Limited Genetic Structure Research Articles

HOW CAN WE EFFICIENTLY CHARACTERIZE GENES OF AGRONOMIC INTEREST IN OLIVE: TOWARDS THE GENETIC ASSOCIATION STUDIES?

Despite the socio-economic importance of olive oil and the need of olive breeding, genetic studies on agronomic traits are restricted to few biparental populations limiting the efficiency of QTL (Quantitative Trait Loci) mapping strategy. Association mapping based on a diversified collection of olive germplasm can be proposed as a complementary strategy to genetically map agronomic traits. Here, we aimed to develop tools for association mapping studies by defining a Mediterranean olive core collection and characterizing a massive set of microsatellite markers (SSRs). The worldwide olive germplasm bank of Marrakech, Morocco (561 accessions from 14 Mediterranean countries) was characterized using 17 nuclear SSRs and cpDNA markers and classified into east, centre and west Mediterranean gene pools. Combining two sampling methods maximizing the capture of diversity and genetic distance, we proposed two core collections of 50 and 94 accessions including all nuclear SSR alleles, cpDNA haplotypes and states of agro-morphology (from Olea databases) from the WOGB Marrakech. These core collections include cultivars considered as the most important in Mediterranean olive producing countries and display a limited genetic structure between east and west/center gene pools. Hence, they are efficient candidates for phenotyping agronomic trait and to explore the largest variability in distinct environmental conditions. Concurrently, we developed a set of genomic and Expressed Sequence Tag (EST)-derived SSRs that were used to complete the genetic map of ‘Oliviere’ × ‘Arbequina’ segregating population. Molecular markers will be used on the proposed core collections to assess the linkage disequilibrium decay according to the genetic distance and to further develop association mapping studies.

Limited genetic structure and diversity in the water rail Rallus aquaticus L., 1758 (Aves: Gruiformes: Rallidae) revealed by mitochondrial DNA analysis

A previous, geographically limited study, has found very little genetic structure in the water rail Rallus aquaticus based on cytochrome oxidase I sequences. Adding samples from Romania, Montenegro, Germany and Spain, we investigated whether the new data confirm the picture of genetic homogeneity or if there is more diverse structure, e.g. due to survival in different Pleistocene refuges. Among 75 studied individuals, there were 12 haplotypes, one of them very common, the others differing in only one or two positions. The high haplotype diversity in Kazakhstan suggested that diversification has been ongoing for a longer time than in the other areas, assuming similar substitution rates across the entire species. Only one rare haplotype was shared between Kazakhstan and another region, specifically Romania. All other rare haplotypes had narrow distributions and probably evolved after the range expansion towards the west. Apparently, gene flow has been restricted in the recent past. The Romanian population was genetically intermediate between Kazakhstan and the western populations. The genetic structure of the populations supported a post-glacial out-of-Central-Asia scenario.

Limited geographic genetic structure detected in a widespread Palearctic corvid, Nucifraga caryocatactes.

The Eurasian or spotted nutcracker (Nucifraga caryocatactes) is a widespread resident corvid found throughout the Palearctic from Central Europe to Japan. Characterized by periodic bouts of irruptive dispersal in search of Pinus seed crops, this species has potential for high levels of gene flow across its range. Previous analysis of 11 individuals did not find significant range-wide population genetic structure. We investigated population structure using 924 base pairs of mitochondrial DNA control region sequence data from 62 individuals from 12 populations distributed throughout the nutcracker’s range. We complemented this analysis by incorporating additional genetic data from previously published sequences. High levels of genetic diversity and limited population genetic structure were detected suggesting that potential barriers to dispersal do not restrict gene flow in nutcrackers.

Gene flow across the N-Atlantic and sex-biased dispersal inferred from mtDNA sequence variation in saithe, Pollachius virens

Genetic variation in saithe Pollachius virens was examined using a 460 base pair fragment of the cytochrome c oxidase subunit I mitochondrial gene in 1163 individuals sampled in Canada, Iceland, Faroe Islands and Norway. In all, 43 segregating sites were observed, almost all synonymous, defining 51 haplotypes. High frequency polymorphism was present at the analyzed fragment making it suitable for population genetic studies. The results showed limited trans Atlantic genetic structure indicating high levels of gene flow. However, a spatial genetic structure was observed when considering the sexes separately. This may suggest sex-biased migration pattern. The data indicate that females may be more philopatric and males more migratory. Such behaviour has rarely been described for marine fish and is worth further research. The observed genetic variation also indicates that saithe has undergone sudden population expansion, reflected in high number of singletons and a shallow genealogy.

Limited genetic structure of Gulf Menhaden (Brevoortia patronus) as revealed by microsatellite markers developed for the genus Brevoortia (Clupeidae)

Long-term sustainable management of wild populations should be based on management actions that account for the genetic structure among populations. Knowledge of genetic structure and of the degree of demographic exchange between discreet [sic] populations allows managers to better define management units. However, adequate gene loci for population assessments are not always available. In this study, variable co-dominant DNA loci in the heavily exploited marine genus Brevoortia were developed with a microsatellite-enriched DNA library for the Gulf Menhaden (Brevoortia patronus). Microsatellite marker discovery was followed by genetic characterization of 4 endemic North American Brevoortia species, by using 14 novel loci as well as 5 previously described loci. Power analysis of these loci for use in species identification and genetic stock structure was used to assess their potential to improve the stock definition in the menhaden fishery of the Gulf of Mexico. These loci could be used to reliably identify menhaden species in the Gulf of Mexico with an estimated error rate of α=0.0001. Similarly, a power analysis completed on the basis of observed allele frequencies in Gulf Menhaden indicated that these markers can be used to detect very small levels of genetic divergence (Fst≈0.004) among simulated populations, with sample sizes as small as n=50 individuals. A cursory analysis of genetic structure among Gulf Menhaden sampled throughout the Gulf of Mexico indicated limited genetic structure among sampling locations, although the available sampling did not reach the target number (n=50) necessary to detect minimal values of significant structure.

Limited genetic structure among broad-scale regions for two commercially harvested, tropical deep-water snappers in New Caledonia

We estimated the spatial population connectivity of Etelis carbunculus and E. coruscans based on measures of population genetic structure using the mitochondrial DNA control region. We collected samples from three areas separated by a minimum of 200 km around New Caledonia. We identified two separate genetic groups for E. carbunculus and a single group for E. coruscans. There were many singleton haplotypes distributed among geographic regions, indicating minimal spatial differentiation in genetic structure between regions for each species, although one of the genetic groups for E. carbunculus was in only two of the three regions. Conservation and management directives should consider both species as a single genetic stock among these three widespread regions. Our results provide evidence that stock structure might be less variable in the South Pacific than reported elsewhere, possibly indicating that trans-boundary management may be required in this region for deep-water snapper fisheries. Further refinement (including taxonomy) is required for E. carbunculus to characterize the different lineages observed.

Evidence for a new introduction of the pitch canker fungus Fusarium circinatum in South Africa

Fusarium circinatum causes pitch canker of Pinus species in many parts of the world. The fungus was first recorded in South Africa in 1990 as a pathogen of P. patula seedlings and emerged later as a pathogen of established plantation trees, especially P. radiata in the Western Cape Province (WCP). In this study the population biology of F. circinatum in the WCP was explored. The aim was to determine the possible origin and reproductive mode of the pathogen, with the ultimate intention of informing disease management strategies in the region. Vegetative compatibility assays, sexual mating studies and amplified fragment length polymorphism analyses were used. For comparative purposes, an isolate collection obtained from diseased P. radiata seedlings in a commercial nursery in the region, as well as a set of isolates from commercial seedling nurseries in the central and northern parts of South Africa, were included. The results showed that the WCP population of F. circinatum employs a predominantly asexual mode of reproduction and that it is highly differentiated from populations of the fungus elsewhere in South Africa. However, limited genetic structure was found within the respective WCP isolate collections. Overall these findings suggest that pitch canker in the WCP originates from one or more separate introductions of the pathogen and that its movement in the region is not restricted. More effective strategies are thus required to limit and manage the effects of F. circinatum in plantations in this region of South Africa.

Diversity and geneflow in a migratory frugivorous fish: implications for Amazonian habitat connectivity

Colossoma macropomum is an ecologically and economically important fish distributed throughout the major tributaries of the Amazon River. C. macropomum require a suite of habitat types for different life stages making them potentially susceptible to the impacts of habitat fragmentation and alteration. As a means of better understanding the potential impacts of development, baseline data on connectivity and patterns of gene flow in species from relatively undisturbed habitat will be of value to monitor potential ecosystem impacts of anthropogenic habitat alteration on native fish communities. We used 13 single sequence repeat markers to determine if fine-scale structuring could be detected at the landscape scale at the Pacaya Samiria National Reserve, Peru. We also applied a model testing approach to evaluate the strength of different migration models, including panmixia, stepping stone and isolation models. Bayesian clustering detected a single genetic grouping across 131 fish. However, a comparison of marginal likelihoods for alternative migration models across PSNR supported a stepping stone model, rather than panmixia (Probability ~1.0). These results demonstrate that even in highly migratory fish with limited genetic structure, the effects of anthropogenic aquatic habitat alterations can be explored using genetic data.

Spatial genetic structure and asymmetrical gene flow within the Pacific walrus

AbstractPacific walruses (Odobenus rosmarus divergens) occupying shelf waters of Pacific Arctic seas migrate during spring and summer from 3 breeding areas in the Bering Sea to form sexually segregated nonbreeding aggregations. We assessed genetic relationships among 2 putative breeding populations and 6 nonbreeding aggregations. Analyses of mitochondrial DNA (mtDNA) control region sequence data suggest that males are distinct among breeding populations (ΦST = 0.051), and between the eastern Chukchi and other nonbreeding aggregations (ΦST = 0.336–0.449). Nonbreeding female aggregations were genetically distinct across marker types (microsatellite FST = 0.019; mtDNA ΦST = 0.313), as was eastern Chukchi and all other nonbreeding aggregations (microsatellite FST = 0.019–0.035; mtDNA ΦST = 0.386–0.389). Gene flow estimates are asymmetrical from St. Lawrence Island into the southeastern Bering breeding population for both sexes. Partitioning of haplotype frequencies among breeding populations suggests that individuals exhibit some degree of philopatry, although weak. High levels of genetic differentiation among eastern Chukchi and all other nonbreeding aggregations, but considerably lower genetic differentiation between breeding populations, suggest that at least 1 genetically distinct breeding population remained unsampled. Limited genetic structure at microsatellite loci between assayed breeding areas can emerge from several processes, including male-mediated gene flow, or population admixture following a decrease in census size (i.e., due to commercial harvest during 1880–1950s) and subsequent recovery. Nevertheless, high levels of genetic diversity in the Pacific walrus, which withstood prolonged decreases in census numbers with little impact on neutral genetic diversity, may reflect resiliency in the face of past environmental challenges.

Limited divergence in the spatially subdivided population of the Hawaiian mushroomRhodocollybia laulaha

Here we report the first population genetic examination of a fungus in Hawaii and, to our knowledge, the only investigation of a saprotrophic fungal population distributed across an oceanic archipelago. Rhodocollybia laulaha fruits abundantly in the native rain forests of Hawaii from June through December. Its range includes the geographic extent of the Hawaiian Archipelago; however, this range is highly fragmented because of the discontinuous distribution of the native forest habitat where R. laulaha occurs. We hypothesized that significant patterns of population structure would be recovered within the geographic range of the Hawaiian mushroom R. laulaha resulting from divergence between isolated subpopulations. We tested for population structure and related inferred patterns of restricted gene flow to geographic distance, major geographic features such as mountain peaks and oceans, elevation zones, and spore morphology. We included 120 R. laulaha collections using data from the rRNA IGS1 region, two microsatellite loci, and 184 AFLP loci. Analyses of these genetic data suggest limited genetic structure among R. laulaha subpopulations in Hawaii correlated mostly with geographic distance. Patterns associated with specialization to elevation or spore morphology were not recovered. The limited geographic structure observed in R. laulaha is consistent with relatively recent population fragmentation.

Hybridization among Arctic white‐headed gulls (Larus spp.) obscures the genetic legacy of the Pleistocene

We studied the influence of glacial oscillations on the genetic structure of seven species of white-headed gull that breed at high latitudes (Larus argentatus, L. canus, L. glaucescens, L. glaucoides, L. hyperboreus, L. schistisagus, and L. thayeri). We evaluated localities hypothesized as ice-free areas or glacial refugia in other Arctic vertebrates using molecular data from 11 microsatellite loci, mitochondrial DNA (mtDNA) control region, and six nuclear introns for 32 populations across the Holarctic. Moderate levels of genetic structure were observed for microsatellites (FST= 0.129), introns (ΦST= 0.185), and mtDNA control region (ΦST= 0.461), with among-group variation maximized when populations were grouped based on subspecific classification. Two haplotype and at least two allele groups were observed across all loci. However, no haplotype/allele group was composed solely of individuals of a single species, a pattern consistent with recent divergence. Furthermore, northernmost populations were not well differentiated and among-group variation was maximized when L. argentatus and L. hyberboreus populations were grouped by locality rather than species, indicating recent hybridization. Four populations are located in putative Pleistocene glacial refugia and had larger τ estimates than the other 28 populations. However, we were unable to substantiate these putative refugia using coalescent theory, as all populations had genetic signatures of stability based on mtDNA. The extent of haplotype and allele sharing among Arctic white-headed gull species is noteworthy. Studies of other Arctic taxa have generally revealed species-specific clusters as well as genetic structure within species, usually correlated with geography. Aspects of white-headed gull behavioral biology, such as colonization ability and propensity to hybridize, as well as their recent evolutionary history, have likely played a large role in the limited genetic structure observed.

Phylogeographic insights into an irruptive pest outbreak

Irruptive forest insect pests cause considerable ecological and economic damage, and their outbreaks have been increasing in frequency and severity. We use a phylogeographic approach to understand the location and progression of an outbreak by the MPB (Dendroctonus ponderosae Hopkins), an irruptive bark beetle that has caused unprecedented damage to lodgepole pine forests in western North America and is poised to expand its range across the boreal forest. We sampled MPB populations across British Columbia and Alberta and used phylogeographic methods to describe lineage diversification, characterize population structure, investigate expansion dynamics, and identify source populations of the outbreak. Using 1181 bp of mitochondrial DNA sequence from 267 individuals, we found high haplotype diversity, low nucleotide diversity, and limited lineage diversification. The overall pattern was consistent with isolation by distance at a continental scale, and with reduced diversity and population structure in the northerly, outbreak regions. Post-Pleistocene expansion was detected, however more recent expansion signals were not detected, potentially due to the size and rapid rate of range expansion. Based on the limited genetic structure, there were likely multiple source populations in southern British Columbia, although the magnitude of the demographic expansion and rate of spread have obscured the signature of these source populations. Our data highlight the need for caution in interpreting phylogeographic results for species with similar demographics.

Very Low Mitochondrial Diversity and Genetic Homogeneity in the Starfish Echinaster sepositus Along the Tunisian Coast

Phylogeographic structure in marine organisms is ascribed to contemporary and/or historical barriers to dispersal (Benzie and Williams 1997; Waters and Roy 2003). In addition, life history mode can exert a strong influence on the genetic structure of populations (Hart et al. 1997; Riginos and Victor 2001), as illustrated by the consequences of the extreme heterogeneity of dispersal capability on geographic distribution of genetic polymorphism (Kinlan and Gaines 2003). For instance, some species with long-lived planktotrophic larvae show vast geographic distributions and limited genetic structure (Booth and Ovenden 2000; Colgan et al. 2005). Conversely, taxa with brief larval stages or direct development often show marked phylogeographic structure (Collin 2001; Planes et al. 2001; Riginos and Victor 2001). Mitochondrial DNA is commonly used as a genetic marker to infer phylogeographic relationships in most marine organisms (Avise 2000). The gene coding for cytochrome c oxidase subunit I (COI) is among the most frequently used markers because of its high degree of variability (e.g., Avise 2000; Duran et al. 2004a; Lee 2000). Among marine invertebrates, few examples of almost negligible levels of intraspecific variation in COI have been reported for basal phyla such as porifera and anthozoa (Duran et al. 2004b; France and Hoover 2002; Shearer et al. 2002). In asteroids, the COI gene has proven to be highly polymorphic (Flowers and Foltz 2001; Waters et al. 2004).

Will all the trees fall? Variable resistance to an introduced forest disease in a highly susceptible host

Although tanoak ( Notholithocarpus densiflorus syn. Lithocarpus densiflorus) is the species most affected by the introduced pathogen Phytophthora ramorum, with demonstrable risk of extirpation, little is known about the origin, range or structuring of the tree's susceptibility. We examined variation in resistance to P. ramorum using a wound inoculation assay of detached leaves from trees at five geographically separated sites, and a non-wound inoculation assay on twigs from trees at two sites. The structure of variation in resistance was compared to the structure at nine nuclear microsatellite markers. Resistance varied quantitatively, with 23% and 12% of the variation among individuals and populations, respectively. There was a significant correlation between resistance in detached leaves and lesion size in non-wounding twig inoculations. Among-population genetic diversity at nine microsatellite loci was weakly structured but significantly non-zero, with 9.5% of variation among populations. Within-population neutral genetic diversity was a poor predictor of resistance, and estimates of phenotypic distances for resistance were no greater than neutral genetic distances. The limited phenotypic and genetic structure we found indicates that tanoaks at all study sites are susceptible, and there is no evidence of prior selection for disease resistance. We conclude that tanoak populations across the species’ range are at risk, but local disease dynamics will depend on both host genetics and environmental conditions.

Matching Management to Biological Scale: Connectivity among Lacustrine Brook Trout Populations

AbstractDetermining appropriate spatial scales for managing fisheries is a key element of sustainable management. For inland fisheries, management or harvest regulations are often implemented as general regional guidelines or on a lake‐by‐lake basis. Wild lacustrine brook trout Salvelinus fontinalis from four waterbodies in the Galipo River watershed of Algonquin Provincial Park, Ontario, were used as a model system to determine the extent of population structure among lakes and to identify appropriate scale(s) for managing inland brook trout fisheries. Individual multilocus genotypes were measured using 10 microsatellite loci and were used to characterize movement and gene flow among lakes. Both population‐ and individual‐based analyses showed very little genetic structure among all pairs of waterbodies, suggesting high levels of movement and gene flow between all pairs of lakes. Varying levels of limited genetic structure between pairs of lakes indicate that gene flow may not be uniform within the study system. These results suggest that contrary to previous studies, local watersheds may be the most appropriate management scale for lacustrine brook trout populations in watersheds where physical characteristics provide the potential for migration and gene flow.

Characterizing dispersal patterns in a threatened seabird with limited genetic structure

Genetic assignment methods provide an appealing approach for characterizing dispersal patterns on ecological time scales, but require sufficient genetic differentiation to accurately identify migrants and a large enough sample size of migrants to, for example, compare dispersal between sexes or age classes. We demonstrate that assignment methods can be rigorously used to characterize dispersal patterns in a marbled murrelet (Brachyramphus marmoratus) population from central California that numbers approximately 600 individuals and is only moderately differentiated (F(ST) approximately 0.03) from larger populations to the north. We used coalescent simulations to select a significance level that resulted in a low and approximately equal expected number of type I and II errors and then used this significance level to identify a population of origin for 589 individuals genotyped at 13 microsatellite loci. The proportion of migrants in central California was greatest during winter when 83% of individuals were classified as migrants compared to lower proportions during the breeding (6%) and post-breeding (8%) seasons. Dispersal was also biased toward young and female individuals, as is typical in birds. Migrants were rarely members of parent-offspring pairs, suggesting that they contributed few young to the central California population. A greater number of migrants than expected under equilibrium conditions, a lack of individuals with mixed ancestry, and a small number of potential source populations (two), likely allowed us to use assignment methods to rigorously characterize dispersal patterns for a population that was larger and less differentiated than typically thought required for the identification of migrants.

Regional Genetic Structure in the Magellanic Penguin (Spheniscus magellanicus) Suggests Metapopulation Dynamics

ABSTRACT. Using microsatellite markers and mitochondrial DNA (mtDNA) sequences (cytochrome oxidase 1 gene), we estimated levels of genetic structuring among nine Magellanic Penguin (Spheniscus magellanicus) colonies distributed throughout three major reproductive regions of the South Atlantic Ocean. Overall, breeding colonies showed relatively high levels of genetic diversity at both nuclear and mtDNA markers (mean heteorzygosity: He = 0.598; mean allelic diversity: A = 7.11; mtDNA haplotype diversity: h = 0.812). A hierarchical analysis of molecular variance based on microsatellite data showed limited genetic structuring of breeding colonies, with 99% of the variation explained by differences among individuals and 0.7–1.0% attributed to differences among the three regions. The mtDNA analysis revealed higher levels of genetic structuring, with 3.43% of the variation explained by regions and 2.24% explained by colonies within the regions. Furthermore, a Mantel test revealed a significant association betwee...

Limited genetic variation and structure in softshell clams (Mya arenaria) across their native and introduced range

To offset declines in commercial landings of the softshell clam, Mya arenaria, resource managers are engaged in extensive stocking of seed clams throughout its range in the northwest Atlantic. Because a mixture of native and introduced stocks can disrupt locally adapted genotypes, we investigated genetic structure in M. arenaria populations across its current distribution to test for patterns of regional differentiation. We sequenced mitochondrial cytochrome oxidase I for a total of 212 individuals from 12 sites in the northwest Atlantic (NW Atlantic), as well as two introduced sites, the northeast Pacific (NE Pacific), and the North Sea Europe (NS Europe). Populations exhibited extremely low genetic variation, with one haplotype dominating (65–100%) at all sites sampled. Despite being introduced in the last 150–400 years, both NE Pacific and NS Europe populations had higher diversity measures than those in the NW Atlantic and both contained private haplotypes at frequencies of 10–27% consistent with their geographic isolation. While significant genetic structure (F ST = 0.159, P < 0.001) was observed between NW Atlantic and NS Europe, there was no evidence for genetic structure across the pronounced environmental clines of the NW Atlantic. Reduced genetic diversity in mtDNA combined with previous studies reporting reduced genetic diversity in nuclear markers strongly suggests a recent population expansion in the NW Atlantic, a pattern that may result from the retreat of ice sheets during Pleistocene glacial periods. Lack of genetic diversity and regional genetic differentiation suggests that present management strategies for the commercially important softshell clam are unlikely to have a significant impact on the regional distribution of genetic variation, although the possibility of disrupting locally adapted stocks cannot be excluded.

Population viscosity can promote the evolution of altruistic sterile helpers and eusociality

Because it increases relatedness between interacting individuals, population viscosity has been proposed to favour the evolution of altruistic helping. However, because it increases local competition between relatives, population viscosity may also act as a brake for the evolution of helping behaviours. In simple models, the kin selected fecundity benefits of helping are exactly cancelled out by the cost of increased competition between relatives when helping occurs after dispersal. This result has lead to the widespread view, especially among people working with social organisms, that special conditions are required for the evolution of altruism. Here, we re-examine this result by constructing a simple population genetic model where we analyse whether the evolution of a sterile worker caste (i.e. an extreme case of altruism) can be selected for by limited dispersal. We show that a sterile worker caste can be selected for even under the simplest life-cycle assumptions. This has relevant consequences for our understanding of the evolution of altruism in social organisms, as many social insects are characterized by limited dispersal and significant genetic population structure.

Limited genetic structure and evidence for dispersal among populations of the endangered Florida grasshopper sparrow, Ammodramus savannarum floridanus

The Florida grasshopper sparrow, Ammodramus savannarum floridanus, is a non-migratory, endangered subspecies endemic to the prairie region of south-central Florida. It has experienced significant population declines and is currently restricted to five locations. We found substantial levels of variation in microsatellites and mtDNA control region sequences, estimates of inbreeding genetic effective population sizes that were much larger than the estimated census size, and no evidence of inbreeding within five sampled populations (n = 105). We also found a lack of genetic structure among populations (FST = 0.0123 for microsatellites and θ = 0.008 for mtDNA), and evidence for dispersal between populations, with 7.6% of all individuals identified as immigrants to their population of capture. We suggest that the subspecies be managed as a single management unit on a regional scale rather than as multiple management units on a local subpopulation scale. There is still a limited opportunity to preserve much of the present genetic variation in this subspecies, if immediate measures are taken to reverse the current population decline before this variation is reduced by genetic drift.