1
|
History cooling events contributed to the endangered status of Pseudotsuga brevifolia endemic to limestone habitats. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
|
2
|
Lott MJ, Wright BR, Neaves LE, Frankham GJ, Dennison S, Eldridge MDB, Potter S, Alquezar-Planas DE, Hogg CJ, Belov K, Johnson RN. Future-proofing the koala: synergising genomic and environmental data for effective species management. Mol Ecol 2022; 31:3035-3055. [PMID: 35344635 DOI: 10.1111/mec.16446] [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: 11/19/2020] [Revised: 02/19/2022] [Accepted: 03/04/2022] [Indexed: 11/30/2022]
Abstract
Climatic and evolutionary processes are inextricably linked to conservation. Avoiding extinction in rapidly changing environments often depends upon a species' capacity to adapt in the face of extreme selective pressures. Here, we employed exon capture and high-throughput next-generation sequencing to investigate the mechanisms underlying population structure and adaptive genetic variation in the koala (Phascolarctos cinereus), an iconic Australian marsupial that represents a unique conservation challenge because it is not uniformly threatened across its range. An examination of 250 specimens representing 91 wild source locations revealed that five major genetic clusters currently exist on a continental scale. The initial divergence of these clusters appears to have been concordant with the Mid-Brunhes Transition (∼ 430-300 kya), a major climatic reorganization that increased the amplitude of Pleistocene glacial-interglacial cycles. While signatures of polygenic selection and environmental adaptation were detected, strong evidence for repeated, climate-associated range contractions and demographic bottleneck events suggests that geographically isolated refugia may have played a more significant role in the survival of the koala through the Pleistocene glaciation than in situ adaptation. Consequently, the conservation of genome-wide genetic variation must be aligned with the protection of core koala habitat to increase the resilience of threatened populations to accelerating anthropogenic threats. Finally, we propose that the five major genetic clusters identified in this study should be accounted for in future koala conservation efforts (e.g. guiding translocations), as existing management divisions in the states of Queensland and New South Wales do not reflect historic or contemporary population structure.
Collapse
Affiliation(s)
- Matthew J Lott
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia
| | - Belinda R Wright
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia.,School of Life and Environmental Sciences, the University of Sydney, 2006, New South Wales, Australia.,Sydney School of Veterinary Sciences, Faculty of Science, the University of Sydney, 2006, New South Wales, Australia
| | - Linda E Neaves
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia.,Fenner School of Environment and Society, the Australian National University, Canberra, Australian Capital Territory, 2600, Australia
| | - Greta J Frankham
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia
| | - Siobhan Dennison
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia
| | - Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia
| | - Sally Potter
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia.,Division of Ecology & Evolution, Research School of Biology, the Australian National University, Australian Capital Territory, Canberra, 2600, Australia
| | - David E Alquezar-Planas
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, the University of Sydney, 2006, New South Wales, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, the University of Sydney, 2006, New South Wales, Australia
| | - Rebecca N Johnson
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia.,National Museum of Natural History, District of Columbia, Washington, 20560, United States
| |
Collapse
|
3
|
Rayne A, Blair S, Dale M, Flack B, Hollows J, Moraga R, Parata RN, Rupene M, Tamati‐Elliffe P, Wehi PM, Wylie MJ, Steeves TE. Weaving place‐based knowledge for culturally significant species in the age of genomics: Looking to the past to navigate the future. Evol Appl 2022; 15:751-772. [PMID: 35603033 PMCID: PMC9108313 DOI: 10.1111/eva.13367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 02/16/2022] [Accepted: 02/24/2022] [Indexed: 11/28/2022] Open
Abstract
Relationships with place provide critical context for characterizing biocultural diversity. Yet, genetic and genomic studies are rarely informed by Indigenous or local knowledge, processes, and practices, including the movement of culturally significant species. Here, we show how place‐based knowledge can better reveal the biocultural complexities of genetic or genomic data derived from culturally significant species. As a case study, we focus on culturally significant southern freshwater kōura (crayfish) in Aotearoa me Te Waipounamu (New Zealand, herein Aotearoa NZ). Our results, based on genotyping‐by‐sequencing markers, reveal strong population genetic structure along with signatures of population admixture in 19 genetically depauperate populations across the east coast of Te Waipounamu. Environment association and differentiation analyses for local adaptation also indicate a role for hydroclimatic variables—including temperature, precipitation, and water flow regimes—in shaping local adaptation in kōura. Through trusted partnerships between community and researchers, weaving genomic markers with place‐based knowledge has both provided invaluable context for the interpretation of data and created opportunities to reconnect people and place. We envisage such trusted partnerships guiding future genomic research for culturally significant species in Aotearoa NZ and beyond.
Collapse
Affiliation(s)
- Aisling Rayne
- University of Canterbury School of Biological Sciences Christchurch New Zealand
| | | | - Matthew Dale
- Waterscape Connections Ltd Dunedin New Zealand
- Te Rūnanga o Ngāi Tahu Dunedin New Zealand
| | - Brendan Flack
- Kāti Huirapa Rūnaka ki Puketeraki Karitane New Zealand
| | | | - Roger Moraga
- Tea Break Bioinformatics Ltd Palmerston North New Zealand
| | | | - Makarini Rupene
- University of Canterbury Ngāi Tahu Research Centre Christchurch New Zealand
- Environment Canterbury Christchurch New Zealand
| | | | - Priscilla M Wehi
- University of Otago, Centre for Sustainability Dunedin New Zealand
| | - Matthew J Wylie
- Kāti Huirapa Rūnaka ki Puketeraki Karitane New Zealand
- The New Zealand Institute for Plant and Food Research Limited Nelson New Zealand
| | - Tammy E Steeves
- University of Canterbury School of Biological Sciences Christchurch New Zealand
| |
Collapse
|
4
|
Revealing the Genetic Structure and Differentiation in Endangered Pinus bungeana by Genome-Wide SNP Markers. FORESTS 2022. [DOI: 10.3390/f13020326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Understanding the genetic variation and differentiation of natural populations is essential for their protection, specifically if the species status is endangered as with Pinus bungeana. Here, we used 346,840 high density and strong specificity SNP loci to carry out genetic analyses (i.e., genetic diversity, genetic structure, phylogeny, and geographical differentiation) on 52 P. bungeana individuals from 5 populations (4 natural and one artificial) representing the main regions of the species distribution in China. Genetic diversity assessment indicated a trend of genetic diversity gradual decrease from west to east across the species distribution areas. Population genetic structure, PCA and phylogenetic analyses consistently indicated that populations in the central and eastern regions were clustered together, while those from the western regions were separated. Mantel test values indicated the presence of geographic isolation among populations, an important factor contributing to the observed genetic differentiation. The maximum likelihood tree and potential migration events inferred from TreeMix analysis indicated the presence of historical genetic exchanges between the west of Qinling Mountains and the Lvliang Mountains populations. Based on the generated genetic information, in situ and ex situ conservation strategies for P.bungeana germplasm resources are proposed, these strategies could be valuable for the conservation, protection and genetic improvement of this endangered species.
Collapse
|
5
|
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] [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.
Collapse
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
| |
Collapse
|
6
|
Genomic Approaches for Conservation Management in Australia under Climate Change. Life (Basel) 2021; 11:life11070653. [PMID: 34357024 PMCID: PMC8304512 DOI: 10.3390/life11070653] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 12/28/2022] Open
Abstract
Conservation genetics has informed threatened species management for several decades. With the advent of advanced DNA sequencing technologies in recent years, it is now possible to monitor and manage threatened populations with even greater precision. Climate change presents a number of threats and challenges, but new genomics data and analytical approaches provide opportunities to identify critical evolutionary processes of relevance to genetic management under climate change. Here, we discuss the applications of such approaches for threatened species management in Australia in the context of climate change, identifying methods of facilitating viability and resilience in the face of extreme environmental stress. Using genomic approaches, conservation management practices such as translocation, targeted gene flow, and gene-editing can now be performed with the express intention of facilitating adaptation to current and projected climate change scenarios in vulnerable species, thus reducing extinction risk and ensuring the protection of our unique biodiversity for future generations. We discuss the current barriers to implementing conservation genomic projects and the efforts being made to overcome them, including communication between researchers and managers to improve the relevance and applicability of genomic studies. We present novel approaches for facilitating adaptive capacity and accelerating natural selection in species to encourage resilience in the face of climate change.
Collapse
|
7
|
Evolutionary history and genetic connectivity across highly fragmented populations of an endangered daisy. Heredity (Edinb) 2021; 126:846-858. [PMID: 33608651 PMCID: PMC8102499 DOI: 10.1038/s41437-021-00413-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 01/31/2023] Open
Abstract
Conservation management can be aided by knowledge of genetic diversity and evolutionary history, so that ecological and evolutionary processes can be preserved. The Button Wrinklewort daisy (Rutidosis leptorrhynchoides) was a common component of grassy ecosystems in south-eastern Australia. It is now endangered due to extensive habitat loss and the impacts of livestock grazing, and is currently restricted to a few small populations in two regions >500 km apart, one in Victoria, the other in the Australian Capital Territory and nearby New South Wales (ACT/NSW). Using a genome-wide SNP dataset, we assessed patterns of genetic structure and genetic differentiation of 12 natural diploid populations. We estimated intrapopulation genetic diversity to scope sources for genetic management. Bayesian clustering and principal coordinate analyses showed strong population genetic differentiation between the two regions, and substantial substructure within ACT/NSW. A coalescent tree-building approach implemented in SNAPP indicated evolutionary divergence between the two distant regions. Among the populations screened, the last two known remaining Victorian populations had the highest genetic diversity, despite having among the lowest recent census sizes. A maximum likelihood population tree method implemented in TreeMix suggested little or no recent gene flow except potentially between very close neighbours. Populations that were more genetically distinctive had lower genetic diversity, suggesting that drift in isolation is likely driving population differentiation though loss of diversity, hence re-establishing gene flow among them is desirable. These results provide background knowledge for evidence-based conservation and support genetic rescue within and between regions to elevate genetic diversity and alleviate inbreeding.
Collapse
|
8
|
Zilko JP, Harley D, Hansen B, Pavlova A, Sunnucks P. Accounting for cryptic population substructure enhances detection of inbreeding depression with genomic inbreeding coefficients: an example from a critically endangered marsupial. Mol Ecol 2020; 29:2978-2993. [PMID: 32627274 DOI: 10.1111/mec.15540] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 05/16/2020] [Accepted: 06/18/2020] [Indexed: 12/21/2022]
Abstract
Characterizing inbreeding depression in wildlife populations can be critical to their conservation. Coefficients of individual inbreeding can be estimated from genome-wide marker data. The degree to which sensitivity of inbreeding coefficients to population genetic substructure alters estimates of inbreeding depression in wild populations is not well understood. Using generalized linear models, we tested the power of two frequently used inbreeding coefficients that are calculated from genome-wide SNP markers, FH and F^III , to predict four fitness traits estimated over two decades in an isolated population of the critically endangered Leadbeater's possum. FH estimates inbreeding as excess observed homozygotes relative to equilibrium expectations, whereas F^III quantifies allelic similarity between the gametes that formed an individual, and upweights rare homozygotes. We estimated FH and F^III from 1,575 genome-wide SNP loci in individuals with fitness trait data (N = 179-237 per trait), and computed revised coefficients, FH by group and F^IIIby group , adjusted for population genetic substructure by calculating them separately within two different genetic groups of individuals identified in the population. Using FH or F^III in the models, inbreeding depression was detected for survival to sexual maturity, longevity and whether individuals bred during their lifetime. F^IIIby group (but not FH by group ) additionally revealed significant inbreeding depression for lifetime reproductive output (total offspring assigned to each individual). Estimates of numbers of lethal equivalents indicated substantial inbreeding load, but differing between inbreeding estimators. Inbreeding depression, declining population size, and low and declining genetic diversity suggest that genetic rescue may assist in preventing extinction of this unique Leadbeater's possum population.
Collapse
Affiliation(s)
- Joseph P Zilko
- School of Biological Sciences, Monash University, Clayton, Vic, Australia
| | - Dan Harley
- Zoos Victoria, Parkville, Vic, Australia
| | - Birgita Hansen
- Centre for eResearch and Digital Innovation, Federation University, Ballarat, Vic, Australia
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Clayton, Vic, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Clayton, Vic, Australia
| |
Collapse
|