A novel framework for evaluating in situ breeding management strategies in endangered populations

Abstract

Human activities have led to the deterioration of natural habitat.As a result, the distributions of many species have been fragmented into small, genetically isolated populations (Ralls et al., 2018). Small populations suffer from inbreeding depression-loss of fitness due to inbreeding-and over generations unavoidably lose genetic diversity, reducing their potential to adapt to changing environments, and increasing their extinction risk (Frankham, 1995(Frankham, , 2010Hedrick & Garcia-Dorado, 2016). Inbreeding has been demonstrated to have harmful effects on survival and reproductive success of all major eukaryotic taxa, and these effects are estimated to be worse in the wild than in captivity (Crnokrak & Roff, 1999).

Not out of the woods yet: Signatures of the prolonged negative genetic consequences of a population bottleneck in a rapidly re‐expanding wader, the black‐faced spoonbill Platalea minor

“…We also suggest that pairwise genetic relatedness (kinship coefficient) between individuals should be calculated routinely for individuals within a small population. Such information could be used to develop manipulative breeding programmes to reduce inbred matings in wild populations (Robledo‐Ruiz et al, 2021). Taken together, our results are especially relevant when anthropogenic environmental changes, such as human‐driven climate change, insecticide pollution and coastal destruction, are increasingly turning incidental natural processes into catastrophic events which put many wildlife species in great peril of population reduction.…”

Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater

“…We sequenced and assembled the nuclear and mitochondrial genomes of a wild-born adult (>10 year old) female helmeted honeyeater, banded on 26 October 2010 (ABBBS metal band 043-00510, colour bands pm:uk, Healesville accession B80296; nicknamed “Helena” by the Helmeted Honeyeater Recovery Team). This female successfully bred for ≥7 breeding seasons at YNCR and was included in 3 genetic studies [ 20 , 21 , 18 ], which revealed that it was genetically diverse and had longer than average life span and higher than average number of fledglings. After presenting symptoms of periarticular gout and nephropathy, this bird was humanely euthanized for animal welfare reasons at Healesville Sanctuary's Australian Wildlife Health Centre on 27 February 2018 under the authority of Zoos Victoria Research and Animal Ethics Committee (approval ZV16010).…”

“…Pedigree . Using the results of a previous parentage analysis [ 18 ], we selected the 36 full-sibling families (father-mother-offspring) that had ≥3 full-siblings (range = 3–14, mean = 5.69 [SD 3.22]; 206 offspring in total). When possible, grandparents and half-siblings of these families were included.…”

“…Genotype posterior probabilities . We used raw sequencing data obtained using DArTseq [ 56 ] from a previous study [ 18 ] for the selected 257 related individuals. Briefly, DArTseq is a reduced-representation sequencing method that uses a combination of PstI and SphI restriction enzymes for DNA digestion, sequencing fragments with both PstI- and SphI-compatible adapters on Illumina HiSeq2500 using single-read configuration (for details see [ 20 ]).…”

“…The helmeted honeyeater has been subject to intensive conservation management, including captive breeding [ 17 ]. Ecological data and genetic samples have been collected for >3 decades, which enabled the recent construction of a multigenerational pedigree spanning 257 helmeted honeyeaters [ 18 ].…”