Individual-based Assignment Research Articles

Two Distinct Life History Strategies of Atlantic Sturgeon in the Ogeechee River, Georgia

Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) is an anadromous, widely distributed, highly migratory sturgeon subspecies that occurs in rivers and marine waters along the North American Atlantic Coast. This fish has shown widespread declines and has been afforded conservation protections, including some based in the U.S. on the delineation of Distinct Population Segments (DPS) under the Endangered Species Act. The management of Atlantic sturgeon will benefit from the knowledge of its population structure as well as the ability to uniquely identify individuals (in relation to population origin) that are vulnerable to anthropogenic stressors at sites outside of their natal estuaries. We used microsatellite analysis to estimate the genetic population structure of Atlantic sturgeon from 13 spawning rivers ranging from the St. Lawrence River, Quebec to the Satilla River, Georgia. Individual Based Assignment (IBA) testing was used to estimate the contribution of each population to mixed-stock aggregations in coastal waters and in a non-natal estuary. An unexpected finding was the discovery of two distinct genetic clusters of juvenile Atlantic sturgeon in the Ogeechee River, Georgia, with specimens in the two clusters differing significantly in terms of mean total length. Additionally, three distinct genetic clusters were detected within the Satilla River juvenile collection, along with two clusters within the Edisto River sample. In F1ST and FST analyses, the extent of the pairwise genetic differentiation between the two genetic clusters in the Ogeechee River and the three in the Satilla River was greater than that between all other pairwise comparisons among rivers in the South Atlantic DPS. In contrast, we found no evidence of the genetic partitioning of juvenile sturgeon within the neighboring Savannah or Altamaha river populations. Using IBA, we found that the overall Ogeechee River population made a moderate contribution (8.3%) to the overall mixed-stock collections (n = 1512) from coastal North Carolina to the Bay of Fundy. Surprisingly, all of the Ogeechee River-assigned specimens (n = 125) in these mixed-stock aggregations were representatives of only one of the two Ogeechee River genetic clusters. These results suggest that the two Ogeechee River genetic clusters exhibit significantly different life history strategies, with one being resident and the second being highly migratory.

Cryptic genetic diversity in the mottled rabbitfish Siganus fuscescens with mitochondrial introgression at a contact zone in the South China Sea

The taxonomy of the mottled rabbitfish Siganus fuscescens species complex has long been challenging. In this study, we analyzed microsatellite genotypes, mitochondrial lineages, and morphometric data from 373 S. fuscescens individuals sampled from the northern Philippines and Hong Kong (South China Sea, Philippine Sea and Sulu Sea basins), to examine putative species boundaries in samples comprising three co-occurring mitochondrial lineages previously reported to characterize S. fuscescens (Clade A and Clade B) or S. canaliculatus (Clade C). We report the existence of two cryptic species within S. fuscescens in the northeast region of the South China Sea and northern Philippine Sea, supported by genetic and morphological differences. Individual-based assignment methods recovered concordant groupings of individuals into two nuclear genotype clusters (Cluster 1, Cluster 2) with (1) limited gene flow, if any, between them (FST = 0.241; P < 0.001); (2) low frequency of later-generation hybrids; (3) significant association with mitochondrial Clade A and Clade B, respectively; and (4) subtle yet significant body shape differences as inferred from geometric morphometric analysis. The divergence between mitochondrial Clade C and the two other clades was not matched by genetic differences at microsatellite marker loci. The occurrence of discordant mitonuclear combinations (20.5% of the total number of individuals) is thought to result from mitochondrial introgression, consistent with a scenario of demographic, and presumably spatial, post-Pleistocene expansion of populations from northern regions into a secondary contact zone in the South China Sea. Mitonuclear discordance due to introgression obscures phylogenetic relationships for recently-diverged lineages, and cautions against the use of mitochondrial markers alone for species identification within the mottled rabbitfish species complex in the South China Sea region.

Origin of Atlantic Sturgeon Collected off the Delaware Coast during Spring Months

AbstractAtlantic Sturgeon Acipenser oxyrinchus oxyrinchus was federally listed under the U.S. Endangered Species Act as five distinct population segments (DPS). Currently, at least 18 estuaries coastwide host spawning populations and the viability of these vary, requiring differing levels of protection. Subadults emigrate from their natal estuaries to marine waters where they are vulnerable to bycatch; one of the major threats to the rebuilding of populations. As a result, identifying the population origin of Atlantic Sturgeon in coastal waters is critical to development of management plans intended to minimize interactions of the most imperiled populations with damaging fisheries. We used mitochondrial DNA control region sequencing and microsatellite DNA analyses to determine the origin of 261 Atlantic Sturgeon collected off the Delaware coast during the spring months. Using individual‐based assignment (IBA) testing and mixed stock analysis, we found that specimens originated from all nine of our reference populations and the five DPSs used in the listing determination. Using IBA, we found that the Hudson River population was the largest contributor (38.3%) to our coastal collection. The James (19.9%) and Delaware (13.8%) river populations, at one time thought to be extirpated or nearly so, were the next largest contributors. The three populations combined in the South Atlantic DPS contributed 21% of specimens; the Altamaha River, the largest population in the South Atlantic DPS, only contributed a single specimen to the collection. While the origin of specimens collected on the Delaware coast was most likely within rivers of the New York Bight DPS (52.1%), specimens that originated elsewhere were also well represented. Genetic analyses provide a robust tool to identify the population origin of individual sturgeon outside of their natal estuaries and to determine the quantitative contributions of individual populations to coastal aggregations that are vulnerable to bycatch and other anthropogenic threats.Received March 17, 2014; accepted September 3, 2014

Genetic diversity and effective size of Atlantic sturgeon, Acipenser oxyrhinchus oxyrhinchus river spawning populations estimated from the microsatellite genotypes of marine-captured juveniles

Juvenile Atlantic sturgeon (Acipenser oxyrhinchus oxyrhinchus) forming aggregations at coastal sites in the mid-Atlantic Bight were subjected to a mixed stock analysis (MSA) and individual-based assignment using twelve microsatellite loci. We confirmed earlier findings from an analysis of mitochondrial DNA that three river spawning populations (Hudson, James and Delaware Rivers) are the primary sources of these particular marine aggregations. Of the 460 individuals sampled 322, 36 and 47 were assigned to the Hudson, James and Delaware Rivers, respectively. MSA estimated that the New York Bight Distinct Population Segment (Hudson River and Delaware River) contributed 83–90 % of individuals to the marine aggregations and the Chesapeake (James River) and Southeast Distinct Population Segments contributed 5.5–11 %. Mean M-ratios were lower than expected at equilibrium in all three rivers (Delaware = 0.726, Hudson = 0.748, James = 0.664), indicative of genetic bottlenecks affecting all three spawning populations. Further, there were low but detectable levels of inbreeding in all three rivers populations. Effective population size (Ne) was estimated for three populations: Hudson River (172–230 individuals), James River (40–100 individuals) and Delaware River (75–186 individuals). Despite these issues, simulations based on life-history information and the Ne estimates suggest that if ongoing management measures are effective, contemporary levels of population genetic diversity are likely to be retained over the next century.

Genetic evidence for male‐biased dispersal in theQinghai toad‐headed agamidPhrynocephalus vlangaliiand its potential link to individual social interactions

Sex-biased dispersal has profound impacts on a species' biology and several factors have been attributed to its evolution, including mating system, inbreeding avoidance, and social complexity. Sex-biased dispersal and its potential link to individual social interactions were examined in the Qinghai toad-headed agamid (Phrynocephalus vlangalii). We first determined the pattern of sex-biased dispersal using population genetic methods. A total of 345 specimens from 32 sites in the Qaidam Basin were collected and genotyped for nine microsatellite DNA loci. Both individual-based assignment tests and allele frequency-based analyses were conducted. Females revealed much more genetic structure than males and all results were consistent with male-biased dispersal. First-generation migrants were also identified by genetic data. We then examined eight social interaction-related morphological traits and explored their potential link to sex-biased dispersal. Female residents had larger heads and longer tails than female migrants. The well-developed signal system among females, coupled with viviparity, might make remaining on natal sites beneficial, and hence promote female philopatry. Dominant females with larger heads were more likely to stay. Contrary to females, male migrants had larger heads and belly patches than residents, suggesting that dispersal might confer selective advantages for males. Such advantages may include opportunities for multiple mating and escaping from crowded sites. Large belly patches and several other morphological traits may assist their success in obtaining mates during dispersal. Furthermore, a relatively high relatedness (R = 0.06) among females suggested that this species might have rudimentary social structure. Case studies in “less” social species may provide important evidence for a better understanding of sex-biased dispersal.

Stock Origins of Subadult and Adult Atlantic Sturgeon, Acipenser oxyrinchus, in a Non-natal Estuary, Long Island Sound

The anadromous acipenserid Atlantic sturgeon Acipenser oxyrinchus was listed in 2012 under the U.S. Endangered Species Act as having four endangered and one threatened distinct population segment (DPS) in American waters. Anthropogenic activities outside of natal estuaries, particularly bycatch, may hinder the abilities of some populations to rebuild. Most Atlantic sturgeon are residential for their first 2–6 years within their natal estuaries, whereas older subadults and adults may migrate to non-natal estuaries and coastal locations. Previous studies demonstrated that subadults and adults aggregate during summer at locations in Long Island Sound (LIS) and its tributary, the Connecticut River; however, the population origin of these fish is unknown. Because of its geographic proximity and relatively robust population, we hypothesized that the LIS and Connecticut River aggregations were almost solely derived from the Hudson River. We used microsatellite nuclear DNA analysis at 11 loci and mitochondrial DNA control region sequence analyses to estimate the relative contributions of nine Atlantic sturgeon populations and the five DPS to these aggregations using individual-based assignment tests and mixed-stock analysis. From 64 to 73 % of specimens from LIS were estimated to be of Hudson origin. Similarly, 66–76 % of specimens from the Connecticut River were of Hudson origin. However, moderate numbers of specimens were detected from distant spawning populations in the southeastern DPS and from two populations once thought to be extirpated or nearly so, the James River (6–7.3 %), and the Delaware River (7.6–12 %). Additionally, specimens were detected from all five DPS in both the LIS and Connecticut River collections. These results highlight the difficulty of evaluating the status of individual Atlantic sturgeon populations because of the propensity of subadults and adults to migrate for extended duration to distant sites where they may be vulnerable to anthropogenic disturbances.

Species identification in the trematomid family using nuclear genetic markers

The Trematominae, a subfamily of the Nototheniidae, are typical of the high-Antarctic shelf waters. Within the Trematominae examples of phenotypic plasticity and possible cryptic speciation have been observed. Morphological identification of adult stages can be problematic in cases of high phenotypic plasticity or cryptic speciation. Additionally, postlarval and juvenile stages often have traits still under development and which lack distinction. A microsatellite DNA multiplex of six markers has been developed for Trematomus newnesi (Van Houdt et al. 2006). This multiplex was tested on five additional trematomid taxa: Pagothenia borchgrevinki, Trematomus bernacchii, Trematomus eulepidotus, Trematomus hansoni and Trematomus scotti. We used these six microsatellite loci to assess the genetic differentiation among species and the resolution power of these loci for individual-based assignment methods. The six species could be well discriminated by conventional methods such as principal component analysis and distance-based methods, and individual Bayesian assignment methods. This marker set can be used for a number of purposes, including the identification of eggs and larval and adult stages. It is also useful for the investigation of recent phylogenetic patterns, as well as the detection of cryptic speciation, which has been suggested for T. bernacchii and T. newnesi but never confirmed with high polymorphic genetic markers.

Candidate loci reveal genetic differentiation between temporally divergent migratory runs of Chinook salmon (Oncorhynchus tshawytscha)

Local adaptation is a dynamic process driven by selection that can vary both in space and time. One important temporal adaptation for migratory animals is the time at which individuals return to breeding sites. Chinook salmon (Oncorhynchus tshawytscha) are excellent subjects for studying the genetic basis of temporal adaptation because their high seasonal homing fidelity promotes reproductive isolation leading to the formation of local populations across diverse environments. We tested for adaptive genetic differentiation between seasonal runs of Chinook salmon using two candidate loci; the circadian rhythm gene, OtsClock1b, and Ots515NWFSC, a microsatellite locus showing sequence identity to three salmonid genes central to reproductive development. We found significant evidence for two genetically distinct migratory runs in the Feather River, California (OtsClock1b: F(ST)=0.042, P=0.02; Ots515NWFSC: F(ST)=0.058, P=0.003). In contrast, the fall and threatened spring runs are genetically homogenous based on neutral microsatellite data (F(ST)=-0.0002). Similarly, two temporally divergent migratory runs of Chinook salmon from New Zealand are genetically differentiated based on polymorphisms in the candidate loci (OtsClock1b: F(ST)=0.083, P-value=0.001; Ots515NWFSC: F(ST)=0.095, P-value=0.000). We used an individual-based assignment method to confirm that these recently diverged populations originated from a single source in California. Tests for selective neutrality indicate that OtsClock1b and Ots515NWFSC exhibit substantial departures from neutral expectations in both systems. The large F(ST )estimates could therefore be the result of directional selection. Evidence presented here suggests that OtsClock1b and Ots515NWFSC may influence migration and spawning timing of Chinook salmon in these river systems.

Demographic bottlenecks and low gene flow in remnant populations of the critically endangered Berchemiella wilsonii var. pubipetiolata (Rhamnaceae) inferred from microsatellite markers

Berchemiella wilsonii var. pubipetiolata (Rhamnaceae) is an endangered plant with only four remnant populations in eastern China. Population genetic information is essential for understanding population history and formulating conservation strategies for this species. Thirteen microsatellite loci were used to investigate genetic variation and population structure of the four remnant populations. Moderate levels of expected heterozygosity (HE = 0.466–0.543) and low allelic diversity (A = 3.1–3.6 and AR = 2.2–2.4, respectively) were observed within populations. Bottleneck tests found three out of four populations to deviate from mutation-drift equilibrium under the two-phase model (TPM), suggesting a recent population decline, which is congruent with known demographic history. The evolutionary history of the species seems dominated by genetic drift rather than gene flow. Low historical gene flow was inferred from several different approaches and Nm ranged from 0.582 by the private allele method to 0.783 by the coalescent method. Contemporary gene flow was also found to be even lower for only one first generation migrant was detected with individual-based assignment analysis. Restricted pollen and seed dispersal as well as a recent decline in population size associated with habitat fragmentation may have contributed to low levels of historical and contemporary gene flow, and resulted in a high genetic differentiation. Under this scenario, Berchemiella wilsonii var. pubipetiolata populations are expected to display more pronounced population genetic structure in the future as a result of increased inbreeding and genetic drift.

Interplay between ecological, behavioural and historical factors in shaping the genetic structure of sympatric walleye populations (Sander vitreus)

Disentangling ecological, behavioural and evolutionary factors responsible for the presence of stable population structure within wild populations has long been challenging to population geneticists. This study primarily aimed at decoding population structure of wild walleye (Sander vitreus) populations of Mistassini Lake (Québec, Canada) in order to define source populations to be used for the study of spatial partitioning using individual-based multilocus assignment methods, and decipher the dynamics of individual dispersal and resulting patterns of spatial resource partitioning and connectivity among populations. A second objective was to elucidate the relationships between biological characteristics (sex, size, age and population of origin) and an individual's probability to migrate and/or disperse. To do so, a total of 780 spawning individuals caught on five distinct spawning sites, and 1165 postspawning individuals, captured over two sampling seasons (2002-2003) were analysed by means of eight microsatellite loci. Four temporally stable walleye populations associated with distinct reproductive grounds were detected. These populations were differentially distributed among lake sectors during their feeding migration and their spatial distribution was stable over the two sampling seasons. Dispersing individuals were identified (n=61); these revealed asymmetrical patterns of dispersal between populations, which was also confirmed by divergent admixture proportions. Regression models underlined population of origin as the only factor explaining differential dispersal of individuals among populations. An analysis of covariance (ancova) indicated that larger individuals tended to migrate from their river of origin further away in the lake relative to smaller fish. In summary, this study underlined the relevance of using individual-based assignment methods for deciphering dynamics of connectivity among wild populations, especially regarding behavioural mechanisms such as differential spatial partitioning and dispersal responsible for the maintenance of genetic population structure.

Intra-annual genetic variation in the downstream larval drift of sutchi catfish (Pangasianodon hypophthalmus) in the Mekong river

Larvae of the sutchi catfish Pangasianodon hypophthalmus were collected during peak downstream drift in the Lower Mekong river on four occasions over an 8-week period during the 2003 spawning season, and genotyped using seven microsatellite loci. We provide evidence for several heterogeneous groups within and among the temporally discrete larval peak samples. Strong evidence for a significant deficit of heterozygotes was observed for each larval sample and the pooled sample, possibly due to population admixture. Although individual-based assignment tests suggested that each larval peak sample was admixed, significant but low genetic differentiation was observed among larval samples (FST = 0.0052, P < 0.01). The lack of significant relatedness confirms the multifamily composition of each larval group, excluding family bias to explain the observed genetic heterogeneity. Both the entire larval peak and each temporally separated larval peak originated from spawning groups with heterogeneous allelic composition involving several distinct spawning events. We propose three explanations to account for our findings: (1) the ecological match/mismatch hypothesis; (2) the genetic 'sweepstakes' selection hypothesis; and (3) life-history-specific characteristics of the spawning populations. Finally, an intra-annual shift in the contribution of the spawning populations to the larval drift was detected on successive occasions.

Microsatellite conservation and Bayesian individual assignment in four Anguilla species

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 319:251-261 (2006) - doi:10.3354/meps319251 Microsatellite conservation and Bayesian individual assignment in four Anguilla species G. E. Maes1,*, J. M. Pujolar1, J. A. M. Raeymaekers1, J. Dannewitz2, F. A. M. Volckaert1 1Laboratory of Aquatic Ecology, Katholieke Universiteit Leuven, Ch. de Bériotstraat, 32, 3000 Leuven, Belgium 2Institute of Freshwater Research, National Board of Fisheries, 178 93 Drottningholm, Sweden *Email: gregory.maes@bio.kuleuven.be ABSTRACT: Microsatellite flanking regions are often highly conserved in fish taxa, enabling their application in other species within or outside the source family. Moderately variable microsatellite markers may also be good candidates for species identification using multi-locus genotypes. We evaluated the degree of conservation of microsatellite flanking regions and the level of polymorphism in 4 commercially important eel species (Anguilla anguilla, A. rostrata, A. japonica and A. marmorata). Using multiplex polymerase chain reactions developed for the first 2 taxa, we assessed the discrimination power of an individual-based assignment method to differentiate all 4 species without initial species information. Detection and classification of each species was performed with high confidence (>90%), as was assignment of randomly sampled individuals to pre-defined species (>95%). Our results demonstrate the highly conserved nature of microsatellites and their level of polymorphism in Anguilla species. Although an inverse relationship was found between genetic diversity and differentiation estimates, likely due to homoplasy, assignment proved to be superior to multivariate and distance-based approaches for identifying the 4 species. The method enables the rapid screening of morphologically similar eel species using only 4 co-dominant nuclear loci and the detection of natural hybridisation or anthropogenic mixing between internationally highly traded species. KEY WORDS: Admixture · Anguillids · Flanking region · Genetic variability · Homoplasy · Multiplex-PCR · Species identification Full text in pdf format Supplementary appendix PreviousNextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 319. Online publication date: August 18, 2006 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2006 Inter-Research.

The effects of gene flow and population isolation on the genetic structure of␣reintroduced wild turkey populations: Are genetic signatures of source populations retained?

To counter losses of genetic diversity in reintroduced populations, species sometimes are reintroduced into networks of populations with the potential to exchange individuals. In reintroduced populations connected by gene flow, patterns of genetic structure initiated by the founding event may become obscured, and populations may eventually follow an isolation-by-distance model of genetic differentiation. Taking advantage of well-documented reintroduction histories of wild turkey populations in Indiana, we assessed the degree to which gene flow among reintroduced populations has obscured genetic signatures left by the founding events. Using a suite of nuclear microsatellite loci and sequence data from the mitochondrial control region, we characterized the level of genetic diversity and degree of genetic structure within and among: (1) reintroduced populations in isolated northern Indiana Fish and Wildlife Areas, (2) reintroduced populations in southern Indiana Fish and Wildlife Areas, where the distribution of populations is more continuous, and (3) source populations used for these reintroductions. We also utilized individual-based assignment tests to determine the relative contribution of source populations to the current distribution of alleles in reintroduced populations. Our results indicate that wild turkey reintroductions in Indiana have left distinct genetic signatures on populations that are detectable even after several decades. Although we found some case-specific evidence for gene flow, particularly in regions where populations are in close proximity, our data indicate on overall paucity of gene flow at a regional scale. Such post-reintroduction genetic monitoring has immediate implications for the design of optimal strategies to reintroduce wildlife for conservation and management.

Genetic Population Structure of Brook Trout Inhabiting a Large River Watershed

Abstract The genetic population structure of brook trout Salvelinus fontinalis inhabiting the Miramichi River, New Brunswick, a large (14,000-km2) river system composed of three main stems, was assessed using six microsatellite DNA loci. Samples from 12 sites incorporating four temporal replicates were analyzed. An individual-based assignment method without a priori knowledge of geographic origin suggested the presence of five candidate source populations within the 12 sites. Drainage structuring based on the 12 sampling sites did not explain the observed patterns of genetic population structure (analysis of molecular variance: 0.74% of variance explained; not significant). Conversely, the five candidate source populations estimated under the assignment approach significantly explained the genetic population structure observed (3.47% of variance explained; P < 0.001), the level of population fragmentation within sampling sites increasing significantly with proximity to the mouth of the watershed (P = 0.01...

Lacustrine spatial distribution of landlocked Atlantic salmon populations assessed across generations by multilocus individual assignment and mixed-stock analyses.

The objective of this study was to assess the spatiotemporal distribution of four landlocked Atlantic salmon (Salmo salar) populations during their sympatric feeding phase in lake St-Jean (Québec, Canada). A total of 1100 fish captured over a period of 25 years was genotyped at six microsatellite loci in order to assess the temporal stability of the relative proportion of each population in different lake sectors using both individual-based assignment and mixed-stock analysis. Estimates of relative proportions obtained from both methods were highly correlated. A nonrandom spatial distribution of populations was observed for each period and, despite the fact that the overall proportion of each population varied over time, the pattern of differential distribution remained generally stable over time. Furthermore, there were indications that the extent of horizontal spatial overlap among populations was negatively correlated with that of their genetic differentiation at both microsatellites and a major histocompatibility complex locus, and independent of the geographical distance between the rivers of origin. We discuss the hypothesis that the temporal stability of spatial distribution, the lack of an association between spatial partitioning and geographical distance between rivers of origin, and the apparent negative correlation between spatial overlap and genetic differentiation, reflect the outcome of selective pressures driving behavioural differences for spatial niche partitioning among populations.