1
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Kendall C, Robinson J, Debortoli G, Nooranikhojasteh A, Christian D, Newman D, Sayers K, Cole S, Parra E, Schillaci M, Viola B. Global and local ancestry estimation in a captive baboon colony. PLoS One 2024; 19:e0305157. [PMID: 38959276 PMCID: PMC11221750 DOI: 10.1371/journal.pone.0305157] [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: 01/15/2024] [Accepted: 05/24/2024] [Indexed: 07/05/2024] Open
Abstract
The last couple of decades have highlighted the importance of studying hybridization, particularly among primate species, as it allows us to better understand our own evolutionary trajectory. Here, we report on genetic ancestry estimates using dense, full genome data from 881 olive (Papio anubus), yellow (Papio cynocephalus), or olive-yellow crossed captive baboons from the Southwest National Primate Research Center. We calculated global and local ancestry information, imputed low coverage genomes (n = 830) to improve marker quality, and updated the genetic resources of baboons available to assist future studies. We found evidence of historical admixture in some putatively purebred animals and identified errors within the Southwest National Primate Research Center pedigree. We also compared the outputs between two different phasing and imputation pipelines along with two different global ancestry estimation software. There was good agreement between the global ancestry estimation software, with R2 > 0.88, while evidence of phase switch errors increased depending on what phasing and imputation pipeline was used. We also generated updated genetic maps and created a concise set of ancestry informative markers (n = 1,747) to accurately obtain global ancestry estimates.
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Affiliation(s)
| | - Jacqueline Robinson
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California, United States of America
| | - Guilherme Debortoli
- Department of Anthropology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Amin Nooranikhojasteh
- Epigenomics Lab, Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Debbie Christian
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Deborah Newman
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Kenneth Sayers
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Shelley Cole
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Esteban Parra
- Department of Anthropology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Michael Schillaci
- Department of Anthropology, University of Toronto Scarborough, Scarborough, Ontario, Canada
| | - Bence Viola
- Department of Anthropology, University of Toronto, Toronto, Ontario, Canada
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2
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Weibel CJ, Dasari MR, Jansen DA, Gesquiere LR, Mututua RS, Warutere JK, Siodi LI, Alberts SC, Tung J, Archie EA. Using non-invasive behavioral and physiological data to measure biological age in wild baboons. GeroScience 2024:10.1007/s11357-024-01157-5. [PMID: 38693466 DOI: 10.1007/s11357-024-01157-5] [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: 01/03/2024] [Accepted: 04/05/2024] [Indexed: 05/03/2024] Open
Abstract
Biological aging is near-ubiquitous in the animal kingdom, but its timing and pace vary between individuals and over lifespans. Prospective, individual-based studies of wild animals-especially non-human primates-help identify the social and environmental drivers of this variation by indicating the conditions and exposure windows that affect aging processes. However, measuring individual biological age in wild primates is challenging because several of the most promising methods require invasive sampling. Here, we leverage observational data on behavior and physiology, collected non-invasively from 319 wild female baboons across 2402 female-years of study, to develop a composite predictor of age: the non-invasive physiology and behavior (NPB) clock. We found that age predictions from the NPB clock explained 51% of the variation in females' known ages. Further, deviations from the clock's age predictions predicted female survival: females predicted to be older than their known ages had higher adult mortality. Finally, females who experienced harsh early-life conditions were predicted to be about 6 months older than those who grew up in more benign conditions. While the relationship between early adversity and NPB age is noisy, this estimate translates to a predicted 2-3 year reduction in mean adult lifespan in our model. A constraint of our clock is that it is tailored to data collection approaches implemented in our study population. However, many of the clock's components have analogs in other populations, suggesting that non-invasive data can provide broadly applicable insight into heterogeneity in biological age in natural populations.
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Affiliation(s)
- Chelsea J Weibel
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Mauna R Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - David A Jansen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | | | - Raphael S Mututua
- Amboseli Baboon Research Project, Amboseli National Park, Kajiado, Kenya
| | - J Kinyua Warutere
- Amboseli Baboon Research Project, Amboseli National Park, Kajiado, Kenya
| | - Long'ida I Siodi
- Amboseli Baboon Research Project, Amboseli National Park, Kajiado, Kenya
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Duke University Population Research Institute, Duke University, Durham, NC, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Duke University Population Research Institute, Duke University, Durham, NC, USA
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
- Canadian Institute for Advanced Research, Toronto, M5G 1M1, Canada
- Faculty of Life Sciences, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
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3
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Gesquiere LR, Adjangba C, Wango TL, Oudu VK, Mututua RS, Warutere JK, Siodi IL, Campos FA, Archie EA, Markham AC, Alberts SC. Thyroid hormone concentrations in female baboons: Metabolic consequences of living in a highly seasonal environment. Horm Behav 2024; 161:105505. [PMID: 38364455 PMCID: PMC11218546 DOI: 10.1016/j.yhbeh.2024.105505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/18/2024]
Abstract
How female mammals adapt metabolically in response to environmental variation remains understudied in the wild, because direct measures of metabolic activity are difficult to obtain in wild populations. However, recent advances in the non-invasive measurement of fecal thyroid hormones, triiodothyronine (T3), an important regulator of metabolism, provide an opportunity to understand how female baboons living in the harsh Amboseli ecosystem in southern Kenya adapt to environmental variability and escape strict reproductive seasonality. Specifically, we assessed how a female's activity budget, diet, and concentrations of fecal T3 metabolites (mT3) changed over the course of the year and between years. We then tested which of several environmental variables (season, rainfall, and temperature) and behavioral variables (female activity budget and diet) best predicted mT3 concentrations. Finally, we determined if two important reproductive events - onset of ovarian cycling and conception of an offspring - were preceded by changes in female mT3 concentrations. We found female baboons' mT3 concentrations varied markedly across the year and between years as a function of environmental conditions. Further, changes in a female's behavior and diet only partially mediated the metabolic response to the environment. Finally, mT3 concentrations increased in the weeks prior to menarche and cycling resumption, regardless of the month or season in which cycling started. This pattern indicates that metabolic activation may be an indicator of reproductive readiness in female baboons as their energy balance is restored.
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Affiliation(s)
| | | | - Tim L Wango
- Amboseli Baboon Research Project, PO Box 72211-0020, Nairobi, Kenya; Department of Veterinary Anatomy and Physiology, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya
| | - Vivian K Oudu
- Amboseli Baboon Research Project, PO Box 72211-0020, Nairobi, Kenya; Department of Veterinary Anatomy and Physiology, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya
| | | | | | - I Long'ida Siodi
- Amboseli Baboon Research Project, PO Box 72211-0020, Nairobi, Kenya
| | - Fernando A Campos
- Department of Anthropology, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - A Catherine Markham
- Department of Anthropology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC 27708, USA; Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
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4
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Rosenbaum S, Malani A, Lea AJ, Tung J, Alberts SC, Archie EA. Testing frameworks for early life effects: the developmental constraints and adaptive response hypotheses do not explain key fertility outcomes in wild female baboons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590627. [PMID: 38712305 PMCID: PMC11071398 DOI: 10.1101/2024.04.23.590627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
In evolutionary ecology, two classes of explanations are frequently invoked to explain "early life effects" on adult outcomes. Developmental constraints (DC) explanations contend that costs of early adversity arise from limitations adversity places on optimal development. Adaptive response (AR) hypotheses propose that later life outcomes will be worse when early and adult environments are poorly "matched." Here, we use recently proposed mathematical definitions for these hypotheses and a quadratic-regression based approach to test the long-term consequences of variation in developmental environments on fertility in wild baboons. We evaluate whether low rainfall and/or dominance rank during development predict three female fertility measures in adulthood, and whether any observed relationships are consistent with DC and/or AR. Neither rainfall during development nor the difference between rainfall in development and adulthood predicted any fertility measures. Females who were low-ranking during development had an elevated risk of losing infants later in life, and greater change in rank between development and adulthood predicted greater risk of infant loss. However, both effects were statistically marginal and consistent with alternative explanations, including adult environmental quality effects. Consequently, our data do not provide compelling support for either of these common explanations for the evolution of early life effects.
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Affiliation(s)
| | - Anup Malani
- University of Chicago Law School & National Bureau of Economic Research
| | - Amanda J Lea
- Department of Biological Sciences, Vanderbilt University
| | - Jenny Tung
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary, Anthropology; Departments of Evolutionary Anthropology & Biology, Duke University
| | - Susan C Alberts
- Departments of Evolutionary Anthropology & Biology, Duke University
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5
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Tellini N, De Chiara M, Mozzachiodi S, Tattini L, Vischioni C, Naumova ES, Warringer J, Bergström A, Liti G. Ancient and recent origins of shared polymorphisms in yeast. Nat Ecol Evol 2024; 8:761-776. [PMID: 38472432 DOI: 10.1038/s41559-024-02352-5] [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: 02/10/2023] [Accepted: 01/30/2024] [Indexed: 03/14/2024]
Abstract
Shared genetic polymorphisms between populations and species can be ascribed to ancestral variation or to more recent gene flow. Here, we mapped shared polymorphisms in Saccharomyces cerevisiae and its sister species Saccharomyces paradoxus, which diverged 4-6 million years ago. We used a dense map of single-nucleotide diagnostic markers (mean distance 15.6 base pairs) in 1,673 sequenced S. cerevisiae isolates to catalogue 3,852 sequence blocks (≥5 consecutive markers) introgressed from S. paradoxus, with most being recent and clade-specific. The highly diverged wild Chinese S. cerevisiae lineages were depleted of introgressed blocks but retained an excess of individual ancestral polymorphisms derived from incomplete lineage sorting, perhaps due to less dramatic population bottlenecks. In the non-Chinese S. cerevisiae lineages, we inferred major hybridization events and detected cases of overlapping introgressed blocks across distinct clades due to either shared histories or convergent evolution. We experimentally engineered, in otherwise isogenic backgrounds, the introgressed PAD1-FDC1 gene pair that independently arose in two S. cerevisiae clades and revealed that it increases resistance against diverse antifungal drugs. Overall, our study retraces the histories of divergence and secondary contacts across S. cerevisiae and S. paradoxus populations and unveils a functional outcome.
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Affiliation(s)
- Nicolò Tellini
- CNRS, INSERM, IRCAN, Côte d'Azur University, Nice, France
| | | | | | | | | | - Elena S Naumova
- Kurchatov Complex for Genetic Research (GosNIIgenetika), National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anders Bergström
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Gianni Liti
- CNRS, INSERM, IRCAN, Côte d'Azur University, Nice, France.
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6
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Groh JS, Coop G. The temporal and genomic scale of selection following hybridization. Proc Natl Acad Sci U S A 2024; 121:e2309168121. [PMID: 38489387 PMCID: PMC10962946 DOI: 10.1073/pnas.2309168121] [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: 05/31/2023] [Accepted: 01/30/2024] [Indexed: 03/17/2024] Open
Abstract
Genomic evidence supports an important role for selection in shaping patterns of introgression along the genome, but frameworks for understanding the evolutionary dynamics within hybrid populations that underlie these patterns have been lacking. Due to the clock-like effect of recombination in hybrids breaking up parental haplotypes, drift and selection produce predictable patterns of ancestry variation at varying spatial genomic scales through time. Here, we develop methods based on the Discrete Wavelet Transform to study the genomic scale of local ancestry variation and its association with recombination rates and show that these methods capture temporal dynamics of drift and genome-wide selection after hybridization. We apply these methods to published datasets from hybrid populations of swordtail fish (Xiphophorus) and baboons (Papio) and to inferred Neanderthal introgression in modern humans. Across systems, upward of 20% of variation in local ancestry at the broadest genomic scales can be attributed to systematic selection against introgressed alleles, consistent with strong selection acting on early-generation hybrids. Signatures of selection at fine genomic scales suggest selection over longer time scales; however, we suggest that our ability to confidently infer selection at fine scales is likely limited by inherent biases in current methods for estimating local ancestry from contiguous segments of genomic similarity. Wavelet approaches will become widely applicable as genomic data from systems with introgression become increasingly available and can help shed light on generalities of the genomic consequences of interspecific hybridization.
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Affiliation(s)
- Jeffrey S. Groh
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA95616
| | - Graham Coop
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA95616
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7
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Anderson JA, Lin D, Lea AJ, Johnston RA, Voyles T, Akinyi MY, Archie EA, Alberts SC, Tung J. DNA methylation signatures of early-life adversity are exposure-dependent in wild baboons. Proc Natl Acad Sci U S A 2024; 121:e2309469121. [PMID: 38442181 PMCID: PMC10945818 DOI: 10.1073/pnas.2309469121] [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: 06/06/2023] [Accepted: 12/13/2023] [Indexed: 03/07/2024] Open
Abstract
The early-life environment can profoundly shape the trajectory of an animal's life, even years or decades later. One mechanism proposed to contribute to these early-life effects is DNA methylation. However, the frequency and functional importance of DNA methylation in shaping early-life effects on adult outcomes is poorly understood, especially in natural populations. Here, we integrate prospectively collected data on fitness-associated variation in the early environment with DNA methylation estimates at 477,270 CpG sites in 256 wild baboons. We find highly heterogeneous relationships between the early-life environment and DNA methylation in adulthood: aspects of the environment linked to resource limitation (e.g., low-quality habitat, early-life drought) are associated with many more CpG sites than other types of environmental stressors (e.g., low maternal social status). Sites associated with early resource limitation are enriched in gene bodies and putative enhancers, suggesting they are functionally relevant. Indeed, by deploying a baboon-specific, massively parallel reporter assay, we show that a subset of windows containing these sites are capable of regulatory activity, and that, for 88% of early drought-associated sites in these regulatory windows, enhancer activity is DNA methylation-dependent. Together, our results support the idea that DNA methylation patterns contain a persistent signature of the early-life environment. However, they also indicate that not all environmental exposures leave an equivalent mark and suggest that socioenvironmental variation at the time of sampling is more likely to be functionally important. Thus, multiple mechanisms must converge to explain early-life effects on fitness-related traits.
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Affiliation(s)
- Jordan A. Anderson
- Department of Evolutionary Anthropology, Duke University, Durham, NC27708
| | - Dana Lin
- Department of Evolutionary Anthropology, Duke University, Durham, NC27708
| | - Amanda J. Lea
- Canadian Institute for Advanced Research, Child & Brain Development Program, Toronto, ONM5G 1M1, Canada
- Department of Biological Sciences, Vanderbilt University, Nashville, TN37235
| | | | - Tawni Voyles
- Department of Evolutionary Anthropology, Duke University, Durham, NC27708
| | - Mercy Y. Akinyi
- Institute of Primate Research, National Museums of Kenya, Nairobi00502, Kenya
| | - Elizabeth A. Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN46556
| | - Susan C. Alberts
- Department of Evolutionary Anthropology, Duke University, Durham, NC27708
- Department of Biology, Duke University, Durham, NC27708
- Duke Population Research Institute, Duke University, Durham, NC27708
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, NC27708
- Canadian Institute for Advanced Research, Child & Brain Development Program, Toronto, ONM5G 1M1, Canada
- Department of Biology, Duke University, Durham, NC27708
- Duke Population Research Institute, Duke University, Durham, NC27708
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig04103, Germany
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8
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Delmore K, Justen H, Kay KM, Kitano J, Moyle LC, Stelkens R, Streisfeld MA, Yamasaki YY, Ross J. Genomic Approaches Are Improving Taxonomic Representation in Genetic Studies of Speciation. Cold Spring Harb Perspect Biol 2024; 16:a041438. [PMID: 37848243 PMCID: PMC10835617 DOI: 10.1101/cshperspect.a041438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Until recently, our understanding of the genetics of speciation was limited to a narrow group of model species with a specific set of characteristics that made genetic analysis feasible. Rapidly advancing genomic technologies are eliminating many of the distinctions between laboratory and natural systems. In light of these genomic developments, we review the history of speciation genetics, advances that have been gleaned from model and non-model organisms, the current state of the field, and prospects for broadening the diversity of taxa included in future studies. Responses to a survey of speciation scientists across the world reveal the ongoing division between the types of questions that are addressed in model and non-model organisms. To bridge this gap, we suggest integrating genetic studies from model systems that can be reared in the laboratory or greenhouse with genomic studies in related non-models where extensive ecological knowledge exists.
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Affiliation(s)
- Kira Delmore
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Hannah Justen
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Kathleen M Kay
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Rike Stelkens
- Division of Population Genetics, Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Matthew A Streisfeld
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
| | - Yo Y Yamasaki
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Joseph Ross
- Department of Biology, California State University, Fresno, California 93740, USA
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9
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Freudiger A, Jovanovic VM, Huang Y, Snyder-Mackler N, Conrad DF, Miller B, Montague MJ, Westphal H, Stadler PF, Bley S, Horvath JE, Brent LJN, Platt ML, Ruiz-Lambides A, Tung J, Nowick K, Ringbauer H, Widdig A. Taking identity-by-descent analysis into the wild: Estimating realized relatedness in free-ranging macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574911. [PMID: 38260273 PMCID: PMC10802400 DOI: 10.1101/2024.01.09.574911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Biological relatedness is a key consideration in studies of behavior, population structure, and trait evolution. Except for parent-offspring dyads, pedigrees capture relatedness imperfectly. The number and length of DNA segments that are identical-by-descent (IBD) yield the most precise estimates of relatedness. Here, we leverage novel methods for estimating locus-specific IBD from low coverage whole genome resequencing data to demonstrate the feasibility and value of resolving fine-scaled gradients of relatedness in free-living animals. Using primarily 4-6× coverage data from a rhesus macaque (Macaca mulatta) population with available long-term pedigree data, we show that we can call the number and length of IBD segments across the genome with high accuracy even at 0.5× coverage. The resulting estimates demonstrate substantial variation in genetic relatedness within kin classes, leading to overlapping distributions between kin classes. They identify cryptic genetic relatives that are not represented in the pedigree and reveal elevated recombination rates in females relative to males, which allows us to discriminate maternal and paternal kin using genotype data alone. Our findings represent a breakthrough in the ability to understand the predictors and consequences of genetic relatedness in natural populations, contributing to our understanding of a fundamental component of population structure in the wild.
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Affiliation(s)
- Annika Freudiger
- Behavioral Ecology Research Group, Faculty of Life Sciences, Institute of Biology, Leipzig University, Leipzig, Germany
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Vladimir M Jovanovic
- Human Biology and Primate Evolution, Institut für Zoologie, Freie Universität Berlin, Berlin, Germany
- Bioinformatics Solution Center, Freie Universität Berlin, Berlin, Germany
| | - Yilei Huang
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Bioinformatics Group, Institute of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Noah Snyder-Mackler
- Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, USA
| | - Donald F Conrad
- Division of Genetics, Oregon National Primate Research Center, Portland, Oregon, USA
| | - Brian Miller
- Division of Genetics, Oregon National Primate Research Center, Portland, Oregon, USA
| | - Michael J Montague
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hendrikje Westphal
- Behavioral Ecology Research Group, Faculty of Life Sciences, Institute of Biology, Leipzig University, Leipzig, Germany
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Bioinformatics Group, Institute of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Institute of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, Austria
- Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
- Santa Fe Institute, Santa Fe, NM, USA
| | - Stefanie Bley
- Behavioral Ecology Research Group, Faculty of Life Sciences, Institute of Biology, Leipzig University, Leipzig, Germany
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julie E Horvath
- Department of Biological and Biomedical Sciences, North Carolina Central University, North Carolina, Durham, USA
- Research and Collections Section, North Carolina Museum of Natural Sciences, North Carolina, Raleigh, USA
- Department of Biological Sciences, North Carolina State University, North Carolina, Raleigh, USA
- Department of Evolutionary Anthropology, Duke University, North Carolina, Durham, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lauren J N Brent
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, UK
| | - Michael L Platt
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Marketing Department, the Wharton School of Business, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Angelina Ruiz-Lambides
- Cayo Santiago Field Station, Caribbean Primate Research Center, University of Puerto Rico, Punta Santiago, Puerto Rico
| | - Jenny Tung
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Evolutionary Anthropology, Duke University, North Carolina, Durham, USA
- Department of Biology, Duke University, Durham, North Carolina, USA
- Duke University Population Research Institute, Durham, North Carolina, USA
| | - Katja Nowick
- Human Biology and Primate Evolution, Institut für Zoologie, Freie Universität Berlin, Berlin, Germany
- Bioinformatics Solution Center, Freie Universität Berlin, Berlin, Germany
| | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anja Widdig
- Behavioral Ecology Research Group, Faculty of Life Sciences, Institute of Biology, Leipzig University, Leipzig, Germany
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Germany
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10
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Langdon QK, Groh JS, Aguillon SM, Powell DL, Gunn T, Payne C, Baczenas JJ, Donny A, Dodge TO, Du K, Schartl M, Ríos-Cárdenas O, Gutierrez-Rodríguez C, Morris M, Schumer M. Genome evolution is surprisingly predictable after initial hybridization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572897. [PMID: 38187753 PMCID: PMC10769416 DOI: 10.1101/2023.12.21.572897] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Over the past two decades, evolutionary biologists have come to appreciate that hybridization, or genetic exchange between distinct lineages, is remarkably common - not just in particular lineages but in taxonomic groups across the tree of life. As a result, the genomes of many modern species harbor regions inherited from related species. This observation has raised fundamental questions about the degree to which the genomic outcomes of hybridization are repeatable and the degree to which natural selection drives such repeatability. However, a lack of appropriate systems to answer these questions has limited empirical progress in this area. Here, we leverage independently formed hybrid populations between the swordtail fish Xiphophorus birchmanni and X. cortezi to address this fundamental question. We find that local ancestry in one hybrid population is remarkably predictive of local ancestry in another, demographically independent hybrid population. Applying newly developed methods, we can attribute much of this repeatability to strong selection in the earliest generations after initial hybridization. We complement these analyses with time-series data that demonstrates that ancestry at regions under selection has remained stable over the past ~40 generations of evolution. Finally, we compare our results to the well-studied X. birchmanni×X. malinche hybrid populations and conclude that deeper evolutionary divergence has resulted in stronger selection and higher repeatability in patterns of local ancestry in hybrids between X. birchmanni and X. cortezi.
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Affiliation(s)
- Quinn K. Langdon
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California
| | - Jeffrey S. Groh
- Center for Population Biology and Department of Evolution and Ecology, University of California, Davis
| | - Stepfanie M. Aguillon
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles
| | - Daniel L. Powell
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Theresa Gunn
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Cheyenne Payne
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | | | - Alex Donny
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Tristram O. Dodge
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Kang Du
- Xiphophorus Genetic Stock Center, Texas State University San Marcos
| | - Manfred Schartl
- Xiphophorus Genetic Stock Center, Texas State University San Marcos
- Developmental Biochemistry, Biocenter, University of Würzburg
| | | | | | | | - Molly Schumer
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
- Freeman Hrabowski Fellow, Howard Hughes Medical Institute
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11
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Kato S, Arakaki S, Nagano AJ, Kikuchi K, Hirase S. Genomic landscape of introgression from the ghost lineage in a gobiid fish uncovers the generality of forces shaping hybrid genomes. Mol Ecol 2023. [PMID: 38047388 DOI: 10.1111/mec.17216] [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: 07/14/2023] [Revised: 09/23/2023] [Accepted: 10/26/2023] [Indexed: 12/05/2023]
Abstract
Extinct lineages can leave legacies in the genomes of extant lineages through ancient introgressive hybridization. The patterns of genomic survival of these extinct lineages provide insight into the role of extinct lineages in current biodiversity. However, our understanding on the genomic landscape of introgression from extinct lineages remains limited due to challenges associated with locating the traces of unsampled 'ghost' extinct lineages without ancient genomes. Herein, we conducted population genomic analyses on the East China Sea (ECS) lineage of Chaenogobius annularis, which was suspected to have originated from ghost introgression, with the aim of elucidating its genomic origins and characterizing its landscape of introgression. By combining phylogeographic analysis and demographic modelling, we demonstrated that the ECS lineage originated from ancient hybridization with an extinct ghost lineage. Forward simulations based on the estimated demography indicated that the statistic γ of the HyDe analysis can be used to distinguish the differences in local introgression rates in our data. Consistent with introgression between extant organisms, we found reduced introgression from extinct lineage in regions with low recombination rates and with functional importance, thereby suggesting a role of linked selection that has eliminated the extinct lineage in shaping the hybrid genome. Moreover, we identified enrichment of repetitive elements in regions associated with ghost introgression, which was hitherto little known but was also observed in the re-analysis of published data on introgression between extant organisms. Overall, our findings underscore the unexpected similarities in the characteristics of introgression landscapes across different taxa, even in cases of ghost introgression.
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Affiliation(s)
- Shuya Kato
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Shizuoka, Japan
| | - Seiji Arakaki
- Amakusa Marine Biological Laboratory, Kyushu University, Amakusa, Kumamoto, Japan
| | - Atsushi J Nagano
- Department of Life Sciences, Faculty of Agriculture, Ryukoku University, Ōtsu, Shiga, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Kiyoshi Kikuchi
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Shizuoka, Japan
| | - Shotaro Hirase
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Shizuoka, Japan
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12
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Lange EC, Griffin M, Fogel AS, Archie EA, Tung J, Alberts SC. Environmental, sex-specific and genetic determinants of infant social behaviour in a wild primate. Proc Biol Sci 2023; 290:20231597. [PMID: 37964524 PMCID: PMC10646456 DOI: 10.1098/rspb.2023.1597] [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: 10/14/2022] [Accepted: 10/23/2023] [Indexed: 11/16/2023] Open
Abstract
Affiliative social bonds are linked to fitness components in many social mammals. However, despite their importance, little is known about how the tendency to form social bonds develops in young animals, or if the timing of development is heritable and thus can evolve. Using four decades of longitudinal observational data from a wild baboon population, we assessed the environmental determinants of an important social developmental milestone in baboons-the age at which a young animal first grooms a conspecific-and we assessed how the rates at which offspring groom their mothers develops during the juvenile period. We found that grooming development differs between the sexes: female infants groom at an earlier age and reach equal rates of grooming with their mother earlier than males. We also found that age at first grooming for both sexes is weakly heritable (h2 = 0.043, 95% CI: 0.002-0.110). These results show that sex differences in grooming emerge at a young age; that strong, equitable social relationships between mothers and daughters begin very early in life; and that age at first grooming is heritable and therefore can be shaped by natural selection.
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Affiliation(s)
- Elizabeth C. Lange
- Department of Biology, Duke University, Durham, NC, USA
- Department of Biological Sciences, SUNY Oswego, Oswego, NY, USA
| | | | - Arielle S. Fogel
- University Program in Genetics and Genomics, Duke University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Elizabeth A. Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Population Research Institute, Duke University, Durham, NC, USA
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Susan C. Alberts
- Department of Biology, Duke University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Population Research Institute, Duke University, Durham, NC, USA
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13
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Levy EJ, Lee A, Siodi IL, Helmich EC, McLean EM, Malone EJ, Pickard MJ, Ranjithkumar R, Tung J, Archie EA, Alberts SC. Early life drought predicts components of adult body size in wild female baboons. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:357-371. [PMID: 37737520 PMCID: PMC10591920 DOI: 10.1002/ajpa.24849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 08/14/2023] [Accepted: 08/28/2023] [Indexed: 09/23/2023]
Abstract
OBJECTIVES In many taxa, adverse early-life environments are associated with reduced growth and smaller body size in adulthood. However, in wild primates, we know very little about whether, where, and to what degree trajectories are influenced by early adversity, or which types of early adversity matter most. Here, we use parallel-laser photogrammetry to assess inter-individual predictors of three measures of body size (leg length, forearm length, and shoulder-rump length) in a population of wild female baboons studied since birth. MATERIALS AND METHODS Using >2000 photogrammetric measurements of 127 females, we present a cross-sectional growth curve of wild female baboons (Papio cynocephalus) from juvenescence through adulthood. We then test whether females exposed to several important sources of early-life adversity-drought, maternal loss, low maternal rank, or a cumulative measure of adversity-were smaller for their age than females who experienced less adversity. Using the "animal model," we also test whether body size is heritable in this study population. RESULTS Prolonged early-life drought predicted shorter limbs but not shorter torsos (i.e., shoulder-rump lengths). Our other measures of early-life adversity did not predict variation in body size. Heritability estimates for body size measures were 36%-67%. Maternal effects accounted for 13%-17% of the variance in leg and forearm length, but no variance in torso length. DISCUSSION Our results suggest that baboon limbs, but not torsos, grow plastically in response to maternal effects and energetic early-life stress. Our results also reveal considerable heritability for all three body size measures in this study population.
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Affiliation(s)
- Emily J. Levy
- Department of Biology, Indiana University, Bloomington IN 47405, USA
- Department of Biology, Duke University, Durham NC 27708, USA
| | - Anna Lee
- Department of Biology, Duke University, Durham NC 27708, USA
| | | | - Emma C. Helmich
- Department of Biology, Duke University, Durham NC 27708, USA
| | - Emily M. McLean
- Division of Natural Sciences, Oxford College of Emory University, Oxford, GA, 30054, USA
| | - Elise J. Malone
- Department of Biology, Duke University, Durham NC 27708, USA
| | | | - Riddhi Ranjithkumar
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham NC 27708, USA
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Evolutionary Anthropology, Duke University, Durham NC 27708, USA
- Canadian Institute for Advanced Research, Toronto, Canada M5G 1M1, Canada
| | - Elizabeth A. Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame IN, 46556, USA
| | - Susan C. Alberts
- Department of Biology, Duke University, Durham NC 27708, USA
- Department of Evolutionary Anthropology, Duke University, Durham NC 27708, USA
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14
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Zipple MN, Archie EA, Tung J, Mututua RS, Warutere JK, Siodi IL, Altmann J, Alberts SC. Five Decades of Data Yield No Support for Adaptive Biasing of Offspring Sex Ratio in Wild Baboons ( Papio cynocephalus). Am Nat 2023; 202:383-398. [PMID: 37792922 PMCID: PMC10998069 DOI: 10.1086/725886] [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: 10/06/2023]
Abstract
AbstractOver the past 50 years, a wealth of testable, often conflicting hypotheses have been generated about the evolution of offspring sex ratio manipulation by mothers. Several of these hypotheses have received support in studies of invertebrates and some vertebrate taxa. However, their success in explaining sex ratios in mammalian taxa-especially in primates-has been mixed. Here, we assess the predictions of four different hypotheses about the evolution of biased offspring sex ratios in the baboons of the Amboseli basin in Kenya: the Trivers-Willard, female rank enhancement, local resource competition, and local resource enhancement hypotheses. Using the largest sample size ever analyzed in a primate population (n = 1,372 offspring), we test the predictions of each hypothesis. Overall, we find no support for adaptive biasing of sex ratios. Offspring sex is not consistently related to maternal dominance rank or biased toward the dispersing sex, nor is it predicted by group size, population growth rates, or their interaction with maternal rank. Because our sample size confers power to detect even subtle biases in sex ratio, including modulation by environmental heterogeneity, these results suggest that adaptive biasing of offspring sex does not occur in this population.
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Affiliation(s)
- Matthew N Zipple
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University
| | | | - Jenny Tung
- Dept of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology
- Department of Evolutionary Anthropology, Duke University
- Department of Biology, Duke University
| | | | | | | | - Jeanne Altmann
- Department of Ecology and Evolutionary Biology, Princeton University
| | - Susan C Alberts
- Department of Evolutionary Anthropology, Duke University
- Department of Biology, Duke University
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15
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Mutti G, Oteo-Garcia G, Caldon M, da Silva MJF, Minhós T, Cowlishaw G, Gottelli D, Huchard E, Carter A, Martinez FI, Raveane A, Capelli C. Assessing the recovery of Y chromosome microsatellites with population genomic data using Papio and Theropithecus genomes. Sci Rep 2023; 13:13839. [PMID: 37620368 PMCID: PMC10449864 DOI: 10.1038/s41598-023-40931-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 08/18/2023] [Indexed: 08/26/2023] Open
Abstract
Y chromosome markers can shed light on male-specific population dynamics but for many species no such markers have been discovered and are available yet, despite the potential for recovering Y-linked loci from available genome sequences. Here, we investigated how effective available bioinformatic tools are in recovering informative Y chromosome microsatellites from whole genome sequence data. In order to do so, we initially explored a large dataset of whole genome sequences comprising individuals at various coverages belonging to different species of baboons (genus: Papio) using Y chromosome references belonging to the same genus and more distantly related species (Macaca mulatta). We then further tested this approach by recovering Y-STRs from available Theropithecus gelada genomes using Papio and Macaca Y chromosome as reference sequences. Identified loci were validated in silico by a) comparing within-species relationships of Y chromosome lineages and b) genotyping male individuals in available pedigrees. Each STR was selected not to extend in its variable region beyond 100 base pairs, so that loci can be developed for PCR-based genotyping of non-invasive DNA samples. In addition to assembling a first set of Papio and Theropithecus Y-specific microsatellite markers, we released TYpeSTeR, an easy-to-use script to identify and genotype Y chromosome STRs using population genomic data which can be modulated according to available male reference genomes and genomic data, making it widely applicable across taxa.
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Affiliation(s)
- Giacomo Mutti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 11/a, 43124, Parma, Italy
- Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Gonzalo Oteo-Garcia
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 11/a, 43124, Parma, Italy
| | - Matteo Caldon
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 11/a, 43124, Parma, Italy
| | - Maria Joana Ferreira da Silva
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Centro de Investigação Em Biodiversidade E Recursos Genéticos, CIBIOInBIO Laboratório AssociadoUniversidade Do Porto, Campus de Vairão, Vairão, Portugal
- ONE ‑ Organisms and Environment Group, School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff, UK
| | - Tânia Minhós
- Centre for Research in Anthropology (CRIA-NOVA FCSH), Av. Forças Armadas, Edifício ISCTE, Sala 2w2, 1649-026, Lisboa, Portugal
- Anthropology Department, School of Social Sciences and Humanities, Universidade Nova de Lisboa (NOVA FCSH), Av. de Berna, 26-C, 1069-061, Lisboa, Portugal
| | - Guy Cowlishaw
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Dada Gottelli
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Elise Huchard
- Institut Des Sciences de L'Evolution, CNRS, Universite de Montpellier, CC 065, 34095, Montpellier 05, France
| | - Alecia Carter
- Department of Anthropology, University College London, 14 Taviton Street, London, WC1H 0BW, UK
| | - Felipe I Martinez
- Escuela de Antropología, Facultad de Ciencias Sociales, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Cristian Capelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 11/a, 43124, Parma, Italy.
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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16
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McLean EM, Moorad JA, Tung J, Archie EA, Alberts SC. Genetic variance and indirect genetic effects for affiliative social behavior in a wild primate. Evolution 2023; 77:1607-1621. [PMID: 37094802 PMCID: PMC10309972 DOI: 10.1093/evolut/qpad066] [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: 09/07/2022] [Revised: 04/11/2023] [Accepted: 04/20/2023] [Indexed: 04/26/2023]
Abstract
Affiliative social behaviors are linked to fitness components in multiple species. However, the role of genetic variance in shaping such behaviors remains largely unknown, limiting our understanding of how affiliative behaviors can respond to natural selection. Here, we employed the "animal model" to estimate environmental and genetic sources of variance and covariance in grooming behavior in the well-studied Amboseli wild baboon population. We found that the tendency for a female baboon to groom others ("grooming given") is heritable (h2 = 0.22 ± 0.048), and that several environmental variables-including dominance rank and the availability of kin as grooming partners-contribute to variance in this grooming behavior. We also detected small but measurable variance due to the indirect genetic effect of partner identity on the amount of grooming given within dyadic grooming partnerships. The indirect and direct genetic effects for grooming given were positively correlated (r = 0.74 ± 0.09). Our results provide insight into the evolvability of affiliative behavior in wild animals, including the possibility for correlations between direct and indirect genetic effects to accelerate the response to selection. As such they provide novel information about the genetic architecture of social behavior in nature, with important implications for the evolution of cooperation and reciprocity.
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Affiliation(s)
- Emily M McLean
- University Program in Genetics and Genomics, Duke University, Durham, NC, United States
- Division of Natural Sciences and Mathematics, Oxford College, Emory University, Oxford, GA, United States
| | - Jacob A Moorad
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, Scotland
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC, United States
- Department of Evolutionary Anthropology, Duke University, Durham, NC, United States
- Population Research Institute, Duke University, Durham, NC, United States
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC, United States
- Department of Evolutionary Anthropology, Duke University, Durham, NC, United States
- Population Research Institute, Duke University, Durham, NC, United States
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17
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Anderson JA, Lin D, Lea AJ, Johnston RA, Voyles T, Akinyi MY, Archie EA, Alberts SC, Tung J. DNA methylation signatures of early life adversity are exposure-dependent in wild baboons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.542485. [PMID: 37333311 PMCID: PMC10274726 DOI: 10.1101/2023.06.05.542485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The early life environment can profoundly shape the trajectory of an animal's life, even years or decades later. One mechanism proposed to contribute to these early life effects is DNA methylation. However, the frequency and functional importance of DNA methylation in shaping early life effects on adult outcomes is poorly understood, especially in natural populations. Here, we integrate prospectively collected data on fitness-associated variation in the early environment with DNA methylation estimates at 477,270 CpG sites in 256 wild baboons. We find highly heterogeneous relationships between the early life environment and DNA methylation in adulthood: aspects of the environment linked to resource limitation (e.g., low-quality habitat, early life drought) are associated with many more CpG sites than other types of environmental stressors (e.g., low maternal social status). Sites associated with early resource limitation are enriched in gene bodies and putative enhancers, suggesting they are functionally relevant. Indeed, by deploying a baboon-specific, massively parallel reporter assay, we show that a subset of windows containing these sites are capable of regulatory activity, and that, for 88% of early drought-associated sites in these regulatory windows, enhancer activity is DNA methylation-dependent. Together, our results support the idea that DNA methylation patterns contain a persistent signature of the early life environment. However, they also indicate that not all environmental exposures leave an equivalent mark and suggest that socioenvironmental variation at the time of sampling is more likely to be functionally important. Thus, multiple mechanisms must converge to explain early life effects on fitness-related traits.
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Affiliation(s)
- Jordan A Anderson
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina 27708, USA
| | - Dana Lin
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina 27708, USA
| | - Amanda J Lea
- Canadian Institute for Advanced Research, Toronto, Canada M5G 1M1, Canada
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, 37235, USA
| | - Rachel A Johnston
- Zoo New England, Stoneham, Massachusetts, 02180
- Broad Institute, Cambridge, Massachusetts, 02142
| | - Tawni Voyles
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina 27708, USA
| | - Mercy Y Akinyi
- Institute of Primate Research, National Museums of Kenya, Nairobi 00502, Kenya
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Susan C Alberts
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina 27708, USA
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
- Duke Population Research Institute, Duke University, Durham, NC 27708, USA
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina 27708, USA
- Canadian Institute for Advanced Research, Toronto, Canada M5G 1M1, Canada
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
- Duke Population Research Institute, Duke University, Durham, NC 27708, USA
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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18
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Sørensen EF, Harris RA, Zhang L, Raveendran M, Kuderna LFK, Walker JA, Storer JM, Kuhlwilm M, Fontsere C, Seshadri L, Bergey CM, Burrell AS, Bergman J, Phillips-Conroy JE, Shiferaw F, Chiou KL, Chuma IS, Keyyu JD, Fischer J, Gingras MC, Salvi S, Doddapaneni H, Schierup MH, Batzer MA, Jolly CJ, Knauf S, Zinner D, Farh KKH, Marques-Bonet T, Munch K, Roos C, Rogers J. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons. Science 2023; 380:eabn8153. [PMID: 37262153 DOI: 10.1126/science.abn8153] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 09/27/2022] [Indexed: 06/03/2023]
Abstract
Baboons (genus Papio) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically distinct phylogenetic species. We used high-coverage whole-genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics and interspecies gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages. The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes.
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Affiliation(s)
- Erik F Sørensen
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Liye Zhang
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lukas F K Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Artificial Intelligence Lab, Illumina Inc., San Diego, CA 92122, USA
| | - Jerilyn A Walker
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | | | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
| | - Claudia Fontsere
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Lakshmi Seshadri
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Christina M Bergey
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Andrew S Burrell
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Jane E Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | - Kenneth L Chiou
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | | | | | - Julia Fischer
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Marie-Claude Gingras
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sejal Salvi
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harshavardhan Doddapaneni
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Kyle K-H Farh
- Artificial Intelligence Lab, Illumina Inc., San Diego, CA 92122, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluis Companys, 23, 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Baldiri i Reixac 4, 08028 Barcelona, Spain
- Institut Catala de Paleontologia Miquel Crusafont, Universitat Autonoma de Barcelona, Edifici ICTA-ICP, cl Columnes s/n, 08193 Cerdanyola del Valles, Barcelona, Spain
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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19
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Groh J, Coop G. The temporal and genomic scale of selection following hybridization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542345. [PMID: 37337589 PMCID: PMC10276902 DOI: 10.1101/2023.05.25.542345] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Genomic evidence supports an important role for selection in shaping patterns of introgression along the genome, but frameworks for understanding the dynamics underlying these patterns within hybrid populations have been lacking. Here, we develop methods based on the Wavelet Transform to understand the spatial genomic scale of local ancestry variation and its association with recombination rates. We present theory and use simulations to show how wavelet-based decompositions of ancestry variance along the genome and the correlation between ancestry and recombination reflect the joint effects of recombination, genetic drift, and genome-wide selection against introgressed alleles. Due to the clock-like effect of recombination in hybrids breaking up parental haplotypes, drift and selection produce predictable patterns of local ancestry variation at varying spatial genomic scales through time. Using wavelet approaches to identify the genomic scale of variance in ancestry and its correlates, we show that these methods can detect temporally localized effects of drift and selection. We apply these methods to previously published datasets from hybrid populations of swordtail fish (Xiphophorus) and baboons (Papio), and to inferred Neanderthal introgression in modern humans. Across systems, we find that upwards of 20% of the variation in local ancestry at the broadest genomic scales can be attributed to systematic selection against introgressed alleles, consistent with strong selection acting on early-generation hybrids. We also see signals of selection at fine genomic scales and much longer time scales. However, we show that our ability to confidently infer selection at fine scales is likely limited by inherent biases in current methods for estimating local ancestry from genomic similarity. Wavelet approaches will become widely applicable as genomic data from systems with introgression become increasingly available, and can help shed light on generalities of the genomic consequences of interspecific hybridization.
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Affiliation(s)
- Jeffrey Groh
- Department of Evolution and Ecology, and Center for Population Biology, University of California, Davis, CA 95616
| | - Graham Coop
- Department of Evolution and Ecology, and Center for Population Biology, University of California, Davis, CA 95616
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20
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Lange EC, Zeng S, Campos FA, Li F, Tung J, Archie EA, Alberts SC. Early life adversity and adult social relationships have independent effects on survival in a wild primate. SCIENCE ADVANCES 2023; 9:eade7172. [PMID: 37196090 PMCID: PMC10191438 DOI: 10.1126/sciadv.ade7172] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 04/11/2023] [Indexed: 05/19/2023]
Abstract
Adverse conditions in early life can have negative consequences for adult health and survival in humans and other animals. What variables mediate the relationship between early adversity and adult survival? Adult social environments represent one candidate: Early life adversity is linked to social adversity in adulthood, and social adversity in adulthood predicts survival outcomes. However, no study has prospectively linked early life adversity, adult social behavior, and adult survival to measure the extent to which adult social behavior mediates this relationship. We do so in a wild baboon population in Amboseli, Kenya. We find weak mediation and largely independent effects of early adversity and adult sociality on survival. Furthermore, strong social bonds and high social status in adulthood can buffer some negative effects of early adversity. These results support the idea that affiliative social behavior is subject to natural selection through its positive relationship with survival, and they highlight possible targets for intervention to improve human health and well-being.
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Affiliation(s)
- Elizabeth C. Lange
- Department of Biology, Duke University, Durham NC, USA
- Department of Biological Sciences, State University of New York at Oswego, Oswego NY, USA
| | - Shuxi Zeng
- Department of Statistical Science, Duke University, Durham NC, USA
| | - Fernando A. Campos
- Department of Anthropology, The University of Texas at San Antonio, San Antonio TX, USA
| | - Fan Li
- Department of Statistical Science, Duke University, Durham NC, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham NC, USA
- Duke Population Research Institute, Duke University, Durham NC, USA
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- University of Leipzig, Faculty of Life Science, Leipzig, Germany
| | - Elizabeth A. Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame IN, USA
| | - Susan C. Alberts
- Department of Biology, Duke University, Durham NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham NC, USA
- Duke Population Research Institute, Duke University, Durham NC, USA
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21
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Sørensen EF, Harris RA, Zhang L, Raveendran M, Kuderna LFK, Walker JA, Storer JM, Kuhlwilm M, Fontsere C, Seshadri L, Bergey CM, Burrell AS, Bergmann J, Phillips-Conroy JE, Shiferaw F, Chiou KL, Chuma IS, Keyyu JD, Fischer J, Gingras MC, Salvi S, Doddapaneni H, Schierup MH, Batzer MA, Jolly CJ, Knauf S, Zinner D, Farh KKH, Marques-Bonet T, Munch K, Roos C, Rogers J. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539112. [PMID: 37205419 PMCID: PMC10187195 DOI: 10.1101/2023.05.02.539112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Baboons (genus Papio ) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically distinct phylogenetic species. We used high coverage whole genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics and inter-species gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal novel patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages. The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes. One-Sentence Summary Genomic data for 225 baboons reveal novel sites of inter-species gene flow and local effects due to differences in admixture.
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22
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Fogel AS, Oduor PO, Nyongesa AW, Kimwele CN, Alberts SC, Archie EA, Tung J. Ecology and age, but not genetic ancestry, predict fetal loss in a wild baboon hybrid zone. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:618-632. [PMID: 38445762 DOI: 10.1002/ajpa.24686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/08/2022] [Accepted: 12/15/2022] [Indexed: 03/07/2024]
Abstract
OBJECTIVES Pregnancy failure represents a major fitness cost for any mammal, particularly those with slow life histories such as primates. Here, we quantified the risk of fetal loss in wild hybrid baboons, including genetic, ecological, and demographic sources of variance. We were particularly interested in testing the hypothesis that hybridization increases fetal loss rates. Such an effect would help explain how baboons may maintain genetic and phenotypic integrity despite interspecific gene flow. MATERIALS AND METHODS We analyzed outcomes for 1020 pregnancies observed over 46 years in a natural yellow baboon-anubis baboon hybrid zone. Fetal losses and live births were scored based on records of female reproductive state and the appearance of live neonates. We modeled the probability of fetal loss as a function of a female's genetic ancestry (the proportion of her genome estimated to be descended from anubis [vs. yellow] ancestors), age, number of previous fetal losses, dominance rank, group size, climate, and habitat quality using binomial mixed effects models. RESULTS Female genetic ancestry did not predict fetal loss. Instead, the risk of fetal loss is elevated for very young and very old females. Fetal loss is most robustly predicted by ecological factors, including poor habitat quality prior to a home range shift and extreme heat during pregnancy. DISCUSSION Our results suggest that gene flow between yellow and anubis baboons is not impeded by an increased risk of fetal loss for hybrid females. Instead, ecological conditions and female age are key determinants of this component of female reproductive success.
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Affiliation(s)
- Arielle S Fogel
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
| | - Peter O Oduor
- Department of Veterinary Anatomy and Physiology, University of Nairobi, Nairobi, Kenya
| | - Albert W Nyongesa
- Department of Veterinary Anatomy and Physiology, University of Nairobi, Nairobi, Kenya
| | - Charles N Kimwele
- Department of Veterinary Anatomy and Physiology, University of Nairobi, Nairobi, Kenya
| | - Susan C Alberts
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
- Department of Biology, Duke University, Durham, North Carolina, USA
- Duke Population Research Institute, Duke University, Durham, North Carolina, USA
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
- Department of Biology, Duke University, Durham, North Carolina, USA
- Duke Population Research Institute, Duke University, Durham, North Carolina, USA
- Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Saxony, Germany
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23
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Kopp GH, Sithaldeen R, Trede F, Grathwol F, Roos C, Zinner D. A Comprehensive Overview of Baboon Phylogenetic History. Genes (Basel) 2023; 14:genes14030614. [PMID: 36980887 PMCID: PMC10048742 DOI: 10.3390/genes14030614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 03/05/2023] Open
Abstract
Baboons (genus Papio) are an intriguing study system to investigate complex evolutionary processes and the evolution of social systems. An increasing number of studies over the last 20 years has shown that considerable incongruences exist between phylogenies based on morphology, mitochondrial, and nuclear sequence data of modern baboons, and hybridization and introgression have been suggested as the main drivers of these patterns. Baboons, therefore, present an excellent opportunity to study these phenomena and their impact on speciation. Advances both in geographic and genomic coverage provide increasing details on the complexity of the phylogeography of baboons. Here, we compile the georeferenced genetic data of baboons and review the current knowledge on baboon phylogeny, discuss the evolutionary processes that may have shaped the patterns that we observe today, and propose future avenues for research.
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Affiliation(s)
- Gisela H. Kopp
- Zukunftskolleg, University of Konstanz, 78457 Konstanz, Germany
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78457 Konstanz, Germany
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
- Correspondence:
| | - Riashna Sithaldeen
- Academic Development Programme, Centre for Higher Education and Development, University of Cape Town, Cape Town 7700, South Africa
| | - Franziska Trede
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Franziska Grathwol
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-University, 37073 Göttingen, Germany
- Leibniz-ScienceCampus Primate Cognition, 37077 Göttingen, Germany
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24
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Boeckx C. What made us "hunter-gatherers of words". Front Neurosci 2023; 17:1080861. [PMID: 36845441 PMCID: PMC9947416 DOI: 10.3389/fnins.2023.1080861] [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: 10/26/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
This paper makes three interconnected claims: (i) the "human condition" cannot be captured by evolutionary narratives that reduce it to a recent 'cognitive modernity', nor by narratives that eliminates all cognitive differences between us and out closest extinct relatives, (ii) signals from paleogenomics, especially coming from deserts of introgression but also from signatures of positive selection, point to the importance of mutations that impact neurodevelopment, plausibly leading to temperamental differences, which may impact cultural evolutionary trajectories in specific ways, and (iii) these trajectories are expected to affect the language phenotypes, modifying what is being learned and how it is put to use. In particular, I hypothesize that these different trajectories influence the development of symbolic systems, the flexible ways in which symbols combine, and the size and configurations of the communities in which these systems are put to use.
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Affiliation(s)
- Cedric Boeckx
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
- Institute of Complex Systems, Universitat de Barcelona, Barcelona, Spain
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
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