2021
DOI: 10.1111/1755-0998.13447
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The endangered White Sands pupfish (Cyprinodon tularosa) genome reveals low diversity and heterogenous patterns of differentiation

Abstract: The integration of genomics into conservation biology has enabled the incorporation of genome-wide diversity metrics within the context of the demographic history of threatened and endangered populations (Leroy et al., 2018). For example, whole-genome sequence analysis of Grey wolf (Canis lupus) revealed patterns of low heterozygosity and high inbreeding depression, despite historical introgression from domestic dog (C. lupus familiaris; Gómez-Sánchez et al., 2018). Such genome-wide assessments can provide key… Show more

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Cited by 4 publications
(6 citation statements)
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“…2 A ). Consistent with Black et al ( 22 ), individual heterozygosity among all 45 samples was very low and varied by a factor of three across sites, ranging from 0.00046 (LR) to 0.00149 (MS). Significant genome-wide differences in heterozygosity were observed across pairwise population comparisons (Wilcoxon signed rank test, W = 0 to 42, P -values < 0.003).…”
Section: Divergence Timessupporting
confidence: 86%
See 2 more Smart Citations
“…2 A ). Consistent with Black et al ( 22 ), individual heterozygosity among all 45 samples was very low and varied by a factor of three across sites, ranging from 0.00046 (LR) to 0.00149 (MS). Significant genome-wide differences in heterozygosity were observed across pairwise population comparisons (Wilcoxon signed rank test, W = 0 to 42, P -values < 0.003).…”
Section: Divergence Timessupporting
confidence: 86%
“…Whole-genome library preparation and sequencing were conducted on individually barcoded samples (n = 15 from each population) and on three pools of samples (n = 30 from each population). Quality controlled reads were aligned to the C. tularosa reference genome ( 22 ) with bwa ( 58 ) and were processed using Poolparty ( 59 ) and Angsd ( 60 ), which were also used to estimate individual heterozygosity and pairwise differentiation. Population structure was evaluated using PCAngsd ( 61 ), NGSadmix ( 62 ), and runs of homozygosity were identified using bcftools ( 63 ).…”
Section: Methodsmentioning
confidence: 99%
See 1 more Smart Citation
“…variegatus mitogenomes, as was also observed by Lema, Wilson, et al (2016). Recent unpublished nuclear DNA analyses suggest possible genetic introgression of C. variegatus into C. tularosa (Black et al 2021), which may explain relationships of those taxa in Figure 1.…”
supporting
confidence: 68%
“…They reinforce Mossop et al’s [ 35 ] conclusion that ephemeral waters represent important dispersal routes in arid ecosystems. Such connections, however fleeting, seem to help freshwater fishes in isolated waters to overcome the small population sizes and low genetic diversity [ 96 99 ] that could otherwise promote a drift towards imperilment or extinction.…”
Section: Discussionmentioning
confidence: 99%