Molecular pedigree analysis in natural populations of fishes: approaches, applications, and practical considerations

Abstract

Molecular markers can provide information on the family structure of natural fish populations through molecular pedigree analysis. This information, which is otherwise difficult to obtain, can give important insights into the expression and evolution of phenotypic traits. We review the literature to provide examples of how molecular pedigree analysis has been used extensively to examine patterns of distribution, dispersal, and social behaviour in fishes and how it provides a tool for the estimation of quantitative genetic parameters. Although multiple methodologies can be used to examine family structure, the efficacy of any molecular pedigree analysis is generally dependent on prior consideration of interrelated statistical and biological factors. Statistical issues stem from the choice of molecular marker type and marker set used, in addition to sampling strategy. We discuss these considerations and additionally emphasize the utility of supplemental nongenetic data for increasing the efficacy of pedigree analysis. We advocate that, where possible, a priori knowledge of the study system's biology should be used to inform study design and further highlight the need for additional empirical testing of methodologies.

Evidence of polygamy in the socially monogamous Amazonian fish Arapaima gigas (Schinz, 1822) (Osteoglossiformes, Arapaimidae)

“…Various authors have discussed the diverse reproductive behaviors and tactics found in fishes through genetic assessments of parentage (Taborsky, 2001(Taborsky, , 2008Wilson & Ferguson, 2002;Hain & Neff, 2007), and their findings have revolutionized the study of reproductive behavior, revealing that individuals of many species engage in extra-pair copulations, including parasitic spawning behavior between satellite and territorial males such as sneaking, egg piracy and female mimicry of cooperative breeding between satellite and territorial males.…”

Marker-assisted estimation of quantitative genetic parameters in rainbow trout, Oncorhynchus mykiss

“…For example, attributed disappointing results in estimating heritability of body weight in Soay sheep to a lack of relatedness structure in the sample, as well as to insufficient amounts of genotypic information. Application to natural populations therefore requires careful consideration of biological processes such as social grouping (Ritland, 2000), as well as appropriate design of sampling strategy (Wilson & Ferguson, 2002), such that significant numbers of relatives are sampled. Since such structure can lead to bias and inaccuracy in the molecular pedigree analysis (discussed above), efficient estimation of genetic parameters in small, highly structured samples may require estimation of allele frequencies from a larger sample more representative of the whole population.…”

Application of microsatellite DNA parentage markers in the swimming crab Portunus trituberculatus

“…Out of the thirty microsatellite loci, only one (P04) is from a congeneric species, P. pelagicus, while eight (E9, E11, E13, E17, E18, E20, E24, and E28) from EST sequences, three (PN22, PN24, and PN27) from GenBank data and eighteen (locus named 'C' and 'H' series) from the enriched genomic library. Genomic DNA was extracted from crab pleopods using a modified CTAB extraction protocol (Wilson 1987) and resuspended at 5-10 ng/ll. PCR was performed in a total of 20 ll reaction mixture containing 1 9 PCR buffer (promega), 2.5 lmol MgCl 2 , 100 lmol each dNTP, 0.5 lmol of each primer, 0.5 U Taq DNA polymerase (promega), and approximately 10 ng template DNA.…”