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von Seth J, van der Valk T, Lord E, Sigeman H, Olsen RA, Knapp M, Kardailsky O, Robertson F, Hale M, Houston D, Kennedy E, Dalén L, Norén K, Massaro M, Robertson BC, Dussex N. Genomic trajectories of a near-extinction event in the Chatham Island black robin. BMC Genomics 2022; 23:747. [PMID: 36357860 PMCID: PMC9647977 DOI: 10.1186/s12864-022-08963-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 10/23/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Understanding the micro--evolutionary response of populations to demographic declines is a major goal in evolutionary and conservation biology. In small populations, genetic drift can lead to an accumulation of deleterious mutations, which will increase the risk of extinction. However, demographic recovery can still occur after extreme declines, suggesting that natural selection may purge deleterious mutations, even in extremely small populations. The Chatham Island black robin (Petroica traversi) is arguably the most inbred bird species in the world. It avoided imminent extinction in the early 1980s and after a remarkable recovery from a single pair, a second population was established and the two extant populations have evolved in complete isolation since then. Here, we analysed 52 modern and historical genomes to examine the genomic consequences of this extreme bottleneck and the subsequent translocation. RESULTS We found evidence for two-fold decline in heterozygosity and three- to four-fold increase in inbreeding in modern genomes. Moreover, there was partial support for temporal reduction in total load for detrimental variation. In contrast, compared to historical genomes, modern genomes showed a significantly higher realised load, reflecting the temporal increase in inbreeding. Furthermore, the translocation induced only small changes in the frequency of deleterious alleles, with the majority of detrimental variation being shared between the two populations. CONCLUSION Our results highlight the dynamics of mutational load in a species that recovered from the brink of extinction, and show rather limited temporal changes in mutational load. We hypothesise that ancestral purging may have been facilitated by population fragmentation and isolation on several islands for thousands of generations and may have already reduced much of the highly deleterious load well before human arrival and introduction of pests to the archipelago. The majority of fixed deleterious variation was shared between the modern populations, but translocation of individuals with low mutational load could possibly mitigate further fixation of high-frequency deleterious variation.
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Affiliation(s)
- Johanna von Seth
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden.
| | - Tom van der Valk
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Edana Lord
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - Hanna Sigeman
- Department of Biology, Lund University, Ecology Building, 223 62, Lund, Sweden
- Ecology and Genetics Research Unit, University of Oulu, 90014, Oulu, Finland
| | - Remi-André Olsen
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 17121, Solna, Sweden
| | - Michael Knapp
- Department of Anatomy, University of Otago, Dunedin, 9054, New Zealand
- Coastal People Southern Skies Centre of Research Excellence, University of Otago, PO Box 56, Dunedin, 9054, Aotearoa, New Zealand
| | - Olga Kardailsky
- Department of Anatomy, University of Otago, Dunedin, 9054, New Zealand
| | - Fiona Robertson
- Department of Zoology, University of Otago, Dunedin, 9054, New Zealand
| | - Marie Hale
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Dave Houston
- Department of Conservation, Biodiversity Group, Auckland, New Zealand
| | - Euan Kennedy
- Department of Conservation, Science and Capability, Christchurch, New Zealand
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - Karin Norén
- Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - Melanie Massaro
- School of Agricultural, Environmental and Veterinary Sciences and Gulbali Institute, Charles Sturt University, PO Box 789, Albury, NSW, Australia
| | - Bruce C Robertson
- Department of Zoology, University of Otago, Dunedin, 9054, New Zealand
| | - Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden.
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Robledo-Ruiz DA, Pavlova A, Clarke RH, Magrath MJL, Quin B, Harrisson KA, Gan HM, Low GW, Sunnucks P. A novel framework for evaluating in situ breeding management strategies in endangered populations. Mol Ecol Resour 2021; 22:239-253. [PMID: 34288508 DOI: 10.1111/1755-0998.13476] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 06/29/2021] [Accepted: 07/15/2021] [Indexed: 11/30/2022]
Abstract
Conservation breeding management aims to reduce inbreeding and maximize the retention of genetic diversity in endangered populations. However, breeding management of wild populations is still rare, and there is a need for approaches that provide data-driven evidence of the likelihood of success of alternative in situ strategies. Here, we provide an analytical framework that uses in silico simulations to evaluate, for real wild populations, (i) the degree of population-level inbreeding avoidance, (ii) the genetic quality of mating pairs, and (iii) the potential genetic benefits of implementing two breeding management strategies. The proposed strategies aim to improve the genetic quality of breeding pairs by splitting detrimental pairs and allowing the members to re-pair in different ways. We apply the framework to the wild population of the Critically Endangered helmeted honeyeater by combining genomic data and field observations to estimate the inbreeding (i.e., pair-kinship) and genetic quality (i.e., Mate Suitability Index) of all mating pairs for seven consecutive breeding seasons. We found no evidence of population-level inbreeding avoidance and that ~91.6% of breeding pairs were detrimental to the genetic health of the population. Furthermore, the framework revealed that neither proposed management strategy would significantly improve the genetic quality or reduce inbreeding of the mating pairs in this population. Our results demonstrate the usefulness of our analytical framework for testing the efficacy of different in situ breeding management strategies and for making evidence-based management decisions.
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Affiliation(s)
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Rohan H Clarke
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Michael J L Magrath
- Department of Wildlife Conservation and Science, Zoos Victoria, Parkville, Vic., Australia.,School of BioSciences, University of Melbourne, Parkville, Vic., Australia
| | - Bruce Quin
- Department of Environment, Land, Water and Planning, Woori Yallock, Vic., Australia
| | - Katherine A Harrisson
- Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Vic., Australia.,Department of Environment, Land, Water and Planning, Arthur Rylah Institute for Environmental Research, Heidelberg, Vic., Australia
| | - Han Ming Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Vic., Australia.,Deakin Genomics Centre, Deakin University, Geelong, Vic., Australia
| | - Gabriel W Low
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
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3
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Kearns AM, Malloy JF, Gobbert MK, Thierry A, Joseph L, Driskell AC, Omland KE. Nuclear introns help unravel the diversification history of the Australo-Pacific Petroica robins. Mol Phylogenet Evol 2018; 131:48-54. [PMID: 30367975 DOI: 10.1016/j.ympev.2018.10.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/15/2018] [Accepted: 10/18/2018] [Indexed: 11/16/2022]
Abstract
Australo-Pacific Petroica robins are known for their striking variability in sexual plumage coloration. Molecular studies in recent years have revised the taxonomy of species and subspecies boundaries across the southwest Pacific and New Guinea. However, these studies have not been able to resolve phylogenetic relationships within Petroica owing to limited sampling of the nuclear genome. Here, we sequence five nuclear introns across all species for which fresh tissue was available. Nuclear loci offer support for major geographic lineages that were first inferred from mtDNA. We find almost no shared nuclear alleles between currently recognized species within the New Zealand and Australian lineages, whereas the Pacific robin radiation has many shared alleles. Multilocus coalescent species trees based on nuclear loci support a sister relationship between the Australian lineage and the Pacific robin radiation-a node that is poorly supported by mtDNA. We also find discordance in support for a sister relationship between the similarly plumaged Rose Robin (P. rosea) and Pink Robin (P. rodinogaster). Our nuclear data complement previous mtDNA studies in suggesting that the phenotypically cryptic eastern and western populations of Australia's Scarlet Robin (P. boodang) are genetically distinct lineages at the early stages of divergence and speciation.
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Affiliation(s)
- Anna M Kearns
- University of Maryland, Baltimore County, Department of Biological Sciences, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
| | - John F Malloy
- University of Maryland, Baltimore County, Department of Biological Sciences, 1000 Hilltop Circle, Baltimore, MD 21250, USA; University of Maryland, Baltimore County, Department of Mathematics and Statistics, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Matthias K Gobbert
- University of Maryland, Baltimore County, Department of Mathematics and Statistics, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Aude Thierry
- University of Canterbury, School of Biological Sciences, Christchurch 8041, New Zealand
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Amy C Driskell
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20013, USA
| | - Kevin E Omland
- University of Maryland, Baltimore County, Department of Biological Sciences, 1000 Hilltop Circle, Baltimore, MD 21250, USA
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Hautphenne S, Massaro M, Taylor P. How old is this bird? The age distribution under some phase sampling schemes. J Math Biol 2017; 75:1319-1347. [PMID: 28374100 DOI: 10.1007/s00285-017-1121-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 03/12/2017] [Indexed: 10/19/2022]
Abstract
In this paper, we use a finite-state continuous-time Markov chain with one absorbing state to model an individual's lifetime. Under this model, the time of death follows a phase-type distribution, and the transient states of the Markov chain are known as phases. We then attempt to provide an answer to the simple question "What is the conditional age distribution of the individual, given its current phase"? We show that the answer depends on how we interpret the question, and in particular, on the phase observation scheme under consideration. We then apply our results to the computation of the age pyramid for the endangered Chatham Island black robin Petroica traversi during the monitoring period 2007-2014.
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Affiliation(s)
- Sophie Hautphenne
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC, 3010, Australia. .,Institute of Mathematics, Ecole polytechnique fédérale de Lausanne, Lausanne, Vaud, Switzerland.
| | - Melanie Massaro
- Institute of Land, Water and Society, School of Environmental Sciences, Charles Sturt University, Albury, NSW, 2640, Australia
| | - Peter Taylor
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC, 3010, Australia
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Genetic diversity and population differentiation within and between island populations of two sympatric Petroica robins, the Chatham Island black robin and tomtit. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0899-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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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] [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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