@article{kuderna_gao_janiak_kuhlwilm_orkin_bataillon_manu_valenzuela_bergman_rousselle_et al._2023, title={A global catalog of whole-genome diversity from 233 primate species}, volume={380}, ISSN={["1095-9203"]}, DOI={10.1126/science.abn7829}, abstractNote={The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.}, number={6648}, journal={SCIENCE}, author={Kuderna, Lukas F. K. and Gao, Hong and Janiak, Mareike C. and Kuhlwilm, Martin and Orkin, Joseph D. and Bataillon, Thomas and Manu, Shivakumara and Valenzuela, Alejandro and Bergman, Juraj and Rousselle, Marjolaine and et al.}, year={2023}, month={Jun}, pages={906–912} }
 @article{watowich_chiou_graves_montague_brent_higham_horvath_lu_martinez_platt_et al._2023, title={Best practices for genotype imputation from low-coverage sequencing data in natural populations}, ISSN={["1755-0998"]}, DOI={10.1111/1755-0998.13854}, abstractNote={Abstract}, journal={MOLECULAR ECOLOGY RESOURCES}, author={Watowich, Marina M. and Chiou, Kenneth L. and Graves, Brian and Montague, Michael J. and Brent, Lauren J. N. and Higham, James P. and Horvath, Julie E. and Lu, Amy and Martinez, Melween I. and Platt, Michael L. and et al.}, year={2023}, month={Aug} }
 @article{kuderna_ulirsch_rashid_ameen_sundaram_hickey_cox_gao_kumar_aguet_et al._2023, title={Identification of constrained sequence elements across 239 primate genomes}, ISSN={["1476-4687"]}, DOI={10.1038/s41586-023-06798-8}, abstractNote={Abstract}, journal={NATURE}, author={Kuderna, Lukas F. K. and Ulirsch, Jacob C. and Rashid, Sabrina and Ameen, Mohamed and Sundaram, Laksshman and Hickey, Glenn and Cox, Anthony J. and Gao, Hong and Kumar, Arvind and Aguet, Francois and et al.}, year={2023}, month={Nov} }
 @article{gao_hamp_ede_schraiber_mcrae_singer-berk_yang_dietrich_fiziev_kuderna_et al._2023, title={The landscape of tolerated genetic variation in humans and primates}, volume={380}, ISSN={["1095-9203"]}, DOI={10.1126/science.abn8197}, abstractNote={Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.}, number={6648}, journal={SCIENCE}, author={Gao, Hong and Hamp, Tobias and Ede, Jeffrey and Schraiber, Joshua G. and McRae, Jeremy and Singer-Berk, Moriel and Yang, Yanshen and Dietrich, Anastasia S. D. and Fiziev, Petko P. and Kuderna, Lukas F. K. and et al.}, year={2023}, month={Jun}, pages={929-+} }
 @article{roche_montague_wang_dickey_ruiz-lambides_brent_platt_horvath_2023, title={Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques}, volume={11}, ISSN={["2165-0497"]}, DOI={10.1128/spectrum.02974-23}, abstractNote={ABSTRACT}, number={5}, journal={MICROBIOLOGY SPECTRUM}, author={Roche, Christina E. and Montague, Michael J. and Wang, JiCi and Dickey, Allison N. and Ruiz-Lambides, Angelina and Brent, Lauren J. N. and Platt, Michael L. and Horvath, Julie E.}, year={2023} }
 @article{kuthyar_watson_huang_brent_platt_horvath_gonzalez-martinez_martinez_godoy-vitorino_knight_et al._2022, title={Limited microbiome differences in captive and semi-wild primate populations consuming similar diets}, volume={98}, ISSN={["1574-6941"]}, DOI={10.1093/femsec/fiac098}, abstractNote={Abstract}, number={10}, journal={FEMS MICROBIOLOGY ECOLOGY}, author={Kuthyar, Sahana and Watson, Karli and Huang, Shi and Brent, Lauren J. N. and Platt, Michael and Horvath, Julie and Gonzalez-Martinez, Janis and Martinez, Melween and Godoy-Vitorino, Filipa and Knight, Rob and et al.}, year={2022}, month={Oct} }
 @article{watowich_chiou_montague_simons_horvath_ruiz-lambides_martinez_higham_brent_platt_et al._2022, title={Natural disaster and immunological aging in a nonhuman primate}, volume={119}, ISSN={["1091-6490"]}, DOI={10.1073/pnas.2121663119}, abstractNote={Significance}, number={8}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Watowich, Marina M. and Chiou, Kenneth L. and Montague, Michael J. and Simons, Noah D. and Horvath, Julie E. and Ruiz-Lambides, Angelina V and Martinez, Melween I and Higham, James P. and Brent, Lauren J. N. and Platt, Michael L. and et al.}, year={2022}, month={Feb} }
 @article{testard_brent_andersson_chiou_negron-del valle_decasien_acevedo-ithier_stock_anton_gonzalez_et al._2022, title={Social connections predict brain structure in a multidimensional free-ranging primate society}, volume={8}, ISSN={["2375-2548"]}, DOI={10.1126/sciadv.abl5794}, abstractNote={Reproduction and survival in most primate species reflects management of both competitive and cooperative relationships. Here, we investigated the links between neuroanatomy and sociality in free-ranging rhesus macaques. In adults, the number of social partners predicted the volume of the mid–superior temporal sulcus and ventral-dysgranular insula, implicated in social decision-making and empathy, respectively. We found no link between brain structure and other key social variables such as social status or indirect connectedness in adults, nor between maternal social networks or status and dependent infant brain structure. Our findings demonstrate that the size of specific brain structures varies with the number of direct affiliative social connections and suggest that this relationship may arise during development. These results reinforce proposed links between social network size, biological success, and the expansion of specific brain circuits.}, number={15}, journal={SCIENCE ADVANCES}, author={Testard, Camille and Brent, Lauren J. N. and Andersson, Jesper and Chiou, Kenneth L. and Negron-Del Valle, Josue E. and DeCasien, Alex R. and Acevedo-Ithier, Arianna and Stock, Michala K. and Anton, Susan C. and Gonzalez, Olga and et al.}, year={2022}, month={Apr} }
 @article{melin_orkin_janiak_valenzuela_kuderna_marrone_ramangason_horvath_roos_kitchener_et al._2021, title={Variation in predicted COVID-19 risk among lemurs and lorises}, volume={83}, ISSN={["1098-2345"]}, DOI={10.1002/ajp.23255}, abstractNote={Abstract}, number={6}, journal={AMERICAN JOURNAL OF PRIMATOLOGY}, author={Melin, Amanda D. and Orkin, Joseph D. and Janiak, Mareike C. and Valenzuela, Alejandro and Kuderna, Lukas and Marrone, Frank, III and Ramangason, Hasinala and Horvath, Julie E. and Roos, Christian and Kitchener, Andrew C. and et al.}, year={2021}, month={Jun} }
 @misc{chiou_montague_goldman_watowich_sams_song_horvath_sterner_ruiz-lambides_martinez_et al._2020, title={Rhesus macaques as a tractable physiological model of human ageing}, volume={375}, ISSN={["1471-2970"]}, DOI={10.1098/rstb.2019.0612}, abstractNote={Research in the basic biology of ageing is increasingly identifying mechanisms and modifiers of ageing in short-lived organisms such as worms and mice. The ultimate goal of such work is to improve human health, particularly in the growing segment of the population surviving into old age. Thus far, few interventions have robustly transcended species boundaries in the laboratory, suggesting that changes in approach are needed to avoid costly failures in translational human research. In this review, we discuss both well-established and alternative model organisms for ageing research and outline how research in nonhuman primates is sorely needed, first, to translate findings from short-lived organisms to humans, and second, to understand key aspects of ageing that are unique to primate biology. We focus on rhesus macaques as a particularly promising model organism for ageing research owing to their social and physiological similarity to humans as well as the existence of key resources that have been developed for this species. As a case study, we compare gene regulatory signatures of ageing in the peripheral immune system between humans and rhesus macaques from a free-ranging study population in Cayo Santiago. We show that both mRNA expression and DNA methylation signatures of immune ageing are broadly shared between macaques and humans, indicating strong conservation of the trajectory of ageing in the immune system. We conclude with a review of key issues in the biology of ageing for which macaques and other nonhuman primates may uniquely contribute valuable insights, including the effects of social gradients on health and ageing. We anticipate that continuing research in rhesus macaques and other nonhuman primates will play a critical role in conjunction with the model organism and human biodemographic research in ultimately improving translational outcomes and extending health and longevity in our ageing population.}, number={1811}, journal={PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES}, author={Chiou, Kenneth L. and Montague, Michael J. and Goldman, Elisabeth A. and Watowich, Marina M. and Sams, Sierra N. and Song, Jeff and Horvath, Julie E. and Sterner, Kirstin N. and Ruiz-Lambides, Angelina V. and Martinez, Melween I. and et al.}, year={2020}, month={Nov} }