Levels Of Population Structure Research Articles

Genetic characterization of two North Italian villages: A story of isolation, ancient admixture, and genetic drift

AbstractObjectivesPopulation isolates represent a focus of interest because of their particular genetic history and the possibility of mapping peculiar deleterious variants. Here we investigated the pattern of genetic variation in two North Italian villages: Rotzo (RTZ) and Stoccareddo (STC), in the Asiago plateau.Materials and methodsWe genotyped over 800 individuals for more than 600.000 markers. We investigated the isolation level by analyzing runs of homozygosity (ROH) and the level of population structure. Then we estimated the time of admixture and the relationship between ancient genomes and these two villages. Finally, we looked at the effect of genetic drift on deleterious variants.ResultsWe highlighted a different isolation level between RTZ and STC; despite the average number of ROH being similar between the two villages, RTZ shows a higher level of total homozygosity. We estimated, from different sources, that the time of admixture for the ancestors of these two populations was between 113 and 88 generations ago.We discovered that a deleterious variant in MCUB gene (rs78025076), which is linked to several lipid traits, is entirely absent in RTZ and at 1%frequency in STC. In contrast, the risk allele frequency is 2% in Europe and 2.4% in North‐East Italy.DiscussionThese results show the importance of a genetic characterization of geographically isolated populations. Their vast array of past history could highlight specific events in the past and help describe deleterious variants and traits distribution in different regions.

Genetic diversity and population structure of orchid bees from the Brazilian savanna

Based on microsatellite markers and non-lethal sampling of orchid bee males, we assessed the genetic diversity and population structure of three species, Euglossa pleosticta, Euglossa imperialis, and Eulaema nigrita, collected from forest remnants in the Brazilian savanna biome. Among these species, El. nigrita has being acknowledged as more tolerant to savanic areas, since it is more frequently found in these habitats than the other two species. Thus, we hypothesized that species more associated with forest areas would show lower levels of genetic diversity and higher levels of population structure, since open areas could represent a barrier to the movement of these species. We observed lower levels of genetic diversity (HE ) in the species highly associated with forest areas (Eg. pleosticta, HE = 0.66; Eg. imperialis, HE = 0.44) compared to El. nigrita (HE = 0.81). Concerning the genetic structure, it was only remarkable among samples of Eg. pleosticta, a species strongly associated with the forest remnants. Despite the documented dispersal capacity of euglossine bees, maintenance of the connections among forest areas in this biome seems to be critical for their conservation in the Brazilian savanna.

Geographic hierarchical population genetic structuring in British European whitefish (Coregonus lavaretus) and its implications for conservation

The European whitefish Coregonus lavaretus complex represents one of the most diverse radiations within salmonids, with extreme morphological and genetic differentiation across its range. Such variation has led to the assignment of many populations to separate species. In Great Britain, the seven native populations of C. lavaretus (two in Scotland, four in England, one in Wales) were previously classified into three species, and recent taxonomic revision resurrected the previous nomenclature. Here we used a dataset of 15 microsatellites to: (1) investigate the genetic diversity of British populations, (2) assess the level of population structure and the relationships between British populations. Genetic diversity was highest in Welsh (HO = 0.50, AR = 5.29), intermediate in English (HO = 0.41–0.50, AR = 2.83–3.88), and lowest in Scottish populations (HO = 0.28–0.35, AR = 2.56–3.04). Population structure analyses indicated high genetic differentiation (global FST = 0.388) between all populations but for the two Scottish populations (FST = 0.063) and two English populations (FST = 0.038). Principal component analysis and molecular ANOVA revealed separation between Scottish, English, and Welsh populations, with the Scottish populations being the most diverged. We argue that the data presented here are not sufficient to support a separation of the British European whitefish populations into three separate species, but support the delineation of different ESUs for these populations.

Recent Out-of-Africa Migration of Human Herpes Simplex Viruses.

Herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) are ubiquitous human pathogens. Both viruses evolved from simplex viruses infecting African primates and they are thus thought to have left Africa during early human migrations. We analyzed the population structure of HSV-1 and HSV-2 circulating strains. Results indicated that HSV-1 populations have limited geographic structure and the most evident clustering by geography is likely due to recent bottlenecks. For HSV-2, the only level of population structure is accounted for by the so-called "worldwide" and "African" lineages. Analysis of ancestry components and nucleotide diversity, however, did not support the view that the worldwide lineage followed early humans during out-of-Africa dispersal. Although phylogeographic analysis confirmed an African origin for both viruses, molecular dating with a method that corrects for the time-dependent rate phenomenon indicated that HSV-1 and HSV-2 migrated from Africa in relatively recent times. In particular, we estimated that the HSV-2 worldwide lineage left the continent in the 18th century, which corresponds to the height of the transatlantic slave trade, possibly explaining the high prevalence of HSV-2 in the Americas (second highest after Africa). The limited geographic clustering of HSV-1 makes it difficult to date its exit from Africa. The split between the basal clade, containing mostly African sequences, and all other strains was dated at ∼5,000 years ago. Our data do not imply that herpes simplex viruses did not infect early humans but show that the worldwide distribution of circulating strains is the result of relatively recent events.

Clonality, spatial structure, and pathogenic variation in Fusarium fujikuroifrom rain-fed rice in southern Laos.

Bakanae disease, caused by the fungal phytopathogen Fusarium fujikuroi, can be detected in most rice (Oryza sativa L.) growing areas worldwide. In this study, we investigated the population structure of this fungus in southern Lao PDR, a country located near the geographic origin of rice domestication. Microsatellites (SSRs) and mating type (MAT) analyses, pathogenicity and fungicide sensitivity tests were integrated in the study. The first key finding is that the population genetic structure of F. fujikuroi in Lao PDR is consistent with high clonal reproduction. Indeed, (i) “true” clones were identified; (ii) within populations, MAT types were frequently skewed from 1:1 ratio, (iii) linkage disequilibrium (among SSRs as also among SSRs and MAT) was present, and (iv) gene-flow between opposite MAT types within the same population is restricted. The presence of genetic divergence among areas and populations and the occurrence of positive spatial autocorrelation of genetic variation, indicate that migration is restricted, and that genetic drift plays an important role in the evolution of this fungus. Two main well-defined groups of isolates were detected (FST = 0.213) that display a non-random spatial distribution. They differ in the ability to induce seedlings death but not seedlings elongation (the typical Bakanae symptom) suggesting that the pathogen’s ability to induce the two symptoms is under different genetic control. Finally, we compared two agroecosystems with contrasting characteristics: low-input and traditional (Lao PDR) vs high-input and modern (Italy). We found differences in the level of population structuring and of spatial autocorrelation. This suggests that the evolutionary potential of the fungus not only depends on its intrinsic characteristics, but is strongly influenced by other external factors, most likely by the dynamics of infested seed exchange. Thus, quarantine and chemical treatments are a way to reduce population connectivity and hence the evolutionary potential of this pathogen.

Territorial Subdivision of the Megalopolis Population by the Ethnic Trait in Relation to the Problem of Creating Genetic Databases. St. Petersburg

On the basis of the materials of the 2010 All-Russia Population Census in St. Petersburg, an analysis of uneven settlement of ethnic groups over the city districts was carried out. Maps reflecting the ethnic topography of the megalopolis have been constructed. Using the trait “ethnicity” as a quasi-genetic marker, territorial stratification of the megacity population was assessed on two levels of population structure: for the level of large units (districts), Fst = 0.310 × 10–2; for the level of small units (municipalities), Fst = 0.659 × 10–2. Sections of the city characterized by the greatest ethnic diversity were identified. These results should be taken into account when forming databases for the purposes of DNA-based identification in the population of St. Petersburg.

Food chain length and trophic niche of a key predator in montane desert streams

Top predator foraging strategy and prey base community composition can influence food web structure and function. To investigate the role of functional trait diversity and taxonomic richness in determining food chain length and energy flow in high elevation desert streams, we examined aquatic invertebrate community data along with carbon and nitrogen stable isotope analysis of a top predator, Abedus herberti (giant water bug). We also examined isotopic niche differences across different levels of population structure and seasons. We hypothesized that communities with higher richness would have longer food chains. We found food chain length did not vary substantially across a wide taxonomic and functional richness gradient, which contradicts theoretical mechanisms stating that more resources or higher functional diversity should lead to longer food chains. The isotopic niche of A. herberti was conserved across seasons and sites, and the majority of carbon in tissues came from allochthonous materials. Stable isotopes suggested that A. herberti occupy similar feeding niches in spring and autumn, despite seasonal changes in stream conditions, leaf litter inputs, and invertebrate community structure. Due to the strong aquatic–terrestrial linkages we identified, human activities and climate-driven alterations to the adjacent terrestrial environment may affect the dynamics and integrity of the within-stream ecosystem.

High-throughput identification of SNPs reveals extensive heterosis with intra-group hybridization and genetic characteristics in a large rapeseed (Brassica napus L.) panel

Genetically diverse germplasm sets are necessary for the identification of heterotic groups in hybrid breeding programs. Assigning parental lines to identified heterotic groups may increase the efficiency of hybrid rapeseed breeding programs. In this study, the genetic diversity, population structure, relationship, and linkage disequilibrium (LD) of 995 rapeseed accessions, including improved breeding lines and parental lines of elite hybrids, were analyzed using a 60K single nucleotide polymorphism array. The whole population was divided into four subgroups according to the parameters of principal component analysis and STRUCTURE. The overall LD decay was fast, and the LD of the A genome decayed faster than that of the C genome. A core set containing 35 accessions was selected using the POWER-CORE program. The heterotic groups were first assessed based on SNPs in the enlarged core set containing core set accessions and parental lines of three elite hybrid. The parental lines were assigned to certain subpopulation (Pop2 in the enlarged core set), in which the accessions are almost the semi-winter or winter OSR lines. The results revealed that the likelihood of developing heterotic hybrids is much higher with intra-group parents. The studies about information regarding the levels of population structure of core sets combined with their ecological adaptability and genetic distance may be useful for the efficient selection of ideal parental lines during rapeseed hybrid breeding program.

Forensic characterization of Brazilian regional populations through massive parallel sequencing of 124 SNPs included in HID ion Ampliseq Identity Panel

Use of Massive Parallel Sequencing (MPS) techniques has been investigated by forensic community aiming introduction of such methods in routine forensic casework analyses. Interesting features presented by MPS include high-throughput, ability to simultaneous genotyping of significant number of samples and forensic markers, workflow automation, among others. Emergence of single nucleotide polymorphism (SNP) as forensic relevant markers was facilitated in this process, since concurrent typing of larger marker sets is necessary for obtaining same levels of individual discrimination provided by other marker categories. In this context, HID Ion Ampliseq Identity Panel is a commercial solution with forensic purposes comprising simultaneous analysis of 90 highly informative autosomal SNPs and 34 Y –chromosome superior clade SNPs for male lineage haplotyping. SNP typing can be obtained with smaller amplicons, and this panel was designed for efficient processing of critical or challenging forensic samples. In this work, a sample of 432 individuals from all five Brazilian geopolitical regions was evaluated with this panel, in order to access feasibility of this panel use in a national basis. Results obtained for all five regions, including forensic parameters, show that this marker set can be efficiently employed for Brazilian nationals in human identification or kinship determination applications, due to high levels of genetic discriminative information content displayed by Brazilians. Interpopulation comparison studies were executed among Brazilian regional populations and 26 worldwide populations, in order to access genetic stratification occurrence. Some levels of population structure were identified, and impact on database design was discussed. Y-chromosome haplotyping of Brazilian samples revealed high levels of European ancestry in Brazilian male lineages, and utility of haplotyping in real forensic casework is addressed. Finally, genotyping and sequencing efficiency with this panel were addressed, as an effort to appraise the adequacy of this panel use in Brazilian national forensic demands.

Demographic history of the Magellanic Penguin (Spheniscus magellanicus) on the Pacific and Atlantic coasts of South America

Spatial subdivision, local extinction and recolonization influence the genetic variation of natural populations. Different levels of population structure can be identified in nature, from panmictic populations, in which high gene flow homogenizes diversity across localities, to metapopulations, where combinations of moderate to high levels of population differentiation and source-sink population dynamics are expected. Gene flow, dispersal and recolonization can be affected by changes in ecological conditions such as climate and resource distribution. Evaluating demographic history is crucial for understanding current population dynamics. We assessed a mitchondrial DNA (mtDNA) control region and microsatellite data for 210 Magellanic Penguins (Spheniscus magellanicus) from 13 breeding colonies on the coastlines of Chile and Argentina, covering a great portion of the species’ distribution. We found high levels of genetic diversity and detected two genetic-geographic regions, Pacific and Atlantic, probably due to interruption of the connection between the oceans during the Last Glacial Maximum (LGM), when several parts of the Magellanic Channel were connected to the continent. The Atlantic ocean colonies showed a slight differentiation between the northern and southern colonies, and the Falkand/Malvinas one seems to be a mix of northern, southern and Pacific colonies. Magellanic Penguins showed intense gene flown among colonies, and exhibited low levels of genetic differentiation in each region. Furthermore, our findings indicate that the Magellanic Penguin experienced a population expansion around 17,500 years ago, which is in agreement with the timing of a decreased sea level and the exposure of the continental shelf along the coast of Argentina and the Falkland/Malvinas Islands at the end of the LGM. Thus, our results suggest that climate changes that affect the sea level in South America can play important roles in the migration of Magellanic Penguins.

Conservation Genetics of the CapercaillieTetrao urogallusin Poland — Diversity of Mitochondrial DNA in Remnant and Extinct Populations

Human-induced changes in the natural environment impact upon a wide variety of genetic processes at all levels of population structure. Insight into these processes is now achieved by analyses of genetic diversity allowing the past and present condition of populations to be assessed and compared. Given its severe fragmentation and small size, the population of the Capercaillie Tetrao urogallus in Poland can be regarded as especially prone to gene-pool alteration. Moreover, this is a region of Europe in which different genetic lineages of the Capercaillie may be present, ensuring that certain conservation decisions may be even more difficult than they otherwise would be. Bearing the above in mind, we decided to study polymorphism of the mitochondrial DNA Control Region (mtDNA CR) in remnant and extinct populations of the Capercaillie in Poland. The extinct population was represented by samples from birds hunted in the Lower Silesian Forest (SW Poland) between 1951–1962. We compared sequences obtained with data from the large, continuous population present in Russia and Scandinavia. Analysing 331 bp of mtDNA CR for 168 individuals, we identified 24 haplotypes, among which only 6 had not been reported previously in the species according to GenBank. Our data confirmed a previous suggestion regarding the genetic structure of the species in Poland, i.e. that birds from Augustow Forest (NE Poland) are related to Russian and Scandinavian populations, constituting a part of the lowland group within the boreal lineage. The Carpathian population is in turn confirmed as an independent genetic group within the boreal lineage, while specimens from the Solska Forest (SE Poland) prove to be highly differentiated from birds in other Polish populations; most likely because they derive from — or have been connected via gene flow with — birds present in the Balkans. Further genetic analysis is necessary to resolve this evolutionary relationship between Capercaillies from south-eastern Poland and those of the Balkans. Where practice is concerned, the overall advice is that three Conservation Units are to be recognised in Poland. In addition to those, the extinct population from the Lower Silesian Forest has been deemed part of the lowland group within the boreal lineage, albeit a distinctive one, given the possibility of gene exchange with Carpathian birds. We further suggest that some aspect of this extinct population's genetic diversity reflects an uncontrolled process of reintroduction taking place in the past.

Community-acquired infection with hypervirulent Clostridium difficile isolates that carry different toxin and antibiotic resistance loci: a case report

BackgroundClostridium difficile infection (CDI) leads to the onset of antibiotic-associated diarrhea (AAD) and a wide range of gastrointestinal pathologies. Currently, CDI is one of the most important opportunistic infections at the intrahospital level and an exponential increase in community-acquired infections has been reported. Herein, we evaluated the relationships (at phylogenetic and genetic population structure levels), as well as the molecular toxigenic and antibiotic resistance profiles of a set of isolates established from a case of community acquired-CDI.Case presentationA 30-year-old woman with no history of hospitalization who was exposed to antibiotics (ampicillin/sulbactam and metronidazole) after a cat-bite wound was presented. The patient had a continuous episode of diarrhea; a stool sample was then collected and community acquired-CDI was confirmed by molecular tests and in vitro culture. Seven isolates were established and subsequently subjected to: (i) Multilocus sequence typing, all isolates belonging to ST-1 (associated with hypervirulent strain (027/BI/NAP1); (ii) description of their toxigenic profile: two of the isolates (Gcol.49 and Gcol.91) were positive for the genes coding for the major toxins (tcdA and tcdB) and their negative regulator (tcdC). All isolates were positive for the cdtB gene encoding one of the binary toxin subunits, while only two (Gcol.51 and Gcol.52) were positive for cdtA; and (iii) identification of antibiotic resistance molecular markers, where there was no difference in gyrA or gyrB gene polymorphisms (related to quinolone resistance), but rather at loci presence/absence, being just one isolate negative, whereas the others showed a differential presence of the tet, ermB and Tn916 regions. The former was associated with resistance to tetracycline and the other two for erythromycin/clindamycin.ConclusionsThis case represents the first report of community acquired-CDI in Colombia associated with hypervirulent strains and shows that isolates obtained from a single patient can carry different toxin and antibiotic resistance loci.

The roles of barriers, refugia, and chromosomal clines underlying diversification in Atlantic Forest social wasps

Phylogeographic studies have sought to explain the genetic imprints of historical climatic changes and geographic barriers within the Brazilian Atlantic Forest (AF) biota, and consequently two processes of diversification (refugia and barriers) have been proposed. Additionally, there is evidence that eustatic changes influenced the biogeographic history of the AF. Here we evaluate these contrasting diversification processes using two AF social wasp species – the mid-montane Synoeca cyanea and the lowland Synoeca aff. septentrionalis. We analyzed several sources of data including multilocus DNA sequence, climatic niche models and chromosomal features. We find support for idiosyncratic phylogeographic patterns between these wasps, involving different levels of population structure and genetic diversity, contrary suitable climatic conditions during the last glaciation, and contrasting historical movements along the AF. Our data indicate that neotectonics and refugia played distinct roles in shaping the genetic structure of these wasps. However, we argue that eustatic changes influenced the demographic expansion but not population structure in AF biota. Notably, these wasps exhibited chromosomal clines, involving chromosome number and decreasing of GC content, latitudinally oriented along the AF. Together, these results reinforce the need to consider individual organismal histories and indicate that barriers and refugia are significant factors in understanding AF evolution.

Exploring the human microbiome from multiple perspectives: factors altering its composition and function.

Our microbiota presents peculiarities and characteristics that may be altered by multiple factors. The degree and consequences of these alterations depend on the nature, strength and duration of the perturbations as well as the structure and stability of each microbiota. The aim of this review is to sketch a very broad picture of the factors commonly influencing different body sites, and which have been associated with alterations in the human microbiota in terms of composition and function. To do so, first, a graphical representation of bacterial, fungal and archaeal genera reveals possible associations among genera affected by different factors. Then, the revision of sequence-based predictions provides associations with functions that become part of the active metabolism. Finally, examination of microbial metabolite contents and fluxes reveals whether metabolic alterations are a reflection of the differences observed at the level of population structure, and in the last step, link microorganisms to functions under perturbations that differ in nature and aetiology. The utilisation of complementary technologies and methods, with a special focus on metabolomics research, is thoroughly discussed to obtain a global picture of microbiota composition and microbiome function and to convey the urgent need for the standardisation of protocols.

Multilocus Phylogeography and Species Delimitation in the Cumberland Plateau Salamander, Plethodon kentucki: Incongruence among Data Sets and Methods.

Species are a fundamental unit of biodiversity, yet can be challenging to delimit objectively. This is particularly true of species complexes characterized by high levels of population genetic structure, hybridization between genetic groups, isolation by distance, and limited phenotypic variation. Previous work on the Cumberland Plateau Salamander, Plethodon kentucki, suggested that it might constitute a species complex despite occupying a relatively small geographic range. To examine this hypothesis, we sampled 135 individuals from 43 populations, and used four mitochondrial loci and five nuclear loci (5693 base pairs) to quantify phylogeographic structure and probe for cryptic species diversity. Rates of evolution for each locus were inferred using the multidistribute package, and time calibrated gene trees and species trees were inferred using BEAST 2 and *BEAST 2, respectively. Because the parameter space relevant for species delimitation is large and complex, and all methods make simplifying assumptions that may lead them to fail, we conducted an array of analyses. Our assumption was that strongly supported species would be congruent across methods. Putative species were first delimited using a Bayesian implementation of the GMYC model (bGMYC), Geneland, and Brownie. We then validated these species using the genealogical sorting index and BPP. We found substantial phylogeographic diversity using mtDNA, including four divergent clades and an inferred common ancestor at 14.9 myr (95% HPD: 10.8–19.7 myr). By contrast, this diversity was not corroborated by nuclear sequence data, which exhibited low levels of variation and weak phylogeographic structure. Species trees estimated a far younger root than did the mtDNA data, closer to 1.0 myr old. Mutually exclusive putative species were identified by the different approaches. Possible causes of data set discordance, and the problem of species delimitation in complexes with high levels of population structure and introgressive hybridization, are discussed.

ANÁLISIS DE LA DIVERSIDAD GENÉTICA DE LA MORA(Rubus spp.)EN EL DEPARTAMENTO DE BOYACÁ

A simple of 21 Rubus spp genetic ecotypes were characterized using markers Random Microsatellite RAMs. The seven primers produced a total of 160 polymorphic bands with molecular weights between 350 and 1500 Kb. RAMs analysis at a level of 55% similarity distinguished the population into five groups generally agree to the site where the ecotypes were collected. The number of polymorphic loci ranged from 16 (ACA) to 27 (CGA). For the total population the percentage of polymorphic loci and the expected average heterozygosity (He) were 88% and 0,29, respectively, much lower than values found in other genetic diversity studies in the genus Rubus. Therefore, strategies must be found to increase genetic variability. The coefficient of genetic differentiation (Fst) obtained in evaluating ecotypes Rubus, with seven RAMs microsatellite markers was 0,29 with a standard deviation of 0,03, values showing high genetic differentiation, which is associated with the level of population structure it tends to stabilize.

Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes.

The spatial structure of the environment (e.g. the configuration of habitat patches) may play an important role in determining the strength of local adaptation. However, previous studies of habitat heterogeneity and local adaptation have largely been limited to simple landscapes, which poorly represent the multiscale habitat structure common in nature. Here, we use simulations to pursue two goals: (i) we explore how landscape heterogeneity, dispersal ability and selection affect the strength of local adaptation, and (ii) we evaluate the performance of several genotype-environment association (GEA) methods for detecting loci involved in local adaptation. We found that the strength of local adaptation increased in spatially aggregated selection regimes, but remained strong in patchy landscapes when selection was moderate to strong. Weak selection resulted in weak local adaptation that was relatively unaffected by landscape heterogeneity. In general, the power of detection methods closely reflected levels of local adaptation. False-positive rates (FPRs), however, showed distinct differences across GEA methods based on levels of population structure. The univariate GEA approach had high FPRs (up to 55%) under limited dispersal scenarios, due to strong isolation by distance. By contrast, multivariate, ordination-based methods had uniformly low FPRs (0-2%), suggesting these approaches can effectively control for population structure. Specifically, constrained ordinations had the best balance of high detection and low FPRs and will be a useful addition to the GEA toolkit. Our results provide both theoretical and practical insights into the conditions that shape local adaptation and how these conditions impact our ability to detect selection.

Population Structure of Vitis rupestris, an Important Resource for Viticulture

The wild North American grapevine Vitis rupestris Scheele is an important genetic resource for viticulture, but its natural populations have been severely depleted. We collected samples from seven V. rupestris populations from the Ozark Plateau in Missouri and the Ouachita Mountains in Oklahoma and genotyped them with 14 microsatellite markers to assess allelic diversity, heterozygosity, and genetic differentiation at various levels of population structure. We found that genetic diversity in V. rupestris was similar to that measured in many V. vinifera L. ssp. sylvestris populations and in other outcrossing angiosperms. We detected significant genetic differentiation among populations (ΦPT = 0.105); there was no significant deviation from Hardy–Weinberg equilibrium in some populations, and there was moderate inbreeding in others. Pronounced differentiation between Missouri and Oklahoma populations was supported by a Bayesian clustering approach and principle coordinate analyses and was apparently a function of geographic distance. Genetic differentiation among Missouri populations was modest. We posit that population differentiation and genetic drift may be inherent characteristics of V. rupestris.

Mitochondrial DNA Structure ofPyganodon grandis(Bivalvia: Unionidae) from the Lake Erie Watershed and Selected Locations in its Northern Distribution

Abstract: The distribution of Pyganodon grandis (Say, 1829) and the entire community of unionid freshwater mussels within the Laurentian Great Lakes became greatly reduced following invasion of dreissenid mussels. While some populations remain, how much gene flow still occurs is not known, nor has the level of population structure been examined within a large lake subsequent to dreissenid infestation. Pyganodon grandis is a common and relatively abundant lacustrine species that utilizes diverse host fish, and, therefore, it may disperse as much as or more than any other unionid species in the region. To test for population structure, we examined a fragment of the maternal mtDNA COI gene from 300 individuals encompassing shallow areas from Lake Erie's western and central basins, Sandusky Bay, Lake St. Clair, and the upper Niagara River. Another 94 individuals from the upper Great Lakes and upper Mississippi River watersheds were added to the analysis. A total of 34 different haplotypes were found for P. gr...

Training set optimization under population structure in genomic selection.

Key message Population structure must be evaluated before optimization of the training set population. Maximizing the phenotypic variance captured by the training set is important for optimal performance. The optimization of the training set (TRS) in genomic selection has received much interest in both animal and plant breeding, because it is critical to the accuracy of the prediction models. In this study, five different TRS sampling algorithms, stratified sampling, mean of the coefficient of determination (CDmean), mean of predictor error variance (PEVmean), stratified CDmean (StratCDmean) and random sampling, were evaluated for prediction accuracy in the presence of different levels of population structure. In the presence of population structure, the most phenotypic variation captured by a sampling method in the TRS is desirable. The wheat dataset showed mild population structure, and CDmean and stratified CDmean methods showed the highest accuracies for all the traits except for test weight and heading date. The rice dataset had strong population structure and the approach based on stratified sampling showed the highest accuracies for all traits. In general, CDmean minimized the relationship between genotypes in the TRS, maximizing the relationship between TRS and the test set. This makes it suitable as an optimization criterion for long-term selection. Our results indicated that the best selection criterion used to optimize the TRS seems to depend on the interaction of trait architecture and population structure.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-014-2418-4) contains supplementary material, which is available to authorized users.