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251 results on '"Perry, George H"'

1. Ecological and anthropogenic effects on the genomic diversity of lemurs in Madagascar

Author

Orkin, Joseph D., Kuderna, Lukas F. K., Hermosilla-Albala, Núria, Fontsere, Claudia, Aylward, Megan L., Janiak, Mareike C., Andriaholinirina, Nicole, Balaresque, Patricia, Blair, Mary E., Fausser, Jean-Luc, Gut, Ivo Glynne, Gut, Marta, Hahn, Matthew W., Harris, R. Alan, Horvath, Julie E., Keyser, Christine, Kitchener, Andrew C., Le, Minh D., Lizano, Esther, Merker, Stefan, Nadler, Tilo, Perry, George H., Rabarivola, Clément J., Rasmussen, Linett, Raveendran, Muthuswamy, Roos, Christian, Wu, Dong Dong, Zaramody, Alphonse, Zhang, Guojie, Zinner, Dietmar, Pozzi, Luca, Rogers, Jeffrey, Farh, Kyle Kai-How, and Marques Bonet, Tomas

Published
2025
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3. An integrative skeletal and paleogenomic analysis of stature variation suggests relatively reduced health for early European farmers

Author

Marciniak, Stephanie, Bergey, Christina M., Silva, Ana Maria, Hałuszko, Agata, Furmanek, Mirosław, Veselka, Barbara, Velemínský, Petr, Vercellotti, Giuseppe, Wahl, Joachim, Zariņa, Gunita, Longhi, Cristina, Kolář, Jan, Garrido-Pena, Rafael, Flores-Fernández, Raúl, Herrero-Corral, Ana M., Simalcsik, Angela, Müller, Werner, Sheridan, Alison, Miliauskienė, Žydrūnė, Jankauskas, Rimantas, Moiseyev, Vyacheslav, Köhler, Kitti, Király, Ágnes, Gamarra, Beatriz, Cheronet, Olivia, Szeverényi, Vajk, Kiss, Viktória, Szeniczey, Tamás, Kiss, Krisztián, Zoffmann, Zsuzsanna K., Koós, Judit, Hellebrandt, Magdolna, Maier, Robert M., Domboróczki, László, Virag, Cristian, Novak, Mario, Reich, David, Hajdu, Tamás, von Cramon-Taubadel, Noreen, Pinhasi, Ron, and Perry, George H.

Published
2022

4. Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant, “subfossil” koala lemur Megaladapis edwardsi

Author

Marciniak, Stephanie, Mughal, Mehreen R., Godfrey, Laurie R., Bankoff, Richard J., Randrianatoandro, Heritiana, Crowley, Brooke E., Bergey, Christina M., Muldoon, Kathleen M., Randrianasy, Jeannot, Raharivololona, Brigitte M., Schuster, Stephan C., Malhi, Ripan S., Yoder, Anne D., Louis, Edward E., Kistler, Logan, and Perry, George H.

Published
2021

5. The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS

Author

Orkin, Joseph D., Montague, Michael J., Tejada-Martinez, Daniela, de Manuel, Marc, del Campo, Javier, Hernandez, Saul Cheves, Di Fiore, Anthony, Fontsere, Claudia, Hodgson, Jason A., Janiak, Mareike C., Kuderna, Lukas F. K., Lizano, Esther, Martin, Maria Pia, Niimura, Yoshihito, Perry, George H., Valverde, Carmen Soto, Tang, Jia, Warren, Wesley C., de Magalhães, João Pedro, Kawamura, Shoji, Marquès-Bonet, Tomàs, Krawetz, Roman, and Melin, Amanda D.

Published
2021

11. Dispersals and genetic adaptation of Bantu-speaking populations in Africa and North America

Author

Patin, Etienne, Lopez, Marie, Grollemund, Rebecca, Verdu, Paul, Harmant, Christine, Quach, Hélène, Laval, Guillaume, Perry, George H., Barreiro, Luis B., Froment, Alain, Heyer, Evelyne, Massougbodji, Achille, Fortes-Lima, Cesar, Migot-Nabias, Florence, Bellis, Gil, Dugoujon, Jean-Michel, Pereira, Joana B., Fernandes, Verónica, Pereira, Luisa, Van der Veen, Lolke, Mouguiama-Daouda, Patrick, Bustamante, Carlos D., Hombert, Jean-Marie, and Quintana-Murci, Lluís

Published
2017

21. Anthropological Genetics

Author

Kitchen, Andrew, Non, Amy L., Gravlee, Clarence C., Mulligan, Connie J., warinner, Christina, Lewis, Cecil M., Bankoff, Richard J., Randrianatoandro, Heritiana D. D., Perry, George H., Malhi, Ripan S., Bader, Alyssa C., and Raff, Jennifer

Published
2015

27. Applying an evolutionary mismatch framework to understand disease susceptibility.

Author

Lea, Amanda J., Clark, Andrew G., Dahl, Andrew W., Devinsky, Orrin, Garcia, Angela R., Golden, Christopher D., Kamau, Joseph, Kraft, Thomas S., Lim, Yvonne A. L., Martins, Dino J., Mogoi, Donald, Pajukanta, Päivi, Perry, George H., Pontzer, Herman, Trumble, Benjamin C., Urlacher, Samuel S., Venkataraman, Vivek V., Wallace, Ian J., Gurven, Michael, and Lieberman, Daniel E.

Subjects
DISEASE susceptibility, TYPE 2 diabetes, NON-communicable diseases, HUMAN ecology
Abstract

Noncommunicable diseases (NCDs) are on the rise worldwide. Obesity, cardiovascular disease, and type 2 diabetes are among a long list of "lifestyle" diseases that were rare throughout human history but are now common. The evolutionary mismatch hypothesis posits that humans evolved in environments that radically differ from those we currently experience; consequently, traits that were once advantageous may now be "mismatched" and disease causing. At the genetic level, this hypothesis predicts that loci with a history of selection will exhibit "genotype by environment" (GxE) interactions, with different health effects in "ancestral" versus "modern" environments. To identify such loci, we advocate for combining genomic tools with partnerships with subsistence-level groups experiencing rapid lifestyle change. In these populations, comparisons of individuals falling on opposite extremes of the "matched" to "mismatched" spectrum are uniquely possible. More broadly, the work we propose will inform our understanding of environmental and genetic risk factors for NCDs across diverse ancestries and cultures. Humans evolved in environments that radically differ from those we currently experience; thus, traits that were once advantageous may now be "mismatched" and disease-causing. In this Essay, the authors advocate for combining genomic tools with partnerships with subsistence-level groups experiencing rapid lifestyle change to identify genetic loci associated with disease risk. [ABSTRACT FROM AUTHOR]

Published
2023
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34. A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology

Author

Westfall, Aundrea K, Telemeco, Rory S, Grizante, Mariana B, Waits, Damien S, Clark, Amanda D, Simpson, Dasia Y, Klabacka, Randy L, Sullivan, Alexis P, Perry, George H, Sears, Michael W, Cox, Christian L, Cox, Robert M, Gifford, Matthew E, John-Alder, Henry B, Langkilde, Tracy, Angilletta, Michael J, Leaché, Adam D, Tollis, Marc, Kusumi, Kenro, and Schwartz, Tonia S

Subjects
reptile, squamate, Genome, AcademicSubjects/SCI02254, AcademicSubjects/SCI00960, Animals, Lizards, Genomics, Data Note, transcriptome, Synteny, Chromosomes
Abstract

Background High-quality genomic resources facilitate investigations into behavioral ecology, morphological and physiological adaptations, and the evolution of genomic architecture. Lizards in the genus Sceloporus have a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources. Findings We present a high-quality chromosome-level reference genome assembly, SceUnd1.0 (using 10X Genomics Chromium, HiC, and Pacific Biosciences data), and tissue/developmental stage transcriptomes for the eastern fence lizard, Sceloporus undulatus. We performed synteny analysis with other snake and lizard assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes. We also used this new assembly to provide improved reference-based genome assemblies for 34 additional Sceloporus species. Finally, we used RNAseq and whole-genome resequencing data to compare 3 assemblies, each representing an increased level of cost and effort: Supernova Assembly with data from 10X Genomics Chromium, HiRise Assembly that added data from HiC, and PBJelly Assembly that added data from Pacific Biosciences sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq and single-nucleotide polymorphism calling, but the chromosome-level scaffolds provided by the addition of HiC data allowed synteny and whole-genome association mapping analyses. The subsequent addition of PacBio data doubled the contig N50 but provided negligible gains in scaffold length. Conclusions These new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.

Published
2021

40. Factors influencing taxonomic unevenness in scientific research: a mixed-methods case study of non-human primate genomic sequence data generation

Author

Hernandez, Margarita, Shenk, Mary K., and Perry, George H.

Subjects
0106 biological sciences, species conservation status, Test data generation, Emerging technologies, Sample (statistics), Biology, 010603 evolutionary biology, 01 natural sciences, Grounded theory, model organisms, 03 medical and health sciences, Data sequences, ethnography of scientists, Relevance (information retrieval), Taxonomic rank, 030304 developmental biology, 0303 health sciences, Multidisciplinary, Massive parallel sequencing, Non human primate, massively parallel sequencing, Genetics and Genomics, Data science, taxonomic bias, Geography, Evolutionary biology, Conservation status, Research Article
Abstract

Scholars have often noted major disparities in the extent of scientific research conducted among taxonomic groups. Such trends may cascade if future scientists gravitate towards study species with more data and resources already available. As new technologies emerge, do research studies employing these technologies continue these disparities? Here, using non-human primates as a case study, we first identified disparities in recently-generated massively-parallel genomic sequencing data and we then conducted interviews with the scientists who produced these data to learn their motivations when selecting species for study. Specifically, we tested whether variables including publication history and conservation status were significantly correlated with publicly-available sequence data in the NCBI Sequence Read Archive. Of the 179.6 terabases (Tb) of sequence data in this database for 519 non-human primate species, 135 Tb (~75%) were from only five species: rhesus macaques, olive baboons, green monkeys, chimpanzees, and crab-eating macaques. The strongest individual predictors of the amount of genomic data were the total number of non-medical scholarly publications (linear regression; r2=0.37; P=6.15×10-12) and number of medical publications (r2=0.27; P=9.27×10-9). In a generalized linear model, the number of non-medical publications (P=0.00064) and closer phylogenetic distance to humans (P=0.024) were the most predictive of the amount of genomic sequence data. We interviewed 33 authors of genomic data-producing publications and analyzed their responses using a grounded theory approach. Consistent with our quantitative results, authors mentioned that their choices of species were motivated by sample accessibility, prior published work, and perceived relevance (especially health-related) to humans. Our mixed-methods approach helped us to identify and contextualize some of the driving factors behind species-uneven patterns of scientific research, which can now be considered by funding agencies, scientific societies, and research teams aiming to align their broader goals with future data generation efforts.SIGNIFICANCE STATEMENTOur study sheds lights on the species-uneven distribution of genomic sequence data generation across the order Primates. We used a combination of quantitative data analyses and qualitative interviews with authors of data-producing studies to identify factors that have driven the observed pattern of unevenness; these included the extent of prior research conducted on each species, the relevance to human medicine, phylogenetic distance to humans, and sample accessibility. While our study focused on factors influencing non-human primate genomic sequence data, similar questions can be asked about how the scientific community engages with research projects more broadly. Our goal is to bring attention to the diversity of factors that influence scientists as they plan their projects, so that this process can be considered in the future by research groups and funding agencies aiming to align their broader goals with future data generation efforts.

Published
2020

41. Global variation in copy number in the human genome

Author

Redon, Richard, Ishikawa, Shumpei, Fitch, Karen R., Feuk, Lars, Perry, George H., Andrews, T. Daniel, Fiegler, Heike, Shapero, Michael H., Carson, Andrew R., Chen, Wenwei, Cho, Eun Kyung, Dallaire, Stephanie, Freeman, Jennifer L., Gonzalez, Juan R., Gratacos, Monica, Huang, Jing, Kalaitzopoulos, Dimitrios, Komura, Daisuke, MacDonald, Jeffrey R., Marshall, Christian R., Mei, Rui, Montgomery, Lyndal, Nishimura, Kunihiro, Okamura, Kohji, Shen, Fan, Somerville, Martin J., Tchinda, Joelle, Valsesia, Armand, Woodwark, Cara, Yang, Fengtang, Zhang, Junjun, Zerjal, Tatiana, Zhang, Jane, Armengol, Lluis, Conrad, Donald F., Estivill, Xavier, Tyler-Smith, Chris, Carter, Nigel P., Aburatani, Hiroyuki, Lee, Charles, Jones, Keith W., Scherer, Stephen W., and Hurles, Matthew E.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Richard Redon [1]; Shumpei Ishikawa [2, 3]; Karen R. Fitch [4]; Lars Feuk [5, 6]; George H. Perry [7]; T. Daniel Andrews [1]; Heike Fiegler [1]; Michael H. Shapero [...]

Published
2006
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42. Potential evolutionary body size reduction in a Malagasy primate (Propithecus verreauxi) in response to human size‐selective hunting pressure.

Author

Sullivan, Alexis P., Godfrey, Laurie R., Lawler, Richard R., Randrianatoandro, Heritiana, Eccles, Laurie, Culleton, Brendan, Ryan, Timothy M., and Perry, George H.

Subjects
BODY size, HUNTING, RADIOCARBON dating, ZOOARCHAEOLOGY, BIODIVERSITY
Abstract

Objectives: The Holocene arrival of humans on Madagascar precipitated major changes to the island's biodiversity. The now‐extinct, endemic "subfossil" megafauna of Madagascar were likely hunted by early human inhabitants. Perhaps in part due to preferential hunting of larger prey, no surviving endemic species on Madagascar is >10 kg. Moreover, some subfossil bones of extant lemurs are considerably larger than those of the modern members of their species, but subfossil versus modern locale differences for the comparisons conducted to date lead to uncertainty about whether these size differences reflect in situ change or pre‐existing ecogeographic variation. Here, we revisited this question with samples from nearby locales. Materials and Methods: We used high‐resolution 3D scan data to conduct comparative morphological analyses of subfossil and modern skeletal remains of one of the larger extant lemurs, Verreaux's sifakas (Propithecus verreauxi) from subfossil and modern sites only ~10 km apart: Taolambiby (bones dated to 725–560—1075–955 cal. years before present) and Beza Mahafaly Special Reserve, respectively. Results: The mean aggregate score for all subfossil elements (n = 12; 0.089 ± 0.117) is significantly greater than that for the modern individuals (n = 31; 0.009 ± 0.045; t‐test; p = 0.039). We found that the average subfossil sifaka bone is ~9% larger than that of modern sifakas (permutation test p = 0.037). Discussion: We cannot yet conclude whether this size difference reflects evolutionary change or an archaeological aggregation/taphonomic process. However, if this is a case of phyletic dwarfism in response to human size‐selective harvesting pressures then the estimated rate of change is greater than those previously calculated for other archaeological cases of this phenomenon. [ABSTRACT FROM AUTHOR]

Published
2022
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