A Comparison of Pedigree, Genetic and Genomic Estimates of Relatedness for Informing Pairing Decisions in Two Critically Endangered Birds: Implications for Conservation Breeding Programmes Worldwide

Stephanie J. Galla; Roger Moraga; Liz Brown; Simone Cleland; Marc P. Hoeppner; Richard F. Maloney; Anne Richardson

doi:10.1111/eva.12916

A Comparison of Pedigree, Genetic and Genomic Estimates of Relatedness for Informing Pairing Decisions in Two Critically Endangered Birds: Implications for Conservation Breeding Programmes Worldwide

Stephanie J. Galla, Roger Moraga, Liz Brown, Simone Cleland, Marc P. Hoeppner, Richard F. Maloney, Anne Richardson

Research output: Contribution to journal › Article › peer-review

54 Scopus citations

Abstract

<div class="line" id="line-5"> Conservation management strategies for many highly threatened species include conservation breeding to prevent extinction and enhance recovery. Pairing decisions for these conservation breeding programmes can be informed by pedigree data to minimize relatedness between individuals in an effort to avoid inbreeding, maximize diversity and maintain evolutionary potential. However, conservation breeding programmes struggle to use this approach when pedigrees are shallow or incomplete. While genetic data (i.e., microsatellites) can be used to estimate relatedness to inform pairing decisions, emerging evidence indicates this approach may lack precision in genetically depauperate species, and more effective estimates will likely be obtained from genomic data (i.e., thousands of genome-wide single nucleotide polymorphisms, or SNPs). Here, we compare relatedness estimates and subsequent pairing decisions using pedigrees, microsatellites and SNPs from whole-genome resequencing approaches in two critically endangered birds endemic to New Zealand: kak&imacr;/black stilt ( Himantopus novaezelandiae ) and k&amacr;k&amacr;riki karaka/orange-fronted parakeet ( Cyanoramphus malherbi ). Our findings indicate that SNPs provide more precise estimates of relatedness than microsatellites when assessing empirical parent–offspring and full sibling relationships. Further, our results show that relatedness estimates and subsequent pairing recommendations using  PMx  are most similar between pedigree- and SNP-based approaches. These combined results indicate that in lieu of robust pedigrees, SNPs are an effective tool for informing pairing decisions, which has important implications for many poorly pedigreed conservation breeding programmes worldwide. </div>

Original language	American English
Journal	Evolutionary Applications
Volume	13
Issue number	5
DOIs	https://doi.org/10.1111/eva.12916
State	Published - May 2020
Externally published	Yes

Keywords

PMx
conservation breeding
conservation genetics
conservation genomics
pairing recommendations
relatedness

EGS Disciplines

Ecology and Evolutionary Biology

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Galla, Stephanie (2020) A comparison of pedigree - pub SelWrks.pdfFinal published version, 1.18 MBLicense: Unspecified

Cite this

Galla, S. J., Moraga, R., Brown, L., Cleland, S., Hoeppner, M. P., Maloney, R. F., & Richardson, A. (2020). A Comparison of Pedigree, Genetic and Genomic Estimates of Relatedness for Informing Pairing Decisions in Two Critically Endangered Birds: Implications for Conservation Breeding Programmes Worldwide. Evolutionary Applications, 13(5). https://doi.org/10.1111/eva.12916

@article{9ef4978ad3ad4ffe960e5eb2d732b34e,

title = "A Comparison of Pedigree, Genetic and Genomic Estimates of Relatedness for Informing Pairing Decisions in Two Critically Endangered Birds: Implications for Conservation Breeding Programmes Worldwide",

abstract = " Conservation management strategies for many highly threatened species include conservation breeding to prevent extinction and enhance recovery. Pairing decisions for these conservation breeding programmes can be informed by pedigree data to minimize relatedness between individuals in an effort to avoid inbreeding, maximize diversity and maintain evolutionary potential. However, conservation breeding programmes struggle to use this approach when pedigrees are shallow or incomplete. While genetic data (i.e., microsatellites) can be used to estimate relatedness to inform pairing decisions, emerging evidence indicates this approach may lack precision in genetically depauperate species, and more effective estimates will likely be obtained from genomic data (i.e., thousands of genome-wide single nucleotide polymorphisms, or SNPs). Here, we compare relatedness estimates and subsequent pairing decisions using pedigrees, microsatellites and SNPs from whole-genome resequencing approaches in two critically endangered birds endemic to New Zealand: kak&imacr;/black stilt ( Himantopus novaezelandiae ) and k&amacr;k&amacr;riki karaka/orange-fronted parakeet ( Cyanoramphus malherbi ). Our findings indicate that SNPs provide more precise estimates of relatedness than microsatellites when assessing empirical parent–offspring and full sibling relationships. Further, our results show that relatedness estimates and subsequent pairing recommendations using  PMx  are most similar between pedigree- and SNP-based approaches. These combined results indicate that in lieu of robust pedigrees, SNPs are an effective tool for informing pairing decisions, which has important implications for many poorly pedigreed conservation breeding programmes worldwide. ",

keywords = "PMx, conservation breeding, conservation genetics, conservation genomics, pairing recommendations, relatedness",

author = "Galla, {Stephanie J.} and Roger Moraga and Liz Brown and Simone Cleland and Hoeppner, {Marc P.} and Maloney, {Richard F.} and Anne Richardson",

note = "Galla, Stephanie J.; Moraga, Roger; Brown, Liz; Cleland, Simone; Hoeppner, Marc P.; Maloney, Richard F.; . . . and Steeves, Tammy E. (2020). {"}A Comparison of Pedigree, Genetic and Genomic Estimates of Relatedness for Informing Pairing Decisions in Two Critically Endangered Birds: Implications for Conservation Breeding Programmes Worldwide{"}. Evolutionary Applications, 13(5), 991-1008. https://doi.org/10.1111/eva.12916",

year = "2020",

month = may,

doi = "10.1111/eva.12916",

language = "American English",

volume = "13",

number = "5",

}

Galla, SJ, Moraga, R, Brown, L, Cleland, S, Hoeppner, MP, Maloney, RF & Richardson, A 2020, 'A Comparison of Pedigree, Genetic and Genomic Estimates of Relatedness for Informing Pairing Decisions in Two Critically Endangered Birds: Implications for Conservation Breeding Programmes Worldwide', Evolutionary Applications, vol. 13, no. 5. https://doi.org/10.1111/eva.12916

A Comparison of Pedigree, Genetic and Genomic Estimates of Relatedness for Informing Pairing Decisions in Two Critically Endangered Birds: Implications for Conservation Breeding Programmes Worldwide. / Galla, Stephanie J.; Moraga, Roger; Brown, Liz et al.
In: Evolutionary Applications, Vol. 13, No. 5, 05.2020.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - A Comparison of Pedigree, Genetic and Genomic Estimates of Relatedness for Informing Pairing Decisions in Two Critically Endangered Birds: Implications for Conservation Breeding Programmes Worldwide

AU - Galla, Stephanie J.

AU - Moraga, Roger

AU - Brown, Liz

AU - Cleland, Simone

AU - Hoeppner, Marc P.

AU - Maloney, Richard F.

AU - Richardson, Anne

N1 - Galla, Stephanie J.; Moraga, Roger; Brown, Liz; Cleland, Simone; Hoeppner, Marc P.; Maloney, Richard F.; . . . and Steeves, Tammy E. (2020). "A Comparison of Pedigree, Genetic and Genomic Estimates of Relatedness for Informing Pairing Decisions in Two Critically Endangered Birds: Implications for Conservation Breeding Programmes Worldwide". Evolutionary Applications, 13(5), 991-1008. https://doi.org/10.1111/eva.12916

PY - 2020/5

Y1 - 2020/5

N2 - Conservation management strategies for many highly threatened species include conservation breeding to prevent extinction and enhance recovery. Pairing decisions for these conservation breeding programmes can be informed by pedigree data to minimize relatedness between individuals in an effort to avoid inbreeding, maximize diversity and maintain evolutionary potential. However, conservation breeding programmes struggle to use this approach when pedigrees are shallow or incomplete. While genetic data (i.e., microsatellites) can be used to estimate relatedness to inform pairing decisions, emerging evidence indicates this approach may lack precision in genetically depauperate species, and more effective estimates will likely be obtained from genomic data (i.e., thousands of genome-wide single nucleotide polymorphisms, or SNPs). Here, we compare relatedness estimates and subsequent pairing decisions using pedigrees, microsatellites and SNPs from whole-genome resequencing approaches in two critically endangered birds endemic to New Zealand: kak&imacr;/black stilt ( Himantopus novaezelandiae ) and k&amacr;k&amacr;riki karaka/orange-fronted parakeet ( Cyanoramphus malherbi ). Our findings indicate that SNPs provide more precise estimates of relatedness than microsatellites when assessing empirical parent–offspring and full sibling relationships. Further, our results show that relatedness estimates and subsequent pairing recommendations using  PMx  are most similar between pedigree- and SNP-based approaches. These combined results indicate that in lieu of robust pedigrees, SNPs are an effective tool for informing pairing decisions, which has important implications for many poorly pedigreed conservation breeding programmes worldwide.

AB - Conservation management strategies for many highly threatened species include conservation breeding to prevent extinction and enhance recovery. Pairing decisions for these conservation breeding programmes can be informed by pedigree data to minimize relatedness between individuals in an effort to avoid inbreeding, maximize diversity and maintain evolutionary potential. However, conservation breeding programmes struggle to use this approach when pedigrees are shallow or incomplete. While genetic data (i.e., microsatellites) can be used to estimate relatedness to inform pairing decisions, emerging evidence indicates this approach may lack precision in genetically depauperate species, and more effective estimates will likely be obtained from genomic data (i.e., thousands of genome-wide single nucleotide polymorphisms, or SNPs). Here, we compare relatedness estimates and subsequent pairing decisions using pedigrees, microsatellites and SNPs from whole-genome resequencing approaches in two critically endangered birds endemic to New Zealand: kak&imacr;/black stilt ( Himantopus novaezelandiae ) and k&amacr;k&amacr;riki karaka/orange-fronted parakeet ( Cyanoramphus malherbi ). Our findings indicate that SNPs provide more precise estimates of relatedness than microsatellites when assessing empirical parent–offspring and full sibling relationships. Further, our results show that relatedness estimates and subsequent pairing recommendations using  PMx  are most similar between pedigree- and SNP-based approaches. These combined results indicate that in lieu of robust pedigrees, SNPs are an effective tool for informing pairing decisions, which has important implications for many poorly pedigreed conservation breeding programmes worldwide.

KW - PMx

KW - conservation breeding

KW - conservation genetics

KW - conservation genomics

KW - pairing recommendations

KW - relatedness

U2 - 10.1111/eva.12916

DO - 10.1111/eva.12916

M3 - Article

VL - 13

JO - Evolutionary Applications

JF - Evolutionary Applications

IS - 5

ER -

A Comparison of Pedigree, Genetic and Genomic Estimates of Relatedness for Informing Pairing Decisions in Two Critically Endangered Birds: Implications for Conservation Breeding Programmes Worldwide

Abstract

Keywords

EGS Disciplines

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