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Article ; Online: Genomes of an endangered rattlesnake show that neutral genetic variation predicts adaptive genetic variation and genetic load.

Kardos, Marty

Proceedings of the National Academy of Sciences of the United States of America

2023 Volume 120, Issue 49, Page(s) e2316880120

MeSH term(s)	Animals ; Genetic Load ; Crotalus ; Genetic Variation
Language	English
Publishing date	2023-11-27
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2316880120
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Article ; Online: Conservation genetics.

Kardos, Marty

Current biology : CB

2021 Volume 31, Issue 19, Page(s) R1185–R1190

Abstract: Natural populations currently face a wide variety of threats including climate change, habitat loss, over-harvesting, invasive species and disease. The most recent report by the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem ... ...

Abstract	Natural populations currently face a wide variety of threats including climate change, habitat loss, over-harvesting, invasive species and disease. The most recent report by the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) found that ecosystems have declined by approximately 50% relative to historical pristine conditions, and that approximately 25% of species are now threatened by extinction. This human-caused biodiversity crisis calls for using all available scientific tools to understand and reverse the increasing rate of extinction. While extinction is inherently a demographic process, being driven by changes in the population growth rate, the field of genetics plays an important role in the conservation of biodiversity. 'Conservation genetics' is a diverse field that applies genetic principles and methods to characterize and advance the preservation of biodiversity. Here, I first provide a short history of the development of the field and then list examples of the most important ways that genetics contributes to conservation.
MeSH term(s)	Biodiversity ; Climate Change ; Conservation of Natural Resources ; Ecosystem ; Humans
Language	English
Publishing date	2021-10-12
Publishing country	England
Document type	Journal Article
ZDB-ID	1071731-6
ISSN	1879-0445 ; 0960-9822
ISSN (online)	1879-0445
ISSN	0960-9822
DOI	10.1016/j.cub.2021.08.047
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Article ; Online: The Genetic Architecture of Fitness Drives Population Viability during Rapid Environmental Change.

Kardos, Marty / Luikart, Gordon

The American naturalist

2021 Volume 197, Issue 5, Page(s) 511–525

Abstract: AbstractThe rapid global loss of biodiversity calls for improved predictions of how populations will evolve and respond demographically to ongoing environmental change. The heritability ( ...

Abstract	AbstractThe rapid global loss of biodiversity calls for improved predictions of how populations will evolve and respond demographically to ongoing environmental change. The heritability (
MeSH term(s)	Alleles ; Biodiversity ; Biological Evolution ; Climate Change ; Computer Simulation ; Gene Frequency ; Genetic Fitness ; Models, Genetic ; Multifactorial Inheritance ; Phenotype ; Selection, Genetic
Language	English
Publishing date	2021-03-22
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	207092-3
ISSN	1537-5323 ; 0003-0147
ISSN (online)	1537-5323
ISSN	0003-0147
DOI	10.1086/713469
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Article ; Online: The Peril of Gene-Targeted Conservation.

Kardos, Marty / Shafer, Aaron B A

Trends in ecology & evolution

2018 Volume 33, Issue 11, Page(s) 827–839

Abstract: The genomics revolution has sparked interest in using our increased understanding of the loci involved in phenotypic variation and adaptation to advance the conservation of biodiversity. Despite much interest and discussion, it remains unclear whether, ... ...

Abstract	The genomics revolution has sparked interest in using our increased understanding of the loci involved in phenotypic variation and adaptation to advance the conservation of biodiversity. Despite much interest and discussion, it remains unclear whether, when, and how such analyses should be used to guide conservation action. Such 'gene-targeted' conservation strategies, while promising, are complicated by several factors including the complex genomic architecture of phenotypic variation and the strong potential for undesirable outcomes such as the loss of genome-wide genetic variation and evolutionary potential. We caution against relying on gene-targeted approaches as a conservation silver bullet and propose rigorous criteria to identify situations where gene-targeted approaches are likely to benefit conservation.
MeSH term(s)	Adaptation, Physiological ; Animals ; Biodiversity ; Biological Evolution ; Conservation of Natural Resources ; Genetic Variation ; Genetics, Population ; Genomics ; Plants
Language	English
Publishing date	2018-09-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	284965-3
ISSN	1872-8383 ; 0169-5347
ISSN (online)	1872-8383
ISSN	0169-5347
DOI	10.1016/j.tree.2018.08.011
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Article ; Online: How should we compare different genomic estimates of the strength of inbreeding depression?

Kardos, Marty / Nietlisbach, Pirmin / Hedrick, Philip W

Proceedings of the National Academy of Sciences of the United States of America

2018 Volume 115, Issue 11, Page(s) E2492–E2493

MeSH term(s)	Consanguinity ; Genomics ; Inbreeding Depression
Language	English
Publishing date	2018-02-21
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1714475115
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Article ; Online: Influence of RNA-Seq library construction, sampling methods, and tissue harvesting time on gene expression estimation.

Chiari, Ylenia / Howard, Leif / Moreno, Nickolas / Relyea, Scott / Dunnigan, James / Boyer, Matthew C / Kardos, Marty / Glaberman, Scott / Luikart, Gordon

Molecular ecology resources

2023 Volume 23, Issue 4, Page(s) 803–817

Abstract: RNA sequencing (RNA-Seq) is popular for measuring gene expression in non-model organisms, including wild populations. While RNA-Seq can detect gene expression variation among wild-caught individuals and yield important insights into biological function, ... ...

Abstract	RNA sequencing (RNA-Seq) is popular for measuring gene expression in non-model organisms, including wild populations. While RNA-Seq can detect gene expression variation among wild-caught individuals and yield important insights into biological function, sampling methods can also affect gene expression estimates. We examined the influence of multiple technical variables on estimated gene expression in a non-model fish, the westslope cutthroat trout (Oncorhynchus clarkii lewisi), using two RNA-Seq library types: 3' RNA-Seq (QuantSeq) and whole mRNA-Seq (NEB). We evaluated effects of dip netting versus electrofishing, and of harvesting tissue immediately versus 5 min after euthanasia on estimated gene expression in blood, gill, and muscle. We found no significant differences in gene expression between sampling methods or tissue collection times with either library type. When library types were compared using the same blood samples, 58% of genes detected by both NEB and QuantSeq showed significantly different expression between library types, and NEB detected 31% more genes than QuantSeq. Although the two library types recovered different numbers of genes and expression levels, results with NEB and QuantSeq were consistent in that neither library type showed differences in gene expression between sampling methods and tissue harvesting times. Our study suggests that researchers can safely rely on different fish sampling strategies in the field. In addition, while QuantSeq is more cost effective, NEB detects more expressed genes. Therefore, when it is crucial to detect as many genes as possible (especially low expressed genes), when alternative splicing is of interest, or when working with an organism lacking good genomic resources, whole mRNA-Seq is more powerful.
MeSH term(s)	Animals ; RNA-Seq ; Sequence Analysis, RNA/methods ; Oncorhynchus/genetics ; Gene Library ; RNA, Messenger/genetics ; Tissue and Organ Harvesting ; Gene Expression ; Gene Expression Profiling/methods ; High-Throughput Nucleotide Sequencing/methods
Chemical Substances	RNA, Messenger
Language	English
Publishing date	2023-02-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2406833-0
ISSN	1755-0998 ; 1755-098X
ISSN (online)	1755-0998
ISSN	1755-098X
DOI	10.1111/1755-0998.13757
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Article: The Peril of Gene-Targeted Conservation

Kardos, Marty / Aaron B.A. Shafer

Trends in ecology & evolution. 2018 Nov., v. 33, no. 11

2018

Abstract	The genomics revolution has sparked interest in using our increased understanding of the loci involved in phenotypic variation and adaptation to advance the conservation of biodiversity. Despite much interest and discussion, it remains unclear whether, when, and how such analyses should be used to guide conservation action. Such ‘gene-targeted’ conservation strategies, while promising, are complicated by several factors including the complex genomic architecture of phenotypic variation and the strong potential for undesirable outcomes such as the loss of genome-wide genetic variation and evolutionary potential. We caution against relying on gene-targeted approaches as a conservation silver bullet and propose rigorous criteria to identify situations where gene-targeted approaches are likely to benefit conservation.
Keywords	biodiversity ; genetic variation ; genomics ; loci ; phenotypic variation
Language	English
Dates of publication	2018-11
Size	p. 827-839.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	284965-3
ISSN	1872-8383 ; 0169-5347
ISSN (online)	1872-8383
ISSN	0169-5347
DOI	10.1016/j.tree.2018.08.011
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Article ; Online: Inferring Individual Inbreeding and Demographic History from Segments of Identity by Descent in

Kardos, Marty / Qvarnström, Anna / Ellegren, Hans

Genetics

2017 Volume 205, Issue 3, Page(s) 1319–1334

Abstract: Individual inbreeding and historical demography can be estimated by analyzing runs of homozygosity (ROH), which are indicative of chromosomal segments of identity by descent (IBD). Such analyses have so far been rare in natural populations due to limited ...

Abstract	Individual inbreeding and historical demography can be estimated by analyzing runs of homozygosity (ROH), which are indicative of chromosomal segments of identity by descent (IBD). Such analyses have so far been rare in natural populations due to limited genomic resources. We analyzed ROH in whole genome sequences from 287
MeSH term(s)	Animals ; Evolution, Molecular ; Founder Effect ; Genome ; Homozygote ; Inbreeding ; Passeriformes/genetics ; Pedigree ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2017-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1534/genetics.116.198861
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Article ; Online: Influence of RNA‐Seq library construction, sampling methods, and tissue harvesting time on gene expression estimation

Chiari, Ylenia / Howard, Leif / Moreno, Nickolas / Relyea, Scott / Dunnigan, James / Boyer, Matthew C. / Kardos, Marty / Glaberman, Scott / Luikart, Gordon

Molecular Ecology Resources. 2023 May, v. 23, no. 4 p.803-817

2023

Abstract: RNA sequencing (RNA‐Seq) is popular for measuring gene expression in non‐model organisms, including wild populations. While RNA‐Seq can detect gene expression variation among wild‐caught individuals and yield important insights into biological function, ... ...

Abstract	RNA sequencing (RNA‐Seq) is popular for measuring gene expression in non‐model organisms, including wild populations. While RNA‐Seq can detect gene expression variation among wild‐caught individuals and yield important insights into biological function, sampling methods can also affect gene expression estimates. We examined the influence of multiple technical variables on estimated gene expression in a non‐model fish, the westslope cutthroat trout (Oncorhynchus clarkii lewisi), using two RNA‐Seq library types: 3′ RNA‐Seq (QuantSeq) and whole mRNA‐Seq (NEB). We evaluated effects of dip netting versus electrofishing, and of harvesting tissue immediately versus 5 min after euthanasia on estimated gene expression in blood, gill, and muscle. We found no significant differences in gene expression between sampling methods or tissue collection times with either library type. When library types were compared using the same blood samples, 58% of genes detected by both NEB and QuantSeq showed significantly different expression between library types, and NEB detected 31% more genes than QuantSeq. Although the two library types recovered different numbers of genes and expression levels, results with NEB and QuantSeq were consistent in that neither library type showed differences in gene expression between sampling methods and tissue harvesting times. Our study suggests that researchers can safely rely on different fish sampling strategies in the field. In addition, while QuantSeq is more cost effective, NEB detects more expressed genes. Therefore, when it is crucial to detect as many genes as possible (especially low expressed genes), when alternative splicing is of interest, or when working with an organism lacking good genomic resources, whole mRNA‐Seq is more powerful.
Keywords	Oncorhynchus clarkii ; RNA ; blood ; cost effectiveness ; ecology ; euthanasia ; fish ; gene expression ; genomics ; muscles ; sequence analysis
Language	English
Dates of publication	2023-05
Size	p. 803-817.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2406816-0
ISSN	1471-8286 ; 1755-098X
ISSN (online)	1471-8286
ISSN	1755-098X
DOI	10.1111/1755-0998.13757
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Article ; Online: Evaluating the outcomes of genetic rescue attempts.

Robinson, Zachary L / Bell, Donovan A / Dhendup, Tashi / Luikart, Gordon / Whiteley, Andrew R / Kardos, Marty

Conservation biology : the journal of the Society for Conservation Biology

2020 Volume 35, Issue 2, Page(s) 666–677

Abstract: Augmenting gene flow is a powerful tool for the conservation of small, isolated populations. However, genetic rescue attempts have largely been limited to populations at the brink of extinction, in part due to concerns over negative outcomes (e.g., ... ...

Abstract	Augmenting gene flow is a powerful tool for the conservation of small, isolated populations. However, genetic rescue attempts have largely been limited to populations at the brink of extinction, in part due to concerns over negative outcomes (e.g., outbreeding depression). Increasing habitat fragmentation may necessitate more proactive genetic management. Broader application of augmented gene flow will, in turn, require rigorous evaluation to increase confidence and identify pitfalls in this approach. To date, there has been no assessment of best monitoring practices for genetic rescue attempts. We used genomically explicit, individual-based simulations to examine the effectiveness of common approaches (i.e., tests for increases in fitness, migrant ancestry, heterozygosity, and abundance) for determining whether genetic rescue or outbreeding depression occurred. Statistical power to detect the effects of gene flow on fitness was high (≥0.8) when effect sizes were large, a finding consistent with those from previous studies on severely inbred populations. However, smaller effects of gene flow on fitness can appreciably affect persistence probability but current evaluation approaches fail to provide results from which reliable inferences can be drawn. The power of the metrics we examined to evaluate genetic rescue attempts depended on the time since gene flow and whether gene flow was beneficial or deleterious. Encouragingly, the use of multiple metrics provided nonredundant information and improved inference reliability, highlighting the importance of intensive monitoring efforts. Further development of best practices for evaluating genetic rescue attempts will be crucial for a responsible transition to increased use of translocations to decrease extinction risk.
MeSH term(s)	Conservation of Natural Resources ; Ecosystem ; Gene Flow ; Genetic Fitness ; Genetic Variation ; Inbreeding ; Reproducibility of Results
Language	English
Publishing date	2020-10-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	58735-7
ISSN	1523-1739 ; 0888-8892
ISSN (online)	1523-1739
ISSN	0888-8892
DOI	10.1111/cobi.13596
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