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Strickland K, Jones ME, Storfer A, Hamede RK, Hohenlohe PA, Margres MJ, McCallum HI, Comte S, Lachish S, Kruuk LEB. Adaptive potential in the face of a transmissible cancer in Tasmanian devils. Mol Ecol 2024; 33:e17531. [PMID: 39340219 PMCID: PMC11521764 DOI: 10.1111/mec.17531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/28/2024] [Accepted: 09/03/2024] [Indexed: 09/30/2024]
Abstract
Emerging infectious diseases (EIDs) not only cause catastrophic declines in wildlife populations but also generate selective pressures that may result in rapid evolutionary responses. One such EID is devil facial tumour disease (DFTD) in the Tasmanian devil. DFTD is almost always fatal and has reduced the average lifespan of individuals by around 2 years, likely causing strong selection for traits that reduce susceptibility to the disease, but population decline has also left Tasmanian devils vulnerable to inbreeding depression. We analysed 22 years of data from an ongoing study of a population of Tasmanian devils on Freycinet Peninsula, Tasmania, to (1) identify whether DFTD may be causing selection on body size, by estimating phenotypic and genetic correlations between DFTD and size traits, (2) estimate the additive genetic variance of susceptibility to DFTD, and (3) investigate whether size traits or susceptibility to DFTD were under inbreeding depression. We found a positive phenotypic relationship between head width and susceptibility to DFTD, but this was not underpinned by a genetic correlation. Conversely, we found a negative phenotypic relationship between body weight and susceptibility to DFTD, and there was evidence for a negative genetic correlation between susceptibility to DFTD and body weight. There was additive genetic variance in susceptibility to DFTD, head width and body weight, but there was no evidence for inbreeding depression in any of these traits. These results suggest that Tasmanian devils have the potential to respond adaptively to DFTD, although the realised evolutionary response will critically further depend on the evolution of DFTD itself.
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Affiliation(s)
- Kasha Strickland
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, UK
| | - Menna E. Jones
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, Washington, USA 99164-4236
| | - Rodrigo K Hamede
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Paul A Hohenlohe
- Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844
| | - Mark J Margres
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Hamish I McCallum
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia
| | - Sebastien Comte
- Vertebrate Pest Research Unit, NSW Department of Primary Industries, 1447 Forest Rd, Orange NSW 2800, Australia
| | - Shelly Lachish
- Public Health Intelligence Branch, Queensland Public Health and Scientific Services Division, Queensland Health, 15 Butterfield Street, Herston, QLD 4006
| | - Loeske E B Kruuk
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, UK
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2
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Hewett AM, Johnston SE, Morris A, Morris S, Pemberton JM. Genetic architecture of inbreeding depression may explain its persistence in a population of wild red deer. Mol Ecol 2024; 33:e17335. [PMID: 38549143 DOI: 10.1111/mec.17335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/01/2024] [Accepted: 03/20/2024] [Indexed: 04/23/2024]
Abstract
Inbreeding depression is of major concern in declining populations, but relatively little is known about its genetic architecture in wild populations, such as the degree to which it is composed of large or small effect loci and their distribution throughout the genome. Here, we combine fitness and genomic data from a wild population of red deer to investigate the genomic distribution of inbreeding effects. Based on the runs of homozygosity (ROH)-based inbreeding coefficient, FROH, we use chromosome-specific inbreeding coefficients (FROHChr) to explore whether the effect of inbreeding varies between chromosomes. Under the assumption that within an individual the probability of being identical-by-descent is equal across all chromosomes, we used a multi-membership model to estimate the deviation of FROHChr from the average inbreeding effect. This novel approach ensures effect sizes are not overestimated whilst maximising the power of our available dataset of >3000 individuals genotyped on >35,000 autosomal SNPs. We find that most chromosomes confer a minor reduction in fitness-related traits, which when these effects are summed, results in the observed inbreeding depression in birth weight, survival and lifetime breeding success. However, no chromosomes had a significant detrimental effect compared to the overall effect of inbreeding, indicating no major effect loci. We conclude that in this population, inbreeding depression is likely the result of multiple mildly or moderately deleterious mutations spread across all chromosomes, which are difficult to detect with statistical confidence. Such mutations will be inefficiently purged, which may explain the persistence of inbreeding depression in this population.
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Affiliation(s)
- Anna M Hewett
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Department of Ecology and Evolution, University of Lausanne (UNIL), Lausanne, Switzerland
| | - Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Alison Morris
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Sean Morris
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Josephine M Pemberton
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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3
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Babarinde IA, Adeola AC, Djagoun CAMS, Nneji LM, Okeyoyin AO, Niba G, Wanzie NK, Oladipo OC, Adebambo AO, Bello SF, Ng’ang’a SI, Olaniyi WA, Okoro VMO, Adedeji BE, Olatunde O, Ayoola AO, Matouke MM, Wang YY, Sanke OJ, Oseni SO, Nwani CD, Murphy RW. Population structure and evolutionary history of the greater cane rat ( Thryonomys swinderianus) from the Guinean Forests of West Africa. Front Genet 2023; 14:1041103. [PMID: 36923796 PMCID: PMC10010571 DOI: 10.3389/fgene.2023.1041103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 02/07/2023] [Indexed: 03/02/2023] Open
Abstract
Grasscutter (Thryonomys swinderianus) is a large-body old world rodent found in sub-Saharan Africa. The body size and the unique taste of the meat of this major crop pest have made it a target of intense hunting and a potential consideration as a micro-livestock. However, there is insufficient knowledge on the genetic diversity of its populations across African Guinean forests. Herein, we investigated the genetic diversity, population structures and evolutionary history of seven Nigerian wild grasscutter populations together with individuals from Cameroon, Republic of Benin, and Ghana, using five mitochondrial fragments, including D-loop and cytochrome b (CYTB). D-loop haplotype diversity ranged from 0.571 (± 0.149) in Republic of Benin to 0.921 (± 0.013) in Ghana. Within Nigeria, the haplotype diversity ranged from 0.659 (± 0.059) in Cross River to 0.837 (± 0.075) in Ondo subpopulation. The fixation index (FST), haplotype frequency distribution and analysis of molecular variance revealed varying levels of population structures across populations. No significant signature of population contraction was detected in the grasscutter populations. Evolutionary analyses of CYTB suggests that South African population might have diverged from other populations about 6.1 (2.6-10.18, 95% CI) MYA. Taken together, this study reveals the population status and evolutionary history of grasscutter populations in the region.
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Affiliation(s)
- Isaac A. Babarinde
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Adeniyi C. Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Kunming, China
- Centre for Biotechnology Research, Bayero University, Kano, Nigeria
| | - Chabi A. M. S. Djagoun
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, Cotonou, Benin
| | - Lotanna M. Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States
| | - Agboola O. Okeyoyin
- National Park Service Headquarters, Federal Capital Territory, Abuja, Nigeria
| | - George Niba
- National Centre for Animal Husbandry and Veterinary Training, Jakiri, North West Region, Cameroon
| | - Ndifor K. Wanzie
- Department of Zoology, University of Douala, Douala, Cameroon
- Department of Zoology, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | | | - Ayotunde O. Adebambo
- Animal Genetics & Biotechnology, Federal University of Agriculture, Abeokuta, Nigeria
| | - Semiu F. Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Said I. Ng’ang’a
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wasiu A. Olaniyi
- Department of Animal Science, Faculty of Agriculture, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| | - Victor M. O. Okoro
- Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | | | - Omotoso Olatunde
- Department of Zoology, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Adeola O. Ayoola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Kunming, China
| | - Moise M. Matouke
- Department of Fisheries and Aquatic Resources Management, University of Buea, Buea, Cameroon
| | | | - Oscar J. Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | - Saidu O. Oseni
- Department of Animal Sciences, Faculty of Agriculture, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Christopher D. Nwani
- Department of Zoology and Environmental Biology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Nigeria
| | - Robert W. Murphy
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada
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4
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Decomposing phenotypic skew and its effects on the predicted response to strong selection. Nat Ecol Evol 2022; 6:774-785. [PMID: 35422480 DOI: 10.1038/s41559-022-01694-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/08/2022] [Indexed: 12/29/2022]
Abstract
The major frameworks for predicting evolutionary change assume that a phenotype's underlying genetic and environmental components are normally distributed. However, the predictions of these frameworks may no longer hold if distributions are skewed. Despite this, phenotypic skew has never been decomposed, meaning the fundamental assumptions of quantitative genetics remain untested. Here we demonstrate that the substantial phenotypic skew in the body size of juvenile blue tits (Cyanistes caeruleus) is driven by environmental factors. Although skew had little impact on our predictions of selection response in this case, our results highlight the impact of skew on the estimation of inheritance and selection. Specifically, the nonlinear parent-offspring regressions induced by skew, alongside selective disappearance, can strongly bias estimates of heritability. The ubiquity of skew and strong directional selection on juvenile body size imply that heritability is commonly overestimated, which may in part explain the discrepancy between predicted and observed trait evolution.
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5
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Khera M, Arbuckle K, Hoffman JI, Sanderson JL, Cant MA, Nichols HJ. Cooperatively breeding banded mongooses do not avoid inbreeding through familiarity-based kin recognition. Behav Ecol Sociobiol 2021. [DOI: 10.1007/s00265-021-03076-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Abstract
In species that live in family groups, such as cooperative breeders, inbreeding is usually avoided through the recognition of familiar kin. For example, individuals may avoid mating with conspecifics encountered regularly in infancy, as these likely include parents, siblings, and closely related alloparents. Other mechanisms have also been reported, albeit rarely; for example, individuals may compare their own phenotype to that of others, with close matches representing likely relatives (“phenotype matching”). However, determinants of the primary inbreeding avoidance mechanisms used by a given species remain poorly understood. We use 24 years of life history and genetic data to investigate inbreeding avoidance in wild cooperatively breeding banded mongooses (Mungos mungo). We find that inbreeding avoidance occurs within social groups but is far from maximised (mean pedigree relatedness between 351 breeding pairs = 0.144). Unusually for a group-living vertebrate, we find no evidence that females avoid breeding with males with which they are familiar in early life. This is probably explained by communal breeding; females give birth in tight synchrony and pups are cared for communally, thus reducing the reliability of familiarity-based proxies of relatedness. We also found little evidence that inbreeding is avoided by preferentially breeding with males of specific age classes. Instead, females may exploit as-yet unknown proxies of relatedness, for example, through phenotype matching, or may employ postcopulatory inbreeding avoidance mechanisms. Investigation of species with unusual breeding systems helps to identify constraints against inbreeding avoidance and contributes to our understanding of the distribution of inbreeding across species.
Significance statement
Choosing the right mate is never easy, but it may be particularly difficult for banded mongooses. In most social animals, individuals avoid mating with those that were familiar to them as infants, as these are likely to be relatives. However, we show that this rule does not work in banded mongooses. Here, the offspring of several mothers are raised in large communal litters by their social group, and parents seem unable to identify or direct care towards their own pups. This may make it difficult to recognise relatives based on their level of familiarity and is likely to explain why banded mongooses frequently inbreed. Nevertheless, inbreeding is lower than expected if mates are chosen at random, suggesting that alternative pre- or post-copulatory inbreeding avoidance mechanisms are used.
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6
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Hajduk GK, Cockburn A, Osmond HL, Kruuk LEB. Complex effects of helper relatedness on female extrapair reproduction in a cooperative breeder. Behav Ecol 2021. [DOI: 10.1093/beheco/araa142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
In cooperatively breeding species, the presence of male helpers in a group often reduces the breeding female’s fidelity to her social partner, possibly because there is more than one potential sire in the group. Using a long-term study of cooperatively breeding superb fairy-wrens (Malurus cyaneus) and records of paternity in 1936 broods, we show that the effect of helpers on rates of extrapair paternity varied according to the helpers’ relatedness to the breeding female. The presence of unrelated male helpers in a group increased average rates of extrapair paternity, from 57% for groups with no unrelated helpers, to 74% with one unrelated helper, to 86% with 2+ unrelated helpers. However, this increase was due in equal part to helpers within the group and males in other groups achieving increased paternity. In contrast, helpers who were sons of the breeding female did not gain paternity, nor did they affect the level of extra-group paternity (which occurred at rates of 60%, 58%, 61% in the presence of 0, 1, 2+ helper sons, respectively). There was no evidence of effects of helpers’ relatedness to the female on nest productivity or nestling performance. Because the presence of helpers per se did not elevate extrapair reproduction rates, our results undermine the “constrained female hypothesis” explanation for an increase in extrapair paternity with helper number in cooperative breeders. However, they indicate that dominant males are disadvantaged by breeding in “cooperative” groups. The reasons why the presence of unrelated helpers, but not of helper-sons, results in higher rates of extra-group reproduction are not clear.
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Affiliation(s)
- Gabriela K Hajduk
- School of Biological Sciences, King’s Buildings, University of Edinburgh, Edinburgh, UK
| | - Andrew Cockburn
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Canberra, ACT, Australia
| | - Helen L Osmond
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Canberra, ACT, Australia
| | - Loeske E B Kruuk
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Canberra, ACT, Australia
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7
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Cockburn A, Peñalba JV, Jaccoud D, Kilian A, Brouwer L, Double MC, Margraf N, Osmond HL, Kruuk LEB, van de Pol M. hiphop: Improved paternity assignment among close relatives using a simple exclusion method for biallelic markers. Mol Ecol Resour 2021; 21:1850-1865. [PMID: 33750003 DOI: 10.1111/1755-0998.13389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/08/2021] [Accepted: 03/15/2021] [Indexed: 11/30/2022]
Abstract
Assignment of parentage with molecular markers is most difficult when the true parents have close relatives in the adult population. Here, we present an efficient solution to that problem by extending simple exclusion approaches to parentage analysis with single nucleotide polymorphic markers (SNPs). We augmented the previously published homozygote opposite test (hot), which counts mismatches due to the offspring and candidate parent having different homozygous genotypes, with an additional test. In this case, parents homozygous for the same SNP are incompatible with heterozygous offspring (i.e., "Homozygous Identical Parents, Heterozygous Offspring are Precluded": hiphop). We tested this approach in a cooperatively breeding bird, the superb fairy-wren, Malurus cyaneus, where rates of extra-pair paternity are exceptionally high, and where paternity assignment is challenging because breeding males typically have first-order adult relatives in their neighbourhood. Combining the tests and conditioning on the maternal genotype with a set of 1376 autosomal SNPs always allowed us to distinguish a single most likely sire from his relatives, and also to identify cases where the true sire must have been unsampled. In contrast, if just the hot test was used, we failed to identify a single most-likely sire in 2.5% of cases. Resampling enabled us to create guidelines for the number of SNPs required when first-order relatives coexist in the mating pool. Our method, implemented in the R package hiphop, therefore provides unambiguous parentage assignments even in systems with complex social organisation. We also identified a suite of Z- and W-linked SNPs that always identified sex correctly.
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Affiliation(s)
- Andrew Cockburn
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Joshua V Peñalba
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia.,Division of Evolutionary Biology, Ludwig Maximilians Universitat Munchen, Munchen, Germany
| | - Damian Jaccoud
- Diversity Arrays Technology Pty Ltd, Bruce, ACT, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, Bruce, ACT, Australia
| | - Lyanne Brouwer
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia.,Department of Animal Ecology and Physiology, Radboud University, Nijmegen, The Netherlands
| | - Michael C Double
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia.,Australian Antarctic Division, Kingston, TAS, Australia
| | - Nicolas Margraf
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia.,Musée d'histoire naturelle de La Chaux-de-Fonds, Neuchatel, Switzerland
| | - Helen L Osmond
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Loeske E B Kruuk
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Martijn van de Pol
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia.,Netherlands Institute of Ecology, Wageningen, The Netherlands
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8
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Cooper EB, Bonnet T, Osmond HL, Cockburn A, Kruuk LEB. Aging and Senescence across Reproductive Traits and Survival in Superb Fairy-Wrens ( Malurus cyaneus). Am Nat 2020; 197:111-127. [PMID: 33417527 DOI: 10.1086/711755] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractWhy do senescence rates of fitness-related traits often vary dramatically? By considering the full aging trajectories of multiple traits, we can better understand how a species' life history shapes the evolution of senescence within a population. Here, we examined age-related changes in sex-specific survival, reproduction, and several components of reproduction using a long-term study of a cooperatively breeding songbird, the superb fairy-wren (Malurus cyaneus). We compared aging patterns between traits by estimating standardized rates of maturation, age of onset of senescence, and rates of senescence while controlling for confounding factors reflecting individual variability in life history. We found striking differences in aging and senescence patterns between survival and reproduction as well as between reproductive traits. In both sexes, survival started to decline from maturity onward. In contrast, all reproductive traits showed improvements into early adulthood, and many showed little or no evidence of senescence. In females, despite senescence in clutch size, number of offspring surviving to independence did not decline in late life, possibly due to improvements in maternal care with age. Superb fairy-wrens have exceptionally high levels of extragroup paternity, and while male within-group reproductive success did not change with age, extragroup reproductive success showed a dramatic increase in early ages, followed by a senescent decline, suggesting that male reproductive aging is driven by sexual selection. We discuss how the superb fairy-wrens' complex life history may contribute to the disparate aging patterns across different traits.
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9
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Cooper EB, Bonnet T, Osmond H, Cockburn A, Kruuk LEB. Do the ages of parents or helpers affect offspring fitness in a cooperatively breeding bird? J Evol Biol 2020; 33:1735-1748. [PMID: 33045108 DOI: 10.1111/jeb.13712] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/31/2020] [Accepted: 09/18/2020] [Indexed: 12/13/2022]
Abstract
Age-related changes in parental phenotypes or genotypes can impact offspring fitness, but separating germline from nongermline transgenerational effects of ageing is difficult for wild populations. Further, in cooperatively breeding species, in addition to parental ages, the age of 'helpers' attending offspring may also affect juvenile performance. Using a 30-year study of a cooperative breeder with very high rates of extra-pair paternity, the superb fairy-wren (Malurus cyaneus), we investigated the effects of maternal, paternal and helper ages on three measures of offspring performance: nestling weight, juvenile survival to independence and recruitment to the breeding population. Mothers with a longer lifespan had offspring with higher juvenile survival, indicating selective disappearance, but the effect of maternal age on juvenile survival was of similar magnitude but negative. For extra-pair offspring, there was no evidence of any effect of the ages of either the genetic sire or the cuckolded 'social' father. However, for within-pair offspring, there was a positive effect of paternal age on juvenile survival, which we suggest may be driven by sexual selection. There were positive associations between the average age of helpers attending a nest and two of the three aspects of offspring performance; these effects were stronger than any of the effects of parental age. In general, the multiple associations between offspring fitness and the ages of adults around them appeared to be driven more by age-related changes in environmental effects than by age-related changes in the germline.
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Affiliation(s)
- Eve B Cooper
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Timothée Bonnet
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Helen Osmond
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Andrew Cockburn
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Loeske E B Kruuk
- Research School of Biology, Australian National University, Canberra, ACT, Australia
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10
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Cost, risk, and avoidance of inbreeding in a cooperatively breeding bird. Proc Natl Acad Sci U S A 2020; 117:15724-15730. [PMID: 32571952 DOI: 10.1073/pnas.1918726117] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inbreeding is often avoided in natural populations by passive processes such as sex-biased dispersal. But, in many social animals, opposite-sexed adult relatives are spatially clustered, generating a risk of incest and hence selection for active inbreeding avoidance. Here we show that, in long-tailed tits (Aegithalos caudatus), a cooperative breeder that risks inbreeding by living alongside opposite-sex relatives, inbreeding carries fitness costs and is avoided by active kin discrimination during mate choice. First, we identified a positive association between heterozygosity and fitness, indicating that inbreeding is costly. We then compared relatedness within breeding pairs to that expected under multiple mate-choice models, finding that pair relatedness is consistent with avoidance of first-order kin as partners. Finally, we show that the similarity of vocal cues offers a plausible mechanism for discrimination against first-order kin during mate choice. Long-tailed tits are known to discriminate between the calls of close kin and nonkin, and they favor first-order kin in cooperative contexts, so we conclude that long-tailed tits use the same kin discrimination rule to avoid inbreeding as they do to direct help toward kin.
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11
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Hajduk GK, Walling CA, Cockburn A, Kruuk LEB. The 'algebra of evolution': the Robertson-Price identity and viability selection for body mass in a wild bird population. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190359. [PMID: 32146880 PMCID: PMC7133512 DOI: 10.1098/rstb.2019.0359] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
By the Robertson–Price identity, the change in a quantitative trait owing to selection, is equal to the trait's covariance with relative fitness. In this study, we applied the identity to long-term data on superb fairy-wrens Malurus cyaneus, to estimate phenotypic and genetic change owing to juvenile viability selection. Mortality in the four-week period between fledging and independence was 40%, and heavier nestlings were more likely to survive, but why? There was additive genetic variance for both nestling mass and survival, and a positive phenotypic covariance between the traits, but no evidence of additive genetic covariance. Comparing standardized gradients, the phenotypic selection gradient was positive, βP = 0.108 (0.036, 0.187 95% CI), whereas the genetic gradient was not different from zero, βA = −0.025 (−0.19, 0.107 95% CI). This suggests that factors other than nestling mass were the cause of variation in survival. In particular, there were temporal correlations between mass and survival both within and between years. We suggest that use of the Price equation to describe cross-generational change in the wild may be challenging, but a more modest aim of estimating its first term, the Robertson–Price identity, to assess within-generation change can provide valuable insights into the processes shaping phenotypic diversity in natural populations. This article is part of the theme issue ‘Fifty years of the Price equation’.
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Affiliation(s)
- G K Hajduk
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - C A Walling
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - A Cockburn
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - L E B Kruuk
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
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12
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Lv L, Liu Y, Osmond HL, Cockburn A, Kruuk LEB. When to start and when to stop: Effects of climate on breeding in a multi-brooded songbird. GLOBAL CHANGE BIOLOGY 2020; 26:443-457. [PMID: 31581368 DOI: 10.1111/gcb.14831] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 08/15/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Abstract
Climate warming has been shown to affect the timing of the onset of breeding of many bird species across the world. However, for multi-brooded species, climate may also affect the timing of the end of the breeding season, and hence also its duration, and these effects may have consequences for fitness. We used 28 years of field data to investigate the links between climate, timing of breeding, and breeding success in a cooperatively breeding passerine, the superb fairy-wren (Malurus cyaneus). This multi-brooded species from southeastern Australia has a long breeding season and high variation in phenology between individuals. By applying a "sliding window" approach, we found that higher minimum temperatures in early spring resulted in an earlier start and a longer duration of breeding, whereas less rainfall and more heatwaves (days > 29°C) in late summer resulted in an earlier end and a shorter duration of breeding. Using a hurdle model analysis, we found that earlier start dates did not predict whether or not females produced any young in a season. However, for successful females who produced at least one young, earlier start dates were associated with higher numbers of young produced in a season. Earlier end dates were associated with a higher probability of producing at least one young, presumably because unsuccessful females kept trying when others had ceased. Despite larger scale trends in climate, climate variables in the windows relevant to this species' phenology did not change across years, and there were no temporal trends in phenology during our study period. Our results illustrate a scenario in which higher temperatures advanced both start and end dates of individuals' breeding seasons, but did not generate an overall temporal shift in breeding times. They also suggest that the complexity of selection pressures on breeding phenology in multi-brooded species may have been underestimated.
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Affiliation(s)
- Lei Lv
- Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Yang Liu
- Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Helen L Osmond
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Andrew Cockburn
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Loeske E B Kruuk
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
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13
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Peñalba JV, Deng Y, Fang Q, Joseph L, Moritz C, Cockburn A. Genome of an iconic Australian bird: High-quality assembly and linkage map of the superb fairy-wren (Malurus cyaneus). Mol Ecol Resour 2020; 20:560-578. [PMID: 31821695 DOI: 10.1111/1755-0998.13124] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/09/2019] [Accepted: 12/02/2019] [Indexed: 12/13/2022]
Abstract
The superb fairy-wren, Malurus cyaneus, is one of the most iconic Australian passerine species. This species belongs to an endemic Australasian clade, Meliphagides, which diversified early in the evolution of the oscine passerines. Today, the oscine passerines comprise almost half of all avian species diversity. Despite the rapid increase of available bird genome assemblies, this part of the avian tree has not yet been represented by a high-quality reference. To rectify that, we present the first high-quality genome assembly of a Meliphagides representative: the superb fairy-wren. We combined Illumina shotgun and mate-pair sequences, PacBio long-reads, and a genetic linkage map from an intensively sampled pedigree of a wild population to generate this genome assembly. Of the final assembled 1.07-Gb genome, 975 Mb (90.4%) was anchored onto 25 pseudochromosomes resulting in a final superscaffold N50 of 68.11 Mb. This high-quality bird genome assembly is one of only a handful which is also accompanied by a genetic map and recombination landscape. In comparison to other pedigree-based bird genetic maps, we find that the fairy-wren genetic map more closely resembles those of Taeniopygia guttata and Parus major maps, unlike the Ficedula albicollis map which more closely resembles that of Gallus gallus. Lastly, we also provide a predictive gene and repeat annotation of the genome assembly. This new high-quality, annotated genome assembly will be an invaluable resource not only regarding the superb fairy-wren species and relatives but also broadly across the avian tree by providing a novel reference point for comparative genomic analyses.
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Affiliation(s)
- Joshua V Peñalba
- Division of Evolutionary Biology, Ludwig Maximilian University of Munich, Munich, Germany
| | | | - Qi Fang
- BGI-Shenzhen, Shenzhen, China
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections, Australia, Canberra, ACT, Australia
| | - Craig Moritz
- Centre for Biodiversity Analysis, Acton, ACT, Australia.,Division of Ecology and Evolution, Australian National University, Acton, ACT, Australia
| | - Andrew Cockburn
- Division of Ecology and Evolution, Australian National University, Acton, ACT, Australia
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14
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Brouwer L, Griffith SC. Extra-pair paternity in birds. Mol Ecol 2019; 28:4864-4882. [PMID: 31587397 PMCID: PMC6899757 DOI: 10.1111/mec.15259] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/05/2019] [Accepted: 09/13/2019] [Indexed: 12/31/2022]
Abstract
Since the first molecular study providing evidence for mating outside the pair bond in birds over 30 years ago, >500 studies have reported rates of extra‐pair paternity (EPP) in >300 bird species. Here, we give a detailed overview of the current literature reporting EPP in birds and highlight the sampling biases and patterns in the data set with respect to taxonomy, avian phylogeny and global regions, knowledge of which will be crucial for correct interpretation of results in future comparative studies. Subsequently, we use this comprehensive dataset to simultaneously test the role of several ecological and life history variables. We do not find clear evidence that variation in EPP across socially monogamous species can be explained by latitude, density (coloniality), migration, generation length, genetic structuring (dispersal distance), or climatic variability, after accounting for phylogeny. These results contrast previous studies, most likely due to the large heterogeneity within species in both EPP and the predictor of interest, indicating that using species averages might be unreliable. Despite the absence of broadscale ecological drivers in explaining interspecific variation in EPP, we suggest that certain behaviours and ecological variables might facilitate or constrain EPP, as indicated by our finding that EPP was negatively associated with latitude within noncolonial species, suggesting a role of breeding synchrony. Thus, rather than focussing on general explanations for variation in EPP across all species, a future focus should be on how various aspects of ecology or life history might have driven variation in EPP among groups of species or populations of the same species. Hence, we argue that variation in EPP can be partly explained when taking the right perspective. This comprehensive overview, and particularly the dataset provided herein will create a foundation for further studies.
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Affiliation(s)
- Lyanne Brouwer
- Department of Animal Ecology & Physiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands.,Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Simon C Griffith
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia
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15
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Raj Pant S, Komdeur J, Burke TA, Dugdale HL, Richardson DS. Socio-ecological conditions and female infidelity in the Seychelles warbler. Behav Ecol 2019; 30:1254-1264. [PMID: 31579133 PMCID: PMC6765383 DOI: 10.1093/beheco/arz072] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 04/05/2019] [Accepted: 05/13/2019] [Indexed: 02/04/2023] Open
Abstract
Within socially monogamous breeding systems, levels of extra-pair paternity can vary not only between species, populations, and individuals, but also across time. Uncovering how different extrinsic conditions (ecological, demographic, and social) influence this behavior will help shed light on the factors driving its evolution. Here, we simultaneously address multiple socio-ecological conditions potentially influencing female infidelity in a natural population of the cooperatively breeding Seychelles warbler, Acrocephalus sechellensis. Our contained study population has been monitored for more than 25 years, enabling us to capture variation in socio-ecological conditions between individuals and across time and to accurately assign parentage. We test hypotheses predicting the influence of territory quality, breeding density and synchrony, group size and composition (number and sex of subordinates), and inbreeding avoidance on female infidelity. We find that a larger group size promotes the likelihood of extra-pair paternity in offspring from both dominant and subordinate females, but this paternity is almost always gained by dominant males from outside the group (not by subordinate males within the group). Higher relatedness between a mother and the dominant male in her group also results in more extra-pair paternity-but only for subordinate females-and this does not prevent inbreeding occurring in this population. Our findings highlight the role of social conditions favoring infidelity and contribute toward understanding the evolution of this enigmatic behavior.
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Affiliation(s)
- Sara Raj Pant
- Centre for Ecology, Evolution and Conservation, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
- Groningen Institute for Evolutionary Life Sciences, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Jan Komdeur
- Groningen Institute for Evolutionary Life Sciences, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Terry A Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Hannah L Dugdale
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - David S Richardson
- Centre for Ecology, Evolution and Conservation, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
- Nature Seychelles, Roche Caiman, Mahe, Republic of Seychelles
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16
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Lichtenauer W, van de Pol M, Cockburn A, Brouwer L. Indirect fitness benefits through extra-pair mating are large for an inbred minority, but cannot explain widespread infidelity among red-winged fairy-wrens. Evolution 2019; 73:467-480. [PMID: 30666623 PMCID: PMC7172280 DOI: 10.1111/evo.13684] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 12/30/2018] [Accepted: 01/03/2019] [Indexed: 11/30/2022]
Abstract
Extra‐pair paternity (EPP) has been suggested to improve the genetic quality of offspring, but evidence has been equivocal. Benefits of EPP may be only available to specific individuals or under certain conditions. Red‐winged fairy‐wrens have extremely high levels of EPP, suggesting fitness benefits might be large and available to most individuals. Furthermore, extreme philopatry commonly leads to incestuous social pairings, so inbreeding avoidance may be an important selection pressure. Here, we quantified the fitness benefits of EPP under varying conditions and across life‐stages. Extra‐pair offspring (EPO) did not appear to have higher fitness than within‐pair offspring (WPO), neither in poor years nor in the absence of helpers‐at‐the‐nest. However, EPP was beneficial for closely related social pairs, because inbred WPO suffered an overall 75% reduction in fitness. Inbreeding depression was nonlinear and reduced nestling body condition, first year survival and reproductive success. Our comprehensive study indicates that EPP should be favored for the 17% of females paired incestuously, but cannot explain the widespread infidelity in this species. Furthermore, our finding that fitness benefits of EPP only become apparent for a small part of the population could potentially explain the apparent absence of fitness differences in population wide comparisons of EPO and WPO.
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Affiliation(s)
- Wendy Lichtenauer
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia.,Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Martijn van de Pol
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia.,Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Andrew Cockburn
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Lyanne Brouwer
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia.,Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Department of Animal Ecology and Physiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
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17
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Bose APH, Henshaw JM, Zimmermann H, Fritzsche K, Sefc KM. Inclusive fitness benefits mitigate costs of cuckoldry to socially paired males. BMC Biol 2019; 17:2. [PMID: 30700283 PMCID: PMC6354359 DOI: 10.1186/s12915-018-0620-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/20/2018] [Indexed: 11/23/2022] Open
Abstract
Background In socially monogamous species, reproduction is not always confined to paired males and females. Extra-pair males commonly also reproduce with paired females, which is traditionally thought to be costly to the females’ social partners. However, we suggest that when the relatedness between reproducing individuals is considered, cuckolded males can suffer lower fitness losses than otherwise expected, especially when the rate of cuckoldry is high. We combine theoretical modeling with a detailed genetic study on a socially monogamous wild fish, Variabilichromis moorii, which displays biparental care despite exceptionally high rates of extra-pair paternity. Results We measured the relatedness between all parties involved in V. moorii spawning events (i.e. between males and females in social pairs, females and their extra-pair partners, and paired males and their cuckolders), and we reveal that males are on average more related to their cuckolders than expected by chance. Queller–Goodnight estimates of relatedness between males and their cuckolders are on average r = 0.038 but can range up to r = 0.64. This also increases the relatedness between males and the extra-pair offspring under their care. These intriguing results are consistent with the predictions of our mathematical model, which shows that elevated relatedness between paired males and their cuckolders can be adaptive for both parties when competition for fertilizations is strong. Conclusions Our results show how cuckoldry by relatives can offset males’ direct fitness losses with inclusive fitness gains, which can be substantial in systems where males face almost certain paternity losses. Electronic supplementary material The online version of this article (10.1186/s12915-018-0620-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aneesh P H Bose
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Jonathan M Henshaw
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Holger Zimmermann
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Karoline Fritzsche
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Kristina M Sefc
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria.
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18
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Petrosky AL. Digest: Extra-pair mating and inbreeding avoidance in a socially monogamous fairy-wren. Evolution 2018; 72:1535-1536. [PMID: 29917238 DOI: 10.1111/evo.13526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 06/11/2018] [Indexed: 11/29/2022]
Abstract
Infidelity in socially monogamous birds may be a mechanism of inbreeding avoidance and may be impacted by cooperative breeding. Hajduk et al. (2018) find that relatedness increases extra-pair mating only in mother-son social pairs of Malurus cyaneus, while a greater number of nest helpers consistently increases the proportion of extra-pair offspring. These findings suggest that there may be multiple explanations for extra-pair mating within a single population.
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Affiliation(s)
- Anna L Petrosky
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois 60637
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