151
|
Genetic monitoring and effects of stocking practices on small Cyprinus carpio populations. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0231-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
152
|
Palstra FP, Ruzzante DE. Demographic and genetic factors shaping contemporary metapopulation effective size and its empirical estimation in salmonid fish. Heredity (Edinb) 2011; 107:444-55. [PMID: 21522167 PMCID: PMC3199926 DOI: 10.1038/hdy.2011.31] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 03/21/2011] [Accepted: 03/24/2011] [Indexed: 11/09/2022] Open
Abstract
The preservation of biodiversity requires an understanding of the maintenance of its components, including genetic diversity. Effective population size determines the amount of genetic variance maintained in populations, but its estimation can be complex, especially when populations are interconnected in a metapopulation. Theory predicts that the effective size of a metapopulation (meta-N(e)) can be decreased or increased by population subdivision, but little empirical work has evaluated these predictions. Here, we use neutral genetic markers and simulations to estimate the effective size of a putative metapopulation in Atlantic salmon (Salmo salar). For a weakly structured set of rivers, we find that meta-N(e) is similar to the sum of local deme sizes, whereas higher genetic differentiation among demes dramatically reduces meta-N(e) estimates. Interdemic demographic processes, such as asymmetrical gene flow, may explain this pattern. However, simulations also suggest that unrecognized population subdivision can also introduce downward bias into empirical estimation, emphasizing the importance of identifying the proper scale of distinct demographic and genetic processes. Under natural patterns of connectivity, evolutionary potential may generally be maintained at higher levels than the local population, with implications for conservation given ongoing species declines and habitat fragmentation.
Collapse
Affiliation(s)
- F P Palstra
- Biology Department, Dalhousie University, Halifax, Nova Scotia, Canada.
| | | |
Collapse
|
153
|
Barker JSF. Effective population size of natural populations of Drosophila buzzatii, with a comparative evaluation of nine methods of estimation. Mol Ecol 2011; 20:4452-71. [PMID: 21951766 DOI: 10.1111/j.1365-294x.2011.05324.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Allozyme and microsatellite data from numerous populations of Drosophila buzzatii have been used (i) to determine to what degree N(e) varies among generations within populations, and among populations, and (ii) to evaluate the congruence of four temporal and five single-sample estimators of N(e) . Effective size of different populations varied over two orders of magnitude, most populations are not temporally stable in genetic composition, and N(e) showed large variation over generations in some populations. Short-term N(e) estimates from the temporal methods were highly correlated, but the smallest estimates were the most precise for all four methods, and the most consistent across methods. Except for one population, N(e) estimates were lower when assuming gene flow than when assuming populations that were closed. However, attempts to jointly estimate N(e) and immigration rate were of little value because the source of migrants was unknown. Correlations among the estimates from the single-sample methods generally were not significant although, as for the temporal methods, estimates were most consistent when they were small. These single-sample estimates of current N(e) are generally smaller than the short-term temporal estimates. Nevertheless, population genetic variation is not being depleted, presumably because of past or ongoing migration. A clearer picture of current and short-term effective population sizes will only follow with better knowledge of migration rates between populations. Different methods are not necessarily estimating the same N(e) , they are subject to different bias, and the biology, demography and history of the population(s) may affect different estimators differently.
Collapse
Affiliation(s)
- J S F Barker
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia.
| |
Collapse
|
154
|
Shama LNS, Kubow KB, Jokela J, Robinson CT. Bottlenecks drive temporal and spatial genetic changes in alpine caddisfly metapopulations. BMC Evol Biol 2011; 11:278. [PMID: 21951631 PMCID: PMC3188517 DOI: 10.1186/1471-2148-11-278] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 09/27/2011] [Indexed: 11/21/2022] Open
Abstract
Background Extinction and re-colonisation of local populations is common in ephemeral habitats such as temporary streams. In most cases, such population turnover leads to reduced genetic diversity within populations and increased genetic differentiation among populations due to stochastic founder events, genetic drift, and bottlenecks associated with re-colonisation. Here, we examined the spatio-temporal genetic structure of 8 alpine caddisfly populations inhabiting permanent and temporary streams from four valleys in two regions of the Swiss Alps in years before and after a major stream drying event, the European heat wave in summer 2003. Results We found that population turnover after 2003 led to a loss of allelic richness and gene diversity but not to significant changes in observed heterozygosity. Within all valleys, permanent and temporary streams in any given year were not differentiated, suggesting considerable gene flow and admixture between streams with differing hydroperiods. Large changes in allele frequencies after 2003 resulted in a substantial increase in genetic differentiation among valleys within one to two years (1-2 generations) driven primarily by drift and immigration. Signatures of genetic bottlenecks were detected in all 8 populations after 2003 using the M-ratio method, but in no populations when using a heterozygosity excess method, indicating differential sensitivity of bottleneck detection methods. Conclusions We conclude that genetic differentiation among A. uncatus populations changed markedly both temporally and spatially in response to the extreme climate event in 2003. Our results highlight the magnitude of temporal population genetic changes in response to extreme events. More specifically, our results show that extreme events can cause rapid genetic divergence in metapopulations. Further studies are needed to determine if recovery from this perturbation through gradual mixing of diverged populations by migration and gene flow leads to the pre-climate event state, or whether the observed changes represent a new genetic equilibrium.
Collapse
Affiliation(s)
- Lisa N S Shama
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland.
| | | | | | | |
Collapse
|
155
|
Endersby NM, Hoffmann AA, White VL, Ritchie SA, Johnson PH, Weeks AR. Changes in the genetic structure of Aedes aegypti (Diptera: Culicidae) populations in Queensland, Australia, across two seasons: implications for potential mosquito releases. JOURNAL OF MEDICAL ENTOMOLOGY 2011; 48:999-1007. [PMID: 21936318 PMCID: PMC3290397 DOI: 10.1603/me10264] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Diseases transmitted by mosquitoes could be controlled if vector populations were replaced with strains that have reduced vector competency. Such a strategy is being developed for control of dengue virus which is transmitted by Aedes aegypti (L.) (Diptera: Culicidae). Mosquitoes artificially infected with the bacterium, Wolbachia pipientis Hertig, are being assessed as candidates for release at the adult stage with the aim of replacement of the wild population. Wolbachia can reduce the capacity of Ae. aegypti to transmit dengue virus and has potential to be driven through the natural population via a system of cytoplasmic incompatibility. Deployment of benign mosquito strains will be influenced by population size and structure of wild-type Ae. aegypti in proposed release areas, as well as rates of gene flow among populations in the wet and dry tropical seasons. Mosquitoes from northern Queensland were screened with genetic markers to find an optimal locality for release of a benign strain of Ae. aegypti. The inland towns of Chillagoe and Charters Towers and the coastal town of Ingham had mosquito populations that were partly genetically isolated from mosquitoes in other areas across both seasons. These locations may be suitable release sites if it is important for the released strain to be restricted during initial phases of implementation. Smaller genetic differences were also evident among other regions and were consistent over two seasons (wet and dry).
Collapse
Affiliation(s)
- N M Endersby
- Centre for Environmental Stress and Adaptation Research, Department of Genetics, Bio21 Institute, The University of Melbourne, Victoria 3010, Australia.
| | | | | | | | | | | |
Collapse
|
156
|
Estimating contemporary effective population size on the basis of linkage disequilibrium in the face of migration. Genetics 2011; 189:633-44. [PMID: 21840864 DOI: 10.1534/genetics.111.132233] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Effective population size (Ne) is an important genetic parameter because of its relationship to loss of genetic variation, increases in inbreeding, accumulation of mutations, and effectiveness of selection. Like most other genetic approaches that estimate contemporary Ne, the method based on linkage disequilibrium (LD) assumes a closed population and (in the most common applications) randomly recombining loci. We used analytical and numerical methods to evaluate the absolute and relative consequences of two potential violations of the closed-population assumption: (1) mixture LD caused by occurrence of more than one gene pool, which would downwardly bias Ne and (2) reductions in drift LD (and hence upward bias in Ne) caused by an increase in the number of parents responsible for local samples. The LD method is surprisingly robust to equilibrium migration. Effects of mixture LD are small for all values of migration rate (m), and effects of additional parents are also small unless m is high in genetic terms. LD estimates of Ne therefore accurately reflect local (subpopulation) Ne unless m>∼5-10%. With higher m, Ne converges on the global (metapopulation) Ne. Two general exceptions were observed. First, equilibrium migration that is rare and hence episodic can occasionally lead to substantial mixture LD, especially when sample size is small. Second, nonequilibrium, pulse migration of strongly divergent individuals can also create strong mixture LD and depress estimates of local Ne. In both cases, assignment tests, Bayesian clustering, and other methods often will allow identification of recent immigrants that strongly influence results. In simulations involving equilibrium migration, the standard LD method performed better than a method designed to jointly estimate Ne and m. The above results assume loci are not physically linked; for tightly linked loci, the LD signal from past migration events can persist for many generations, with consequences for Ne estimates that remain to be evaluated.
Collapse
|
157
|
Rougeron V, Bañuls AL, Carme B, Simon S, Couppié P, Nacher M, Hide M, De Meeûs T. Reproductive strategies and population structure in Leishmania: substantial amount of sex in Leishmania Viannia guyanensis. Mol Ecol 2011; 20:3116-27. [PMID: 21722225 DOI: 10.1111/j.1365-294x.2011.05162.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Leishmania species of the subgenus Viannia and especially Leishmania Viannia guyanensis are responsible for a large proportion of New World leishmaniasis cases. Since a recent publication on Leishmania Viannia braziliensis, the debate on the mode of reproduction of Leishmania parasites has been reopened. A predominant endogamic reproductive mode (mating with relatives), together with strong Wahlund effects (sampling of strains from heterogeneous subpopulations), was indeed evidenced. To determine whether this hypothesis can be generalized to other Leishmania Viannia species, we performed a population genetic study on 153 human strains of L. (V.) guyanensis from French Guiana based on 12 microsatellite loci. The results revealed important homozygosity and very modest linkage disequilibrium, which is in agreement with a high level of sexual recombination and substantial endogamy. These results also revealed a significant isolation by distance with relatively small neighbourhoods and hence substantial viscosity of Leishmania populations in French Guiana. These results are of epidemiological relevance and suggest a major role for natural hosts and/or vectors in parasite strain diffusion across the country as compared to human hosts.
Collapse
Affiliation(s)
- Virginie Rougeron
- Laboratoire MIVEGEC (UMR IRD 224-CNRS 5290-Université Montpellier 1) Montpellier, France.
| | | | | | | | | | | | | | | |
Collapse
|
158
|
Crumbling diversity: comparison of historical archived and contemporary natural populations indicate reduced genetic diversity and increasing genetic differentiation in the golden-cheeked warbler. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0235-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
159
|
Population genetics of Schistosoma haematobium: development of novel microsatellite markers and their application to schistosomiasis control in Mali. Parasitology 2011; 138:978-94. [PMID: 21679489 DOI: 10.1017/s0031182011000722] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The recent implementation of mass drug administration (MDA) for control of uro-genital schistosomiasis has identified an urgent need for molecular markers to both directly monitor the impact of MDA, for example to distinguish re-infections from uncleared infections, as well as understand aspects of parasite reproduction and gene flow which might predict evolutionary change, such as the development and spread of drug resistance. We report the development of a novel microsatellite tool-kit allowing, for the first time, robust genetic analysis of individual S. haematobium larvae collected directly from infected human hosts. We genotyped the parasite populations of 47 children from 2 schools in the Ségou region of Mali, the first microsatellite study of this highly neglected parasite. There was only limited evidence of population subdivision between individual children or between the two schools, suggesting that few barriers to gene flow exist in this population. Complex relationships between parasite reproductive success, infection intensity and host age and gender were identified. Older children and boys harboured more diverse infections, as measured by the number of unique adult genotypes present. Individual parasite genotypes had variable reproductive success both across hosts, a pre-requisite for evolutionary selection, and, phenotypically, in hosts of different ages and genders. These data serve as a baseline against which to measure the effect of treatment on parasite population genetics in this region of Mali, and the tools developed are suitable to further investigate this important pathogen, and its close relatives, throughout their range.
Collapse
|
160
|
Phillipsen IC, Funk WC, Hoffman EA, Monsen KJ, Blouin MS. Comparative analyses of effective population size within and among species: ranid frogs as a case study. Evolution 2011; 65:2927-45. [PMID: 21967433 DOI: 10.1111/j.1558-5646.2011.01356.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
It has recently become practicable to estimate the effective sizes (N(e) ) of multiple populations within species. Such efforts are valuable for estimating N(e) in evolutionary modeling and conservation planning. We used microsatellite loci to estimate N(e) of 90 populations of four ranid frog species (20-26 populations per species, mean n per population = 29). Our objectives were to determine typical values of N(e) for populations of each species, compare N(e) estimates among the species, and test for correlations between several geographic variables and N(e) within species. We used single-sample linkage disequilibrium (LD), approximate Bayesian computation (ABC), and sibship assignment (SA) methods to estimate contemporary N(e) for each population. Three of the species-Rana pretiosa, R. luteiventris, and R. cascadae- have consistently small effective population sizes (<50). N(e) in Lithobates pipiens spans a wider range, with some values in the hundreds or thousands. There is a strong east-to-west trend of decreasing N(e) in L. pipiens. The smaller effective sizes of western populations of this species may be related to habitat fragmentation and population bottlenecking.
Collapse
Affiliation(s)
- Ivan C Phillipsen
- Department of Zoology, Oregon State University, 3029 Cordley Hall, Corvallis, Oregon 97331-2914, USA.
| | | | | | | | | |
Collapse
|
161
|
Hare MP, Nunney L, Schwartz MK, Ruzzante DE, Burford M, Waples RS, Ruegg K, Palstra F. Understanding and estimating effective population size for practical application in marine species management. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2011; 25:438-449. [PMID: 21284731 DOI: 10.1111/j.1523-1739.2010.01637.x] [Citation(s) in RCA: 170] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Effective population size (N(e)) determines the strength of genetic drift in a population and has long been recognized as an important parameter for evaluating conservation status and threats to genetic health of populations. Specifically, an estimate of N(e) is crucial to management because it integrates genetic effects with the life history of the species, allowing for predictions of a population's current and future viability. Nevertheless, compared with ecological and demographic parameters, N(e) has had limited influence on species management, beyond its application in very small populations. Recent developments have substantially improved N(e) estimation; however, some obstacles remain for the practical application of N(e) estimates. For example, the need to define the spatial and temporal scale of measurement makes the concept complex and sometimes difficult to interpret. We reviewed approaches to estimation of N(e) over both long-term and contemporary time frames, clarifying their interpretations with respect to local populations and the global metapopulation. We describe multiple experimental factors affecting robustness of contemporary N(e) estimates and suggest that different sampling designs can be combined to compare largely independent measures of N(e) for improved confidence in the result. Large populations with moderate gene flow pose the greatest challenges to robust estimation of contemporary N(e) and require careful consideration of sampling and analysis to minimize estimator bias. We emphasize the practical utility of estimating N(e) by highlighting its relevance to the adaptive potential of a population and describing applications in management of marine populations, where the focus is not always on critically endangered populations. Two cases discussed include the mechanisms generating N(e) estimates many orders of magnitude lower than census N in harvested marine fishes and the predicted reduction in N(e) from hatchery-based population supplementation.
Collapse
Affiliation(s)
- Matthew P Hare
- Department of Natural Resources, Cornell University, Ithaca NY 14853, USA.
| | | | | | | | | | | | | | | |
Collapse
|
162
|
Cox K, Vanden Broeck A, Van Calster H, Mergeay J. Temperature-related natural selection in a wind-pollinated tree across regional and continental scales. Mol Ecol 2011; 20:2724-38. [PMID: 21623981 DOI: 10.1111/j.1365-294x.2011.05137.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Adaptive genetic variation is a key factor in evolutionary biology, but the detection of signatures of natural selection remains challenging in nonmodel organisms. We used a genome scan approach to detect signals of natural selection in the Black alder (Alnus glutinosa), a widespread wind-pollinated tree. Gene flow through pollen dispersal is believed to be high in this species, and we therefore expected to find a clear response to natural selection. In combination with two different landscape genetic approaches, we determined which environmental variables were most associated with the inferred selection. This analysis was performed on a regional scale (northern Belgium) and on a continental scale (Europe). Because climate-related differences are much more pronounced at the continental scale, we expected to find more selection-sensitive genetic markers across Europe than across northern Belgium. At both spatial scales, a substantial number of genetic loci were considered outliers, with respect to neutral expectations, and were therefore identified as selective. Based on results from our combined approach, four putative selective loci (or 2.5%) were recovered with high statistical support. Although these loci seemed to be associated with different environmental variables, they were mainly temperature-related. Our study demonstrates that the use of complementary methods in landscape genetics allows the discovery of selective loci which otherwise might stay hidden. In combination with a genome scan, the selective loci can be verified and the nature of the selection pressure can be identified.
Collapse
Affiliation(s)
- K Cox
- Research Institute for Nature and Forest, Gaverstraat 4, B-9500 Geraardsbergen, Belgium.
| | | | | | | |
Collapse
|
163
|
Kobayashi Y, Achaz G, Telschow A. Effect of parasitic sex-ratio distorters on host gene frequencies in a mainland-island context. J Evol Biol 2011; 24:1695-705. [PMID: 21605214 DOI: 10.1111/j.1420-9101.2011.02296.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
It was previously argued that infection by parasitic sex-ratio distorters can enhance both random genetic drift and genetic influx from outside the population. However, these two enhancement effects have been studied independently. Here, we study the equilibrium frequencies of alleles (neutral and selected) in a mainland-island scenario where both genetic drift and genetic influx are enhanced due to infection by a cytoplasmic feminizing element. Interestingly, our model reveals that at neutral loci, the two effects almost exactly cancel each other out, such that infection has only a very minor effect on the equilibrium frequency distributions of alleles. At selected loci, in contrast, the two effects are unbalanced and infection has conspicuous effects. Despite the cryptic effects of infection at neutral loci, we demonstrate that temporally spaced data can be used to evaluate the effect of infection on genetic drift and that on gene flow separately.
Collapse
Affiliation(s)
- Y Kobayashi
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan.
| | | | | |
Collapse
|
164
|
Campos JL, Bellocq JGD, Schaschl H, Suchentrunk F. MHC class II DQA gene variation across cohorts of brown hares (Lepus europaeus) from eastern Austria: Testing for different selection hypotheses. Mamm Biol 2011. [DOI: 10.1016/j.mambio.2010.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
165
|
Junge C, Vøllestad LA, Barson NJ, Haugen TO, Otero J, Sætre GP, Leder EH, Primmer CR. Strong gene flow and lack of stable population structure in the face of rapid adaptation to local temperature in a spring-spawning salmonid, the European grayling (Thymallus thymallus). Heredity (Edinb) 2011; 106:460-71. [PMID: 21224882 PMCID: PMC3131973 DOI: 10.1038/hdy.2010.160] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 11/19/2010] [Accepted: 11/22/2010] [Indexed: 11/09/2022] Open
Abstract
Gene flow has the potential to both constrain and facilitate adaptation to local environmental conditions. The early stages of population divergence can be unstable because of fluctuating levels of gene flow. Investigating temporal variation in gene flow during the initial stages of population divergence can therefore provide insights to the role of gene flow in adaptive evolution. Since the recent colonization of Lake Lesjaskogsvatnet in Norway by European grayling (Thymallus thymallus), local populations have been established in over 20 tributaries. Multiple founder events appear to have resulted in reduced neutral variation. Nevertheless, there is evidence for local adaptation in early life-history traits to different temperature regimes. In this study, microsatellite data from almost a decade of sampling were assessed to infer population structuring and its temporal stability. Several alternative analyses indicated that spatial variation explained 2-3 times more of the divergence in the system than temporal variation. Over all samples and years, there was a significant correlation between genetic and geographic distance. However, decomposed pairwise regression analysis revealed differing patterns of genetic structure among local populations and indicated that migration outweighs genetic drift in the majority of populations. In addition, isolation by distance was observable in only three of the six years, and signals of population bottlenecks were observed in the majority of samples. Combined, the results suggest that habitat-specific adaptation in this system has preceded the development of consistent population substructuring in the face of high levels of gene flow from divergent environments.
Collapse
Affiliation(s)
- C Junge
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway.
| | | | | | | | | | | | | | | |
Collapse
|
166
|
Drees C, Hüfner S, Matern A, Nève G, Assmann T. Repeated sampling detects gene flow in a flightless ground beetle in a fragmented landscape. Hereditas 2011; 148:36-45. [PMID: 21410469 DOI: 10.1111/j.1601-5223.2010.02212.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Secondary clines level down in the course of time if the gene flow is not interrupted. Temporally repeated sampling of populations in a cline allows the investigation not only of its occurrence but also of the estimation of the amount of ongoing gene flow. We reinvestigated an allozyme gradient in Carabus auronitens populations in the Westphalian Lowlands (northwestern Germany) 15 to 20 years after it had originally been recorded. A total of 977 individuals of this flightless woodland species from 29 sample sites were genotyped at the diallelic Est-1 locus in 2005-2006 and compared to former findings, collected in 1985-1994 from the same populations. Both data sets showed clinal variation. Pairwise differences between the samples of both data sets indicated significant decrease in the steepness of the cline during the past 15 to 20 years. The estimated average gene flow per generation is 0.6% of each beetle population. Ongoing gene flow in the flightless ground beetle C. auronitens led to a less pronounced cline despite a stable degree of fragmentation (and connectivity) of the landscape. Migration and gene flow were obviously enabled by the numerous hedgerows. The corridors are seen to be a prerequisite for migration between populations and for possible future range shifts of forest insect species.
Collapse
Affiliation(s)
- Claudia Drees
- Institute of Ecology, Leuphana University Lüneburg, Lüneburg, Germany.
| | | | | | | | | |
Collapse
|
167
|
Nock CJ, Ovenden JR, Butler GL, Wooden I, Moore A, Baverstock PR. Population structure, effective population size and adverse effects of stocking in the endangered Australian eastern freshwater cod Maccullochella ikei. JOURNAL OF FISH BIOLOGY 2011; 78:303-321. [PMID: 21235562 DOI: 10.1111/j.1095-8649.2010.02865.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Microsatellite markers were used to examine spatio-temporal genetic variation in the endangered eastern freshwater cod Maccullochella ikei in the Clarence River system, eastern Australia. High levels of population structure were detected. A model-based clustering analysis of multilocus genotypes identified four populations that were highly differentiated by F-statistics (F(ST) = 0·09 - 0·49; P < 0·05), suggesting fragmentation and restricted dispersal particularly among upstream sites. Hatchery breeding programmes were used to re-establish locally extirpated populations and to supplement remnant populations. Bayesian and frequency-based analyses of hatchery fingerling samples provided evidence for population admixture in the hatchery, with the majority of parental stock sourced from distinct upstream sites. Comparison between historical and contemporary wild-caught samples showed a significant loss of heterozygosity (21%) and allelic richness (24%) in the Mann and Nymboida Rivers since the commencement of stocking. Fragmentation may have been a causative factor; however, temporal shifts in allele frequencies suggest swamping with hatchery-produced M. ikei has contributed to the genetic decline in the largest wild population. This study demonstrates the importance of using information on genetic variation and population structure in the management of breeding and stocking programmes, particularly for threatened species.
Collapse
Affiliation(s)
- C J Nock
- Centres for Animal and Plant Conservation Genetics, Southern Cross University, P. O. Box 157 Lismore, NSW, Australia.
| | | | | | | | | | | |
Collapse
|
168
|
Knutsen H, Olsen EM, Jorde PE, Espeland SH, André C, Stenseth NC. Are low but statistically significant levels of genetic differentiation in marine fishes 'biologically meaningful'? A case study of coastal Atlantic cod. Mol Ecol 2010; 20:768-83. [PMID: 21199035 DOI: 10.1111/j.1365-294x.2010.04979.x] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A key question in many genetic studies on marine organisms is how to interpret a low but statistically significant level of genetic differentiation. Do such observations reflect a real phenomenon, or are they caused by confounding factors such as unrepresentative sampling or selective forces acting on the marker loci? Further, are low levels of differentiation biologically trivial, or can they represent a meaningful and perhaps important finding? We explored these issues in an empirical study on coastal Atlantic cod, combining temporally replicated genetic samples over a 10-year period with an extensive capture-mark-recapture study of individual mobility and population size. The genetic analyses revealed a pattern of differentiation between the inner part of the fjord and the open skerries area at the fjord entrance. Overall, genetic differentiation was weak (average F(ST) = 0.0037), but nevertheless highly statistical significant and did not depend on particular loci that could be subject to selection. This spatial component dominated over temporal change, and temporal replicates clustered together throughout the 10-year period. Consistent with genetic results, the majority of the recaptured fish were found close to the point of release, with <1% of recaptured individuals dispersing between the inner fjord and outer skerries. We conclude that low levels of genetic differentiation in this marine fish can indeed be biologically meaningful, corresponding to separate, temporally persistent, local populations. We estimated the genetically effective sizes (N(e) ) of the two coastal cod populations to 198 and 542 and found a N(e) /N (spawner) ratio of 0.14.
Collapse
Affiliation(s)
- H Knutsen
- Institute of Marine Research, Flødevigen, N-4817 His, Norway.
| | | | | | | | | | | |
Collapse
|
169
|
Johnson JA, Talbot SL, Sage GK, Burnham KK, Brown JW, Maechtle TL, Seegar WS, Yates MA, Anderson B, Mindell DP. The use of genetics for the management of a recovering population: temporal assessment of migratory peregrine falcons in North America. PLoS One 2010; 5:e14042. [PMID: 21124969 PMCID: PMC2987794 DOI: 10.1371/journal.pone.0014042] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 10/26/2010] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Our ability to monitor populations or species that were once threatened or endangered and in the process of recovery is enhanced by using genetic methods to assess overall population stability and size over time. This can be accomplished most directly by obtaining genetic measures from temporally-spaced samples that reflect the overall stability of the population as given by changes in genetic diversity levels (allelic richness and heterozygosity), degree of population differentiation (F(ST) and D(EST)), and effective population size (N(e)). The primary goal of any recovery effort is to produce a long-term self-sustaining population, and these genetic measures provide a metric by which we can gauge our progress and help make important management decisions. METHODOLOGY/PRINCIPAL FINDINGS The peregrine falcon in North America (Falco peregrinus tundrius and anatum) was delisted in 1994 and 1999, respectively, and its abundance will be monitored by the species Recovery Team every three years until 2015. Although the United States Fish and Wildlife Service makes a distinction between tundrius and anatum subspecies, our genetic results based on eleven microsatellite loci suggest limited differentiation that can be attributed to an isolation by distance relationship and warrant no delineation of these two subspecies in its northern latitudinal distribution from Alaska through Canada into Greenland. Using temporal samples collected at Padre Island, Texas during migration (seven temporal time periods between 1985-2007), no significant differences in genetic diversity or significant population differentiation in allele frequencies between time periods were observed and were indistinguishable from those obtained from tundrius/anatum breeding locations throughout their northern distribution. Estimates of harmonic mean N(e) were variable and imprecise, but always greater than 500 when employing multiple temporal genetic methods. CONCLUSIONS/SIGNIFICANCE These results, including those from simulations to assess the power of each method to estimate N(e), suggest a stable or growing population, which is consistent with ongoing field-based monitoring surveys. Therefore, historic and continuing efforts to prevent the extinction of the peregrine falcon in North America appear successful with no indication of recent decline, at least from the northern latitude range-wide perspective. The results also further highlight the importance of archiving samples and their use for continual assessment of population recovery and long-term viability.
Collapse
Affiliation(s)
- Jeff A Johnson
- Department of Biological Sciences, Institute of Applied Sciences, University of North Texas, Denton, Texas, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
170
|
KOBAYASHI Y, TELSCHOW A. Cytoplasmic feminizing elements in a two-population model: infection dynamics, gene flow modification, and the spread of autosomal suppressors. J Evol Biol 2010; 23:2558-68. [DOI: 10.1111/j.1420-9101.2010.02116.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
171
|
Bataille A, Cunningham AA, Cruz M, Cedeno V, Goodman SJ. Seasonal effects and fine-scale population dynamics of Aedes taeniorhynchus, a major disease vector in the Galapagos Islands. Mol Ecol 2010; 19:4491-504. [PMID: 20875066 DOI: 10.1111/j.1365-294x.2010.04843.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Characterization of the fine-scale population dynamics of the mosquito Aedes taeniorhynchus is needed to improve our understanding of its role as a disease vector in the Galapagos Islands. We used microsatellite data to assess the genetic structure of coastal and highland mosquito populations and patterns of gene flow between the two habitats through time on Santa Cruz Island. In addition, we assessed possible associations of mosquito abundance and genetic diversity with environmental variables. The coastal and highland mosquito populations were highly differentiated from each other all year round, with some gene flow detected only during periods of increased precipitation. The results support the hypothesis that selection arising from ecological differences between habitats is driving adaptation and divergence in A. taeniorhynchus, and maintaining long-term genetic differentiation of the populations against gene flow. The highland and lowland populations may constitute an example of incipient speciation in progress. Highland populations were characterized by lower observed heterozygosity and allelic richness, suggesting a founder effect and/or lower breeding site availability in the highlands. A lack of reduction in genetic diversity over time in highland populations suggests that they survive dry periods as dormant eggs. Association between mosquito abundance and precipitation was strong in the highlands, whereas tide height was the main factor affecting mosquito abundance on the coast. Our findings suggests differences in the infection dynamics of mosquito-borne parasites in the highlands compared to the coast, and a higher risk of mosquito-driven disease spread across these habitats during periods of increased precipitation.
Collapse
Affiliation(s)
- Arnaud Bataille
- Institute of Integrative and Comparative Biology, University of Leeds, Leeds LS2 9JT, UK
| | | | | | | | | |
Collapse
|
172
|
Pinsky ML, Montes Jr. HR, Palumbi SR. USING ISOLATION BY DISTANCE AND EFFECTIVE DENSITY TO ESTIMATE DISPERSAL SCALES IN ANEMONEFISH. Evolution 2010; 64:2688-700. [DOI: 10.1111/j.1558-5646.2010.01003.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
173
|
Genetic diversity of the killifish Aphanius fasciatus paralleling the environmental changes of Tarquinia salterns habitat. Genetica 2010; 138:1011-21. [DOI: 10.1007/s10709-010-9487-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Accepted: 08/09/2010] [Indexed: 10/19/2022]
|
174
|
Antao T, Pérez-Figueroa A, Luikart G. Early detection of population declines: high power of genetic monitoring using effective population size estimators. Evol Appl 2010; 4:144-54. [PMID: 25567959 PMCID: PMC3352520 DOI: 10.1111/j.1752-4571.2010.00150.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 06/25/2010] [Indexed: 11/28/2022] Open
Abstract
Early detection of population declines is essential to prevent extinctions and to ensure sustainable harvest. We evaluated the performance of two Ne estimators to detect population declines: the two-sample temporal method and a one-sample method based on linkage disequilibrium (LD). We used simulated data representing a wide range of population sizes, sample sizes and number of loci. Both methods usually detect a population decline only one generation after it occurs if Ne drops to less than approximately 100, and 40 microsatellite loci and 50 individuals are sampled. However, the LD method often out performed the temporal method by allowing earlier detection of less severe population declines (Ne approximately 200). Power for early detection increased more rapidly with the number of individuals sampled than with the number of loci genotyped, primarily for the LD method. The number of samples available is therefore an important criterion when choosing between the LD and temporal methods. We provide guidelines regarding design of studies targeted at monitoring for population declines. We also report that 40 single nucleotide polymorphism (SNP) markers give slightly lower precision than 10 microsatellite markers. Our results suggest that conservation management and monitoring strategies can reliably use genetic based methods for early detection of population declines.
Collapse
Affiliation(s)
- Tiago Antao
- Liverpool School of Tropical Medicine Liverpool, UK
| | - Andrés Pérez-Figueroa
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo Vigo, Spain
| | - Gordon Luikart
- Flathead Lake Biological Station and Division of Biological Sciences, University of Montana Polson, MT, USA ; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão Vairão, Portugal
| |
Collapse
|
175
|
MAGALHAES IS, MWAIKO S, SEEHAUSEN O. Sympatric colour polymorphisms associated with nonrandom gene flow in cichlid fish of Lake Victoria. Mol Ecol 2010; 19:3285-300. [DOI: 10.1111/j.1365-294x.2010.04751.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
176
|
Osborne MJ, Davenport SR, Hoagstrom CW, Turner TF. Genetic effective size, N(e), tracks density in a small freshwater cyprinid, Pecos bluntnose shiner (Notropis simus pecosensis). Mol Ecol 2010; 19:2832-44. [PMID: 20579288 DOI: 10.1111/j.1365-294x.2010.04695.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Genetic monitoring tracks changes in measures of diversity including allelic richness, heterozygosity and genetic effective size over time, and has emerged as an important tool for understanding evolutionary consequences of population management. One proposed application of genetic monitoring has been to estimate abundance and its trajectory through time. Here, genetic monitoring was conducted across five consecutive year for the Pecos bluntnose shiner, a federally threatened minnow. Temporal changes in allele frequencies at seven microsatellite DNA loci were used to estimate variance effective size (N(eV)) across adjacent years in the time series. Likewise, effective size was computed using the linkage disequilibrium method (N(eD)) for each sample. Estimates of N(e) were then compared to estimates of adult fish density obtained from traditional demographic monitoring. For Pecos bluntnose shiner, density (catch-per-unit-effort), N(eV) and N(eD) were positively associated across this time series. Results for Pecos bluntnose shiner were compared to a related and ecologically similar species, the Rio Grande silvery minnow. In this species, density and N(eV) were negatively associated, which suggested decoupling of abundance and effective size trajectories. Conversely, density and N(eD) were positively associated. For Rio Grande silvery minnow, discrepancies among estimates of N(e) and their relationships with adult fish density could be related to effects of high variance in reproductive success in the wild and/or effects of supplementation of the wild population with captive-bred and reared fish. The efficacy of N(e) as a predictor of density and abundance may depend on intrinsic population dynamics of the species and how these dynamics are influenced by the landscape features, management protocols and other factors.
Collapse
Affiliation(s)
- Megan J Osborne
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
| | | | | | | |
Collapse
|
177
|
Pilot M, Dabrowski MJ, Jancewicz E, Schtickzelle N, Gliwicz J. Temporally stable genetic variability and dynamic kinship structure in a fluctuating population of the root vole Microtus oeconomus. Mol Ecol 2010; 19:2800-12. [PMID: 20561198 DOI: 10.1111/j.1365-294x.2010.04692.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genetic variability, kin structure and demography of a population are mutually dependent. Population genetic theory predicts that under demographically stable conditions, neutral genetic variability reaches equilibrium between gene flow and drift. However, density fluctuations and non-random mating, resulting e.g. from kin clustering, may lead to changes in genetic composition over time. Theoretical models also predict that changes in kin structure may affect aggression level and recruitment, leading to density fluctuations. These predictions have been rarely tested in natural populations. The aim of this study was to analyse changes in genetic variability and kin structure in a local population of the root vole (Microtus oeconomus) that underwent a fourfold change in mean density over a 6-year period. Intensive live-trapping resulted in sampling 88% of individuals present in the study area, as estimated from mark-recapture data. Based on 642 individual genotypes at 20 microsatellite loci, we compared genetic variability and kin structure of this population between consecutive years. We found that immigration was negatively correlated with density, while the number of kin groups was positively correlated with density. This is consistent with theoretical predictions that changes in kin structure play an important role in population fluctuations. Despite the changes in density and kin structure, there was no genetic differentiation between years. Population-level genetic diversity measures did not significantly vary in time and remained relatively high (H(E) range: 0.72-0.78). These results show that a population that undergoes significant demographic and social changes may maintain high genetic variability and stable genetic composition.
Collapse
Affiliation(s)
- Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679 Warsaw, Poland.
| | | | | | | | | |
Collapse
|
178
|
Sacks BN, Statham MJ, Perrine JD, Wisely SM, Aubry KB. North American montane red foxes: expansion, fragmentation, and the origin of the Sacramento Valley red fox. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0053-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
179
|
Boettcher PJ, Tixier-Boichard M, Toro MA, Simianer H, Eding H, Gandini G, Joost S, Garcia D, Colli L, Ajmone-Marsan P. Objectives, criteria and methods for using molecular genetic data in priority setting for conservation of animal genetic resources. Anim Genet 2010; 41 Suppl 1:64-77. [PMID: 20500756 DOI: 10.1111/j.1365-2052.2010.02050.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The genetic diversity of the world's livestock populations is decreasing, both within and across breeds. A wide variety of factors has contributed to the loss, replacement or genetic dilution of many local breeds. Genetic variability within the more common commercial breeds has been greatly decreased by selectively intense breeding programmes. Conservation of livestock genetic variability is thus important, especially when considering possible future changes in production environments. The world has more than 7500 livestock breeds and conservation of all of them is not feasible. Therefore, prioritization is needed. The objective of this article is to review the state of the art in approaches for prioritization of breeds for conservation, particularly those approaches that consider molecular genetic information, and to identify any shortcomings that may restrict their application. The Weitzman method was among the first and most well-known approaches for utilization of molecular genetic information in conservation prioritization. This approach balances diversity and extinction probability to yield an objective measure of conservation potential. However, this approach was designed for decision making across species and measures diversity as distinctiveness. For livestock, prioritization will most commonly be performed among breeds within species, so alternatives that measure diversity as co-ancestry (i.e. also within-breed variability) have been proposed. Although these methods are technically sound, their application has generally been limited to research studies; most existing conservation programmes have effectively primarily based decisions on extinction risk. The development of user-friendly software incorporating these approaches may increase their rate of utilization.
Collapse
Affiliation(s)
- P J Boettcher
- Animal Production and Health Division, Food and Agriculture Organization of the United Nations, Rome 00153, Italy.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
180
|
Waples RS. Spatial-temporal stratifications in natural populations and how they affect understanding and estimation of effective population size. Mol Ecol Resour 2010; 10:785-96. [PMID: 21565090 DOI: 10.1111/j.1755-0998.2010.02876.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The concept of effective population size (N(e) ) is based on an elegantly simple idea which, however, rapidly becomes very complex when applied to most real-world situations. In natural populations, spatial and temporal stratifications create different classes of individuals with different vital rates, and this in turn affects (generally reduces) N(e) in complex ways. I consider how these natural stratifications influence our understanding of effective size and how to estimate it, and what the consequences are for conservation and management of natural populations. Important points that emerge include the following: 1 The relative influences of local vs metapopulation N(e) depend on a variety of factors, including the time frame of interest. 2 Levels of diversity in local populations are strongly influenced by even low levels of migration, so these measures are not reliable indicators of local N(e) . 3 For long-term effective size, obtaining a reliable estimate of mutation rate is the most important consideration; unless this is accomplished, estimates can be biased by orders of magnitude. 4 At least some estimators of contemporary N(e) appear to be robust to relatively high (approximately 10%) equilibrium levels of migration, so under many realistic scenarios they might yield reliable estimates of local N(e) . 5 Age structure probably has little effect on long-term estimators of N(e) but can strongly influence contemporary estimates. 6 More research is needed in several key areas: (i) to disentangle effects of selection and drift in metapopulations connected by intermediate levels of migration; (ii) to elucidate the relationship between N(b) (effective number of breeders per year) and N(e) per generation in age-structured populations; (iii) to perform rigorous sensitivity analyses of new likelihood and coalescent-based methods for estimating demographic and evolutionary histories.
Collapse
Affiliation(s)
- Robin S Waples
- NOAA Fisheries, Northwest Fisheries Science Center, 2725 Montlake Blvd. East, Seattle, WA 98112, USA
| |
Collapse
|
181
|
An examination of genetic diversity and effective population size in Atlantic salmon populations. Genet Res (Camb) 2010; 91:395-412. [PMID: 20122296 DOI: 10.1017/s0016672309990346] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Effective population size (Ne) is an important parameter in the conservation of genetic diversity. Comparative studies of empirical data that gauge the relative accuracy of Ne methods are limited, and a better understanding of the limitations and potential of Ne estimators is needed. This paper investigates genetic diversity and Ne in four populations of wild anadromous Atlantic salmon (Salmo salar L.) in Europe, from the Rivers Oir and Scorff (France) and Spey and Shin (Scotland). We aimed to understand present diversity and historical processes influencing current population structure. Our results showed high genetic diversity for all populations studied, despite their wide range of current effective sizes. To improve understanding of high genetic diversity observed in the populations with low effective size, we developed a model predicting present diversity as a function of past demographic history. This suggested that high genetic diversity could be explained by a bottleneck occurring within recent centuries rather than by gene flow. Previous studies have demonstrated the efficiency of coalescence models to estimate Ne. Using nine subsets from 37 microsatellite DNA markers from the four salmon populations, we compared three coalescence estimators based on single and dual samples. Comparing Ne estimates confirmed the efficiency of increasing the number and variability of microsatellite markers. This efficiency was more accentuated for the smaller populations. Analysis with low numbers of neutral markers revealed uneven distributions of allelic frequencies and overestimated short-term Ne. In addition, we found evidence of artificial stock enhancement using native and non-native origin. We propose estimates of Ne for the four populations, and their applications for salmon conservation and management are discussed.
Collapse
|
182
|
COOMBS JASONA, LETCHER BH, NISLOW KH. pedagog: software for simulating eco‐evolutionary population dynamics. Mol Ecol Resour 2010; 10:558-63. [DOI: 10.1111/j.1755-0998.2009.02803.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- JASON A. COOMBS
- Program In Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - B. H. LETCHER
- S.O. Conte Anadromous Fish Research Center, US Geological Survey/Leetown Science Center, One Migratory Way, Turners Falls, MA 01376, USA
| | - K. H. NISLOW
- Northern Research Station, US Forest Service, University of Massachusetts, Amherst, MA 01003, USA
| |
Collapse
|
183
|
Peery MZ, Hall LA, Sellas A, Beissinger SR, Moritz C, Bérubé M, Raphael MG, Nelson SK, Golightly RT, McFarlane-Tranquilla L, Newman S, Palsbøll PJ. Genetic analyses of historic and modern marbled murrelets suggest decoupling of migration and gene flow after habitat fragmentation. Proc Biol Sci 2010; 277:697-706. [PMID: 19906669 PMCID: PMC2842750 DOI: 10.1098/rspb.2009.1666] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 10/19/2009] [Indexed: 11/12/2022] Open
Abstract
The dispersal of individuals among fragmented populations is generally thought to prevent genetic and demographic isolation, and ultimately reduce extinction risk. In this study, we show that a century of reduction in coastal old-growth forests, as well as a number of other environmental factors, has probably resulted in the genetic divergence of marbled murrelets (Brachyramphus marmoratus) in central California, despite the fact that 7 per cent of modern-sampled murrelets in this population were classified as migrants using genetic assignment tests. Genetic differentiation appears to persist because individuals dispersing from northern populations contributed relatively few young to the central California population, as indicated by the fact that migrants were much less likely to be members of parent-offspring pairs than residents (10.5% versus 45.4%). Moreover, a recent 1.4 per cent annual increase in the proportion of migrants in central California, without appreciable reproduction, may have masked an underlying decline in the resident population without resulting in demographic rescue. Our results emphasize the need to understand the behaviour of migrants and the extent to which they contribute offspring in order to determine whether dispersal results in gene flow and prevents declines in resident populations.
Collapse
Affiliation(s)
- M Zachariah Peery
- Department of Forest and Wildlife Ecology, 1630 Linden Drive Madison, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
184
|
Temporally stable genetic structure of heavily exploited Atlantic herring (Clupea harengus) in Swedish waters. Heredity (Edinb) 2010; 104:40-51. [PMID: 19654606 DOI: 10.1038/hdy.2009.98] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Information on the temporal stability of genetic structures is important to permit detection of changes that can constitute threats to biological resources. Large-scale harvesting operations are known to potentially alter the composition and reduce the variability of populations, and Atlantic herring (Clupea harengus) has a long history of heavy exploitation. In the Baltic Sea and Skagerrak waters, the census population sizes have declined by 35-50% over the last three decades. We compared the genetic structure of Atlantic herring in these waters sampled at least two different times between 1979 and 2003 by assaying 11 allozyme and nine microsatellite loci. We cannot detect any changes in the amount of genetic variation or spatial structure, and differentiation is weak with overall F(ST)=0.003 among localities for the older samples and F(ST)=0.002 for the newer ones. There are indications of temporal allele frequency changes, particularly in one of five sampling localities that is reflected in a relatively small local N(e) estimate of c. 400. The previously identified influence of selection at the microsatellite locus Cpa112 remains stable over the 24-year period studied here. Despite little genetic differentiation, migration among localities appears small enough to permit demographic independence between populations.
Collapse
|
185
|
Ríos M, Monleón-Getino T. Application of a Markovian process to the calculation of mean time equilibrium in a genetic drift model. J Appl Stat 2010. [DOI: 10.1080/02664760902889981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
186
|
Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0050-7] [Citation(s) in RCA: 214] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
187
|
Larmuseau MHD, Raeymaekers JAM, Hellemans B, Van Houdt JKJ, Volckaert FAM. Mito-nuclear discordance in the degree of population differentiation in a marine goby. Heredity (Edinb) 2010; 105:532-42. [PMID: 20145668 DOI: 10.1038/hdy.2010.9] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
An increasing number of phylogeographic studies on marine species shows discordant patterns in the degree of population differentiation between nuclear and mitochondrial markers. To understand better which factors have the potential to cause these patterns of discordance in marine organisms, a population genetic study was realized on the sand goby Pomatoschistus minutus (Pallas 1770; Gobiidae, Teleostei). Sand gobies from eight European locations were genotyped at eight microsatellite markers. Microsatellites confirmed the global phylogeographical pattern of P. minutus observed with mitochondrial DNA (mtDNA) markers and nuclear allozyme markers. Three groups consistent with the mitochondrial lineages were defined (the Mediterranean, Iberian and North Atlantic groups) and indications of a recent founder event in the northern Baltic Sea were found. Nevertheless, differences in the degree of population differentiation between the nuclear and mitochondrial markers were large (global F(ST)-values for microsatellites=0.0121; for allozymes=0.00831; for mtDNA=0.4293). Selection, sex-biased dispersal, homoplasy and a high effective population size are generally accepted as explanations for this mitonuclear discrepancy in the degree of population differentiation. In this study, selection on mtDNA and microsatellites, male-biased dispersal and homoplasy on microsatellite markers are unlikely to be a main cause for this discrepancy. The most likely reason for the discordant pattern is a recent demographical expansion of the sand goby, resulting in high effective population sizes slowing down the differentiation of nuclear DNA.
Collapse
Affiliation(s)
- M H D Larmuseau
- Laboratory of Animal Diversity and Systematics, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | | | | | | |
Collapse
|
188
|
Demandt MH. Temporal changes in genetic diversity of isolated populations of perch and roach. CONSERV GENET 2010. [DOI: 10.1007/s10592-009-0027-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
189
|
Blank WA, Reis EAG, Thiong'o FW, Braghiroli JF, Santos JM, Melo PRS, Guimarães ICS, Silva LK, Carmo TMA, Reis MG, Blanton RE. Analysis of Schistosoma mansoni population structure using total fecal egg sampling. J Parasitol 2010; 95:881-9. [PMID: 20049994 DOI: 10.1645/ge-1895.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Many parasite populations are difficult to sample because they are not uniformly distributed between several host species and are often not easily collected from the living host, thereby limiting sample size and possibly distorting the representation of the population. For the parasite Schistosoma mansoni, we investigated the use of eggs, in aggregate, from the stools of infected individuals as a simple and representative sample. Previously, we demonstrated that microsatellite allele frequencies can be accurately estimated from pooled DNA of cloned S. mansoni adults. Here, we show that genotyping of parasite populations from reproductively isolated laboratory strains can be used to identify these specific populations based on characteristic patterns of allele frequencies, as observed by polyacrylamide gel electrophoresis and automated sequencer analysis of fluorescently labeled PCR products. Microsatellites used to genotype aggregates of eggs collected from stools of infected individuals produced results consistent with the geographic distribution of the samples. Preferential amplification of smaller alleles, and stutter PCR products, had negligible effect on measurement of genetic differentiation. Direct analysis of total stool eggs can be an important approach to questions of population genetics for this parasite by increasing the sample size to thousands per infected individual and by reducing bias.
Collapse
Affiliation(s)
- Walter A Blank
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
190
|
Saarinen EV, Austin JD, Daniels JC. Genetic estimates of contemporary effective population size in an endangered butterfly indicate a possible role for genetic compensation. Evol Appl 2010; 3:28-39. [PMID: 25567901 PMCID: PMC3352457 DOI: 10.1111/j.1752-4571.2009.00096.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Accepted: 06/29/2009] [Indexed: 11/28/2022] Open
Abstract
The effective population size (N e ) is a critical evolutionary and conservation parameter that can indicate the adaptive potential of populations. Robust estimates of N e of endangered taxa have been previously hampered by estimators that are sensitive to sample size. We estimated N e on two remaining populations of the endangered Miami blue butterfly, a formerly widespread taxon in Florida. Our goal was to determine the consistency of various temporal and point estimators on inferring N e and to determine the utility of this information for understanding the role of genetic stochasticity. We found that recently developed 'unbiased estimators' generally performed better than some older methods in that the former had more realistic N e estimates and were more consistent with what is known about adult population size. Overall, N e /N ratios based on census point counts were high. We suggest that this pattern may reflect genetic compensation caused by reduced reproductive variance due to breeding population size not being limited by resources. Assuming N e and N are not heavily biased, it appears that the lack of gene flow between distant populations may be a greater genetic threat in the short term than the loss of heterozygosity due to inbreeding.
Collapse
Affiliation(s)
- Emily V Saarinen
- Department of Wildlife Ecology and Conservation, University of Florida Gainesville, FL, USA ; McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History Gainesville, FL, USA
| | - James D Austin
- Department of Wildlife Ecology and Conservation, University of Florida Gainesville, FL, USA
| | - Jaret C Daniels
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History Gainesville, FL, USA ; Department of Entomology and Nematology, University of Florida Gainesville, FL, USA
| |
Collapse
|
191
|
The genetic structure of populations of an invading pest fruit fly, Bactrocera tryoni, at the species climatic range limit. Heredity (Edinb) 2009; 105:165-72. [PMID: 19997126 DOI: 10.1038/hdy.2009.163] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Previous population genetic studies of the Queensland fruit fly, Bactrocera tryoni Froggatt (Diptera: Tephritidae), in its central range have shown barely detectable genetic differentiation across distances of almost 3000 km (F(st)=0.003). In this study, we investigated the genetic structuring of southern border populations of B. tryoni, in the region extending from the central population to the recently colonized southern range limit. The expectation was that marginal populations would be small, fragmented population sinks, with local adaptation limited by gene flow or drift. Unexpectedly, we found that the population at the southern extreme of the range was a source population, rather than a sink, for the surrounding region. This was shown by assignment testing of recent outbreaks in an adjoining quarantine area and by indirect migration estimates. Furthermore, populations in the region had formed a latitudinal cline in microsatellite allele frequencies, spanning the region between the central population and the southern range limit. The cline has formed within 250 generations of the initial invasion and appears stable between years. We show that there is restricted gene flow in the region and that effective population sizes are of the order of 10(2)-10(3). Although the cline may result from natural selection, neutral evolutionary processes may also explain our findings.
Collapse
|
192
|
Temporal genetic samples indicate small effective population size of the endangered yellow-eyed penguin. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9988-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
193
|
Broquet T, Petit EJ. Molecular Estimation of Dispersal for Ecology and Population Genetics. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2009. [DOI: 10.1146/annurev.ecolsys.110308.120324] [Citation(s) in RCA: 209] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Thomas Broquet
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland;
| | - Eric J. Petit
- INRA/Agrocampus Ouest/Univ. Rennes 1, UMR 1099 BiO3P (Biology of Organisms and Populations applied to Plant Protection), Domaine de la Motte, 35653 Le Rheu, France;
- University Rennes 1/CNRS, UMR 6553 ECOBIO, Campus de Beaulieu, 35042 Rennes Cedex, France
| |
Collapse
|
194
|
Tepolt CK, Darling JA, Bagley MJ, Geller JB, Blum MJ, Grosholz ED. European green crabs (Carcinus maenas) in the northeastern Pacific: genetic evidence for high population connectivity and current-mediated expansion from a single introduced source population. DIVERS DISTRIB 2009. [DOI: 10.1111/j.1472-4642.2009.00605.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
|
195
|
Beebee TJC. A comparison of single-sample effective size estimators using empirical toad (Bufo calamita) population data: genetic compensation and population size-genetic diversity correlations. Mol Ecol 2009; 18:4790-7. [PMID: 19863715 DOI: 10.1111/j.1365-294x.2009.04398.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The accuracy and precision of four single-sample estimators of effective population size, N(e) (heterozygote excess, linkage disequilibrium, Bayesian partial likelihood and sibship analysis) were compared using empirical data (microsatellite genotypes) from multiple natterjack toad (Bufo calamita) populations in Britain (n = 16) and elsewhere in Europe (n = 10). Census size data were available for the British populations. Because toads have overlapping generations, all of these methods estimated the number of effective breeders N(b) rather than N(e). The heterozygote excess method only provided results, without confidence limits, for nine of the British populations. Linkage disequilibrium gave estimates for 10 British populations, but only six had finite confidence limits. The Bayesian and sibship methods both produced estimates with finite confidence limits for all the populations. Although the Bayesian method was the most precise, on most criteria (insensitivity to locus number, correlation with other effective and census size estimates and correlation with genetic diversity) the sibship method performed best. The results also provided evidence of genetic compensation in natterjack toads, and highlighted how the relationship between effective size and genetic diversity can vary as a function of geographical scale.
Collapse
Affiliation(s)
- T J C Beebee
- School of Life Sciences, University of Sussex, Falmer, Brighton BN19QG, UK.
| |
Collapse
|
196
|
Balkenhol N, Waits LP. Molecular road ecology: exploring the potential of genetics for investigating transportation impacts on wildlife. Mol Ecol 2009; 18:4151-64. [PMID: 19732335 DOI: 10.1111/j.1365-294x.2009.04322.x] [Citation(s) in RCA: 168] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Transportation infrastructures such as roads, railroads and canals can have major environmental impacts. Ecological road effects include the destruction and fragmentation of habitat, the interruption of ecological processes and increased erosion and pollution. Growing concern about these ecological road effects has led to the emergence of a new scientific discipline called road ecology. The goal of road ecology is to provide planners with scientific advice on how to avoid, minimize or mitigate negative environmental impacts of transportation. In this review, we explore the potential of molecular genetics to contribute to road ecology. First, we summarize general findings from road ecology and review studies that investigate road effects using genetic data. These studies generally focus only on barrier effects of roads on local genetic diversity and structure and only use a fraction of available molecular approaches. Thus, we propose additional molecular applications that can be used to evaluate road effects across multiple scales and dimensions of the biodiversity hierarchy. Finally, we make recommendations for future research questions and study designs that would advance molecular road ecology. Our review demonstrates that molecular approaches can substantially contribute to road ecology research and that interdisciplinary, long-term collaborations will be particularly important for realizing the full potential of molecular road ecology.
Collapse
Affiliation(s)
- Niko Balkenhol
- Department of Fish & Wildlife Resources, University of Idaho, Moscow, ID 83844-1136, USA.
| | | |
Collapse
|
197
|
Kim KS, Bagley MJ, Coates BS, Hellmich RL, Sappington TW. Spatial and temporal genetic analyses show high gene flow among European corn borer (Lepidoptera: Crambidae) populations across the central U.S. corn belt. ENVIRONMENTAL ENTOMOLOGY 2009; 38:1312-1323. [PMID: 19689914 DOI: 10.1603/022.038.0443] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
European corn borer, Ostrinia nubilalis (Hübner), adults were sampled at 13 sites along two perpendicular 720-km transects intersecting in central Iowa and for the following two generations at four of the same sites separated by 240 km in the cardinal directions. More than 50 moths from each sample location and time were genotyped at eight microsatellite loci. Spatial analyses indicated that there is no spatial genetic structuring between European corn borer populations sampled 720 km apart at the extremes of the transects and no pattern of genetic isolation by distance at that geographic scale. Although these results suggest high gene flow over the spatial scale tested, it is possible that populations have not had time to diverge since the central Corn Belt was invaded by this insect approximately 60 yr ago. However, temporal analyses of genetic changes in single locations over time suggest that the rate of migration is indeed very high. The results of this study suggest that the geographic dimensions of European corn borer populations are quite large, indicating that monitoring for resistance to transgenic Bt corn at widely separated distances is justified, at least in the central Corn Belt. High gene flow further implies that resistance to Bt corn may be slow to evolve, but once it does develop, it may spread geographically with such speed that mitigation strategies will have to be implemented quickly to be effective.
Collapse
Affiliation(s)
- Kyung Seok Kim
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, IA 50011, USA
| | | | | | | | | |
Collapse
|
198
|
Palstra FP, O'Connell MF, Ruzzante DE. Age structure, changing demography and effective population size in Atlantic salmon (Salmo salar). Genetics 2009; 182:1233-49. [PMID: 19528328 PMCID: PMC2728862 DOI: 10.1534/genetics.109.101972] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Accepted: 06/04/2009] [Indexed: 11/18/2022] Open
Abstract
Effective population size (N(e)) is a central evolutionary concept, but its genetic estimation can be significantly complicated by age structure. Here we investigate N(e) in Atlantic salmon (Salmo salar) populations that have undergone changes in demography and population dynamics, applying four different genetic estimators. For this purpose we use genetic data (14 microsatellite markers) from archived scale samples collected between 1951 and 2004. Through life table simulations we assess the genetic consequences of life history variation on N(e). Although variation in reproductive contribution by mature parr affects age structure, we find that its effect on N(e) estimation may be relatively minor. A comparison of estimator models suggests that even low iteroparity may upwardly bias N(e) estimates when ignored (semelparity assumed) and should thus empirically be accounted for. Our results indicate that N(e) may have changed over time in relatively small populations, but otherwise remained stable. Our ability to detect changes in N(e) in larger populations was, however, likely hindered by sampling limitations. An evaluation of N(e) estimates in a demographic context suggests that life history diversity, density-dependent factors, and metapopulation dynamics may all affect the genetic stability of these populations.
Collapse
Affiliation(s)
- Friso P Palstra
- Biology Department, Life Sciences Centre, Dalhousie University, 1355 Oxford St., Halifax, Nova Scotia B3H AJ1, Canada.
| | | | | |
Collapse
|
199
|
Gene flow and natal dispersal in the Siberian flying squirrel based on direct and indirect data. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9954-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
200
|
Kuparinen A, Tufto J, Consuegra S, Hindar K, Merilä J, Garcia de Leaniz C. Effective size of an Atlantic salmon (Salmo salar L.) metapopulation in Northern Spain. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9945-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|