A comparison of microsatellites and SNPs in parental assignment in the GIFT strain of Nile tilapia (Oreochromis niloticus): The power of exclusion
Trong, T.Q. ; Bers, N.E.M. van; Crooijmans, R.P.M.A. ; Dibbits, B.W. ; Komen, J. - \ 2013
Aquaculture 388-391 (2013). - ISSN 0044-8486 - p. 14 - 23.
genotyping errors - computer-program - empirical-evaluation - natural-populations - markers - wild - inference - paternity - sibship - salmon
In this study, parental assignment was studied in the 10th generation of a pedigreed selected Nile tilapia (Oreochromis niloticus) population (GIFT) and their offspring, by comparing two types of molecular markers, microsatellites and SNPs, using an exclusion-based (Vitassign) and a likelihood-based (Cervus) method. For the experiment, G10 parents were divided in 4 groups (cohorts) and allowed to produce offspring by natural group mating. In total 173 offspring were tested against 238 parents, using either 12 microsatellites (PIC = 0.639; exclusion power 68.0%) or 122 SNPs (PIC = 0.341; exclusion power 99.9%). In this study, more than half of the candidate parents were either full- or half-sibs with other parents. Furthermore, 13.8% of the parents died before being sampled for DNA. When offspring were assigned to parents in the same cohort, using Vitassign, for microsatellites, allowing up to 2 mismatches, 37.6% offspring got unique assignments, 45.1% got multiple assignments, and 17.3% were not assigned; for SNPs with up to 15 mismatches allowed, 83.8% offspring got unique assignments while 13.9% got multiple assignments. Only 2.3% were not assigned. Using Cervus, for microsatellites, the mean ‘strict’ (> 95% CF) assignment rate across the 4 cohorts was 18%, the ‘relax’ (80–95% CF) assignment rate was 43%, and 39% were not assigned; for SNPs, 39% ‘strict’ assignments were obtained (mean across 4 cohorts); the remaining offspring were not assigned. In general assignment rates were higher when cohort offspring were assigned to all parents combined, irrespective of method (Vitassign or Cervus) or marker used. However, consistency of assignments between microsatellites and SNPs was low: 28% with Vitassign and 16% with Cervus. Consistency of assignments between Cervus and Vitassign was high with SNPs (65%), but was low with microsatellites (31%). We conclude that missing parents and relatedness among candidate parents resulted in low assignment rates. Furthermore, low exclusion power of the microsatellite set resulted in low assignment rates and multiple parent pair assignments irrespective of method used. Exclusion methods and likelihood-based methods can be equally good for parental assignments, providing that good marker sets with high exclusion power are available.
Genetic relationships in an international collection of Puccinia horiana isolates based on newly identified molecular markers and demonstration of recombination
Backer, M. de; Bonants, P.J.M. ; Pedley, K.F. ; Maes, M. ; Roldan-Ruiz, I. ; Bockstaele, E. van; Heungens, K. ; Lee, T.A.J. van der - \ 2013
Phytopathology 103 (2013)11. - ISSN 0031-949X - p. 1169 - 1179.
chrysanthemum white rust - multilocus genotype data - single nucleotide polymorphisms - whole genome amplification - f-sp tritici - parentage analysis - computer-program - x morifolium - resistance - pathogens
The obligate biotrophic pathogen Puccinia horiana is the causal agent of chrysanthemum white rust. Although P. horiana is a quarantine organism, it has been able to spread to most chrysanthemum-producing regions in the world since the 1960s; however, the transfer routes are largely obscure. An extremely low level of allelic diversity was observed in a geographically diverse set of eight isolates using complexity reduction of polymorphic sequences (CRoPS) technology. Only 184 of the 16,196 contigs (1.1%) showed one or more single-nucleotide polymorphisms (SNPs). Thirty-two SNPs and one simple-sequence repeat were translated into molecular markers and used to genotype 45 isolates originating from North and South America, Asia, and Europe. In most cases, phylogenetic clustering was related to geographic origin, indicating local establishment. The European isolates mostly grouped in two major populations that may relate to the two historic introductions previously reported. However, evidence of recent geographic transfer was also observed, including transfer events between Europe and South America and between Southeast Asia and Europe. In contrast with the presumed clonal propagation of this microcyclic rust, strong indications of marker recombination were observed, presumably as a result of anastomosis, karyogamy, and somatic meiosis. Recombination and transfer also explain the geographic dispersal of specific markers. A near-to-significant correlation between the genotypic data and previously obtained pathotype data was observed and one marker was associated with the most virulent pathotype group. In combination with a fast SNP detection method, the markers presented here will be helpful tools to further elucidate the transfer pathways and local survival of this pathogen
Potential barriers to gene flow in the endangered European wildcat (Felis silvestris)
Hartmann, S.A. ; Steyer, K. ; Kraus, R.H.S. ; Segelbacher, G. ; Nowak, C. - \ 2013
Conservation Genetics 14 (2013)2. - ISSN 1566-0621 - p. 413 - 426.
maximum-likelihood-estimation - population-structure - computer-program - domestic cats - southern california - coalescent approach - landscape genetics - differentiation - hybridization - conservation
The European wildcat (Felis silvestris silvestris) is a focal species for conservation in many European countries. After a severe population decline during the 19th century, many populations became extinct or isolated. Within Germany, suitable wildcat habitat is assumed to be highly fragmented. We thus investigated fine-scale genetic structure of wildcat populations in Central Germany across two major potential barriers, the Rhine River with its valley and a major highway. We analyzed 260 hair and tissue samples collected between 2006 and 2011 in the Taunus and Hunsrück mountain ranges (3,500 km2 study area). We identified 188 individuals by genotyping 14 microsatellite loci, and found significant genetic substructure in the study area. Both the Rhine River and the highway were identified as significant barrier to gene flow. While the long-term effect of the river has led to stronger genetic differentiation in the river compared to the highway, estimates of current gene flow and relatedness across barriers indicated a similar or even stronger barrier effect to ongoing wildcat dispersal of the highway. Despite these barrier effects, we found evidence for the presence of recent migration across both the river and the highway. Our study thus suggests that although wildcats have the capability of dispersal across major anthropogenic and natural landscape barriers, these structures still lead to an effective isolation of populations as reflected by genetic analysis. The results strengthen the need for currently ongoing national strategies of wildcat conservation aiming for large scale habitat connectivity.
Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus): direct, simultaneous evaluation of neutral vs putatively selected loci
Andre, C. ; Larsson, L.C. ; Laikre, L. ; Bekkevold, D. ; Brigham, J. ; Carvalho, G.R. ; Dahlgren, T.G. ; Hutchinson, W.F. ; Mariani, S. ; Mudde, C.M. ; Ruzzante, D.E. ; Ryman, N. - \ 2011
Heredity 106 (2011)2. - ISSN 0018-067X - p. 270 - 280.
cod gadus-morhua - salmon salmo-salar - histocompatibility class-i - mitochondrial-dna - north-sea - molecular markers - balancing selection - statistical power - natural-selection - computer-program
In many marine fish species, genetic population structure is typically weak because populations are large, evolutionarily young and have a high potential for gene flow. We tested whether genetic markers influenced by natural selection are more efficient than the presumed neutral genetic markers to detect population structure in Atlantic herring (Clupea harengus), a migratory pelagic species with large effective population sizes. We compared the spatial and temporal patterns of divergence and statistical power of three traditional genetic marker types, microsatellites, allozymes and mitochondrial DNA, with one microsatellite locus, Cpa112, previously shown to be influenced by divergent selection associated with salinity, and one locus located in the major histocompatibility complex class IIA (MHC-IIA) gene, using the same individuals across analyses. Samples were collected in 2002 and 2003 at two locations in the North Sea, one location in the Skagerrak and one location in the low-saline Baltic Sea. Levels of divergence for putatively neutral markers were generally low, with the exception of single outlier locus/sample combinations; microsatellites were the most statistically powerful markers under neutral expectations. We found no evidence of selection acting on the MHC locus. Cpa112, however, was highly divergent in the Baltic samples. Simulations addressing the statistical power for detecting population divergence showed that when using Cpa112 alone, compared with using eight presumed neutral microsatellite loci, sample sizes could be reduced by up to a tenth while still retaining high statistical power. Our results show that the loci influenced by selection can serve as powerful markers for detecting population structure in high gene-flow marine fish species. Heredity (2011) 106, 270-280; doi:10.1038/hdy.2010.71; published online 16 June 2010
The east-west-north colonization history of the Mediterranean and Europe by the coastal plant Carex extensa (Cyperaceae)
Escudero, M. ; Vargas, P. ; Arens, P. ; Ouborg, N.J. ; Luceno, M. - \ 2010
Molecular Ecology 19 (2010)2. - ISSN 0962-1083 - p. 352 - 370.
population genetic-structure - length polymorphism markers - messinian salinity crisis - sedges carex - phylogeographical structure - molecular evolution - microsatellite data - computer-program - chloroplast dna - cakile-maritima
Coastal plants are ideal models for studying the colonization routes of species because of the simple linear distributions of these species. Carex extensa occurs mainly in salt marshes along the Mediterranean and European coasts. Variation in cpDNA sequences, amplified fragment length polymorphisms (AFLPs) and simple sequence repeats (SSRs) of 24 populations were analysed to reconstruct its colonization history. Phylogenetic relationships indicate that C. extensa together with the South American Carex vixdentata and the southern African Carex ecklonii form a monophyletic group of halophilic species. Analyses of divergence times suggest that early lineage diversification may have occurred between the late Miocene and the late Pliocene (Messinian crisis). Phylogenetic and network analyses of cpDNA variation revealed the monophyly of the species and an ancestral haplotype contained in populations of the eastern Mediterranean. The AFLP and SSR analyses support a pattern of variation compatible with these two lineages. These analyses also show higher levels of genetic diversity and differentiation in the eastern population group, which underwent an east-to-west Mediterranean colonization. Quaternary climatic oscillations appear to have been responsible for the split between these two lineages. Secondary contacts may have taken place in areas near the Ligurian Sea in agreement with the gene flow detected in Corsican populations. The AFLP and SSR data accord with the 'tabula rasa' hypothesis in which a recent and rapid colonization of northern Europe took place from the western Mediterranean after the Last Glacial Maximum. The unbalanced west-east vs. west-north colonization may be as a result of 'high density blocking' effect
Estimating Breeding Values With Molecular Relatedness and Reconstructed Pedigrees in Natural Mating Populations of Common Sole, Solea Solea
Blonk, R.J.W. ; Komen, J. ; Kamstra, A. ; Arendonk, J.A.M. van - \ 2010
Genetics 184 (2010). - ISSN 0016-6731 - p. 213 - 219.
cod gadus-morhua - quantitative genetic-parameters - turbot scophthalmus-maximus - marker-inferred relatedness - pairwise relatedness - oncorhynchus-mykiss - computer-program - rainbow-trout - body-weight - heritability
Captive populations where natural mating in groups is used to obtain offspring typically yield unbalanced population structures with highly skewed parental contributions and unknown pedigrees. Consequently, for genetic parameter estimation, relationships need to be reconstructed or estimated using DNA marker data. With missing parents and natural mating groups, commonly used pedigree reconstruction methods are not accurate and lead to loss of data. Relatedness estimators, however, infer relationships between all animals sampled. In this study, we compared a pedigree relatedness method and a relatedness estimator ("molecular relatedness") method using accuracy of estimated breeding values. A commercial data set of common sole, Solea solea, with 51 parents and 1953 offspring ("full data set") was used. Due to missing parents, for 1338 offspring, a pedigree could be reconstructed with 10 microsatellite markers ("reduced data set"). Cross-validation of both methods using the reduced data set showed an accuracy of estimated breeding values of 0.54 with pedigree reconstruction and 0.55 with molecular relatedness. Accuracy of estimated breeding values increased to 0.60 when applying molecular relatedness to the full data set. Our results indicate that pedigree reconstruction and molecular relatedness predict breeding values equally well in a population with skewed contributions to families. This is probably due to the presence of few large full-sib families. However, unlike methods with pedigree reconstruction, molecular relatedness methods ensure availability of all genotyped selection candidates, which results in higher accuracy of breeding value estimation
Estimates of heritability and genetic correlation for body length and resistance to fish pasteurellosis in the gilthead sea bream (Sparus aurata L.)
Antonello, J. ; Massault, C. ; Francha, R. ; Haley, C.S. ; Pellizzari, C. ; Bovo, G. ; Atarnello, Th. ; Koning, D.J. de; Bargelloni, L. - \ 2009
Aquaculture 298 (2009)1-2. - ISSN 0044-8486 - p. 29 - 35.
salmon salmo-salar - bass dicentrarchus-labrax - challenge-test data - gadus-morhua l. - atlantic salmon - disease resistance - statistical-models - computer-program - rainbow-trout - seabream
Fish pasteurellosis is an infectious disease that affects several fish species living in marine temperate waters. Its causative agent is the Gram-negative bacterium Photobacterium damselae subsp. piscicida (Phdp). Fish pasteurellosis represents a serious health problem for the majority of intensive sea bream hatcheries, with 90–100% mortality during disease outbreaks. Larvae and juveniles are the most susceptible stages. A potential strategy to prevent fish pasteurellosis is to select for animals that are genetically resistant to it. The aim of this work was to evaluate the genetic variation of disease resistance and growth in the gilthead sea bream (Sparus aurata L.). An experimental population, approximately 3500 animals originating from mass spawning of four broodstocks, was experimentally infected with a highly virulent strain of Phdp. Mortality was monitored daily for 19 days. Upon completion of the challenge experiment, genetic profiles at nine microsatellite loci were obtained for 1753 animals and for all (256) broodstock fish, for parentage assignment. A subset of families defined by means of genetic analysis was used to calculate heritability for survival to infection. For body length (measured post-mortem), heritability was 0.38 ± 0.07. The heritability for disease resistance varied depending on how resistance was defined. Heritability was 0.12 ± 0.04 for days of survival post challenge, defined as a continuous trait, while it ranged from 0.45 ± 0.04 to 0.18 ± 0.08 for the binary trait dead/alive at a specific day. The genetic correlation between body length and survival was positive and significant (r = 0.61 ± 0.16). These results confirm the existence of genetic variation for growth and resistance against Phpd and highlight also the potential for selective breeding programs to improve these traits
Polyandry and polygyny in an African rodent pest species, Mastomys natalensis
Kennis, J. ; Sluydts, V. ; Leirs, H. ; Hooft, W.F. van - \ 2008
Mammalia 72 (2008)3. - ISSN 0025-1461 - p. 150 - 160.
squirrels sciurus-vulgaris - reproductive success - computer-program - mating systems - small mammals - population-dynamics - social-organization - parental genotypes - spacing behavior - southern-africa
Males and females use different mating strategies and seldom have these strategies been studied on the field for cryptic rodent species. We studied the breeding strategies of both males and females of the sub-Sahara African rodent pest species, Mastomys natalensis, in the field using capture removal and capture-mark-recapture techniques combined with microsatellite analyses. In total, 36 litters (359 young) and 94 candidate fathers were genotyped. Multiple paternity (more than one male per litter) occurs frequently in all sampled grids (>47% of all litters). Paternity assignment success rates are relatively high (mean 69%). Males are polygynous, but this is less frequent than female polyandry. Large differences in male reproductive success exist with a large part of the male population without offspring in our sample. Larger males father significantly more offspring. Spatial analyses do not show a strict spatial organisation. Our data suggest male M. natalensis roam around to mate with as many females as possible, while females also mate with several males to produce litters fathered by several males. This species could be an interesting candidate for testing virally vectored immunocontraception as a pest management technique due to the promiscuous mating and high frequency of sexual contacts.