Using genomic tools to maintain diversity and fitness in conservation programmes

Abstract

Conservation programmes aim at maximizing the survival probability of populations, by minimizing the loss of genetic diversity, which allows populations to adapt to changes, and controlling inbreeding increases. The best known strategy to achieve these goals is optimizing the contributions of the parents to minimize global coancestry in their offspring. Results on neutral scenarios showed that management based on molecular coancestry could maintain more diversity than management based on genealogical coancestry when a large number of markers were available. However, if the population has deleterious mutations, managing using optimal contributions can lead to a decrease in fitness, especially using molecular coancestry, because both beneficial and harmful alleles are maintained, compromising the long-term viability of the population. We introduce here two strategies to avoid this problem: The first one uses molecular coancestry calculated removing markers with low minor allele frequencies, as they could be linked to selected loci. The second one uses a coancestry based on segments of identity by descent, which measures the proportion of genome segments shared by two individuals because of a common ancestor. We compare these strategies under two contrasting mutational models of fitness effects, one assuming many mutations of small effect and another with few mutations of large effect. Using markers at intermediate frequencies maintains a larger fitness than using all markers, but leads to maintaining less diversity. Using the segment-based coancestry provides a compromise solution between maintaining diversity and fitness, especially when the population has some inbreeding load.

Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations

“…5B,C): The lower the mean h value, the larger the decline in fitness after 10 generations (about 0.08 for h = 0.35 and 0.006 for h = 0.5). Based on predictions made on simulated data (de Cara et al 2013b), we expected that the strategy that maintained the most diversity would be the one that performed the worst in terms of fitness. However, and maybe partly due to the small population size here managed, genealogical management resulted both in maintaining less fitness and diversity than any marker-based strategy ( Fig.…”

“…Our first objective was to determine whether the use of marker-by-marker based coancestry in management strategies outperforms genealogical coancestry and the recently postulated IBD-based coancestry (de Cara et al 2013b) in terms of maintaining variation in a population. By managing the two pig populations through in silico management, with their actual genotypes, we have shown that the best management strategy in terms of maintaining diversity was using molecular coancestry.…”

“…However, management of populations using OC with molecular coancestry may lead to a fitness decrease, since deleterious alleles linked to the markers used to measure coancestry will be maintained (de Cara et al 2013a). Recently, a measure of coancestry based on shared genomic regions has been proposed as a compromise to maintain both fitness and genetic diversity when the population in the program has a medium to high inbreeding load (de Cara et al 2013b). One of the aims of this approach is to avoid the occurrence of long runs of homozygosity (ROH) in the offspring, which are characteristic of reduced diversity, due either to selection or bottlenecks and therefore, may confer inbreeding depression (Keller and Waller 2002;Szpiech et al 2013;Curik et al 2014).…”

“…Predictions for management based on genealogical, molecular, or IBD segments have been made with simulated data (de Cara et al 2013b), but have so far not been tested with actual genotype data. Pigs are an excellent model for testing the use of genetic data in population management.…”

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“…Utilization of small number of fish brooders, generation after generation, may cause reduction in genetic variability and result in indiscriminate hybridization, inbreeding and loss of genetic purity of Chinese fish species (Ellergern & Galtier, 2016). Therefore, regular monitoring of genetic variability in fish hatchery stock is essential to detect whether breeding programs are affecting genetic integrity by reducing genetic variation (De-Cara, Villanueva, Toro, & Fernandez, 2013) which is lacking in Pakistan. By upgrading and managing standards of breeding activities and brood stock in hatchery operations, aquaculture outputs can be enhanced and their influence on capture fisheries biodiversity can be reduced (Xu et al, 2015).…”