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Hernandez KM, O'Neill KB, Bors EK, Steel D, Zoller JA, Constantine R, Horvath S, Baker CS. Using epigenetic clocks to investigate changes in the age structure of critically endangered Māui dolphins. Ecol Evol 2023; 13:e10562. [PMID: 37780090 PMCID: PMC10534197 DOI: 10.1002/ece3.10562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 10/03/2023] Open
Abstract
The age of an individual is an essential demographic parameter but is difficult to estimate without long-term monitoring or invasive sampling. Epigenetic approaches are increasingly used to age organisms, including nonmodel organisms such as cetaceans. Māui dolphins (Cephalorhynchus hectori maui) are a critically endangered subspecies endemic to Aotearoa New Zealand, and the age structure of this population is important for informing conservation. Here we present an epigenetic clock for aging Māui and Hector's dolphins (C. h. hectori) developed from methylation data using DNA from tooth aged individuals (n = 48). Based on this training data set, the optimal model required only eight methylation sites, provided an age correlation of .95, and had a median absolute age error of 1.54 years. A leave-one-out cross-validation analysis with the same parameters resulted in an age correlation of .87 and median absolute age error of 2.09 years. To improve age estimation, we included previously published beluga whale (Delphinapterus leucas) data to develop a joint beluga/dolphin clock, resulting in a clock with comparable performance and improved estimation of older individuals. Application of the models to DNA from skin biopsy samples of living Māui dolphins revealed a shift from a median age of 8-9 years to a younger population aged 7-8 years 10 years later. These models could be applied to other dolphin species and demonstrate the ability to construct a clock even when the number of known age samples is limited, removing this impediment to estimating demographic parameters vital to the conservation of critically endangered species.
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Affiliation(s)
| | | | - Eleanor K. Bors
- Marine Mammal InstituteOregon State UniversityOregonNewportUSA
| | - Debbie Steel
- Marine Mammal InstituteOregon State UniversityOregonNewportUSA
| | - Joseph A. Zoller
- Fielding School of Public Health, Department of BiostatisticsUniversity of CaliforniaCaliforniaLos AngelesUSA
| | - Rochelle Constantine
- School of Biological Sciences & Institute of Marine ScienceUniversity of Auckland – Waipapa Taumata RauAucklandNew Zealand
| | - Steve Horvath
- Fielding School of Public Health, Department of BiostatisticsUniversity of CaliforniaCaliforniaLos AngelesUSA
- David Geffen School of Medicine, Department of Human GeneticsUniversity of CaliforniaCaliforniaLos AngelesUSA
- Altos LabsCaliforniaSan DiegoUSA
| | - C. Scott Baker
- Marine Mammal InstituteOregon State UniversityOregonNewportUSA
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2
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Reproductive timing as an explanation for skewed parentage assignment ratio in a bisexually philopatric population. Behav Ecol Sociobiol 2022. [DOI: 10.1007/s00265-022-03233-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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3
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Affiliation(s)
- Jan Komdeur
- Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
| | - Long Ma
- Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
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4
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Martien KK, Taylor BL, Chivers SJ, Mahaffy SD, Gorgone AM, Baird RW. Fidelity to natal social groups and mating within and between social groups in an endangered false killer whale population. ENDANGER SPECIES RES 2019. [DOI: 10.3354/esr00995] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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5
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Townsend AK, Taff CC, Jones ML, Getman KH, Wheeler SS, Hinton MG, Logsdon RM. Apparent inbreeding preference despite inbreeding depression in the American crow. Mol Ecol 2019; 28:1116-1126. [PMID: 30222228 DOI: 10.1111/mec.14866] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 08/18/2018] [Accepted: 09/04/2018] [Indexed: 11/28/2022]
Abstract
Although matings between relatives can have negative effects on offspring fitness, apparent inbreeding preference has been reported in a growing number of systems, including those with documented inbreeding depression. Here, we examined evidence for inbreeding depression and inbreeding preference in two populations (Clinton, New York, and Davis, California, USA) of the cooperatively breeding American crow (Corvus brachyrhynchos). We then compared observed inbreeding strategies with theoretical expectations for optimal, adaptive levels of inbreeding, given the inclusive fitness benefits and population-specific magnitude of inbreeding depression. We found that low heterozygosity at a panel of 33 microsatellite markers was associated with low survival probability (fledging success) and low white blood cell counts among offspring in both populations. Despite these costs, our data were more consistent with inbreeding preference than avoidance: The observed heterozygosity among 396 sampled crow offspring was significantly lower than expected if local adults were mating by random chance. This pattern was consistent across a range of spatial scales in both populations. Adaptive levels of inbreeding, given the magnitude of inbreeding depression, were predicted to be very low in the California population, whereas complete disassortative mating was predicted in the New York population. Sexual conflict might have contributed to the apparent absence of inbreeding avoidance in crows. These data add to an increasing number of examples of an "inbreeding paradox," where inbreeding appears to be preferred despite inbreeding depression.
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Affiliation(s)
| | - Conor C Taff
- Cornell University Laboratory of Ornithology, Ithaca, New York
| | - Melissa L Jones
- Avian Sciences Graduate Group, University of California, Davis, California
| | | | - Sarah S Wheeler
- Sacramento-Yolo Mosquito and Vector Control District, Elk Grove, California
| | - Mitch G Hinton
- Animal Behavior Graduate Group, University of California, Davis, California
| | - Ryane M Logsdon
- Animal Behavior Graduate Group, University of California, Davis, California
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6
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Karniski C, Krzyszczyk E, Mann J. Senescence impacts reproduction and maternal investment in bottlenose dolphins. Proc Biol Sci 2018; 285:20181123. [PMID: 30051841 PMCID: PMC6083244 DOI: 10.1098/rspb.2018.1123] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 06/22/2018] [Indexed: 01/13/2023] Open
Abstract
Reproductive senescence is evident across many mammalian species. An emerging perspective considers components of reproductive senescence as evolutionarily distinct phenomena: fertility senescence and maternal-effect senescence. While fertility senescence is regarded as the ageing of reproductive physiology, maternal-effect senescence pertains to the declining capacity to provision and rear surviving offspring due to age. Both contribute to reproductive failure in utero making it difficult to differentiate between the two prenatally in the wild. We investigated both components in a long-lived mammal with prolonged maternal care through three parameters: calf survival, interbirth interval (IBI) and lactation period. We provide clear evidence for reproductive senescence in a wild population of bottlenose dolphins (Tursiops aduncus) using 34+ years of longitudinal data on 229 adult females and 562 calves. Calf survival decreased with maternal age, and calves with older mothers had lower survival than predicted by birth order, suggesting maternal-effect senescence. Both lactation period and IBIs increased with maternal age, and IBIs increased regardless of calf mortality, indicating interactions between fertility and maternal-effect senescence. Of calves that survived to weaning, last-born calves weaned later than earlier-born calves, evidence of terminal investment, a mitigating strategy given reduced reproductive value caused by either components of reproductive senescence.
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Affiliation(s)
- Caitlin Karniski
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | - Ewa Krzyszczyk
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | - Janet Mann
- Department of Biology, Georgetown University, Washington, DC 20057, USA
- Department of Psychology, Georgetown University, Washington, DC 20057, USA
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7
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de Boer RA, Eens M, Müller W. Sex-specific effects of inbreeding on reproductive senescence. Proc Biol Sci 2018; 285:20180231. [PMID: 29794043 PMCID: PMC5998105 DOI: 10.1098/rspb.2018.0231] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/24/2018] [Indexed: 01/29/2023] Open
Abstract
Inbreeding depression plays a significant role in evolutionary biology and ecology. However, we lack a clear understanding of the fitness consequences of inbreeding depression. Studies often focus on short-term effects of inbreeding in juvenile offspring, whereas inbreeding depression in adult traits and the interplay between inbreeding depression and age are rarely addressed. Inbreeding depression may increase with age and accelerate the decline in reproductive output in ageing individuals (reproductive senescence), which could be subject to sex-specific dynamics. We test this hypothesis with a longitudinal experimental study in a short-lived songbird. Adult inbred and outbred male and female canaries were paired in a 2 × 2 factorial design, and survival and annual reproductive performance were studied for 3 years. We found inbreeding depression in female egg-laying ability, male fertilization success and survival of both sexes. Annual reproductive success of both males and females declined when paired with an inbred partner independent of their own inbreeding status. This shows that inbreeding can have fitness costs in outbred individuals when they mate with an inbred individual. Further, inbred females showed faster reproductive senescence than outbred females, confirming that inbreeding depression and age can interact to affect fitness. By contrast, there was no evidence for an interaction between inbreeding depression and reproductive senescence in male fertilization success. Our findings highlight the importance of considering sex-specific effects and age to determine the full range of fitness consequences of inbreeding and demonstrate that inbreeding depression can accelerate reproductive senescence.
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Affiliation(s)
- Raïssa A de Boer
- Behavioural Ecology and Ecophysiology Group, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Marcel Eens
- Behavioural Ecology and Ecophysiology Group, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Wendt Müller
- Behavioural Ecology and Ecophysiology Group, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
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8
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Pérez-Alvarez MJ, Vásquez RA, Moraga R, Santos-Carvallo M, Kraft S, Sabaj V, Capella J, Gibbons J, Vilina Y, Poulin E. Home sweet home: social dynamics and genetic variation of a long-term resident bottlenose dolphin population off the Chilean coast. Anim Behav 2018. [DOI: 10.1016/j.anbehav.2018.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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9
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Mating in a bisexually philopatric society: bottlenose dolphin females associate with adult males but not adult sons during estrous. Behav Ecol Sociobiol 2017. [DOI: 10.1007/s00265-017-2380-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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Robinson KP, Sim TMC, Culloch RM, Bean TS, Cordoba Aguilar I, Eisfeld SM, Filan M, Haskins GN, Williams G, Pierce GJ. Female reproductive success and calf survival in a North Sea coastal bottlenose dolphin (Tursiops truncatus) population. PLoS One 2017; 12:e0185000. [PMID: 28931081 PMCID: PMC5607131 DOI: 10.1371/journal.pone.0185000] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 09/04/2017] [Indexed: 11/18/2022] Open
Abstract
Between-female variation in reproductive output provides a strong measure of individual fitness and a quantifiable measure of the health of a population which may be highly informative to management. In the present study, we examined reproductive traits in female bottlenose dolphins from the east coast of Scotland using longitudinal sightings data collected over twenty years. From a total of 102 females identified between 1997 and 2016, 74 mothers produced a collective total of 193 calves. Females gave birth from 6 to 13 years of age with a mean age of 8. Calves were produced during all study months, May to October inclusive, but showed a seasonal birth pulse corresponding to the regional peak in summer water temperatures. Approximately 83% (n = 116) of the calves of established fate were successfully raised to year 2-3. Of the known mortalities, ~45% were first-born calves. Calf survival rates were also lower in multiparous females who had previously lost calves. A mean inter-birth interval (IBI) of 3.80 years (n = 110) and mean fecundity of 0.16 was estimated for the population. Calf loss resulted in shortened IBIs, whilst longer IBIs were observed in females assumed to be approaching reproductive senescence. Maternal age and size, breeding experience, dominance, individual associations, group size and other social factors, were all concluded to influence reproductive success (RS) in this population. Some females are likely more important than others for the future viability of the population. Consequently, a better knowledge of the demographic groups containing those females showing higher reproductive success would be highly desirable for conservation efforts aimed at their protection.
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Affiliation(s)
- Kevin P. Robinson
- Cetacean Research & Rescue Unit (CRRU), Banff, Scotland, United Kingdom
| | - Texa M. C. Sim
- Cetacean Research & Rescue Unit (CRRU), Banff, Scotland, United Kingdom
- Oceanlab, University of Aberdeen, Newburgh, Scotland, United Kingdom
| | - Ross M. Culloch
- Cetacean Research & Rescue Unit (CRRU), Banff, Scotland, United Kingdom
| | - Thomas S. Bean
- Cetacean Research & Rescue Unit (CRRU), Banff, Scotland, United Kingdom
| | | | - Sonja M. Eisfeld
- Cetacean Research & Rescue Unit (CRRU), Banff, Scotland, United Kingdom
| | - Miranda Filan
- Cetacean Research & Rescue Unit (CRRU), Banff, Scotland, United Kingdom
| | - Gary N. Haskins
- Cetacean Research & Rescue Unit (CRRU), Banff, Scotland, United Kingdom
| | | | - Graham J. Pierce
- Oceanlab, University of Aberdeen, Newburgh, Scotland, United Kingdom
- CESAM and Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
- Instituto de Investigacións Mariñas (CSIC), Vigo, Spain
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11
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Emami-Khoyi A, Paterson AM, Hartley DA, Boren LJ, Cruickshank RH, Ross JG, Murphy EC, Else TA. Mitogenomics data reveal effective population size, historical bottlenecks, and the effects of hunting on New Zealand fur seals (Arctocephalus forsteri). Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:567-580. [PMID: 28539070 DOI: 10.1080/24701394.2017.1325478] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The New Zealand fur seal (Arctocephalus forsteri) passed through a population bottleneck due to commercial sealing during the eighteenth to nineteenth centuries. To facilitate future management options, we reconstructed the demographic history of New Zealand fur seals in a Bayesian framework using maternally inherited, mitochondrial DNA sequences. Mitogenomic data suggested two separate clades (most recent common ancestor 5000 years ago) of New Zealand fur seals that survived large-scale human harvest. Mitochondrial haplotype diversity was high, with 45 singletons identified from 46 individuals although mean nucleotide diversity was low (0.012 ± 0.0061). Variation was not constrained geographically. Analyses of mitogenomes support the hypothesis for a population bottleneck approximately 35 generations ago, which coincides with the peak of commercial sealing. Mitogenomic data are consistent with a pre-human effective population size of approximately 30,000 that first declined to around 10,000 (due to the impact of Polynesian colonization, particularly in the first 100 years of their arrival into New Zealand), and then to 100-200 breeding individuals during peak of commercial sealing.
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Affiliation(s)
- Arsalan Emami-Khoyi
- a Center for Ecological Genomics and Wildlife Conservation , University of Johannesburg , Auckland Park , South Africa.,b Department of Ecology , Lincoln University , Lincoln , New Zealand
| | - Adrian M Paterson
- b Department of Ecology , Lincoln University , Lincoln , New Zealand
| | | | - Laura J Boren
- d New Zealand Department of Conservation , Wellington-Te Aro , New Zealand
| | | | - James G Ross
- b Department of Ecology , Lincoln University , Lincoln , New Zealand.,e Centre for Wildlife Management and Conservation , Lincoln University , Lincoln , New Zealand
| | - Elaine C Murphy
- b Department of Ecology , Lincoln University , Lincoln , New Zealand.,e Centre for Wildlife Management and Conservation , Lincoln University , Lincoln , New Zealand
| | - Terry-Ann Else
- f Department of Basic Science , Touro University , NV , USA
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12
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Dunn SJ, Byers JA. How Pronghorn Females Avoid Inbreeding Depression. Ethology 2016. [DOI: 10.1111/eth.12567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Stacey J. Dunn
- Department of Biological Sciences University of Idaho Moscow ID USA
| | - John A. Byers
- Department of Biological Sciences University of Idaho Moscow ID USA
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13
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Bouchebti S, Durier V, Pasquaretta C, Rivault C, Lihoreau M. Subsocial Cockroaches Nauphoeta cinerea Mate Indiscriminately with Kin Despite High Costs of Inbreeding. PLoS One 2016; 11:e0162548. [PMID: 27655156 PMCID: PMC5031396 DOI: 10.1371/journal.pone.0162548] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 08/24/2016] [Indexed: 11/26/2022] Open
Abstract
Many animals have evolved strategies to reduce risks of inbreeding and its deleterious effects on the progeny. In social arthropods, such as the eusocial ants and bees, inbreeding avoidance is typically achieved by the dispersal of breeders from their native colony. However studies in presocial insects suggest that kin discrimination during mate choice may be a more common mechanism in socially simpler species with no reproductive division of labour. Here we examined this possibility in the subsocial cockroach Nauphoeta cinerea, a model species for research in sexual selection, where males establish dominance hierarchies to access females and control breeding territories. When given a binary choice between a sibling male and a non-sibling male that had the opportunity to establish a hierarchy prior to the tests, females mated preferentially with the dominant male, irrespective of kinship or body size. Despite the lack of kin discrimination during mate choice, inbred-mated females incurred significant fitness costs, producing 20% less offspring than outbred-mated females. We discuss how the social mating system of this territorial cockroach may naturally limit the probability of siblings to encounter and reproduce, without the need for evolving active inbreeding avoidance mechanisms, such as kin recognition.
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Affiliation(s)
- Sofia Bouchebti
- Research Center on Animal Cognition (CRCA), Center for Integrative Biology (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Virginie Durier
- CNRS UMR 6552 Ethologie Animale et Humaine, Université de Rennes 1, Avenue du Général Leclerc, Rennes, France
| | - Cristian Pasquaretta
- Research Center on Animal Cognition (CRCA), Center for Integrative Biology (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Colette Rivault
- CNRS UMR 6552 Ethologie Animale et Humaine, Université de Rennes 1, Avenue du Général Leclerc, Rennes, France
| | - Mathieu Lihoreau
- Research Center on Animal Cognition (CRCA), Center for Integrative Biology (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
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14
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Allen SJ, Bryant KA, Kraus RHS, Loneragan NR, Kopps AM, Brown AM, Gerber L, Krützen M. Genetic isolation between coastal and fishery-impacted, offshore bottlenose dolphin (Tursiopsspp.) populations. Mol Ecol 2016; 25:2735-53. [DOI: 10.1111/mec.13622] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/17/2016] [Accepted: 03/11/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Simon J. Allen
- Cetacean Research Unit; School of Veterinary and Life Sciences; Murdoch University; Perth Western Australia 6150 Australia
- Centre for Marine Futures; School of Animal Biology and Oceans Institute; University of Western Australia; Perth Western Australia 6009 Australia
| | - Kate A. Bryant
- School of Veterinary and Life Sciences; Murdoch University; Murdoch Western Australia 6150 Australia
| | - Robert H. S. Kraus
- Department of Biology; University of Konstanz; 78457 Konstanz Germany
- Department of Migration and Immuno-Ecology; Max Planck Institute for Ornithology; Am Obstberg 1 78315 Radolfzell Germany
| | - Neil R. Loneragan
- School of Veterinary and Life Sciences; Murdoch University; Murdoch Western Australia 6150 Australia
| | - Anna M. Kopps
- Evolutionary Genetics Group; Department of Anthropology; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
- Evolution and Ecology Research Centre; School of Biological; Earth and Environmental Sciences; University of New South Wales; Sydney New South Wales 2052 Australia
| | - Alexander M. Brown
- Cetacean Research Unit; School of Veterinary and Life Sciences; Murdoch University; Perth Western Australia 6150 Australia
| | - Livia Gerber
- Evolutionary Genetics Group; Department of Anthropology; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Michael Krützen
- Evolutionary Genetics Group; Department of Anthropology; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
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15
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16
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Manlik O, McDonald JA, Mann J, Raudino HC, Bejder L, Krützen M, Connor RC, Heithaus MR, Lacy RC, Sherwin WB. The relative importance of reproduction and survival for the conservation of two dolphin populations. Ecol Evol 2016; 6:3496-3512. [PMID: 28725349 PMCID: PMC5513288 DOI: 10.1002/ece3.2130] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 03/19/2016] [Accepted: 03/21/2016] [Indexed: 11/23/2022] Open
Abstract
It has been proposed that in slow‐growing vertebrate populations survival generally has a greater influence on population growth than reproduction. Despite many studies cautioning against such generalizations for conservation, wildlife management for slow‐growing populations still often focuses on perturbing survival without careful evaluation as to whether those changes are likely or feasible. Here, we evaluate the relative importance of reproduction and survival for the conservation of two bottlenose dolphin (Tursiops cf aduncus) populations: a large, apparently stable population and a smaller one that is forecast to decline. We also assessed the feasibility and effectiveness of wildlife management objectives aimed at boosting either reproduction or survival. Consistent with other analytically based elasticity studies, survival had the greatest effect on population trajectories when altering vital rates by equal proportions. However, the findings of our alternative analytical approaches are in stark contrast to commonly used proportional sensitivity analyses and suggest that reproduction is considerably more important. We show that in the stable population reproductive output is higher, and adult survival is lower; the difference in viability between the two populations is due to the difference in reproduction; reproductive rates are variable, whereas survival rates are relatively constant over time; perturbations on the basis of observed, temporal variation indicate that population dynamics are much more influenced by reproduction than by adult survival; for the apparently declining population, raising reproductive rates would be an effective and feasible tool to reverse the forecast population decline; increasing survival would be ineffective.
Our findings highlight the importance of reproduction – even in slow‐growing populations – and the need to assess the effect of natural variation in vital rates on population viability. We echo others in cautioning against generalizations based on life‐history traits and recommend that population modeling for conservation should also take into account the magnitude of vital rate changes that could be attained under alternative management scenarios.
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Affiliation(s)
- Oliver Manlik
- Evolution and Ecology Research Centre School of Biological, Earth and Environmental Sciences University of New South Wales Sydney New South Wales 2052 Australia
| | - Jane A McDonald
- Evolution and Ecology Research Centre School of Biological, Earth and Environmental Sciences University of New South Wales Sydney New South Wales 2052 Australia.,Present address: School of Biological Sciences University of Queensland St Lucia Queensland 4067 Australia
| | - Janet Mann
- Evolution and Ecology Research Centre School of Biological, Earth and Environmental Sciences University of New South Wales Sydney New South Wales 2052 Australia.,Department of Biology and Psychology Georgetown University 37th and O St. NW Washington DC 20057
| | - Holly C Raudino
- Cetacean Research Unit School of Veterinary and Life Sciences Murdoch University South Street Murdoch Western Australia 6150 Australia.,Marine Science Program Department of Parks and Wildlife 17 Dick Perry Avenue. Perth Western Australia 6151 Australia
| | - Lars Bejder
- Cetacean Research Unit School of Veterinary and Life Sciences Murdoch University South Street Murdoch Western Australia 6150 Australia
| | - Michael Krützen
- Evolution and Ecology Research Centre School of Biological, Earth and Environmental Sciences University of New South Wales Sydney New South Wales 2052 Australia.,Anthropological Institute and Museum University of Zurich Winterthurerstrasse 1908057 Zurich Switzerland
| | - Richard C Connor
- Evolution and Ecology Research Centre School of Biological, Earth and Environmental Sciences University of New South Wales Sydney New South Wales 2052 Australia.,Biology Department UMASS-Dartmouth Dartmouth Massachusetts 02747
| | - Michael R Heithaus
- Department of Biological Science School of Environment Arts and Society Florida International University North Miami Florida 33181
| | - Robert C Lacy
- Chicago Zoological Society Brookfield Illinois 60513
| | - William B Sherwin
- Evolution and Ecology Research Centre School of Biological, Earth and Environmental Sciences University of New South Wales Sydney New South Wales 2052 Australia.,Cetacean Research Unit School of Veterinary and Life Sciences Murdoch University South Street Murdoch Western Australia 6150 Australia
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17
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Abstract
Inbreeding depression is of major concern for the conservation of threatened species, and inbreeding avoidance is thought to be a key driver in the evolution of mating systems. However, the estimation of individual inbreeding coefficients in natural populations has been challenging, and, consequently, the full effect of inbreeding on fitness remains unclear. Genomic inbreeding coefficients may resolve the long-standing paucity of data on inbreeding depression in adult traits and total fitness. Here we investigate inbreeding depression in a range of life history traits and fitness in a wild population of red deer (Cervus elaphus) in Scotland using individual inbreeding coefficients derived from dense Single-Nucleotide Polymorphism (SNP) data (Fgrm). We find associations between[Formula: see text]and annual breeding success in both sexes, and between maternal inbreeding coefficient and offspring survival. We also confirm previous findings of inbreeding depression in birth weight and juvenile survival. In contrast, inbreeding coefficients calculated from a deep and comparatively complete pedigree detected inbreeding depression in juvenile survival, but not in any adult fitness component. The total effect of inbreeding on lifetime breeding success (LBS) was substantial in both sexes: for Fgrm = 0.125, a value resulting from a half-sib mating, LBS declined by 72% for females and 95% for males. Our results demonstrate that SNP-based estimates of inbreeding provide a powerful tool for evaluating inbreeding depression in natural populations, and suggest that, to date, the prevalence of inbreeding depression in adult traits may have been underestimated.
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18
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Brough TE, Henderson S, Guerra M, Dawson SM. Factors influencing heterogeneity in female reproductive success in a Critically Endangered population of bottlenose dolphins. ENDANGER SPECIES RES 2016. [DOI: 10.3354/esr00715] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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20
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Frère CH, Chandrasoma D, Whiting MJ. Polyandry in dragon lizards: inbred paternal genotypes sire fewer offspring. Ecol Evol 2015; 5:1686-92. [PMID: 25937911 PMCID: PMC4409416 DOI: 10.1002/ece3.1447] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 02/01/2015] [Accepted: 02/08/2015] [Indexed: 11/11/2022] Open
Abstract
Multiple mating in female animals is something of a paradox because it can either be risky (e.g., higher probability of disease transmission, social costs) or provide substantial fitness benefits (e.g., genetic bet hedging whereby the likelihood of reproductive failure is lowered). The genetic relatedness of parental units, particularly in lizards, has rarely been studied in the wild. Here, we examined levels of multiple paternity in Australia's largest agamid lizard, the eastern water dragon (Intellagama lesueurii), and determined whether male reproductive success is best explained by its heterozygosity coefficient or the extent to which it is related to the mother. Female polyandry was the norm: 2/22 clutches (9.2%) were sired by three or more fathers, 17/22 (77.2%) were sired by two fathers, and only 3/22 (13.6%) clutches were sired by one father. Moreover, we reconstructed the paternal genotypes for 18 known mother–offspring clutches and found no evidence that females were favoring less related males or that less related males had higher fitness. However, males with greater heterozygosity sired more offspring. While the postcopulatory mechanisms underlying this pattern are not understood, female water dragons likely represent another example of reproduction through cryptic means (sperm selection/sperm competition) in a lizard, and through which they may ameliorate the effects of male-driven precopulatory sexual selection.
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Affiliation(s)
- Celine H Frère
- GeneCology Research Centre, University of the Sunshine Coast Maroochydore DC, Sunshine Coast, Queensland, 4558, Australia
| | - Dani Chandrasoma
- Department of Biological Sciences, Macquarie University Sydney, New South Wales, 2109, Australia
| | - Martin J Whiting
- Department of Biological Sciences, Macquarie University Sydney, New South Wales, 2109, Australia
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Kopps AM, Ackermann CY, Sherwin WB, Allen SJ, Bejder L, Krützen M. Cultural transmission of tool use combined with habitat specializations leads to fine-scale genetic structure in bottlenose dolphins. Proc Biol Sci 2014; 281:20133245. [PMID: 24648223 DOI: 10.1098/rspb.2013.3245] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Socially learned behaviours leading to genetic population structure have rarely been described outside humans. Here, we provide evidence of fine-scale genetic structure that has probably arisen based on socially transmitted behaviours in bottlenose dolphins (Tursiops sp.) in western Shark Bay, Western Australia. We argue that vertical social transmission in different habitats has led to significant geographical genetic structure of mitochondrial DNA (mtDNA) haplotypes. Dolphins with mtDNA haplotypes E or F are found predominantly in deep (more than 10 m) channel habitat, while dolphins with a third haplotype (H) are found predominantly in shallow habitat (less than 10 m), indicating a strong haplotype-habitat correlation. Some dolphins in the deep habitat engage in a foraging strategy using tools. These 'sponging' dolphins are members of one matriline, carrying haplotype E. This pattern is consistent with what had been demonstrated previously at another research site in Shark Bay, where vertical social transmission of sponging had been shown using multiple lines of evidence. Using an individual-based model, we found support that in western Shark Bay, socially transmitted specializations may have led to the observed genetic structure. The reported genetic structure appears to present an example of cultural hitchhiking of mtDNA haplotypes on socially transmitted foraging strategies, suggesting that, as in humans, genetic structure can be shaped through cultural transmission.
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Affiliation(s)
- Anna M Kopps
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, , Sydney, New South Wales 2052, Australia, Evolutionary Genetics Group, Anthropological Institute and Museum, University of Zurich, , Winterthurerstrasse 190, Zurich 8057, Switzerland, Murdoch University Cetacean Research Unit, Centre for Fish, Fisheries and Aquatic Ecosystems Research, School of Veterinary and Life Sciences, Murdoch University, , South Street, Murdoch, Western Australia 6150, Australia
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Mourier J, Buray N, Schultz JK, Clua E, Planes S. Genetic network and breeding patterns of a sicklefin lemon shark (Negaprion acutidens) population in the Society Islands, French Polynesia. PLoS One 2013; 8:e73899. [PMID: 23967354 PMCID: PMC3742621 DOI: 10.1371/journal.pone.0073899] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 07/23/2013] [Indexed: 11/19/2022] Open
Abstract
Human pressures have put many top predator populations at risk of extinction. Recent years have seen alarming declines in sharks worldwide, while their resilience remains poorly understood. Studying the ecology of small populations of marine predators is a priority to better understand their ability to withstand anthropogenic and environmental stressors. In the present study, we monitored a naturally small island population of 40 adult sicklefin lemon sharks in Moorea, French Polynesia over 5 years. We reconstructed the genetic relationships among individuals and determined the population's mating system. The genetic network illustrates that all individuals, except one, are interconnected at least through one first order genetic relationship. While this species developed a clear inbreeding avoidance strategy involving dispersal and migration, the small population size, low number of breeders, and the fragmented environment characterizing these tropical islands, limits its complete effectiveness.
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Affiliation(s)
- Johann Mourier
- LabEx CORAIL - USR 3278 CNRS-EPHE, Centre de Recherche Insulaire et Observatoire de l'Environnement (CRIOBE), Papetoai, Moorea, French Polynesia.
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Szulkin M, Stopher KV, Pemberton JM, Reid JM. Inbreeding avoidance, tolerance, or preference in animals? Trends Ecol Evol 2013. [DOI: 10.1016/j.tree.2012.10.016] [Citation(s) in RCA: 158] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Loyau A, Cornuau JH, Clobert J, Danchin E. Incestuous sisters: mate preference for brothers over unrelated males in Drosophila melanogaster. PLoS One 2012; 7:e51293. [PMID: 23251487 PMCID: PMC3519633 DOI: 10.1371/journal.pone.0051293] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 11/01/2012] [Indexed: 11/20/2022] Open
Abstract
The literature is full of examples of inbreeding avoidance, while recent mathematical models predict that inbreeding tolerance or even inbreeding preference should be expected under several realistic conditions like e.g. polygyny. We investigated male and female mate preferences with respect to relatedness in the fruit fly D. melanogaster. Experiments offered the choice between a first order relative (full-sibling or parent) and an unrelated individual with the same age and mating history. We found that females significantly preferred mating with their brothers, thus supporting inbreeding preference. Moreover, females did not avoid mating with their fathers, and males did not avoid mating with their sisters, thus supporting inbreeding tolerance. Our experiments therefore add empirical evidence for inbreeding preference, which strengthens the prediction that inbreeding tolerance and preference can evolve under specific circumstances through the positive effects on inclusive fitness.
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Affiliation(s)
- Adeline Loyau
- CNRS, Station d'Ecologie Expérimentale du CNRS à Moulis, USR 2936, Saint Girons, France.
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Mourier J, Planes S. Direct genetic evidence for reproductive philopatry and associated fine-scale migrations in female blacktip reef sharks (Carcharhinus melanopterus) in French Polynesia. Mol Ecol 2012; 22:201-14. [PMID: 23130666 DOI: 10.1111/mec.12103] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 09/19/2012] [Accepted: 09/24/2012] [Indexed: 11/29/2022]
Abstract
Conservation of top predators has been emphasized as essential in an ecosystem due to their role in trophic chain regulation. Optimizing conservation strategies for these endangered marine top predators requires direct estimates of breeding patterns and connectivity as these are essential to understanding the population dynamics. There have been some attempts to investigate breeding patterns of reef sharks from litter reconstruction using molecular analyses. However, direct fine-scale migrations of female sharks for parturition as well as connectivity at a medium scale like between islands remain mostly unknown. We used microsatellite DNA markers and a likelihood-based parentage analysis to determine breeding patterns of female blacktip reef sharks in Moorea (Society Islands, French Polynesia). Most females gave birth at their home island but some migrated to specific nursery areas outside the area they are attached to, sometimes going to another island 50 km away across deep ocean. Our analysis also revealed that females migrated to the same nursery for every birthing event. Many offspring showed a high level of inbreeding indicating an overall reduced population size, restricted movements and dispersal, or specific mating behaviour. Females represent the vectors that transport the genes at nursery grounds, and their fidelity should thus define reproductive units. As females seem to be philopatric, males could be the ones dispersing genes between populations. These results highlight the need to conserve coastal zones where female reef sharks seem to exhibit philopatry during the breeding season.
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Affiliation(s)
- Johann Mourier
- Laboratoire d'Excellence CORAIL, USR 3278 CNRS-EPHE, CRIOBE, BP 1013, 98729, Moorea, French Polynesia.
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Ringler E, Ringler M, Jehle R, Hödl W. The female perspective of mating in A. femoralis, a territorial frog with paternal care--a spatial and genetic analysis. PLoS One 2012; 7:e40237. [PMID: 22768260 PMCID: PMC3386955 DOI: 10.1371/journal.pone.0040237] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 06/03/2012] [Indexed: 11/25/2022] Open
Abstract
The adaptive significance of sequential polyandry is a challenging question in evolutionary and behavioral biology. Costs and benefits of different mating patterns are shaped by the spatial distribution of individuals and by genetic parameters such as the pairwise relatedness between potential mating partners. Thus, females should become less choosy as costs of mating and searching for mates increase. We used parentage assignments to investigate spatial and genetic patterns of mating across a natural population of the Neotropical frog Allobates femoralis, a species characterized by male territoriality and care and female iteroparity. There was no correlation between genetic and spatial distances between adult individuals across the population. In 72% of cases, females mated with males available within a radius of 20 m. Mean pairwise relatedness coefficients of successful reproducers did not differ from random mating but had a lower variance than expected by chance, suggesting maximal reproductive output at intermediate genetic divergence. We also found evidence for selection in favor of more heterozygous individuals between the embryo and adult stage. The level of sequential polyandry significantly increased with the number of spatially available males. Females that had more candidate males also produced more adult progeny. We hypothesize that the benefits associated with female multiple mating outweigh the costs of in- and outbreeding depression, and consequently precluded the evolution of 'choosy' mate selection in this species.
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Affiliation(s)
- Eva Ringler
- University of Vienna, Department of Evolutionary Biology, Vienna, Austria.
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Affiliation(s)
- S. J. Dunn
- Department of Biological Sciences University of Idaho Moscow ID USA
| | - E. Clancey
- Department of Biological Sciences University of Idaho Moscow ID USA
| | - L. P. Waits
- Department of Fish and Wildlife Resources University of Idaho Moscow ID USA
| | - J. A. Byers
- Department of Biological Sciences University of Idaho Moscow ID USA
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Chapman DD, Simpfendorfer CA, Wiley TR, Poulakis GR, Curtis C, Tringali M, Carlson JK, Feldheim KA. Genetic diversity despite population collapse in a critically endangered marine fish: the smalltooth sawfish (Pristis pectinata). ACTA ACUST UNITED AC 2011; 102:643-52. [PMID: 21926063 DOI: 10.1093/jhered/esr098] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Sawfish (family Pristidae) are among the most critically endangered marine fish in the world, yet very little is known about how genetic bottlenecks, genetic drift, and inbreeding depression may be affecting these elasmobranchs. In the US Atlantic, the smalltooth sawfish (Pristis pectinata) has declined to 1-5% of its abundance in the 1900s, and its core distribution has contracted to southwest Florida. We used 8 polymorphic microsatellite markers to show that this remnant population still exhibits high genetic diversity in terms of average allelic richness (18.23), average alleles per locus (18.75, standard deviation [SD] 6.6) and observed heterozygosity (0.43-0.98). Inbreeding is rare (mean individual internal relatedness = -0.02, SD 0.14; F(IS) = -0.011, 95% confidence interval [CI] = -0.039 to 0.011), even though the estimated effective population size (N(e)) is modest (250-350, 95% CI = 142-955). Simulations suggest that the remnant smalltooth sawfish population will probably retain >90% of its current genetic diversity over the next century even at the lower estimate of N(e). There is no evidence of a genetic bottleneck accompanying last century's demographic bottleneck, and we discuss hypotheses that could explain this. We also discuss features of elasmobranch life history and population biology that could make them less vulnerable than other large marine vertebrates to genetic change associated with reduced population size.
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Affiliation(s)
- Demian D Chapman
- Institute for Ocean Conservation Science & School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, NY 11794, USA.
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Ford MJ, Hanson MB, Hempelmann JA, Ayres KL, Emmons CK, Schorr GS, Baird RW, Balcomb KC, Wasser SK, Parsons KM, Balcomb-Bartok K. Inferred Paternity and Male Reproductive Success in a Killer Whale (Orcinus orca) Population. ACTA ACUST UNITED AC 2011; 102:537-53. [PMID: 21757487 DOI: 10.1093/jhered/esr067] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We used data from 78 individuals at 26 microsatellite loci to infer parental and sibling relationships within a community of fish-eating ("resident") eastern North Pacific killer whales (Orcinus orca). Paternity analysis involving 15 mother/calf pairs and 8 potential fathers and whole-pedigree analysis of the entire sample produced consistent results. The variance in male reproductive success was greater than expected by chance and similar to that of other aquatic mammals. Although the number of confirmed paternities was small, reproductive success appeared to increase with male age and size. We found no evidence that males from outside this small population sired any of the sampled individuals. In contrast to previous results in a different population, many offspring were the result of matings within the same "pod" (long-term social group). Despite this pattern of breeding within social groups, we found no evidence of offspring produced by matings between close relatives, and the average internal relatedness of individuals was significantly less than expected if mating were random. The population's estimated effective size was <30 or about 1/3 of the current census size. Patterns of allele frequency variation were consistent with a population bottleneck.
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Affiliation(s)
- Michael J Ford
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, Seattle, WA 98112, USA.
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Fríre CH, Mann J, Krützen M, Connor RC, Bejder L, Sherwin WB. Nature and nurture: A step towards investigating their interactions in the wild. Commun Integr Biol 2011; 4:192-3. [PMID: 21655437 DOI: 10.4161/cib.4.2.14297] [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: 11/25/2010] [Accepted: 11/26/2010] [Indexed: 11/19/2022] Open
Abstract
The debate about the relative importance of nature versus nurture has been around for decades, but despite this, there has been very little evidence about how these might in fact interact to drive evolution in the wild. Recently, the identification of a comparable methodology for analyzing both genetic and social effects of phenotypic variation revealed that fitness variation in a free-living population of dolphin was driven by a strong social and genetic interaction. This study not only provides evidence that nature and nurture do interact to drive phenotypic evolution but also represents a step towards partitioning the effects of genetic, social, environmental factors and their multiway interactions to better understand phenotypic evolution in the wild.
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Affiliation(s)
- Celine H Fríre
- School of Biological Earth and Ecological Sciences; University of New South Wales; Sydney, Australia
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Rioux-Paquette E, Festa-Bianchet M, Coltman DW. No inbreeding avoidance in an isolated population of bighorn sheep. Anim Behav 2010. [DOI: 10.1016/j.anbehav.2010.08.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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