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Webster TH, Vannan A, Pinto BJ, Denbrock G, Morales M, Dolby GA, Fiddes IT, DeNardo DF, Wilson MA. Lack of Dosage Balance and Incomplete Dosage Compensation in the ZZ/ZW Gila Monster (Heloderma suspectum) Revealed by De Novo Genome Assembly. Genome Biol Evol 2024; 16:evae018. [PMID: 38319079 PMCID: PMC10950046 DOI: 10.1093/gbe/evae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/07/2024] Open
Abstract
Reptiles exhibit a variety of modes of sex determination, including both temperature-dependent and genetic mechanisms. Among those species with genetic sex determination, sex chromosomes of varying heterogamety (XX/XY and ZZ/ZW) have been observed with different degrees of differentiation. Karyotype studies have demonstrated that Gila monsters (Heloderma suspectum) have ZZ/ZW sex determination and this system is likely homologous to the ZZ/ZW system in the Komodo dragon (Varanus komodoensis), but little else is known about their sex chromosomes. Here, we report the assembly and analysis of the Gila monster genome. We generated a de novo draft genome assembly for a male using 10X Genomics technology. We further generated and analyzed short-read whole genome sequencing and whole transcriptome sequencing data for three males and three females. By comparing female and male genomic data, we identified four putative Z chromosome scaffolds. These putative Z chromosome scaffolds are homologous to Z-linked scaffolds identified in the Komodo dragon. Further, by analyzing RNAseq data, we observed evidence of incomplete dosage compensation between the Gila monster Z chromosome and autosomes and a lack of balance in Z-linked expression between the sexes. In particular, we observe lower expression of the Z in females (ZW) than males (ZZ) on a global basis, though we find evidence suggesting local gene-by-gene compensation. This pattern has been observed in most other ZZ/ZW systems studied to date and may represent a general pattern for female heterogamety in vertebrates.
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Affiliation(s)
- Timothy H Webster
- Department of Anthropology, University of Utah, Salt Lake City, UT, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Annika Vannan
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Brendan J Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
| | - Grant Denbrock
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Matheo Morales
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Genetics, Yale University, New Haven, CT, USA
| | - Greer A Dolby
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Dale F DeNardo
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ, USA
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2
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Cotter DJ, Webster TH, Wilson MA. Genomic and demographic processes differentially influence genetic variation across the human X chromosome. PLoS One 2023; 18:e0287609. [PMID: 37910456 PMCID: PMC10619814 DOI: 10.1371/journal.pone.0287609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 06/08/2023] [Indexed: 11/03/2023] Open
Abstract
Many forces influence genetic variation across the genome including mutation, recombination, selection, and demography. Increased mutation and recombination both lead to increases in genetic diversity in a region-specific manner, while complex demographic patterns shape patterns of diversity on a more global scale. While these processes act across the entire genome, the X chromosome is particularly interesting because it contains several distinct regions that are subject to different combinations and strengths of these forces: the pseudoautosomal regions (PARs) and the X-transposed region (XTR). The X chromosome thus can serve as a unique model for studying how genetic and demographic forces act in different contexts to shape patterns of observed variation. We therefore sought to explore diversity, divergence, and linkage disequilibrium in each region of the X chromosome using genomic data from 26 human populations. Across populations, we find that both diversity and substitution rate are consistently elevated in PAR1 and the XTR compared to the rest of the X chromosome. In contrast, linkage disequilibrium is lowest in PAR1, consistent with the high recombination rate in this region, and highest in the region of the X chromosome that does not recombine in males. However, linkage disequilibrium in the XTR is intermediate between PAR1 and the autosomes, and much lower than the non-recombining X. Finally, in addition to these global patterns, we also observed variation in ratios of X versus autosomal diversity consistent with population-specific evolutionary history as well. While our results were generally consistent with previous work, two unexpected observations emerged. First, our results suggest that the XTR does not behave like the rest of the recombining X and may need to be evaluated separately in future studies. Second, the different regions of the X chromosome appear to exhibit unique patterns of linked selection across different human populations. Together, our results highlight profound regional differences across the X chromosome, simultaneously making it an ideal system for exploring the action of evolutionary forces as well as necessitating its careful consideration and treatment in genomic analyses.
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Affiliation(s)
- Daniel J. Cotter
- Department of Genetics, Stanford University, Stanford, CA, United States of America
| | - Timothy H. Webster
- Department of Anthropology, University of Utah, Salt Lake City, UT, United States of America
- School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
| | - Melissa A. Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
- Center for Evolution and Medicine, Biodesign Institute, Arizona State University, Tempe, AZ, United States of America
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Brand CM, Kuang S, Gilbertson EN, McArthur E, Pollard KS, Webster TH, Capra JA. Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees. bioRxiv 2023:2023.10.26.564272. [PMID: 37961120 PMCID: PMC10634871 DOI: 10.1101/2023.10.26.564272] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Phenotypic divergence between closely related species, including bonobos and chimpanzees (genus Pan), is largely driven by variation in gene regulation. The 3D structure of the genome mediates gene expression; however, genome folding differences in Pan are not well understood. Here, we apply machine learning to predict genome-wide 3D genome contact maps from DNA sequence for 56 bonobos and chimpanzees, encompassing all five extant lineages. We use a pairwise approach to estimate 3D divergence between individuals from the resulting contact maps in 4,420 1 Mb genomic windows. While most pairs were similar, ∼17% were predicted to be substantially divergent in genome folding. The most dissimilar maps were largely driven by single individuals with rare variants that produce unique 3D genome folding in a region. We also identified 89 genomic windows where bonobo and chimpanzee contact maps substantially diverged, including several windows harboring genes associated with traits implicated in Pan phenotypic divergence. We used in silico mutagenesis to identify 51 3D-modifying variants in these bonobo-chimpanzee divergent windows, finding that 34 or 66.67% induce genome folding changes via CTCF binding motif disruption. Our results reveal 3D genome variation at the population-level and identify genomic regions where changes in 3D folding may contribute to phenotypic differences in our closest living relatives.
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Affiliation(s)
- Colin M. Brand
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA
| | - Shuzhen Kuang
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
| | - Erin N. Gilbertson
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA
- Biomedical Informatics Graduate Program, University of California San Francisco, San Francisco, CA
| | - Evonne McArthur
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN
| | - Katherine S. Pollard
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
- Biomedical Informatics Graduate Program, University of California San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA
| | | | - John A. Capra
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA
- Biomedical Informatics Graduate Program, University of California San Francisco, San Francisco, CA
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4
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Webster TH, Vannan A, Pinto BJ, Denbrock G, Morales M, Dolby GA, Fiddes IT, DeNardo DF, Wilson MA. Incomplete dosage balance and dosage compensation in the ZZ/ZW Gila monster ( Heloderma suspectum) revealed by de novo genome assembly. bioRxiv 2023:2023.04.26.538436. [PMID: 37163099 PMCID: PMC10168389 DOI: 10.1101/2023.04.26.538436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Reptiles exhibit a variety of modes of sex determination, including both temperature-dependent and genetic mechanisms. Among those species with genetic sex determination, sex chromosomes of varying heterogamety (XX/XY and ZZ/ZW) have been observed with different degrees of differentiation. Karyotype studies have demonstrated that Gila monsters (Heloderma suspectum) have ZZ/ZW sex determination and this system is likely homologous to the ZZ/ZW system in the Komodo dragon (Varanus komodoensis), but little else is known about their sex chromosomes. Here, we report the assembly and analysis of the Gila monster genome. We generated a de novo draft genome assembly for a male using 10X Genomics technology. We further generated and analyzed short-read whole genome sequencing and whole transcriptome sequencing data for three males and three females. By comparing female and male genomic data, we identified four putative Z-chromosome scaffolds. These putative Z-chromosome scaffolds are homologous to Z-linked scaffolds identified in the Komodo dragon. Further, by analyzing RNAseq data, we observed evidence of incomplete dosage compensation between the Gila monster Z chromosome and autosomes and a lack of balance in Z-linked expression between the sexes. In particular, we observe lower expression of the Z in females (ZW) than males (ZZ) on a global basis, though we find evidence suggesting local gene-by-gene compensation. This pattern has been observed in most other ZZ/ZW systems studied to date and may represent a general pattern for female heterogamety in vertebrates.
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Affiliation(s)
- Timothy H. Webster
- Department of Anthropology, University of Utah, Salt Lake City, UT
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Annika Vannan
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Brendan J. Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
| | - Grant Denbrock
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Matheo Morales
- School of Life Sciences, Arizona State University, Tempe, AZ
- Department of Genetics, Yale University, New Haven, CT
| | - Greer A. Dolby
- School of Life Sciences, Arizona State University, Tempe, AZ
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ
| | | | - Dale F. DeNardo
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Melissa A. Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ
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5
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Lasisi T, Zaidi AA, Webster TH, Stephens NB, Routch K, Jablonski NG, Shriver MD. High-throughput phenotyping methods for quantifying hair fiber morphology. Sci Rep 2021; 11:11535. [PMID: 34075066 PMCID: PMC8169905 DOI: 10.1038/s41598-021-90409-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/10/2021] [Indexed: 11/18/2022] Open
Abstract
Quantifying the continuous variation in human scalp hair morphology is of interest to anthropologists, geneticists, dermatologists and forensic scientists, but existing methods for studying hair form are time-consuming and not widely used. Here, we present a high-throughput sample preparation protocol for the imaging of both longitudinal (curvature) and cross-sectional scalp hair morphology. Additionally, we describe and validate a new Python package designed to process longitudinal and cross-sectional hair images, segment them, and provide measurements of interest. Lastly, we apply our methods to an admixed African-European sample (n = 140), demonstrating the benefit of quantifying hair morphology over classification, and providing evidence that the relationship between cross-sectional morphology and curvature may be an artefact of population stratification rather than a causal link.
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Affiliation(s)
- Tina Lasisi
- Department of Anthropology, Pennsylvania State University, Philadelphia, USA.
| | - Arslan A Zaidi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | | | - Nicholas B Stephens
- Department of Anthropology, Pennsylvania State University, Philadelphia, USA
| | - Kendall Routch
- Department of Anthropology, Pennsylvania State University, Philadelphia, USA
| | - Nina G Jablonski
- Department of Anthropology, Pennsylvania State University, Philadelphia, USA
| | - Mark D Shriver
- Department of Anthropology, Pennsylvania State University, Philadelphia, USA
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6
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Guevara EE, Webster TH, Lawler RR, Bradley BJ, Greene LK, Ranaivonasy J, Ratsirarson J, Harris RA, Liu Y, Murali S, Raveendran M, Hughes DST, Muzny DM, Yoder AD, Worley KC, Rogers J. Comparative genomic analysis of sifakas ( Propithecus) reveals selection for folivory and high heterozygosity despite endangered status. Sci Adv 2021; 7:7/17/eabd2274. [PMID: 33893095 PMCID: PMC8064638 DOI: 10.1126/sciadv.abd2274] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 03/08/2021] [Indexed: 05/12/2023]
Abstract
Sifakas (genus Propithecus) are critically endangered, large-bodied diurnal lemurs that eat leaf-based diets and show corresponding anatomical and microbial adaptations to folivory. We report on the genome assembly of Coquerel's sifaka (P. coquereli) and the resequenced genomes of Verreaux's (P. verreauxi), the golden-crowned (P. tattersalli), and the diademed (P. diadema) sifakas. We find high heterozygosity in all sifakas compared with other primates and endangered mammals. Demographic reconstructions nevertheless suggest declines in effective population size beginning before human arrival on Madagascar. Comparative genomic analyses indicate pervasive accelerated evolution in the ancestral sifaka lineage affecting genes in several complementary pathways relevant to folivory, including nutrient absorption and xenobiotic and fatty acid metabolism. Sifakas show convergent evolution at the level of the pathway, gene family, gene, and amino acid substitution with other folivores. Although sifakas have relatively generalized diets, the physiological challenges of habitual folivory likely led to strong selection.
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Affiliation(s)
- Elaine E Guevara
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.
- Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA
| | - Timothy H Webster
- Department of Anthropology, University of Utah, Salt Lake City, UT 84112, USA
| | - Richard R Lawler
- Department of Sociology and Anthropology, James Madison University, Harrisonburg, VA 22807, USA
| | - Brenda J Bradley
- Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA
| | - Lydia K Greene
- Duke Lemur Center, Duke University, Durham, NC 27705, USA
- Department of Biology, Duke University, Durham, NC 27708-0338, USA
| | - Jeannin Ranaivonasy
- Département Agroécologie, Biodiversité et Changement Climatique, ESSA, University of Antananarivo, Antananarivo, Madagascar
| | - Joelisoa Ratsirarson
- Département Agroécologie, Biodiversité et Changement Climatique, ESSA, University of Antananarivo, Antananarivo, Madagascar
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yue Liu
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shwetha Murali
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Donna M Muzny
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708-0338, USA
| | - Kim C Worley
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA
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7
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Ozga AT, Webster TH, Gilby IC, Wilson MA, Nockerts RS, Wilson ML, Pusey AE, Li Y, Hahn BH, Stone AC. Urine as a high-quality source of host genomic DNA from wild populations. Mol Ecol Resour 2021; 21:170-182. [PMID: 32985084 PMCID: PMC7746602 DOI: 10.1111/1755-0998.13260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 08/13/2020] [Accepted: 09/03/2020] [Indexed: 12/28/2022]
Abstract
The ability to generate genomic data from wild animal populations has the potential to give unprecedented insight into the population history and dynamics of species in their natural habitats. However, for many species, it is impossible legally, ethically or logistically to obtain tissue samples of quality sufficient for genomic analyses. In this study we evaluate the success of multiple sources of genetic material (faeces, urine, dentin and dental calculus) and several capture methods (shotgun, whole-genome, exome) in generating genome-scale data in wild eastern chimpanzees (Pan troglodytes schweinfurthii) from Gombe National Park, Tanzania. We found that urine harbours significantly more host DNA than other sources, leading to broader and deeper coverage across the genome. Urine also exhibited a lower rate of allelic dropout. We found exome sequencing to be far more successful than both shotgun sequencing and whole-genome capture at generating usable data from low-quality samples such as faeces and dental calculus. These results highlight urine as a promising and untapped source of DNA that can be noninvasively collected from wild populations of many species.
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Affiliation(s)
- Andrew T. Ozga
- Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University
- Center for Evolution and Medicine, Arizona State University
| | - Timothy H. Webster
- Department of Anthropology, University of Utah
- School of Life Sciences, Arizona State University
| | - Ian C. Gilby
- School of Human Evolution and Social Change, Arizona State University
- Institute of Human Origins, Arizona State University
| | - Melissa A. Wilson
- Center for Evolution and Medicine, Arizona State University
- School of Life Sciences, Arizona State University
| | | | - Michael L. Wilson
- Department of Anthropology, University of Minnesota
- Department of Ecology, Evolution and Behavior, University of Minnesota
| | | | - Yingying Li
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania
| | - Anne C. Stone
- Center for Evolution and Medicine, Arizona State University
- School of Human Evolution and Social Change, Arizona State University
- Institute of Human Origins, Arizona State University
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8
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Torosin NS, Argibay H, Webster TH, Corneli PS, Knapp LA. Comparing the selective landscape of TLR7 and TLR8 across primates reveals unique sites under positive selection in Alouatta. Mol Phylogenet Evol 2020; 152:106920. [PMID: 32768453 DOI: 10.1016/j.ympev.2020.106920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 03/06/2020] [Accepted: 07/31/2020] [Indexed: 11/24/2022]
Abstract
Among primates, susceptibility to yellow fever (YFV), a single-stranded (ss) RNA virus, ranges from complete resistance to high susceptibility. Howler monkeys (genus Alouatta) are the most susceptible to YFV. In order to identify Alouatta-specific genetic factors that may be responsible for their susceptibility, we collected skin samples from howler monkey museum specimens of the species A. caraya and A. guariba clamitans. We compared the rate of nonsynonymous to synonymous (dN/dS) changes of Toll-like receptor (TLR) 7 and TLR8, the two genes responsible for detecting all ssRNA viruses, across the Primate order. Overall, we found that the TLR7 gene is under stronger purifying selection in howler monkeys compared to other New World and Old World primates, but TLR8 is under the same selective pressure. When we evaluated dN/dS at each codon, we found six codons under positive selection in Alouatta TLR8 and two codons under positive selection in TLR7. The changes in TLR7 are unique to A. guariba clamitans and are found in functionally important regions likely to affect detection of ssRNA viruses by TLR7/TLR8, as well as downstream signaling. These amino acid differences in A. guariba clamitans may play a role in YFV susceptibility. These results have implications for identifying genetic factors affecting YFV susceptibility in primates.
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Affiliation(s)
- Nicole S Torosin
- Department of Anthropology, University of Utah, 260 S. Central Campus Dr., Salt Lake City, UT 84112, United States.
| | - Hernan Argibay
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA-CONICET), Intendente Güiraldes 2160 - Ciudad Universitaria (C1428EGA) Ciudad Autónoma de Buenos Aires, Argentina
| | - Timothy H Webster
- Department of Anthropology, University of Utah, 260 S. Central Campus Dr., Salt Lake City, UT 84112, United States
| | - Patrice Showers Corneli
- Department of Biology, University of Utah, 257 S. 1400 E., Salt Lake City, UT 84112, United States
| | - Leslie A Knapp
- Department of Anthropology, University of Utah, 260 S. Central Campus Dr., Salt Lake City, UT 84112, United States
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9
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Torosin NS, Webster TH, Argibay H, Sanchez Fernandez C, Ferreyra H, Uhart M, Agostini I, Knapp LA. Positively selected variants in functionally important regions of TLR7 in Alouatta guariba clamitans with yellow fever virus exposure in Northern Argentina. Am J Phys Anthropol 2020; 173:50-60. [PMID: 32583896 DOI: 10.1002/ajpa.24086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 04/28/2020] [Accepted: 05/10/2020] [Indexed: 01/15/2023]
Abstract
BACKGROUND In 2007-2009, a major yellow fever virus (YFV) outbreak in Northern Argentina decimated the local howler monkey (Alouatta) population. AIMS To evaluate whether the surviving howler monkeys possess advantageous genetic variants inherited from monkeys alive prior to the YFV outbreak, we explored the relationship between Toll-like receptor (TLR) 7 and TLR8 gene variation and YFV susceptibility. METHODS We used samples from Alouatta individuals in Misiones, Argentina alive before the YFV outbreak, individuals that died during the outbreak, and individuals that survived the outbreak and are alive today. We measured genetic divergence between Alouatta YFV exposure groups and evaluated Alouatta-specific substitutions for functional consequences. RESULTS We did not find different allele frequencies in the post-YFV exposure Alouatta group compared to the pre-exposure group. We identified three nonsynonymous variants in TLR7 in Alouatta guariba clamitans. Two of these substitutions are under positive selection in functionally important regions of the gene. DISCUSSION AND CONCLUSIONS Our results did not indicate that surviving howler monkey spossess advantageous genetic variants at greater frequency than those alive before the YFV outbreak. However, the positively selected unique coding differences in A. guariba clamitans are in the region important in pathogen detection which may affect YFV resistance. Morework is necessary to fully explore this hypothesis.
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Affiliation(s)
- Nicole S Torosin
- Department of Anthropology, University of Utah, Salt Lake City, Utah, USA
| | - Timothy H Webster
- Department of Anthropology, University of Utah, Salt Lake City, Utah, USA
| | - Hernán Argibay
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA-CONICET), Intendente Güiraldes 2160 - Ciudad Universitaria (C1428EGA), Buenos Aires, Argentina
| | - Candelaria Sanchez Fernandez
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina
| | - Hebe Ferreyra
- Global Health Program, Wildlife Conservation Society, Buenos Aires, Argentina
| | - Marcela Uhart
- One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Ilaria Agostini
- Instituto de Biología Subtropical (IBS), Universidad Nacional de Misiones (UNaM), Consejo Nacional de Investigaciones Científcas y Técnicas (CONICET), Puerto Iguazú, Argentina
| | - Leslie A Knapp
- Department of Anthropology, University of Utah, Salt Lake City, Utah, USA
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10
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Dolby GA, Morales M, Webster TH, DeNardo DF, Wilson MA, Kusumi K. Discovery of a New TLR Gene and Gene Expansion Event through Improved Desert Tortoise Genome Assembly with Chromosome-Scale Scaffolds. Genome Biol Evol 2020; 12:3917-3925. [PMID: 32011707 PMCID: PMC7058155 DOI: 10.1093/gbe/evaa016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2020] [Indexed: 12/11/2022] Open
Abstract
Toll-like receptors (TLRs) are a complex family of innate immune genes that are well characterized in mammals and birds but less well understood in nonavian sauropsids (reptiles). The advent of highly contiguous draft genomes of nonmodel organisms enables study of such gene families through analysis of synteny and sequence identity. Here, we analyze TLR genes from the genomes of 22 tetrapod species. Findings reveal a TLR8 gene expansion in crocodilians and turtles (TLR8B), and a second duplication (TLR8C) specifically within turtles, followed by pseudogenization of that gene in the nonfreshwater species (desert tortoise and green sea turtle). Additionally, the Mojave desert tortoise (Gopherus agassizii) has a stop codon in TLR8B (TLR8-1) that is polymorphic among conspecifics. Revised orthology further reveals a new TLR homolog, TLR21-like, which is exclusive to lizards, snakes, turtles, and crocodilians. These analyses were made possible by a new draft genome assembly of the desert tortoise (gopAga2.0), which used chromatin-based assembly to yield draft chromosomal scaffolds (L50 = 26 scaffolds, N50 = 28.36 Mb, longest scaffold = 107 Mb) and an enhanced de novo genome annotation with 25,469 genes. Our three-step approach to orthology curation and comparative analysis of TLR genes shows what new insights are possible using genome assemblies with chromosome-scale scaffolds that permit integration of synteny conservation data.
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Affiliation(s)
- Greer A Dolby
- School of Life Sciences, Arizona State University
- Center for Mechanisms of Evolution, Arizona State University
| | | | - Timothy H Webster
- School of Life Sciences, Arizona State University
- Department of Anthropology, University of Utah
| | | | - Melissa A Wilson
- School of Life Sciences, Arizona State University
- Center for Evolution and Medicine, Arizona State University
| | - Kenro Kusumi
- School of Life Sciences, Arizona State University
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11
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Orton JP, Morales M, Fontenele RS, Schmidlin K, Kraberger S, Leavitt DJ, Webster TH, Wilson MA, Kusumi K, Dolby GA, Varsani A. Virus Discovery in Desert Tortoise Fecal Samples: Novel Circular Single-Stranded DNA Viruses. Viruses 2020; 12:v12020143. [PMID: 31991902 PMCID: PMC7077246 DOI: 10.3390/v12020143] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 01/18/2020] [Accepted: 01/21/2020] [Indexed: 12/25/2022] Open
Abstract
The Sonoran Desert tortoise Gopherus morafkai is adapted to the desert, and plays an important ecological role in this environment. There is limited information on the viral diversity associated with tortoises (family Testudinidae), and to date no DNA virus has been identified associated with these animals. This study aimed to assess the diversity of DNA viruses associated with the Sonoran Desert tortoise by sampling their fecal matter. A viral metagenomics approach was used to identify the DNA viruses in fecal samples from wild Sonoran Desert tortoises in Arizona, USA. In total, 156 novel single-stranded DNA viruses were identified from 40 fecal samples. Those belonged to two known viral families, the Genomoviridae (n = 27) and Microviridae (n = 119). In addition, 10 genomes were recovered that belong to the unclassified group of circular-replication associated protein encoding single-stranded (CRESS) DNA virus and five circular molecules encoding viral-like proteins.
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Affiliation(s)
- Joseph P. Orton
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (J.P.O.); (M.M.); (R.S.F.); (K.S.); (M.A.W.); (K.K.)
| | - Matheo Morales
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (J.P.O.); (M.M.); (R.S.F.); (K.S.); (M.A.W.); (K.K.)
| | - Rafaela S. Fontenele
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (J.P.O.); (M.M.); (R.S.F.); (K.S.); (M.A.W.); (K.K.)
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA;
| | - Kara Schmidlin
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (J.P.O.); (M.M.); (R.S.F.); (K.S.); (M.A.W.); (K.K.)
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA;
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA;
| | - Daniel J. Leavitt
- Natural Resources Program, Naval Facilities Engineering Command-Navy Region Southwest, San Diego, CA 92101, USA, USA;
| | - Timothy H. Webster
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (J.P.O.); (M.M.); (R.S.F.); (K.S.); (M.A.W.); (K.K.)
- Department of Anthropology, University of Utah, Salt Lake City, UT 84112, USA
| | - Melissa A. Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (J.P.O.); (M.M.); (R.S.F.); (K.S.); (M.A.W.); (K.K.)
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA
| | - Kenro Kusumi
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (J.P.O.); (M.M.); (R.S.F.); (K.S.); (M.A.W.); (K.K.)
| | - Greer A. Dolby
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (J.P.O.); (M.M.); (R.S.F.); (K.S.); (M.A.W.); (K.K.)
- Correspondence: (G.A.D.); (A.V.); Tel.: +1-480-965-7456 (G.A.D.); +1-480-727-2093 (A.V.)
| | - Arvind Varsani
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (J.P.O.); (M.M.); (R.S.F.); (K.S.); (M.A.W.); (K.K.)
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA;
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town 7925, South Africa
- Correspondence: (G.A.D.); (A.V.); Tel.: +1-480-965-7456 (G.A.D.); +1-480-727-2093 (A.V.)
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12
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Webster TH, Couse M, Grande BM, Karlins E, Phung TN, Richmond PA, Whitford W, Wilson MA. Identifying, understanding, and correcting technical artifacts on the sex chromosomes in next-generation sequencing data. Gigascience 2020; 8:5530326. [PMID: 31289836 PMCID: PMC6615978 DOI: 10.1093/gigascience/giz074] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 12/04/2018] [Accepted: 06/03/2019] [Indexed: 11/25/2022] Open
Abstract
Background Mammalian X and Y chromosomes share a common evolutionary origin and retain regions of high sequence similarity. Similar sequence content can confound the mapping of short next-generation sequencing reads to a reference genome. It is therefore possible that the presence of both sex chromosomes in a reference genome can cause technical artifacts in genomic data and affect downstream analyses and applications. Understanding this problem is critical for medical genomics and population genomic inference. Results Here, we characterize how sequence homology can affect analyses on the sex chromosomes and present XYalign, a new tool that (1) facilitates the inference of sex chromosome complement from next-generation sequencing data; (2) corrects erroneous read mapping on the sex chromosomes; and (3) tabulates and visualizes important metrics for quality control such as mapping quality, sequencing depth, and allele balance. We find that sequence homology affects read mapping on the sex chromosomes and this has downstream effects on variant calling. However, we show that XYalign can correct mismapping, resulting in more accurate variant calling. We also show how metrics output by XYalign can be used to identify XX and XY individuals across diverse sequencing experiments, including low- and high-coverage whole-genome sequencing, and exome sequencing. Finally, we discuss how the flexibility of the XYalign framework can be leveraged for other uses including the identification of aneuploidy on the autosomes. XYalign is available open source under the GNU General Public License (version 3). Conclusions Sex chromsome sequence homology causes the mismapping of short reads, which in turn affects downstream analyses. XYalign provides a reproducible framework to correct mismapping and improve variant calling on the sex chromsomes.
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Affiliation(s)
- Timothy H Webster
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85281, USA.,Department of Anthropology, University of Utah, 260 S Central Drive, Carolyn and Kem Gardner Commons, Suite 4625, Salt Lake City, UT 84112, USA
| | - Madeline Couse
- University of British Columbia, 2329 West Mall, Vancouver, BC, V6T 1Z4, Canada.,BC Children's Hospital Research Institute, 950 W 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, MSC 9776, Bethesda, MD 20892, USA
| | - Tanya N Phung
- Interdepartmental Program in Bioinformatics, UCLA, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Phillip A Richmond
- BC Children's Hospital Research Institute, 950 W 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.,Centre for Molecular Medicine and Therapeutics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V52 4H4, Canada
| | - Whitney Whitford
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.,Centre for Brain Research, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85281, USA.,Center for Evolution and Medicine, Arizona State University, 401 E. Tyler Mall, Tempe, AZ 85287, USA
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13
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Rupp SM, Webster TH, Olney KC, Hutchins ED, Kusumi K, Wilson Sayres MA. Evolution of Dosage Compensation in Anolis carolinensis, a Reptile with XX/XY Chromosomal Sex Determination. Genome Biol Evol 2018; 9:231-240. [PMID: 28206607 PMCID: PMC5381669 DOI: 10.1093/gbe/evw263] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2016] [Indexed: 12/11/2022] Open
Abstract
In species with highly heteromorphic sex chromosomes, the degradation of one of the sex chromosomes will result in unequal gene expression between the sexes (e.g. between XX females and XY males) and between the sex chromosomes and the autosomes. Dosage compensation is a process whereby genes on the sex chromosomes achieve equal gene expression. We compared genome-wide levels of transcription between males and females, and between the X chromosome and the autosomes in the green anole, Anolis carolinensis. We present evidence for dosage compensation between the sexes, and between the sex chromosomes and the autosomes. When dividing the X chromosome into regions based on linkage groups, we discovered that genes in the first reported X-linked region, anole linkage group b (LGb), exhibit complete dosage compensation, although the rest of the X-linked genes exhibit incomplete dosage compensation. Our data further suggest that the mechanism of this dosage compensation is upregulation of the X chromosome in males. We report that approximately 10% of coding genes, most of which are on the autosomes, are differentially expressed between males and females. In addition, genes on the X chromosome exhibited higher ratios of nonsynonymous to synonymous substitution than autosomal genes, consistent with the fast-X effect. Our results from the green anole add an additional observation of dosage compensation in a species with XX/XY sex determination.
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Affiliation(s)
- Shawn M Rupp
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | | | - Kimberly C Olney
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | | | - Kenro Kusumi
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Melissa A Wilson Sayres
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.,Center for Evolution and Medicine, The Biodesign Institute at Arizona State University, Tempe, AZ, USA
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14
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Olney KC, Narang P, Taravella AM, Webster TH, Wilson Sayres MA. EvSex16: Evolutionary Genomics of Sex. J Hered 2017; 108:707-708. [PMID: 29096011 DOI: 10.1093/jhered/esx084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kimberly C Olney
- School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Pooja Narang
- School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | | | | | - Melissa A Wilson Sayres
- School of Life Sciences, Arizona State University, Tempe, AZ 85287.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287
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15
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Webster TH, Wilson Sayres MA. Genomic signatures of sex-biased demography: progress and prospects. Curr Opin Genet Dev 2016; 41:62-71. [PMID: 27599147 DOI: 10.1016/j.gde.2016.08.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 07/06/2016] [Accepted: 08/02/2016] [Indexed: 01/09/2023]
Abstract
Sex-biased demographic events have played a crucial role in shaping human history. Many of these processes affect genetic variation and can therefore leave detectable signatures in the genome because autosomal, X-linked, Y-linked, and mitochondrial DNA inheritance differ between sexes. Here, we discuss how sex-biased processes shape patterns of genetic diversity across the genome, review recent genomic evidence for sex-biased demography in modern human populations, and suggest directions for future research.
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Affiliation(s)
- Timothy H Webster
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Melissa A Wilson Sayres
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; Center for Evolution and Medicine, The Biodesign Institute at Arizona State University, Tempe, AZ 85287, USA.
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16
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Baden AL, Webster TH, Kamilar JM. Resource seasonality and reproduction predict fission–fusion dynamics in black‐and‐white ruffed lemurs (
Varecia variegata
). Am J Primatol 2015; 78:256-79. [DOI: 10.1002/ajp.22507] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 10/04/2015] [Accepted: 10/30/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Andrea L. Baden
- Department of AnthropologyHunter CollegeNew YorkNew York
- Graduate CenterCity University of New YorkNew YorkNew York
- New York Consortium in Evolutionary Primatology (NYCEP)New YorkNew York
| | | | - Jason M. Kamilar
- Department of AnthropologyUniversity of MassachusettsAmherstMassachusetts
- Graduate Program in Organismic and Evolutionary BiologyUniversity of MassachusettsAmherstMassachusetts
- School of Human Evolution and Social ChangeArizona State UniversityTempeArizona
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17
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Hsiang AY, Field DJ, Webster TH, Behlke ADB, Davis MB, Racicot RA, Gauthier JA. The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record. BMC Evol Biol 2015; 15:87. [PMID: 25989795 PMCID: PMC4438441 DOI: 10.1186/s12862-015-0358-5] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 04/22/2015] [Indexed: 11/17/2022] Open
Abstract
Background The highly derived morphology and astounding diversity of snakes has long inspired debate regarding the ecological and evolutionary origin of both the snake total-group (Pan-Serpentes) and crown snakes (Serpentes). Although speculation abounds on the ecology, behavior, and provenance of the earliest snakes, a rigorous, clade-wide analysis of snake origins has yet to be attempted, in part due to a dearth of adequate paleontological data on early stem snakes. Here, we present the first comprehensive analytical reconstruction of the ancestor of crown snakes and the ancestor of the snake total-group, as inferred using multiple methods of ancestral state reconstruction. We use a combined-data approach that includes new information from the fossil record on extinct crown snakes, new data on the anatomy of the stem snakes Najash rionegrina, Dinilysia patagonica, and Coniophis precedens, and a deeper understanding of the distribution of phenotypic apomorphies among the major clades of fossil and Recent snakes. Additionally, we infer time-calibrated phylogenies using both new ‘tip-dating’ and traditional node-based approaches, providing new insights on temporal patterns in the early evolutionary history of snakes. Results Comprehensive ancestral state reconstructions reveal that both the ancestor of crown snakes and the ancestor of total-group snakes were nocturnal, widely foraging, non-constricting stealth hunters. They likely consumed soft-bodied vertebrate and invertebrate prey that was subequal to head size, and occupied terrestrial settings in warm, well-watered, and well-vegetated environments. The snake total-group – approximated by the Coniophis node – is inferred to have originated on land during the middle Early Cretaceous (~128.5 Ma), with the crown-group following about 20 million years later, during the Albian stage. Our inferred divergence dates provide strong evidence for a major radiation of henophidian snake diversity in the wake of the Cretaceous-Paleogene (K-Pg) mass extinction, clarifying the pattern and timing of the extant snake radiation. Although the snake crown-group most likely arose on the supercontinent of Gondwana, our results suggest the possibility that the snake total-group originated on Laurasia. Conclusions Our study provides new insights into when, where, and how snakes originated, and presents the most complete picture of the early evolution of snakes to date. More broadly, we demonstrate the striking influence of including fossils and phenotypic data in combined analyses aimed at both phylogenetic topology inference and ancestral state reconstruction. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0358-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Allison Y Hsiang
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut, 06520, USA.
| | - Daniel J Field
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut, 06520, USA. .,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA.
| | - Timothy H Webster
- Department of Anthropology, Yale University, New Haven, Connecticut, 06520, USA.
| | - Adam D B Behlke
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut, 06520, USA.
| | - Matthew B Davis
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut, 06520, USA.
| | - Rachel A Racicot
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut, 06520, USA.
| | - Jacques A Gauthier
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut, 06520, USA. .,Yale Peabody Museum of Natural History, Yale University, New Haven, Connecticut, 06520, USA.
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18
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Webster TH, McGrew WC, Marchant LF, Payne CLR, Hunt KD. Selective insectivory at Toro-Semliki, Uganda: comparative analyses suggest no 'savanna' chimpanzee pattern. J Hum Evol 2014; 71:20-7. [PMID: 24792877 DOI: 10.1016/j.jhevol.2014.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 08/16/2013] [Accepted: 02/04/2014] [Indexed: 11/26/2022]
Abstract
Chimpanzee (Pan troglodytes) insectivory across Africa is ubiquitous. Insects provide a significant nutritional payoff and may be important for chimpanzees in dry, open habitats with narrow diets. We tested this hypothesis at Semliki, Uganda, a long-term dry study site. We evaluated prospects for insectivory by measuring insect abundance along de novo transects and trails, monitoring social insect colonies, and surveying available raw materials for elementary technology. We determined the frequency and nature of insectivory through behavioral observation and fecal analysis. We then compared our results with those from 15 other long-term chimpanzee study sites using a cluster analysis. We found that Semliki chimpanzees are one of the most insectivorous populations studied to date in terms of frequency of consumption, but they are very selective in their insectivory, regularly consuming only weaver ants (Oecophylla longinoda) and honey and bees from hives of Apis mellifera. This selectivity obtains despite having a full range of typical prey species available in harvestable quantities. We suggest that Semliki chimpanzees may face ecological time constraints and therefore bias their predation toward prey taxa that can be quickly consumed. Geographical proximity correlated with the results of the cluster analysis, while rainfall, a relatively gross measure of environment, did not. Because broad taxonomic groups of insects were used in analyses, prey availability was unlikely to have a strong effect on this pattern. Instead, we suggest that transmission of cultural knowledge may play a role in determining chimpanzee prey selection across Africa. Further study is needed to test these hypotheses.
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Affiliation(s)
- Timothy H Webster
- Department of Anthropology, Miami University, 120 Upham Hall, 100 Bishop Circle, Oxford, OH 45056-1879, USA; Division of Biological Anthropology, Department of Archaeology and Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 IQH, UK; Department of Anthropology, Yale University, 10 Sachem Street, New Haven, CT 06511-3707, USA.
| | - William C McGrew
- Division of Biological Anthropology, Department of Archaeology and Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 IQH, UK
| | - Linda F Marchant
- Department of Anthropology, Miami University, 120 Upham Hall, 100 Bishop Circle, Oxford, OH 45056-1879, USA
| | - Charlotte L R Payne
- Division of Biological Anthropology, Department of Archaeology and Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 IQH, UK
| | - Kevin D Hunt
- Department of Anthropology, Indiana University, Student Building 130, 701 E Kirkwood, Bloomington, IN 47405, USA
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19
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McIntosh AM, Bennett C, Dickson D, Anestis SF, Watts DP, Webster TH, Fontenot MB, Bradley BJ. The apolipoprotein E (APOE) gene appears functionally monomorphic in chimpanzees (Pan troglodytes). PLoS One 2012; 7:e47760. [PMID: 23112842 PMCID: PMC3480407 DOI: 10.1371/journal.pone.0047760] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 09/20/2012] [Indexed: 12/21/2022] Open
Abstract
Background The human apolipoprotein E (APOE) gene is polymorphic, with three primary alleles (E2, E3, E4) that differ at two key non-synonymous sites. These alleles are functionally different in how they bind to lipoproteins, and this genetic variation is associated with phenotypic variation for several medical traits, including cholesterol levels, cardiovascular health, Alzheimer’s disease risk, and longevity. The relative frequencies of these alleles vary across human populations, and the evolution and maintenance of this diversity is much debated. Previous studies comparing human and chimpanzee APOE sequences found that the chimpanzee sequence is most similar to the human E4 allele, although the resulting chimpanzee protein might function like the protein coded for by the human E3 allele. However, these studies have used sequence data from a single chimpanzee and do not consider whether chimpanzees, like humans, show intra-specific and subspecific variation at this locus. Methodology and Principal Findings To examine potential intraspecific variation, we sequenced the APOE gene of 32 chimpanzees. This sample included 20 captive individuals representing the western subspecies (P. troglodytes verus) and 12 wild individuals representing the eastern subspecies (P. t. schweinfurthii). Variation in our resulting sequences was limited to one non-coding, intronic SNP, which showed fixed differences between the two subspecies. We also compared APOE sequences for all available ape genera and fossil hominins. The bonobo APOE protein is identical to that of the chimpanzee, and the Denisovan APOE exhibits all four human-specific, non-synonymous changes and appears functionally similar to the human E4 allele. Conclusions We found no coding variation within and between chimpanzee populations, suggesting that the maintenance of functionally diverse APOE polymorphisms is a unique feature of human evolution.
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Affiliation(s)
- Annick M. McIntosh
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
| | - Calvin Bennett
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
| | - Dara Dickson
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
| | - Stephanie F. Anestis
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
| | - David P. Watts
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
| | - Timothy H. Webster
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
| | - M. Babette Fontenot
- Division of Behavioral Sciences, New Iberia Research Center, University of Louisiana at Lafayette, Lafayette, Louisiana, United States of America
| | - Brenda J. Bradley
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
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20
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Abstract
Midazolam is a commonly used benzodiazepine that is ideal for conscious sedation during a variety of procedures. Laryngospasm is listed by the manufacturer as a rare side effect of midazolam. Flumazenil is a competitive inhibitor of the benzodiazepines that is available for reversal at the end of such a procedure or when too much sedation has been achieved. We present a case of a 61-year-old man who was to undergo conscious sedation before cardioversion. Shortly after receiving midazolam, he developed laryngospasm and resultant respiratory distress; the laryngospasm was reversed by a small dose of flumazenil. The symptoms recurred after approximately 25 minutes and were again reversed with flumazenil. Neither midazolam-induced laryngospasm nor its reversal with flumazenil have previously been reported. A brief discussion regarding laryngospasm and the use of flumazenil are included.
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Affiliation(s)
- D P Davis
- Department of Emergency Medicine, University of California at San Diego, USA.
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