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Adomako K, Sovi S, Kyei B, Hamidu JA, Olympio OS, Aggrey SE. Phenotypic characterization and analysis of genetic diversity between commercial crossbred and indigenous chickens from three different agro-ecological zones using DArT-Seq technology. PLoS One 2024; 19:e0297643. [PMID: 38696379 PMCID: PMC11065228 DOI: 10.1371/journal.pone.0297643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 01/05/2024] [Indexed: 05/04/2024] Open
Abstract
Indigenous and were used to study genetic diversity and population structure analyses. Polymorphism information content (PIC) values ranged from 0.0 to 0.5, with 21,285 SNP markers (35%) being in the lowest PIC value range (0 to 0.15) while 13,511 (commercial chickens have developed unique adaptations to their environments, which may include nutrition, pathogens, and thermal stress. Besides, environmental pressures and artificial selection have generated significant genome-wide divergence in chickens, as those selection pressures contribute a considerable evolutionary force to phenotypic and genotypic differentiation. Herein, we determined genomic diversity of indigenous chickens from semi-deciduous rainforest (SDR), coastal savannah (CS) and Guinea savannah (GS) agro-ecological zones (AEZs) in Ghana and commercial crossbreds (CC) reared at the Kwame Nkrumah University of Science and Technology (KNUST). We generated SNP markers from 82 chickens (62 indigenous chicken ecotypes and 26 commercial crossbred ecotype) using DArT-Seq technology. A total of 85,396 SNP markers were generated and after filtering the data, 58,353 markers 21%) were in the highest PIC value range (0.45 to 0.50). The CC were more genetically diverse than the indigenous birds, with the highest expected heterozygosity value of 0.220. Between the commercial crossbreds population and the indigenous ecotypes, pairwise FST values were estimated to be 0.105 between CS, 0.096 between SDF, and 0.133 between GS. Furthermore, PCA analysis showed that the CC, SDF and GS chickens clustered together and are genetically distant from the commercial crossbred. We herein show that chickens from the AEZs studied can be considered as one population. However, due the abundance of agro-byproducts in the SDR compared to the CS and GS, chickens from the SDR AEZ had better growth compared to their counterparts. It is suggested that the genetic diversity within the local ecotypes could form the basis for genetic improvement.
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Affiliation(s)
- Kwaku Adomako
- Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Selorm Sovi
- Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Nutrigenomics Laboratory, Department of Poultry Science, University of Georgia, Athens, Georgia, United States of America
| | - Bismark Kyei
- Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jacob Alhassan Hamidu
- Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Oscar Simon Olympio
- Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Samuel E. Aggrey
- Nutrigenomics Laboratory, Department of Poultry Science, University of Georgia, Athens, Georgia, United States of America
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2
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Sopniewski J, Catullo RA. Estimates of heterozygosity from single nucleotide polymorphism markers are context-dependent and often wrong. Mol Ecol Resour 2024; 24:e13947. [PMID: 38433491 DOI: 10.1111/1755-0998.13947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/18/2024] [Accepted: 02/21/2024] [Indexed: 03/05/2024]
Abstract
Genetic diversity is frequently described using heterozygosity, particularly in a conservation context. Often, it is estimated using single nucleotide polymorphisms (SNPs); however, it has been shown that heterozygosity values calculated from SNPs can be biased by both study design and filtering parameters. Though solutions have been proposed to address these issues, our own work has found them to be inadequate in some circumstances. Here, we aimed to improve the reliability and comparability of heterozygosity estimates, specifically by investigating how sample size and missing data thresholds influenced the calculation of autosomal heterozygosity (heterozygosity calculated from across the genome, i.e. fixed and variable sites). We also explored how the standard practice of tri- and tetra-allelic site exclusion could bias heterozygosity estimates and influence eventual conclusions relating to genetic diversity. Across three distinct taxa (a frog, Litoria rubella; a tree, Eucalyptus microcarpa; and a grasshopper, Keyacris scurra), we found heterozygosity estimates to be meaningfully affected by sample size and missing data thresholds, partly due to the exclusion of tri- and tetra-allelic sites. These biases were inconsistent both between species and populations, with more diverse populations tending to have their estimates more severely affected, thus having potential to dramatically alter interpretations of genetic diversity. We propose a modified framework for calculating heterozygosity that reduces bias and improves the utility of heterozygosity as a measure of genetic diversity, whilst also highlighting the need for existing population genetic pipelines to be adjusted such that tri- and tetra-allelic sites be included in calculations.
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Affiliation(s)
- Jarrod Sopniewski
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Renee A Catullo
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, Australia
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3
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Schmidt TL, Thia JA, Hoffmann AA. How Can Genomics Help or Hinder Wildlife Conservation? Annu Rev Anim Biosci 2024; 12:45-68. [PMID: 37788416 DOI: 10.1146/annurev-animal-021022-051810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Genomic data are becoming increasingly affordable and easy to collect, and new tools for their analysis are appearing rapidly. Conservation biologists are interested in using this information to assist in management and planning but are typically limited financially and by the lack of genomic resources available for non-model taxa. It is therefore important to be aware of the pitfalls as well as the benefits of applying genomic approaches. Here, we highlight recent methods aimed at standardizing population assessments of genetic variation, inbreeding, and forms of genetic load and methods that help identify past and ongoing patterns of genetic interchange between populations, including those subjected to recent disturbance. We emphasize challenges in applying some of these methods and the need for adequate bioinformatic support. We also consider the promises and challenges of applying genomic approaches to understand adaptive changes in natural populations to predict their future adaptive capacity.
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Affiliation(s)
- Thomas L Schmidt
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
| | - Joshua A Thia
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
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4
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Ghildiyal K, Nayak SS, Rajawat D, Sharma A, Chhotaray S, Bhushan B, Dutt T, Panigrahi M. Genomic insights into the conservation of wild and domestic animal diversity: A review. Gene 2023; 886:147719. [PMID: 37597708 DOI: 10.1016/j.gene.2023.147719] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/20/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
Due to environmental change and anthropogenic activities, global biodiversity has suffered an unprecedented loss, and the world is now heading toward the sixth mass extinction event. This urges the need to step up our efforts to promote the sustainable use of animal genetic resources and plan effective strategies for their conservation. Although habitat preservation and restoration are the primary means of conserving biodiversity, genomic technologies offer a variety of novel tools for identifying biodiversity hotspots and thus, support conservation efforts. Conservation genomics is a broad area of science that encompasses the application of genomic data from thousands or tens of thousands of genome-wide markers to address important conservation biology concerns. Genomic approaches have revolutionized the way we understand and manage animal populations, providing tools to identify and preserve unique genetic variants and alleles responsible for adaptive genetic variation, reducing the deleterious consequences of inbreeding, and increasing the adaptive potential of threatened species. The advancement of genomic technologies, particularly comparative genomic approaches, and the increased accessibility of genomic resources in the form of genome-enabled taxa for non-model organisms, provides a distinct advantage in defining conservation units over traditional genetics approaches. The objective of this review is to provide an exhaustive overview of the concept of conservation genomics, discuss the rationale behind the transition from conservation genetics to genomic approaches, and emphasize the potential applications of genomic techniques for conservation purposes. We also highlight interesting case studies in both livestock and wildlife species where genomic techniques have been used to accomplish conservation goals. Finally, we address some challenges and future perspectives in this field.
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Affiliation(s)
- Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Supriya Chhotaray
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
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5
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Li C, Xiao H, Zhang X, Lin H, Elmer KR, Zhao J. Deep genome-wide divergences among species in White Cloud Mountain minnow Tanichthys albonubes (Cypriniformes: Tanichthyidae) complex: Conservation and species management implications. Mol Phylogenet Evol 2023; 182:107734. [PMID: 36804428 DOI: 10.1016/j.ympev.2023.107734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
Abstract
Identifying cryptic species is important for the assessments of biodiversity. Further, untangling mechanisms underlying the origins of cryptic species can facilitate our understanding of evolutionary processes. Advancements in genomic approaches for non-model systems have offered unprecedented opportunities to investigate these areas. The White Cloud Mountain minnow (Tanichthys albonubes) is a popular freshwater pet fish worldwide but its wild populations in China are critically endangered. Recent research based on a few molecular markers suggested that this species in fact comprised seven cryptic species, of which six were previously unknown. Here, we tested six of these cryptic species and quantified genomic interspecific divergences between species in the T. albonubes complex by analyzing genome-wide restriction site-associated DNA sequencing (RADseq) data generated from 189 individuals sampled from seven populations (including an outgroup congeneric species, T. micagemmae). We found that six cryptic species previously suggested were well supported by RADseq data. The genetic diversity of each species in the T. albonubes complex was low compared with T. micagemmae and the contemporary effective population sizes (Ne) of each cryptic species were small. Phylogenetic analysis showed seven clades with high support values confirmed with Neighbor-Net trees. The pairwise divergences between species in T. albonubes complex were deep and the highly differentiated loci were evenly distributed across the genome. We proposed that the divergence level of T. albonubes complex is at a late stage of cryptic speciation and lacking gene flow. Our findings provide new insights into cryptic speciation and have important implications for conservation and species management of T. albonubes complex.
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Affiliation(s)
- Chao Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China; Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Han Xiao
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Xiuxia Zhang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Hungdu Lin
- The Affiliated School of National Tainan First Senior High School, Tainan, Taiwan
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jun Zhao
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China.
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6
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Butterworth NJ, Wallman JF, Johnston NP, Dawson BM, Sharp-Heward J, McGaughran A. The blowfly Chrysomya latifrons inhabits fragmented rainforests, but shows no population structure. Oecologia 2023; 201:703-719. [PMID: 36773072 PMCID: PMC10038970 DOI: 10.1007/s00442-023-05333-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/27/2023] [Indexed: 02/12/2023]
Abstract
Climate change and deforestation are causing rainforests to become increasingly fragmented, placing them at heightened risk of biodiversity loss. Invertebrates constitute the greatest proportion of this biodiversity, yet we lack basic knowledge of their population structure and ecology. There is a compelling need to develop our understanding of the population dynamics of a wide range of rainforest invertebrates so that we can begin to understand how rainforest fragments are connected, and how they will cope with future habitat fragmentation and climate change. Blowflies are an ideal candidate for such research because they are widespread, abundant, and can be easily collected within rainforests. We genotyped 188 blowflies (Chrysomya latifrons) from 15 isolated rainforests and found high levels of gene flow, a lack of genetic structure between rainforests, and low genetic diversity - suggesting the presence of a single large genetically depauperate population. This highlights that: (1) the blowfly Ch. latifrons inhabits a ~ 1000 km stretch of Australian rainforests, where it plays an important role as a nutrient recycler; (2) strongly dispersing flies can migrate between and connect isolated rainforests, likely carrying pollen, parasites, phoronts, and pathogens along with them; and (3) widely dispersing and abundant insects can nevertheless be genetically depauperate. There is an urgent need to better understand the relationships between habitat fragmentation, genetic diversity, and adaptive potential-especially for poorly dispersing rainforest-restricted insects, as many of these may be particularly fragmented and at highest risk of local extinction.
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Affiliation(s)
- Nathan J Butterworth
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia.
- Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
| | - James F Wallman
- Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
- Centre for Sustainable Ecosystem Solutions, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Nikolas P Johnston
- Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
- Department of Ecology and Biogeography, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, 87-100, Toruń, Poland
- Centre for Sustainable Ecosystem Solutions, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Blake M Dawson
- Centre for Sustainable Ecosystem Solutions, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Joshua Sharp-Heward
- Centre for Sustainable Ecosystem Solutions, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Angela McGaughran
- Te Aka Mātuatua - School of Science, University of Waikato, Private Bag 3105, Hamilton, 3240, New Zealand
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7
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Abstract
Insects constitute vital components of ecosystems. There is alarming evidence for global declines in insect species diversity, abundance, and biomass caused by anthropogenic drivers such as habitat degradation or loss, agricultural practices, climate change, and environmental pollution. This raises important concerns about human food security and ecosystem functionality and calls for more research to assess insect population trends and identify threatened species and the causes of declines to inform conservation strategies. Analysis of genetic diversity is a powerful tool to address these goals, but so far animal conservation genetics research has focused strongly on endangered vertebrates, devoting less attention to invertebrates, such as insects, that constitute most biodiversity. Insects' shorter generation times and larger population sizes likely necessitate different analytical methods and management strategies. The availability of high-quality reference genome assemblies enables population genomics to address several key issues. These include precise inference of past demographic fluctuations and recent declines, measurement of genetic load levels, delineation of evolutionarily significant units and cryptic species, and analysis of genetic adaptation to stressors. This enables identification of populations that are particularly vulnerable to future threats, considering their potential to adapt and evolve. We review the application of population genomics to insect conservation and the outlook for averting insect declines.
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Affiliation(s)
- Matthew T Webster
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
| | - Alexis Beaurepaire
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Agroscope, Swiss Bee Research Centre, Bern, Switzerland
| | - Peter Neumann
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Agroscope, Swiss Bee Research Centre, Bern, Switzerland
| | - Eckart Stolle
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
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8
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Xu X, Schmidt TL, Liang J, Ridland PM, Chung J, Yang Q, Jasper M, Umina PA, Liu W, Hoffmann AA. Genome‐wide
SNPs
of vegetable leafminer,
Liriomyza sativae
: insights into the recent Australian invasion. Evol Appl 2022; 15:1129-1140. [PMID: 35899255 PMCID: PMC9309458 DOI: 10.1111/eva.13430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 05/26/2022] [Accepted: 05/29/2022] [Indexed: 11/28/2022] Open
Abstract
Liriomyza sativae, the vegetable leafminer, is an important agricultural pest originally from the Americas, which has now colonized all continents except Antarctica. In 2015, L. sativae arrived on the Australian mainland and established on the Cape York Peninsula in the northeast of the country near the Torres Strait, which provides a possible pathway for pests to enter Australia and evade biosecurity efforts. Here, we assessed genetic variation in L. sativae based on genome‐wide single nucleotide polymorphisms (SNPs) generated by double digest restriction‐site‐associated DNA sequencing (ddRAD‐seq), aiming to uncover the potential origin(s) of this pest in Australia and contribute to reconstructing its global invasion history. Our fineRADstructure results and principal component analysis suggest Australian mainland populations were genetically close to populations from the Torres Strait, whereas populations from Asia, Africa, and Papua New Guinea (PNG) were more distantly related. Hawaiian populations were genetically distinct from all other populations of L. sativae included in our study. Admixture analyses further revealed that L. sativae from the Torres Strait may have genetic variation originating from multiple sources including Indonesia and PNG, and which has now spread to the Australian mainland. The L. sativae lineages from Asia and Africa appear closely related. Isolation‐by‐distance (IBD) was found at a broad global scale, but not within small regions, suggesting that human‐mediated factors likely contribute to the local spread of this pest. Overall, our findings suggest that an exotic Liriomyza pest invaded Australia through the Indo‐Papuan conduit, highlighting the importance of biosecurity programs aimed at restricting the movement of pests and diseases through this corridor.
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Affiliation(s)
- Xuefen Xu
- Bio21 Institute, School of BioSciences The University of Melbourne Parkville Victoria Australia
| | - Tom L. Schmidt
- Bio21 Institute, School of BioSciences The University of Melbourne Parkville Victoria Australia
| | - Jiaxin Liang
- Bio21 Institute, School of BioSciences The University of Melbourne Parkville Victoria Australia
| | - Peter M. Ridland
- Bio21 Institute, School of BioSciences The University of Melbourne Parkville Victoria Australia
| | - Jessica Chung
- Bio21 Institute, School of BioSciences The University of Melbourne Parkville Victoria Australia
| | - Qiong Yang
- Bio21 Institute, School of BioSciences The University of Melbourne Parkville Victoria Australia
| | - Moshe Jasper
- Bio21 Institute, School of BioSciences The University of Melbourne Parkville Victoria Australia
| | - Paul A. Umina
- Bio21 Institute, School of BioSciences The University of Melbourne Parkville Victoria Australia
- Cesar Australia Brunswick Victoria Australia
| | - Wanxue Liu
- Chinese Academy of Agricultural Sciences Beijing China
| | - Ary A. Hoffmann
- Bio21 Institute, School of BioSciences The University of Melbourne Parkville Victoria Australia
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9
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Kearney MR, Jasper ME, White VL, Aitkenhead IJ, Blacket MJ, Kong JD, Chown SL, Hoffmann AA. Parthenogenesis without costs in a grasshopper with hybrid origins. Science 2022; 376:1110-1114. [PMID: 35653484 DOI: 10.1126/science.abm1072] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The rarity of parthenogenetic species is typically attributed to the reduced genetic variability that accompanies the absence of sex, yet natural parthenogens can be surprisingly successful. Ecological success is often proposed to derive from hybridization through enhanced genetic diversity from repetitive origins or enhanced phenotypic breadth from heterosis. Here, we tested and rejected both hypotheses in a classic parthenogen, the diploid grasshopper Warramaba virgo. Genetic data revealed a single hybrid mating origin at least 0.25 million years ago, and comparative analyses of 14 physiological and life history traits showed no evidence for altered fitness relative to its sexual progenitors. Our findings imply that the rarity of parthenogenesis is due to constraints on origin rather than to rapid extinction.
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Affiliation(s)
- Michael R Kearney
- School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Moshe E Jasper
- Bio21 Institute, School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Vanessa L White
- School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Ian J Aitkenhead
- School of Biological Sciences, Monash University, Victoria 3800, Australia
| | - Mark J Blacket
- School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Jacinta D Kong
- School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Steven L Chown
- School of Biological Sciences, Monash University, Victoria 3800, Australia
| | - Ary A Hoffmann
- Bio21 Institute, School of BioSciences, The University of Melbourne, Victoria 3010, Australia
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10
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Willi Y, Kristensen TN, Sgrò CM, Weeks AR, Ørsted M, Hoffmann AA. Conservation genetics as a management tool: The five best-supported paradigms to assist the management of threatened species. Proc Natl Acad Sci U S A 2022; 119:e2105076119. [PMID: 34930821 PMCID: PMC8740573 DOI: 10.1073/pnas.2105076119] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
About 50 y ago, Crow and Kimura [An Introduction to Population Genetics Theory (1970)] and Ohta and Kimura [Genet. Res. 22, 201-204 (1973)] laid the foundations of conservation genetics by predicting the relationship between population size and genetic marker diversity. This work sparked an enormous research effort investigating the importance of population dynamics, in particular small population size, for population mean performance, population viability, and evolutionary potential. In light of a recent perspective [J. C. Teixeira, C. D. Huber, Proc. Natl. Acad. Sci. U.S.A. 118, 10 (2021)] that challenges some fundamental assumptions in conservation genetics, it is timely to summarize what the field has achieved, what robust patterns have emerged, and worthwhile future research directions. We consider theory and methodological breakthroughs that have helped management, and we outline some fundamental and applied challenges for conservation genetics.
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Affiliation(s)
- Yvonne Willi
- Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Torsten N Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
| | - Carla M Sgrò
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Andrew R Weeks
- School of BioSciences, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
- Cesar Australia, Brunswick, VIC 3056, Australia
| | - Michael Ørsted
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
- Department of Biology, Aarhus University, Aarhus 8000, Denmark
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia;
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11
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Schmidt TL, Jasper M, Weeks AR, Hoffmann AA. Unbiased population heterozygosity estimates from genome‐wide sequence data. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13659] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Thomas L. Schmidt
- School of BioSciences Bio21 InstituteUniversity of Melbourne Parkville VIC Australia
| | - Moshe‐Elijah Jasper
- School of BioSciences Bio21 InstituteUniversity of Melbourne Parkville VIC Australia
| | - Andrew R Weeks
- School of BioSciences Bio21 InstituteUniversity of Melbourne Parkville VIC Australia
- cesar Pty Ltd Parkville VIC Australia
| | - Ary A Hoffmann
- School of BioSciences Bio21 InstituteUniversity of Melbourne Parkville VIC Australia
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