1
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Guhlin J, Le Lec MF, Wold J, Koot E, Winter D, Biggs PJ, Galla SJ, Urban L, Foster Y, Cox MP, Digby A, Uddstrom LR, Eason D, Vercoe D, Davis T, Howard JT, Jarvis ED, Robertson FE, Robertson BC, Gemmell NJ, Steeves TE, Santure AW, Dearden PK. Species-wide genomics of kākāpō provides tools to accelerate recovery. Nat Ecol Evol 2023; 7:1693-1705. [PMID: 37640765 DOI: 10.1038/s41559-023-02165-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 07/11/2023] [Indexed: 08/31/2023]
Abstract
The kākāpō is a critically endangered, intensively managed, long-lived nocturnal parrot endemic to Aotearoa New Zealand. We generated and analysed whole-genome sequence data for nearly all individuals living in early 2018 (169 individuals) to generate a high-quality species-wide genetic variant callset. We leverage extensive long-term metadata to quantify genome-wide diversity of the species over time and present new approaches using probabilistic programming, combined with a phenotype dataset spanning five decades, to disentangle phenotypic variance into environmental and genetic effects while quantifying uncertainty in small populations. We find associations for growth, disease susceptibility, clutch size and egg fertility within genic regions previously shown to influence these traits in other species. Finally, we generate breeding values to predict phenotype and illustrate that active management over the past 45 years has maintained both genome-wide diversity and diversity in breeding values and, hence, evolutionary potential. We provide new pathways for informing future conservation management decisions for kākāpō, including prioritizing individuals for translocation and monitoring individuals with poor growth or high disease risk. Overall, by explicitly addressing the challenge of the small sample size, we provide a template for the inclusion of genomic data that will be transformational for species recovery efforts around the globe.
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Affiliation(s)
- Joseph Guhlin
- Genomics Aotearoa, Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand
| | - Marissa F Le Lec
- Genomics Aotearoa, Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand
| | - Jana Wold
- School of Biological Sciences, University of Canterbury, Christchurch, Aotearoa New Zealand
| | - Emily Koot
- The New Zealand Institute for Plant and Food Research Ltd, Palmerston North, Aotearoa New Zealand
| | - David Winter
- School of Natural Sciences, Massey University, Palmerston North, Aotearoa New Zealand
| | - Patrick J Biggs
- School of Natural Sciences, Massey University, Palmerston North, Aotearoa New Zealand
- School of Veterinary Science, Massey University, Palmerston North, Aotearoa New Zealand
| | - Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Christchurch, Aotearoa New Zealand
- Department of Biological Sciences, Boise State University, Boise, ID, USA
| | - Lara Urban
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand
- Helmholtz Pioneer Campus, Helmholtz Zentrum Muenchen, Neuherberg, Germany
- Helmholtz AI, Helmholtz Zentrum Muenchen, Neuherberg, Germany
- School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Yasmin Foster
- Department of Zoology, University of Otago, Dunedin, Aotearoa New Zealand
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North, Aotearoa New Zealand
- Department of Statistics, University of Auckland, Auckland, Aotearoa New Zealand
| | - Andrew Digby
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand
| | - Lydia R Uddstrom
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand
| | - Daryl Eason
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand
| | - Deidre Vercoe
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand
| | - Tāne Davis
- Rakiura Tītī Islands Administering Body, Invercargill, Aotearoa New Zealand
| | - Jason T Howard
- Neurogenetics of Language Lab, The Rockefeller University, New York, NY, USA
- Mirxes, Cambridge, MA, USA
| | - Erich D Jarvis
- The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Fiona E Robertson
- Department of Zoology, University of Otago, Dunedin, Aotearoa New Zealand
| | - Bruce C Robertson
- Department of Zoology, University of Otago, Dunedin, Aotearoa New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, Aotearoa New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa New Zealand
| | - Peter K Dearden
- Genomics Aotearoa, Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand.
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2
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Rayne A, Arahanga-Doyle H, Cox B, Cox MP, Febria CM, Galla SJ, Hendy SC, Locke K, Matheson A, Pawlik A, Roa T, Sharp EL, Walker LA, Watene K, Wehi PM, Steeves TE. Collective action is needed to build a more just science system. Nat Hum Behav 2023:10.1038/s41562-023-01635-4. [PMID: 37291438 DOI: 10.1038/s41562-023-01635-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Aisling Rayne
- Te Pūnaha Matatini Centre for Research Excellence, Auckland, New Zealand.
- Centre for Sustainability, University of Otago, Dunedin, New Zealand.
- Cawthron Institute, Nelson, New Zealand.
| | - Hitaua Arahanga-Doyle
- Te Pūnaha Matatini Centre for Research Excellence, Auckland, New Zealand
- Department of Psychology, University of Otago, Dunedin, New Zealand
| | - Bethany Cox
- Te Pūnaha Matatini Centre for Research Excellence, Auckland, New Zealand
- School of Environment, Waipapa Taumata Rau University of Auckland, Auckland, New Zealand
| | - Murray P Cox
- Te Pūnaha Matatini Centre for Research Excellence, Auckland, New Zealand
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- School of Statistics, Waipapa Taumata Rau University of Auckland, Auckland, New Zealand
| | - Catherine M Febria
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
- Department of Integrative Biology, University of Windsor, Windsor, Ontario, Canada
| | - Stephanie J Galla
- Department of Biological Sciences, Boise State University, Boise, ID, USA
| | - Shaun C Hendy
- Te Pūnaha Matatini Centre for Research Excellence, Auckland, New Zealand
- Toha Science, Nelson, New Zealand
- Centre for Science in Society, Te Herenga Waka Victoria University of Wellington, Wellington, New Zealand
| | - Kirsten Locke
- Te Pūnaha Matatini Centre for Research Excellence, Auckland, New Zealand
- School of Critical Studies in Education, Waipapa Taumata Rau University of Auckland, Auckland, New Zealand
| | - Anna Matheson
- Te Pūnaha Matatini Centre for Research Excellence, Auckland, New Zealand
- School of Health, Te Herenga Waka Victoria University of Wellington, Wellington, New Zealand
| | | | - Tom Roa
- Te Pūnaha Matatini Centre for Research Excellence, Auckland, New Zealand
- Te Pua Wānanga ki te Ao - Faculty of Māori and Indigenous Studies, University of Waikato, Hamilton, New Zealand
| | - Emma L Sharp
- Te Pūnaha Matatini Centre for Research Excellence, Auckland, New Zealand
- School of Environment, Waipapa Taumata Rau University of Auckland, Auckland, New Zealand
| | - Leilani A Walker
- Te Pūnaha Matatini Centre for Research Excellence, Auckland, New Zealand
- Department of Environmental Science, Auckland University of Technology, Auckland, New Zealand
| | - Krushil Watene
- Te Pūnaha Matatini Centre for Research Excellence, Auckland, New Zealand
- Department of Philosophy, Waipapa Taumata Rau University of Auckland, Auckland, New Zealand
| | - Priscilla M Wehi
- Te Pūnaha Matatini Centre for Research Excellence, Auckland, New Zealand
- Centre for Sustainability, University of Otago, Dunedin, New Zealand
| | - Tammy E Steeves
- Te Pūnaha Matatini Centre for Research Excellence, Auckland, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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3
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Galla SJ, Mittan-Moreau CS, Barbosa S. Capturing conservation in the post-genomics era: a book review of “Conservation and Genomics of Populations.”. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01481-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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4
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Hauser S, Galla SJ, Putnam AS, Steeves TE, Latch EK. Comparing genome-based estimates of relatedness for use in pedigree-based conservation management. Mol Ecol Resour 2022; 22:2546-2558. [PMID: 35510790 DOI: 10.1111/1755-0998.13630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 02/28/2022] [Accepted: 03/30/2022] [Indexed: 12/01/2022]
Abstract
Researchers have long debated which estimator of relatedness best captures the degree of relationship between two individuals. In the genomics era, this debate continues, with relatedness estimates being sensitive to the methods used to generate markers, marker quality, and levels of diversity in sampled individuals. Here, we compare six commonly used genome-based relatedness estimators (kinship genetic distance (KGD), Wang Maximum Likelihood (TrioML), Queller and Goodnight (Rxy ), Kinship INference for Genome-wide association studies (KING-robust), and Pairwise Relatedness (RAB ), allele-sharing co-ancestry (AS)) across five species bred in captivity-including three birds and two mammals-with varying degrees of reliable pedigree data, using reduced-representation and whole genome resequencing data. Genome-based relatedness estimates varied widely across estimators, sequencing methods, and species, yet the most consistent results for known first order relationships were found using Rxy , RAB , and AS. However, AS was found to be less consistently correlated with known pedigree relatedness than either Rxy or RAB . Our combined results indicate there is not a single genome-based estimator that is ideal across different species and data types. To determine the most appropriate genome-based relatedness estimator for each new dataset, we recommend assessing the relative: (1) correlation of candidate estimators with known relationships in the pedigree and (2) precision of candidate estimators with known first-order relationships. These recommendations are broadly applicable to conservation breeding programs, particularly where genome-based estimates of relatedness can complement and complete poorly pedigreed populations. Given a growing interest in the application of wild pedigrees, our results are also applicable to in-situ wildlife management.
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Affiliation(s)
- Samantha Hauser
- Department of Biological Sciences, University of Wisconsin, Milwaukee, Wisconsin, USA.,Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Stephanie J Galla
- School of Biological Sciences, University of Canterbury, New Zealand.,Department of Biological Sciences, Boise State University, Boise, Idaho, USA
| | - Andrea S Putnam
- Department of Exhibit-Curators, San Diego Zoo Wildlife Alliance, San Diego, California, USA
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, New Zealand
| | - Emily K Latch
- Department of Biological Sciences, University of Wisconsin, Milwaukee, Wisconsin, USA
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5
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Robb BC, Olsoy PJ, Mitchell JJ, Caughlin TT, Delparte DM, Galla SJ, Fremgen‐Tarantino MR, Nobler JD, Rachlow JL, Shipley LA, Forbey JS. Near‐infrared spectroscopy aids ecological restoration by classifying variation of taxonomy and phenology of a native shrub. Restor Ecol 2021. [DOI: 10.1111/rec.13584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Brecken C. Robb
- Department of Biological Sciences Boise State University 1910 W University Drive Boise ID 83725 U.S.A
| | - Peter J. Olsoy
- Department of Biological Sciences Boise State University 1910 W University Drive Boise ID 83725 U.S.A
| | - Jessica J. Mitchell
- Department of Ecosystem and Conservation Science University of Montana 32 Campus Drive Missoula MT 59812 U.S.A
| | - T. Trevor Caughlin
- Department of Biological Sciences Boise State University 1910 W University Drive Boise ID 83725 U.S.A
| | - Donna M. Delparte
- Department of Geosciences Idaho State University 921 S 8th Avenue Pocatello ID 83209 U.S.A
| | - Stephanie J. Galla
- Department of Biological Sciences Boise State University 1910 W University Drive Boise ID 83725 U.S.A
| | | | - Jordan D. Nobler
- Department of Biological Sciences Boise State University 1910 W University Drive Boise ID 83725 U.S.A
| | - Janet L. Rachlow
- Department of Fish and Wildlife Sciences University of Idaho 875 Perimeter Drive Moscow ID 83844 U.S.A
| | - Lisa A. Shipley
- School of the Environment Washington State University 100 Dairy Road/1228 Webster Pullman WA 99164 U.S.A
| | - Jennifer S. Forbey
- Department of Biological Sciences Boise State University 1910 W University Drive Boise ID 83725 U.S.A
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6
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Melton AE, Beck J, Galla SJ, Jenkins J, Handley L, Kim M, Grimwood J, Schmutz J, Richardson BA, Serpe M, Novak S, Buerki S. A draft genome provides hypotheses on drought tolerance in a keystone plant species in Western North America threatened by climate change. Ecol Evol 2021; 11:15417-15429. [PMID: 34765187 PMCID: PMC8571618 DOI: 10.1002/ece3.8245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/12/2021] [Accepted: 10/01/2021] [Indexed: 11/17/2022] Open
Abstract
Climate change presents distinct ecological and physiological challenges to plants as extreme climate events become more common. Understanding how species have adapted to drought, especially ecologically important nonmodel organisms, will be crucial to elucidate potential biological pathways for drought adaptation and inform conservation strategies. To aid in genome-to-phenome research, a draft genome was assembled for a diploid individual of Artemisia tridentata subsp. tridentata, a threatened keystone shrub in western North America. While this taxon has few genetic resources available and genetic/genomics work has proven difficult due to genetic heterozygosity in the past, a draft genome was successfully assembled. Aquaporin (AQP) genes and their promoter sequences were mined from the draft genome to predict mechanisms regulating gene expression and generate hypotheses on key genes underpinning drought response. Fifty-one AQP genes were fully assembled within the draft genome. Promoter and phylogenetic analyses revealed putative duplicates of A. tridentata subsp. tridentata AQPs which have experienced differentiation in promoter elements, potentially supporting novel biological pathways. Comparison with nondrought-tolerant congener supports enrichments of AQP genes in this taxon during adaptation to drought stress. Differentiation of promoter elements revealed that paralogues of some genes have evolved to function in different pathways, highlighting these genes as potential candidates for future research and providing critical hypotheses for future genome-to-phenome work.
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Affiliation(s)
- Anthony E. Melton
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - James Beck
- Department of ComputingBoise State UniversityBoiseIdahoUSA
| | | | - Jerry Jenkins
- HudsonAlpha Institute for BiotechnologyHuntsvilleAlabamaUSA
| | - Lori Handley
- HudsonAlpha Institute for BiotechnologyHuntsvilleAlabamaUSA
| | - Min Kim
- HudsonAlpha Institute for BiotechnologyHuntsvilleAlabamaUSA
| | - Jane Grimwood
- HudsonAlpha Institute for BiotechnologyHuntsvilleAlabamaUSA
| | - Jeremy Schmutz
- HudsonAlpha Institute for BiotechnologyHuntsvilleAlabamaUSA
| | | | - Marcelo Serpe
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Stephen Novak
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Sven Buerki
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
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7
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Rohn TT, Beck JD, Galla SJ, Isho NF, Pollock TB, Suresh T, Kulkarni A, Sanghal T, Hayden EJ. Fragmentation of Apolipoprotein E4 is Required for Differential Expression of Inflammation and Activation Related Genes in Microglia Cells. ACTA ACUST UNITED AC 2021; 4. [PMID: 34693295 DOI: 10.23937/2643-4539/1710020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The apolipoprotein E4 (APOE4) allele represents the single greatest risk factor for late-onset Alzheimer's disease (AD) and accumulating evidence suggests that fragmentation with a toxic-gain of function may be a key molecular step associated with this risk. Recently, we demonstrated strong immunoreactivity of a 151 amino-terminal fragment of apoE4 (E4-fragment) within the nucleus of microglia in the human AD brain. In vitro, this fragment led to toxicity and activation of inflammatory processes in BV2 microglia cells. Additionally, a transcriptome analysis following exogenous treatment of BV2 microglia cells with this E4 fragment led to a > 2-fold up regulation of 1,608 genes, with many genes playing a role in inflammation and microglia activation. To extend these findings, we here report a similar transcriptome analysis in BV2 microglia cells following treatment with full-length ApoE4 (FL-ApoE4). The results indicated that full-length ApoE4 had a very small effect on gene expression compared to the fragment. Only 48 differentially expressed genes (DEGs) were identified (p < 0.05, and greater than 2-fold change). A gene ontology analysis of these DEGs indicated that they are not involved in inflammatory and activation processes, in contrast to the genes up regulated by the E4-fragment. In addition, genes that showed a negative fold-change upon FL-E4 treatment typically showed a strong positive fold-change upon treatment with the fragment (Pearson's r = -0.7). Taken together, these results support the hypothesis that a key step in the conversion of microglia to an activated phenotype is proteolytic cleavage of FL-ApoE4. Therefore, the neutralization of this amino-terminal fragment of ApoE4, specifically, may serve as an important therapeutic strategy in the treatment of AD.
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Affiliation(s)
- Troy T Rohn
- Department of Biological Sciences, Boise State University, USA
| | - James D Beck
- Department of Biological Sciences, Boise State University, USA
| | | | - Noail F Isho
- University of Washington School of Medicine, University of Washington, USA
| | | | - Tarun Suresh
- Department of Biological Sciences, Boise State University, USA
| | - Arni Kulkarni
- Department of Biological Sciences, Boise State University, USA
| | - Tanya Sanghal
- Department of Biological Sciences, Boise State University, USA
| | - Eric J Hayden
- Department of Biological Sciences, Boise State University, USA
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8
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Galla SJ, Brown L, Couch-Lewis Ngāi Tahu Te Hapū O Ngāti Wheke Ngāti Waewae Y, Cubrinovska I, Eason D, Gooley RM, Hamilton JA, Heath JA, Hauser SS, Latch EK, Matocq MD, Richardson A, Wold JR, Hogg CJ, Santure AW, Steeves TE. The relevance of pedigrees in the conservation genomics era. Mol Ecol 2021; 31:41-54. [PMID: 34553796 PMCID: PMC9298073 DOI: 10.1111/mec.16192] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/12/2021] [Accepted: 09/17/2021] [Indexed: 01/21/2023]
Abstract
Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long‐standing tools available to manage genetics—the pedigree—has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing to estimate relatedness, inbreeding, and genome‐wide functional diversity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic management. Genomic data can address pedigree pitfalls (e.g., founder relatedness, missing data, uncertainty), and in return robust pedigrees allow for more nuanced research design, including well‐informed sampling strategies and quantitative analyses (e.g., heritability, linkage) to better inform genomic inquiry. We further contend that building and maintaining pedigrees provides an opportunity to strengthen trusted relationships among conservation researchers, practitioners, Indigenous Peoples, and Local Communities.
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Affiliation(s)
- Stephanie J Galla
- Department of Biological Sciences, Boise State University, Boise, Idaho, USA.,School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
| | - Liz Brown
- New Zealand Department of Conservation, Twizel, Canterbury, New Zealand
| | | | - Ilina Cubrinovska
- School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
| | - Daryl Eason
- New Zealand Department of Conservation, Invercargill, Southland, New Zealand
| | - Rebecca M Gooley
- Smithsonian-Mason School of Conservation, Front Royal, Maryland, USA.,Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
| | - Jill A Hamilton
- Department of Biological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Julie A Heath
- Department of Biological Sciences, Boise State University, Boise, Idaho, USA
| | - Samantha S Hauser
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Emily K Latch
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science, Program in Ecology, Evolution and Conservation Biology, University of Nevada Reno, Reno, Nevada, USA
| | - Anne Richardson
- The Isaac Conservation and Wildlife Trust, Christchurch, Canterbury, New Zealand
| | - Jana R Wold
- School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, Auckland, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
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9
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Wold J, Koepfli KP, Galla SJ, Eccles D, Hogg CJ, Le Lec MF, Guhlin J, Santure AW, Steeves TE. Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern. Mol Ecol 2021; 30:5949-5965. [PMID: 34424587 PMCID: PMC9290615 DOI: 10.1111/mec.16141] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 07/28/2021] [Accepted: 08/18/2021] [Indexed: 12/28/2022]
Abstract
Structural variants (SVs) are large rearrangements (>50 bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, that is, variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While there are increasing opportunities to investigate functional genomic variation in threatened species via single nucleotide polymorphism (SNP) data sets, SVs remain understudied despite their potential influence on fitness traits of conservation interest. In this future-focused Opinion, we contend that characterizing SVs offers the conservation genomics community an exciting opportunity to complement SNP-based approaches to enhance species recovery. We also leverage the existing literature-predominantly in human health, agriculture and ecoevolutionary biology-to identify approaches for readily characterizing SVs and consider how integrating these into the conservation genomics toolbox may transform the way we manage some of the world's most threatened species.
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Affiliation(s)
- Jana Wold
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, Front Royal, Virginia, USA.,Centre for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA.,Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russia
| | - Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biological Sciences, Boise State University, Boise, Idaho, USA
| | - David Eccles
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Marissa F Le Lec
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand
| | - Joseph Guhlin
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand.,Genomics Aotearoa, Dunedin, Otago, New Zealand
| | - Anna W Santure
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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10
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Wojahn JMA, Galla SJ, Melton AE, Buerki S. G2PMineR: A Genome to Phenome Literature Review Approach. Genes (Basel) 2021; 12:genes12020293. [PMID: 33672535 PMCID: PMC7923769 DOI: 10.3390/genes12020293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 11/21/2022] Open
Abstract
There is a gap in the conceptual framework linking genes to phenotypes (G2P) for non-model organisms, as most non-model organisms do not yet have genomic resources readily available. To address this, researchers often perform literature reviews to understand G2P linkages by curating a list of likely gene candidates, hinging upon other studies already conducted in closely related systems. Sifting through hundreds to thousands of articles is a cumbersome task that slows down the scientific process and may introduce bias into a study. To fill this gap, we created G2PMineR, a free and open source literature mining tool developed specifically for G2P research. This R package uses automation to make the G2P review process efficient and unbiased, while also generating hypothesized associations between genes and phenotypes within a taxonomical framework. We applied the package to a literature review for drought-tolerance in plants. The analysis provides biologically meaningful results within the known framework of drought tolerance in plants. Overall, the package is useful for conducting literature reviews for genome to phenome projects, and also has broad appeal to scientists investigating a wide range of study systems as it can conduct analyses under the auspices of three different kingdoms (Plantae, Animalia, and Fungi).
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11
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Galla SJ, Moraga R, Brown L, Cleland S, Hoeppner MP, Maloney RF, Richardson A, Slater L, Santure AW, Steeves TE. 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. Evol Appl 2020; 13:991-1008. [PMID: 32431748 PMCID: PMC7232769 DOI: 10.1111/eva.12916] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 12/27/2019] [Accepted: 01/02/2020] [Indexed: 12/18/2022] Open
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: kakī/black stilt (Himantopus novaezelandiae) and kākāriki 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.
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Affiliation(s)
- Stephanie J. Galla
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | - Roger Moraga
- Tea Break Bioinformatics, LtdPalmerston NorthNew Zealand
| | - Liz Brown
- New Zealand Department of ConservationTwizelNew Zealand
| | | | - Marc P. Hoeppner
- Institute for Clinical Molecular BiologyChristian‐Albrechts‐University KielKielGermany
| | | | - Anne Richardson
- The Isaac Conservation and Wildlife TrustChristchurchNew Zealand
| | - Lyndon Slater
- New Zealand Department of ConservationRangioraNew Zealand
| | - Anna W. Santure
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Tammy E. Steeves
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
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Galla SJ, Buckley TR, Elshire R, Hale ML, Knapp M, McCallum J, Moraga R, Santure AW, Wilcox P, Steeves TE. Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances. Mol Ecol 2016; 25:5267-5281. [PMID: 27641156 DOI: 10.1111/mec.13837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 02/06/2023]
Abstract
Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here, we demonstrate how building strong relationships between conservation geneticists and primary industry scientists is leading to mutually-beneficial outcomes for both disciplines. Based on our collective experience as collaborative New Zealand-based scientists, we also provide insight for forging these cross-sector relationships.
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Affiliation(s)
- Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand.
| | - Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland Mail Centre, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Rob Elshire
- The Elshire Group, Ltd., 52 Victoria Avenue, Palmerston North, 4410, New Zealand
| | - Marie L Hale
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago, P.O. Box 913, Dunedin, 9054, New Zealand
| | - John McCallum
- Breeding and Genomics, New Zealand Institute for Plant and Food Research, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Roger Moraga
- AgResearch, Ruakura Research Centre, Bisley Road, Private Bag 3115, Hamilton, 3240, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Phillip Wilcox
- Department of Mathematics and Statistics, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin, 9054, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
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Leenen FH, Galla SJ, Geyskes GG, Murdaugh HV, Shapiro AP. Effects of hemodialysis and saline loading on body fluid compartments, plasma renin activity and blood pressure in patients on chronic hemodialysis. Nephron Clin Pract 1977; 18:93-100. [PMID: 857177 DOI: 10.1159/000180782] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The influence of one hemodialysis session and of subsequent loading by 1.5-2 liters N saline on blood pressure, PRA and body fluid compartments was assessed in seven patients with chronic renal failure on maintenance hemodialysis. Dialysis caused only slight decreases in plasma volume, ECV and in TEBS. Lying mean blood pressure by 5-10 mm Hg and PRA increased by 30%. Saline loading resulted in a significant increase in plasma volume by 0.4 liters and in blood pressure by 10-5 mm Hg, but in a decrease in PRA by 40%. The changes in mean blood pressure correlated positively with the changes in plasma volume, and negatively with the changes in PRA. It is concluded that the renin-angiotensin system in patients on chronic hemodialysis still functions as one of the adjustment mechanisms for the circulatory homeostasis, when challenged by volume loss or volume and sodium loading.
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Leenen FH, Galla SJ, Redmond DP, Vagnucci AH, McDonald RH, Shapiro AP. Relationships of the renin-angiotensin-aldosterone system and sodium balance to blood pressure regulation in chronic renal failure of polycystic kidney disease. Metabolism 1975; 24:589-603. [PMID: 1128229 DOI: 10.1016/0026-0495(75)90139-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In 5 patients with polycystic kidney disease and creatinine clearances ranging from 4 to 40 ml/min, relationships between changes in blood pressure, sodium balance, body fluid compartments, plasma renin activity (PRA), urinary aldosterone excretion, and plasma aldosterone concentrations were studied during periods of low, medium, and high sodium intake. Total body water (TBW), total exchangeable body sodium (TEBS), and extracellular volume (ECV) were measured by isotope dilution techniques, plasma volume with Evan's blue dye, and PRA and aldosterone by radioimmunoassay. Low sodium intake reduced kidney function, blood pressure, and serum sodium, while PRA reached its highest levels. Subsequent increases in sodium intake improved kidney function and increased blood pressure. Plasma volume increased slightly and ECV markedly, while PRA dropped to 15 percent of the value noted after the low sodium intake. TBW and TEBS showed inconsistent changes. Aldosterone changes correlated closely with PRA. Blood pressure showed a negative correlation with PRA, but a positive one with body weight and cumulative sodium balance, and with plasma and extracellular volumes.it is suggested that whereas renin and aldosterone are involved in the maintenance of circulatory homeostasis during sodium loss, sodium retention causes an increase in blood pressure by concomitant changes in body fluids.
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Galla SJ. Techniques of anesthesia. Fed Proc 1969; 28:1404-9. [PMID: 5798888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Takaori M, Safar P, Galla SJ. Comparison of hydroxyethyl starch with plasma and dextrans in severe haemodilution. Can Anaesth Soc J 1968; 15:347-56. [PMID: 5661386 DOI: 10.1007/bf03006959] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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