySNP23 and BARCSoySSR13 were highly congruent relative to identifying genotypes and for estimating population genetic differences.