201
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Castellanos MC, Alcántara JM, Rey PJ, Bastida JM. Intra-population comparison of vegetative and floral trait heritabilities estimated from molecular markers in wild Aquilegia populations. Mol Ecol 2011; 20:3513-24. [PMID: 21504491 DOI: 10.1111/j.1365-294x.2011.05094.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Measuring heritable genetic variation is important for understanding patterns of trait evolution in wild populations, and yet studies of quantitative genetic parameters estimated directly in the field are limited by logistic constraints, such as the difficulties of inferring relatedness among individuals in the wild. Marker-based approaches have received attention because they can potentially be applied directly to wild populations. For long-lived, self-compatible plant species where pedigrees are inadequate, the regression-based method proposed by Ritland has the appeal of estimating heritabilities from marker-based estimates of relatedness. The method has been difficult to implement in some plant populations, however, because it requires significant variance in relatedness across the population. Here, we show that the method can be readily applied to compare the ability of different traits to respond to selection, within populations. For several taxa of the perennial herb genus Aquilegia, we estimated heritabilities of floral and vegetative traits and, combined with estimates of natural selection, compared the ability to respond to selection of both types of traits under current conditions. The intra-population comparisons showed that vegetative traits have a higher potential for evolution, because although they are as heritable as floral traits, selection on them is stronger. These patterns of potential evolution are consistent with macroevolutionary trends in the European lineage of the genus.
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Affiliation(s)
- Maria Clara Castellanos
- Consejo Superior de Investigaciones Científicas, Centro de Investigaciones sobre Desertificación, 46470 Albal, Valencia, Spain.
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202
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203
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Chancellor RL, Satkoski J, George D, Olupot W, Lichti N, Smith DG, Waser PM. Do Dispersing Monkeys Follow Kin? Evidence from Gray-cheeked Mangabeys (Lophocebus albigena). INT J PRIMATOL 2011; 32:474-490. [PMID: 21475401 PMCID: PMC3047692 DOI: 10.1007/s10764-010-9483-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 07/22/2010] [Indexed: 11/26/2022]
Abstract
Among social vertebrates, immigrants may incur a substantial fitness cost when they attempt to join a new group. Dispersers could reduce that cost, or increase their probability of mating via coalition formation, by immigrating into groups containing first- or second-degree relatives. We here examine whether dispersing males tend to move into groups containing fathers or brothers in gray-cheeked mangabeys (Lophocebus albigena) in Kibale National Park, Uganda. We sampled blood from 21 subadult and adult male mangabeys in 7 social groups and genotyped them at 17 microsatellite loci. Twelve genotyped males dispersed to groups containing other genotyped adult males during the study; in only 1 case did the group contain a probable male relative. Contrary to the prediction that dispersing males would follow kin, relatively few adult male dyads were likely first- or second-degree relatives; opportunities for kin-biased dispersal by mangabeys appear to be rare. During 4 yr of observation, adult brothers shared a group only once, and for only 6 wk. Mean relatedness among adult males sharing a group was lower than that among males in different groups. Randomization tests indicate that closely related males share groups no more often than expected by chance, although these tests had limited power. We suggest that the demographic conditions that allow kin-biased dispersal to evolve do not occur in mangabeys, may be unusual among primates, and are worth further attention.
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Affiliation(s)
- Rebecca L. Chancellor
- Department of Anthropology, University of California, Davis, Davis, CA 95616 USA
- Gishwati Area Conservation Program, Great Ape Trust, P.O. Box 538, Gisenyi, Rwanda
| | - Jessica Satkoski
- Department of Anthropology, University of California, Davis, Davis, CA 95616 USA
| | - Debbie George
- Department of Anthropology, University of California, Davis, Davis, CA 95616 USA
| | - William Olupot
- Wildlife Conservation Society, P.O. Box 7487, Kampala, Uganda
| | - Nathanael Lichti
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907 USA
| | - David G. Smith
- Department of Anthropology, University of California, Davis, Davis, CA 95616 USA
- California National Primate Research Center, University of California, Davis, CA 95616 USA
| | - Peter M. Waser
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 USA
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204
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Rew MB, Robbins J, Mattila D, Palsbøll PJ, Bérube M. How many genetic markers to tag an individual? An empirical assessment of false matching rates among close relatives. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2011; 21:877-887. [PMID: 21639051 DOI: 10.1890/10-0348.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Genetic identification of individuals is now commonplace, enabling the application of tagging methods to elusive species or species that cannot be tagged by traditional methods. A key aspect is determining the number of loci required to ensure that different individuals have non-matching multi-locus genotypes. Closely related individuals are of particular concern because of elevated matching probabilities caused by their recent co-ancestry. This issue may be addressed by increasing the number of loci to a level where full siblings (the relatedness category with the highest matching probability) are expected to have non-matching multi-locus genotypes. However, increasing the number of loci to meet this "full-sib criterion" greatly increases the laboratory effort, which in turn may increase the genotyping error rate resulting in an upward-biased mark-recapture estimate of abundance as recaptures are missed due to genotyping errors. We assessed the contribution of false matches from close relatives among 425 maternally related humpback whales, each genotyped at 20 microsatellite loci. We observed a very low (0.5-4%) contribution to falsely matching samples from pairs of first-order relatives (i.e., parent and offspring or full siblings). The main contribution to falsely matching individuals from close relatives originated from second-order relatives (e.g., half siblings), which was estimated at 9%. In our study, the total number of observed matches agreed well with expectations based upon the matching probability estimated for unrelated individuals, suggesting that the full-sib criterion is overly conservative, and would have required a 280% relative increase in effort. We suggest that, under most circumstances, the overall contribution to falsely matching samples from close relatives is likely to be low, and hence applying the full-sib criterion is unnecessary. In those cases where close relatives may present a significant issue, such as unrepresentative sampling, we propose three different genotyping strategies requiring only a modest increase in effort, which will greatly reduce the number of false matches due to the presence of related individuals.
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Affiliation(s)
- Mary Beth Rew
- Department of Environmental Science, Policy and Management, University of California, 137 Mulford Hall, Berkeley, California 94720-3110, USA
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205
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Characterization of paternity relationships in the mole rat Spalax ehrenbergi by microsatellite genotyping. POPUL ECOL 2011. [DOI: 10.1007/s10144-011-0264-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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206
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Green ML, Herzing DL, Baldwin JD. Reproductive success of male Atlantic spotted dolphins (Stenella frontalis) revealed by noninvasive genetic analysis of paternity. CAN J ZOOL 2011. [DOI: 10.1139/z10-111] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cetaceans are known to frequently engage in sexual behavior; however, the lack of male parental investment in offspring makes assessment of male reproductive success difficult. We assessed paternity in a small population (mean individuals sighted per year = 93) of Atlantic spotted dolphins ( Stenella frontalis (G. Cuvier, 1829)) utilizing noninvasively collected fecal material. Samples (n = 88) were collected from dolphins from four social clusters. Of the 29 offspring tested, 34.5% were assigned paternity, resulting in 10 paternities assigned to seven males. Our study indicates that achieving a certain age is a potential precursor for males to mate successfully, as 18 years was the youngest estimated age of a male at the time of calf conception. In all pairings but one, the males were older than the female (mean age difference = 7.7+ years). Successful males were from two of the four social clusters and males most often mated within their social group or with females from the next geographically closest group. The study combines genetic data with known maternal pedigree information and reveals patterns in the overall mating system in a cetacean species where reproductive success of males was previously unknown.
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Affiliation(s)
- Michelle L. Green
- Department of Biology, Florida Atlantic University, 3200 College Avenue, Davie, FL 33314, USA
- Wild Dolphin Project, P.O. Box 8436, Jupiter, FL 33468, USA
- Department of Biology, Department of Psychology, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Denise L. Herzing
- Department of Biology, Florida Atlantic University, 3200 College Avenue, Davie, FL 33314, USA
- Wild Dolphin Project, P.O. Box 8436, Jupiter, FL 33468, USA
- Department of Biology, Department of Psychology, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - John D. Baldwin
- Department of Biology, Florida Atlantic University, 3200 College Avenue, Davie, FL 33314, USA
- Wild Dolphin Project, P.O. Box 8436, Jupiter, FL 33468, USA
- Department of Biology, Department of Psychology, Florida Atlantic University, Boca Raton, FL 33431, USA
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207
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Fabiani A, Trucchi E, Rosa S, Marquez C, Snell HL, Snell HM, Tapia Aguilera W, Gentile G. Conservation of Galápagos land iguanas: genetic monitoring and predictions of a long-term program on the island of Santa Cruz. Anim Conserv 2011. [DOI: 10.1111/j.1469-1795.2011.00442.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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208
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209
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HAUSER LORENZ, BAIRD MELISSA, HILBORN RAY, SEEB LISAW, SEEB JAMESE. An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population. Mol Ecol Resour 2011; 11 Suppl 1:150-61. [DOI: 10.1111/j.1755-0998.2010.02961.x] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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210
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Kim YK, Hong YJ, Min MS, Kim KS, Kim YJ, Voloshina I, Myslenkov A, Smith GJD, Cuong ND, Tho HH, Han SH, Yang DH, Kim CB, Lee H. Genetic status of Asiatic black bear (Ursus thibetanus) reintroduced into South Korea based on mitochondrial DNA and microsatellite loci analysis. ACTA ACUST UNITED AC 2011; 102:165-74. [PMID: 21325020 DOI: 10.1093/jhered/esq121] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Asiatic black bear is one of the most endangered mammals in South Korea owing to population declines resulting from human exploitation and habitat fragmentation. To restore the black bear population in South Korea, 27 bear cubs from North Korea and Russian Far East (Primorsky Krai) were imported and released into Jirisan National Park, a reservoir of the largest wild population in South Korea, in 2004. To monitor the success of this reintroduction, the genetic diversity and population structure of the reintroduced black bears were measured using both mitochondrial and nuclear DNA markers. Mitochondrial D-loop region DNA sequences (615 bp) of 43 Japanese black bears from previous study and 14 Southeast Asian black bears in this study were employed to obtain phylogenetic inference of the reintroduced black bears. The mitochondrial phylogeny indicated Asiatic black bear populations from Russian Far East and North Korea form a single evolutionary unit distinct from populations from Japan and Southeast Asia. Mean expected heterozygosity (H(E)) across 16 microsatellite loci was 0.648 for Russian and 0.676 for North Korean populations. There was a moderate but significant level of microsatellite differentiation (F(ST) = 0.063) between black bears from the 2 source areas. In addition, genetic evidences revealed that 2 populations are represented as diverging groups, with lingering genetic admixture among individuals of 2 source populations. Relatedness analysis based on genetic markers indicated several discrepancies with the pedigree records. Implication of the phylogenetic and genetic evidences on long-term management of Asiatic black bears in South Korea is discussed.
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Affiliation(s)
- Yung-Kun Kim
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 151-742, Korea
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211
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Mitchell AA, Lau J, Chemnick LG, Thompson EA, Alberts AC, Ryder OA, Gerber GP. Using microsatellite diversity in wild Anegada iguanas (Cyclura pinguis) to establish relatedness in a captive breeding group of this critically endangered species. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0184-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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212
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Characterisation of twenty-one European badger (Meles meles) microsatellite loci facilitates the discrimination of second-order relatives. CONSERV GENET RESOUR 2011. [DOI: 10.1007/s12686-011-9392-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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213
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A Demo-Genetic Analysis of a Small Reintroduced Carnivore Population: The Otter (Lutra lutra) in The Netherlands. INTERNATIONAL JOURNAL OF ECOLOGY 2011. [DOI: 10.1155/2011/870853] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Assessing the viability of reintroduced animal populations is a complicated task. Reintroductions are usually carried out with a small number of individuals, thereby, limiting the possibilities for monitoring because of the possible negative effects of intensive monitoring on survival and reproduction. Moreover, reintroduction studies are part of a socioeconomic interplay of forces, thereby, also limiting monitoring possibilities. Also, knowledge of population demography and abundance can be incomplete or unattainable. Here, we illustrate how we combined traditional telemetry and novel non-invasive genetic methodology to construct a detailed life table of a small reintroduced otter population in The Netherlands. Combining an appropriate capture-mark-recapture framework with a matrix modelling approach provides, in general, useful insights for such populations. The data indicated that (i) male survival is lower than female survival, (ii) the reintroduced population is currently growing (estimatedλ=1.26: range [1.06, 1.42]) and seems viable, (iii) increasing adult survival is currently the critical stage at which efforts of field managers should concentrate, and (iv) the modelling framework allowed us to determine the boundary conditions for the vital rates under which the population would go extinct. The applied approach directs at measurements that help field managers to implement the right conservation strategy after reintroductions.
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214
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Wolf JBW, Traulsen A, James R. Exploring the Link between Genetic Relatedness r and Social Contact Structure k in Animal Social Networks. Am Nat 2010; 177:135-42. [PMID: 21117963 DOI: 10.1086/657442] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Our understanding of how cooperation can arise in a population of selfish individuals has been greatly advanced by theory. More than one approach has been used to explore the effect of population structure. Inclusive fitness theory uses genetic relatedness r to express the role of population structure. Evolutionary graph theory models the evolution of cooperation on network structures and focuses on the number of interacting partners k as a quantity of interest. Here we use empirical data from a hierarchically structured animal contact network to examine the interplay between independent, measurable proxies for these key parameters. We find strong inverse correlations between estimates of r and k over three levels of social organization, suggesting that genetic relatedness and social contact structure capture similar structural information in a real population.
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Affiliation(s)
- Jochen B W Wolf
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany.
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215
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Grueber CE, Waters JM, Jamieson IG. The imprecision of heterozygosity-fitness correlations hinders the detection of inbreeding and inbreeding depression in a threatened species. Mol Ecol 2010; 20:67-79. [PMID: 21087447 DOI: 10.1111/j.1365-294x.2010.04930.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In nonpedigreed wild populations, inbreeding depression is often quantified through the use of heterozygosity-fitness correlations (HFCs), based on molecular estimates of relatedness. Although such correlations are typically interpreted as evidence of inbreeding depression, by assuming that the marker heterozygosity is a proxy for genome-wide heterozygosity, theory predicts that these relationships should be difficult to detect. Until now, the vast majority of empirical research in this area has been performed on generally outbred, nonbottlenecked populations, but differences in population genetic processes may limit extrapolation of results to threatened populations. Here, we present an analysis of HFCs, and their implications for the interpretation of inbreeding, in a free-ranging pedigreed population of a bottlenecked species: the endangered takahe (Porphyrio hochstetteri). Pedigree-based inbreeding depression has already been detected in this species. Using 23 microsatellite loci, we observed only weak evidence of the expected relationship between multilocus heterozygosity and fitness at individual life-history stages (such as survival to hatching and fledging), and parameter estimates were imprecise (had high error). Furthermore, our molecular data set could not accurately predict the inbreeding status of individuals (as 'inbred' or 'outbred', determined from pedigrees), nor could we show that the observed HFCs were the result of genome-wide identity disequilibrium. These results may be attributed to high variance in heterozygosity within inbreeding classes. This study is an empirical example from a free-ranging endangered species, suggesting that even relatively large numbers (>20) of microsatellites may give poor precision for estimating individual genome-wide heterozygosity. We argue that pedigree methods remain the most effective method of quantifying inbreeding in wild populations, particularly those that have gone through severe bottlenecks.
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216
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Lee DH, Cho CI, Kim NS. Prediction of Genomic Relationship Matrices using Single Nucleotide Polymorphisms in Hanwoo. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2010. [DOI: 10.5187/jast.2010.52.5.357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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217
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Serbezov D, Bernatchez L, Olsen EM, Vøllestad LA. Mating patterns and determinants of individual reproductive success in brown trout (Salmo trutta) revealed by parentage analysis of an entire stream living population. Mol Ecol 2010; 19:3193-205. [PMID: 20629953 DOI: 10.1111/j.1365-294x.2010.04744.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Reproductive success and its determinants are difficult to infer for wild populations of species with no parental care where behavioural observations are difficult or impossible. In this study, we characterized the breeding system and provide estimates of individual reproductive success under natural conditions for an exhaustively sampled stream-resident brown trout (Salmo trutta) population. We inferred parentage using a full probability Bayesian model that combines genetic (microsatellite) with phenotypic data. By augmenting the potential parents file with inferred parental genotypes from sib-ship analysis in cases where large families had unsampled parents, we could make more precise inference on variance of family size. We observed both polygamous and monogamous matings and large reproductive skew for both sexes, particularly in males. Correspondingly, we found evidence for sexual selection on body size for both sexes. We show that the mating system of brown trout has the potential to be very flexible and we conjecture that environmental uncertainty could be driving the evolution and perhaps select for the maintenance of plasticity of the mating system in this species.
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Affiliation(s)
- Dimitar Serbezov
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, P.O. Box 1066, Blindern, 0316 Oslo, Norway.
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218
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Allendorf FW, Hohenlohe PA, Luikart G. Genomics and the future of conservation genetics. Nat Rev Genet 2010; 11:697-709. [DOI: 10.1038/nrg2844] [Citation(s) in RCA: 939] [Impact Index Per Article: 67.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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219
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Ledoux JB, Garrabou J, Bianchimani O, Drap P, Féral JP, Aurelle D. Fine-scale genetic structure and inferences on population biology in the threatened Mediterranean red coral, Corallium rubrum. Mol Ecol 2010; 19:4204-16. [PMID: 20854271 DOI: 10.1111/j.1365-294x.2010.04814.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Identifying microevolutionary processes acting in populations of marine species with larval dispersal is a challenging but crucial task because of its conservation implications. In this context, recent improvements in the study of spatial genetic structure (SGS) are particularly promising because they allow accurate insights into the demographic and evolutionary processes at stake. Using an exhaustive sampling and a combination of image processing and population genetics, we highlighted significant SGS between colonies of Corallium rubrum over an area of half a square metre, which sheds light on a number of aspects of its population biology. Based on this SGS, we found the mean dispersal range within sites to be between 22.6 and 32.1 cm, suggesting that the surveyed area approximately corresponded to a breeding unit. We then conducted a kinship analysis, which revealed a complex half-sib family structure and allowed us to quantify the level of self-recruitment and to characterize aspects of the mating system of this species. Furthermore, significant temporal variations in allele frequencies were observed, suggesting low genetic drift. These results have important conservation implications for the red coral and further our understanding of the microevolutionary processes acting within populations of sessile marine species with a larval phase.
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Affiliation(s)
- J-B Ledoux
- Aix-Marseille Université, CNRS UMR 6540 DIMAR, Centre d'Océanologie de Marseille, Station Marine d'Endoume, Chemin de la Batterie des Lions, 13007 Marseille, FranceEcole d'ingénieur de Luminy, CNRS UMR 6168 LSIS Avenue de Luminy 13288 Marseille Cedex 09, France
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220
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Abstract
Grouping provides many potential benefits to individuals in terms of foraging and anti-predator protection. However, it has been suggested that individuals could gain additional benefits in terms of indirect fitness by grouping with kin. Surprisingly, the genetic composition of wild fish shoals and the importance of kin-associated shoaling remain poorly understood. The Trinidadian guppy (Poecilia reticulata) has life history traits that might promote kin structure of shoals such as internal fertilisation and small brood size in contrast to many other fish species. Even though previous studies did not find any indication of kin structure in shoals of adult guppies, it is possible that related juveniles remain together in shoals, partly because of lower mobility and because the advantages of kin association may change with age. Using 10 microsatellite markers, we conducted a genetic analysis on 40 shoals from four populations. Pair-wise relatedness was inferred using a modified version of the software package COLONY and permutation tests were conducted to test the hypothesis that kin occur together in juvenile shoals more often than expected by chance. The frequency of sib dyads among juveniles within shoals was significantly larger than that between shoals in two high predation populations but not in two low predation populations. This finding contributes to the understanding of factors underlying shoal composition and highlights the potential of recent methodological advances for detecting such relationships.
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221
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Anderson TJC, Williams JT, Nair S, Sudimack D, Barends M, Jaidee A, Price RN, Nosten F. Inferred relatedness and heritability in malaria parasites. Proc Biol Sci 2010; 277:2531-40. [PMID: 20392725 PMCID: PMC2894920 DOI: 10.1098/rspb.2010.0196] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 03/22/2010] [Indexed: 12/22/2022] Open
Abstract
Malaria parasites vary in phenotypic traits of biomedical or biological interest such as growth rate, virulence, sex ratio and drug resistance, and there is considerable interest in identifying the genes that underlie this variation. An important first step is to determine trait heritability (H(2)). We evaluate two approaches to measuring H(2) in natural parasite populations using relatedness inferred from genetic marker data. We collected single-clone Plasmodium falciparum infections from 185 patients from the Thailand-Burma border, monitored parasite clearance following treatment with artemisinin combination therapy (ACT), measured resistance to six antimalarial drugs and genotyped parasites using 335 microsatellites. We found strong relatedness structure. There were 27 groups of two to eight clonally identical (CI) parasites, and 74 per cent of parasites showed significant relatedness to one or more other parasites. Initially, we used matrices of allele sharing and variance components (VC) methods to estimate H(2). Inhibitory concentrations (IC(50)) for six drugs showed significant H(2) (0.24 to 0.79, p = 0.06 to 2.85 x 10(-9)), demonstrating that this study design has adequate power. However, a phenotype of current interest--parasite clearance following ACT--showed no detectable heritability (H(2) = 0-0.09, ns) in this population. The existence of CI parasites allows the use of a simple ANOVA approach for quantifying H(2), analogous to that used in human twin studies. This gave similar results to the VC method and requires considerably less genotyping information. We conclude (i) that H(2) can be effectively measured in malaria parasite populations using minimal genotype data, allowing rational design of genome-wide association studies; and (ii) while drug response (IC(50)) shows significant H(2), parasite clearance following ACT was not heritable in the population studied.
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Affiliation(s)
- Tim J C Anderson
- Southwest Foundation for Biomedical Research, San Antonio, TX, USA.
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222
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Gonçalves da Silva A, Russello MA. iR el: software for implementing pairwise relatedness estimators and evaluating their performance. CONSERV GENET RESOUR 2010. [DOI: 10.1007/s12686-010-9292-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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223
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Sheikh SI, Berger-Wolf TY, Khokhar AA, Caballero IC, Ashley MV, Chaovalitwongse W, Chou CA, Dasgupta B. Combinatorial reconstruction of half-sibling groups from microsatellite data. J Bioinform Comput Biol 2010; 8:337-56. [PMID: 20401949 DOI: 10.1142/s0219720010004793] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2009] [Revised: 12/08/2009] [Accepted: 12/08/2009] [Indexed: 11/18/2022]
Abstract
While full-sibling group reconstruction from microsatellite data is a well-studied problem, reconstruction of half-sibling groups is much less studied, theoretically challenging, and computationally demanding. In this paper, we present a formulation of the half-sibling reconstruction problem and prove its APX-hardness. We also present exact solutions for this formulation and develop heuristics. Using biological and synthetic datasets we present experimental results and compare them with the leading alternative software COLONY. We show that our results are competitive and allow half-sibling group reconstruction in the presence of polygamy, which is prevalent in nature.
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Affiliation(s)
- Saad I Sheikh
- Department of Computer Science, University of Illinois at Chicago, 851 S. Morgan St (M/C 152), Chicago, IL 60607, USA.
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224
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Sillanpää MJ. Overview of techniques to account for confounding due to population stratification and cryptic relatedness in genomic data association analyses. Heredity (Edinb) 2010; 106:511-9. [PMID: 20628415 DOI: 10.1038/hdy.2010.91] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Population-based genomic association analyses are more powerful than within-family analyses. However, population stratification (unknown or ignored origin of individuals from multiple source populations) and cryptic relatedness (unknown or ignored covariance between individuals because of their relatedness) are confounding factors in population-based genomic association analyses, which inflate the false-positive rate. As a consequence, false association signals may arise in genomic data association analyses for reasons other than true association between the tested genomic factor (marker genotype, gene or protein expression) and the study phenotype. It is therefore important to correct or account for these confounders in population-based genomic data association analyses. The common correction techniques for population stratification and cryptic relatedness problems are presented here in the phenotype-marker association analysis context, and comments on their suitability for other types of genomic association analyses (for example, phenotype-expression association) are also provided. Even though many of these techniques have originally been developed in the context of human genetics, most of them are also applicable to model organisms and breeding populations.
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Affiliation(s)
- M J Sillanpää
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
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225
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SKAUG HJ, BÉRUBÉ M, PALSBØLL PJ. Detecting dyads of related individuals in large collections of DNA‐profiles by controlling the false discovery rate. Mol Ecol Resour 2010; 10:693-700. [DOI: 10.1111/j.1755-0998.2010.02833.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- H. J. SKAUG
- Department of Mathematics, University of Bergen, Box 7803, 5020 Bergen, Norway
| | - M. BÉRUBÉ
- Department of Genetics, Microbiology, and Toxicology, Stockholm University, 106 91 Stockholm, Sweden
| | - P. J. PALSBØLL
- Department of Genetics, Microbiology, and Toxicology, Stockholm University, 106 91 Stockholm, Sweden
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227
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Population substructure in continuous and fragmented stands of Populus trichocarpa. Heredity (Edinb) 2010; 105:348-57. [PMID: 20531447 DOI: 10.1038/hdy.2010.73] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Population substructure has important implications for both basic and applied genetic research. We used 10 microsatellite markers to characterize population substructure in two ecologically and demographically contrasting populations of the model tree Populus trichocarpa. The Marchel site was a continuous stand growing in a mesic habitat in western Oregon, whereas the Vinson site consisted of three disjunct and isolated stands in the high desert of eastern Oregon. A previous study revealed that pollen-mediated gene flow is extensive in both populations. Surprisingly, model-based clustering, principal components analysis and analyses of molecular variance provided overwhelming support for the existence of at least two intermingled sub-populations within the continuous Marchel population (F(ST)=0.026, P<0.001), which occupied an area with a radius of only about 250 m. Genets in these two sub-populations appeared to have different relative clone ages and phenologies, leading us to hypothesize that they correspond to different seedling cohorts, each established from seeds produced by relatively few mothers. As expected, substructure was stronger in the fragmented Vinson population (F(ST)=0.071, P=0.001), and this difference appeared to result from the more extensive family structure in this population. Using group-likelihood methods, we reconstructed multiple interconnected half-sib families in the Vinson population, with some genets having as many as eight putative siblings. Researchers involved in ongoing and future association studies in P. trichocarpa should account for the likely presence of subtle but practically significant substructure in populations throughout the range of this species.
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228
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Palsbøll PJ, Zachariah Peery M, Bérubé M. Detecting populations in the 'ambiguous' zone: kinship-based estimation of population structure at low genetic divergence. Mol Ecol Resour 2010; 10:797-805. [PMID: 21565091 DOI: 10.1111/j.1755-0998.2010.02887.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Identifying population structure is one of the most common and important objectives of spatial analyses using population genetic data. Population structure is detected either by rejecting the null hypothesis of a homogenous distribution of genetic variation, or by estimating low migration rates. Issues arise with most current population genetic inference methods when the genetic divergence is low among putative populations. Low levels of genetic divergence may be as a result of either high ongoing migration or historic high migration but no current, ongoing migration. We direct attention to recent developments in the use of the tempo-spatial distribution of closely related individuals to detect population structure or estimate current migration rates. These 'kinship-based' approaches complement more traditional population-based genetic inference methods by providing a means to detect population structure and estimate current migration rates when genetic divergence is low. However, for kinship-based methods to become widely adopted, formal estimation procedures applicable to a range of species life histories are needed.
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Affiliation(s)
- Per J Palsbøll
- Department of Genetics, Microbiology and Toxicology, Stockholm University, SE-106 91 Stockholm, Sweden Department of Forest and Wildlife Ecology, University of Wisconsin Madison, 1630 Linden Drive, Madison, WI 53706, USA
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229
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Croteau EK, Heist EJ, Nielsen CK. Fine-scale population structure and sex-biased dispersal in bobcats (Lynx rufus) from southern Illinois. CAN J ZOOL 2010. [DOI: 10.1139/z10-024] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In mammal populations, the spatial and genetic structure can be affected by dispersal, philopatry, and relatedness. Bobcats ( Lynx rufus (Schreber, 1777)) are thought to exhibit typical mammalian dispersal behaviour where males disperse and females are philopatric, potentially leading to higher relatedness among females compared with males. We used 10 microsatellite loci to examine population structure and sex-biased dispersal in 146 bobcats sampled in southern Illinois during 1993–2001 using population genetic descriptive statistics, a Bayesian clustering algorithm, relatedness (rxy), and autocorrelation analyses. A randomization test demonstrated that female dyads had significantly higher rxy values with respect to randomly selected dyads (rxy = 0.093 ± 0.222, P = 0.012) and spatial autocorrelation analyses determined that females in close proximity (<5 km) had a high probability of being related (P = 0.001). Conversely, rxy values for males were not different from the null distribution (rxy = 0.019 ± 0.122, P = 0.3158) and no significant relationships were found with spatial autocorrelation analysis. Additionally, it was demonstrated that bobcats in southern Illinois approximated a panmictic population with no obvious barriers to gene flow. The pattern of relatedness observed in this study confirmed that females were philopatric and males dispersed, corroborating existing observational data for this species.
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Affiliation(s)
- Emily K. Croteau
- Cooperative Wildlife Research Laboratory, Southern Illinois University – Carbondale, Life Sciences II, Carbondale, IL 62901-6504, USA
- Fisheries and Illinois Aquaculture Center, Southern Illinois University – Carbondale, Life Sciences III, 1125 Lincoln Drive, Carbondale, IL 62901-6511, USA
| | - Edward J. Heist
- Cooperative Wildlife Research Laboratory, Southern Illinois University – Carbondale, Life Sciences II, Carbondale, IL 62901-6504, USA
- Fisheries and Illinois Aquaculture Center, Southern Illinois University – Carbondale, Life Sciences III, 1125 Lincoln Drive, Carbondale, IL 62901-6511, USA
| | - Clayton K. Nielsen
- Cooperative Wildlife Research Laboratory, Southern Illinois University – Carbondale, Life Sciences II, Carbondale, IL 62901-6504, USA
- Fisheries and Illinois Aquaculture Center, Southern Illinois University – Carbondale, Life Sciences III, 1125 Lincoln Drive, Carbondale, IL 62901-6511, USA
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230
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Goncalves da Silva A, Lalonde DR, Quse V, Shoemaker A, Russello MA. Genetic Approaches Refine Ex Situ Lowland Tapir (Tapirus terrestris) Conservation. J Hered 2010; 101:581-90. [DOI: 10.1093/jhered/esq055] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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231
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Steinauer ML, Blouin MS, Criscione CD. Applying evolutionary genetics to schistosome epidemiology. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2010; 10:433-43. [PMID: 20176142 PMCID: PMC2861999 DOI: 10.1016/j.meegid.2010.02.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 02/09/2010] [Accepted: 02/15/2010] [Indexed: 10/19/2022]
Abstract
We review how molecular markers and evolutionary analysis have been applied to the study of schistosome parasites, important pathogens that infect over 200 million people worldwide. Topics reviewed include phylogenetics and biogeography, hybridization, infection within snails, mating systems, and genetic structure. Some interesting generalizations include that schistosome species hybridize frequently and have switched definitive hosts repeatedly in evolutionary time. We show that molecular markers can be used to infer epidemiologically relevant processes such as spatial variation in transmission, or to reveal complex patterns of mate choice. Analysis of genetic structure data shows that transmission foci can be structured by watershed boundaries, habitat types, and host species. We also discuss sampling and analytical problems that arise when using larvae to estimate genetic parameters of adult schistosome populations. Finally, we review pitfalls in methodologies such as genotyping very small individuals, statistical methods for identifying clonemates or for identifying sibling groups, and estimating allele frequencies from pooled egg samples.
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Affiliation(s)
- Michelle L Steinauer
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, 105 Magruder Hall, Corvallis, OR 97331, United States.
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232
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WALLING CRAIGA, PEMBERTON JOSEPHINEM, HADFIELD JARRODD, KRUUK LOESKEEB. Comparing parentage inference software: reanalysis of a red deer pedigree. Mol Ecol 2010; 19:1914-28. [DOI: 10.1111/j.1365-294x.2010.04604.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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233
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JONES OWENR, WANG JINLIANG. COLONY: a program for parentage and sibship inference from multilocus genotype data. Mol Ecol Resour 2010; 10:551-5. [DOI: 10.1111/j.1755-0998.2009.02787.x] [Citation(s) in RCA: 1204] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- OWEN R. JONES
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | - JINLIANG WANG
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
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234
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Lebigre C, Alatalo RV, Siitari H. Female-biased dispersal alone can reduce the occurrence of inbreeding in black grouse (Tetrao tetrix). Mol Ecol 2010; 19:1929-39. [PMID: 20345672 DOI: 10.1111/j.1365-294x.2010.04614.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although inbreeding depression and mechanisms for kin recognition have been described in natural bird populations, inbreeding avoidance through mate choice has rarely been reported suggesting that sex-biased dispersal is the main mechanism reducing the risks of inbreeding. However, a full understanding of the effect of dispersal on the occurrence of inbred matings requires estimating the inbreeding risks prior to dispersal. Combining pairwise relatedness measures and kinship assignments, we investigated in black grouse whether the observed occurrence of inbred matings was explained by active kin discrimination or by female-biased dispersal. In this large continuous population, copulations between close relatives were rare. As female mate choice was random for relatedness, females with more relatives in the local flock tended to mate with genetically more similar males. To quantify the initial risks of inbreeding, we measured the relatedness to the males of females captured in their parental flock and virtually translocated female hatchlings in their parental and to more distant flocks. These tests indicated that dispersal decreased the likelihood of mating with relatives and that philopatric females had higher inbreeding risks than the actual breeding females. As females do not discriminate against relatives, the few inbred matings were probably due to the variance in female dispersal propensity and dispersal distance. Our results support the view that kin discrimination mate choice is of little value if dispersal effectively reduces the risks of inbreeding.
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Affiliation(s)
- C Lebigre
- School of Biological Sciences, University of Aberdeen, Tillydrone avenue, Aberdeen, AB24 2TZ, UK.
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235
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Fantin C, Farias IP, Monjeló LAS, Hrbek T. Polyandry in the red-headed river turtle Podocnemis erythrocephala (Testudines, Podocnemididae) in the Brazilian Amazon. GENETICS AND MOLECULAR RESEARCH 2010; 9:435-40. [PMID: 20391328 DOI: 10.4238/vol9-1gmr749] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The genus Podocnemis comprises six living species, including P. erythrocephala (irapuca-red-headed river turtle). Data are available concerning the reproductive biology of the species of the genus Podocnemis, but little is known about their reproductive strategies. Considering the total lack of such data for P. erythrocephala, and with the goal of contributing information on their mode of reproduction, we examined the relationships among individuals of nests of this turtle, using microsatellite markers. Using four microsatellite loci, we analyzed the progeny in six nests from two localities in the Brazilian Amazon (Santa Isabel do rio Negro and Parintins). All juveniles from each nest were analyzed. The genotypes of each juvenile from each nest were identified, and because a sample of female DNA was not available, the maternal genotype was inferred from homozygous individuals in each nest. We found that this species is promiscuous; there was multiple paternity in five of the six nests analyzed. In addition to being important for the understanding of evolutionary and genetic processes, this type of information will be useful for chelonian management projects. Our data suggest one possible difference between reproductive patterns of the different populations. This multi-paternal condition may be a natural reproductive strategy for the preservation of the genetic diversity of this species.
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Affiliation(s)
- C Fantin
- Departamento de Biologia, Laboratório de Evolução e Genética Animal, Universidade Federal do Amazonas, Manaus, AM, Brasil.
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236
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Faircloth BC, Title A, Tan K, Welty J, Belthoff JR, Gowaty PA. Eighteen microsatellite loci developed from western burrowing owls (Athene cunicularia hypugaea). CONSERV GENET RESOUR 2010. [DOI: 10.1007/s12686-010-9214-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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237
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Israel JA, May B. Indirect genetic estimates of breeding population size in the polyploid green sturgeon (Acipenser medirostris). Mol Ecol 2010; 19:1058-70. [PMID: 20149090 DOI: 10.1111/j.1365-294x.2010.04533.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J A Israel
- Genomic Variation Laboratory, Department of Animal Science, University of California, Davis, CA 95616, USA.
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238
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Koelewijn HP, Pérez-Haro M, Jansman HAH, Boerwinkel MC, Bovenschen J, Lammertsma DR, Niewold FJJ, Kuiters AT. The reintroduction of the Eurasian otter (Lutra lutra) into the Netherlands: hidden life revealed by noninvasive genetic monitoring. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0051-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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239
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Kinship Analysis of One Broodstock Population of Large Yellow Croaker<I>Pseudosciaena crocea</I>. Zool Res 2010. [DOI: 10.3724/sp.j.1141.2009.06620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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240
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DUNCAN SARAHI, RIECHERT SUSANE, FITZPATRICK BENJAMINM, FORDYCE JAMESA. Relatedness and genetic structure in a socially polymorphic population of the spiderAnelosimus studiosus. Mol Ecol 2010; 19:810-8. [DOI: 10.1111/j.1365-294x.2010.04523.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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241
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Coleman C, Copetti D, Cipriani G, Hoffmann S, Kozma P, Kovács L, Morgante M, Testolin R, Di Gaspero G. The powdery mildew resistance gene REN1 co-segregates with an NBS-LRR gene cluster in two Central Asian grapevines. BMC Genet 2009; 10:89. [PMID: 20042081 PMCID: PMC2814809 DOI: 10.1186/1471-2156-10-89] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2009] [Accepted: 12/30/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Grape powdery mildew is caused by the North American native pathogen Erysiphe necator. Eurasian Vitis vinifera varieties were all believed to be susceptible. REN1 is the first resistance gene naturally found in cultivated plants of Vitis vinifera. RESULTS REN1 is present in 'Kishmish vatkana' and 'Dzhandzhal kara', two grapevines documented in Central Asia since the 1920's. These cultivars have a second-degree relationship (half sibs, grandparent-grandchild, or avuncular), and share by descent the chromosome on which the resistance allele REN1 is located. The REN1 interval was restricted to 1.4 cM using 38 SSR markers distributed across the locus and the segregation of the resistance phenotype in two progenies of collectively 461 offspring, derived from either resistant parent. The boundary markers delimit a 1.4-Mbp sequence in the PN40024 reference genome, which contains 27 genes with known functions, 2 full-length coiled-coil NBS-LRR genes, and 9 NBS-LRR pseudogenes. In the REN1 locus of PN40024, NBS genes have proliferated through a mixture of segmental duplications, tandem gene duplications, and intragenic recombination between paralogues, indicating that the REN1 locus has been inherently prone to producing genetic variation. Three SSR markers co-segregate with REN1, the outer ones confining the 908-kb array of NBS-LRR genes. Kinship and clustering analyses based on genetic distances with susceptible cultivars representative of Central Asian Vitis vinifera indicated that 'Kishmish vatkana' and 'Dzhandzhal kara' fit well into local germplasm. 'Kishmish vatkana' also has a parent-offspring relationship with the seedless table grape 'Sultanina'. In addition, the distant genetic relatedness to rootstocks, some of which are derived from North American species resistant to powdery mildew and have been used worldwide to guard against phylloxera since the late 1800's, argues against REN1 being infused into Vitis vinifera from a recent interspecific hybridisation. CONCLUSION The REN1 gene resides in an NBS-LRR gene cluster tightly delimited by two flanking SSR markers, which can assist in the selection of this DNA block in breeding between Vitis vinifera cultivars. The REN1 locus has multiple layers of structural complexity compared with its two closely related paralogous NBS clusters, which are located some 5 Mbp upstream and 4 Mbp downstream of the REN1 interval on the same chromosome.
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Affiliation(s)
- Courtney Coleman
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze 208, 33100 Udine, Italy.
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242
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JONES ADAMG, SMALL CLAYTONM, PACZOLT KIMBERLYA, RATTERMAN NICHOLASL. A practical guide to methods of parentage analysis. Mol Ecol Resour 2009; 10:6-30. [PMID: 21564987 DOI: 10.1111/j.1755-0998.2009.02778.x] [Citation(s) in RCA: 239] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- ADAM G. JONES
- Department of Biology, 3258 TAMU, Texas A&M University, College Station, TX 77843, USA
| | - CLAYTON M. SMALL
- Department of Biology, 3258 TAMU, Texas A&M University, College Station, TX 77843, USA
| | - KIMBERLY A. PACZOLT
- Department of Biology, 3258 TAMU, Texas A&M University, College Station, TX 77843, USA
| | - NICHOLAS L. RATTERMAN
- Department of Biology, 3258 TAMU, Texas A&M University, College Station, TX 77843, USA
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243
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Remotely plucked hair genotyping: a reliable and non-invasive method for censusing pine marten (Martes martes, L. 1758) populations. EUR J WILDLIFE RES 2009. [DOI: 10.1007/s10344-009-0332-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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244
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Wittemyer G, Okello JBA, Rasmussen HB, Arctander P, Nyakaana S, Douglas-Hamilton I, Siegismund HR. Where sociality and relatedness diverge: the genetic basis for hierarchical social organization in African elephants. Proc Biol Sci 2009; 276:3513-21. [PMID: 19605399 PMCID: PMC2817196 DOI: 10.1098/rspb.2009.0941] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 06/24/2009] [Indexed: 11/12/2022] Open
Abstract
Hierarchical properties characterize elephant fission-fusion social organization whereby stable groups of individuals coalesce into higher order groups or split in a predictable manner. This hierarchical complexity is rare among animals and, as such, an examination of the factors driving its emergence offers unique insight into the evolution of social behaviour. Investigation of the genetic basis for such social affiliation demonstrates that while the majority of core social groups (second-tier affiliates) are significantly related, this is not exclusively the case. As such, direct benefits received through membership of these groups appear to be salient to their formation and maintenance. Further analysis revealed that the majority of groups in the two higher social echelons (third and fourth tiers) are typically not significantly related. The majority of third-tier members are matrilocal, carrying the same mtDNA control region haplotype, while matrilocality among fourth-tier groups was slightly less than expected at random. Comparison of results to those from a less disturbed population suggests that human depredation, leading to social disruption, altered the genetic underpinning of social relations in the study population. These results suggest that inclusive fitness benefits may crystallize elephant hierarchical social structuring along genetic lines when populations are undisturbed. However, indirect benefits are not critical to the formation and maintenance of second-, third- or fourth-tier level bonds, indicating the importance of direct benefits in the emergence of complex, hierarchical social relations among elephants. Future directions and conservation implications are discussed.
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Affiliation(s)
- George Wittemyer
- Department of Fish, Wildlife and Conservation Biology, Colorado State University, 1474 Campus Delivery, Fort Collins, CO 80523, USA.
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245
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Cowell RG. Efficient maximum likelihood pedigree reconstruction. Theor Popul Biol 2009; 76:285-91. [PMID: 19781561 DOI: 10.1016/j.tpb.2009.09.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 09/10/2009] [Accepted: 09/16/2009] [Indexed: 11/24/2022]
Abstract
A simple and efficient algorithm is presented for finding a maximum likelihood pedigree using microsatellite (STR) genotype information on a complete sample of related individuals. The computational complexity of the algorithm is at worst (O(n(3)2(n))), where n is the number of individuals. Thus it is possible to exhaustively search the space of all pedigrees of up to thirty individuals for one that maximizes the likelihood. A priori age and sex information can be used if available, but is not essential. The algorithm is applied in a simulation study, and to some real data on humans.
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Affiliation(s)
- Robert G Cowell
- Faculty of Actuarial Science and Insurance, Cass Business School, 106 Bunhill Row, London EC1Y 8TZ, UK.
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246
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Liu JX, Ely B. Sibship reconstruction demonstrates the extremely low effective population size of striped bass Morone saxatilis in the Santee-Cooper system, South Carolina, USA. Mol Ecol 2009; 18:4112-20. [PMID: 19735452 DOI: 10.1111/j.1365-294x.2009.04343.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For organisms with great fecundity and high mortality in early life stages, such as shellfish or fishes, the need to match reproductive activity with environmental conditions conducive to spawning, fertilization, larval development and recruitment may result in extreme variance in reproductive success among individuals. The main objective of this study was to investigate evidence of large variance in the reproductive success of the striped bass Morone saxatilis in the Santee-Cooper system, South Carolina, USA. Seven microsatellite loci were analysed in 603 recruits representing three yearly cohorts from 1992 to 1994, and a group analysis was performed to identify full-sib families. Large variance in reproductive success was detected, with a few large, full-sib families contributing disproportionately to each of the cohorts. The severity of sweepstakes reproductive success varied among cohorts depending on environmentally imposed mortality. Estimations of the effective number of breeders in these long-lived fish ranged from 24 in 1992 to 44 in 1994. Furthermore, the estimated genetic effective population size (N(e) = 93) is approximately four orders of magnitude lower than estimates of adult census size (N = 362 000). Furthermore, the presence of large full-sib families indicates that striped bass engage in pair mating in the wild. Heterogeneity in genetic composition was also observed among cohorts, suggesting that genetically different adults contribute to different cohorts and that chance rather than fitness variation determines reproductive success.
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Affiliation(s)
- Jin-Xian Liu
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
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247
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BERG EC, EADIE JM, LANGEN TA, RUSSELL AF. Reverse sex-biased philopatry in a cooperative bird: genetic consequences and a social cause. Mol Ecol 2009; 18:3486-99. [DOI: 10.1111/j.1365-294x.2009.04284.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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248
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Abstract
MOTIVATION Family relationships can be estimated from DNA marker data. Applications arise in a large number of areas including evolution and conservation research, genealogical research in human, plant and animal populations, forensic problems and genetic mapping via linkage and association analyses. Traditionally, likelihood-based approaches to relationship estimation have used unlinked genetic markers. Due to the fact that some relationships cannot be distinguished from data at unlinked markers, and given the limited number of such markers available, there are considerable constraints on the type of identification problem that can be satisfactorily addressed with such approaches. The aim of this article is to explore the potential of linked autosomal single nucleotide polymorphism markers in this context. Throughout, we will view the problem of relationship estimation as one of pedigree identification rather than identity-by-descent, and thus focus on applications where determination of the exact relationship is important. RESULTS We show that the increase in information obtained by exploiting large sets of linked markers substantially increases the number of problems that can be solved. Results are presented based on simulations as well as on real data. AVAILABILITY The R library FEST is freely available from http://folk.uio.no/thoree/FEST.
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Affiliation(s)
- Øivind Skare
- Norwegian Institute of Public Health, 0403 Oslo, Norway
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249
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ASHLEY MV, CABALLERO IC, CHAOVALITWONGSE W, DASGUPTA B, GOVINDAN P, SHEIKH SI, BERGER-WOLF TY. KINALYZER, a computer program for reconstructing sibling groups. Mol Ecol Resour 2009; 9:1127-31. [DOI: 10.1111/j.1755-0998.2009.02562.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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250
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Yue LF, Wang DAW, Huang BH, Liu XH. Characterization of nine novel microsatellite markers from Brandt's vole (Lasiopodomys brandtii). Mol Ecol Resour 2009; 9:1194-6. [PMID: 21564873 DOI: 10.1111/j.1755-0998.2009.02601.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: 11/27/2022]
Abstract
Highly polymorphic microsatellite markers are the most powerful tools to infer kinship relations. In this study, a library enriched for (AC)(n) (AG)(n) and (AGAT)(n) was constructed for screening microsatellite markers in Brandt's vole (Lasiopodomys brandtii), and nine novel polymorphic microsatellite markers were developed and characterized. The number of alleles ranged from 4 to 11 per locus and the mean polymorphism information content was 0.7535. The observed and the expected heterozygosity values averaged 0.760 (0.554-0.908) and 0.7914 (0.718-0.845), respectively. Average nonexclusion probability for one candidate parent varied from 0.485 to 0.716. These nine novel markers are highly polymorphic and powerful enough for our future kinship analysis.
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Affiliation(s)
- Ling-Fen Yue
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2, Haidian District, Beijing 100193, China
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