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Ginther SC, Cameron H, White CR, Marshall DJ. Metabolic loads and the costs of metazoan reproduction. Science 2024; 384:763-767. [PMID: 38753775 DOI: 10.1126/science.adk6772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 04/09/2024] [Indexed: 05/18/2024]
Abstract
Reproduction includes two energy investments-the energy in the offspring and the energy expended to make them. The former is well understood, whereas the latter is unquantified but often assumed to be small. Without understanding both investments, the true energy costs of reproduction are unknown. We present a framework for estimating the total energy costs of reproduction by combining data on the energy content of offspring (direct costs) and the metabolic load of bearing them (indirect costs). We find that direct costs typically represent the smaller fraction of the energy expended on reproduction. Mammals pay the highest reproductive costs (excluding lactation), ~90% of which are indirect. Ectotherms expend less on reproduction overall, and live-bearing ectotherms pay higher indirect costs compared with egg-layers. We show that the energy demands of reproduction exceed standard assumptions.
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Affiliation(s)
- Samuel C Ginther
- Centre for Geometric Biology, School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Hayley Cameron
- Centre for Geometric Biology, School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
- School of Biosciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Craig R White
- Centre for Geometric Biology, School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Dustin J Marshall
- Centre for Geometric Biology, School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
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2
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Ricolfi L, Taylor MD, Yang Y, Lagisz M, Nakagawa S. Maternal transfer of per- and polyfluoroalkyl substances (PFAS) in wild birds: A systematic review and meta-analysis. CHEMOSPHERE 2024; 361:142346. [PMID: 38759804 DOI: 10.1016/j.chemosphere.2024.142346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are synthetic chemicals widely used in consumer products. PFAS can accumulate in animal tissues, resulting in biomagnification and adverse effects on wildlife, such as reproductive impairment. In bird species, PFAS are transferred from mothers to eggs along with essential nutrients and may affect embryo development. However, the extent of maternal PFAS transfer across different species and compounds remains poorly understood. Here, we conducted a systematic review and meta-analysis to quantify maternal PFAS transfer in wild birds and investigate potential sources of variation. We tested the moderating effects of compounds' physicochemical properties and biological traits of studied birds. The dataset included 505 measurements of PFAS concentration and 371 effect sizes derived from 13 studies on 16 bird species and 25 compounds. Overall, across all studies and species, we found a 41% higher concentration of PFAS in offspring than in mothers. Specifically, contaminants were concentrated in the yolk, longer and heavier compounds showed preferential transfer, larger clutch size was associated with decreased PFAS transfer and a higher transfer rate was shown in species with piscivorous and opportunistic/diverse diets. A validation assessment showed good robustness of the overall meta-analytic result. Given the crucial role of birds in maintaining ecological balance, this research article has relevant implications for modelling the impacts of PFAS on wildlife, ecosystems, and human health.
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Affiliation(s)
- Lorenzo Ricolfi
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales Sydney, Sydney, NSW, 2052, Australia.
| | - Matthew D Taylor
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales Sydney, Sydney, NSW, 2052, Australia; Port Stephens Fisheries Institute, New South Wales Department of Primary Industries, Nelson Bay, Australia; Queensland Alliance for Environmental Health Sciences, Faculty of Health and Behavioural Sciences, The University of Queensland, Brisbane, Australia.
| | - Yefeng Yang
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales Sydney, Sydney, NSW, 2052, Australia.
| | - Malgorzata Lagisz
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales Sydney, Sydney, NSW, 2052, Australia.
| | - Shinichi Nakagawa
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales Sydney, Sydney, NSW, 2052, Australia.
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3
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Li S, Liu Y, DU X, Li G, Liao W. Nest complexity correlates with larger brain size but smaller body mass across bird species. Integr Zool 2024; 19:496-504. [PMID: 37378973 DOI: 10.1111/1749-4877.12744] [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] [Indexed: 06/29/2023]
Abstract
Amniotes differ substantially in absolute and relative brain size after controlling for allometry, and numerous hypotheses have been proposed to explain brain size evolution. Brain size is thought to correlate with processing capacity and the brain's ability to support complex manipulation such as nest-building skills. The increased complexity of nest structure is supposed to be a measure of an ability to manipulate nesting material into the required shape. The degree of nest-structure complexity is also supposed to be associated with body mass, partly because small species lose heat faster and delicate and insulated nests are more crucial for temperature control of eggs during incubation by small birds. Here, we conducted comparative analyses to test these hypotheses by investigating whether the complexity of species-typical nest structure can be explained by brain size and body mass (a covariate also to control for allometric effects on brain size) across 1353 bird species from 147 families. Consistent with these hypotheses, our results revealed that avian brain size increases as the complexity of the nest structure increases after controlling for a significant effect of body size, and also that a negative relationship exists between nest complexity and body mass.
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Affiliation(s)
- Shaobin Li
- College of Life Science, Yangtze University, Jingzhou, China
| | - Yuxin Liu
- College of Life Science, Yangtze University, Jingzhou, China
| | - Xiaolong DU
- College of Life Science, Yangtze University, Jingzhou, China
| | - Guopan Li
- College of Life Science, Yangtze University, Jingzhou, China
| | - Wenbo Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
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4
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Pottier P, Noble DWA, Seebacher F, Wu NC, Burke S, Lagisz M, Schwanz LE, Drobniak SM, Nakagawa S. New horizons for comparative studies and meta-analyses. Trends Ecol Evol 2024; 39:435-445. [PMID: 38216408 DOI: 10.1016/j.tree.2023.12.004] [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: 09/25/2023] [Revised: 11/29/2023] [Accepted: 12/08/2023] [Indexed: 01/14/2024]
Abstract
Comparative analyses and meta-analyses are key tools to elucidate broad biological principles, yet the two approaches often appear different in purpose. We propose an integrated approach that can generate deeper insights into ecoevolutionary processes. Marrying comparative and meta-analytic approaches will allow for (i) a more accurate investigation of drivers of biological variation, (ii) a greater ability to account for sources of non-independence in experimental data, (iii) more effective control of publication bias, and (iv) improved transparency and reproducibility. Stronger integration of meta-analytic and comparative studies can also broaden the scope from species-centric investigations to community-level responses and function-valued traits (e.g., reaction norms). We illuminate commonalities, differences, and the transformative potential of combining these methodologies for advancing ecology and evolutionary biology.
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Affiliation(s)
- Patrice Pottier
- Evolution and Ecology Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.
| | - Daniel W A Noble
- Division of Ecology and Evolution, Research School of Biology, College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Frank Seebacher
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Nicholas C Wu
- Hawkesbury Institute for the Environment, Western Sydney University, New South Wales, Australia
| | - Samantha Burke
- Evolution and Ecology Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Malgorzata Lagisz
- Evolution and Ecology Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia; Theoretical Sciences Visiting Program, Okinawa Institute of Science and Technology Graduate University, Onna 904-0495, Japan
| | - Lisa E Schwanz
- Evolution and Ecology Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Szymon M Drobniak
- Evolution and Ecology Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia; Institute of Environmental Sciences, Jagiellonian University, Krakow, Poland
| | - Shinichi Nakagawa
- Evolution and Ecology Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia; Theoretical Sciences Visiting Program, Okinawa Institute of Science and Technology Graduate University, Onna 904-0495, Japan
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5
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Smith SM, Heaney LR, Angielczyk KD. Small skeletons show size-specific scaling: an exploration of allometry in the mammalian lumbar spine. Proc Biol Sci 2024; 291:20232868. [PMID: 38628132 PMCID: PMC11021941 DOI: 10.1098/rspb.2023.2868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/14/2024] [Indexed: 04/19/2024] Open
Abstract
Studies of vertebrate bone biomechanics often focus on skeletal adaptations at upper extremes of body mass, disregarding the importance of skeletal adaptations at lower extremes. Yet mammals are ancestrally small and most modern species have masses under 5 kg, so the evolution of morphology and function at small size should be prioritized for understanding how mammals subsist. We examined allometric scaling of lumbar vertebrae in the small-bodied Philippine endemic rodents known as cloud rats, which vary in mass across two orders of magnitude (15.5 g-2700 g). External vertebral dimensions scale with isometry or positive allometry, likely relating to body size and nuances in quadrupedal posture. In contrast to most mammalian trabecular bone studies, bone volume fraction and trabecular thickness scale with positive allometry and isometry, respectively. It is physiologically impossible for these trends to continue to the upper extremes of mammalian body size, and we demonstrate a fundamental difference in trabecular bone allometry between large- and small-bodied mammals. These findings have important implications for the biomechanical capabilities of mammalian bone at small body size; for the selective pressures that govern skeletal evolution in small mammals; and for the way we define 'small' and 'large' in the context of vertebrate skeletons.
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Affiliation(s)
- S. M. Smith
- Field Museum of Natural History, 1400 S DuSable Lake Shore Drive, Chicago, IL 60605, USA
| | - L. R. Heaney
- Field Museum of Natural History, 1400 S DuSable Lake Shore Drive, Chicago, IL 60605, USA
| | - K. D. Angielczyk
- Field Museum of Natural History, 1400 S DuSable Lake Shore Drive, Chicago, IL 60605, USA
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6
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Martins PM, Anderson MJ, Sweatman WL, Punnett AJ. Significant shifts in latitudinal optima of North American birds. Proc Natl Acad Sci U S A 2024; 121:e2307525121. [PMID: 38557189 PMCID: PMC11009622 DOI: 10.1073/pnas.2307525121] [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: 05/04/2023] [Accepted: 12/25/2023] [Indexed: 04/04/2024] Open
Abstract
Changes in climate can alter environmental conditions faster than most species can adapt. A prediction under a warming climate is that species will shift their distributions poleward through time. While many studies focus on range shifts, latitudinal shifts in species' optima can occur without detectable changes in their range. We quantified shifts in latitudinal optima for 209 North American bird species over the last 55 y. The latitudinal optimum (m) for each species in each year was estimated using a bespoke flexible non-linear zero-inflated model of abundance vs. latitude, and the annual shift in m through time was quantified. One-third (70) of the bird species showed a significant shift in their optimum. Overall, mean peak abundances of North American birds have shifted northward, on average, at a rate of 1.5 km per year (±0.58 SE), corresponding to a total distance moved of 82.5 km (±31.9 SE) over the last 55 y. Stronger poleward shifts at the continental scale were linked to key species' traits, including thermal optimum, habitat specialization, and territoriality. Shifts in the western region were larger and less variable than in the eastern region, and they were linked to species' thermal optimum, habitat density preference, and habitat specialization. Individual species' latitudinal shifts were most strongly linked to their estimated thermal optimum, clearly indicating a climate-driven response. Displacement of species from their historically optimal realized niches can have dramatic ecological consequences. Effective conservation must consider within-range abundance shifts. Areas currently deemed "optimal" are unlikely to remain so.
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Affiliation(s)
- Paulo Mateus Martins
- New Zealand Institute for Advanced Study, Massey University, Auckland0745, New Zealand
- PRIMER-e, Quest Research Limited, Auckland0793, New Zealand
| | - Marti J. Anderson
- New Zealand Institute for Advanced Study, Massey University, Auckland0745, New Zealand
- PRIMER-e, Quest Research Limited, Auckland0793, New Zealand
| | - Winston L. Sweatman
- School of Mathematical and Computational Sciences, Massey University, Auckland0745, New Zealand
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7
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Feltes GL, Campos GS, Raidan FSS, Feres LFR, Ribeiro VMP, Cobuci JA. Comparing Bayesian models for the genetic evaluation of oocytes and embryo counts in Dairy Gir cattle. J Appl Genet 2024:10.1007/s13353-024-00862-3. [PMID: 38570427 DOI: 10.1007/s13353-024-00862-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/08/2024] [Accepted: 03/21/2024] [Indexed: 04/05/2024]
Abstract
Count traits are usually explored in livestock breeding programs, and they usually do not fit into normal distribution, requiring alternatives to adjust the phenotype to estimate accurate genetic parameters and breeding values. Alternatively, distribution such as Poisson can be used to evaluate count traits. This study aimed to compare and discuss the genetic evaluation for oocyte and embryo counts considering Gaussian (untransformed variable - LIN; transformed by logarithm - LOG; transformed by Anscombe - ANS) and Poisson (POI) distributions. The data comprised 11,343 total oocytes (TO), viable oocytes (VO), cleaved embryos (CE), and viable embryo (VE) records of ovum pick-up from 1740 Dairy Gir heifers and cows. The genetic parameters and breeding values were estimated by the MCMCglmm package of the R software. The posterior means of heritability varied from 0.40 (LIN) to 0.49 (POI) for TO, 0.39 (LIN) to 0.49 (POI) for VO, 0.30 (LOG) to 0.41 (POI) for cleaved embryos, and 0.19 (LIN) to 0.32 (POI) for viable embryos. The posterior means of repeatability varied from 0.56 (LIN) to 0.65 (POI) for TO, 0.53 (LOG) to 0.63 (POI) for VO, 0.44 (LOG) to 0.60 (POI) for CE, and 0.36 (LOG) to 0.56 (POI) for VE. Deviance information criterion and mean squared residuals indicated that POI model should be used for the genetic evaluation of embryo and oocyte count traits. Spearman's rank correlation between estimated breeding value (EBV) for embryo and oocyte count traits computed by POI, LOG, and ANS models was high (ranging from 0.77 to 0.99), indicating little reranking among the best animals. The POI model is the most adequate for genetic evaluation, resulting in more reliable EBV of oocyte and embryo count traits for Dairy Gir cattle.
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Affiliation(s)
- Giovani Luis Feltes
- Departamento de Zootecnia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 7712 Agronomia, Porto Alegre, RS, CEP 91509-900, Brazil
| | - Gabriel Soares Campos
- Departamento de Zootecnia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 7712 Agronomia, Porto Alegre, RS, CEP 91509-900, Brazil
| | | | | | | | - Jaime Araújo Cobuci
- Departamento de Zootecnia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 7712 Agronomia, Porto Alegre, RS, CEP 91509-900, Brazil.
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8
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Gross IP, Wilson AE, Wolak ME. The fitness consequences of wildlife conservation translocations: a meta-analysis. Biol Rev Camb Philos Soc 2024; 99:348-371. [PMID: 37844577 DOI: 10.1111/brv.13025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 10/01/2023] [Accepted: 10/04/2023] [Indexed: 10/18/2023]
Abstract
Conservation translocation is a common strategy to offset mounting rates of population declines through the transfer of captive- or wild-origin organisms into areas where conspecific populations are imperilled or completely extirpated. Translocations that supplement existing populations are referred to as reinforcements and can be conducted using captive-origin animals [ex situ reinforcement (ESR)] or wild-origin animals without any captive ancestry [in situ reinforcement (ISR)]. These programs have been criticized for low success rates and husbandry practices that produce individuals with genetic and performance deficits, but the post-release performance of captive-origin or wild-origin translocated groups has not been systematically reviewed to quantify success relative to wild-resident control groups. To assess the disparity in post-release performance of translocated organisms relative to wild-resident conspecifics and examine the association of performance disparity with organismal and methodological factors across studies, we conducted a systematic review and meta-analysis of 821 performance comparisons from 171 studies representing nine animal classes (101 species). We found that translocated organisms have 64% decreased odds of out-performing their wild-resident counterparts, supporting claims of systemic issues hampering conservation translocations. To help identify translocation practices that could maximize program success in the future, we further quantified the impact of broad organismal and methodological factors on the disparity between translocated and wild-resident conspecific performance. Pre-release animal enrichment significantly reduced performance disparities, whereas our results suggest no overall effects of taxonomic group, sex, captive generation time, or the type of fitness surrogate measured. This work is the most comprehensive systematic review to date of animal conservation translocations in which wild conspecifics were used as comparators, thereby facilitating an evaluation of the overall impact of this conservation strategy and identifying specific actions to increase success. Our review highlights the need for conservation managers to include both sympatric and allopatric wild-reference groups to ensure the post-release performance of translocated animals can be evaluated. Further, our analyses identify pre-release animal enrichment as a particular strategy for improving the outcomes of animal conservation translocations, and demonstrate how meta-analysis can be used to identify implementation choices that maximize translocated animal contributions to recipient population growth and viability.
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Affiliation(s)
- Iwo P Gross
- Department of Biological Sciences, Auburn University, 120 W. Samford Avenue, Auburn, AL, 36849, USA
| | - Alan E Wilson
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, 382 Mell Street, Auburn, AL, 36849, USA
| | - Matthew E Wolak
- Department of Biological Sciences, Auburn University, 120 W. Samford Avenue, Auburn, AL, 36849, USA
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9
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Wan JSH, Bonser SP, Pang CK, Fazlioglu F, Rutherford S. Adaptive responses to living in stressful habitats: Do invasive and native plant populations use different strategies? Ecol Lett 2024; 27:e14419. [PMID: 38613177 DOI: 10.1111/ele.14419] [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: 10/19/2023] [Revised: 02/08/2024] [Accepted: 03/05/2024] [Indexed: 04/14/2024]
Abstract
Plants inhabit stressful environments characterized by a variety of stressors, including mine sites, mountains, deserts, and high latitudes. Populations from stressful and reference (non-stressful) sites often have performance differences. However, while invasive and native species may respond differently to stressful environments, there is limited understanding of the patterns in reaction norms of populations from these sites. Here, we use phylogenetically controlled meta-analysis to assess the performance of populations under stress and non-stress conditions. We ask whether stress populations of natives and invasives differ in the magnitude of lowered performance under non-stress conditions and if they vary in the degree of performance advantage under stress. We also assessed whether these distinctions differ with stress intensity. Our findings revealed that natives not only have greater adaptive advantages but also more performance reductions than invasives. Populations from very stressful sites had more efficient adaptations, and performance costs increased with stress intensity in natives only. Overall, the results support the notion that adaptation is frequently costless. Reproductive output was most closely associated with adaptive costs and benefits. Our study characterized the adaptive strategies used by invasive and native plants under stressful conditions, thereby providing important insights into the limitations of adaptation to extreme sites.
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Affiliation(s)
- Justin S H Wan
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Sydney, New South Wales, Australia
| | - Stephen P Bonser
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales (UNSW), Sydney, New South Wales, Australia
| | - Clara K Pang
- PlantClinic, Australian Institute of Botanical Science, Royal Botanic Garden, Sydney, New South Wales, Australia
| | | | - Susan Rutherford
- Center for Sustainable Environmental and Ecosystem Research, Department of Environmental Science, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
- Department of Environmental and Sustainability Sciences, The Dorothy and George Hennings College of Science, Mathematics and Technology, Kean University, Union, New Jersey, USA
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou, Zhejiang Province, China
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10
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Kandza VH, Jang H, Kiabiya Ntamboudila F, Lew-Levy S, Boyette AH. Dyadic inter-group cooperation in shotgun hunting activities in a Congo Basin village. EVOLUTIONARY HUMAN SCIENCES 2024; 6:e22. [PMID: 38689891 PMCID: PMC11058523 DOI: 10.1017/ehs.2024.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 02/19/2024] [Accepted: 03/13/2024] [Indexed: 05/02/2024] Open
Abstract
Understanding the dynamics of inter-group cooperation in human adaptation has been the subject of recent empirical and theoretical studies in evolutionary anthropology, beginning to fill gaps in our knowledge of how interactions across political, economic and social domains can - and often do - lead to stable, large-scale cooperation. Here we investigate dyadic intergroup cooperation in shotgun hunting in the Republic of the Congo. In the Congo Basin, inter-group cooperation between foragers and farmers is at the centre of an exchange system maintained by traditional norms and institutions such as fictive kinship. Here, we focused on what factors predict cooperative shotgun hunting exchanges between BaYaka and Yambe. We conducted structured interviews with 48 BaYaka hunters and 18 Yambe men who organise hunts in a village along the Motaba River. We used Bayesian multilevel regression models to investigate the influence of Yambe and BaYaka attributes on probability of dyadic cooperation. We found that BaYaka men's reputations as skilled hunters and their family size each predicted cooperation in shotgun hunting, whereas there was no effect of Yambe attributes (status, wealth, family size). We discuss the results in terms of evolutionary models of men as hunters and inter-group cooperation, as well as biodiversity conservation implications.
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Affiliation(s)
- Vidrige H. Kandza
- Department of Human Behavior, Ecology and Culture Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Haneul Jang
- Department of Human Behavior, Ecology and Culture Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institute for Advances Studies, Toulouse, France
| | - Francy Kiabiya Ntamboudila
- Faculte des Lettres, Arts et Sciences Humaines Marien Ngouabi University, Brazzaville, Republic of the Congo
| | | | - Adam H. Boyette
- Department of Human Behavior, Ecology and Culture Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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11
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Kojima Y, Ito RK, Fukuyama I, Ohkubo Y, Durso AM. Foraging predicts the evolution of warning coloration and mimicry in snakes. Proc Natl Acad Sci U S A 2024; 121:e2318857121. [PMID: 38437547 PMCID: PMC10945821 DOI: 10.1073/pnas.2318857121] [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: 11/17/2023] [Accepted: 01/16/2024] [Indexed: 03/06/2024] Open
Abstract
Warning coloration and Batesian mimicry are classic examples of Darwinian evolution, but empirical evolutionary patterns are often paradoxical. We test whether foraging costs predict the evolution of striking coloration by integrating genetic and ecological data for aposematic and mimetic snakes (Elapidae and Dipsadidae). Our phylogenetic comparison on a total of 432 species demonstrated that dramatic changes in coloration were well predicted by foraging strategy. Multiple tests consistently indicated that warning coloration and conspicuous mimicry were more likely to evolve in species where foraging costs of conspicuous appearance were relaxed by poor vision of their prey, concealed habitat, or nocturnal activity. Reversion to crypsis was also well predicted by ecology for elapids but not for dipsadids. In contrast to a theoretical prediction and general trends, snakes' conspicuous coloration was correlated with secretive ecology, suggesting that a selection regime underlies evolutionary patterns. We also found evidence that mimicry of inconspicuous models (pitvipers) may have evolved in association with foraging demand for crypsis. These findings demonstrate that foraging is an important factor necessary to understand the evolution, persistence, and diversity of warning coloration and mimicry of snakes, highlighting the significance of additional selective factors in solving the warning coloration paradox.
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Affiliation(s)
- Yosuke Kojima
- Department of Biology, Toho University, Funabashi274-8510, Japan
| | - Ryosuke K. Ito
- Division of Forest & Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan
| | - Ibuki Fukuyama
- Division of Earth, Life and Environment, Graduate School of Human and Environmental Studies, Kyoto University, Kyoto606-8501, Japan
| | - Yusaku Ohkubo
- Department of Human Ecology, Graduate School of Environmental and Life Science, Okayama University, Okayama700-8530, Japan
| | - Andrew M. Durso
- Department of Biological Sciences, Florida Gulf Coast University, Ft. Myers, FL33965
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12
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Schraiber JG, Edge MD, Pennell M. Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.10.579721. [PMID: 38496530 PMCID: PMC10942266 DOI: 10.1101/2024.02.10.579721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
In both statistical genetics and phylogenetics, a major goal is to identify correlations between genetic loci or other aspects of the phenotype or environment and a focal trait. In these two fields, there are sophisticated but disparate statistical traditions aimed at these tasks. The disconnect between their respective approaches is becoming untenable as questions in medicine, conservation biology, and evolutionary biology increasingly rely on integrating data from within and among species, and once-clear conceptual divisions are becoming increasingly blurred. To help bridge this divide, we derive a general model describing the covariance between the genetic contributions to the quantitative phenotypes of different individuals. Taking this approach shows that standard models in both statistical genetics (e.g., Genome-Wide Association Studies; GWAS) and phylogenetic comparative biology (e.g., phylogenetic regression) can be interpreted as special cases of this more general quantitative-genetic model. The fact that these models share the same core architecture means that we can build a unified understanding of the strengths and limitations of different methods for controlling for genetic structure when testing for associations. We develop intuition for why and when spurious correlations may occur using analytical theory and conduct population-genetic and phylogenetic simulations of quantitative traits. The structural similarity of problems in statistical genetics and phylogenetics enables us to take methodological advances from one field and apply them in the other. We demonstrate this by showing how a standard GWAS technique-including both the genetic relatedness matrix (GRM) as well as its leading eigenvectors, corresponding to the principal components of the genotype matrix, in a regression model-can mitigate spurious correlations in phylogenetic analyses. As a case study of this, we re-examine an analysis testing for co-evolution of expression levels between genes across a fungal phylogeny, and show that including covariance matrix eigenvectors as covariates decreases the false positive rate while simultaneously increasing the true positive rate. More generally, this work provides a foundation for more integrative approaches for understanding the genetic architecture of phenotypes and how evolutionary processes shape it.
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13
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Pawar S, Huxley PJ, Smallwood TRC, Nesbit ML, Chan AHH, Shocket MS, Johnson LR, Kontopoulos DG, Cator LJ. Variation in temperature of peak trait performance constrains adaptation of arthropod populations to climatic warming. Nat Ecol Evol 2024; 8:500-510. [PMID: 38273123 DOI: 10.1038/s41559-023-02301-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 12/07/2023] [Indexed: 01/27/2024]
Abstract
The capacity of arthropod populations to adapt to long-term climatic warming is currently uncertain. Here we combine theory and extensive data to show that the rate of their thermal adaptation to climatic warming will be constrained in two fundamental ways. First, the rate of thermal adaptation of an arthropod population is predicted to be limited by changes in the temperatures at which the performance of four key life-history traits can peak, in a specific order of declining importance: juvenile development, adult fecundity, juvenile mortality and adult mortality. Second, directional thermal adaptation is constrained due to differences in the temperature of the peak performance of these four traits, with these differences expected to persist because of energetic allocation and life-history trade-offs. We compile a new global dataset of 61 diverse arthropod species which provides strong empirical evidence to support these predictions, demonstrating that contemporary populations have indeed evolved under these constraints. Our results provide a basis for using relatively feasible trait measurements to predict the adaptive capacity of diverse arthropod populations to geographic temperature gradients, as well as ongoing and future climatic warming.
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Affiliation(s)
- Samraat Pawar
- Department of Life Sciences, Imperial College London, Ascot, UK.
| | - Paul J Huxley
- Department of Life Sciences, Imperial College London, Ascot, UK.
- Department of Statistics, Virginia Tech, Blacksburg, VA, USA.
| | - Thomas R C Smallwood
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Miles L Nesbit
- Department of Life Sciences, Imperial College London, Ascot, UK
- The Pirbright Institute, Woking, UK
| | - Alex H H Chan
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Marta S Shocket
- Department of Geography, University of Florida, Gainesville, FL, USA
| | - Leah R Johnson
- Department of Statistics, Virginia Tech, Blacksburg, VA, USA
| | | | - Lauren J Cator
- Department of Life Sciences, Imperial College London, Ascot, UK.
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14
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Nagy J, Hauber ME, Löki V, Mainwaring MC. Plumage and eggshell colouration covary with the level of sex-specific parental contributions to nest building in birds. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2024; 111:12. [PMID: 38411714 PMCID: PMC10899274 DOI: 10.1007/s00114-024-01899-4] [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: 08/01/2023] [Revised: 12/19/2023] [Accepted: 02/19/2024] [Indexed: 02/28/2024]
Abstract
Interspecific variation in sex-specific contributions to prenatal parental care, including avian nest building, is becoming increasingly better understood as we amass more information on more species. We examined whether sex-specific nest building contributions covary with the colouration of parents and their eggs in 521 species of Western Palearctic birds. Having colourful plumage and laying colourful eggs are costly because of the deposition of pigments in feathers and eggs and/or forming costly nanostructural substrates in feathers, and so it might be expected that those costs covary with the costs of nest building at the level of individuals and/or across species to produce of a suite of codivergent traits. Using a phylogenetically informed approach, we tested the hypothesis that species in which females alone invest energy building nests exhibit less sexual plumage dichromatism. However, we found comparative support for the opposite of this prediction. We then tested that species in which females alone build nests lay more colourful, and costlier, eggs because the dual costs of building nests and laying colourful eggs can only be borne by higher quality individuals. As expected, we found that species in which females build nests alone or together with males are more likely to lay colourfully pigmented eggs relative to species in which only males build nests. Finally, stochastic character mapping provided evidence of the repeated evolution of female-only nest building. Interspecific sex differences in plumage colouration therefore covary in a complex manner with female pre- (nest building) and post-copulatory (egg production) investment in reproduction.
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Affiliation(s)
- Jenő Nagy
- HUN-REN-UD Conservation Biology Research Group, Department of Botany, University of Debrecen, Egyetem tér 1., H-4032, Debrecen, Hungary
| | - Mark E Hauber
- Advanced Science Research Center and Program in Psychology, Graduate Center of the City University of New York, New York, NY, 10031, USA
| | - Viktor Löki
- Wetland Ecology Research Group, HUN-REN Centre for Ecological Research, Institute of Aquatic Ecology, Bem tér 18/C, H-4026, Debrecen, Hungary
| | - Mark C Mainwaring
- School of Environmental and Natural Sciences, Bangor University, Bangor, LL57 2DG, UK.
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15
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Pepke ML. Telomere length is not a useful tool for chronological age estimation in animals. Bioessays 2024; 46:e2300187. [PMID: 38047504 DOI: 10.1002/bies.202300187] [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: 09/27/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/05/2023]
Abstract
Telomeres are short repetitive DNA sequences capping the ends of chromosomes. Telomere shortening occurs during cell division and may be accelerated by oxidative damage or ameliorated by telomere maintenance mechanisms. Consequently, telomere length changes with age, which was recently confirmed in a large meta-analysis across vertebrates. However, based on the correlation between telomere length and age, it was concluded that telomere length can be used as a tool for chronological age estimation in animals. Correlation should not be confused with predictability, and the current data and studies suggest that telomeres cannot be used to reliably predict individual chronological age. There are biological reasons for why there is large individual variation in telomere dynamics, which is mainly due to high susceptibility to a wide range of environmental, but also genetic factors, rendering telomeres unfeasible as a tool for age estimation. The use of telomeres for chronological age estimation is largely a misguided effort, but its occasional reappearance in the literature raises concerns that it will mislead resources in wildlife conservation.
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Affiliation(s)
- Michael L Pepke
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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16
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Leonti M, Baker J, Staub P, Casu L, Hawkins J. Taste shaped the use of botanical drugs. eLife 2024; 12:RP90070. [PMID: 38265283 PMCID: PMC10945733 DOI: 10.7554/elife.90070] [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] [Indexed: 01/25/2024] Open
Abstract
The perception of taste and flavour (a combination of taste, smell, and chemesthesis), here also referred to as chemosensation, enables animals to find high-value foods and avoid toxins. Humans have learned to use unpalatable and toxic substances as medicines, yet the importance of chemosensation in this process is poorly understood. Here, we generate tasting-panel data for botanical drugs and apply phylogenetic generalised linear mixed models to test whether intensity and complexity of chemosensory qualities as well as particular tastes and flavours can predict ancient Graeco-Roman drug use. We found chemosensation to be strongly predictive of therapeutic use: botanical drugs with high therapeutic versatility have simple yet intense tastes and flavours, and 21 of 22 chemosensory qualities predicted at least one therapeutic use. In addition to the common notion of bitter tasting medicines, we also found starchy, musky, sweet, and soapy drugs associated with versatility. In ancient Greece and Rome, illness was thought to arise from imbalance in bodily fluids or humours, yet our study suggests that uses of drugs were based on observed physiological effects that are often consistent with modern understanding of chemesthesis and taste receptor pharmacology.
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Affiliation(s)
- Marco Leonti
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, Monserrato, Italy
| | - Joanna Baker
- School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Peter Staub
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, Monserrato, Italy
| | - Laura Casu
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria, Monserrato, Italy
| | - Julie Hawkins
- School of Biological Sciences, University of Reading, Reading, United Kingdom
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17
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Olivier CA, Martin JS, Pilisi C, Agnani P, Kauffmann C, Hayes L, Jaeggi AV, Schradin C. Primate social organization evolved from a flexible pair-living ancestor. Proc Natl Acad Sci U S A 2024; 121:e2215401120. [PMID: 38154063 PMCID: PMC10769843 DOI: 10.1073/pnas.2215401120] [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: 09/09/2022] [Accepted: 10/26/2023] [Indexed: 12/30/2023] Open
Abstract
Explaining the evolution of primate social organization has been fundamental to understand human sociality and social evolution more broadly. It has often been suggested that the ancestor of all primates was solitary and that other forms of social organization evolved later, with transitions being driven by various life history traits and ecological factors. However, recent research showed that many understudied primate species previously assumed to be solitary actually live in pairs, and intraspecific variation in social organization is common. We built a detailed database from primary field studies quantifying the number of social units expressing different social organizations in each population. We used Bayesian phylogenetic models to infer the probability of each social organization, conditional on several socioecological and life history predictors. Here, we show that when intraspecific variation is accounted for, the ancestral social organization of primates was inferred to be variable, with the most common social organization being pair-living but with approximately 10 to 20% of social units of the ancestral population deviating from this pattern by being solitary living. Body size and activity patterns had large effects on transitions between types of social organizations. As in other mammalian clades, pair-living is closely linked to small body size and likely more common in ancestral species. Our results challenge the assumption that ancestral primates were solitary and that pair-living evolved afterward emphasizing the importance of focusing on field data and accounting for intraspecific variation, providing a flexible statistical framework for doing so.
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Affiliation(s)
- Charlotte-Anaïs Olivier
- Institut Pluridisciplinaire Hubert Curien, CNRS, Department of Ethology and Evolutionary Physiology, University of Strasbourg, Strasbourg67200, France
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg2050, South Africa
| | - Jordan S. Martin
- Human Ecology Group, Institute of Evolutionary Medicine, University of Zurich, ZurichCH-8057, Switzerland
| | - Camille Pilisi
- Institut Pluridisciplinaire Hubert Curien, CNRS, Department of Ethology and Evolutionary Physiology, University of Strasbourg, Strasbourg67200, France
| | - Paul Agnani
- Institut Pluridisciplinaire Hubert Curien, CNRS, Department of Ethology and Evolutionary Physiology, University of Strasbourg, Strasbourg67200, France
| | - Cécile Kauffmann
- Institut Pluridisciplinaire Hubert Curien, CNRS, Department of Ethology and Evolutionary Physiology, University of Strasbourg, Strasbourg67200, France
| | - Loren Hayes
- Department of Biology, Geology, and Environmental Science, University of Tennessee, Chattanooga37403, TN
| | - Adrian V. Jaeggi
- Human Ecology Group, Institute of Evolutionary Medicine, University of Zurich, ZurichCH-8057, Switzerland
| | - C. Schradin
- Institut Pluridisciplinaire Hubert Curien, CNRS, Department of Ethology and Evolutionary Physiology, University of Strasbourg, Strasbourg67200, France
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg2050, South Africa
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18
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Hake A, Germann A, de Beer C, Thielen A, Däumer M, Preiser W, von Briesen H, Pfeifer N. Insights to HIV-1 coreceptor usage by estimating HLA adaptation with Bayesian generalized linear mixed models. PLoS Comput Biol 2023; 19:e1010355. [PMID: 38127856 PMCID: PMC10769057 DOI: 10.1371/journal.pcbi.1010355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 01/05/2024] [Accepted: 11/06/2023] [Indexed: 12/23/2023] Open
Abstract
The mechanisms triggering the human immunodeficiency virus type I (HIV-1) to switch the coreceptor usage from CCR5 to CXCR4 during the course of infection are not entirely understood. While low CD4+ T cell counts are associated with CXCR4 usage, a predominance of CXCR4 usage with still high CD4+ T cell counts remains puzzling. Here, we explore the hypothesis that viral adaptation to the human leukocyte antigen (HLA) complex, especially to the HLA class II alleles, contributes to the coreceptor switch. To this end, we sequence the viral gag and env protein with corresponding HLA class I and II alleles of a new cohort of 312 treatment-naive, subtype C, chronically-infected HIV-1 patients from South Africa. To estimate HLA adaptation, we develop a novel computational approach using Bayesian generalized linear mixed models (GLMMs). Our model allows to consider the entire HLA repertoire without restricting the model to pre-learned HLA-polymorphisms. In addition, we correct for phylogenetic relatedness of the viruses within the model itself to account for founder effects. Using our model, we observe that CXCR4-using variants are more adapted than CCR5-using variants (p-value = 1.34e-2). Additionally, adapted CCR5-using variants have a significantly lower predicted false positive rate (FPR) by the geno2pheno[coreceptor] tool compared to the non-adapted CCR5-using variants (p-value = 2.21e-2), where a low FPR is associated with CXCR4 usage. Consequently, estimating HLA adaptation can be an asset in predicting not only coreceptor usage, but also an approaching coreceptor switch in CCR5-using variants. We propose the usage of Bayesian GLMMs for modeling virus-host adaptation in general.
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Affiliation(s)
- Anna Hake
- Research Group Computational Biology, Max Planck Institute for Informatics, Saarbrücken, Germany
- Saarbrücken Graduate School of Computer Science, Saarland University, Saarbrücken, Germany
| | - Anja Germann
- Main Department Medical Biotechnology, Fraunhofer Institute for Biomedical Engineering, Sulzbach, Germany
| | - Corena de Beer
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- National Health Laboratory Service, Tygerberg Business Unit, Cape Town, South Africa
| | | | - Martin Däumer
- Institute of Immunology and Genetics, Kaiserslautern, Germany
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- National Health Laboratory Service, Tygerberg Business Unit, Cape Town, South Africa
| | - Hagen von Briesen
- Main Department Medical Biotechnology, Fraunhofer Institute for Biomedical Engineering, Sulzbach, Germany
| | - Nico Pfeifer
- Research Group Computational Biology, Max Planck Institute for Informatics, Saarbrücken, Germany
- German Center for Infection Research, Partner Site Tübingen, Tübingen, Germany
- Methods in Medical Informatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
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19
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Fletcher LE, Martin LB, Downs CJ. Leukocyte Concentrations Are Isometric in Reptiles Unlike in Endotherms. Physiol Biochem Zool 2023; 96:405-417. [PMID: 38237194 DOI: 10.1086/727050] [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: 01/23/2024]
Abstract
AbstractHow do large and small reptiles defend against infections, given the consequences of body mass for physiology and disease transmission? Functionally equivalent mammalian and avian granulocytes increased disproportionately with body mass (i.e., scaled hypermetrically), such that large organisms had higher concentrations than expected by a prediction of proportional protection across sizes. However, as these scaling relationships were derived from endothermic animals, they do not necessarily inform the scaling of leukocyte concentration for ectothermic reptiles that have a different physiology and evolutionary history. Here, we asked whether and how lymphocyte and heterophil concentrations relate to body mass among more than 120 reptile species. We compared these relationships to those found in birds and mammals and to existing scaling frameworks (i.e., protecton, complexity, rate of metabolism, or safety factor hypotheses). Both lymphocyte and heterophil concentrations scaled almost isometrically among reptiles. In contrast, functionally equivalent granulocytes scaled hypermetrically and lymphocytes scaled isometrically in birds and mammals. Life history traits were also poor predictors of variation in reptilian heterophil and lymphocyte concentrations. Our results provide insight into differences in immune protection in birds and mammals relative to that in reptiles through a comparative lens. The shape of scaling relationships differs, which should be considered when modeling disease dynamics among these groups.
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20
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Eliason CM, Mellenthin LE, Hains T, McCullough JM, Pirro S, Andersen MJ, Hackett SJ. Genomic signatures of convergent shifts to plunge-diving behavior in birds. Commun Biol 2023; 6:1011. [PMID: 37875535 PMCID: PMC10598022 DOI: 10.1038/s42003-023-05359-z] [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: 05/17/2023] [Accepted: 09/14/2023] [Indexed: 10/26/2023] Open
Abstract
Understanding the genetic basis of convergence at broad phylogenetic scales remains a key challenge in biology. Kingfishers (Aves: Alcedinidae) are a cosmopolitan avian radiation with diverse colors, diets, and feeding behaviors-including the archetypal plunge-dive into water. Given the sensory and locomotor challenges associated with air-water transitions, kingfishers offer a powerful opportunity to explore the effects of convergent behaviors on the evolution of genomes and phenotypes, as well as direct comparisons between continental and island lineages. Here, we use whole-genome sequencing of 30 diverse kingfisher species to identify the genomic signatures associated with convergent feeding behaviors. We show that species with smaller ranges (i.e., on islands) have experienced stronger demographic fluctuations than those on continents, and that these differences have influenced the dynamics of molecular evolution. Comparative genomic analyses reveal positive selection and genomic convergence in brain and dietary genes in plunge-divers. These findings enhance our understanding of the connections between genotype and phenotype in a diverse avian radiation.
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Affiliation(s)
- Chad M Eliason
- Grainger Bioinformatics Center, The Field Museum, Chicago, IL, USA.
- Negaunee Integrative Research Center, The Field Museum, Chicago, IL, USA.
| | - Lauren E Mellenthin
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Taylor Hains
- Grainger Bioinformatics Center, The Field Museum, Chicago, IL, USA
- Negaunee Integrative Research Center, The Field Museum, Chicago, IL, USA
- Committee on Evolution Biology, University of Chicago, Chicago, IL, USA
| | - Jenna M McCullough
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Stacy Pirro
- Iridian Genomes, Inc., 6213 Swords Way, Bethesda, MD, USA
| | - Michael J Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Shannon J Hackett
- Committee on Evolution Biology, University of Chicago, Chicago, IL, USA
- Negaunee Integrative Research Center, The Field Museum, Chicago, IL, USA
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21
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Horváth G, Garamszegi LZ, Herczeg G. Phylogenetic meta-analysis reveals system-specific behavioural type-behavioural predictability correlations. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230303. [PMID: 37680498 PMCID: PMC10480700 DOI: 10.1098/rsos.230303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/24/2023] [Indexed: 09/09/2023]
Abstract
The biological significance of behavioural predictability (environment-independent within-individual behavioural variation) became accepted recently as an important part of an individual's behavioural strategy besides behavioural type (individual mean behaviour). However, we do not know how behavioural type and predictability evolve. Here, we tested different evolutionary scenarios: (i) the two traits evolve independently (lack of correlations) and (ii) the two traits' evolution is constrained (abundant correlations) due to either (ii/a) proximate constraints (direction of correlations is similar) or (ii/b) local adaptations (direction of correlations is variable). We applied a set of phylogenetic meta-analyses based on 93 effect sizes across 44 vertebrate and invertebrate species, focusing on activity and risk-taking. The general correlation between behavioural type and predictability did not differ from zero. Effect sizes for correlations showed considerable heterogeneity, with both negative and positive correlations occurring. The overall absolute (unsigned) effect size was high (Zr = 0.58), and significantly exceeded the null expectation based on randomized data. Our results support the adaptive scenario: correlations between behavioural type and predictability are abundant in nature, but their direction is variable. We suggest that the evolution of these behavioural components might be constrained in a system-specific way.
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Affiliation(s)
- Gergely Horváth
- Department of Systematic Zoology and Ecology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
- ELKH-ELTE-MTM Integrative Ecology Research Group, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - László Zsolt Garamszegi
- Centre for Ecological Research, Institute of Ecology and Botany, Alkotmány u. 2-4, 2163 Vácrátót, Hungary
- National Laboratory for Health Security, Centre for Ecological Research, Budapest, Hungary
| | - Gábor Herczeg
- Department of Systematic Zoology and Ecology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
- ELKH-ELTE-MTM Integrative Ecology Research Group, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
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22
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Lobos‐Catalán P, Jiménez‐Castillo M. The functional mechanism behind the latitudinal pattern of liana diversity: Freeze-thaw embolism reduces the ecological performance of liana species. Ecol Evol 2023; 13:e10486. [PMID: 37736281 PMCID: PMC10509155 DOI: 10.1002/ece3.10486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 09/23/2023] Open
Abstract
There is a strong decrease in liana diversity along latitudinal and altitudinal gradients at a global scale, and there is a marked difference in liana diversity between tropical and temperate ecosystems. From these observations, it has been proposed that cold temperatures would restrict the ecological patterns of liana because of their vascular system's vulnerability to freeze-thaw embolism. Our objective was to establish the functional mechanism that drives the loss of liana diversity along a latitudinal temperature gradient. We evaluate the ecological performance of liana in 10 different species based on the apical growth rate, as well as functional traits associated with efficiency (maximum hydraulic conductivity and percentage conductivity lost) and safety of water transport (vessel diameter, vessel density, wood density, and root pressure). We found that at the colder (more southern) site within the latitudinal gradient, liana species showed lower performance, with a fivefold decrease in their apical growth rate as compared to the warmer (more northern) sites. We postulate that this lower performance results from a much lower water transport efficiency (26.1-fold decrease as compared to liana species that inhabit warmer sites) that results from higher freeze-thaw (37.5% of PLC) and reduction of vessel diameter (3 times narrower). These results are unmistakable evidence that cold temperature restricts liana performance: in a cold environment, liana species exhibit a strong decrease in performance, low efficiency, and higher safety of water transport. Conversely, at warmer sites, we found that liana species exhibit functional strategies associated with higher performance, higher efficiency, and lower safety of water transport capacity. This trade-off between efficiency and safety of water transport and their effects on performance could explain the latitudinal pattern of liana diversity.
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Affiliation(s)
- Paulina Lobos‐Catalán
- Instituto de Ciencias Ambientales y EvolutivasUniversidad Austral de ChileValdiviaChile
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23
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Sweeny AR, Lemon H, Ibrahim A, Watt KA, Wilson K, Childs DZ, Nussey DH, Free A, McNally L. A mixed-model approach for estimating drivers of microbiota community composition and differential taxonomic abundance. mSystems 2023; 8:e0004023. [PMID: 37489890 PMCID: PMC10469806 DOI: 10.1128/msystems.00040-23] [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: 02/08/2023] [Accepted: 05/08/2023] [Indexed: 07/26/2023] Open
Abstract
Next-generation sequencing (NGS) and metabarcoding approaches are increasingly applied to wild animal populations, but there is a disconnect between the widely applied generalized linear mixed model (GLMM) approaches commonly used to study phenotypic variation and the statistical toolkit from community ecology typically applied to metabarcoding data. Here, we describe the suitability of a novel GLMM-based approach for analyzing the taxon-specific sequence read counts derived from standard metabarcoding data. This approach allows decomposition of the contribution of different drivers to variation in community composition (e.g., age, season, individual) via interaction terms in the model random-effects structure. We provide guidance to implementing this approach and show how these models can identify how responsible specific taxonomic groups are for the effects attributed to different drivers. We applied this approach to two cross-sectional data sets from the Soay sheep population of St. Kilda. GLMMs showed agreement with dissimilarity-based approaches highlighting the substantial contribution of age and minimal contribution of season to microbiota community compositions, and simultaneously estimated the contribution of other technical and biological factors. We further used model predictions to show that age effects were principally due to increases in taxa of the phylum Bacteroidetes and declines in taxa of the phylum Firmicutes. This approach offers a powerful means for understanding the influence of drivers of community structure derived from metabarcoding data. We discuss how our approach could be readily adapted to allow researchers to estimate contributions of additional factors such as host or microbe phylogeny to answer emerging questions surrounding the ecological and evolutionary roles of within-host communities. IMPORTANCE NGS and fecal metabarcoding methods have provided powerful opportunities to study the wild gut microbiome. A wealth of data is, therefore, amassing across wild systems, generating the need for analytical approaches that can appropriately investigate simultaneous factors at the host and environmental scale that determine the composition of these communities. Here, we describe a generalized linear mixed-effects model (GLMM) approach to analyze read count data from metabarcoding of the gut microbiota, allowing us to quantify the contributions of multiple host and environmental factors to within-host community structure. Our approach provides outputs that are familiar to a majority of field ecologists and can be run using any standard mixed-effects modeling packages. We illustrate this approach using two metabarcoding data sets from the Soay sheep population of St. Kilda investigating age and season effects as worked examples.
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Affiliation(s)
- Amy R. Sweeny
- Institute of Ecology & Evolution, University of Edinburgh, Edinburgh, United Kingdom
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Hannah Lemon
- Institute of Ecology & Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Anan Ibrahim
- Biochemistry and Biotechnology, Institute of Quantitative Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Kathryn A. Watt
- Institute of Ecology & Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Kenneth Wilson
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Dylan Z. Childs
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Daniel H. Nussey
- Institute of Ecology & Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew Free
- Biochemistry and Biotechnology, Institute of Quantitative Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Luke McNally
- Institute of Ecology & Evolution, University of Edinburgh, Edinburgh, United Kingdom
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24
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Huang S, Edie SM, Collins KS, Crouch NMA, Roy K, Jablonski D. Diversity, distribution and intrinsic extinction vulnerability of exploited marine bivalves. Nat Commun 2023; 14:4639. [PMID: 37582749 PMCID: PMC10427664 DOI: 10.1038/s41467-023-40053-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/10/2023] [Indexed: 08/17/2023] Open
Abstract
Marine bivalves are important components of ecosystems and exploited by humans for food across the world, but the intrinsic vulnerability of exploited bivalve species to global changes is poorly known. Here, we expand the list of shallow-marine bivalves known to be exploited worldwide, with 720 exploited bivalve species added beyond the 81 in the United Nations FAO Production Database, and investigate their diversity, distribution and extinction vulnerability using a metric based on ecological traits and evolutionary history. The added species shift the richness hotspot of exploited species from the northeast Atlantic to the west Pacific, with 55% of bivalve families being exploited, concentrated mostly in two major clades but all major body plans. We find that exploited species tend to be larger in size, occur in shallower waters, and have larger geographic and thermal ranges-the last two traits are known to confer extinction-resistance in marine bivalves. However, exploited bivalve species in certain regions such as the tropical east Atlantic and the temperate northeast and southeast Pacific, are among those with high intrinsic vulnerability and are a large fraction of regional faunal diversity. Our results pinpoint regional faunas and specific taxa of likely concern for management and conservation.
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Affiliation(s)
- Shan Huang
- School of Geography, Earth & Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
- Senckenberg Biodiversity and Climate Research Center (SBiK-F), Frankfurt (Main), Germany.
| | - Stewart M Edie
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, USA
| | | | - Nicholas M A Crouch
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Kaustuv Roy
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - David Jablonski
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL, 60637, USA
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Mascaro O, Goupil N, Pantecouteau H, Depierreux A, Van der Henst JB, Claidière N. Human and animal dominance hierarchies show a pyramidal structure guiding adult and infant social inferences. Nat Hum Behav 2023; 7:1294-1306. [PMID: 37386104 DOI: 10.1038/s41562-023-01634-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/17/2023] [Indexed: 07/01/2023]
Abstract
This study investigates the structure of social hierarchies. We hypothesized that if social dominance relations serve to regulate conflicts over resources, then hierarchies should converge towards pyramidal shapes. Structural analyses and simulations confirmed this hypothesis, revealing a triadic-pyramidal motif across human and non-human hierarchies (114 species). Phylogenetic analyses showed that this pyramidal motif is widespread, with little influence of group size or phylogeny. Furthermore, nine experiments conducted in France found that human adults (N = 120) and infants (N = 120) draw inferences about dominance relations that are consistent with hierarchies' pyramidal motif. By contrast, human participants do not draw equivalent inferences based on a tree-shaped pattern with a similar complexity to pyramids. In short, social hierarchies exhibit a pyramidal motif across a wide range of species and environments. From infancy, humans exploit this regularity to draw systematic inferences about unobserved dominance relations, using processes akin to formal reasoning.
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Affiliation(s)
- Olivier Mascaro
- Université Paris Cité, CNRS, Integrative Neuroscience and Cognition Center, Paris, France.
| | - Nicolas Goupil
- Institut des Sciences Cognitives-Marc Jeannerod, UMR5229, CNRS and Université Claude Bernard Lyon 1, Bron, France
| | | | - Adeline Depierreux
- Université Paris Cité, CNRS, Integrative Neuroscience and Cognition Center, Paris, France
| | - Jean-Baptiste Van der Henst
- Université Claude Bernard Lyon 1, CNRS, INSERM, Centre de Recherche en Neurosciences de Lyon, U1028, UMR5292, Trajectoires, Bron, France
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26
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Mora-Poblete F, Maldonado C, Henrique L, Uhdre R, Scapim CA, Mangolim CA. Multi-trait and multi-environment genomic prediction for flowering traits in maize: a deep learning approach. FRONTIERS IN PLANT SCIENCE 2023; 14:1153040. [PMID: 37593046 PMCID: PMC10428628 DOI: 10.3389/fpls.2023.1153040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 07/12/2023] [Indexed: 08/19/2023]
Abstract
Maize (Zea mays L.), the third most widely cultivated cereal crop in the world, plays a critical role in global food security. To improve the efficiency of selecting superior genotypes in breeding programs, researchers have aimed to identify key genomic regions that impact agronomic traits. In this study, the performance of multi-trait, multi-environment deep learning models was compared to that of Bayesian models (Markov Chain Monte Carlo generalized linear mixed models (MCMCglmm), Bayesian Genomic Genotype-Environment Interaction (BGGE), and Bayesian Multi-Trait and Multi-Environment (BMTME)) in terms of the prediction accuracy of flowering-related traits (Anthesis-Silking Interval: ASI, Female Flowering: FF, and Male Flowering: MF). A tropical maize panel of 258 inbred lines from Brazil was evaluated in three sites (Cambira-2018, Sabaudia-2018, and Iguatemi-2020 and 2021) using approximately 290,000 single nucleotide polymorphisms (SNPs). The results demonstrated a 14.4% increase in prediction accuracy when employing multi-trait models compared to the use of a single trait in a single environment approach. The accuracy of predictions also improved by 6.4% when using a single trait in a multi-environment scheme compared to using multi-trait analysis. Additionally, deep learning models consistently outperformed Bayesian models in both single and multiple trait and environment approaches. A complementary genome-wide association study identified associations with 26 candidate genes related to flowering time traits, and 31 marker-trait associations were identified, accounting for 37%, 37%, and 22% of the phenotypic variation of ASI, FF and MF, respectively. In conclusion, our findings suggest that deep learning models have the potential to significantly improve the accuracy of predictions, regardless of the approach used and provide support for the efficacy of this method in genomic selection for flowering-related traits in tropical maize.
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Affiliation(s)
| | - Carlos Maldonado
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Luma Henrique
- Department of Agronomy, State University of Maringá, Paraná, Brazil
| | - Renan Uhdre
- Department of Agronomy, State University of Maringá, Paraná, Brazil
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Wang Y, Obbard DJ. Experimental estimates of germline mutation rate in eukaryotes: a phylogenetic meta-analysis. Evol Lett 2023; 7:216-226. [PMID: 37475753 PMCID: PMC10355183 DOI: 10.1093/evlett/qrad027] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/08/2023] [Accepted: 06/08/2023] [Indexed: 07/22/2023] Open
Abstract
Mutation is the ultimate source of all genetic variation, and over the last 10 years the ready availability of whole-genome sequencing has permitted direct estimation of mutation rate for many non-model species across the tree of life. In this meta-analysis, we make a comprehensive search of the literature for mutation rate estimates in eukaryotes, identifying 140 mutation accumulation (MA) and parent-offspring (PO) sequencing studies covering 134 species. Based on these data, we revisit differences in the single-nucleotide mutation (SNM) rate between different phylogenetic lineages and update the known relationships between mutation rate and generation time, genome size, and nucleotide diversity-while accounting for phylogenetic nonindependence. We do not find a significant difference between MA and PO in estimated mutation rates, but we confirm that mammal and plant lineages have higher mutation rates than arthropods and that unicellular eukaryotes have the lowest mutation rates. We find that mutation rates are higher in species with longer generation times and larger genome sizes, even when accounting for phylogenetic relationships. Moreover, although nucleotide diversity is positively correlated with mutation rate, the gradient of the relationship is significantly less than one (on a logarithmic scale), consistent with higher mutation rates in populations with smaller effective size. For the 29 species for which data are available, we find that indel mutation rates are positively correlated with nucleotide mutation rates and that short deletions are generally more common than short insertions. Nevertheless, despite recent progress, no estimates of either SNM or indel mutation rates are available for the majority of deeply branching eukaryotic lineages-or even for most animal phyla. Even among charismatic megafauna, experimental mutation rate estimates remain unknown for amphibia and scarce for reptiles and fish.
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Affiliation(s)
- Yiguan Wang
- Corresponding author: Institute of Ecology and Evolution, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, United Kingdom.
| | - Darren J Obbard
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
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28
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Cornwallis CK, van 't Padje A, Ellers J, Klein M, Jackson R, Kiers ET, West SA, Henry LM. Symbioses shape feeding niches and diversification across insects. Nat Ecol Evol 2023; 7:1022-1044. [PMID: 37202501 PMCID: PMC10333129 DOI: 10.1038/s41559-023-02058-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 03/15/2023] [Indexed: 05/20/2023]
Abstract
For over 300 million years, insects have relied on symbiotic microbes for nutrition and defence. However, it is unclear whether specific ecological conditions have repeatedly favoured the evolution of symbioses, and how this has influenced insect diversification. Here, using data on 1,850 microbe-insect symbioses across 402 insect families, we found that symbionts have allowed insects to specialize on a range of nutrient-imbalanced diets, including phloem, blood and wood. Across diets, the only limiting nutrient consistently associated with the evolution of obligate symbiosis was B vitamins. The shift to new diets, facilitated by symbionts, had mixed consequences for insect diversification. In some cases, such as herbivory, it resulted in spectacular species proliferation. In other niches, such as strict blood feeding, diversification has been severely constrained. Symbioses therefore appear to solve widespread nutrient deficiencies for insects, but the consequences for insect diversification depend on the feeding niche that is invaded.
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Affiliation(s)
| | - Anouk van 't Padje
- Amsterdam Institute for Life and Environment, section Ecology and Evolution, Vrije Universiteit, Amsterdam, the Netherlands
- Laboratory of Genetics, Wageningen University and Research, Wageningen, the Netherlands
| | - Jacintha Ellers
- Amsterdam Institute for Life and Environment, section Ecology and Evolution, Vrije Universiteit, Amsterdam, the Netherlands
| | - Malin Klein
- Amsterdam Institute for Life and Environment, section Ecology and Evolution, Vrije Universiteit, Amsterdam, the Netherlands
| | - Raphaella Jackson
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - E Toby Kiers
- Amsterdam Institute for Life and Environment, section Ecology and Evolution, Vrije Universiteit, Amsterdam, the Netherlands
| | - Stuart A West
- Department of Biology, University of Oxford, Oxford, UK
| | - Lee M Henry
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
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29
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Qiu T, Aravena MC, Ascoli D, Bergeron Y, Bogdziewicz M, Boivin T, Bonal R, Caignard T, Cailleret M, Calama R, Calderon SD, Camarero JJ, Chang-Yang CH, Chave J, Chianucci F, Courbaud B, Cutini A, Das AJ, Delpierre N, Delzon S, Dietze M, Dormont L, Espelta JM, Fahey TJ, Farfan-Rios W, Franklin JF, Gehring CA, Gilbert GS, Gratzer G, Greenberg CH, Guignabert A, Guo Q, Hacket-Pain A, Hampe A, Han Q, Holik J, Hoshizaki K, Ibanez I, Johnstone JF, Journé V, Kitzberger T, Knops JMH, Kunstler G, Kurokawa H, Lageard JGA, LaMontagne JM, Lefevre F, Leininger T, Limousin JM, Lutz JA, Macias D, Marell A, McIntire EJB, Moore CM, Moran E, Motta R, Myers JA, Nagel TA, Naoe S, Noguchi M, Oguro M, Parmenter R, Pearse IS, Perez-Ramos IM, Piechnik L, Podgorski T, Poulsen J, Redmond MD, Reid CD, Rodman KC, Rodriguez-Sanchez F, Samonil P, Sanguinetti JD, Scher CL, Seget B, Sharma S, Shibata M, Silman M, Steele MA, Stephenson NL, Straub JN, Sutton S, Swenson JJ, Swift M, Thomas PA, Uriarte M, Vacchiano G, Whipple AV, Whitham TG, Wion AP, Wright SJ, Zhu K, Zimmerman JK, Zywiec M, Clark JS. Masting is uncommon in trees that depend on mutualist dispersers in the context of global climate and fertility gradients. NATURE PLANTS 2023:10.1038/s41477-023-01446-5. [PMID: 37386149 DOI: 10.1038/s41477-023-01446-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 05/17/2023] [Indexed: 07/01/2023]
Abstract
The benefits of masting (volatile, quasi-synchronous seed production at lagged intervals) include satiation of seed predators, but these benefits come with a cost to mutualist pollen and seed dispersers. If the evolution of masting represents a balance between these benefits and costs, we expect mast avoidance in species that are heavily reliant on mutualist dispersers. These effects play out in the context of variable climate and site fertility among species that vary widely in nutrient demand. Meta-analyses of published data have focused on variation at the population scale, thus omitting periodicity within trees and synchronicity between trees. From raw data on 12 million tree-years worldwide, we quantified three components of masting that have not previously been analysed together: (i) volatility, defined as the frequency-weighted year-to-year variation; (ii) periodicity, representing the lag between high-seed years; and (iii) synchronicity, indicating the tree-to-tree correlation. Results show that mast avoidance (low volatility and low synchronicity) by species dependent on mutualist dispersers explains more variation than any other effect. Nutrient-demanding species have low volatility, and species that are most common on nutrient-rich and warm/wet sites exhibit short periods. The prevalence of masting in cold/dry sites coincides with climatic conditions where dependence on vertebrate dispersers is less common than in the wet tropics. Mutualist dispersers neutralize the benefits of masting for predator satiation, further balancing the effects of climate, site fertility and nutrient demands.
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Affiliation(s)
- Tong Qiu
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, USA.
| | - Marie-Claire Aravena
- Facultad de Ciencias Forestales y de la Conservacion de la Naturaleza (FCFCN), Universidad de Chile, La Pintana, Santiago, Chile
| | - Davide Ascoli
- Department of Agriculture, Forest and Food Sciences, University of Torino, Grugliasco, Torino, Italy
| | - Yves Bergeron
- Forest Research Institute, University of Quebec in Abitibi-Temiscamingue, Rouyn-Noranda, Quebec, Canada
| | - Michal Bogdziewicz
- Department of Systematic Zoology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Thomas Boivin
- Institut National de Recherche pour Agriculture, Alimentation et Environnement (INRAE), Ecologie des Forets Mediterranennes, Avignon, France
| | - Raul Bonal
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, Madrid, Spain
| | - Thomas Caignard
- Universite Bordeaux, Institut National de Recherche pour Agriculture, Alimentation et Environnement (INRAE), Biodiversity, Genes, and Communities (BIOGECO), Pessac, France
| | - Maxime Cailleret
- NRAE, Aix-Marseille University, UMR RECOVER, Aix-en-Provence, France
| | - Rafael Calama
- Centro de Investigacion Forestal (INIA-CSIC), Madrid, Spain
| | - Sergio Donoso Calderon
- Facultad de Ciencias Forestales y de la Conservacion de la Naturaleza (FCFCN), Universidad de Chile, La Pintana, Santiago, Chile
| | - J Julio Camarero
- Instituto Pirenaico de Ecologla, Consejo Superior de Investigaciones Cientificas (IPE-CSIC), Zaragoza, Spain
| | - Chia-Hao Chang-Yang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Jerome Chave
- Laboratoire Evolution et Diversite Biologique, Toulouse, France
| | | | - Benoit Courbaud
- Universite Grenoble Alpes, Institut National de Recherche pour Agriculture, Alimentation et Environnement (INRAE), Laboratoire EcoSystemes et Societes En Montagne (LESSEM), St. Martin-d'Heres, France
| | - Andrea Cutini
- Research Centre for Forestry and Wood, Arezzo, Italy
| | - Adrian J Das
- U.S. Geological Survey Western Ecological Research Center, Three Rivers, CA, USA
| | - Nicolas Delpierre
- Universite Paris-Saclay, Centre national de la recherche scientifique, AgroParisTech, Ecologie Systematique et Evolution, Orsay, France
| | - Sylvain Delzon
- Universite Bordeaux, Institut National de Recherche pour Agriculture, Alimentation et Environnement (INRAE), Biodiversity, Genes, and Communities (BIOGECO), Pessac, France
| | - Michael Dietze
- Earth and Environment, Boston University, Boston, MA, USA
| | - Laurent Dormont
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS), Montpellier, France
| | - Josep Maria Espelta
- Centre de Recerca Ecologica i Aplicacions Forestals (CREAF), Bellaterra, Catalunya, Spain
| | | | - William Farfan-Rios
- Washington University in Saint Louis, Center for Conservation and Sustainable Development, Missouri Botanical Garden, St Louis, MO, USA
| | | | - Catherine A Gehring
- Department of Biological Sciences and Center for Adaptive Western Landscapes, Flagstaff, AZ, USA
| | - Gregory S Gilbert
- Department of Environmental Studies, University of California, Santa Cruz, CA, USA
| | - Georg Gratzer
- Institute of Forest Ecology, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Wien, Austria
| | | | | | - Qinfeng Guo
- Eastern Forest Environmental Threat Assessment Center, USDA Forest Service, Southern Research Station, Research Triangle Park, NC, USA
| | - Andrew Hacket-Pain
- Department of Geography and Planning, School of Environmental Sciences, University of Liverpool, Liverpool, UK
| | - Arndt Hampe
- Universite Bordeaux, Institut National de Recherche pour Agriculture, Alimentation et Environnement (INRAE), Biodiversity, Genes, and Communities (BIOGECO), Pessac, France
| | - Qingmin Han
- Department of Plant Ecology Forestry and Forest Products Research Institute (FFPRI), Tsukuba, Ibaraki, Japan
| | - Jan Holik
- Department of Forest Ecology, Silva Tarouca Research Institute, Brno, Czech Republic
| | - Kazuhiko Hoshizaki
- Department of Biological Environment, Akita Prefectural University, Akita, Japan
| | - Ines Ibanez
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
| | - Jill F Johnstone
- Institute of Arctic Biology, University of Alaska, Fairbanks, AK, USA
| | - Valentin Journé
- Universite Grenoble Alpes, Institut National de Recherche pour Agriculture, Alimentation et Environnement (INRAE), Laboratoire EcoSystemes et Societes En Montagne (LESSEM), St. Martin-d'Heres, France
| | - Thomas Kitzberger
- Department of Ecology, Instituto de Investigaciones en Biodiversidad y Medioambiente (Consejo Nacional de Investigaciones Cientificas y Tecnicas - Universidad Nacional del Comahue), Bariloche, Argentina
| | - Johannes M H Knops
- Health and Environmental Sciences Department, Xian Jiaotong-Liverpool University, Suzhou, China
| | - Georges Kunstler
- Universite Grenoble Alpes, Institut National de Recherche pour Agriculture, Alimentation et Environnement (INRAE), Laboratoire EcoSystemes et Societes En Montagne (LESSEM), St. Martin-d'Heres, France
| | - Hiroko Kurokawa
- Department of Forest Vegetation, Forestry and Forest Products Research Institute, Tsukuba, Japan, Ibaraki
| | - Jonathan G A Lageard
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK
| | | | - Francois Lefevre
- Institut National de Recherche pour Agriculture, Alimentation et Environnement (INRAE), Ecologie des Forets Mediterranennes, Avignon, France
| | - Theodor Leininger
- USDA, Forest Service, Southern Research Station, Stoneville, MS, USA
| | | | - James A Lutz
- Department of Wildland Resources, and the Ecology Center, Utah State University, Logan, UT, USA
| | - Diana Macias
- Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | | | | | | | - Emily Moran
- School of Natural Sciences, UC Merced, Merced, CA, USA
| | - Renzo Motta
- Department of Agriculture, Forest and Food Sciences, University of Torino, Grugliasco, Torino, Italy
| | - Jonathan A Myers
- Department of Biology, Washington University in St Louis, St Louis, MO, USA
| | - Thomas A Nagel
- Department of Forestry and Renewable Forest Resources, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Shoji Naoe
- Tohoku Research Center, Forestry and Forest Products Research Institute, Morioka, Iwate, Japan
| | - Mahoko Noguchi
- Tohoku Research Center, Forestry and Forest Products Research Institute, Morioka, Iwate, Japan
| | - Michio Oguro
- Department of Forest Vegetation, Forestry and Forest Products Research Institute, Tsukuba, Japan, Ibaraki
| | - Robert Parmenter
- Valles Caldera National Preserve, National Park Service, Jemez Springs, NM, USA
| | - Ian S Pearse
- U.S. Geological Survey Fort Collins Science Center, Fort Collins, CO, USA
| | - Ignacio M Perez-Ramos
- Instituto de Recursos Naturales y Agrobiologia de Sevilla, Consejo Superior de Investigaciones Cientificas (IRNAS-CSIC), Seville, Andalucia, Spain
| | - Lukasz Piechnik
- W. Szafer Institute of Botany, Polish Academy of Sciences, Krakow, Poland
| | - Tomasz Podgorski
- Mammal Research Institute, Polish Academy of Sciences, Bialowieza, Poland
| | - John Poulsen
- Nicholas School of the Environment, Duke University, Durham, NC, USA
| | - Miranda D Redmond
- Department of Forest and Rangeland Stewardship, Colorado State University, Fort Collins, CO, USA
| | - Chantal D Reid
- Nicholas School of the Environment, Duke University, Durham, NC, USA
| | - Kyle C Rodman
- Ecological Restoration Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Pavel Samonil
- Department of Forest Ecology, Silva Tarouca Research Institute, Brno, Czech Republic
| | - Javier D Sanguinetti
- Bilogo Dpto. Conservacin y Manejo, Parque Nacional Lanin Elordi y Perito Moreno, San Marten de los Andes, Neuqun, Argentina
| | - C Lane Scher
- Nicholas School of the Environment, Duke University, Durham, NC, USA
| | - Barbara Seget
- W. Szafer Institute of Botany, Polish Academy of Sciences, Krakow, Poland
| | - Shubhi Sharma
- Nicholas School of the Environment, Duke University, Durham, NC, USA
| | - Mitsue Shibata
- Department of Forest Vegetation, Forestry and Forest Products Research Institute, Tsukuba, Japan, Ibaraki
| | - Miles Silman
- Department of Biology, Wake Forest University, Winston-Salem, NC, USA
| | | | - Nathan L Stephenson
- U.S. Geological Survey Western Ecological Research Center, Three Rivers, CA, USA
| | - Jacob N Straub
- Department of Environmental Science and Ecology, State University of New York-Brockport, Brockport, NY, USA
| | - Samantha Sutton
- Nicholas School of the Environment, Duke University, Durham, NC, USA
| | | | - Margaret Swift
- Nicholas School of the Environment, Duke University, Durham, NC, USA
| | - Peter A Thomas
- School of Life Sciences, Keele University, Staffordshire, UK
| | - Maria Uriarte
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Giorgio Vacchiano
- Department of Agricultural and Environmental Sciences - Production, Territory, Agroenergy (DISAA), University of Milan, Milano, Italy
| | - Amy V Whipple
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Thomas G Whitham
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Andreas P Wion
- Department of Forest and Rangeland Stewardship, Colorado State University, Fort Collins, CO, USA
| | - S Joseph Wright
- Smithsonian Tropical Research Institute, Balboa, Republic of Panama
| | - Kai Zhu
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
| | - Jess K Zimmerman
- Department of Environmental Sciences, University of Puerto Rico, Rio Piedras, PR, USA
| | - Magdalena Zywiec
- W. Szafer Institute of Botany, Polish Academy of Sciences, Krakow, Poland
| | - James S Clark
- Universite Grenoble Alpes, Institut National de Recherche pour Agriculture, Alimentation et Environnement (INRAE), Laboratoire EcoSystemes et Societes En Montagne (LESSEM), St. Martin-d'Heres, France
- Nicholas School of the Environment, Duke University, Durham, NC, USA
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30
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Marshall AF, Balloux F, Hemmings N, Brekke P. Systematic review of avian hatching failure and implications for conservation. Biol Rev Camb Philos Soc 2023; 98:807-832. [PMID: 36635252 DOI: 10.1111/brv.12931] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 12/21/2022] [Accepted: 12/30/2022] [Indexed: 01/14/2023]
Abstract
Avian hatching failure is a widespread phenomenon, affecting around 10% of all eggs that are laid and not lost to predation, damage, or desertion. Our understanding of hatching failure is limited in terms of both its underpinning mechanisms and its occurrence across different populations. It is widely acknowledged that rates of hatching failure are higher in threatened species and in populations maintained in captivity compared to wild, non-threatened species, but these differences have rarely been quantified and any broader patterns remain unexplored. To examine the associations between threat status, management interventions, and hatching failure across populations we conducted a phylogenetically controlled multilevel meta-analysis across 231 studies and 241 species of birds. Our data set included both threatened (Critically Endangered, Endangered, and Vulnerable) and non-threatened (Near Threatened and Least Concern) species across wild and captive populations, as well as 'wild managed' ('free-living') populations. We found the mean overall rate of hatching failure across all populations to be 16.79%, with the hatching failure rate of wild, non-threatened species being 12.40%. We found that populations of threatened species experienced significantly higher mean hatching failure than populations of non-threatened species. Different levels of management were also associated with different rates of hatching failure, with wild populations experiencing the lowest rate of hatching failure, followed by wild managed populations, and populations in captivity experiencing the highest rate. Similarly, populations that were subject to the specific management interventions of artificial incubation, supplementary feeding, and artificial nest provision displayed significantly higher rates of hatching failure than populations without these interventions. The driver of this correlation between hatching failure and management remains unclear, but could be an indirect result of threatened species being more likely to have lower hatching success and also being more likely to be subject to management, indicating that conservation efforts are fittingly being focused towards the species potentially most at risk from extinction. This is the most comprehensive comparative analysis of avian hatching failure that has been conducted to date, and the first to quantify explicitly how threat status and management are associated with the rate of hatching failure in a population. We discuss the implications of our results, focusing on their potential applications to conservation. Although we identified several factors clearly associated with variation in hatching failure, a significant amount of heterogeneity was not explained by our meta-analytical model, indicating that other factors influencing hatching failure were not included here. We discuss what these factors might be and suggest avenues for further research. Finally, we discuss the inconsistency in how hatching failure is defined and reported within the literature, and propose a standardised definition to be used in future studies which will enable better comparison across populations and ensure that the most accurate information is used to support management decisions.
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Affiliation(s)
- Ashleigh F Marshall
- Institute of Zoology, Zoological Society of London, Outer Circle, Regent's Park, London, NW1 4RY, UK
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - François Balloux
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Nicola Hemmings
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, Outer Circle, Regent's Park, London, NW1 4RY, UK
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Dougherty LR, Rovenolt F, Luyet A, Jokela J, Stephenson JF. Ornaments indicate parasite load only if they are dynamic or parasites are contagious. Evol Lett 2023; 7:176-190. [PMID: 37251584 PMCID: PMC10210455 DOI: 10.1093/evlett/qrad017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 05/31/2023] Open
Abstract
Choosing to mate with an infected partner has several potential fitness costs, including disease transmission and infection-induced reductions in fecundity and parental care. By instead choosing a mate with no, or few, parasites, animals avoid these costs and may also obtain resistance genes for offspring. Within a population, then, the quality of sexually selected ornaments on which mate choice is based should correlate negatively with the number of parasites with which a host is infected ("parasite load"). However, the hundreds of tests of this prediction yield positive, negative, or no correlation between parasite load and ornament quality. Here, we use phylogenetically controlled meta-analysis of 424 correlations from 142 studies on a wide range of host and parasite taxa to evaluate explanations for this ambiguity. We found that ornament quality is weakly negatively correlated with parasite load overall, but the relationship is more strongly negative among ornaments that can dynamically change in quality, such as behavioral displays and skin pigmentation, and thus can accurately reflect current parasite load. The relationship was also more strongly negative among parasites that can transmit during sex. Thus, the direct benefit of avoiding parasite transmission may be a key driver of parasite-mediated sexual selection. No other moderators, including methodological details and whether males exhibit parental care, explained the substantial heterogeneity in our data set. We hope to stimulate research that more inclusively considers the many and varied ways in which parasites, sexual selection, and epidemiology intersect.
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Affiliation(s)
- Liam R Dougherty
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, United Kingdom
| | - Faith Rovenolt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Alexia Luyet
- Department of Aquatic Ecology, EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Institute for Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Jukka Jokela
- Department of Aquatic Ecology, EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Institute for Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Jessica F Stephenson
- Corresponding author: University of Pittsburgh Department of Biological Sciences, Clapp Hall, 4249 Fifth Avenue, Pittsburgh, PA 15260 USA.
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32
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Hibbins MS, Breithaupt LC, Hahn MW. Phylogenomic comparative methods: Accurate evolutionary inferences in the presence of gene tree discordance. Proc Natl Acad Sci U S A 2023; 120:e2220389120. [PMID: 37216509 PMCID: PMC10235958 DOI: 10.1073/pnas.2220389120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Phylogenetic comparative methods have long been a mainstay of evolutionary biology, allowing for the study of trait evolution across species while accounting for their common ancestry. These analyses typically assume a single, bifurcating phylogenetic tree describing the shared history among species. However, modern phylogenomic analyses have shown that genomes are often composed of mosaic histories that can disagree both with the species tree and with each other-so-called discordant gene trees. These gene trees describe shared histories that are not captured by the species tree, and therefore that are unaccounted for in classic comparative approaches. The application of standard comparative methods to species histories containing discordance leads to incorrect inferences about the timing, direction, and rate of evolution. Here, we develop two approaches for incorporating gene tree histories into comparative methods: one that constructs an updated phylogenetic variance-covariance matrix from gene trees, and another that applies Felsenstein's pruning algorithm over a set of gene trees to calculate trait histories and likelihoods. Using simulation, we demonstrate that our approaches generate much more accurate estimates of tree-wide rates of trait evolution than standard methods. We apply our methods to two clades of the wild tomato genus Solanum with varying rates of discordance, demonstrating the contribution of gene tree discordance to variation in a set of floral traits. Our approaches have the potential to be applied to a broad range of classic inference problems in phylogenetics, including ancestral state reconstruction and the inference of lineage-specific rate shifts.
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Affiliation(s)
- Mark S. Hibbins
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ONM5S 3B2, Canada
- Department of Biology, Indiana University, Bloomington, IN47405
| | - Lara C. Breithaupt
- Department of Biology, Indiana University, Bloomington, IN47405
- Department of Computer Science, Duke University, Durham, NC27710
| | - Matthew W. Hahn
- Department of Biology, Indiana University, Bloomington, IN47405
- Department of Computer Science, Indiana University, Bloomington, IN47405
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33
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McClelland SC, Attard MRG, Bowen J, Horrocks NPC, Jamie GA, Dixit T, Spottiswoode CN, Portugal SJ. Eggshell composition and surface properties of avian brood-parasitic species compared with non-parasitic species. ROYAL SOCIETY OPEN SCIENCE 2023; 10:221023. [PMID: 37234505 PMCID: PMC10206472 DOI: 10.1098/rsos.221023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 05/05/2023] [Indexed: 05/28/2023]
Abstract
The eggs of avian obligate brood-parasitic species have multiple adaptations to deceive hosts and optimize development in host nests. While the structure and composition of the eggshell in all birds is essential for embryo growth and protection from external threats, parasitic eggs may face specific challenges such as high microbial loads, rapid laying and ejection by the host parents. We set out to assess whether eggshells of avian brood-parasitic species have either (i) specialized structural properties, to meet the demands of a brood-parasitic strategy or (ii) similar structural properties to eggs of their hosts, due to the similar nest environment. We measured the surface topography (roughness), wettability (how well surfaces repel water) and calcium content of eggshells of a phylogenetically and geographically diverse range of brood-parasitic species (representing four of the seven independent lineages of avian brood-parasitic species), their hosts and close relatives of the parasites. These components of the eggshell structure have been demonstrated previously to influence such factors as the risk of microbial infection and overall shell strength. Within a phylogenetically controlled framework, we found no overall significant differences in eggshell roughness, wettability and calcium content between (i) parasitic and non-parasitic species, or (ii) parasitic species and their hosts. Both the wettability and calcium content of the eggs from brood-parasitic species were not more similar to those of their hosts' eggs than expected by chance. By contrast, the mean surface roughness of the eggs of brood-parasitic species was more similar to that of their hosts' eggs than expected by chance, suggesting brood-parasitic species may have evolved to lay eggs that match the host nest environment for this trait. The lack of significant overall differences between parasitic and non-parasitic species, including hosts, in the traits we measured, suggests that phylogenetic signal, as well as general adaptations to the nest environment and for embryo development, outweigh any influence of a parasitic lifestyle on these eggshell properties.
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Affiliation(s)
- Stephanie C. McClelland
- Department of Biological Sciences, School of Life and Environmental Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Marie R. G. Attard
- Department of Biological Sciences, School of Life and Environmental Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
- School of Engineering and Innovation, Open University, Milton Keynes MK7 6AA, UK
| | - James Bowen
- School of Engineering and Innovation, Open University, Milton Keynes MK7 6AA, UK
| | - Nicholas P. C. Horrocks
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge University, Cambridge CB2 0AW, UK
| | - Gabriel A. Jamie
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
- FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch 7701, Cape Town, South Africa
| | - Tanmay Dixit
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
- FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch 7701, Cape Town, South Africa
| | - Claire N. Spottiswoode
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
- FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch 7701, Cape Town, South Africa
| | - Steven J. Portugal
- Department of Biological Sciences, School of Life and Environmental Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
- The Natural History Museum, Tring, Herts HP23 6AP, UK
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34
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Healy K, Kelly R, Carnevale A, Buckley YM. Measuring the shape of mortality across animals and plants: Alternatives to H entropy metrics reveal hidden type IV survivorship curves and associations with parental care at macro-ecological scales. Ecol Evol 2023; 13:e10076. [PMID: 37206684 PMCID: PMC10191775 DOI: 10.1002/ece3.10076] [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: 01/23/2023] [Revised: 04/15/2023] [Accepted: 04/25/2023] [Indexed: 05/21/2023] Open
Abstract
The shape of mortality, or how mortality is spread across an organism's life course, is fundamental to a range of biological processes, with attempts to quantify it rooted in ecology, evolution, and demography. One approach to quantify the distribution of mortality over an organism's life is the use of entropy metrics whose values are interpreted within the classical framework of survivorship curves ranging from type I distributions, with mortality concentrated in late life stages, to type III survivorship curves associated with high early stage mortality. However, entropy metrics were originally developed using restricted taxonomic groups and the behavior of entropy metrics over larger scales of variation may make them unsuitable for wider-ranging contemporary comparative studies. Here, we revisit the classic survivorship framework and, using a combination of simulations and comparative analysis of demography data spanning the animal and plant kingdoms, we show that commonly used entropy metrics cannot distinguish between the most extreme survivorship curves, which in turn can mask important macroecological patterns. We show how using H entropy masks a macroecological pattern of how parental care is associated with type I and type II species and for macroecological studies recommend the use of metrics, such as measures of area under the curve. Using frameworks and metrics that capture the full range of variation of survivorship curves will aid in our understanding of the links between the shape of mortality, population dynamics, and life history traits.
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Affiliation(s)
- Kevin Healy
- School of Natural Sciences, Ollscoil na GaillimheUniversity of GalwayGalwayIreland
- School of Natural Sciences, ZoologyTrinity College DublinDublinIreland
| | - Ruth Kelly
- School of Natural Sciences, ZoologyTrinity College DublinDublinIreland
- Environment and Marine Sciences DivisionAgri‐Food and Biosciences InstituteBelfastUK
| | - Angela Carnevale
- School of Mathematical and Statistical Sciences, Ollscoil na GaillimheUniversity of GalwayGalwayIreland
| | - Yvonne M. Buckley
- School of Natural Sciences, ZoologyTrinity College DublinDublinIreland
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35
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Osmanski AB, Paulat NS, Korstian J, Grimshaw JR, Halsey M, Sullivan KAM, Moreno-Santillán DD, Crookshanks C, Roberts J, Garcia C, Johnson MG, Densmore LD, Stevens RD, Rosen J, Storer JM, Hubley R, Smit AFA, Dávalos LM, Karlsson EK, Lindblad-Toh K, Ray DA. Insights into mammalian TE diversity through the curation of 248 genome assemblies. Science 2023; 380:eabn1430. [PMID: 37104570 PMCID: PMC11103246 DOI: 10.1126/science.abn1430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 10/28/2022] [Indexed: 04/29/2023]
Abstract
We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion and quiescence events across the mammalian tree. Young TEs, particularly long interspersed elements, drive increases in genome size, whereas DNA transposons are associated with smaller genomes. Mammals tend to accumulate only a few types of TEs at any given time, with one TE type dominating. We also found association between dietary habit and the presence of DNA transposon invasions. These detailed annotations will serve as a benchmark for future comparative TE analyses among placental mammals.
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Affiliation(s)
- Austin B. Osmanski
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Nicole S. Paulat
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Jenny Korstian
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Jenna R. Grimshaw
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Michaela Halsey
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | | | | | | | - Jacquelyn Roberts
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Carlos Garcia
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Matthew G. Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | | | - Richard D. Stevens
- Department of Natural Resources Management and Natural Science Research Laboratory, Museum of Texas Tech University, Lubbock, TX, USA
| | | | - Jeb Rosen
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | | | - Liliana M. Dávalos
- Department of Ecology & Evolution, Stony Brook University, Stony Brook, NY, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, USA
| | - Elinor K. Karlsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA
| | - David A. Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
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36
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Yim AD, Cowgill L, Katz DC, Roseman CC. Variation in ontogenetic trajectories of limb dimensions in humans is attributable to both climatic effects and neutral evolution. J Hum Evol 2023; 179:103369. [PMID: 37104893 DOI: 10.1016/j.jhevol.2023.103369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 03/26/2023] [Accepted: 03/26/2023] [Indexed: 04/29/2023]
Abstract
Previous studies showed that there is variation in ontogenetic trajectories of human limb dimensions and proportions. However, little is known about the evolutionary significance of this variation. This study used a global sample of modern human immature long bone measurements and a multivariate linear mixed-effects model to study 1) whether the variation in ontogenetic trajectories of limb dimensions is consistent with ecogeographic predictions and 2) the effects of different evolutionary forces on the variation in ontogenetic trajectories. We found that genetic relatedness arising from neutral (nonselective) evolution, allometric variation associated with the change in size, and directional effects from climate all contributed to the variation in ontogenetic trajectories of all major long bone dimensions in modern humans. After accounting for the effects of neutral evolution and holding other effects considered in the current study constant, extreme temperatures have weak, positive associations with diaphyseal length and breadth measurements, while mean temperature shows negative associations with diaphyseal dimensions. The association with extreme temperatures fits the expectations of ecogeographic rules, while the association with mean temperature may explain the observed among-group variation in intralimb indices. The association with climate is present throughout ontogeny, suggesting an explanation of adaptation by natural selection as the most likely cause. On the other hand, genetic relatedness among groups, as structured by neutral evolutionary factors, is an important consideration when interpreting skeletal morphology, even for nonadult individuals.
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Affiliation(s)
- An-Di Yim
- Department of Health and Exercise Sciences, Truman State University, 100 E Normal Ave, Kirksville, MO, USA; Department of Biology, Truman State University, 100 E Normal Ave, Kirksville, MO, USA; Department of Anthropology, University of Illinois at Urbana-Champaign, 109 Davenport Hall, 607 S Mathews Ave, Urbana, IL, USA.
| | - Libby Cowgill
- Department of Anthropology, University of Missouri, 112 Swallow Hall, Columbia, MO, USA
| | - David C Katz
- Department of Cell Biology and Anatomy, University of Calgary, 2500 University Drive NW, Calgary, Canada
| | - Charles C Roseman
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, 515 Morrill Hall, 505 S Goodwin Ave, Urbana, IL, USA
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37
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Eliason CM, McCullough JM, Hackett SJ, Andersen MJ. Complex plumages spur rapid color diversification in kingfishers (Aves: Alcedinidae). eLife 2023; 12:83426. [PMID: 37083474 PMCID: PMC10121218 DOI: 10.7554/elife.83426] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/22/2023] [Indexed: 04/22/2023] Open
Abstract
Colorful signals in nature provide some of the most stunning examples of rapid phenotypic evolution. Yet, studying color pattern evolution has been historically difficult owing to differences in perceptual ability of humans and analytical challenges with studying how complex color patterns evolve. Island systems provide a natural laboratory for testing hypotheses about the direction and magnitude of phenotypic change. A recent study found that plumage colors of island species are darker and less complex than continental species. Whether such shifts in plumage complexity are associated with increased rates of color evolution remains unknown. Here, we use geometric morphometric techniques to test the hypothesis that plumage complexity and insularity interact to influence color diversity in a species-rich clade of colorful birds-kingfishers (Aves: Alcedinidae). In particular, we test three predictions: (1) plumage complexity enhances interspecific rates of color evolution, (2) plumage complexity is lower on islands, and (3) rates of plumage color evolution are higher on islands. Our results show that more complex plumages result in more diverse colors among species and that island species have higher rates of color evolution. Importantly, we found that island species did not have more complex plumages than their continental relatives. Thus, complexity may be a key innovation that facilitates evolutionary response of individual color patches to distinct selection pressures on islands, rather than being a direct target of selection itself. This study demonstrates how a truly multivariate treatment of color data can reveal evolutionary patterns that might otherwise go unnoticed.
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Affiliation(s)
- Chad M Eliason
- Grainger Bioinformatics Center, Field Museum of Natural History, Chicago, United States
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, United States
| | - Jenna M McCullough
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, United States
| | - Shannon J Hackett
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, United States
| | - Michael J Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, United States
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38
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Caicoya AL, Schaffer A, Holland R, von Fersen L, Colell M, Amici F. Innovation across 13 ungulate species: problem solvers are less integrated in the social group and less neophobic. Proc Biol Sci 2023; 290:20222384. [PMID: 37015274 PMCID: PMC10072937 DOI: 10.1098/rspb.2022.2384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023] Open
Abstract
Innovation is the ability to solve new problems or find novel solutions to familiar problems, and it is known to provide animals with crucial fitness benefits. Although this ability has been extensively studied in some taxa, the factors that predict innovation within and across species are still largely unclear. In this study, we used a novel foraging task to test 111 individuals belonging to 13 ungulate species-a still understudied taxon. To solve the task, individuals had to open transparent and opaque cups with food rewards, by removing their cover. We assessed whether individual factors (neophobia, social integration, sex, age, rank) and socio-ecological factors (dietary breadth, fission-fusion dynamics, domestication, group size) predicted participation and performance in the task. Using a phylogenetic approach, we showed that success was higher for less neophobic and socially less integrated individuals. Moreover, less neophobic individuals, individuals of domesticated species and having higher fission-fusion dynamics were more likely to participate in the task. These results are in line with recent literature suggesting a central role of sociality and personality traits to successfully deal with novel challenges, and confirm ungulates as a promising taxon to test evolutionary theories with a comparative approach.
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Affiliation(s)
- Alvaro L Caicoya
- Department of Clinical Psychology and Psychobiology, Faculty of Psychology, University of Barcelona, 08007 Barcelona, Spain
- Institute of Neurosciences, University of Barcelona, 08021 Barcelona, Spain
| | - Alina Schaffer
- Behavioral Ecology Research Group, Institute of Biology, University of Leipzig, 04103 Leipzig, Germany
- Zoo Leipzig, 04015 Leipzig, Germany
| | - Ruben Holland
- Research Group Human Biology and Primate Cognition, Institute of Biology, University of Leipzig, 04103 Leipzig, Germany
| | - Lorenzo von Fersen
- Department of Comparative Cultural Psychology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Montserrat Colell
- Institute of Neurosciences, University of Barcelona, 08021 Barcelona, Spain
- Behavioral Ecology Research Group, Institute of Biology, University of Leipzig, 04103 Leipzig, Germany
| | - Federica Amici
- Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Nuremberg Zoo, 90480 Nuremberg, Germany
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39
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Advanced methods and implementations for the meta-analyses of animal models: Current practices and future recommendations. Neurosci Biobehav Rev 2023; 146:105016. [PMID: 36566804 DOI: 10.1016/j.neubiorev.2022.105016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
Meta-analytic techniques have been widely used to synthesize data from animal models of human diseases and conditions, but these analyses often face two statistical challenges due to complex nature of animal data (e.g., multiple effect sizes and multiple species): statistical dependency and confounding heterogeneity. These challenges can lead to unreliable and less informative evidence, which hinders the translation of findings from animal to human studies. We present a literature survey of meta-analysis using animal models (animal meta-analysis), showing that these issues are not adequately addressed in current practice. To address these challenges, we propose a meta-analytic framework based on multilevel (linear mixed-effects) models. Through conceptualization, formulations, and worked examples, we illustrate how this framework can appropriately address these issues while allowing for testing new questions. Additionally, we introduce other advanced techniques such as multivariate models, robust variance estimation, and meta-analysis of emergent effect sizes, which can deliver robust inferences and novel biological insights. We also provide a tutorial with annotated R code to demonstrate the implementation of these techniques.
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40
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Pestana C, de Sousa AA, Todorov OS, Beaudet A, Benoit J. Evolutionary history of hominin brain size and phylogenetic comparative methods. PROGRESS IN BRAIN RESEARCH 2023; 275:217-232. [PMID: 36841569 DOI: 10.1016/bs.pbr.2022.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
An absolutely and relatively large brain has traditionally been viewed as a distinctive characteristic of the Homo genus, with anatomically modern humans presented at the apex of a long line of progressive increases in encephalization. Many studies continue to focus attention on increasing brain size in the Homo genus, while excluding measures of absolute and relative brain size of more geologically recent, smaller brained, hominins such as Homo floresiensis, and Homo naledi and smaller brained Homo erectus specimens. This review discusses the benefits of using phylogenetic comparative methods to trace the diverse changes in hominin brain evolution and the drawbacks of not doing so.
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Affiliation(s)
- Christopher Pestana
- Evolutionary Studies Institute, School of Geosciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Orlin S Todorov
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Amélie Beaudet
- Department of Archaeology, University of Cambridge, Cambridge, United Kingdom; School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, Johannesburg, South Africa; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Julien Benoit
- Evolutionary Studies Institute, School of Geosciences, University of the Witwatersrand, Johannesburg, South Africa
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41
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Minias P, Janiszewski T. Ground nesting in passerine birds: evolution, biogeography and life history correlates. OIKOS 2023. [DOI: 10.1111/oik.09870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- Piotr Minias
- Dept of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, Univ. of Łódź Łódź Poland
| | - Tomasz Janiszewski
- Dept of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, Univ. of Łódź Łódź Poland
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42
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Abstract
Large brains provide adaptive cognitive benefits but require unusually high, near-constant energy inputs and become fully functional well after their growth is completed. Consequently, young of most larger-brained endotherms should not be able to independently support the growth and development of their own brains. This paradox is solved if the evolution of extended parental provisioning facilitated brain size evolution. Comparative studies indeed show that extended parental provisioning coevolved with brain size and that it may improve immature survival. The major role of extended parental provisioning supports the idea that the ability to sustain the costs of brains limited brain size evolution.
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43
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Zhu P, Liu W, Zhang X, Li M, Liu G, Yu Y, Li Z, Li X, Du J, Wang X, Grueter CC, Li M, Zhou X. Correlated evolution of social organization and lifespan in mammals. Nat Commun 2023; 14:372. [PMID: 36720880 PMCID: PMC9889386 DOI: 10.1038/s41467-023-35869-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 01/05/2023] [Indexed: 02/02/2023] Open
Abstract
Discerning the relationship between sociality and longevity would permit a deeper understanding of how animal life history evolved. Here, we perform a phylogenetic comparative analysis of ~1000 mammalian species on three states of social organization (solitary, pair-living, and group-living) and longevity. We show that group-living species generally live longer than solitary species, and that the transition rate from a short-lived state to a long-lived state is higher in group-living than non-group-living species, altogether supporting the correlated evolution of social organization and longevity. The comparative brain transcriptomes of 94 mammalian species identify 31 genes, hormones and immunity-related pathways broadly involved in the association between social organization and longevity. Further selection features reveal twenty overlapping pathways under selection for both social organization and longevity. These results underscore a molecular basis for the influence of the social organization on longevity.
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Affiliation(s)
- Pingfen Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Weiqiang Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxiao Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meng Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Gaoming Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Yang Yu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Zihao Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuanjing Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Du
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Cyril C Grueter
- School of Human Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Centre for Evolutionary Biology, School of Biological Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,International Center of Biodiversity and Primate Conservation, Dali University, Dali, Yunnan, 671003, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.
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44
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Street SE, Gutiérrez JS, Allen WL, Capellini I. Human activities favour prolific life histories in both traded and introduced vertebrates. Nat Commun 2023; 14:262. [PMID: 36650141 PMCID: PMC9845321 DOI: 10.1038/s41467-022-35765-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 12/28/2022] [Indexed: 01/19/2023] Open
Abstract
Species' life histories determine population demographics and thus the probability that introduced populations establish and spread. Life histories also influence which species are most likely to be introduced, but how such 'introduction biases' arise remains unclear. Here, we investigate how life histories affect the probability of trade and introduction in phylogenetic comparative analyses across three vertebrate classes: mammals, reptiles and amphibians. We find that traded species have relatively high reproductive rates and long reproductive lifespans. Within traded species, introduced species have a more extreme version of this same life history profile. Species in the pet trade also have long reproductive lifespans but lack 'fast' traits, likely reflecting demand for rare species which tend to have slow life histories. We identify multiple species not yet traded or introduced but with life histories indicative of high risk of future trade, introduction and potentially invasion. Our findings suggest that species with high invasion potential are favoured in the wildlife trade and therefore that trade regulation is crucial for preventing future invasions.
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Affiliation(s)
- Sally E Street
- Department of Anthropology, Durham University, Durham, DH1 3LE, UK.
| | - Jorge S Gutiérrez
- Department of Anatomy, Cell Biology and Zoology, University of Extremadura, Badajoz, 06006, Spain
| | - William L Allen
- Department of Biosciences, Swansea University, Swansea, SA2 8PP, UK
| | - Isabella Capellini
- School of Biological Sciences, Queens University Belfast, Belfast, BT9 5DL, UK.
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45
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Smith JE, Jaeggi AV, Holmes RK, Silk JB. Sex differences in cooperative coalitions: a mammalian perspective. Philos Trans R Soc Lond B Biol Sci 2023; 378:20210426. [PMID: 36440559 PMCID: PMC9703251 DOI: 10.1098/rstb.2021.0426] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/09/2022] [Indexed: 11/29/2022] Open
Abstract
In group-living species, cooperative tactics can offset asymmetries in resource-holding potential between individuals and alter the outcome of intragroup conflicts. Differences in the kinds of competitive pressures that males and females face might influence the benefits they gain from forming intragroup coalitions. We predicted that there would be a female bias in intragroup coalitions because females (1) are more like to live with kin than males are, and (2) compete over resources that are more readily shared than resources males compete over. We tested this main prediction using information about coalition formation across mammalian species and phylogenetic comparative analyses. We found that for nearly all species in which intragroup coalitions occur, members of both sexes participate, making this the typical mammalian pattern. The presence and frequency of female or male coalitions were not strongly associated with key socio-ecological factors like resource defensibility, sexual dimorphism or philopatry. This suggests that once the ability to form intragroup coalitions emerges in one sex, it is likely to emerge in the other sex as well and that there is no strong phylogenetic legacy of sex differences in this form of cooperation. This article is part of the theme issue 'Cooperation among women: evolutionary and cross-cultural perspectives'.
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Affiliation(s)
- Jennifer E. Smith
- Biology Department, University of Wisconsin Eau Claire, 105 Garfield Avenue, Eau Claire, WI 54702, USA
- Biology Department, Mills College, 5000 MacArthur Boulevard, Oakland, CA 94631, USA
| | - Adrian V. Jaeggi
- Institute of Evolutionary Medicine, University of Zurich, Zurich 8057, Switzerland
| | - Rose K. Holmes
- Biology Department, University of Wisconsin Eau Claire, 105 Garfield Avenue, Eau Claire, WI 54702, USA
| | - Joan B. Silk
- School of Human Evolution and Social Change, Institute of Human Origins, Arizona State University, Tempe, AZ 85287-2402, USA
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46
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Bastide P, Soneson C, Stern DB, Lespinet O, Gallopin M. A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data. Mol Biol Evol 2023; 40:6889356. [PMID: 36508357 DOI: 10.1093/molbev/msac269] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/14/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Interspecies RNA-Seq datasets are increasingly common, and have the potential to answer new questions about the evolution of gene expression. Single-species differential expression analysis is now a well-studied problem that benefits from sound statistical methods. Extensive reviews on biological or synthetic datasets have provided the community with a clear picture on the relative performances of the available methods in various settings. However, synthetic dataset simulation tools are still missing in the interspecies gene expression context. In this work, we develop and implement a new simulation framework. This tool builds on both the RNA-Seq and the phylogenetic comparative methods literatures to generate realistic count datasets, while taking into account the phylogenetic relationships between the samples. We illustrate the usefulness of this new framework through a targeted simulation study, that reproduces the features of a recently published dataset, containing gene expression data in adult eye tissue across blind and sighted freshwater crayfish species. Using our simulated datasets, we perform a fair comparison of several approaches used for differential expression analysis. This benchmark reveals some of the strengths and weaknesses of both the classical and phylogenetic approaches for interspecies differential expression analysis, and allows for a reanalysis of the crayfish dataset. The tool has been integrated in the R package compcodeR, freely available on Bioconductor.
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Affiliation(s)
- Paul Bastide
- IMAG, Université de Montpellier, CNRS, Montpellier, France
| | - Charlotte Soneson
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - David B Stern
- Department of Integrative Biology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Olivier Lespinet
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Mélina Gallopin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
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47
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Beltrán DF, Araya-Salas M, Parra JL, Stiles FG, Rico-Guevara A. The evolution of sexually dimorphic traits in ecological gradients: an interplay between natural and sexual selection in hummingbirds. Proc Biol Sci 2022; 289:20221783. [PMID: 36515116 PMCID: PMC9748779 DOI: 10.1098/rspb.2022.1783] [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: 09/08/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
Traits that exhibit differences between the sexes have been of special interest in the study of phenotypic evolution. Classic hypotheses explain sexually dimorphic traits via intra-sexual competition and mate selection, yet natural selection may also act differentially on the sexes to produce dimorphism. Natural selection can act either through physiological and ecological constraints on one of the sexes, or by modulating the strength of sexual/social selection. This predicts an association between the degree of dimorphism and variation in ecological environments. Here, we characterize the variation in hummingbird dimorphism across ecological gradients using rich databases of morphology, colouration and song. We show that morphological dimorphism decreases with elevation in the understorey and increases with elevation in mixed habitats, that dichromatism increases at high altitudes in open and mixed habitats, and that song is less complex in mixed habitats. Our results are consistent with flight constraints, lower predation pressure at high elevations and with habitat effects on song transmission. We also show that dichromatism and song complexity are positively associated, while tail dimorphism and song complexity are negatively associated. Our results suggest that key ecological factors shape sexually dimorphic traits, and that different communication modalities do not always evolve in tandem.
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Affiliation(s)
- Diego F. Beltrán
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Marcelo Araya-Salas
- Centro de Investigación en Neurociencias, Universidad de Costa Rica, San José, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
| | - Juan L. Parra
- Grupo de Ecología y Evolución de Vertebrados, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - F. Gary Stiles
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Alejandro Rico-Guevara
- Department of Biology, University of Washington, Seattle, WA 98195, USA
- Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98105, USA
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48
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Vargas G. G, Kunert N, Hammond WM, Berry ZC, Werden LK, Smith‐Martin CM, Wolfe BT, Toro L, Mondragón‐Botero A, Pinto‐Ledezma JN, Schwartz NB, Uriarte M, Sack L, Anderson‐Teixeira KJ, Powers JS. Leaf habit affects the distribution of drought sensitivity but not water transport efficiency in the tropics. Ecol Lett 2022; 25:2637-2650. [PMID: 36257904 PMCID: PMC9828425 DOI: 10.1111/ele.14128] [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: 06/18/2022] [Revised: 08/11/2022] [Accepted: 09/10/2022] [Indexed: 01/12/2023]
Abstract
Considering the global intensification of aridity in tropical biomes due to climate change, we need to understand what shapes the distribution of drought sensitivity in tropical plants. We conducted a pantropical data synthesis representing 1117 species to test whether xylem-specific hydraulic conductivity (KS ), water potential at leaf turgor loss (ΨTLP ) and water potential at 50% loss of KS (ΨP50 ) varied along climate gradients. The ΨTLP and ΨP50 increased with climatic moisture only for evergreen species, but KS did not. Species with high ΨTLP and ΨP50 values were associated with both dry and wet environments. However, drought-deciduous species showed high ΨTLP and ΨP50 values regardless of water availability, whereas evergreen species only in wet environments. All three traits showed a weak phylogenetic signal and a short half-life. These results suggest strong environmental controls on trait variance, which in turn is modulated by leaf habit along climatic moisture gradients in the tropics.
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Affiliation(s)
- German Vargas G.
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA,School of Biological SciencesThe University of UtahSalt Lake CityUtahUSA
| | - Norbert Kunert
- Conservation Ecology CenterSmithsonian National Zoo and Conservation Biology InstituteFront RoyalVirginiaUSA,Forest Global Earth ObservatorySmithsonian Tropical Research InstitutePanamaRepublic of Panama,Department of Integrative Biology and Biodiversity Research, Institute of BotanyUniversity of Natural Resources and Life Sciences ViennaViennaAustria
| | - William M. Hammond
- Agronomy Department, Institute of Food and Agricultural SciencesUniversity of FloridaGainesvilleFloridaUSA
| | - Z. Carter Berry
- Department of BiologyWake Forest UniversityWinston‐SalemNorth CarolinaUSA
| | - Leland K. Werden
- Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
| | - Chris M. Smith‐Martin
- Department of Ecology Evolution and Environmental BiologyColumbia UniversityNew YorkNew YorkUSA
| | - Brett T. Wolfe
- School of Renewable Natural ResourcesLouisiana State University Agricultural CenterBaton RougeLouisianaUSA,Smithsonian Tropical Research InstitutePanamaRepublic of Panama
| | - Laura Toro
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA
| | | | - Jesús N. Pinto‐Ledezma
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt. PaulMinnesotaUSA
| | - Naomi B. Schwartz
- Department of GeographyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - María Uriarte
- Department of Ecology Evolution and Environmental BiologyColumbia UniversityNew YorkNew YorkUSA
| | - Lawren Sack
- Department of Ecology and EvolutionUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Kristina J. Anderson‐Teixeira
- Conservation Ecology CenterSmithsonian National Zoo and Conservation Biology InstituteFront RoyalVirginiaUSA,Forest Global Earth ObservatorySmithsonian Tropical Research InstitutePanamaRepublic of Panama
| | - Jennifer S. Powers
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt. PaulMinnesotaUSA
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49
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Macedo G, Marcondes RS, Biondo C, Bravo GA, Derryberry EP. The evolution of sex similarities in social signals: Climatic seasonality is associated with lower sexual dimorphism and greater elaboration of female and male signals in antbirds (Thamnophilidae). Evolution 2022; 76:2893-2915. [PMID: 36237126 DOI: 10.1111/evo.14638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 01/22/2023]
Abstract
Selection on signals that mediate social competition varies with resource availability. Climate regulates resource availability, which may affect the strength of competition and selection on signals. Traditionally, this meant that more seasonal, colder, or dryer-overall harsher-environments should favor the elaboration of male signals under stronger male-male competition, increasing sexual dimorphism. However, females also use signals to compete; thus, harsher environments could strengthen competition and favor elaboration of signals in both sexes, decreasing sexual dimorphism. Alternatively, harsher environments could decrease sexual dimorphism due to scarcer resources to invest in signal elaboration in both sexes. We evaluated these contrasting hypotheses in antbirds, a family of Neotropical passerines that varies in female and male signals and occurs across diverse climatic regimes. We tested the association of sexual dimorphism of plumage coloration and songs with temperature, precipitation, and their seasonality. We found that greater seasonality is associated with lower sexual dimorphism in plumage coloration and greater elaboration of visual signals in both sexes, but not acoustic signals. Our results suggest that greater seasonality may be associated with convergent elaboration of female and male visual signals, highlighting the role of signals of both sexes in the evolution of sexual dimorphism.
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Affiliation(s)
- Gabriel Macedo
- Center for Natural Sciences and Humanities, Federal University of ABC (UFABC), São Bernardo do Campo, SP, 09606-045, Brazil.,Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Rafael S Marcondes
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, 70803.,Current Address: Department of Biosciences, Rice University, Houston, Texas, 77005
| | - Cibele Biondo
- Center for Natural Sciences and Humanities, Federal University of ABC (UFABC), São Bernardo do Campo, SP, 09606-045, Brazil
| | - Gustavo A Bravo
- Sección de Ornitología, Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Villa de Leyva, 154001, Colombia.,Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, 02138
| | - Elizabeth P Derryberry
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, 37996
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50
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Kärkkäinen T, Briga M, Laaksonen T, Stier A. Within-individual repeatability in telomere length: A meta-analysis in nonmammalian vertebrates. Mol Ecol 2022; 31:6339-6359. [PMID: 34455645 DOI: 10.1111/mec.16155] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 07/27/2021] [Accepted: 08/23/2021] [Indexed: 01/31/2023]
Abstract
Telomere length is increasingly used as a biomarker of long-term somatic state and future survival prospects. While most studies have overlooked this aspect, biological interpretations based on a given telomere length will benefit from considering the level of within-individual repeatability of telomere length through time. Therefore, we conducted a meta-analysis on 74 longitudinal studies in nonmammalian vertebrates, with the aim to establish the current pattern of within-individual repeatability in telomere length and to identify the methodological (e.g., qPCR/TRF) and biological factors (e.g., age class, phylogeny) that may affect it. While the median within-individual repeatability of telomere length was moderate to high (R = 0.55; 95% CI: 0.05-0.95; N = 82), marked heterogeneity between studies was evident. Measurement method affected the repeatability estimate strongly, with TRF-based studies exhibiting high repeatability (R = 0.80; 95% CI: 0.34-0.96; N = 25), while repeatability of qPCR-based studies was markedly lower and more variable (R = 0.46; 95% CI: 0.04-0.82; N = 57). While phylogeny explained some variance in repeatability, phylogenetic signal was not significant (λ = 0.32; 95% CI: 0.00-0.83). None of the biological factors investigated here significantly explained variation in the repeatability of telomere length, being potentially obscured by methodological differences. Our meta-analysis highlights the high variability in within-individual repeatability estimates between studies and the need to put more effort into separating technical and biological explanations. This is important to better understand to what extent biological factors can affect the repeatability of telomere length and thus the interpretation of telomere length data.
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Affiliation(s)
| | - Michael Briga
- Department of Biology, University of Turku, Turku, Finland
| | - Toni Laaksonen
- Department of Biology, University of Turku, Turku, Finland
| | - Antoine Stier
- Department of Biology, University of Turku, Turku, Finland
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