Effectiveness of managed gene flow in reducing genetic divergence associated with captive breeding

Abstract

Captive breeding has the potential to rebuild depressed populations. However, associated genetic changes may decrease restoration success and negatively affect the adaptive potential of the entire population. Thus, approaches that minimize genetic risks should be tested in a comparative framework over multiple generations. Genetic diversity in two captive-reared lines of a species of conservation interest, Chinook salmon (Oncorhynchus tshawytscha), was surveyed across three generations using genome-wide approaches. Genetic divergence from the source population was minimal in an integrated line, which implemented managed gene flow by using only naturally-born adults as captive broodstock, but significant in a segregated line, which bred only captive-origin individuals. Estimates of effective number of breeders revealed that the rapid divergence observed in the latter was largely attributable to genetic drift. Three independent tests for signatures of adaptive divergence also identified temporal change within the segregated line, possibly indicating domestication selection. The results empirically demonstrate that using managed gene flow for propagating a captive-reared population reduces genetic divergence over the short term compared to one that relies solely on captive-origin parents. These findings complement existing studies of captive breeding, which typically focus on a single management strategy and examine the fitness of one or two generations.

Genomewide association analyses of fitness traits in captive‐reared Chinook salmon: Applications in evaluating conservation strategies

“…The observed phenotypic and genomic divergence in certain traits, most notably spawn timing, may also have more immediate impacts on specific management practices at CESRF to further reduce possible effects of captive rearing, as the program is adaptively managed (Fast et al., ). Lastly, the results support previous work demonstrating the effectiveness of managed gene flow in conservation‐focused breeding programs (Waters et al., , ) and will provide additional information that managers can use to assess the relative advantages and disadvantages of different captive rearing approaches.…”

“…The ecological background of the study population and the initiation of the integrated and segregated hatchery lines at CESRF have been described in previous publications (Fast et al., ; Knudsen et al., ; Waters et al., ). Briefly, wild adults returning from the ocean to their freshwater spawning grounds were collected for founding broodstock (Figure ) from the upper Yakima River, WA, USA, population from 1997 to 2002 as they passed the Roza Dam Adult Monitoring Facility (RAMF), located 90 river kilometers south of CESRF.…”

Initial founders of captive populations are genetically representative of natural populations in critically endangered dusky gopher frogs,Lithobates sevosus

“…Following our study, additional natural individuals were used to augment the ex situ population for 5 years until successful breeding via IVF occurred. These additions likely maintained the genetic composition of the captive population because integrated captive populations tend to have reduced amounts of genetic divergence from natural populations [Waters et al, ]. Thus, we can speculate that the captive individuals used in IVF continued to maintain genetic variation present in the natural population in terms of heterozygosity and allelic richness.…”

Genetic and morphological divergences between wild and captive-bred populations ofSalmo trutta abanticus

“…Waters et al. () recorded a significant genetic divergence just in the first generation of small number of captive breeder in chinook salmon populations. Furthermore, it has been widely documented that genetic diversity of captive‐breed population tends to decrease due to genetic drift and inbreeding when the broodstock of parental population is small (Fraser, ).…”