Robustness of linkage maps in natural populations: a simulation study

Abstract

In a number of long-term individual-based studies of vertebrate populations, the genealogical relationships between individuals have been established with molecular markers. As a result, it is possible to construct genetic linkage maps of these study populations by examining the co-segregation of markers through the pedigree. There are now four free-living vertebrate study populations for whom linkage maps have been built. In this study, simulation was used to investigate whether these linkage maps are likely to be accurate. In all four populations, the probability of assigning markers to the correct chromosome is high and framework maps are generally inferred correctly. However, genotyping error can result in incorrect maps being built with very strong statistical support over the correct order. Future applications of linkage maps of natural populations are discussed.

Extensive linkage disequilibrium in a wild bird population

“…The linkage map was composed using 107 polymorphic microsatellite loci typed on ca. 350 animals, making it one of the most detailed linkage maps available for natural animal popu- lations [28]. In fact, it is one of only a few genetic linkage maps of wild bird species to date.…”

“…Among the most important applications of genetic maps in genomic analyses is in that they provide a platform to support studies utilizing or aiming to apply candidate gene approaches [21,23], QTL mapping [24], comparative genomics [25], and genome annotation [26]. However, construction of genetic linkage maps for non-model organisms is complicated by several factors [27,28]. One of the major obstacles for the construction of linkage maps in passerine birds (but see [4]) is the scarcity of informative genetic markers.…”

Introduction. Evolutionary dynamics of wild populations: the use of long-term pedigree data

“…Exploration of several important current challenges in evolutionary biology are still in their infancy, including the analysis of sexually antagonistic genetic variance (Poissant et al 2008), the genetic basis of responses to changing environmental conditions (Brommer et al 2008;Visser 2008), exploration of the genetic basis of senescence (Keller et al 2008;Nussey et al 2008) and the exploitation of rapid advancements in molecular genetic technology (Slate 2008). The questions being asked of datasets from natural populations have clearly moved considerably beyond simply estimating the heritability of a trait or the selection pressures to which it is subject.…”

A genetic linkage map for the South African Angora goat

“…The marker order on chromosomes CHI2, CHI4, CHI5, CHI11, CHI13 and CHI19 however varied from those reported by Schibler et al (1998). The relative marker distances between the studies also differed, which was expected as chromosome lengths is a property of the population under study (Slate, 2008) and incorrect mapping usually result in inflated maps. The average number of informative meiosis (518 ± 179) in our study was much higher than the 114 ± 70 reported by Schibler et al (1998), resulting in a more accurate linkage map.…”

“…The previously published goat maps (Vaiman et al, 1996;Schibler et al, 1998) made use of this design, as did the current study. Although marker phase is difficult to infer in natural populations, it was shown through simulation studies by Slate (2008) that linkage maps constructed from natural populations are reasonable robust and accurate.…”