Contrasting results from molecular and pedigree-based population diversity measures in captive zebra highlight challenges facing genetic management of zoo populations

Abstract

Zoo conservation breeding programs manage the retention of population genetic diversity through analysis of pedigree records. The range of demographic and genetic indices determined through pedigree analysis programs allows the conservation of diversity to be monitored relative to the particular founder population for a species. Such approaches are based on a number of well-documented founder assumptions, however without knowledge of actual molecular genetic diversity there is a risk that pedigree-based measures will be misinterpreted and population genetic diversity misunderstood. We examined the genetic diversity of the captive populations of Grevy's zebra, Hartmann's mountain zebra and plains zebra in Japan and the United Kingdom through analysis of mitochondrial DNA sequences. Very low nucleotide variability was observed in Grevy's zebra. The results were evaluated with respect to current and historic diversity in the wild, and indicate that low genetic diversity in the captive population is likely a result of low founder diversity, which in turn suggests relatively low wild genetic diversity prior to recent population declines. Comparison of molecular genetic diversity measures with analogous diversity indices generated from the studbook data for Grevy's zebra and Hartmann's mountain zebra show contrasting patterns, with Grevy's zebra displaying markedly less molecular diversity than mountain zebra, despite studbook analysis indicating that the Grevy's zebra population has substantially more founders, greater effective population size, lower mean kinship, and has suffered less loss of gene diversity. These findings emphasize the need to validate theoretical estimates of genetic diversity in captive breeding programs with empirical molecular genetic data. Zoo Biol. 36:87-94, 2017. © 2016 Wiley Periodicals, Inc.

Genetic Diversity and Genetic Structure of the Wild Tsushima Leopard Cat from Genome-Wide Analysis

“…However, because the genetic relationship between founders in captive populations is unknown, breeding plans are designed assuming that there is no kinship between the founders. Therefore, it is important to note the difference between genetic diversity based on pedigree and genetic diversity based on genetic analysis [ 57 ]. This is the case especially when the wild population is small, such that the difference between the two genetic diversities may be large [ 57 ].…”

“…Therefore, it is important to note the difference between genetic diversity based on pedigree and genetic diversity based on genetic analysis [ 57 ]. This is the case especially when the wild population is small, such that the difference between the two genetic diversities may be large [ 57 ]. The Tsushima leopard cat also has a small population size, so the genetic diversity it actually retains is likely to be lower than the genetic diversity based on pedigrees, and a more careful breeding plan is needed.…”

Studbook and molecular analyses for the endangered black-lion-tamarin; an integrative approach for assessing genetic diversity and driving management in captivity

“…According to recommendations of the ISFG (International Society for Forensic Genetics) for the area of non-human DNA typing 34 , they have also potential to be used, by the community of forensic scientist, for investigations involving poaching, smuggling and illegal trade of protected species 32,54,55 DNA-based studies can still simulate, estimate and compare genetic diversity levels in breeding programs 56 . Genetic management of threatened species has experienced an increase in the last few years 6,29,57,58 , and more recently has been improved by a combination of pedigree and molecular information 59 . For the BLT captive breeding program, we highlight that an integrative approach could be of benefit in terms of allele representativeness and also for considering a more plausible genetic diversity estimate for the founding population.…”

“…Overall, to promote the long-term success of the BLT conservation program, we recommend including genetic diversity parameters based on molecular data, in addition to the pedigree analyses and MSI scores. Microsatellite-based values of expected heterozygosity, individual heterozygosity, allele richness, private alleles, population structure, inbreeding and kinship could be monitored over generations, helping to evaluate gains and losses of genetic diversity more effectively, and identifying individuals potentially better suited for reproduction and for relocation in captivity 29,42,47 . Finally, we must take into account that an integrated in situ and ex situ approach is strongly indicated for the metapopulation management of BLTs and to help shield this species from its imminent risk of extinction, since in nature L. chrysopygus has a small population size and a very low genetic diversity level.…”

“…To compensate for the lack of knowledge about the initial genetic diversity and relationships between the founders, various institutions that manage endangered species have recently tried to combine molecular data with pedigree analyses 6,[24][25][26][27][28] , although studies integrating both types of data are still scarce 29 .…”