Evaluating sources of bias in pedigree‐based estimates of breeding population size

White, Shannon L.; Sard, Nicholas M.; Brundage, Harold M.; Johnson, Robin L.; Lubinski, Barbara A.; Eackles, Michael S.; Park, Ian A.; Fox, Dewayne A.; Kazyak, David C.

doi:10.1002/eap.2602

Cited by 7 publications

(2 citation statements)

References 45 publications

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“…However, microhaplotypes also contained higher inter‐laboratory scoring errors. These data could provide new opportunities to assess the abundance of local walleye populations using genetic techniques such as close‐kin mark‐recapture (CKMR) and rarefaction, which benefit from multiallelic markers (Bravington et al, 2016 ; White et al, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

A new GTSeq resource to facilitate multijurisdictional research and management of walleye Sander vitreus

Euclide

Larson

Bootsma

et al. 2022

Ecology and Evolution

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Conservation and management professionals often work across jurisdictional boundaries to identify broad ecological patterns. These collaborations help to protect populations whose distributions span political borders. One common limitation to multijurisdictional collaboration is consistency in data recording and reporting. This limitation can impact genetic research, which relies on data about specific markers in an organism's genome. Incomplete overlap of markers between separate studies can prevent direct comparisons of results. Standardized marker panels can reduce the impact of this issue and provide a common starting place for new research. Genotyping‐in‐thousands (GTSeq) is one approach used to create standardized marker panels for nonmodel organisms. Here, we describe the development, optimization, and early assessments of a new GTSeq panel for use with walleye ( Sander vitreus ) from the Great Lakes region of North America. High genome‐coverage sequencing conducted using RAD capture provided genotypes for thousands of single nucleotide polymorphisms (SNPs). From these markers, SNP and microhaplotype markers were chosen, which were informative for genetic stock identification (GSI) and kinship analysis. The final GTSeq panel contained 500 markers, including 197 microhaplotypes and 303 SNPs. Leave‐one‐out GSI simulations indicated that GSI accuracy should be greater than 80% in most jurisdictions. The false‐positive rates of parent‐offspring and full‐sibling kinship identification were found to be low. Finally, genotypes could be consistently scored among separate sequencing runs >94% of the time. Results indicate that the GTSeq panel that we developed should perform well for multijurisdictional walleye research throughout the Great Lakes region.

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Section: Discussionmentioning

confidence: 99%

A new GTSeq resource to facilitate multijurisdictional research and management of walleye Sander vitreus

Euclide

Larson

Bootsma

et al. 2022

Ecology and Evolution

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“…Approximately 25 rivers still support their reproduction [7,8]. The abundances of adult sturgeon in these spawning populations vary greatly, with census estimates ranging from the low hundreds for the Delaware River [9] to less than a thousand for the Hudson River, New York [10] and Altamaha River, Georgia [11,12] and about 20,000 for the Saint John River, New Brunswick [13]. Because population sizes vary so greatly [1], the vulnerabilities of individual populations to more severe declines and extirpation also differ.…”

Section: Introductionmentioning

confidence: 99%

Two Distinct Life History Strategies of Atlantic Sturgeon in the Ogeechee River, Georgia

et al. 2023

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Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) is an anadromous, widely distributed, highly migratory sturgeon subspecies that occurs in rivers and marine waters along the North American Atlantic Coast. This fish has shown widespread declines and has been afforded conservation protections, including some based in the U.S. on the delineation of Distinct Population Segments (DPS) under the Endangered Species Act. The management of Atlantic sturgeon will benefit from the knowledge of its population structure as well as the ability to uniquely identify individuals (in relation to population origin) that are vulnerable to anthropogenic stressors at sites outside of their natal estuaries. We used microsatellite analysis to estimate the genetic population structure of Atlantic sturgeon from 13 spawning rivers ranging from the St. Lawrence River, Quebec to the Satilla River, Georgia. Individual Based Assignment (IBA) testing was used to estimate the contribution of each population to mixed-stock aggregations in coastal waters and in a non-natal estuary. An unexpected finding was the discovery of two distinct genetic clusters of juvenile Atlantic sturgeon in the Ogeechee River, Georgia, with specimens in the two clusters differing significantly in terms of mean total length. Additionally, three distinct genetic clusters were detected within the Satilla River juvenile collection, along with two clusters within the Edisto River sample. In F1ST and FST analyses, the extent of the pairwise genetic differentiation between the two genetic clusters in the Ogeechee River and the three in the Satilla River was greater than that between all other pairwise comparisons among rivers in the South Atlantic DPS. In contrast, we found no evidence of the genetic partitioning of juvenile sturgeon within the neighboring Savannah or Altamaha river populations. Using IBA, we found that the overall Ogeechee River population made a moderate contribution (8.3%) to the overall mixed-stock collections (n = 1512) from coastal North Carolina to the Bay of Fundy. Surprisingly, all of the Ogeechee River-assigned specimens (n = 125) in these mixed-stock aggregations were representatives of only one of the two Ogeechee River genetic clusters. These results suggest that the two Ogeechee River genetic clusters exhibit significantly different life history strategies, with one being resident and the second being highly migratory.

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DnaDot - fixing ecology and evolution’s blind spot, population size

Sherwin

2024

Ecological Indicators

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Evaluating sources of bias in pedigree‐based estimates of breeding population size

Cited by 7 publications

References 45 publications

A new GTSeq resource to facilitate multijurisdictional research and management of walleye Sander vitreus

A new GTSeq resource to facilitate multijurisdictional research and management of walleye Sander vitreus

Two Distinct Life History Strategies of Atlantic Sturgeon in the Ogeechee River, Georgia

DnaDot - fixing ecology and evolution’s blind spot, population size

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