1
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Forsdick NJ, Wold J, Angelo A, Bissey F, Hart J, Head M, Liggins L, Senanayake D, Steeves TE. Journeying towards best practice data management in biodiversity genomics. Mol Ecol Resour 2023. [PMID: 37873890 DOI: 10.1111/1755-0998.13880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/15/2023] [Accepted: 10/03/2023] [Indexed: 10/25/2023]
Abstract
Advances in sequencing technologies and declining costs are increasing the accessibility of large-scale biodiversity genomic datasets. To maximize the impact of these data, a careful, considered approach to data management is essential. However, challenges associated with the management of such datasets remain, exacerbated by uncertainty among the research community as to what constitutes best practices. As an interdisciplinary team with diverse data management experience, we recognize the growing need for guidance on comprehensive data management practices that minimize the risks of data loss, maximize efficiency for stand-alone projects, enhance opportunities for data reuse, facilitate Indigenous data sovereignty and uphold the FAIR and CARE Guiding Principles. Here, we describe four fictional personas reflecting differing user experiences with data management to identify data management challenges across the biodiversity genomics research ecosystem. We then use these personas to demonstrate realistic considerations, compromises and actions for biodiversity genomic data management. We also launch the Biodiversity Genomics Data Management Hub (https://genomicsaotearoa.github.io/data-management-resources/), containing tips, tricks and resources to support biodiversity genomics researchers, especially those new to data management, in their journey towards best practice. The Hub also provides an opportunity for those biodiversity researchers whose expertise lies beyond genomics and are keen to advance their data management journey. We aim to support the biodiversity genomics community in embedding data management throughout the research lifecycle to maximize research impact and outcomes.
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Affiliation(s)
- Natalie J Forsdick
- Manaaki Whenua-Landcare Research, Lincoln, New Zealand
- Genomics Aotearoa, Dunedin, New Zealand
| | - Jana Wold
- Genomics Aotearoa, Dunedin, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Anton Angelo
- Library, University of Canterbury, Christchurch, New Zealand
| | - François Bissey
- Digital Services, University of Canterbury, Christchurch, New Zealand
| | - Jamie Hart
- Digital Services, University of Canterbury, Christchurch, New Zealand
| | - Mitchell Head
- Ngaati Mahuta, Waikato, New Zealand
- Ngaati Naho, Waikato, New Zealand
- Te Kotahi Research Institute, University of Waikato, Hamilton, New Zealand
| | - Libby Liggins
- Genomics Aotearoa, Dunedin, New Zealand
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | | | - Tammy E Steeves
- Genomics Aotearoa, Dunedin, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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2
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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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3
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Wylie MJ, Kitson J, Russell K, Yoshizaki G, Yazawa R, Steeves TE, Wellenreuther M. Fish germ cell cryobanking and transplanting for conservation. Mol Ecol Resour 2023. [PMID: 37712134 DOI: 10.1111/1755-0998.13868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 05/26/2023] [Accepted: 07/18/2023] [Indexed: 09/16/2023]
Abstract
The unprecedented loss of global biodiversity is linked to multiple anthropogenic stressors. New conservation technologies are urgently needed to mitigate this loss. The rights, knowledge and perspectives of Indigenous peoples in biodiversity conservation-including the development and application of new technologies-are increasingly recognised. Advances in germplasm cryopreservation and germ cell transplantation (termed 'broodstock surrogacy') techniques offer exciting tools to preserve biodiversity, but their application has been underappreciated. Here, we use teleost fishes as an exemplar group to outline (1) the power of these techniques to preserve genome-wide genetic diversity, (2) the need to apply a conservation genomic lens when selecting individuals for germplasm cryobanking and broodstock surrogacy and (3) the value of considering the cultural significance of these genomic resources. We conclude by discussing the opportunities and challenges of these techniques for conserving biodiversity in threatened teleost fish and beyond.
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Affiliation(s)
- Matthew J Wylie
- The New Zealand Institute for Plant & Food Research Limited, Nelson, New Zealand
| | - Jane Kitson
- Kitson Consulting Ltd, Invercargill, New Zealand
| | - Khyla Russell
- Kāti Huirapa Rūnaka ki Puketeraki, Karitane, New Zealand
| | - Goro Yoshizaki
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ryosuke Yazawa
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Maren Wellenreuther
- The New Zealand Institute for Plant & Food Research Limited, Nelson, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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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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5
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Wold JR, Guhlin JG, Dearden PK, Santure AW, Steeves TE. The promise and challenges of characterizing genome-wide structural variants: A case study in a critically endangered parrot. Mol Ecol Resour 2023. [PMID: 36916824 DOI: 10.1111/1755-0998.13783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/24/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023]
Abstract
There is growing interest in the role of structural variants (SVs) as drivers of local adaptation and speciation. From a biodiversity genomics perspective, the characterization of genome-wide SVs provides an exciting opportunity to complement single nucleotide polymorphisms (SNPs). However, little is known about the impacts of SV discovery and genotyping strategies on the characterization of genome-wide SV diversity within and among populations. Here, we explore a near whole-species resequence data set, and long-read sequence data for a subset of highly represented individuals in the critically endangered kākāpō (Strigops habroptilus). We demonstrate that even when using a highly contiguous reference genome, different discovery and genotyping strategies can significantly impact the type, size and location of SVs characterized genome-wide. Further, we found that the mean number of SVs in each of two kākāpō lineages differed both within and across generations. These combined results suggest that genome-wide characterization of SVs remains challenging at the population-scale. We are optimistic that increased accessibility to long-read sequencing and advancements in bioinformatic approaches including multireference approaches like genome graphs will alleviate at least some of the challenges associated with resolving SV characteristics below the species level. In the meantime, we address caveats, highlight considerations, and provide recommendations for the characterization of genome-wide SVs in biodiversity genomic research.
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Affiliation(s)
- Jana R Wold
- University of Canterbury, Christchurch, New Zealand
| | - Joseph G Guhlin
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Peter K Dearden
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
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6
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Digby A, Eason D, Catalina A, Lierz M, Galla S, Urban L, Le Lec MF, Guhlin J, Steeves TE, Dearden PK, Joustra T, Lees C, Davis T, Vercoe D. Hidden impacts of conservation management on fertility of the critically endangered kākāpō. PeerJ 2023; 11:e14675. [PMID: 36755872 PMCID: PMC9901309 DOI: 10.7717/peerj.14675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/11/2022] [Indexed: 02/05/2023] Open
Abstract
Background Animal conservation often requires intensive management actions to improve reproductive output, yet any adverse effects of these may not be immediately apparent, particularly in threatened species with small populations and long lifespans. Hand-rearing is an example of a conservation management strategy which, while boosting populations, can cause long-term demographic and behavioural problems. It is used in the recovery of the critically endangered kākāpō (Strigops habroptilus), a flightless parrot endemic to New Zealand, to improve the slow population growth that is due to infrequent breeding, low fertility and low hatching success. Methods We applied Bayesian mixed models to examine whether hand-rearing and other factors were associated with clutch fertility in kākāpō. We used projection predictive variable selection to compare the relative contributions to fertility from the parents' rearing environment, their age and previous copulation experience, the parental kinship, and the number of mates and copulations for each clutch. We also explored how the incidence of repeated copulations and multiple mates varied with kākāpō density. Results The rearing status of the clutch father and the number of mates and copulations of the clutch mother were the dominant factors in predicting fertility. Clutches were less likely to be fertile if the father was hand-reared compared to wild-reared, but there was no similar effect for mothers. Clutches produced by females copulating with different males were more likely to be fertile than those from repeated copulations with one male, which in turn had a higher probability of fertility than those from a single copulation. The likelihood of multiple copulations and mates increased with female:male adult sex ratio, perhaps as a result of mate guarding by females. Parental kinship, copulation experience and age all had negligible associations with clutch fertility. Conclusions These results provide a rare assessment of factors affecting fertility in a wild threatened bird species, with implications for conservation management. The increased fertility due to multiple mates and copulations, combined with the evidence for mate guarding and previous results of kākāpō sperm morphology, suggests that an evolutionary mechanism exists to optimise fertility through sperm competition in kākāpō. The high frequency of clutches produced from single copulations in the contemporary population may therefore represent an unnatural state, perhaps due to too few females. This suggests that opportunity for sperm competition should be maximised by increasing population densities, optimising sex ratios, and using artificial insemination. The lower fertility of hand-reared males may result from behavioural defects due to lack of exposure to conspecifics at critical development stages, as seen in other taxa. This potential negative impact of hand-rearing must be balanced against the short-term benefits it provides.
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Affiliation(s)
- Andrew Digby
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, New Zealand
| | - Daryl Eason
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, New Zealand
| | | | - Michael Lierz
- Clinic for Birds, Reptiles, Amphibians and Fish, Justus-Liebig University Giessen, Giessen, Germany
| | - Stephanie Galla
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand,Department of Biological Sciences, Boise State University, Boise, ID, United States of America
| | - Lara Urban
- Genomics Aotearoa, Dunedin, New Zealand,Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Marissa F. Le Lec
- Genomics Aotearoa, Dunedin, New Zealand,Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Joseph Guhlin
- Genomics Aotearoa, Dunedin, New Zealand,Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Tammy E. Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand,Genomics Aotearoa, Christchurch, New Zealand
| | - Peter K. Dearden
- Genomics Aotearoa, Dunedin, New Zealand,Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | - Caroline Lees
- IUCN SSC Conservation Planning Specialist Group, Auckland, New Zealand
| | - Tane Davis
- Te Rūnanga o Ngāi Tahu, Christchurch, New Zealand
| | - Deidre Vercoe
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, New Zealand
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7
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Magid M, Wold JR, Moraga R, Cubrinovska I, Houston DM, Gartrell BD, Steeves TE. Leveraging an existing whole genome resequencing population dataset to characterize toll‐like receptor gene diversity in a threatened bird. Mol Ecol Resour 2022; 22:2810-2825. [PMID: 35635119 PMCID: PMC9543821 DOI: 10.1111/1755-0998.13656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/29/2022] [Accepted: 05/26/2022] [Indexed: 11/27/2022]
Abstract
Species recovery programs are increasingly using genomic data to measure neutral genetic diversity and calculate metrics like relatedness. While these measures can inform conservation management, determining the mechanisms underlying inbreeding depression requires information about functional genes associated with adaptive or maladaptive traits. Toll‐like receptors (TLRs) are one family of functional genes, which play a crucial role in recognition of pathogens and activation of the immune system. Previously, these genes have been analysed using species‐specific primers and PCR. Here, we leverage an existing short‐read reference genome, whole‐genome resequencing population data set, and bioinformatic tools to characterize TLR gene diversity in captive and wild tchūriwat’/tūturuatu/shore plover (Thinornis novaeseelandiae), a threatened bird endemic to Aotearoa New Zealand. Our results show that TLR gene diversity in tchūriwat’/tūturuatu is low, and forms two distinct captive and wild genetic clusters. The bioinformatic approach presented here has broad applicability to other threatened species with existing genomic resources in Aotearoa New Zealand and beyond.
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Affiliation(s)
- Molly Magid
- University of Canterbury School of Biological Sciences Christchurch NZ
| | - Jana R. Wold
- University of Canterbury School of Biological Sciences Christchurch NZ
| | - Roger Moraga
- Tea Break Bioinformatics, Ltd Palmerston North NZ
| | - Ilina Cubrinovska
- University of Canterbury School of Biological Sciences Christchurch NZ
| | | | - Brett D. Gartrell
- Wildbase Massey University Institute of Veterinary, Animal, and Biomedical Sciences, Palmerston North, Manawatu NZ
| | - Tammy E. Steeves
- University of Canterbury School of Biological Sciences Christchurch NZ
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8
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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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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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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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11
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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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12
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Forsdick NJ, Martini D, Brown L, Cross HB, Maloney RF, Steeves TE, Knapp M. Genomic sequencing confirms absence of introgression despite past hybridisation between a critically endangered bird and its common congener. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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13
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Schori JC, Steeves TE, Murray TJ. Designing monitoring protocols to measure population trends of threatened insects: A case study of the cryptic, flightless grasshopper Brachaspis robustus. PLoS One 2020; 15:e0238636. [PMID: 32970696 PMCID: PMC7514004 DOI: 10.1371/journal.pone.0238636] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 08/20/2020] [Indexed: 11/18/2022] Open
Abstract
Statistically robust monitoring of threatened populations is essential for effective conservation management because the population trend data that monitoring generates is often used to make decisions about when and how to take action. Despite representing the highest proportion of threatened animals globally, the development of best practice methods for monitoring populations of threatened insects is relatively uncommon. Traditionally, population trend data for the Nationally Endangered New Zealand grasshopper Brachaspis robustus has been determined by counting all adults and nymphs seen on a single ~1.5 km transect searched once annually. This method lacks spatial and temporal replication, both of which are essential to overcome detection errors in highly cryptic species like B. robustus. It also provides no information about changes in the grasshopper’s distribution throughout its range. Here, we design and test new population density and site occupancy monitoring protocols by comparing a) comprehensive plot and transect searches at one site and b) transect searches at two sites representing two different habitats (gravel road and natural riverbed) occupied by the species across its remaining range. Using power analyses, we determined a) the number of transects, b) the number of repeated visits and c) the grasshopper demographic to count to accurately detect long term change in relative population density. To inform a monitoring protocol design to track trends in grasshopper distribution, we estimated the probability of detecting an individual with respect to a) search area, b) weather and c) the grasshopper demographic counted at each of the two sites. Density estimates from plots and transects did not differ significantly. Population density monitoring was found to be most informative when large adult females present in early summer were used to index population size. To detect a significant change in relative density with power > 0.8 at the gravel road habitat, at least seventeen spatial replicates (transects) and four temporal replicates (visits) were required. Density estimates at the natural braided river site performed poorly and likely require a much higher survey effort. Detection of grasshopper presence was highest (pg > 0.6) using a 100 m x 1 m transect at both sites in February under optimal (no cloud) conditions. At least three visits to a transect should be conducted per season for distribution monitoring. Monitoring protocols that inform the management of threatened species are crucial for better understanding and mitigation of the current global trends of insect decline. This study provides an exemplar of how appropriate monitoring protocols can be developed for threatened insect species.
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Affiliation(s)
- Jennifer C. Schori
- School of Biological Sciences, College of Science, University of Canterbury, Christchurch, New Zealand
- * E-mail:
| | - Tammy E. Steeves
- School of Biological Sciences, College of Science, University of Canterbury, Christchurch, New Zealand
| | - Tara J. Murray
- School of Forestry, College of Engineering, University of Canterbury, Christchurch, New Zealand
- Department of Conservation, Biodiversity Group, Dunedin, New Zealand
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14
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Rayne A, Byrnes G, Collier‐Robinson L, Hollows J, McIntosh A, Ramsden M, Rupene M, Tamati‐Elliffe P, Thoms C, Steeves TE. Centring Indigenous knowledge systems to re‐imagine conservation translocations. People and Nature 2020. [DOI: 10.1002/pan3.10126] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Aisling Rayne
- School of Biological Sciences University of Canterbury Christchurch New Zealand
| | - Greg Byrnes
- Te Kōhaka o Tūhaitara Trust Christchurch New Zealand
| | | | | | - Angus McIntosh
- School of Biological Sciences University of Canterbury Christchurch New Zealand
| | | | - Makarini Rupene
- Environment Canterbury Christchurch New Zealand
- Ngāi Tahu Research Centre University of Canterbury Christchurch New Zealand
| | | | - Channell Thoms
- School of Biological Sciences University of Canterbury Christchurch New Zealand
| | - Tammy E. Steeves
- School of Biological Sciences University of Canterbury Christchurch New Zealand
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15
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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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16
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Schori JC, Maloney RF, Steeves TE, Murray TJ. Evidence that reducing mammalian predators is beneficial for threatened and declining New Zealand grasshoppers. New Zealand Journal of Zoology 2018. [DOI: 10.1080/03014223.2018.1523201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Jennifer C. Schori
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Richard F. Maloney
- Department of Conservation, Biodiversity Group, Christchurch, New Zealand
| | - Tammy E. Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Tara J. Murray
- School of Forestry, University of Canterbury, Christchurch, New Zealand
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17
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Bartlett MJ, Steeves TE, Gemmell NJ, Rosengrave PC. Sperm competition risk drives rapid ejaculate adjustments mediated by seminal fluid. eLife 2017; 6:e28811. [PMID: 29084621 PMCID: PMC5669631 DOI: 10.7554/elife.28811] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/13/2017] [Indexed: 12/15/2022] Open
Abstract
In many species, males can make rapid adjustments to ejaculate performance in response to sperm competition risk; however, the mechanisms behind these changes are not understood. Here, we manipulate male social status in an externally fertilising fish, chinook salmon (Oncorhynchus tshawytscha), and find that in less than 48 hr, males can upregulate sperm velocity when faced with an increased risk of sperm competition. Using a series of in vitro sperm manipulation and competition experiments, we show that rapid changes in sperm velocity are mediated by seminal fluid and the effect of seminal fluid on sperm velocity directly impacts paternity share and therefore reproductive success. These combined findings, completely consistent with sperm competition theory, provide unequivocal evidence that sperm competition risk drives plastic adjustment of ejaculate quality, that seminal fluid harbours the mechanism for the rapid adjustment of sperm velocity and that fitness benefits accrue to males from such adjustment.
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Affiliation(s)
- Michael J Bartlett
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | - Tammy E Steeves
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | - Neil J Gemmell
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
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18
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Steeves TE, Johnson JA, Hale ML. Maximising evolutionary potential in functional proxies for extinct species: a conservation genetic perspective on de‐extinction. Funct Ecol 2017. [DOI: 10.1111/1365-2435.12843] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Tammy E. Steeves
- School of Biological Sciences University of Canterbury Private Bag 4800 Christchurch8140 New Zealand
| | - Jeff A. Johnson
- Department of Biological Sciences and Institute of Applied Science University of North Texas 1155 Union Circle Denton TX76203 USA
| | - Marie L. Hale
- School of Biological Sciences University of Canterbury Private Bag 4800 Christchurch8140 New Zealand
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19
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Bennett JR, Maloney RF, Steeves TE, Brazill-Boast J, Possingham HP, Seddon PJ. Spending limited resources on de-extinction could lead to net biodiversity loss. Nat Ecol Evol 2017; 1:53. [DOI: 10.1038/s41559-016-0053] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 12/13/2016] [Indexed: 01/30/2023]
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20
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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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21
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Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JMD, Wragg D, Zhou H. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res 2015; 145:78-179. [PMID: 26282327 PMCID: PMC5120589 DOI: 10.1159/000430927] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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22
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Gardner PP, Fasold M, Burge SW, Ninova M, Hertel J, Kehr S, Steeves TE, Griffiths-Jones S, Stadler PF. Conservation and losses of non-coding RNAs in avian genomes. PLoS One 2015; 10:e0121797. [PMID: 25822729 PMCID: PMC4378963 DOI: 10.1371/journal.pone.0121797] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/03/2015] [Indexed: 11/21/2022] Open
Abstract
Here we present the results of a large-scale bioinformatics annotation of non-coding RNA loci in 48 avian genomes. Our approach uses probabilistic models of hand-curated families from the Rfam database to infer conserved RNA families within each avian genome. We supplement these annotations with predictions from the tRNA annotation tool, tRNAscan-SE and microRNAs from miRBase. We identify 34 lncRNA-associated loci that are conserved between birds and mammals and validate 12 of these in chicken. We report several intriguing cases where a reported mammalian lncRNA, but not its function, is conserved. We also demonstrate extensive conservation of classical ncRNAs (e.g., tRNAs) and more recently discovered ncRNAs (e.g., snoRNAs and miRNAs) in birds. Furthermore, we describe numerous “losses” of several RNA families, and attribute these to either genuine loss, divergence or missing data. In particular, we show that many of these losses are due to the challenges associated with assembling avian microchromosomes. These combined results illustrate the utility of applying homology-based methods for annotating novel vertebrate genomes.
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Affiliation(s)
- Paul P. Gardner
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- * E-mail:
| | - Mario Fasold
- Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany
- ecSeq Bioinformatics, Brandvorwerkstr.43, D-04275 Leipzig, Germany
| | - Sarah W. Burge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Maria Ninova
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Jana Hertel
- Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Stephanie Kehr
- Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Tammy E. Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Sam Griffiths-Jones
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, D-04103 Leipzig, Germany
- Department of Theoretical Chemistry of the University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria
- Center for RNA in Technology and Health, Univ. Copenhagen, Grønnegårdsvej 3, Frederiksberg C, Denmark
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe NM 87501, USA
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany
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23
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Steeves TE, Hale ML, Gemmell NJ. Development of polymorphic microsatellite markers for the New Zealand black stilt (Himantopus novaezelandiae) and cross-amplification in the pied stilt (Himantopus himantopus leucocephalus). Mol Ecol Resour 2013; 8:1105-7. [PMID: 21585985 DOI: 10.1111/j.1755-0998.2008.02170.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Eight polymorphic microsatellite primer pairs were developed for the critically endangered New Zealand black stilt, Himantopus novaezelandiae, representing the first microsatellite markers available for birds in the family Recurvirostridae. The number of alleles ranged from two to four per locus. Observed and expected heterozygosities ranged from 0.30 to 0.80 and from 0.37 to 0.70, respectively. All eight loci were polymorphic in the related species Himantopus himantopus leucocephalus, indicating these primer pairs may be useful for additional taxa in the globally distributed genus Himantopus.
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Affiliation(s)
- Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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Andrews BJ, Hale ML, Steeves TE. Characterisation of microsatellite loci in the critically endangered orange-fronted kākāriki (Cyanoramphus malherbi) isolated using genomic next generation sequencing. CONSERV GENET RESOUR 2012. [DOI: 10.1007/s12686-012-9777-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Hale ML, Burg TM, Steeves TE. Sampling for microsatellite-based population genetic studies: 25 to 30 individuals per population is enough to accurately estimate allele frequencies. PLoS One 2012; 7:e45170. [PMID: 22984627 PMCID: PMC3440332 DOI: 10.1371/journal.pone.0045170] [Citation(s) in RCA: 291] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 08/17/2012] [Indexed: 11/29/2022] Open
Abstract
One of the most common questions asked before starting a new population genetic study using microsatellite allele frequencies is "how many individuals do I need to sample from each population?" This question has previously been answered by addressing how many individuals are needed to detect all of the alleles present in a population (i.e. rarefaction based analyses). However, we argue that obtaining accurate allele frequencies and accurate estimates of diversity are much more important than detecting all of the alleles, given that very rare alleles (i.e. new mutations) are not very informative for assessing genetic diversity within a population or genetic structure among populations. Here we present a comparison of allele frequencies, expected heterozygosities and genetic distances between real and simulated populations by randomly subsampling 5-100 individuals from four empirical microsatellite genotype datasets (Formica lugubris, Sciurus vulgaris, Thalassarche melanophris, and Himantopus novaezelandia) to create 100 replicate datasets at each sample size. Despite differences in taxon (two birds, one mammal, one insect), population size, number of loci and polymorphism across loci, the degree of differences between simulated and empirical dataset allele frequencies, expected heterozygosities and pairwise F(ST) values were almost identical among the four datasets at each sample size. Variability in allele frequency and expected heterozygosity among replicates decreased with increasing sample size, but these decreases were minimal above sample sizes of 25 to 30. Therefore, there appears to be little benefit in sampling more than 25 to 30 individuals per population for population genetic studies based on microsatellite allele frequencies.
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Affiliation(s)
- Marie L Hale
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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Steeves TE, Maloney RF, Hale ML, Tylianakis JM, Gemmell NJ. Genetic analyses reveal hybridization but no hybrid swarm in one of the world's rarest birds. Mol Ecol 2010; 19:5090-100. [PMID: 21050294 DOI: 10.1111/j.1365-294x.2010.04895.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hybridization facilitated by human activities has dramatically altered the evolutionary trajectories of threatened taxa around the globe. Whereas introduced mammalian predators and widespread habitat loss and degradation clearly imperil the recovery and survival of the New Zealand endemic black stilt or kakī (Himantopus novaezelandiae), the risk associated with hybridization between this critically endangered endemic and its self-introduced congener, the pied stilt or poaka (Himantopus himantopus leucocephalus) is less clear. Here, we combine Bayesian admixture analyses of microsatellite data with mitochondrial DNA sequence data to assess the levels of hybridization and introgression between kakī and poaka. We show that birds classified as hybrids on the basis of adult plumage are indeed of hybrid origin and that hybridization between kakī and poaka is both extensive and bidirectional. Despite this, we found almost no evidence for introgression from poaka to kakī, thus negating the popular belief that kakī represent a hybrid swarm. To our knowledge, ours represents the first comprehensive study to document a lack of widespread introgression for a species at risk despite a recent history of extensive bidirectional human-induced hybridization. We attribute this rather surprising result, in part, to reduced reproductive success in female hybrids combined with a transient male-biased kakī sex ratio. To maximize the evolutionary potential of kakī, we use these data to recommend conservation management activities aimed to maintain the genetic integrity and to maximize the genetic diversity of this iconic rare bird.
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Affiliation(s)
- Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand.
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Morris-Pocock JA, Steeves TE, Estela FA, Anderson DJ, Friesen VL. Comparative phylogeography of brown (Sula leucogaster) and red-footed boobies (S. sula): the influence of physical barriers and habitat preference on gene flow in pelagic seabirds. Mol Phylogenet Evol 2009; 54:883-96. [PMID: 19931624 DOI: 10.1016/j.ympev.2009.11.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2009] [Revised: 11/11/2009] [Accepted: 11/13/2009] [Indexed: 12/16/2022]
Abstract
To test the hypothesis that both physical and ecological barriers to gene flow drive population differentiation in tropical seabirds, we surveyed mitochondrial control region variation in 242 brown boobies (Sula leucogaster), which prefer inshore habitat, and 271 red-footed boobies (S. sula), which prefer pelagic habitat. To determine the relative influence of isolation and gene flow on population structure, we used both traditional methods and a recently developed statistical method based on coalescent theory and Bayesian inference (Isolation with Migration). We found that global population genetic structure was high in both species, and that female-mediated gene flow among ocean basins apparently has been restricted by major physical barriers including the Isthmus of Panama, and the periodic emergence of the Sunda and Sahul Shelves in Southeast Asia. In contrast, the evolutionary history of populations within ocean basins differed markedly between the two species. In brown boobies, we found high levels of population genetic differentiation and limited gene flow among colonies, even at spatial scales as small as 500km. Although red-footed booby colonies were also genetically differentiated within ocean basins, coalescent analyses indicated that populations have either diverged in the face of ongoing gene flow, or diverged without gene flow but recently made secondary contact. Regardless, gene flow among red-footed booby populations was higher than among brown booby populations. We suggest that these contrasting patterns of gene flow within ocean basins may be explained by the different habitat preferences of brown and red-footed boobies.
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Affiliation(s)
- J A Morris-Pocock
- Department of Biology, Queen's University, Kingston, Ont. K7L 3N6, Canada.
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Steeves TE, Holdaway RN, Hale ML, McLay E, McAllan IAW, Christian M, Hauber ME, Bunce M. Merging ancient and modern DNA: extinct seabird taxon rediscovered in the North Tasman Sea. Biol Lett 2009; 6:94-7. [PMID: 19675005 DOI: 10.1098/rsbl.2009.0478] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ancient DNA has revolutionized the way in which evolutionary biologists research both extinct and extant taxa, from the inference of evolutionary history to the resolution of taxonomy. Here, we present, to our knowledge, the first study to report the rediscovery of an 'extinct' avian taxon, the Tasman booby (Sula tasmani), using classical palaeontological data combined with ancient and modern DNA data. Contrary to earlier work, we show an overlap in size between fossil and modern birds in the North Tasman Sea (classified currently as S. tasmani and Sula dactylatra fullagari, respectively). In addition, we show that Holocene fossil birds have mitochondrial control region sequences that are identical to those found in modern birds. These results indicate that the Tasman booby is not an extinct taxon: S. dactylatra fullagari O'Brien & Davies, 1990 is therefore a junior synonym of Sula tasmani van Tets, Meredith, Fullagar & Davidson, 1988 and all North Tasman Sea boobies should be known as S. d. tasmani. In addition to reporting the rediscovery of an extinct avian taxon, our study highlights the need for researchers to be cognizant of multidisciplinary approaches to understanding taxonomy and past biodiversity.
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Affiliation(s)
- Tammy E Steeves
- School of Biological Sciences, University of Canterbury, , Private Bag 4800, Christchurch 8140, New Zealand.
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Robertson BC, Steeves TE, McBride KP, Goldstien SJ, Williams M, Gemmell NJ. Phylogeography of the New Zealand blue duck (Hymenolaimus malacorhynchos): implications for translocation and species recovery. CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9294-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Steeves TE, Anderson DJ, Friesen VL. A role for nonphysical barriers to gene flow in the diversification of a highly vagile seabird, the masked booby (Sula dactylatra). Mol Ecol 2006; 14:3877-87. [PMID: 16202102 DOI: 10.1111/j.1365-294x.2005.02713.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
To test the hypothesis that nonphysical barriers to gene flow play a role in the divergence of low-latitude seabird populations, we applied phylogeographic methods to mitochondrial control region sequence variation in a global sample of masked boobies (Sula dactylatra). In accord with previous studies, we found that Indo-Pacific and Atlantic haplotypes form two divergent lineages, excluding one haplotype previously attributed to secondary contact between the Indian Ocean and the Caribbean Sea. Within the Indo-Pacific and the Atlantic, we found a relatively large number of haplotypes, many of which were unique to a single population. Although haplotypes from most populations were found in more than one higher-level clade, nested clade analysis revealed a significant association between clades and geography for the majority of higher-level clades, most often interpreted as a consequence of isolation by distance. We found low levels of gene flow within Indo-Pacific and Atlantic populations, and a significant correlation between gene flow and geographical distance among Indo-Pacific populations. We estimate that Indo-Pacific masked boobies experienced rapid population growth approximately 180,000 years ago and that the majority of Indo-Pacific and Atlantic populations diverged within the last approximately 115,000 years. These combined data suggest that the predominant pattern between Indo-Pacific and Atlantic populations is long-term isolation by physical barriers to gene flow. In contrast, populations within these regions appear to have diverged despite few obvious physical barriers to gene flow, perhaps as a consequence of limited natal dispersal combined with local adaptation and/or genetic drift.
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Affiliation(s)
- Tammy E Steeves
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada.
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Abstract
To further test the hypothesis that the Isthmus of Panama is a major barrier to gene flow in pantropical seabirds, we applied phylogeographic methods to mitochondrial control sequence variation in masked booby (Sula dactylatra) populations on either side of the Isthmus of Panama and the southern tip of Africa. In accord with Steeves et al. (2003), we found that all Caribbean masked boobies with the 'secondary contact' cytochrome b haplotype (m-B) shared a control region haplotype (Sd_100), which grouped with Indian-Pacific haplotypes and not Caribbean-Atlantic haplotypes. In addition, Sd_100 was more closely related to control region haplotypes in the Indian Ocean than in the Pacific. We also found that the 'secondary contact' birds diverged more recently from extant populations in the Indian Ocean than in the Pacific. Thus, it appears that these masked boobies did not breach the Isthmus of Panama. Rather, birds likely dispersed around the southern tip of Africa during favourable oceanographic conditions in the Pleistocene.
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Affiliation(s)
- T E Steeves
- Department of Biology, Queen's University, Kingston, ON, Canada.
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Abstract
The present study compared the developmental potential and uptake of nutrients by embryos from pre-pubertal and adult cows. Oocytes retrieved from ovaries of 5 to 7 month old calves and adult cows were matured and fertilized in vitro. Embryos were cultured in SOFaa to the blastocyst stage (7 days post-insemination). At successive stages of development, rates of glucose and pyruvate uptake were measured non-invasively by microfluorescence for individual embryos. Fertilization was equivalent in embryos from pre-pubertal and adult cows (P > 0.05), however development to blastocyst was significantly lower in embryos from pre-pubertal cows (9.8% versus 33.7%, respectively; P < 0.05). Total blastocyst cell number was not different between pre-pubertal and adult material (P > 0.05). Glucose uptake was exponential (pre-pubertal, r = 0.82; adult, r = 0. 82; P < 0.05), with an increase in uptake beyond the 8- to 16-cell stage. Glucose uptake was significantly lower in embryos from pre-pubertal cows at the 2- to 4-cell stages (1.5 versus 3.0 pmoles/embryo/hr; P < 0.05), but was equivalent to the adult cow at all other stages of development (P > 0.05). Pyruvate uptake was low until the blastocyst stage. Pyruvate uptake by embryos from pre-pubertal cows was significantly different to adult cows at the 1-cell stage (2.7 versus 4.6 pmoles/embryo/hr, respectively; P < 0. 05) and 2- to 4-cell stages (4.9 versus 3.6 pmoles/embryo/hr, respectively; P < 0.05). Pyruvate uptake was equivalent in the two groups in the later stages of development (P > 0.05). Perturbations in the uptake of nutrients by embryos from pre-pubertal cows were most likely due to the presence of a high proportion of developmentally incompetent embryos. Further, embryos from pre-pubertal cows that did develop to the blastocyst were as viable as blastocysts from adult cows with respect to nutrient uptakes and total cell number.
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Affiliation(s)
- T E Steeves
- Centre for Early Human Development, Institute of Reproduction and Development, Monash Medical Centre, Clayton, Victoria, Australia.
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Abstract
The aim of the study was to compare the energy metabolism of oocytes from pre-pubertal (2 to 3 months) and adult cows during maturation, to identify the cause of poor developmental potential in many pre-pubertal oocytes. The metabolism of [5-(3)H] glucose, [2-(14)C] pyruvate, and [G-(3)H] glutamine was measured at 0 hr, 12 hr, and 24 hr maturation. Oxidative metabolism was important during maturation of oocytes from both pre-pubertal and adult cows, with pyruvate metabolism peaking at 12 hr and glutamine metabolism increasing linearly and peaking at 24 hr. Peak oxidative metabolism was significantly lower in oocytes from pre-pubertal animals, for both pyruvate and glutamine (P < 0.05). Glucose metabolism increased significantly during oocyte maturation in both groups (0hr to 24 hr). Glucose metabolism was significantly lower in oocytes from pre-pubertal cows at 12 hr (P < 0.05). Oocytes from pre-pubertal animals were significantly smaller than oocytes from adult cows at 0 hr, 12 hr, and 24 hr maturation (P < 0.05). When metabolic rates were corrected for oocyte volume, there were no significant differences in substrate metabolism between oocytes from pre-pubertal and adult cows. There was however, a delay in the increase in glucose metabolism in pre-pubertal oocytes 0 hr to 12 hr maturation. Germinal vesicle breakdown was slower in oocytes from pre-pubertal animals with more oocytes still at the germinal vesicle stage approximately 5 hr post-aspiration, compared to oocytes from adult cows (P < 0.05). By 24 hr, development to metaphase II was equivalent for pre-pubertal and adult oocytes. This study identified differences in energy metabolism, oocyte size, and meiotic progression between the oocytes from pre-pubertal and adult cows that may account for the poor developmental potential of many pre-pubertal oocytes.
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Affiliation(s)
- T E Steeves
- Centre for Early Human Development, Institute of Reproduction and Development, Monash University, Monash Medical Centre, Clayton, Victoria, Australia.
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Abstract
The aim of the study was to determine the amino acid requirements of the in vitro-produced bovine embryo as it develops from the zygote to the blastocyst, using a two-step culture system. When added to synthetic oviduct fluid (SOF) for the first 72-h culture, Eagle's nonessential amino acids and glutamine (NeGln) significantly increased development to the 8- to 16-cell stage (Day 4 postinsemination [pi]) and subsequent blastocyst development (Day 7 pi). Glutamine alone during the first 72-h culture did not stimulate development to the 8- to 16-cell stage (p > 0.05); however, the removal of glutamine from NeGln reduced the stimulatory effects of the nonessential amino acids. Replacing glutamine with betaine (an organic osmolyte) in NeGln did not stimulate development to the 8- to 16-cell stage compared to culture in SOF, but it did improve subsequent blastocyst development, indicating an osmolytic function of glutamine during the first 72-h culture. The addition of Eagle's essential amino acids and glutamine to SOF, or to medium already containing nonessential amino acids and glutamine for the first 72-h culture, did not affect cleavage to the 8- to 16-cell stage or subsequent blastocyst development (p > 0.05). Beyond Day 4 pi, culture with 20aa (nonessential and essential amino acids and glutamine) increased blastocyst development, total cell number, and the number of cells in both the trophectoderm and inner cell mass, compared to culture with other groups of amino acids (p < 0.05). Substituting betaine for glutamine in 20aa reduced blastocyst formation, indicating a non-osmolytic function of glutamine during the second 72-h culture. Further, there was a significant negative correlation between the concentration of essential amino acids (quarter, half, or single strength) and embryo development during both the first 72-h and second 72-h culture (p < 0.01), indicating that the concentration of essential amino acids was too high during culture of the bovine embryo. This study identified the temporal and differential effects of amino acids during development of the bovine embryo from the zygote to the blastocyst.
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Affiliation(s)
- T E Steeves
- Centre for Early Human Development, Institute of Reproduction and Development, Monash University, Monash Medical Centre, Clayton, Victoria 3168, Australia.
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