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Macedo-Rego RC, Jennions MD, Santos ESA. Does the potential strength of sexual selection differ between mating systems with and without defensive behaviours? A meta-analysis. Biol Rev Camb Philos Soc 2024; 99:1504-1523. [PMID: 38597347 DOI: 10.1111/brv.13078] [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: 04/10/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/11/2024]
Abstract
The Darwin-Bateman paradigm predicts that females enhance their fitness by being choosy and mating with high-quality males, while males should compete to mate with as many females as possible. In many species, males enhance their fitness by defending females and/or resources used by females. That is, males directly defend access to mating opportunities. However, paternity analyses have repeatedly shown that females in most species mate polyandrously, which contradicts traditional expectations that male defensive behaviours lead to monandry. Here, in an extensive meta-analysis, encompassing 109 species and 1026 effect sizes from across the animal kingdom, we tested if the occurrence of defensive behaviours modulates sexual selection on females and males. If so, we can illuminate the extent to which males really succeed in defending access to mating and fertilisation opportunities. We used four different indices of the opportunity for sexual selection that comprise pre-mating and/or post-mating episodes of selection. We found, for both sexes, that the occurrence of defensive behaviours does not modulate the potential strength of sexual selection. This implies that male defensive behaviours do not predict the true intensity of sexual selection. While the most extreme levels of sexual selection on males are in species with male defensive behaviours, which indicates that males do sometimes succeed in restricting females' re-mating ability (e.g. elephant seals, Mirounga leonina), estimates of the opportunity for sexual selection vary greatly across species, regardless of whether or not defensive behaviours occur. Indeed, widespread polyandry shows that females are usually not restricted by male defensive behaviours. In addition, our results indicate that post-mating episodes of selection, such as cryptic female choice and sperm competition, might be important factors modulating the opportunity for sexual selection. We discuss: (i) why male defensive behaviours fail to lower the opportunity for sexual selection among females or fail to elevate it for males; (ii) how post-mating events might influence sexual selection; and (iii) the role of females as active participants in sexual selection. We also highlight that inadequate data reporting in the literature prevented us from extracting effect sizes from many studies that had presumably collected the relevant data.
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Affiliation(s)
- Renato C Macedo-Rego
- Programa de Pós-graduação em Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, trav. 14, no. 321, São Paulo, SP 05508-090, Brazil
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Michael D Jennions
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Centre, 10 Marais Street, Stellenbosch, 7600, South Africa
| | - Eduardo S A Santos
- Programa de Pós-graduação em Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, trav. 14, no. 321, São Paulo, SP 05508-090, Brazil
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2
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Olah G, Waples RS, Stojanovic D. Influence of molecular marker type on estimating effective population size and other genetic parameters in a critically endangered parrot. Ecol Evol 2024; 14:e11102. [PMID: 38524913 PMCID: PMC10961163 DOI: 10.1002/ece3.11102] [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: 08/01/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 03/26/2024] Open
Abstract
Genetics is a fast-moving field, and for conservation practitioners or ecologists, it can be bewildering. The choice of marker used in studies is fundamental; in the literature, preference has recently shifted from microsatellites to single nucleotide polymorphism (SNP) loci. Understanding how marker type affects estimates of population genetic parameters is important in the context of conservation, especially because the accuracy of estimates has a bearing on the actions taken to protect threatened species. We compare parameter estimates between seven microsatellites, 3761 SNP loci, and a random subset of 100 SNPs for the exact same 324 individual swift parrots, Lathamus discolor, and also use 457 additional samples from subsequent years to compare SNP estimates. Both marker types estimated a lower H O than H E. We show that microsatellites and SNPs mainly indicate a lack of spatial genetic structure, except when a priori collection locations were used on the SNP data in a discriminant analysis of principal components (DAPC). The 100-SNP subset gave comparable results to when the full dataset was used. Estimates of effective population size (N e) were comparable between markers when the same individuals were considered, but SNPs had narrower confidence intervals. This is reassuring because conservation assessments that rely on population genetic estimates based on a few microsatellites are unlikely to be nullified by the general shift toward SNPs in the literature. However, estimates between markers and datasets varied considerably when only adult samples were considered; hence, including samples of all age groups is recommended to be used when available. The estimated N e was higher for the full SNP dataset (2010-2019) than the smaller comparison data (2010-2015), which might be a better reflection of the species status. The lower precision of microsatellites may not necessarily be a barrier for most conservation applications; however, SNPs will improve confidence limits, which may be useful for practitioners.
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Affiliation(s)
- George Olah
- Fenner School of Environment and SocietyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and MedicineKing's College LondonLondonUK
| | - Robin S. Waples
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Dejan Stojanovic
- Fenner School of Environment and SocietyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
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3
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Wang J, Bourke AFG. Parentage exclusion of close relatives in haplodiploid species. Theor Popul Biol 2023; 154:40-50. [PMID: 37640113 DOI: 10.1016/j.tpb.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023]
Abstract
Parentage exclusion probability is usually calculated to evaluate the informativeness of a set of markers for, and the statistical power of, a parentage analysis. Equations for parentage exclusion probability have been derived in various scenarios such as paternity exclusion when maternity is known or unknown or when candidate males are unrelated or loosely related (being from the same subpopulation) to the father. All previous work assumes a diploid species. Although marker-based parentage analyses have been conducted in haploidiploid species (such as ants, bees and wasps) for diploid offspring at the individual level or haploid offspring at the class level, rigorously derived formulations of parentage exclusion probability for haploid offspring at the individual level are lacking, which prevents the precise evaluation of the informativeness for and the statistical power of a parentage analysis. In this study we derive equations for the exclusion probability of maternity of a haploid male when multiple mother candidates (workers or queens) are unrelated or fullsibs to the mother. The usefulness of the equations is exemplified by numerical examples, and the results are discussed in the context of the study of worker reproductivity in eusocial haplodiploid species. The results are especially valuable for an optimal experimental design in determining sampling intensities (e.g. number of markers and number of individuals) to achieve satisfactory statistical power of a parentage analysis in investigating workers' reproductivity in eusocial haplodiploid species.
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Affiliation(s)
- Jinliang Wang
- Institute of Zoology, Zoological Society of London, London NW1 4RY, United Kingdom.
| | - Andrew F G Bourke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
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4
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Coombs KR, Weladji RB, Holand Ø, Røed KH. Mismatch between calf paternity and observed copulations between male and female reindeer: Multiple mating in a polygynous ungulate? Curr Zool 2023; 69:377-384. [PMID: 37614915 PMCID: PMC10443607 DOI: 10.1093/cz/zoac054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/05/2022] [Indexed: 08/25/2023] Open
Abstract
In polygynous systems, such as that exhibited by reindeer Rangifer tarandus, mate choice can be difficult to disentangle from male intrasexual competition because male behavior may constrain female choice. Multiple mating may provide an avenue for female mate choice, though it is difficult to identify using behavioral estimators alone. Molecular techniques address this issue by affording ecologists an opportunity to reassess mating systems from a genetic perspective. We assessed the frequency and possible explanations for multiple mating in reindeer using a genetic approach to determine the success of observed copulations in a semi-domesticated herd in Kaamanen, Finland. Behavioral and genetic data were synthesized with population characteristics over a 7-year period to test the hypothesis that, if present, polyandry in reindeer is driven by sexual harassment from sub-dominant males. We observed multiple mating in 42% of females, with as many as 60% exhibiting multiple mating in certain years. We found no evidence that multiple mating resulted from sexual harassment by sub-dominant males, suggesting that it is likely a deliberate strategy among females. Conversion rate of copulations into paternities varied with male size, with smaller males more likely to experience mismatch than larger males. Female preference for larger males persisted despite the occurrence of multiple mating, possibly suggesting a mechanism for cryptic post-copulatory selection. We suggest further research to delineate the possible influence of cryptic post-copulatory selection and multiple mating to defend against infertility in exhausted males.
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Affiliation(s)
- Keenin R Coombs
- Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, QC, H4B1R6, Canada
| | - Robert B Weladji
- Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, QC, H4B1R6, Canada
| | - Øystein Holand
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Oluf Thesens vei 6, 1433 Ås, Norway
| | - Knut H Røed
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Veterinærbygningen, Elizabeth Stephansens vei 15, N-1430 Ås, Norway
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5
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Chapman EG, Pilkington JG, Pemberton JM. Correlates of early reproduction and apparent fitness consequences in male Soay sheep. Ecol Evol 2023; 13:e10058. [PMID: 37168987 PMCID: PMC10164647 DOI: 10.1002/ece3.10058] [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: 12/16/2022] [Revised: 04/05/2023] [Accepted: 04/17/2023] [Indexed: 05/13/2023] Open
Abstract
Life history trade-offs are ubiquitous across species and place constraints on the timing of life history events, including the optimal age at first reproduction. However, studies on lifetime breeding success of male mammals are rare due to sex-biased dispersal and the requirement for genetic paternity inferences. We studied the correlates and apparent fitness consequences of early life reproduction among males in a free-living population of Soay sheep (Ovis aries) on St Kilda, Scotland. We investigated the factors associated with early breeding success and the apparent consequences of early success for survival and future reproduction. We used genetic paternity inferences, population data, and individual morphology measurements collected over 30 years. We found that individuals born in years with low-density population size had the highest early life breeding success and singletons were more likely to be successful than twins. Individuals that bred successfully at 7 months were more likely to survive their first winter. For individuals that survived their first winter, early breeding success was not associated with later breeding success. As individual heterogeneity affects breeding success, we believe that variation in individual quality masks the costs of early reproduction in this population. Our findings provide no evidence for selection for delayed age at reproduction in male Soay sheep.
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Affiliation(s)
- Elisabeth G. Chapman
- School of Biological Sciences, Institute of Ecology and EvolutionUniversity of EdinburghEdinburghUK
| | - Jill G. Pilkington
- School of Biological Sciences, Institute of Ecology and EvolutionUniversity of EdinburghEdinburghUK
| | - Josephine M. Pemberton
- School of Biological Sciences, Institute of Ecology and EvolutionUniversity of EdinburghEdinburghUK
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6
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Mauleón K, Sánchez-Dávila F, Ungerfeld R. Rams' reproductive status during a controlled breeding period: effect of social dominance. Trop Anim Health Prod 2023; 55:164. [PMID: 37079200 DOI: 10.1007/s11250-023-03584-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/12/2023] [Indexed: 04/21/2023]
Abstract
The aim of this study was to compare the variation in body weight, scrotal circumference (SC), and seminal quality during a breeding period in dominant and subordinate rams. Data were collected from 12 dyads of rams, each bred with 15 ewes for 7 weeks. Before joining, the dominance relationship between both rams from each dyad was determined. Body weight and SC were recorded weekly in the morning, and semen was collected by electroejaculation, determining the volume, sperm concentration, mass motility, and percentage of sperm with progressive motility. In addition, the total number of sperm and sperm with progressive motility ejaculated were calculated. Dominance had no direct effect or interaction with time on any of the variables analyzed. Body weight, seminal volume, sperm concentration, mass motility, percentage of sperm with progressive motility, and total ejaculated sperm varied with time (p < 0.05), and scrotal circumference and total ejaculated sperm with progressive motility tended to vary with time. In general, all indicators evaluated were affected in the first weeks, when most ewes were cycling, recovering as the breeding progressed. It was concluded that, at least under the conditions of this study, dominance position did not affect the profile of the reproductive variables evaluated, although all of them were affected during the breeding period.
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Affiliation(s)
- Keyla Mauleón
- Universidad Autónoma de Nuevo León, Posgrado Conjunto Facultad de Medicina Veterinaria y Zootecnia y Facultad de Agronomía, CP. 66050, General Escobedo, N.L., Mexico
| | - Fernando Sánchez-Dávila
- Universidad Autónoma de Nuevo León, Posgrado Conjunto Facultad de Medicina Veterinaria y Zootecnia y Facultad de Agronomía, CP. 66050, General Escobedo, N.L., Mexico
| | - Rodolfo Ungerfeld
- Facultad de Veterinaria, Universidad de La República, Ruta 8 Kilómetro 18, 13000, Montevideo, Uruguay.
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Papach A, Beaurepaire A, Yañez O, Huwiler M, Williams GR, Neumann P. Multiple mating by both sexes in an invasive insect species, Aethina tumida (Coleoptera: Nitidulidae). INSECT SCIENCE 2023; 30:517-529. [PMID: 36097706 DOI: 10.1111/1744-7917.13112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/11/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Multiple mating by both sexes is common among sexually reproducing animals. Small hive beetles (SHB), Aethina tumida, are parasites of bee nests endemic to sub-Saharan Africa and have become a widespread invasive species. Despite the considerable economic damages they can cause, their basic biology remains poorly understood. Here we show that male and female small hive beetles can mate multiple times, suggesting that costs for mating are low in this species. In an invasive A. tumida population in the United States, a combination of laboratory experiments for males and paternity analysis with eight polymorphic DNA microsatellite markers for field-caught females were used to estimate the number of mating by both sexes. The data show that females and males can mate multiple times-females mated with up to eight males, whereas males mated with at least seven females. The results also showed that A. tumida displayed a skewed paternity, although this was not consistent among the tested females. Thus, first or last male advantage seem to be unlikely in A. tumida. Our observations that individuals of both sexes of A. tumida can mate multiple times opens new research avenues for examining drivers of multiple mating and determining the role it may play in promoting biological invasions.
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Affiliation(s)
- Anna Papach
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Agroscope, Swiss Bee Research Centre, Bern, Switzerland
| | - Alexis Beaurepaire
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Agroscope, Swiss Bee Research Centre, Bern, Switzerland
| | - Orlando Yañez
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Agroscope, Swiss Bee Research Centre, Bern, Switzerland
| | - Meret Huwiler
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Geoffrey R Williams
- Department of Entomology & Plant Pathology, Auburn University, Auburn, Alabama, USA
| | - Peter Neumann
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Agroscope, Swiss Bee Research Centre, Bern, Switzerland
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8
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Jing M, Chen Y, Yao K, Wang Y, Huang L. Comparative phylogeography of two commensal rat species ( Rattus tanezumi and Rattus norvegicus) in China: Insights from mitochondrial DNA, microsatellite, and 2b-RAD data. Ecol Evol 2022; 12:e9409. [PMID: 36254297 PMCID: PMC9557235 DOI: 10.1002/ece3.9409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/09/2022] [Accepted: 09/20/2022] [Indexed: 11/10/2022] Open
Abstract
Rattus norvegicus and Rattus tanezumi are dominant species of Chinese house rats, but the colonization and demographic history of two species in China have not been thoroughly explored. Phylogenetic analyses with mitochondrial DNA including 486 individuals from 31 localities revealed that R. norvegicus is widely distributed in China, R. tanezumi is mainly distributed in southern China with currently invading northward; northeast China was the natal region of R. norvegicus, while the spread of R. tanezumi in China most likely started from the southeast coast. A total of 123 individuals from 18 localities were subjected to 2b-RAD analyses. In neighbor-joining tree, individuals of R. tanezumi grouped into geographic-specific branches, and populations from southeast coast were ancestral groups, which confirmed the colonization route from southeast coast to central and western China. However, individuals of R. norvegicus were generally grouped into two clusters instead of geographic-specific branches. One cluster comprised inland populations, and another cluster included both southeast coast and inland populations, which indicated that spread history of R. norvegicus in China was complex; in addition to on-land colonization, shipping transportation also have played great roles. ADMIXTURE and principal component analyses provided further supports for the colonization history. Demographic analyses revealed that climate changes at ~40,000 to 18,000 years ago and ~4000 years ago had led to population declines of both species; the R. norvegicus declined rapidly while the population of R. tanezumi continuously expanded since ~1500 years ago, indicating the importance of interspecies' competition in their population size changes. Our study provided a valuable framework for further investigation on phylogeography of two species in China.
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Affiliation(s)
- Meidong Jing
- School of Life SciencesNantong UniversityNantongChina
| | - Yingjie Chen
- School of Life SciencesNantong UniversityNantongChina
| | - Keying Yao
- School of Life SciencesNantong UniversityNantongChina
| | - Youming Wang
- School of Life SciencesNantong UniversityNantongChina
| | - Ling Huang
- School of Life SciencesNantong UniversityNantongChina
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9
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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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10
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Leimar O, Bshary R. Reproductive skew, fighting costs, and winner-loser effects in social-dominance evolution. J Anim Ecol 2022; 91:1036-1046. [PMID: 35304750 PMCID: PMC9315160 DOI: 10.1111/1365-2656.13691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/02/2022] [Indexed: 11/28/2022]
Abstract
1. Social hierarchies are often found in group-living animals and can be formed through pairwise aggressive interactions. The dominance rank can influence reproductive success (RS) with a skew towards high-ranking individuals. 2. Using game theory we investigate how the opportunity for differently ranked individuals to achieve RS influences the costs of hierarchy formation and the strength of winner and loser effects. 3. In our model, individuals adjust their aggressive and submissive behaviour towards others through reinforcement learning. The learning is based on rewards and penalties, which depend on relative fighting ability. From individual-based simulations we determine evolutionary equilibria of traits such as learning rates. We examine situations that differ in the extent of monopolisation of contested RS by dominants and in the proportion of total RS that is contested. 4. The model implements two kinds of fighting costs: a decrease in effective fighting ability from damage (loss of condition), and a risk of mortality that increases with the total accumulated damage. Either of these costs can limit the amount of fighting. 5. We find that stable dominance hierarchies form, with a positive correlation between dominance position and fighting ability. The accumulated costs differ between dominance positions, with the highest costs paid by low or intermediately ranked individuals. Costs tend to be higher in high-skew situations. 6. We identify a 'stay-in, opt-out' syndrome, comprising a range from weaker (stay-in) to stronger (opt-out) winner-loser effects. We interpret the opt-out phenotype to be favoured by selection on lower-ranked individuals to opt out of contests over social dominance, because it is more pronounced when more of the total RS is uncontested. 7. We discuss our results in relation to field and experimental observations and argue that there is a need for empirical investigation of the behaviour and reproductive success of lower-ranked individuals.
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Affiliation(s)
- Olof Leimar
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Redouan Bshary
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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11
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Lee KD, Millar CD, Brekke P, Whibley A, Ewen JG, Hingston M, Zhu A, Santure AW. The design and application of a 50 K SNP chip for a threatened Aotearoa New Zealand passerine, the hihi. Mol Ecol Resour 2021; 22:415-429. [PMID: 34323011 DOI: 10.1111/1755-0998.13480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 11/30/2022]
Abstract
Next-generation sequencing has transformed the fields of ecological and evolutionary genetics by allowing for cost-effective identification of genome-wide variation. Single nucleotide polymorphism (SNP) arrays, or "SNP chips", enable very large numbers of individuals to be consistently genotyped at a selected set of these identified markers, and also offer the advantage of being able to analyse samples of variable DNA quality. We used reduced representation restriction-aided digest sequencing (RAD-seq) of 31 birds of the threatened hihi (Notiomystis cincta; stitchbird) and low-coverage whole genome sequencing (WGS) of 10 of these birds to develop an Affymetrix 50 K SNP chip. We overcame the limitations of having no hihi reference genome and a low quantity of sequence data by separate and pooled de novo assembly of each of the 10 WGS birds. Reads from all individuals were mapped back to these de novo assemblies to identify SNPs. A subset of RAD-seq and WGS SNPs were selected for inclusion on the chip, prioritising SNPs with the highest quality scores whose flanking sequence uniquely aligned to the zebra finch (Taeniopygia guttata) genome. Of the 58,466 SNPs manufactured on the chip, 72% passed filtering metrics and were polymorphic. By genotyping 1,536 hihi on the array, we found that SNPs detected in multiple assemblies were more likely to successfully genotype, representing a cost-effective approach to identify SNPs for genotyping. Here, we demonstrate the utility of the SNP chip by describing the high rates of linkage disequilibrium in the hihi genome, reflecting the history of population bottlenecks in the species.
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Affiliation(s)
- Kate D Lee
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Craig D Millar
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, Regent's Park, London, UK
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - John G Ewen
- Institute of Zoology, Zoological Society of London, Regent's Park, London, UK
| | - Melanie Hingston
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Amy Zhu
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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12
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McFarlane S, Manseau M, Wilson PJ. Spatial familial networks to infer demographic structure of wild populations. Ecol Evol 2021; 11:4507-4519. [PMID: 33976826 PMCID: PMC8093719 DOI: 10.1002/ece3.7345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 11/08/2022] Open
Abstract
In social species, reproductive success and rates of dispersal vary among individuals resulting in spatially structured populations. Network analyses of familial relationships may provide insights on how these parameters influence population-level demographic patterns. These methods, however, have rarely been applied to genetically derived pedigree data from wild populations.Here, we use parent-offspring relationships to construct familial networks from polygamous boreal woodland caribou (Rangifer tarandus caribou) in Saskatchewan, Canada, to inform recovery efforts. We collected samples from 933 individuals at 15 variable microsatellite loci along with caribou-specific primers for sex identification. Using network measures, we assess the contribution of individual caribou to the population with several centrality measures and then determine which measures are best suited to inform on the population demographic structure. We investigate the centrality of individuals from eighteen different local areas, along with the entire population.We found substantial differences in centrality of individuals in different local areas, that in turn contributed differently to the full network, highlighting the importance of analyzing networks at different scales. The full network revealed that boreal caribou in Saskatchewan form a complex, interconnected familial network, as the removal of edges with high betweenness did not result in distinct subgroups. Alpha, betweenness, and eccentricity centrality were the most informative measures to characterize the population demographic structure and for spatially identifying areas of highest fitness levels and family cohesion across the range. We found varied levels of dispersal, fitness, and cohesion in family groups. Synthesis and applications: Our results demonstrate the value of different network measures in assessing genetically derived familial networks. The spatial application of the familial networks identified individuals presenting different fitness levels, short- and long-distance dispersing ability across the range in support of population monitoring and recovery efforts.
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Affiliation(s)
- Samantha McFarlane
- Environmental and Life Sciences DepartmentTrent UniversityPeterboroughONCanada
- Landscape Science and Technology DivisionEnvironment and Climate Change CanadaOttawaONCanada
| | - Micheline Manseau
- Environmental and Life Sciences DepartmentTrent UniversityPeterboroughONCanada
- Landscape Science and Technology DivisionEnvironment and Climate Change CanadaOttawaONCanada
| | - Paul J. Wilson
- Environmental and Life Sciences DepartmentTrent UniversityPeterboroughONCanada
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13
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Cayuela H, Dorant Y, Mérot C, Laporte M, Normandeau E, Gagnon-Harvey S, Clément M, Sirois P, Bernatchez L. Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish. Mol Ecol 2021; 30:1624-1641. [PMID: 33565147 DOI: 10.1111/mec.15835] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 01/15/2021] [Accepted: 02/01/2021] [Indexed: 12/22/2022]
Abstract
Increasing evidence shows that structural variants represent an overlooked aspect of genetic variation with consequential evolutionary roles. Among those, copy number variants (CNVs), including duplicated genomic regions and transposable elements (TEs), may contribute to local adaptation and/or reproductive isolation among divergent populations. Those mechanisms suppose that CNVs could be used to infer neutral and/or adaptive population genetic structure, whose study has been restricted to microsatellites, mitochondrial DNA and Amplified fragment length polymorphism markers in the past and more recently the use of single nucleotide polymorphisms (SNPs). Taking advantage of recent developments allowing CNV analysis from RAD-seq data, we investigated how variation in fitness-related traits, local environmental conditions and demographic history are associated with CNVs, and how subsequent copy number variation drives population genetic structure in a marine fish, the capelin (Mallotus villosus). We collected 1538 DNA samples from 35 sampling sites in the north Atlantic Ocean and identified 6620 putative CNVs. We found associations between CNVs and the gonadosomatic index, suggesting that six duplicated regions could affect female fitness by modulating oocyte production. We also detected 105 CNV candidates associated with water temperature, among which 20% corresponded to genomic regions located within the sequence of protein-coding genes, suggesting local adaptation to cold water by means of gene sequence amplification. We also identified 175 CNVs associated with the divergence of three previously defined parapatric glacial lineages, of which 24% were located within protein-coding genes, making those loci potential candidates for reproductive isolation. Lastly, our analyses unveiled a hierarchical, complex CNV population structure determined by temperature and local geography, which was in stark contrast to that inferred based on SNPs in a previous study. Our findings underline the complementarity of those two types of genomic variation in population genomics studies.
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Affiliation(s)
- Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Yann Dorant
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Stéphane Gagnon-Harvey
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Marie Clément
- Center for Fisheries Ecosystems Research, Fisheries and Marine Institute of Memorial, University of Newfoundland, St. John's, NL, Canada.,Labrador Institute of Memorial University of Newfoundland, Happy Valley-Goose Bay, NL, Canada
| | - Pascal Sirois
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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14
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Gutiérrez EG, Vivas-Toro I, Carmona-Ruíz D, Villalobos-Chaves D, Rodríguez-Herrera B, Real-Monroy MD, León-Avila G, Ortega J. Socio-spatial organization reveals paternity and low kinship in the Honduran white bat (Ectophylla alba) in Costa Rica. Integr Zool 2021; 16:646-658. [PMID: 33411951 DOI: 10.1111/1749-4877.12514] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ectophylla alba is a tent-making bat that roosts in mixed-sex clusters comprising adults and offspring. Our goal was to determine the genetic identity of individuals belonging to different roosting groups. We tested the hypothesis of kin selection as a major force structuring group composition. We used 9 microsatellites designed for E. alba to determine the genetic identity and probability of parentage of individuals. We analyzed parentage and kinship using the software ML-Relate, GenAIEx, and Cervus. The obtained relationship probabilities (0.5) revealed a clear maternal relationship between female adults and offspring with allele compatibility, and at least 5 relationships between male adults and pups. We found a low degree of relatedness within roosting groups. Between roosting groups at different sites, the mean probability of a half-sibling relationship ranged from 0.214 to 0.244 and, for full-sibling relationship, from 0.383 to 0.553. Genetically, adult individuals were poorly related within clusters, and kinship as an evolutionary force could not explain group membership.
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Affiliation(s)
- Edgar G Gutiérrez
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Isabela Vivas-Toro
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Daniela Carmona-Ruíz
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | | | | | - Melina Del Real-Monroy
- Laboratorio de Genómica Evolutiva, Doctorado en Ciencias Básicas, Universidad Autónoma de Zacatecas, Zacatecas, Zac., México
| | - Gloria León-Avila
- Laboratorio de Genética, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Jorge Ortega
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
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15
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Behringer V, Krumbholz A, Stevens JMG, Keiler AM, Zierau O, Hohmann G. Exploring the Utility of Hair Endocannabinoids for Monitoring Homeostasis in Bonobos. Physiol Biochem Zool 2021; 94:83-98. [PMID: 33434116 DOI: 10.1086/712658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractQuantifying physiological challenges has gained increasing importance in evolutionary biology, behavioral physiology, and conservation. One matrix that is particularly useful for obtaining long-term records of physiological changes in mammals is hair. Potential markers are components of the endocannabinoid (EC) system, which regulates homeostasis of the brain as well as the endocrine and immune systems. Here, we present results from the first study to measure ECs (anandamide [AEA], 2-archidonyl glycerol [2-AG]) and EC-like compounds (N-palmitoylethanolamine [PEA], N-oleoylethanolamine [OEA], N-stearoylethanolamine [SEA]) in the hair of a nonhuman primate. We found that AEA, SEA, PEA, and OEA can be reliably measured in hair samples. When comparing the measurements of hair from different body parts, we found that variations of some analytes suggest that hair location is likely to affect results. For changes in health status, measurements of ECs and EC-like compounds reflected differences at both intra- and interindividual levels. We concluded that the EC system potentially provides novel tools to assess well-being, health status, and metabolic stress-not only in the hair of humans but also in that of domestic and wild animals. Measuring changes in ECs and EC-like compounds may improve the long-term monitoring of health status in captive and wild primates and may serve as a useful measure in animal welfare programs.
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16
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Airst JI, Lingle S. Male size and alternative mating tactics in white-tailed deer and mule deer. J Mammal 2020. [DOI: 10.1093/jmammal/gyaa109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Within populations, individual males adopt different courtship tactics due to differences in their competitive ability, which may vary depending on the animal’s age and size. To test the hypothesis that mule deer (Odocoileus hemionus) and white-tailed deer (O. virginianus) males vary their courtship behavior based on their size, we conducted focal observations of 144 mule deer and 85 white-tailed males that varied in size, at a large grassland site in southern Alberta. The smallest mule deer males devoted more time to feeding, were less likely to engage in late-stage courtship than larger males and were less likely to move among female groups. Other males, including small white-tailed males, appeared to use a roving strategy to search for estrous females in different groups, which is consistent with recent research on male movements. Both medium and large males increased the time they spent in one-male groups, and specifically isolated pairs, as courtship advanced, presumably to reduce competition with other males. However, this trend was most pronounced for medium mule deer males, and for all size classes of white-tailed deer. In contrast, large mule deer males spent a similar proportion of time tending females in all group types. Our results identified potential size-dependent tactics for mule deer males. In contrast, white-tailed males of all sizes appeared to rely on a tactic of finding and tending estrous females in isolation from other males.
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Affiliation(s)
- Jason I Airst
- Department of Biology, The University of Winnipeg, Winnipeg, MB, Canada
| | - Susan Lingle
- Department of Biology, The University of Winnipeg, Winnipeg, MB, Canada
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17
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Jensen EL, Tschritter C, de Groot PVC, Hayward KM, Branigan M, Dyck M, Clemente‐Carvalho RBG, Lougheed SC. Canadian polar bear population structure using genome-wide markers. Ecol Evol 2020; 10:3706-3714. [PMID: 32313629 PMCID: PMC7160183 DOI: 10.1002/ece3.6159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/23/2020] [Accepted: 02/18/2020] [Indexed: 12/01/2022] Open
Abstract
Predicting the consequences of environmental changes, including human-mediated climate change on species, requires that we quantify range-wide patterns of genetic diversity and identify the ecological, environmental, and historical factors that have contributed to it. Here, we generate baseline data on polar bear population structure across most Canadian subpopulations (n = 358) using 13,488 genome-wide single nucleotide polymorphisms (SNPs) identified with double-digest restriction site-associated DNA sequencing (ddRAD). Our ddRAD dataset showed three genetic clusters in the sampled Canadian range, congruent with previous studies based on microsatellites across the same regions; however, due to a lack of sampling in Norwegian Bay, we were unable to confirm the existence of a unique cluster in that subpopulation. These data on the genetic structure of polar bears using SNPs provide a detailed baseline against which future shifts in population structure can be assessed, and opportunities to develop new noninvasive tools for monitoring polar bears across their range.
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Affiliation(s)
- Evelyn L. Jensen
- Department of BiologyQueen’s UniversityKingstonONCanada
- Present address:
Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | | | | | | | - Marsha Branigan
- Department of Environment and Natural ResourcesGovernment of the Northwest TerritoriesInuvikNTCanada
| | - Markus Dyck
- Department of EnvironmentGovernment of NunavutIgloolikNUCanada
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18
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von Thaden A, Nowak C, Tiesmeyer A, Reiners TE, Alves PC, Lyons LA, Mattucci F, Randi E, Cragnolini M, Galián J, Hegyeli Z, Kitchener AC, Lambinet C, Lucas JM, Mölich T, Ramos L, Schockert V, Cocchiararo B. Applying genomic data in wildlife monitoring: Development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism panels. Mol Ecol Resour 2020; 20. [PMID: 31925943 DOI: 10.1111/1755-0998.13136] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/24/2019] [Accepted: 01/05/2020] [Indexed: 01/16/2023]
Abstract
The genomic era has led to an unprecedented increase in the availability of genome-wide data for a broad range of taxa. Wildlife management strives to make use of these vast resources to enable refined genetic assessments that enhance biodiversity conservation. However, as new genomic platforms emerge, problems remain in adapting the usually complex approaches for genotyping of noninvasively collected wildlife samples. Here, we provide practical guidelines for the standardized development of reduced single nucleotide polymorphism (SNP) panels applicable for microfluidic genotyping of degraded DNA samples, such as faeces or hairs. We demonstrate how microfluidic SNP panels can be optimized to efficiently monitor European wildcat (Felis silvestris S.) populations. We show how panels can be set up in a modular fashion to accommodate informative markers for relevant population genetics questions, such as individual identification, hybridization assessment and the detection of population structure. We discuss various aspects regarding the implementation of reduced SNP panels and provide a framework that will allow both molecular ecologists and practitioners to help bridge the gap between genomics and applied wildlife conservation.
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Affiliation(s)
- Alina von Thaden
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Annika Tiesmeyer
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Tobias E Reiners
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Wildlife Biology Program, University of Montana, Missoula, MT, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Federica Mattucci
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia, Bologna, Italy
| | - Ettore Randi
- Department BIGEA, University of Bologna, Bologna, Italy.,Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, Denmark
| | - Margherita Cragnolini
- Institut für Spezielle Zoologie und Evolutionsbiologie, Biologisch-Pharmazeutische Fakultät, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - José Galián
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - Zsolt Hegyeli
- "Milvus Group" Bird and Nature Protection Association, Tîrgu Mureş, Romania
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK.,Institute of Geography, School of Geosciences, University of Edinburgh, Edinburgh, UK
| | - Clotilde Lambinet
- Department of Science and Environmental Management, University of Liège, Liège, Belgium
| | - José M Lucas
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - Thomas Mölich
- Landesverband Thüringen e.V., BUND für Umwelt und Naturschutz Deutschland (BUND), Erfurt, Germany
| | - Luana Ramos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Vinciane Schockert
- Department of Science and Environmental Management, University of Liège, Liège, Belgium
| | - Berardino Cocchiararo
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
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19
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Erofeeva MN, Naidenko SV. Interspecific Variation in the Relationships of Mating Partners in Felids. BIOL BULL+ 2020. [DOI: 10.1134/s1062359019060062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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Wellenreuther M, Mérot C, Berdan E, Bernatchez L. Going beyond SNPs: The role of structural genomic variants in adaptive evolution and species diversification. Mol Ecol 2019; 28:1203-1209. [PMID: 30834648 DOI: 10.1111/mec.15066] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 02/28/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Maren Wellenreuther
- The New Zealand Institute for Plant & Food Research Ltd, Nelson, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Emma Berdan
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
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21
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Minkner MMI, Young C, Amici F, McFarland R, Barrett L, Grobler JP, Henzi SP, Widdig A. Assessment of Male Reproductive Skew via Highly Polymorphic STR Markers in Wild Vervet Monkeys, Chlorocebus pygerythrus. J Hered 2019; 109:780-790. [PMID: 30272235 DOI: 10.1093/jhered/esy048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 09/28/2018] [Indexed: 11/12/2022] Open
Abstract
Male reproductive strategies have been well studied in primate species where the ability of males to monopolize reproductive access is high. Less is known about species where males cannot monopolize mating access. Vervet monkeys (Chlorocebus pygerythrus) are interesting in this regard as female codominance reduces the potential for male monopolization. Under this condition, we assessed whether male dominance rank still influences male mating and reproductive success, by assigning paternities to infants in a population of wild vervets in the Eastern Cape, South Africa. To determine paternity, we established microsatellite markers from noninvasive fecal samples via cross-species amplification. In addition, we evaluated male mating and reproductive success for 3 groups over 4 mating seasons. We identified 21 highly polymorphic microsatellites (number of alleles = 7.5 ± 3.1 [mean ± SD], observed heterozygosity = 0.691 ± 0.138 [mean ± SD]) and assigned paternity to 94 of 97 sampled infants (96.9%) with high confidence. Matings pooled over 4 seasons were significantly skewed across 3 groups, although skew indices were low (B index = 0.023-0.030) and mating success did not correlate with male dominance. Paternities pooled over 4 seasons were not consistently significantly skewed (B index = 0.005-0.062), with high-ranking males siring more offspring than subordinates only in some seasons. We detected 6 cases of extra-group paternity (6.4%) and 4 cases of natal breeding (4.3%). Our results suggest that alternative reproductive strategies besides priority of access for dominant males are likely to affect paternity success, warranting further investigation into the determinants of paternity among species with limited male monopolization potential.
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Affiliation(s)
- Mirjam M I Minkner
- Behavioural Ecology, Institute of Biology, Faculty of Life Sciences, Leipzig University, Talstr, Leipzig, Germany.,Research Group Primate Kin Selection, Department of Primatology, Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany.,Applied Behavioural Ecology and Ecosystems Research Unit, University of South Africa, Christiaan de Wet Road and Pioneer Avenue, Florida, Gauteng, South Africa
| | - Christopher Young
- Applied Behavioural Ecology and Ecosystems Research Unit, University of South Africa, Christiaan de Wet Road and Pioneer Avenue, Florida, Gauteng, South Africa.,Department of Psychology, University of Lethbridge, Lethbridge, AB, Canada.,Department of Anatomy and Physiology, Faculty of Veterinary Science, University of Pretoria, Private Bag, Onderstepoort, South Africa
| | - Federica Amici
- Behavioural Ecology, Institute of Biology, Faculty of Life Sciences, Leipzig University, Talstr, Leipzig, Germany.,Research Group Primate Kin Selection, Department of Primatology, Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany
| | - Richard McFarland
- Department of Anthropology, University of Wisconsin-Madison, Madison, WI, USA.,Brain Function Research Group, School of Physiology, University of the Witwatersrand, Parktown, Johannesburg, Gauteng, South Africa
| | - Louise Barrett
- Applied Behavioural Ecology and Ecosystems Research Unit, University of South Africa, Christiaan de Wet Road and Pioneer Avenue, Florida, Gauteng, South Africa.,Department of Psychology, University of Lethbridge, Lethbridge, AB, Canada
| | - J Paul Grobler
- and Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, Nelson Mandela Drive, Park West, Bloemfontein, South Africa
| | - S Peter Henzi
- Applied Behavioural Ecology and Ecosystems Research Unit, University of South Africa, Christiaan de Wet Road and Pioneer Avenue, Florida, Gauteng, South Africa.,Department of Psychology, University of Lethbridge, Lethbridge, AB, Canada
| | - Anja Widdig
- Behavioural Ecology, Institute of Biology, Faculty of Life Sciences, Leipzig University, Talstr, Leipzig, Germany.,Research Group Primate Kin Selection, Department of Primatology, Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany
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22
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Ewart KM, Johnson RN, Ogden R, Joseph L, Frankham GJ, Lo N. Museum specimens provide reliable SNP data for population genomic analysis of a widely distributed but threatened cockatoo species. Mol Ecol Resour 2019; 19:1578-1592. [PMID: 31484222 DOI: 10.1111/1755-0998.13082] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 12/20/2022]
Abstract
Natural history museums harbour a plethora of biological specimens which are of potential use in population and conservation genetic studies. Although technical advancements in museum genomics have enabled genome-wide markers to be generated from aged museum specimens, the suitability of these data for robust biological inference is not well characterized. The aim of this study was to test the utility of museum specimens in population and conservation genomics by assessing the biological and technical validity of single nucleotide polymorphism (SNP) data derived from such samples. To achieve this, we generated thousands of SNPs from 47 red-tailed black cockatoo (Calyptorhychus banksii) traditional museum samples (i.e. samples that were not collected with the primary intent of DNA analysis) and 113 fresh tissue samples (cryopreserved liver/muscle) using a restriction site-associated DNA marker approach (DArTseq™ ). Thousands of SNPs were successfully generated from most of the traditional museum samples (with a mean age of 44 years, ranging from 5 to 123 years), although 38% did not provide useful data. These SNPs exhibited higher error rates and contained significantly more missing data compared with SNPs from fresh tissue samples, likely due to considerable DNA fragmentation. However, based on simulation results, the level of genotyping error had a negligible effect on inference of population structure in this species. We did identify a bias towards low diversity SNPs in older samples that appears to compromise temporal inferences of genetic diversity. This study demonstrates the utility of a RADseq-based method to produce reliable genome-wide SNP data from traditional museum specimens.
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Affiliation(s)
- Kyle M Ewart
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.,Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Rebecca N Johnson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.,Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO, Canberra, Australia
| | - Greta J Frankham
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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23
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Foroughirad V, Levengood AL, Mann J, Frère CH. Quality and quantity of genetic relatedness data affect the analysis of social structure. Mol Ecol Resour 2019; 19:1181-1194. [PMID: 31056823 DOI: 10.1111/1755-0998.13028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 02/06/2023]
Abstract
Kinship plays a fundamental role in the evolution of social systems and is considered a key driver of group living. To understand the role of kinship in the formation and maintenance of social bonds, accurate measures of genetic relatedness are critical. Genotype-by-sequencing technologies are rapidly advancing the accuracy and precision of genetic relatedness estimates for wild populations. The ability to assign kinship from genetic data varies depending on a species' or population's mating system and pattern of dispersal, and empirical data from longitudinal studies are crucial to validate these methods. We use data from a long-term behavioural study of a polygynandrous, bisexually philopatric marine mammal to measure accuracy and precision of parentage and genetic relatedness estimation against a known partial pedigree. We show that with moderate but obtainable sample sizes of approximately 4,235 SNPs and 272 individuals, highly accurate parentage assignments and genetic relatedness coefficients can be obtained. Additionally, we subsample our data to quantify how data availability affects relatedness estimation and kinship assignment. Lastly, we conduct a social network analysis to investigate the extent to which accuracy and precision of relatedness estimation improve statistical power to detect an effect of relatedness on social structure. Our results provide practical guidance for minimum sample sizes and sequencing depth for future studies, as well as thresholds for post hoc interpretation of previous analyses.
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Affiliation(s)
- Vivienne Foroughirad
- Division of Marine Science and Conservation, Duke University Marine Laboratory, Beaufort, North Carolina
| | - Alexis L Levengood
- Global Change Ecology Research Group, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
| | - Janet Mann
- Departments of Biology and Psychology, Georgetown University, Washington, District of Columbia
| | - Céline H Frère
- Global Change Ecology Research Group, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
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24
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Andrews KR, Adams JR, Cassirer EF, Plowright RK, Gardner C, Dwire M, Hohenlohe PA, Waits LP. A bioinformatic pipeline for identifying informative SNP panels for parentage assignment from RADseq data. Mol Ecol Resour 2018; 18:1263-1281. [PMID: 29870119 PMCID: PMC6207459 DOI: 10.1111/1755-0998.12910] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 05/18/2018] [Accepted: 05/24/2018] [Indexed: 11/30/2022]
Abstract
The development of high-throughput sequencing technologies is dramatically increasing the use of single nucleotide polymorphisms (SNPs) across the field of genetics, but most parentage studies of wild populations still rely on microsatellites. We developed a bioinformatic pipeline for identifying SNP panels that are informative for parentage analysis from restriction site-associated DNA sequencing (RADseq) data. This pipeline includes options for analysis with or without a reference genome, and provides methods to maximize genotyping accuracy and select sets of unlinked loci that have high statistical power. We test this pipeline on small populations of Mexican gray wolf and bighorn sheep, for which parentage analyses are expected to be challenging due to low genetic diversity and the presence of many closely related individuals. We compare the results of parentage analysis across SNP panels generated with or without the use of a reference genome, and between SNPs and microsatellites. For Mexican gray wolf, we conducted parentage analyses for 30 pups from a single cohort where samples were available from 64% of possible mothers and 53% of possible fathers, and the accuracy of parentage assignments could be estimated because true identities of parents were known a priori based on field data. For bighorn sheep, we conducted maternity analyses for 39 lambs from five cohorts where 77% of possible mothers were sampled, but true identities of parents were unknown. Analyses with and without a reference genome produced SNP panels with ≥95% parentage assignment accuracy for Mexican gray wolf, outperforming microsatellites at 78% accuracy. Maternity assignments were completely consistent across all SNP panels for the bighorn sheep, and were 74.4% consistent with assignments from microsatellites. Accuracy and consistency of parentage analysis were not reduced when using as few as 284 SNPs for Mexican gray wolf and 142 SNPs for bighorn sheep, indicating our pipeline can be used to develop SNP genotyping assays for parentage analysis with relatively small numbers of loci.
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Affiliation(s)
- Kimberly R. Andrews
- Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844, USA
- Current address: Genetics and Genomics Group, University of Washington JISAO and NOAA Pacific Marine Environmental Lab, Seattle, WA 98115, USA
| | - Jennifer R. Adams
- Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844, USA
| | - E. Frances Cassirer
- Idaho Department of Fish and Game, 3316 16th Street, Lewiston, ID 83501, USA
| | - Raina K. Plowright
- Department of Microbiology and Immunology, Montana State University, 109 Lewis Hall, Bozeman, MT 59717, USA
| | - Colby Gardner
- U.S. Fish and Wildlife Service, 2105 Osuna Road NE, Albuquerque, NM 87113, USA
| | - Maggie Dwire
- U.S. Fish and Wildlife Service, 2105 Osuna Road NE, Albuquerque, NM 87113, USA
| | - Paul A. Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844, USA
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25
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Carroll EL, Bruford MW, DeWoody JA, Leroy G, Strand A, Waits L, Wang J. Genetic and genomic monitoring with minimally invasive sampling methods. Evol Appl 2018; 11:1094-1119. [PMID: 30026800 PMCID: PMC6050181 DOI: 10.1111/eva.12600] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 01/02/2018] [Indexed: 12/12/2022] Open
Abstract
The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high-quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low-quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here, we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy data sets and recommend how to address the challenges of moving between traditional and next-generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.
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Affiliation(s)
- Emma L. Carroll
- Scottish Oceans Institute and Sea Mammal Research UnitUniversity of St AndrewsSt AndrewsUK
| | - Mike W. Bruford
- Cardiff School of Biosciences and Sustainable Places Research InstituteCardiff UniversityCardiff, WalesUK
| | - J. Andrew DeWoody
- Department of Forestry and Natural Resources and Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
| | - Gregoire Leroy
- Animal Production and Health DivisionFood and Agriculture Organization of the United NationsRomeItaly
| | - Alan Strand
- Grice Marine LaboratoryDepartment of BiologyCollege of CharlestonCharlestonSCUSA
| | - Lisette Waits
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIDUSA
| | - Jinliang Wang
- Institute of ZoologyZoological Society of LondonLondonUK
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26
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Delord C, Lassalle G, Oger A, Barloy D, Coutellec M, Delcamp A, Evanno G, Genthon C, Guichoux E, Le Bail P, Le Quilliec P, Longin G, Lorvelec O, Massot M, Reveillac E, Rinaldo R, Roussel J, Vigouroux R, Launey S, Petit EJ. A cost‐and‐time effective procedure to develop
SNP
markers for multiple species: A support for community genetics. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.13034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Chrystelle Delord
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
- HYDRECO Guyane SARLLaboratoire‐Environnement de Petit Saut Kourou France
| | - Gilles Lassalle
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
| | - Adrien Oger
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
| | - Dominique Barloy
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
| | | | | | - Guillaume Evanno
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
| | | | | | | | | | | | - Olivier Lorvelec
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
| | | | - Elodie Reveillac
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
| | | | | | - Regis Vigouroux
- HYDRECO Guyane SARLLaboratoire‐Environnement de Petit Saut Kourou France
| | - Sophie Launey
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
| | - Eric J. Petit
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
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27
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Lucena-Perez M, Soriano L, López-Bao JV, Marmesat E, Fernández L, Palomares F, Godoy JA. Reproductive biology and genealogy in the endangered Iberian lynx: Implications for conservation. Mamm Biol 2018. [DOI: 10.1016/j.mambio.2017.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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28
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Thrasher DJ, Butcher BG, Campagna L, Webster MS, Lovette IJ. Double-digest RAD sequencing outperforms microsatellite loci at assigning paternity and estimating relatedness: A proof of concept in a highly promiscuous bird. Mol Ecol Resour 2018; 18:953-965. [PMID: 29455472 DOI: 10.1111/1755-0998.12771] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 01/31/2018] [Accepted: 02/04/2018] [Indexed: 12/17/2022]
Abstract
Information on genetic relationships among individuals is essential to many studies of the behaviour and ecology of wild organisms. Parentage and relatedness assays based on large numbers of single nucleotide polymorphism (SNP) loci hold substantial advantages over the microsatellite markers traditionally used for these purposes. We present a double-digest restriction site-associated DNA sequencing (ddRAD-seq) analysis pipeline that, as such, simultaneously achieves the SNP discovery and genotyping steps and which is optimized to return a statistically powerful set of SNP markers (typically 150-600 after stringent filtering) from large numbers of individuals (up to 240 per run). We explore the trade-offs inherent in this approach through a set of experiments in a species with a complex social system, the variegated fairy-wren (Malurus lamberti) and further validate it in a phylogenetically broad set of other bird species. Through direct comparisons with a parallel data set from a robust panel of highly variable microsatellite markers, we show that this ddRAD-seq approach results in substantially improved power to discriminate among potential relatives and considerably more precise estimates of relatedness coefficients. The pipeline is designed to be universally applicable to all bird species (and with minor modifications to many other taxa), to be cost- and time-efficient, and to be replicable across independent runs such that genotype data from different study periods can be combined and analysed as field samples are accumulated.
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Affiliation(s)
- Derrick J Thrasher
- Macaulay Library, Cornell Laboratory of Ornithology, Ithaca, NY, USA
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA
| | - Bronwyn G Butcher
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Ithaca, NY, USA
| | - Leonardo Campagna
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Ithaca, NY, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Michael S Webster
- Macaulay Library, Cornell Laboratory of Ornithology, Ithaca, NY, USA
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA
| | - Irby J Lovette
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Ithaca, NY, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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29
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Jacobs RL, Frankel DC, Rice RJ, Kiefer VJ, Bradley BJ. Parentage complexity in socially monogamous lemurs (Eulemur rubriventer
): Integrating genetic and observational data. Am J Primatol 2018; 80. [DOI: 10.1002/ajp.22738] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 12/24/2017] [Accepted: 01/07/2018] [Indexed: 01/05/2023]
Affiliation(s)
- Rachel L. Jacobs
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology; The George Washington University; Washington District of Columbia
| | - David C. Frankel
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology; The George Washington University; Washington District of Columbia
| | - Riley J. Rice
- Department of Anthropology; Yale University; New Haven Connecticut
| | - Vera J. Kiefer
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology; The George Washington University; Washington District of Columbia
| | - Brenda J. Bradley
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology; The George Washington University; Washington District of Columbia
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30
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Microhaplotypes provide increased power from short‐read
DNA
sequences for relationship inference. Mol Ecol Resour 2017; 18:296-305. [DOI: 10.1111/1755-0998.12737] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/19/2017] [Accepted: 11/01/2017] [Indexed: 12/17/2022]
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31
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Escudero PC, Tucker DB, Avila LJ, Sites JW, Morando M. Distribution of Genetic Diversity within a Population ofLiolaemus xanthoviridisand an Assessment of its Mating System, as Inferred with Microsatellite Markers. J HERPETOL 2017. [DOI: 10.2994/sajh-d-16-00037.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Paula C. Escudero
- Grupo de Herpetología Patagónica. Instituto Patagónico para el Estudio de los Ecosistemas Continentales. Centro Nacional Patagónico- Consejo Nacional de Investigaciones Científicas. Puerto Madryn, Argentina
| | - Derek B. Tucker
- Department of Biology 4102 LSB, Brigham Young University, Provo, USA
| | - Luciano J. Avila
- Grupo de Herpetología Patagónica. Instituto Patagónico para el Estudio de los Ecosistemas Continentales. Centro Nacional Patagónico- Consejo Nacional de Investigaciones Científicas. Puerto Madryn, Argentina
| | - Jack W. Sites
- Department of Biology 4102 LSB, Brigham Young University, Provo, USA
| | - Mariana Morando
- Grupo de Herpetología Patagónica. Instituto Patagónico para el Estudio de los Ecosistemas Continentales. Centro Nacional Patagónico- Consejo Nacional de Investigaciones Científicas. Puerto Madryn, Argentina
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32
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Fountain T, Husby A, Nonaka E, DiLeo MF, Korhonen JH, Rastas P, Schulz T, Saastamoinen M, Hanski I. Inferring dispersal across a fragmented landscape using reconstructed families in the Glanville fritillary butterfly. Evol Appl 2017. [DOI: 10.1111/eva.12552] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Toby Fountain
- Department of Biosciences; University of Helsinki; Helsinki Finland
- Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Arild Husby
- Department of Biosciences; University of Helsinki; Helsinki Finland
| | - Etsuko Nonaka
- Department of Biosciences; University of Helsinki; Helsinki Finland
- Department of Biology; Lund University; Lund Sweden
| | | | - Janne H. Korhonen
- Department of Biosciences; University of Helsinki; Helsinki Finland
- Department of Computer Science; Aalto University; Aalto Finland
| | - Pasi Rastas
- Department of Biosciences; University of Helsinki; Helsinki Finland
- Department of Zoology; University of Cambridge; Cambridge UK
| | - Torsti Schulz
- Department of Biosciences; University of Helsinki; Helsinki Finland
| | | | - Ilkka Hanski
- Department of Biosciences; University of Helsinki; Helsinki Finland
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33
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Head ML, Kahn AT, Henshaw JM, Keogh JS, Jennions MD. Sexual selection on male body size, genital length and heterozygosity: Consistency across habitats and social settings. J Anim Ecol 2017; 86:1458-1468. [PMID: 28815592 DOI: 10.1111/1365-2656.12742] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/30/2017] [Indexed: 12/22/2022]
Abstract
Spatial and temporal variation in environmental factors and the social setting can help to maintain genetic variation in sexually selected traits if it affects the strength of directional selection. A key social parameter which affects the intensity of, and sometimes predicts the response to, mating competition is the operational sex ratio (OSR; ratio of receptive males to females). How the OSR affects selection for specific male traits is poorly understood. It is also unclear how sexual selection is affected by interactions between the OSR and environmental factors, such as habitat complexity, that alter key male-female interactions such as mate encounter rates. Here, we experimentally manipulated the OSR and habitat complexity and quantified sexual selection on male mosquitofish (Gambusia holbrooki) by directly measuring male reproductive success (i.e. paternity). We show that despite a more equitable sharing of paternity (i.e. higher levels of multiple paternity) under a male-biased OSR, selection on focal male traits was unaffected by the OSR or habitat complexity. Instead, sexual selection consistently, and significantly, favoured smaller bodied males, males with higher genome wide heterozygosity (based on >3,000 SNP markers) and males with a relatively long gonopodium (intromittent organ). Our results show that sexual selection on male body size, relative genital size and heterozygosity in this system is consistent across environments that vary in ecological parameters that are expected to influence mate encounter rates.
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Affiliation(s)
- Megan L Head
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australia
| | - Andrew T Kahn
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australia
| | - Jonathan M Henshaw
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australia
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australia
| | - Michael D Jennions
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australia
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34
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Festa-Bianchet M, Douhard M, Gaillard JM, Pelletier F. Successes and challenges of long-term field studies of marked ungulates. J Mammal 2017. [DOI: 10.1093/jmammal/gyw227] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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35
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Allendorf FW. Genetics and the conservation of natural populations: allozymes to genomes. Mol Ecol 2017; 26:420-430. [DOI: 10.1111/mec.13948] [Citation(s) in RCA: 180] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 11/28/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Fred W. Allendorf
- Division of Biological Sciences University of Montana Missoula MT 59812 USA
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36
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Newbolt CH, Acker PK, Neuman TJ, Hoffman SI, Ditchkoff SS, Steury TD. Factors influencing reproductive success in male white-tailed deer. J Wildl Manage 2016. [DOI: 10.1002/jwmg.21191] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Chad H. Newbolt
- School of Forestry and Wildlife Sciences; Auburn University; AL 36849 USA
| | - Peter K. Acker
- School of Forestry and Wildlife Sciences; Auburn University; AL 36849 USA
| | - Timothy J. Neuman
- School of Forestry and Wildlife Sciences; Auburn University; AL 36849 USA
| | | | | | - Todd D. Steury
- School of Forestry and Wildlife Sciences; Auburn University; AL 36849 USA
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37
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Sato N, Yoshida MA, Kasugai T. Impact of cryptic female choice on insemination success: Larger sized and longer copulating male squid ejaculate more, but females influence insemination success by removing spermatangia. Evolution 2016; 71:111-120. [PMID: 27805265 DOI: 10.1111/evo.13108] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 10/12/2016] [Accepted: 10/21/2016] [Indexed: 11/28/2022]
Abstract
In polyandrous mating systems, sperm competition and cryptic female choice (CFC) are well recognized as postcopulatory evolutionary forces. However, it remains challenging to separate CFC from sperm competition and to estimate how much CFC influences insemination success because those processes usually occur inside the female's body. The Japanese pygmy squid, Idiosepius paradoxus, is an ideal species in which to separate CFC from sperm competition because sperm transfer by the male and sperm displacement by the female can be observed directly at an external location on the female's body. Here, we counted the number of spermatangia transferred to, removed from, and remaining on the female body during single copulation episodes. We measured behavioral and morphological characteristics of the male, such as duration of copulation and body size. Although males with larger body size and longer copulation time were capable of transferring larger amounts of sperm, females preferentially eliminated sperm from males with larger body size and shorter copulation time by spermatangia removal; thus, CFC could attenuate sperm precedence by larger males, whereas it reinforces sperm precedence by males with longer copulation time. Genetic paternity analysis revealed that fertilisation success for each male was correlated with remaining sperm volume that is adjusted by females after copulation.
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Affiliation(s)
- Noriyosi Sato
- Graduate School of Fisheries Science and Environmental Studies, Nagasaki University, Nagasaki, Nagasaki, Japan.,Current Address: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, United Kingdom
| | - Masa-Aki Yoshida
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan.,Current Address: Marine Biological Science Section, Education and Research Center for Biological Resources, Faculty of Life and Environmental Science, Shimane University, Kamo 194, Okinoshima-cho, Oki, Shimane, Japan
| | - Takashi Kasugai
- Port of Nagoya Public Aquarium, 1-3 Minato-machi, Minato-ku, Nagoya, Aichi, Japan
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38
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Viengkone M, Derocher AE, Richardson ES, Malenfant RM, Miller JM, Obbard ME, Dyck MG, Lunn NJ, Sahanatien V, Davis CS. Assessing polar bear ( Ursus maritimus) population structure in the Hudson Bay region using SNPs. Ecol Evol 2016; 6:8474-8484. [PMID: 28031799 PMCID: PMC5167041 DOI: 10.1002/ece3.2563] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 09/14/2016] [Accepted: 09/20/2016] [Indexed: 12/28/2022] Open
Abstract
Defining subpopulations using genetics has traditionally used data from microsatellite markers to investigate population structure; however, single‐nucleotide polymorphisms (SNPs) have emerged as a tool for detection of fine‐scale structure. In Hudson Bay, Canada, three polar bear (Ursus maritimus) subpopulations (Foxe Basin (FB), Southern Hudson Bay (SH), and Western Hudson Bay (WH)) have been delineated based on mark–recapture studies, radiotelemetry and satellite telemetry, return of marked animals in the subsistence harvest, and population genetics using microsatellites. We used SNPs to detect fine‐scale population structure in polar bears from the Hudson Bay region and compared our results to the current designations using 414 individuals genotyped at 2,603 SNPs. Analyses based on discriminant analysis of principal components (DAPC) and STRUCTURE support the presence of four genetic clusters: (i) Western—including individuals sampled in WH, SH (excluding Akimiski Island in James Bay), and southern FB (south of Southampton Island); (ii) Northern—individuals sampled in northern FB (Baffin Island) and Davis Strait (DS) (Labrador coast); (iii) Southeast—individuals from SH (Akimiski Island in James Bay); and (iv) Northeast—individuals from DS (Baffin Island). Population structure differed from microsatellite studies and current management designations demonstrating the value of using SNPs for fine‐scale population delineation in polar bears.
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Affiliation(s)
- Michelle Viengkone
- Department of Biological Sciences University of Alberta Edmonton AB Canada
| | | | - Evan Shaun Richardson
- Wildlife Research Division Science and Technology Branch Environment and Climate Change Canada University of Alberta Edmonton AB Canada
| | - René Michael Malenfant
- Department of Biological Sciences University of Alberta Edmonton AB Canada; Department of Biology University of New Brunswick Fredericton NB Canada
| | - Joshua Moses Miller
- Department of Biological Sciences University of Alberta Edmonton AB Canada; Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
| | - Martyn E Obbard
- Wildlife Research and Monitoring Section Ontario Ministry of Natural Resources and Forestry Trent University Peterborough ON Canada
| | - Markus G Dyck
- Department of Environment Government of Nunavut Igloolik NU Canada
| | - Nick J Lunn
- Wildlife Research Division Science and Technology Branch Environment and Climate Change Canada University of Alberta Edmonton AB Canada
| | - Vicki Sahanatien
- Department of Biological Sciences University of Alberta Edmonton AB Canada
| | - Corey S Davis
- Department of Biological Sciences University of Alberta Edmonton AB Canada
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39
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Setchell JM. Sexual Selection and the differences between the sexes in Mandrills (Mandrillus sphinx). AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 159:S105-29. [PMID: 26808101 DOI: 10.1002/ajpa.22904] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Sexual selection has become a major focus in evolutionary and behavioral ecology. It is also a popular research topic in primatology. I use studies of mandrills (Mandrillus sphinx), a classic example of extravagant armaments and ornaments in animals, to exemplify how a long-term, multidisciplinary approach that integrates field observations with laboratory methods can contribute to on-going theoretical debates in the field of sexual selection. I begin with a brief summary of the main concepts of sexual selection theory and the differences between the sexes. I then introduce mandrills and the study population and review mandrill life history, the ontogeny of sex differences, and maternal effects. Next, I focus on male-male competition and female choice, followed by the less well-studied questions of female-female competition and male choice. This review shows how different reproductive priorities lead to very different life histories and divergent adaptations in males and females. It demonstrates how broadening traditional perspectives on sexual selection beyond the ostentatious results of intense sexual selection on males leads to an understanding of more subtle and cryptic forms of competition and choice in both sexes and opens many productive avenues in the study of primate reproductive strategies. These include the potential for studies of postcopulatory selection, female intrasexual competition, and male choice. These studies of mandrills provide comparison and, I hope, inspiration for studies of both other polygynandrous species and species with mating systems less traditionally associated with sexual selection.
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Affiliation(s)
- Joanna M Setchell
- Department of Anthropology, Evolutionary Anthropology Research Group, Behaviour Ecology and Evolution Research (BEER) Centre, Durham University, Durham, DH1 3LE, UK
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40
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Kaiser SA, Taylor SA, Chen N, Sillett TS, Bondra ER, Webster MS. A comparative assessment of
SNP
and microsatellite markers for assigning parentage in a socially monogamous bird. Mol Ecol Resour 2016; 17:183-193. [DOI: 10.1111/1755-0998.12589] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/14/2016] [Accepted: 07/19/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Sara A. Kaiser
- Macaulay Library Cornell Lab of Ornithology 159 Sapsucker Woods Rd Ithaca NY 14850 USA
- Migratory Bird Center Center for Conservation Genomics Smithsonian Conservation Biology Institute National Zoological Park MRC 5503 Washington DC 20013 USA
| | - Scott A. Taylor
- Fuller Evolutionary Biology Program Cornell Lab of Ornithology 159 Sapsucker Woods Rd Ithaca NY 14850 USA
- Department of Ecology and Evolutionary Biology University of Colorado at Boulder 1900 Pleasant Street 334 UCB Boulder CO 80309 USA
| | - Nancy Chen
- Fuller Evolutionary Biology Program Cornell Lab of Ornithology 159 Sapsucker Woods Rd Ithaca NY 14850 USA
- Department of Ecology and Evolutionary Biology Cornell University E145 Corson Hall 215 Tower Road Ithaca NY 14853 USA
| | - T. Scott Sillett
- Migratory Bird Center Center for Conservation Genomics Smithsonian Conservation Biology Institute National Zoological Park MRC 5503 Washington DC 20013 USA
| | - Eliana R. Bondra
- Department of Ecology and Evolutionary Biology Cornell University E145 Corson Hall 215 Tower Road Ithaca NY 14853 USA
| | - Michael S. Webster
- Macaulay Library Cornell Lab of Ornithology 159 Sapsucker Woods Rd Ithaca NY 14850 USA
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41
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Individual, social, and sexual niche traits affect copulation success in a polygynandrous mating system. Behav Ecol Sociobiol 2016. [DOI: 10.1007/s00265-016-2112-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Turner MM, Deperno CS, Booth W, Vargo EL, Conner MC, Lancia RA. The mating system of white-tailed deer under Quality Deer Management. J Wildl Manage 2016. [DOI: 10.1002/jwmg.1067] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Melissa M. Turner
- Department of Forestry and Environmental Resources, Fisheries, Wildlife, and Conservation Biology Program; North Carolina State University; Raleigh NC 27695 USA
| | - Christopher S. Deperno
- Department of Forestry and Environmental Resources, Fisheries, Wildlife, and Conservation Biology Program; North Carolina State University; Raleigh NC 27695 USA
| | - Warren Booth
- Department of Biological Science; The University of Tulsa; Tulsa OK 74104 USA
| | - Edward L. Vargo
- Department of Entomology; Texas A&M University; College Station TX 77843 USA
| | - Mark C. Conner
- DuPont Crop Protection, Chesapeake Farms; Chestertown MD 21620 USA
| | - Richard A. Lancia
- Department of Forestry and Environmental Resources, Fisheries, Wildlife, and Conservation Biology Program; North Carolina State University; Raleigh NC 27695 USA
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Kervinen M, Lebigre C, Soulsbury CD. Simultaneous age‐dependent and age‐independent sexual selection in the lekking black grouse(Lyrurus tetrix). J Anim Ecol 2016; 85:715-25. [DOI: 10.1111/1365-2656.12496] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 12/11/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Matti Kervinen
- Department of Biological and Environmental Science University of Jyväskylä P. O. Box 35 Jyväskylä FI‐40014 Finland
| | - Christophe Lebigre
- Earth and Life Institute Place de la Croix du Sud 4 Carnoy building B‐1348 Louvain‐la‐Neuve Belgium
| | - Carl D. Soulsbury
- Joseph Banks Laboratories School of Life Sciences University of Lincoln Lincoln LN6 7TS UK
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Kin competition drives the evolution of sex-biased dispersal under monandry and polyandry, not under monogamy. Anim Behav 2016. [DOI: 10.1016/j.anbehav.2016.01.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Regan CE, Pilkington JG, Pemberton JM, Crawley MJ. Sex differences in relationships between habitat use and reproductive performance in Soay sheep (Ovis aries). Ecol Lett 2015; 19:171-179. [DOI: 10.1111/ele.12550] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/02/2015] [Accepted: 10/22/2015] [Indexed: 02/05/2023]
Affiliation(s)
- Charlotte. E. Regan
- Institute of Evolutionary Biology; School of Biological Sciences; University of Edinburgh; Ashworth Laboratories; Charlotte Auerbach Road Edinburgh EH9 3FL UK
| | - Jill. G. Pilkington
- Institute of Evolutionary Biology; School of Biological Sciences; University of Edinburgh; Ashworth Laboratories; Charlotte Auerbach Road Edinburgh EH9 3FL UK
| | - Josephine. M. Pemberton
- Institute of Evolutionary Biology; School of Biological Sciences; University of Edinburgh; Ashworth Laboratories; Charlotte Auerbach Road Edinburgh EH9 3FL UK
| | - Michael. J. Crawley
- Faculty of Natural Sciences; Department of Life Sciences; Imperial College London; Silwood Park Ascot Berkshire UK
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Hayward AD, Moorad J, Regan CE, Berenos C, Pilkington JG, Pemberton JM, Nussey DH. Asynchrony of senescence among phenotypic traits in a wild mammal population. Exp Gerontol 2015; 71:56-68. [PMID: 26277618 PMCID: PMC4661475 DOI: 10.1016/j.exger.2015.08.003] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/14/2015] [Accepted: 08/04/2015] [Indexed: 01/10/2023]
Abstract
The degree to which changes in lifespan are coupled to changes in senescence in different physiological systems and phenotypic traits is a central question in biogerontology. It is underpinned by deeper biological questions about whether or not senescence is a synchronised process, or whether levels of synchrony depend on species or environmental context. Understanding how natural selection shapes patterns of synchrony in senescence across physiological systems and phenotypic traits demands the longitudinal study of many phenotypes under natural conditions. Here, we examine the patterns of age-related variation in late adulthood in a wild population of Soay sheep (Ovis aries) that have been the subject of individual-based monitoring for thirty years. We examined twenty different phenotypic traits in both males and females, encompassing vital rates (survival and fecundity), maternal reproductive performance (offspring birth weight, birth date and survival), male rutting behaviour, home range measures, parasite burdens, and body mass. We initially quantified age-related variation in each trait having controlled for annual variation in the environment, among-individual variation and selective disappearance effects. We then standardised our age-specific trait means and tested whether age trajectories could be meaningfully grouped according to sex or the type of trait. Whilst most traits showed age-related declines in later life, we found striking levels of asynchrony both within and between the sexes. Of particular note, female fecundity and reproductive performance declined with age, but male annual reproductive success did not. We also discovered that whilst home range size and quality decline with age in females, home range size increases with age in males. Our findings highlight the complexity of phenotypic ageing under natural conditions and, along with emerging data from other wild populations and laboratory models, suggest that the long-standing hypothesis within evolutionary biology that fitness-related traits should senesce in a synchronous manner is seriously flawed.
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Affiliation(s)
- Adam D Hayward
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, United Kingdom
| | - Jacob Moorad
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, United Kingdom
| | - Charlotte E Regan
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, United Kingdom
| | - Camillo Berenos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, United Kingdom
| | - Jill G Pilkington
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, United Kingdom
| | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, United Kingdom
| | - Daniel H Nussey
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, United Kingdom.
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Davis NG, Houston DD, Nason JD. Transcriptome-facilitated development of SNPs for the Sonoran Desert rock fig, Ficus petiolaris (Moraceae). APPLICATIONS IN PLANT SCIENCES 2015; 3:apps1500028. [PMID: 26191464 PMCID: PMC4504724 DOI: 10.3732/apps.1500028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY Single-nucleotide polymorphism (SNP) primers were developed for a native North American desert fig, Ficus petiolaris (Moraceae), to provide markers for population genetic studies designed to quantify patterns of gene flow across a complex landscape. METHODS AND RESULTS Transcriptome sequencing and bioinformatic protocols were implemented to discover SNPs in single-copy protein-coding genes. Multiplexes of 30 nuclear and 24 organellar (chloroplast and mitochondrial) SNPs were selected for primer development and genotyping on the Sequenom MASSArray System. Of these 54 loci, 49 reliably amplified across a panel of 96 F. petiolaris individuals. CONCLUSIONS This study has provided SNP primers that can be applied in future studies investigating population genetics of F. petiolaris and its coevolution with associated pollinating and nonpollinating fig wasps.
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Affiliation(s)
- Nicholas G. Davis
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, Iowa 50011 USA
| | - Derek D. Houston
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, Iowa 50011 USA
| | - John D. Nason
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, Iowa 50011 USA
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Isaksson C. Urbanization, oxidative stress and inflammation: a question of evolving, acclimatizing or coping with urban environmental stress. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12477] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Corlatti L, Bassano B, Poláková R, Fattorini L, Pagliarella MC, Lovari S. Preliminary analysis of reproductive success in a large mammal with alternative mating tactics, the Northern chamois,Rupicapra rupicapra. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12569] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Luca Corlatti
- Research Unit of Behavioural Ecology, Ethology and Wildlife Management; Department of Life Sciences; University of Siena; Via P. A. Mattioli 4 53100 Siena Italy
- Institute of Wildlife Biology and Game Management; University of Natural Resources and Life Sciences Vienna; Gregor-Mendel Strasse 33 A-1180 Vienna Austria
| | - Bruno Bassano
- Alpine Wildlife Research Centre; Gran Paradiso National Park; Via della Rocca 47 10123 Torino Italy
| | - Radka Poláková
- Institute of Vertebrate Biology; Academy of Sciences of the Czech Republic; Květná 8 CZ-603 65 Brno Czech Republic
| | - Lorenzo Fattorini
- Department of Economics and Statistics; University of Siena; Piazza S. Francesco 8 53100 Siena Italy
| | - Maria Chiara Pagliarella
- Department of Economics and Statistics; University of Siena; Piazza S. Francesco 8 53100 Siena Italy
| | - Sandro Lovari
- Research Unit of Behavioural Ecology, Ethology and Wildlife Management; Department of Life Sciences; University of Siena; Via P. A. Mattioli 4 53100 Siena Italy
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