Estimating divergence time for two evolutionarily significant units of a protected fish species

Stockwell, Craig A.; Heilveil, Jeffrey S.; Purcell, Kevin M.

doi:10.1007/s10592-013-0447-1

Cited by 18 publications

(14 citation statements)

References 46 publications

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“…; Stockwell et al. ). Evolutionarily divergent populations, even if divergence is determined with noncoding genetic markers, likely encompass adaptive differences (Fraser and Bernatchez ; Hedrick et al.…”

Section: Discussionmentioning

confidence: 98%

“…The ESU concept has been widely embraced by the conservation biology community (Moritz 1994;Peacock et al 2010;Bristol et al 2013;Lumley and Cusson 2013;Olivares et al 2013;Stockwell et al 2013). Evolutionarily divergent populations, even if divergence is determined with noncoding genetic markers, likely encompass adaptive differences (Fraser and Bernatchez 2001;Hedrick et al 2001).…”

Section: Discussionmentioning

confidence: 99%

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Genetic variation and population structure in a threatened species, the Utah prairie dog Cynomys parvidens: the use of genetic data to inform conservation actions

Brown

Peacock

Ritchie

2016

Ecology and Evolution

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The Utah prairie dog (Cynomys parvidens), listed as threatened under the United States Endangered Species Act, was the subject of an extensive eradication program throughout its range during the 20th century. Eradication campaigns, habitat destruction/fragmentation/conversion, and epizootic outbreaks (e.g., sylvatic plague) have reduced prairie dog numbers from an estimated 95,000 individuals in the 1920s to approximately 14,000 (estimated adult spring count) today. As a result of these anthropogenic actions, the species is now found in small isolated sets of subpopulations. We characterized the levels of genetic diversity and population genetic structure using 10 neutral nuclear microsatellite loci for twelve populations (native and transplanted) representative of the three management designated “recovery units,” found in three distinct biogeographic regions, sampled across the species' range. The results indicate (1) low levels of genetic diversity within colonies (H e = 0.109–0.357; H o = 0.106‐ 0.313), (2) high levels of genetic differentiation among colonies (global F ST = 0.296), (3) very small genetic effective population sizes, and (4) evidence of genetic bottlenecks. The genetic data reveal additional subdivision such that colonies within recovery units do not form single genotype clusters consistent with recovery unit boundaries. Genotype cluster membership support historical gene flow among colonies in the easternmost West Desert Recovery Unit with the westernmost Pausaugunt colonies and among the eastern Pausaugunt colonies and the Awapa Recovery unit to the north. In order to maintain the long‐term viability of the species, there needs to be an increased focus on maintaining suitable habitat between groups of existing populations that can act as connective corridors. The location of future translocation sites should be located in areas that will maximize connectivity, leading to maintenance of genetic variation and evolutionary potential.

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Section: Discussionmentioning

confidence: 98%

Section: Discussionmentioning

confidence: 99%

Genetic variation and population structure in a threatened species, the Utah prairie dog Cynomys parvidens: the use of genetic data to inform conservation actions

Brown

Peacock

Ritchie

2016

Ecology and Evolution

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“…Therefore, we hypothesise that reductions in snowy plover population size may have resulted from the combined impacts of increasing anthropogenic modification of habitats. Estimating demographic histories is becoming more common in conservation genetic studies (Carnaval et al 2009;Palsbøll et al 2013;Shafer et al 2015;Stoffel et al 2018) and can be used among other to prioritize conservation units (Stockwell et al 2013).…”

Section: Discussionmentioning

confidence: 99%

Population differentiation and historical demography of the threatened snowy plover Charadrius nivosus (Cassin, 1858)

et al. 2020

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Delineating conservation units is a complex and often controversial process that is particularly challenging for highly vagile species. Here, we reassess population genetic structure and identify those populations of highest conservation value in the threatened snowy plover (Charadrius nivosus, Cassin, 1858), a partial migrant shorebird endemic to the Americas. We use four categories of genetic data-mitochondrial DNA (mtDNA), microsatellites, Z-linked and autosomal single nucleotide polymorphisms (SNPs)-to: (1) assess subspecies delineation and examine population structure (2) compare the sensitivity of the different types of genetic data to detect spatial genetic patterns, and (3) reconstruct demographic history of the populations analysed. Delineation of two traditionally recognised subspecies was broadly supported by all data. In addition, microsatellite and SNPs but not mtDNA supported the recognition of Caribbean snowy plovers (C. n. tenuirostris) and Floridian populations (eastern C. n. nivosus) as distinct genetic lineage and deme, respectively. Low migration rates estimated from autosomal SNPs (m < 0.03) reflect a general paucity of exchange between genetic lineages. In contrast, we detected strong unidirectional migration (m = 0.26) from the western into the eastern nivosus deme. Within western nivosus, we found no genetic differentiation between coastal Pacific and inland populations. The correlation between geographic and genetic distances was weak but significant for all genetic data sets. All demes showed signatures of bottlenecks occurring during the past 1000 years. We conclude that at least four snowy plover conservation units are warranted: in addition to subspecies nivosus and occidentalis, a third unit comprises the Caribbean tenuirostris lineage and a fourth unit the distinct eastern nivosus deme.

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“…Estimation of species divergence time is critical not only for understanding the evolutionary history of a group (Drummond & Rambaut, ; Edwards, ) and testing fundamental concepts in evolutionary ecology (Coyne & Orr, ; Hendry & Kinnison, ; Schluter, ) but also for the management of small populations and their future conservation (Kinnison, Hendry, & Stockwell, ; Martin, Crawford, Turner, & Simons, ; Reed & Stockwell, ; Stockwell, Heilveil, & Purcell, ). Older lineages—particularly relict lineages such as the coelacanth and tuatara—are widely regarded as higher conservation value due to their greater reservoir of evolutionary history and unique traits (Faith, Reid, & Hunter, ; Vane‐Wright, Humphries, & Williams, ).…”

Section: Introductionmentioning

confidence: 99%

New evidence for the recent divergence of Devil's Hole pupfish and the plausibility of elevated mutation rates in endangered taxa

Martin

Höhna

2017

Molecular Ecology

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Sa glam et al. recently argued that the Devil's Hole pupfish (Cyprinodon diabolis), a conservation icon with the smallest known species range, was isolated 60 kya based on a new genomic data set. If true, this would be a radically long timescale for any species to persist at population sizes <500 individuals, in contrast to conservation genetics theory. However, here we argue that their analyses and interpretation are inappropriate. They placed highly restrictive prior distributions on divergence times, which do not appropriately model the large uncertainty and result in removing nearly all uncertainty from their analyses, and chose among models by assuming that pupfishes exhibit human mutation rates. We reanalysed their data with their same methods, only using an informative prior for the plausible range of mutation rates observed across vertebrates, including an estimate of the genomewide mutation rate from a pedigree analysis of cichlid fishes. In fact, Saglam et al.'s phylogenetic data support much younger median divergence times for C. diabolis, ranging from 6.2 to 19.9 kya, overlapping with our previous phylogenetic divergence time estimates of 2.5-6.5 kya. There are many reasons to suspect an even younger age and higher mutation rate in C. diabolis, as we previously estimated, due to their high metabolism, small adult size, small population size and severe environmental stressors. In conclusion, our results highlight the need for measuring mutation rate in this fascinating species and suggest that the ages of endangered taxa present in small, isolated populations may frequently be overestimated.

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Estimating divergence time for two evolutionarily significant units of a protected fish species

Cited by 18 publications

References 46 publications

Genetic variation and population structure in a threatened species, the Utah prairie dog Cynomys parvidens: the use of genetic data to inform conservation actions

Genetic variation and population structure in a threatened species, the Utah prairie dog Cynomys parvidens: the use of genetic data to inform conservation actions

Population differentiation and historical demography of the threatened snowy plover Charadrius nivosus (Cassin, 1858)

New evidence for the recent divergence of Devil's Hole pupfish and the plausibility of elevated mutation rates in endangered taxa

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