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Cauret CMS, Jordan DC, Kukoly LM, Burton SR, Anele EU, Kwiecien JM, Gansauge MT, Senthillmohan S, Greenbaum E, Meyer M, Horb ME, Evans BJ. Functional dissection and assembly of a small, newly evolved, W chromosome-specific genomic region of the African clawed frog Xenopus laevis. PLoS Genet 2023; 19:e1010990. [PMID: 37792893 PMCID: PMC10578606 DOI: 10.1371/journal.pgen.1010990] [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: 03/07/2023] [Revised: 10/16/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023] Open
Abstract
Genetic triggers for sex determination are frequently co-inherited with other linked genes that may also influence one or more sex-specific phenotypes. To better understand how sex-limited regions evolve and function, we studied a small W chromosome-specific region of the frog Xenopus laevis that contains only three genes (dm-w, scan-w, ccdc69-w) and that drives female differentiation. Using gene editing, we found that the sex-determining function of this region requires dm-w but that scan-w and ccdc69-w are not essential for viability, female development, or fertility. Analysis of mesonephros+gonad transcriptomes during sexual differentiation illustrates masculinization of the dm-w knockout transcriptome, and identifies mostly non-overlapping sets of differentially expressed genes in separate knockout lines for each of these three W-specific gene compared to wildtype sisters. Capture sequencing of almost all Xenopus species and PCR surveys indicate that the female-determining function of dm-w is present in only a subset of species that carry this gene. These findings map out a dynamic evolutionary history of a newly evolved W chromosome-specific genomic region, whose components have distinctive functions that frequently degraded during Xenopus diversification, and evidence the evolutionary consequences of recombination suppression.
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Affiliation(s)
- Caroline M. S. Cauret
- Biology Department, McMaster University, Hamilton, Ontario, Canada
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Danielle C. Jordan
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, Massachusetts United States of America
- The School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | | | - Sarah R. Burton
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, Massachusetts United States of America
| | - Emmanuela U. Anele
- Biology Department, McMaster University, Hamilton, Ontario, Canada
- Department Zoology, Ahmadu Bello University, Zaria, Nigeria
| | - Jacek M. Kwiecien
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Marie-Theres Gansauge
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Eli Greenbaum
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, United States of America
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marko E. Horb
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, Massachusetts United States of America
| | - Ben J. Evans
- Biology Department, McMaster University, Hamilton, Ontario, Canada
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Mcguire JA, Huang X, Reilly SB, Iskandar DT, Wang-Claypool CY, Werning S, Chong RA, Lawalata SZS, Stubbs AL, Frederick JH, Brown RM, Evans BJ, Arifin U, Riyanto A, Hamidy A, Arida E, Koo MS, Supriatna J, Andayani N, Hall R. Species Delimitation, Phylogenomics, and Biogeography of Sulawesi Flying Lizards: A Diversification History Complicated by Ancient Hybridization, Cryptic Species, and Arrested Speciation. Syst Biol 2023; 72:885-911. [PMID: 37074804 PMCID: PMC10405571 DOI: 10.1093/sysbio/syad020] [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: 07/16/2022] [Revised: 03/14/2023] [Accepted: 04/13/2023] [Indexed: 04/20/2023] Open
Abstract
The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island's long period of isolation and dynamic tectonic history have been implicated as drivers of the regional diversification, this has rarely been tested in the context of an explicit geological framework. Here, we provide a tectonically informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands. We employ a framework for inferring cryptic speciation that involves phylogeographic and genetic clustering analyses as a means of identifying potential species followed by population demographic assessment of divergence-timing and rates of bi-directional migration as means of confirming lineage independence (and thus species status). Using this approach, phylogenetic and population genetic analyses of mitochondrial sequence data obtained for 613 samples, a 50-SNP data set for 370 samples, and a 1249-locus exon-capture data set for 106 samples indicate that the current taxonomy substantially understates the true number of Sulawesi Draco species, that both cryptic and arrested speciations have taken place, and that ancient hybridization confounds phylogenetic analyses that do not explicitly account for reticulation. The Draco lineatus Group appears to comprise 15 species-9 on Sulawesi proper and 6 on peripheral islands. The common ancestor of this group colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two ancestral islands, and began to radiate ~6 Ma as new islands formed and were colonized via overwater dispersal. The enlargement and amalgamation of many of these proto-islands into modern Sulawesi, especially during the past 3 Ma, set in motion dynamic species interactions as once-isolated lineages came into secondary contact, some of which resulted in lineage merger, and others surviving to the present. [Genomics; Indonesia; introgression; mitochondria; phylogenetics; phylogeography; population genetics; reptiles.].
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Affiliation(s)
- Jimmy A Mcguire
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Xiaoting Huang
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Qindao, Shandong, 266003, PR China
| | - Sean B Reilly
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA
| | - Djoko T Iskandar
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
| | - Cynthia Y Wang-Claypool
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Sarah Werning
- Department of Anatomy, Des Moines University, 3200 Grand Avenue, Des Moines, IA 50312-4198, USA
| | - Rebecca A Chong
- Department of Biology, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Shobi Z S Lawalata
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- United in Diversity Foundation, Jalan Hayam Wuruk, Jakarta, Indonesia
| | - Alexander L Stubbs
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Jeffrey H Frederick
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, 1345 Jayhawk Blvd., University of Kansas, Lawrence, KS 66045, USA
| | - Ben J Evans
- Biology Department, McMaster University, Hamilton, Ontario, Canada
| | - Umilaela Arifin
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
- Center for Taxonomy and Morphology, Zoologisches Museum Hamburg, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, R230 20146 Hamburg, Germany
| | - Awal Riyanto
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Amir Hamidy
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Evy Arida
- Research Center for Applied Zoology, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Michelle S Koo
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Jatna Supriatna
- Department of Biology, Institute for Sustainable Earth and Resources (I-SER), Gedung Laboratorium Multidisiplin, and Research Center for Climate Change (RCCC-UI), Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Noviar Andayani
- Department of Biology, Institute for Sustainable Earth and Resources (I-SER), Gedung Laboratorium Multidisiplin, and Research Center for Climate Change (RCCC-UI), Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Robert Hall
- SE Asia Research Group (SEARG), Department of Earth Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
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Fornaini NR, Bergelová B, Gvoždík V, Černohorská H, Krylov V, Kubíčková S, Fokam EB, Badjedjea G, Evans BJ, Knytl M. Consequences of polyploidy and divergence as revealed by cytogenetic mapping of tandem repeats in African clawed frogs ( Xenopus, Pipidae). EUR J WILDLIFE RES 2023; 69:81. [PMID: 37483536 PMCID: PMC10361878 DOI: 10.1007/s10344-023-01709-8] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/13/2023] [Accepted: 06/27/2023] [Indexed: 07/25/2023]
Abstract
Repetitive elements have been identified in several amphibian genomes using whole genome sequencing, but few studies have used cytogenetic mapping to visualize these elements in this vertebrate group. Here, we used fluorescence in situ hybridization and genomic data to map the U1 and U2 small nuclear RNAs and histone H3 in six species of African clawed frog (genus Xenopus), including, from subgenus Silurana, the diploid Xenopus tropicalis and its close allotetraploid relative X. calcaratus and, from subgenus Xenopus, the allotetraploid species X. pygmaeus, X. allofraseri, X. laevis, and X. muelleri. Results allowed us to qualitatively evaluate the relative roles of polyploidization and divergence in the evolution of repetitive elements because our focal species include allotetraploid species derived from two independent polyploidization events - one that is relatively young that gave rise to X. calcaratus and another that is older that gave rise to the other (older) allotetraploids. Our results demonstrated conserved loci number and position of signals in the species from subgenus Silurana; allotetraploid X. calcaratus has twice as many signals as diploid X. tropicalis. However, the content of repeats varied among the other allotetraploid species. We detected almost same number of signals in X. muelleri as in X. calcaratus and same number of signals in X. pygmaeus, X. allofraseri, X. laevis as in the diploid X. tropicalis. Overall, these results are consistent with the proposal that allopolyploidization duplicated these tandem repeats and that variation in their copy number was accumulated over time through reduction and expansion in a subset of the older allopolyploids.
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Affiliation(s)
- Nicola R. Fornaini
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 12843 Czech Republic
| | - Barbora Bergelová
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 12843 Czech Republic
| | - Václav Gvoždík
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Zoology, National Museum of the Czech Republic, Prague, Czech Republic
| | - Halina Černohorská
- Department of Genetics and Reproduction, CEITEC - Veterinary Research Institute, Hudcova 296/70, Brno, 62100 Czech Republic
| | - Vladimír Krylov
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 12843 Czech Republic
| | - Svatava Kubíčková
- Department of Genetics and Reproduction, CEITEC - Veterinary Research Institute, Hudcova 296/70, Brno, 62100 Czech Republic
| | - Eric B. Fokam
- Department of Animal Biology and Conservation, University of Buea, PO Box 63, Buea, 00237 Cameroon
| | - Gabriel Badjedjea
- Department of Aquatic Ecology, Biodiversity Monitoring Center, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Ben J. Evans
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S4K1 Canada
| | - Martin Knytl
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 12843 Czech Republic
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S4K1 Canada
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Rong S, Neil CR, Welch A, Duan C, Maguire S, Meremikwu IC, Meyerson M, Evans BJ, Fairbrother WG. Large-scale functional screen identifies genetic variants with splicing effects in modern and archaic humans. Proc Natl Acad Sci U S A 2023; 120:e2218308120. [PMID: 37192163 PMCID: PMC10214146 DOI: 10.1073/pnas.2218308120] [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: 11/07/2022] [Accepted: 04/12/2023] [Indexed: 05/18/2023] Open
Abstract
Humans coexisted and interbred with other hominins which later became extinct. These archaic hominins are known to us only through fossil records and for two cases, genome sequences. Here, we engineer Neanderthal and Denisovan sequences into thousands of artificial genes to reconstruct the pre-mRNA processing patterns of these extinct populations. Of the 5,169 alleles tested in this massively parallel splicing reporter assay (MaPSy), we report 962 exonic splicing mutations that correspond to differences in exon recognition between extant and extinct hominins. Using MaPSy splicing variants, predicted splicing variants, and splicing quantitative trait loci, we show that splice-disrupting variants experienced greater purifying selection in anatomically modern humans than that in Neanderthals. Adaptively introgressed variants were enriched for moderate-effect splicing variants, consistent with positive selection for alternative spliced alleles following introgression. As particularly compelling examples, we characterized a unique tissue-specific alternative splicing variant at the adaptively introgressed innate immunity gene TLR1, as well as a unique Neanderthal introgressed alternative splicing variant in the gene HSPG2 that encodes perlecan. We further identified potentially pathogenic splicing variants found only in Neanderthals and Denisovans in genes related to sperm maturation and immunity. Finally, we found splicing variants that may contribute to variation among modern humans in total bilirubin, balding, hemoglobin levels, and lung capacity. Our findings provide unique insights into natural selection acting on splicing in human evolution and demonstrate how functional assays can be used to identify candidate causal variants underlying differences in gene regulation and phenotype.
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Affiliation(s)
- Stephen Rong
- Center for Computational Molecular Biology, Brown University, Providence, RI02912
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Christopher R. Neil
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Anastasia Welch
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Chaorui Duan
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Samantha Maguire
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Ijeoma C. Meremikwu
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Malcolm Meyerson
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Ben J. Evans
- Department of Biology, McMaster University, Hamilton, ONL8S 4K1, Canada
| | - William G. Fairbrother
- Center for Computational Molecular Biology, Brown University, Providence, RI02912
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
- Hassenfeld Child Health Innovation Institute of Brown University, Providence, RI02912
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Zhu J, Evans BJ. Mitonuclear Interactions and the Origin of Macaque Societies. Genome Biol Evol 2023; 15:7033213. [PMID: 36757387 PMCID: PMC9937042 DOI: 10.1093/gbe/evad010] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 01/12/2023] [Accepted: 01/21/2023] [Indexed: 02/10/2023] Open
Abstract
In most eukaryotes, aerobic respiration requires interactions between autosomally encoded genes (Ninteract genes) and mitochondrial DNA, RNA, and protein. In species where females are philopatric, contrasting distributions of genetic variation in mitochondrial and nuclear genomes create variation in mitonuclear interactions that may be subject to natural selection. To test this expectation, we turned to a group with extreme female philopatry: the macaque monkeys. We examined four genomic data sets from (1) wild caught and (2) captive populations of rhesus macaque, which is the most widely distributed nonhuman primate, and (3) the stump-tailed macaque and (4) a subspecies of longtail macaque, both of whose mitochondrial DNA is introgressed from a highly diverged ancestor. We identified atypically long runs of homozygosity, low polymorphism, high differentiation, and/or rapid protein evolution associated with Ninteract genes compared with non-Ninteract genes. These metrics suggest a subset of Ninteract genes were independently subject to atypically pervasive natural selection in multiple species. These findings suggest that natural selection on mitonuclear interactions could have influenced several aspects of macaque societies including species diversity, ecological breadth, female-biased adult sex ratio and demography, sexual dimorphism, and mitonuclear phylogenomics.
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Affiliation(s)
- Jianlong Zhu
- Biology Department, McMaster University, Hamilton, Ontario, Canada
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Knytl M, Fornaini NR, Bergelová B, Gvoždík V, Černohorská H, Kubíčková S, Fokam EB, Evans BJ, Krylov V. Divergent subgenome evolution in the allotetraploid frog Xenopus calcaratus. Gene X 2023; 851:146974. [DOI: 10.1016/j.gene.2022.146974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
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Premachandra T, Cauret CMS, Conradie W, Measey J, Evans BJ. Population genomics and subgenome evolution of the allotetraploid frog Xenopus laevis in southern Africa. G3 (Bethesda) 2022; 13:6916838. [PMID: 36524354 PMCID: PMC9911082 DOI: 10.1093/g3journal/jkac325] [Citation(s) in RCA: 1] [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] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/02/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022]
Abstract
Allotetraploid genomes have two distinct genomic components called subgenomes that are derived from separate diploid ancestral species. Many genomic characteristics such as gene function, expression, recombination, and transposable element mobility may differ significantly between subgenomes. To explore the possibility that subgenome population structure and gene flow may differ as well, we examined genetic variation in an allotetraploid frog-the African clawed frog (Xenopus laevis)-over the dynamic and varied habitat of its native range in southern Africa. Using reduced representation genome sequences from 91 samples from 12 localities, we found no strong evidence that population structure and gene flow differed substantially by subgenome. We then compared patterns of population structure in the nuclear genome to the mitochondrial genome using Sanger sequences from 455 samples from 183 localities. Our results provide further resolution to the geographic distribution of mitochondrial and nuclear diversity in this species and illustrate that population structure in both genomes corresponds roughly with variation in seasonal rainfall and with the topography of southern Africa.
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Affiliation(s)
- Tharindu Premachandra
- Department of Biology, McMaster University, Life Sciences Building Room 328, 1280 Main Street West, Hamilton, ON L8S4K1, Canada
| | - Caroline M S Cauret
- Department of Biology, McMaster University, Life Sciences Building Room 328, 1280 Main Street West, Hamilton, ON L8S4K1, Canada,Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Werner Conradie
- Port Elizabeth Museum (Bayworld), P.O. Box 13147, Humewood, Gqeberha 6013, South Africa,Department of Conservation Management, Natural Resource Science and Management Cluster, Faculty of Science, Nelson Mandela University, George Campus, George 6019, South Africa
| | - John Measey
- Corresponding author: Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa.
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Evans BJ, Mudd AB, Bredeson JV, Furman BLS, Wasonga DV, Lyons JB, Harland RM, Rokhsar DS. New insights into Xenopus sex chromosome genomics from the Marsabit clawed frog X. borealis. J Evol Biol 2022; 35:1777-1790. [PMID: 36054077 PMCID: PMC9722552 DOI: 10.1111/jeb.14078] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 02/08/2022] [Revised: 06/23/2022] [Accepted: 07/14/2022] [Indexed: 11/26/2022]
Abstract
In many groups, sex chromosomes change frequently but the drivers of their rapid evolution are varied and often poorly characterized. With an aim of further understanding sex chromosome turnover, we investigated the polymorphic sex chromosomes of the Marsabit clawed frog, Xenopus borealis, using genomic data and a new chromosome-scale genome assembly. We confirmed previous findings that 54.1 Mb of chromosome 8L is sex-linked in animals from east Kenya and a laboratory strain, but most (or all) of this region is not sex-linked in natural populations from west Kenya. Previous work suggests possible degeneration of the Z chromosomes in the east population because many sex-linked transcripts of this female heterogametic population have female-biased expression, and we therefore expected this chromosome to not be present in the west population. In contrast, our simulations support a model where most or all of the sex-linked portion of the Z chromosome from the east acquired autosomal segregation in the west, and where much genetic variation specific to the large sex-linked portion of the W chromosome from the east is not present in the west. These recent changes are consistent with the hot-potato model, wherein sex chromosome turnover is favoured by natural selection if it purges a (minimally) degenerate sex-specific sex chromosome, but counterintuitively suggest natural selection failed to purge a Z chromosome that has signs of more advanced and possibly more ancient regulatory degeneration. These findings highlight complex evolutionary dynamics of young, rapidly evolving Xenopus sex chromosomes and set the stage for mechanistic work aimed at pinpointing additional sex-determining genes in this group.
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Affiliation(s)
- Ben J Evans
- Biology Department, Life Sciences Building Room 328, McMaster University, Hamilton, Ontario, Canada
| | - Austin B Mudd
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Jessen V Bredeson
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Benjamin L S Furman
- Biology Department, Life Sciences Building Room 328, McMaster University, Hamilton, Ontario, Canada
- Canexia Health, Vancouver, British Columbia, Canada
| | | | - Jessica B Lyons
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Richard M Harland
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Dan S Rokhsar
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
- Okinawa Institute of Science and Technology Graduate University, Onna, Japan
- Chan-Zuckerberg BioHub, San Francisco, California, USA
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Hayashi S, Suda K, Fujimura F, Fujikawa M, Tamura K, Tsukamoto D, Evans BJ, Takamatsu N, Ito M. Neofunctionalization of a non-coding portion of a DNA transposon in the coding region of the chimerical sex-determining gene dm-W in Xenopus frogs. Mol Biol Evol 2022; 39:6613159. [PMID: 35763822 PMCID: PMC9250109 DOI: 10.1093/molbev/msac138] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Most vertebrate sex-determining genes (SDGs) emerge as neofunctionalized genes through duplication and/or mutation of ancestral genes that are involved with sexual differentiation. We previously demonstrated dm-W to be the SDG in the African clawed frog Xenopus laevis and found that a portion of this gene emerged from the masculinization gene dmrt1 after allotetraploidization by interspecific hybridization between two ancestral species around 17–18 Ma. dm-W has four exons consisting of a noncoding exon 1, dmrt1-derived exons 2 and 3, and an orphan exon 4 (Ex4) of unknown origin that includes coding sequence (CDS). In this study, we searched for the origin of Ex4 and investigated the function of the CDS of this exon. We found that the Ex4-CDS is derived from a noncoding portion of the hAT-10 family of DNA transposon. Evolutionary analysis of transposons and determination of the Ex4 sequences from three other species indicated that Ex4 was generated before the diversification of most or all extant allotetraploid species in subgenus Xenopus, during which time we hypothesize that transposase activity of this hAT superfamily was active. Using DNA–protein binding and transfection assays, we further demonstrate that the Ex4-encoded amino acid sequence increases the DNA-binding ability and transrepression activity of DM-W. These findings suggest that the conversion of the noncoding transposon sequence to the CDS of dm-W contributed to neofunctionalization of a new chimeric SDG in the ancestor of the allotetraploid Xenopus species, offering new insights into de novo origin and functional evolution of chimerical genes.
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Affiliation(s)
- Shun Hayashi
- Department of Bioscience, School of Science, Kitasato University, 1-15-1 Kitasato, Minamiku Sagamihara, Kanagawa 252-0373, Japan
| | - Kosuke Suda
- Department of Bioscience, School of Science, Kitasato University, 1-15-1 Kitasato, Minamiku Sagamihara, Kanagawa 252-0373, Japan
| | - Fuga Fujimura
- Department of Bioscience, School of Science, Kitasato University, 1-15-1 Kitasato, Minamiku Sagamihara, Kanagawa 252-0373, Japan
| | - Makoto Fujikawa
- Department of Bioscience, School of Science, Kitasato University, 1-15-1 Kitasato, Minamiku Sagamihara, Kanagawa 252-0373, Japan
| | - Kei Tamura
- Department of Bioscience, School of Science, Kitasato University, 1-15-1 Kitasato, Minamiku Sagamihara, Kanagawa 252-0373, Japan
| | - Daisuke Tsukamoto
- Department of Bioscience, School of Science, Kitasato University, 1-15-1 Kitasato, Minamiku Sagamihara, Kanagawa 252-0373, Japan
| | - Ben J Evans
- Department of Biology, Life Sciences Room 328, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Nobuhiko Takamatsu
- Department of Bioscience, School of Science, Kitasato University, 1-15-1 Kitasato, Minamiku Sagamihara, Kanagawa 252-0373, Japan
| | - Michihiko Ito
- Department of Bioscience, School of Science, Kitasato University, 1-15-1 Kitasato, Minamiku Sagamihara, Kanagawa 252-0373, Japan
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Stevison LS, Bailey NP, Szpiech ZA, Novak TE, Melnick DJ, Evans BJ, Wall JD. Evolution of genes involved in the unusual genitals of the bear macaque, Macaca arctoides. Ecol Evol 2022; 12:e8897. [PMID: 35646310 PMCID: PMC9130562 DOI: 10.1002/ece3.8897] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 11/30/2022] Open
Abstract
Genital divergence is thought to contribute to reproductive barriers by establishing a “lock‐and‐key" mechanism for reproductive compatibility. One such example, Macaca arctoides, the bear macaque, has compensatory changes in both male and female genital morphology as compared to close relatives. M. arctoides also has a complex evolutionary history, having extensive introgression between the fascicularis and sinica macaque species groups. Here, phylogenetic relationships were analyzed via whole‐genome sequences from five species, including M. arctoides, and two species each from the putative parental species groups. This analysis revealed ~3x more genomic regions supported placement in the sinica species group as compared to the fascicularis species group. Additionally, introgression analysis of the M. arctoides genome revealed it is a mosaic of recent polymorphisms shared with both species groups. To examine the evolution of their unique genital morphology further, the prevalence of candidate genes involved in genital morphology was compared against genome‐wide outliers in various population genetic metrics of diversity, divergence, introgression, and selection, while accounting for background variation in recombination rate. This analysis identified 67 outlier genes, including several genes that influence baculum morphology in mice, which were of interest since the bear macaque has the longest primate baculum. The mean of four of the seven population genetic metrics was statistically different in the candidate genes as compared to the rest of the genome, suggesting that genes involved in genital morphology have increased divergence and decreased diversity beyond expectations. These results highlight specific genes that may have played a role in shaping the unique genital morphology in the bear macaque.
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Affiliation(s)
- Laurie S Stevison
- Department of Biological Sciences Auburn University Auburn Alabama USA
| | - Nick P Bailey
- Department of Biological Sciences Auburn University Auburn Alabama USA
| | - Zachary A Szpiech
- Department of Biological Sciences Auburn University Auburn Alabama USA.,Department of Biology Pennsylvania State University University Park Pennsylvania USA.,Institute for Computational and Data Sciences Pennsylvania State University University Park Pennsylvania USA
| | - Taylor E Novak
- Department of Biological Sciences Auburn University Auburn Alabama USA
| | - Don J Melnick
- Department of Ecology, Evolution, and Environmental Biology Columbia University New York New York USA
| | - Ben J Evans
- Biology Department McMaster University Hamilton Ontario Canada
| | - Jeffrey D Wall
- Institute for Human Genetics University of California, San Francisco San Francisco California USA
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11
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Evans BJ, Peter BM, Melnick DJ, Andayani N, Supriatna J, Zhu J, Tosi AJ. Mitonuclear interactions and introgression genomics of macaque monkeys ( Macaca) highlight the influence of behaviour on genome evolution. Proc Biol Sci 2021; 288:20211756. [PMID: 34610767 PMCID: PMC8493204 DOI: 10.1098/rspb.2021.1756] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 08/05/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022] Open
Abstract
In most macaques, females are philopatric and males migrate from their natal ranges, which results in pronounced divergence of mitochondrial genomes within and among species. We therefore predicted that some nuclear genes would have to acquire compensatory mutations to preserve compatibility with diverged interaction partners from the mitochondria. We additionally expected that these sex-differences would have distinctive effects on gene flow in the X and autosomes. Using new genomic data from 29 individuals from eight species of Southeast Asian macaque, we identified evidence of natural selection associated with mitonuclear interactions, including extreme outliers of interspecies differentiation and metrics of positive selection, low intraspecies polymorphism and atypically long runs of homozygosity associated with nuclear-encoded genes that interact with mitochondria-encoded genes. In one individual with introgressed mitochondria, we detected a small but significant enrichment of autosomal introgression blocks from the source species of her mitochondria that contained genes which interact with mitochondria-encoded loci. Our analyses also demonstrate that sex-specific demography sculpts genetic exchange across multiple species boundaries. These findings show that behaviour can have profound but indirect effects on genome evolution by influencing how interacting components of different genomic compartments (mitochondria, the autosomes and the sex chromosomes) move through time and space.
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Affiliation(s)
- Ben J. Evans
- Biology Department, Life Sciences Building Room 328, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Benjamin M. Peter
- Department of Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig Germany
| | - Don J. Melnick
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 10th floor Schermerhorn Extension, 119th Street and Amsterdam Avenue, New York, NY 10027 USA
| | - Noviar Andayani
- Department of Biology, Universitas Indonesia, Gedung E, Kampus UI Depok, Depok 16424, Indonesia
| | - Jatna Supriatna
- Department of Biology, Universitas Indonesia, Gedung E, Kampus UI Depok, Depok 16424, Indonesia
- Institute for Sustainable Earth and Resources (I-SER), Gedung Laboratorium Multidisiplin, Universitas Indonesia, Gedung E, Kampus UI Depok, Depok 16424, Indonesia
- Research Center for Climate Change (RCCC-UI), Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Gedung E, Kampus UI Depok, Depok 16424, Indonesia
| | - Jianlong Zhu
- Biology Department, Life Sciences Building Room 328, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Anthony J. Tosi
- Anthropology Department, Kent State University, 238 Lowry Hall, Kent, OH 44242, USA
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12
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Stöck M, Kratochvíl L, Kuhl H, Rovatsos M, Evans BJ, Suh A, Valenzuela N, Veyrunes F, Zhou Q, Gamble T, Capel B, Schartl M, Guiguen Y. A brief review of vertebrate sex evolution with a pledge for integrative research: towards ' sexomics'. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200426. [PMID: 34247497 PMCID: PMC8293304 DOI: 10.1098/rstb.2020.0426] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 03/08/2021] [Indexed: 02/07/2023] Open
Abstract
Triggers and biological processes controlling male or female gonadal differentiation vary in vertebrates, with sex determination (SD) governed by environmental factors or simple to complex genetic mechanisms that evolved repeatedly and independently in various groups. Here, we review sex evolution across major clades of vertebrates with information on SD, sexual development and reproductive modes. We offer an up-to-date review of divergence times, species diversity, genomic resources, genome size, occurrence and nature of polyploids, SD systems, sex chromosomes, SD genes, dosage compensation and sex-biased gene expression. Advances in sequencing technologies now enable us to study the evolution of SD at broader evolutionary scales, and we now hope to pursue a sexomics integrative research initiative across vertebrates. The vertebrate sexome comprises interdisciplinary and integrated information on sexual differentiation, development and reproduction at all biological levels, from genomes, transcriptomes and proteomes, to the organs involved in sexual and sex-specific processes, including gonads, secondary sex organs and those with transcriptional sex-bias. The sexome also includes ontogenetic and behavioural aspects of sexual differentiation, including malfunction and impairment of SD, sexual differentiation and fertility. Starting from data generated by high-throughput approaches, we encourage others to contribute expertise to building understanding of the sexomes of many key vertebrate species. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.
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Affiliation(s)
- Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries—IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czech Republic
| | - Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries—IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
| | - Michail Rovatsos
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Ben J. Evans
- Department of Biology, McMaster University, Life Sciences Building Room 328, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
- Department of Organismal Biology—Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Frédéric Veyrunes
- Institut des Sciences de l'Evolution de Montpellier, ISEM UMR 5554 (CNRS/Université de Montpellier/IRD/EPHE), Montpellier, France
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
- Department of Neuroscience and Developmental Biology, University of Vienna, A-1090 Vienna, Austria
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
| | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Würzburg, 97074 Würzburg, Germany
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
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13
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Song XY, Furman BLS, Premachandra T, Knytl M, Cauret CMS, Wasonga DV, Measey J, Dworkin I, Evans BJ. Sex chromosome degeneration, turnover, and sex-biased expression of sex-linked transcripts in African clawed frogs ( Xenopus). Philos Trans R Soc Lond B Biol Sci 2021; 376:20200095. [PMID: 34247503 DOI: 10.1098/rstb.2020.0095] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The tempo of sex chromosome evolution-how quickly, in what order, why and how their particular characteristics emerge during evolution-remains poorly understood. To understand this further, we studied three closely related species of African clawed frog (genus Xenopus), that each has independently evolved sex chromosomes. We identified population polymorphism in the extent of sex chromosome differentiation in wild-caught Xenopus borealis that corresponds to a large, previously identified region of recombination suppression. This large sex-linked region of X. borealis has an extreme concentration of genes that encode transcripts with sex-biased expression, and we recovered similar findings in the smaller sex-linked regions of Xenopus laevis and Xenopus tropicalis. In two of these species, strong skews in expression (mostly female-biased in X. borealis, mostly male-biased in X. tropicalis) are consistent with expectations associated with recombination suppression, and in X. borealis, we hypothesize that a degenerate ancestral Y-chromosome transitioned into its contemporary Z-chromosome. These findings indicate that Xenopus species are tolerant of differences between the sexes in dosage of the products of multiple genes, and offer insights into how evolutionary transformations of ancestral sex chromosomes carry forward to affect the function of new sex chromosomes. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.
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Affiliation(s)
- Xue-Ying Song
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Benjamin L S Furman
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1.,Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, Canada V6T 1Z4
| | - Tharindu Premachandra
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Martin Knytl
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1.,Department of Cell Biology, Charles University, 7 Vinicna Street, Prague 12843, Czech Republic
| | - Caroline M S Cauret
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | | | - John Measey
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602 Stellenbosch, South Africa
| | - Ian Dworkin
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Ben J Evans
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
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14
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Furman BLS, Cauret CMS, Knytl M, Song XY, Premachandra T, Ofori-Boateng C, Jordan DC, Horb ME, Evans BJ. A frog with three sex chromosomes that co-mingle together in nature: Xenopus tropicalis has a degenerate W and a Y that evolved from a Z chromosome. PLoS Genet 2020; 16:e1009121. [PMID: 33166278 PMCID: PMC7652241 DOI: 10.1371/journal.pgen.1009121] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 04/23/2020] [Accepted: 09/16/2020] [Indexed: 11/18/2022] Open
Abstract
In many species, sexual differentiation is a vital prelude to reproduction, and disruption of this process can have severe fitness effects, including sterility. It is thus interesting that genetic systems governing sexual differentiation vary among-and even within-species. To understand these systems more, we investigated a rare example of a frog with three sex chromosomes: the Western clawed frog, Xenopus tropicalis. We demonstrate that natural populations from the western and eastern edges of Ghana have a young Y chromosome, and that a male-determining factor on this Y chromosome is in a very similar genomic location as a previously known female-determining factor on the W chromosome. Nucleotide polymorphism of expressed transcripts suggests genetic degeneration on the W chromosome, emergence of a new Y chromosome from an ancestral Z chromosome, and natural co-mingling of the W, Z, and Y chromosomes in the same population. Compared to the rest of the genome, a small sex-associated portion of the sex chromosomes has a 50-fold enrichment of transcripts with male-biased expression during early gonadal differentiation. Additionally, X. tropicalis has sex-differences in the rates and genomic locations of recombination events during gametogenesis that are similar to at least two other Xenopus species, which suggests that sex differences in recombination are genus-wide. These findings are consistent with theoretical expectations associated with recombination suppression on sex chromosomes, demonstrate that several characteristics of old and established sex chromosomes (e.g., nucleotide divergence, sex biased expression) can arise well before sex chromosomes become cytogenetically distinguished, and show how these characteristics can have lingering consequences that are carried forward through sex chromosome turnovers.
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Affiliation(s)
- Benjamin L. S. Furman
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
- Department of Zoology, University of British Columbia, 6270 University Blvd Vancouver, British Columbia, V6T 1Z4 Canada
| | - Caroline M. S. Cauret
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Martin Knytl
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
- Department of Cell Biology, Charles University, 7 Vinicna Street, Prague, 12843, Czech Republic
| | - Xue-Ying Song
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Tharindu Premachandra
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | | | - Danielle C. Jordan
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, 7 MBL St, Woods Hole, MA 02543 USA
| | - Marko E. Horb
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, 7 MBL St, Woods Hole, MA 02543 USA
| | - Ben J. Evans
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
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15
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Cauret CMS, Gansauge MT, Tupper AS, Furman BLS, Knytl M, Song X, Greenbaum E, Meyer M, Evans BJ. Erratum to: Developmental systems drift and the drivers of sex chromosome evolution. Mol Biol Evol 2020; 37:1844. [DOI: 10.1093/molbev/msz286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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16
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Cauret CMS, Gansauge MT, Tupper AS, Furman BLS, Knytl M, Song XY, Greenbaum E, Meyer M, Evans BJ. Developmental Systems Drift and the Drivers of Sex Chromosome Evolution. Mol Biol Evol 2019; 37:799-810. [DOI: 10.1093/molbev/msz268] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
AbstractPhenotypic invariance—the outcome of purifying selection—is a hallmark of biological importance. However, invariant phenotypes might be controlled by diverged genetic systems in different species. Here, we explore how an important and invariant phenotype—the development of sexually differentiated individuals—is controlled in over two dozen species in the frog family Pipidae. We uncovered evidence in different species for 1) an ancestral W chromosome that is not found in many females and is found in some males, 2) independent losses and 3) autosomal segregation of this W chromosome, 4) changes in male versus female heterogamy, and 5) substantial variation among species in recombination suppression on sex chromosomes. We further provide evidence of, and evolutionary context for, the origins of at least seven distinct systems for regulating sex determination among three closely related genera. These systems are distinct in their genomic locations, evolutionary origins, and/or male versus female heterogamy. Our findings demonstrate that the developmental control of sexual differentiation changed via loss, sidelining, and empowerment of a mechanistically influential gene, and offer insights into novel factors that impinge on the diverse evolutionary fates of sex chromosomes.
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Affiliation(s)
| | - Marie-Theres Gansauge
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Andrew S Tupper
- Origins Institute and Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Canada
| | - Benjamin L S Furman
- Biology Department, McMaster University, Hamilton, Canada
- Department of Zoology, Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Martin Knytl
- Biology Department, McMaster University, Hamilton, Canada
- Department of Cell Biology, Charles University, Prague 2, Czech Republic
| | - Xue-Ying Song
- Biology Department, McMaster University, Hamilton, Canada
| | - Eli Greenbaum
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Ben J Evans
- Biology Department, McMaster University, Hamilton, Canada
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17
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Evans BJ, Gansauge MT, Stanley EL, Furman BLS, Cauret CMS, Ofori-Boateng C, Gvoždík V, Streicher JW, Greenbaum E, Tinsley RC, Meyer M, Blackburn DC. Xenopus fraseri: Mr. Fraser, where did your frog come from? PLoS One 2019; 14:e0220892. [PMID: 31509539 PMCID: PMC6738922 DOI: 10.1371/journal.pone.0220892] [Citation(s) in RCA: 19] [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: 07/04/2019] [Accepted: 07/23/2019] [Indexed: 01/06/2023] Open
Abstract
A comprehensive, accurate, and revisable alpha taxonomy is crucial for biodiversity studies, but is challenging when data from reference specimens are difficult to collect or observe. However, recent technological advances can overcome some of these challenges. To illustrate this, we used modern approaches to tackle a centuries-old taxonomic enigma presented by Fraser’s Clawed Frog, Xenopus fraseri, including whether X. fraseri is different from other species, and if so, where it is situated geographically and phylogenetically. To facilitate these inferences, we used high-resolution techniques to examine morphological variation, and we generated and analyzed complete mitochondrial genome sequences from all Xenopus species, including >150-year-old type specimens. Our results demonstrate that X. fraseri is indeed distinct from other species, firmly place this species within a phylogenetic context, and identify its minimal geographic distribution in northern Ghana and northern Cameroon. These data also permit novel phylogenetic resolution into this intensively studied and biomedically important group. Xenopus fraseri was formerly thought to be a rainforest endemic placed alongside species in the amieti species group; in fact this species occurs in arid habitat on the borderlands of the Sahel, and is the smallest member of the muelleri species group. This study illustrates that the taxonomic enigma of Fraser’s frog was a combined consequence of sparse collection records, interspecies conservation and intraspecific polymorphism in external anatomy, and type specimens with unusual morphology.
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Affiliation(s)
- Ben J. Evans
- Department of Biology, McMaster University, Hamilton, ON, Canada
- * E-mail:
| | - Marie-Theres Gansauge
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany
| | - Edward L. Stanley
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of America
| | - Benjamin L. S. Furman
- Department of Biology, McMaster University, Hamilton, ON, Canada
- Department of Zoology, Beaty Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Václav Gvoždík
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Czech Republic
- Department of Zoology, National Museum, Prague, Czech Republic
| | | | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, El Paso, United States of America
| | - Richard C. Tinsley
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany
| | - David C. Blackburn
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of America
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18
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Ackermann RR, Arnold ML, Baiz MD, Cahill JA, Cortés-Ortiz L, Evans BJ, Grant BR, Grant PR, Hallgrimsson B, Humphreys RA, Jolly CJ, Malukiewicz J, Percival CJ, Ritzman TB, Roos C, Roseman CC, Schroeder L, Smith FH, Warren KA, Wayne RK, Zinner D. Hybridization in human evolution: Insights from other organisms. Evol Anthropol 2019; 28:189-209. [PMID: 31222847 PMCID: PMC6980311 DOI: 10.1002/evan.21787] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [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: 08/31/2018] [Revised: 01/30/2019] [Accepted: 04/30/2019] [Indexed: 12/14/2022]
Abstract
During the late Pleistocene, isolated lineages of hominins exchanged genes thus influencing genomic variation in humans in both the past and present. However, the dynamics of this genetic exchange and associated phenotypic consequences through time remain poorly understood. Gene exchange across divergent lineages can result in myriad outcomes arising from these dynamics and the environmental conditions under which it occurs. Here we draw from our collective research across various organisms, illustrating some of the ways in which gene exchange can structure genomic/phenotypic diversity within/among species. We present a range of examples relevant to questions about the evolution of hominins. These examples are not meant to be exhaustive, but rather illustrative of the diverse evolutionary causes/consequences of hybridization, highlighting potential drivers of human evolution in the context of hybridization including: influences on adaptive evolution, climate change, developmental systems, sex-differences in behavior, Haldane's rule and the large X-effect, and transgressive phenotypic variation.
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Affiliation(s)
- Rebecca R. Ackermann
- Department of Archaeology, University of Cape Town, Rondebosch, South Africa
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa
| | | | - Marcella D. Baiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - James A. Cahill
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California
| | - Liliana Cortés-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Ben J. Evans
- Biology Department, Life Sciences Building, McMaster University, Hamilton, Canada
| | - B. Rosemary Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey
| | - Peter R. Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey
| | - Benedikt Hallgrimsson
- Department of Cell Biology and Anatomy and the Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Robyn A. Humphreys
- Department of Archaeology, University of Cape Town, Rondebosch, South Africa
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa
| | - Clifford J. Jolly
- Center for the Study of Human Origins, Department of Anthropology, New York University, and NYCEP, New York, New York
| | - Joanna Malukiewicz
- Biodesign Institute, Arizona State University, Tempe, Arizona
- Federal University of Vicosa, Department of Animal Biology, Brazil
| | - Christopher J. Percival
- Department of Cell Biology and Anatomy and the Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
- Department of Anthropology, Stony Brook University, New York
| | - Terrence B. Ritzman
- Department of Archaeology, University of Cape Town, Rondebosch, South Africa
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa
- Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri
- Department of Anthropology, Washington University, St. Louis, Missouri
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center (DPZ), Leibniz Institute for Primate Research, Göttingen, Germany
| | - Charles C. Roseman
- Department of Animal Biology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Lauren Schroeder
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa
- Department of Anthropology, University of Toronto Mississauga, Mississauga, Canada
| | - Fred H. Smith
- Department of Sociology and Anthropology, Illinois State University, Normal, Illinois
| | - Kerryn A. Warren
- Department of Archaeology, University of Cape Town, Rondebosch, South Africa
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa
| | | | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center (DPZ), Leibniz Institute for Primate Research, Göttingen, Germany
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19
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Schreeg ME, Evans BJ, Allen J, Lewis MC, Luckring E, Evola M, Richard DK, Piner K, Thompson EM, Adin DB, Tokarz DA. Cardiac Leiomyosarcoma in a Cat Presenting for Bilateral Renal Neoplasia. J Comp Pathol 2019; 168:19-24. [PMID: 31103054 DOI: 10.1016/j.jcpa.2019.02.005] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/21/2019] [Accepted: 02/25/2019] [Indexed: 11/27/2022]
Abstract
A 10-year-old neutered female domestic longhair cat was presented to a tertiary care veterinary hospital for evaluation of a right renal mass that was identified incidentally on abdominal radiographs and classified further as a sarcoma based on fine needle aspiration cytology. Further diagnostic workup, including ultrasound and cytology, identified a sarcoma in the left kidney. After approximately 1 month of conservative medical management, the clinical condition deteriorated and the cat was humanely destroyed. Post-mortem examination confirmed bilateral renal masses with multifocal infarction and extensive necrosis, and further identified a large mass at the apex of the heart as well as multiple pulmonary nodules. Microscopical examination of the masses identified a population of poorly-differentiated neoplastic spindle cells, consistent with sarcoma. Immunohistochemically, the neoplastic cells expressed smooth muscle actin and muscle-specific actin, but were negative for myoglobin and factor VIII. Phosphotungstic acid-haematoxylin staining was unable to identify cross-striations in the neoplastic cells. Based on these results and the pattern of lesion distribution, the cat was diagnosed with cardiac leiomyosarcoma with pulmonary and bilateral renal metastasis.
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Affiliation(s)
- M E Schreeg
- North Carolina State University, College of Veterinary Medicine, 1060 William Moore Drive, Raleigh, USA
| | - B J Evans
- North Carolina State University, College of Veterinary Medicine, 1060 William Moore Drive, Raleigh, USA
| | - J Allen
- North Carolina State University, College of Veterinary Medicine, 1060 William Moore Drive, Raleigh, USA
| | - M C Lewis
- North Carolina State University, College of Veterinary Medicine, 1060 William Moore Drive, Raleigh, USA
| | - E Luckring
- North Carolina State University, College of Veterinary Medicine, 1060 William Moore Drive, Raleigh, USA
| | - M Evola
- North Carolina State University, College of Veterinary Medicine, 1060 William Moore Drive, Raleigh, USA
| | - D K Richard
- Cleveland School Animal Hospital, 79 Oxholm Circle, Garner, USA
| | - K Piner
- Veterinary Specialty Hospital of the Carolinas, 6405 Tryon Rd, Cary, North Carolina, USA
| | - E M Thompson
- North Carolina State University, College of Veterinary Medicine, 1060 William Moore Drive, Raleigh, USA
| | - D B Adin
- North Carolina State University, College of Veterinary Medicine, 1060 William Moore Drive, Raleigh, USA
| | - D A Tokarz
- North Carolina State University, College of Veterinary Medicine, 1060 William Moore Drive, Raleigh, USA.
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20
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Furman BLS, Dang UJ, Evans BJ, Golding GB. Divergent subgenome evolution after allopolyploidization in African clawed frogs (Xenopus). J Evol Biol 2018; 31:1945-1958. [DOI: 10.1111/jeb.13391] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/26/2018] [Accepted: 10/06/2018] [Indexed: 12/22/2022]
Affiliation(s)
| | - Utkarsh J. Dang
- Department of Health Outcomes and Administrative Sciences; School of Pharmacy and Pharmaceutical Sciences; Binghamton University; State University of New York; Binghamton NY USA
| | - Ben J. Evans
- Department of Biology; McMaster University; Hamilton ON Canada
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21
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Furman BLS, Evans BJ. Divergent Evolutionary Trajectories of Two Young, Homomorphic, and Closely Related Sex Chromosome Systems. Genome Biol Evol 2018; 10:742-755. [PMID: 29608717 PMCID: PMC5841384 DOI: 10.1093/gbe/evy045] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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: 02/20/2018] [Indexed: 02/02/2023] Open
Abstract
There exists extraordinary variation among species in the degree and nature of sex chromosome divergence. However, much of our knowledge about sex chromosomes is based on comparisons between deeply diverged species with different ancestral sex chromosomes, making it difficult to establish how fast and why sex chromosomes acquire variable levels of divergence. To address this problem, we studied sex chromosome evolution in two species of African clawed frog (Xenopus), both of whom acquired novel systems for sex determination from a recent common ancestor, and both of whom have female (ZW/ZZ) heterogamy. Derived sex chromosomes of one species, X. laevis, have a small region of suppressed recombination that surrounds the sex determining locus, and have remained this way for millions of years. In the other species, X. borealis, a younger sex chromosome system exists on a different pair of chromosomes, but the region of suppressed recombination surrounding an unidentified sex determining gene is vast, spanning almost half of the sex chromosomes. Differences between these sex chromosome systems are also apparent in the extent of nucleotide divergence between the sex chromosomes carried by females. Our analyses also indicate that in autosomes of both of these species, recombination during oogenesis occurs more frequently and in different genomic locations than during spermatogenesis. These results demonstrate that new sex chromosomes can assume radically different evolutionary trajectories, with far-reaching genomic consequences. They also suggest that in some instances the origin of new triggers for sex determination may be coupled with rapid evolution sex chromosomes, including recombination suppression of large genomic regions.
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Affiliation(s)
| | - Ben J Evans
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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22
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Evans BJ, Hall S, Tuckwood L, Grant F, Williams S, Gordon AL. 93THE IMPACT OF INTEGRATING GERIATRIC MEDICINE WITH UROLOGY TEAMS TO REALISE MULTIDISCIPLINARY WORKING ON AN ACUTE UROLOGY WARD AT ROYAL DERBY HOSPITAL. Age Ageing 2018. [DOI: 10.1093/ageing/afy126.09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- B J Evans
- Department of Medicine for the Elderly, Royal Derby Hospital
| | - S Hall
- Department of Urology, Royal Derby Hospital
| | - L Tuckwood
- Department of Urology, Royal Derby Hospital
| | - F Grant
- Department of Medicine for the Elderly, Royal Derby Hospital
| | - S Williams
- Department of Urology, Royal Derby Hospital
| | - A L Gordon
- Department of Medicine for the Elderly, Royal Derby Hospital
- Division of Medical Sciences and Graduate Entry Medicine, University of Nottingham
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23
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Evans BJ, Grant F, Shah T, Gordon AL. 129NELA LIAISON TEAM: DEVELOPING COLLABORATIVE PARTNERSHIPS WITH SURGICAL AND CRITICAL CARE TEAMS IN DERBY FOR OLDER PEOPLE UNDERGOING EMERGENCY SURGERY. Age Ageing 2018. [DOI: 10.1093/ageing/afy126.45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- B J Evans
- Department of Medicine for the Elderly, Royal Derby Hospital
| | - F Grant
- Department of Medicine for the Elderly, Royal Derby Hospital
| | - T Shah
- Department of Medicine for the Elderly, Royal Derby Hospital
| | - A L Gordon
- Department of Medicine for the Elderly, Royal Derby Hospital
- Division of Medical Sciences and Graduate Entry Medicine, University of Nottingham
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24
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Evans BJ, Tosi AJ, Zeng K, Dushoff J, Corvelo A, Melnick DJ. Correction to 'Speciation over the edge: gene flow among non-human primate species across a formidable biogeographic barrier'. R Soc Open Sci 2018; 5:180736. [PMID: 30110472 PMCID: PMC6030316 DOI: 10.1098/rsos.180736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
[This corrects the article DOI: 10.1098/rsos.170351.].
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Abstract
The genome of the red vizcacha rat (Rodentia, Octodontidae, Tympanoctomys barrerae) is the largest of all mammals, and about double the size of their close relative, the mountain vizcacha rat Octomys mimax, even though the lineages that gave rise to these species diverged from each other only about 5 Ma. The mechanism for this rapid genome expansion is controversial, and hypothesized to be a consequence of whole genome duplication or accumulation of repetitive elements. To test these alternative but nonexclusive hypotheses, we gathered and evaluated evidence from whole transcriptome and whole genome sequences of T. barrerae and O. mimax. We recovered support for genome expansion due to accumulation of a diverse assemblage of repetitive elements, which represent about one half and one fifth of the genomes of T. barrerae and O. mimax, respectively, but we found no strong signal of whole genome duplication. In both species, repetitive sequences were rare in transcribed regions as compared with the rest of the genome, and mostly had no close match to annotated repetitive sequences from other rodents. These findings raise new questions about the genomic dynamics of these repetitive elements, their connection to widespread chromosomal fissions that occurred in the T. barrerae ancestor, and their fitness effects—including during the evolution of hypersaline dietary tolerance in T. barrerae.
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Affiliation(s)
- Ben J Evans
- Biology Department, McMaster University, Hamilton, Ontario, Canada
| | - Nathan S Upham
- Biology Department, McMaster University, Hamilton, Ontario, Canada.,Field Museum of Natural History, Chicago, IL.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
| | | | - Ricardo A Ojeda
- Grupo de Investigaciones de la Biodiversidad (GIB), Instituto Argentino de Investigaciones de Zonas Áridas (IADIZA), Mendoza, Argentina
| | - Agustina A Ojeda
- Grupo de Investigaciones de la Biodiversidad (GIB), Instituto Argentino de Investigaciones de Zonas Áridas (IADIZA), Mendoza, Argentina
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26
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Frantz LAF, Rudzinski A, Nugraha AMS, Evin A, Burton J, Hulme-Beaman A, Linderholm A, Barnett R, Vega R, Irving-Pease EK, Haile J, Allen R, Leus K, Shephard J, Hillyer M, Gillemot S, van den Hurk J, Ogle S, Atofanei C, Thomas MG, Johansson F, Mustari AH, Williams J, Mohamad K, Damayanti CS, Wiryadi ID, Obbles D, Mona S, Day H, Yasin M, Meker S, McGuire JA, Evans BJ, von Rintelen T, Ho SYW, Searle JB, Kitchener AC, Macdonald AA, Shaw DJ, Hall R, Galbusera P, Larson G. Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events. Proc Biol Sci 2018; 285:rspb.2017.2566. [PMID: 29643207 PMCID: PMC5904307 DOI: 10.1098/rspb.2017.2566] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 11/30/2017] [Accepted: 03/16/2018] [Indexed: 11/13/2022] Open
Abstract
The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back to 40 Ma. Recent studies, however, suggest that much of Sulawesi's fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric datasets derived from Sulawesi's three largest mammals: the babirusa, anoa and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Ma to 2–3 Ma), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (approx. 1–2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years.
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Affiliation(s)
- Laurent A F Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK .,The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Anna Rudzinski
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | | | - Allowen Evin
- Institut des Sciences de l'Evolution, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095 Montpellier, Cedex 05, France.,Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK
| | - James Burton
- Royal (Dick) School of Veterinary Studies & The Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Edinburgh EH25 9RG, UK.,IUCN SSC Asian Wild Cattle Specialist Group and Chester Zoo, Cedar House, Caughall Road, Upton by Chester, Chester CH2 1LH, UK
| | - Ardern Hulme-Beaman
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK.,Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK
| | - Anna Linderholm
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK.,Department of Anthropology, Texas A&M University, College Station, TX 77843-4352, USA
| | - Ross Barnett
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Rodrigo Vega
- Ecology Research Group, Section of Life Sciences, School of Human and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury CT1 1QU, Kent, UK
| | - Evan K Irving-Pease
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - James Haile
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Richard Allen
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Kristin Leus
- Copenhagen Zoo, IUCN SSC Conservation Breeding Specialist Group-Europe, Roskildevej 38, Postboks 7, 2000 Frederiksberg, Denmark.,European Association of Zoos and Aquaria, PO Box 20164, 1000 HD Amsterdam, The Netherlands
| | - Jill Shephard
- Centre for Research and Conservation (CRC), Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, 2018 Antwerp, Belgium.,Environment and Conservation Sciences, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia 6150, Australia
| | - Mia Hillyer
- Centre for Research and Conservation (CRC), Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, 2018 Antwerp, Belgium.,Molecular Systematics Unit/Terrestrial Zoology, Western Australian Museum, Welshpool, Western Australia, Australia
| | - Sarah Gillemot
- Centre for Research and Conservation (CRC), Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, 2018 Antwerp, Belgium
| | - Jeroen van den Hurk
- Centre for Research and Conservation (CRC), Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, 2018 Antwerp, Belgium
| | - Sharron Ogle
- Edinburgh Medical School: BMTO, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Cristina Atofanei
- Ecology Research Group, Section of Life Sciences, School of Human and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury CT1 1QU, Kent, UK
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | | | - Abdul Haris Mustari
- Department of Forest Resources Conservation and Ecotourism, Faculty of Forestry, Bogor Agricultural University, PO Box 168, Bogor 16001, Indonesia
| | - John Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, Faculty of Sciences, University of Adelaide, Roseworthy, Southern Australia 5371, Australia
| | - Kusdiantoro Mohamad
- Faculty of Veterinary Medicine, Bogor Agricultural University, Jalan Agatis, IPB Campus, Darmaga, Bogor 16680, Indonesia
| | - Chandramaya Siska Damayanti
- Faculty of Veterinary Medicine, Bogor Agricultural University, Jalan Agatis, IPB Campus, Darmaga, Bogor 16680, Indonesia
| | | | - Dagmar Obbles
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Ch. Deberiotstraat 32, 3000 Leuven, Belgium
| | - Stephano Mona
- Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, 16 rue Buffon, CP39, 75005 Paris, France.,EPHE, PSL Research University, Paris, France
| | | | | | - Stefan Meker
- Department of Zoology, State Museum of Natural History Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Ben J Evans
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Thomas von Rintelen
- Museum für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, NY 14853, USA
| | - Andrew C Kitchener
- Department of Natural Sciences, Chambers Street, National Museums Scotland, Edinburgh EH1 1JF, UK.,Institute of Geography, School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
| | - Alastair A Macdonald
- Royal (Dick) School of Veterinary Studies & The Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Edinburgh EH25 9RG, UK
| | - Darren J Shaw
- Royal (Dick) School of Veterinary Studies & The Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Edinburgh EH25 9RG, UK
| | - Robert Hall
- SE Asia Research Group, Department of Earth Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Peter Galbusera
- Centre for Research and Conservation (CRC), Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, 2018 Antwerp, Belgium
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK
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27
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Evans BJ, Tosi AJ, Zeng K, Dushoff J, Corvelo A, Melnick DJ. Speciation over the edge: gene flow among non-human primate species across a formidable biogeographic barrier. R Soc Open Sci 2017; 4:170351. [PMID: 29134059 PMCID: PMC5666242 DOI: 10.1098/rsos.170351] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/18/2017] [Indexed: 05/30/2023]
Abstract
Many genera of terrestrial vertebrates diversified exclusively on one or the other side of Wallace's Line, which lies between Borneo and Sulawesi islands in Southeast Asia, and demarcates one of the sharpest biogeographic transition zones in the world. Macaque monkeys are unusual among vertebrate genera in that they are distributed on both sides of Wallace's Line, raising the question of whether dispersal across this barrier was an evolutionary one-off or a more protracted exchange-and if the latter, what were the genomic consequences. To explore the nature of speciation over the edge of this biogeographic divide, we used genomic data to test for evidence of gene flow between macaque species across Wallace's Line after macaques colonized Sulawesi. We recovered evidence of post-colonization gene flow, most prominently on the X chromosome. These results are consistent with the proposal that gene flow is a pervasive component of speciation-even when barriers to gene flow seem almost insurmountable.
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Affiliation(s)
- Ben J. Evans
- Biology Department, Life Sciences Building Room 328, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S4K1
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 10th floor Schermerhorn Extension, 119th Street and Amsterdam Avenue, New York, NY 10027, USA
| | - Anthony J. Tosi
- Anthropology Department, Kent State University, 238 Lowry Hall, Kent, OH 44242, USA
| | - Kai Zeng
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Jonathan Dushoff
- Biology Department, Life Sciences Building Room 328, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S4K1
| | - André Corvelo
- New York Genome Center, 101 Avenue of the Americas, New York, NY 10013, USA
| | - Don J. Melnick
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 10th floor Schermerhorn Extension, 119th Street and Amsterdam Avenue, New York, NY 10027, USA
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28
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Kelley DB, Elliott TM, Evans BJ, Hall IC, Leininger EC, Rhodes HJ, Yamaguchi A, Zornik E. Probing forebrain to hindbrain circuit functions in Xenopus. Genesis 2017; 55. [PMID: 28095617 DOI: 10.1002/dvg.22999] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 11/15/2016] [Accepted: 11/16/2016] [Indexed: 12/25/2022]
Abstract
The vertebrate hindbrain includes neural circuits that govern essential functions including breathing, blood pressure and heart rate. Hindbrain circuits also participate in generating rhythmic motor patterns for vocalization. In most tetrapods, sound production is powered by expiration and the circuitry underlying vocalization and respiration must be linked. Perception and arousal are also linked; acoustic features of social communication sounds-for example, a baby's cry-can drive autonomic responses. The close links between autonomic functions that are essential for life and vocal expression have been a major in vivo experimental challenge. Xenopus provides an opportunity to address this challenge using an ex vivo preparation: an isolated brain that generates vocal and breathing patterns. The isolated brain allows identification and manipulation of hindbrain vocal circuits as well as their activation by forebrain circuits that receive sensory input, initiate motor patterns and control arousal. Advances in imaging technologies, coupled to the production of Xenopus lines expressing genetically encoded calcium sensors, provide powerful tools for imaging neuronal patterns in the entire fictively behaving brain, a goal of the BRAIN Initiative. Comparisons of neural circuit activity across species (comparative neuromics) with distinctive vocal patterns can identify conserved features, and thereby reveal essential functional components.
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Affiliation(s)
- Darcy B Kelley
- Department of Biological Sciences, Columbia University, New York, New York, 10027
| | - Taffeta M Elliott
- Department of Psychology, New Mexico Tech, Socorro, New Mexico, 87801
| | - Ben J Evans
- Department of Biology, McMaster University, Hamilton, Ontario, Ontario, L8S4K1, Canada
| | - Ian C Hall
- Department of Biology, Benedictine University, Lisle, Illinois
| | | | - Heather J Rhodes
- Department of Biology, Denison University, Granville, Ohio, 43023
| | - Ayako Yamaguchi
- Department of Biology, University of Utah, Salt Lake City, Utah, 84112
| | - Erik Zornik
- Biology Department, Reed College, Portland, Oregon, 97201
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29
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Knytl M, Smolík O, Kubíčková S, Tlapáková T, Evans BJ, Krylov V. Chromosome divergence during evolution of the tetraploid clawed frogs, Xenopus mellotropicalis and Xenopus epitropicalis as revealed by Zoo-FISH. PLoS One 2017; 12:e0177087. [PMID: 28545147 PMCID: PMC5436656 DOI: 10.1371/journal.pone.0177087] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 08/18/2016] [Accepted: 04/21/2017] [Indexed: 02/04/2023] Open
Abstract
Whole genome duplication (WGD) generates new species and genomic redundancy. In African clawed frogs of the genus Xenopus, this phenomenon has been especially important in that (i) all but one extant species are polyploid and (ii) whole genome sequences of some species provide an evidence for genomic rearrangements prior to or after WGD. Within Xenopus in the subgenus Silurana, at least one allotetraploidization event gave rise to three extant tetraploid (2n = 4x = 40) species–Xenopus mellotropicalis, X. epitropicalis, and X. calcaratus–but it is not yet clear the degree to which these tetraploid genomes experienced rearrangements prior to or after allotetraploidization. To explore genome evolution during diversification of these species, we performed cytogenetic analyses of X. mellotropicalis, including assessment of the localization of nucleolar organizer region, chromosome banding, and determination of the p/q arm ratios for each chromosome pair. We compared these data to a previously characterized karyotype of X. epitropicalis. Morphometric, C-banding and Zoo-FISH data support a previously hypothesized common allotetraploid predecessor of these species. Zoo-FISH with whole chromosome painting (WCP) probes derived from the closely related diploid species X. tropicalis confirmed the existence of ten chromosomal quartets in X. mellotropicalis somatic cells, as expected by its ploidy level and tetraploid ancestry. The p/q arm ratio of chromosome 2a was found to be substantially different between X. mellotropicalis (0.81) and X. epitropicalis (0.67), but no substantial difference between these two species was detected in this ratio for the homoeologous chromosome pair 2b, or for other chromosome pairs. Additionally, we identified variation between these two species in the locations of a heterochromatic block on chromosome pair 2a. These results are consistent with a dynamic history of genomic rearrangements before and/or after genome duplication, a surprising finding given the otherwise relatively conserved genomic structure of most frogs.
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Affiliation(s)
- Martin Knytl
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
- * E-mail:
| | - Ondřej Smolík
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Svatava Kubíčková
- Department of Genetics and Reproduction, CEITEC -Veterinary Research Institute, Brno, Czech Republic
| | - Tereza Tlapáková
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ben J. Evans
- Department of Biology, Life Sciences Building Room 328, Mc Master University, Hamilton, Ontario, Canada
| | - Vladimír Krylov
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
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30
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Evans BJ, O'Brien D, Allstadt SD, Gregor TP, Sorenmo KU. Treatment outcomes and prognostic factors of feline splenic mast cell tumors: A multi-institutional retrospective study of 64 cases. Vet Comp Oncol 2017; 16:20-27. [PMID: 28168776 DOI: 10.1111/vco.12305] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 08/02/2016] [Revised: 11/07/2016] [Accepted: 12/20/2016] [Indexed: 11/29/2022]
Abstract
BACKGROUND Mast cell tumors (MCT) are common splenic tumors in cats, but there is limited information on treatment outcomes of cats with this disease. MATERIALS AND METHODS This retrospective study evaluated treatment outcomes in 64 cats with splenic MCT. Cats were categorized into the following treatment groups: splenectomy (A, n = 20); splenectomy with chemotherapy (B, n = 20); chemotherapy alone (C, n = 15); or supportive care (D, n = 9). RESULTS Median tumor specific survival (MTSS) was: 856, 853, 244, 365 days for groups A, B, C, and D, respectively. The MTSS was not significantly different between the 4 groups. However, comparing cats that had splenectomy (A and B) versus those that did not (C and D), the MTSS was 856 and 342 days, respectively (p=0.008). None of the prognostic factors analyzed significantly influenced survival. CONCLUSION Splenectomy (+/- chemotherapy) significantly prolongs survival in cats with mast cell tumors. The role of chemotherapy remains unknown.
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Affiliation(s)
- B J Evans
- College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - D O'Brien
- Vista Veterinary Specialists, Sacramento, California
| | - S D Allstadt
- Veterinary Specialists of North Texas, Dallas, Texas
| | - T P Gregor
- Antech Veterinary Services, Irvine, California
| | - K U Sorenmo
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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Russell JNH, Marsh AK, Willer DO, Ambagala APN, Dzamba M, Chan JK, Pilon R, Fournier J, Brudno M, Antony JM, Sandstrom P, Evans BJ, MacDonald KS. A novel strain of cynomolgus macaque cytomegalovirus: implications for host-virus co-evolution. BMC Genomics 2016; 17:277. [PMID: 27044312 PMCID: PMC4820910 DOI: 10.1186/s12864-016-2588-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 10/09/2015] [Accepted: 03/14/2016] [Indexed: 12/20/2022] Open
Abstract
Background Cytomegaloviruses belong to a large, ancient, genus of DNA viruses comprised of a wide array of species-specific strains that occur in diverse array of hosts. Methods In this study we sequenced the ~217 Kb genome of a cytomegalovirus isolated from a Mauritius cynomolgus macaque, CyCMV Mauritius, and compared it to previously sequenced cytomegaloviruses from a cynomolgus macaque of Filipino origin (CyCMV Ottawa) and two from Indian rhesus macaques (RhCMV 180.92 and RhCMV 68–1). Results Though more closely related to CyCMV Ottawa, CyCMV Mauritius is less genetically distant from both RhCMV strains than is CyCMV Ottawa. Several individual genes, including homologues of CMV genes RL11B, UL123, UL83b, UL84 and a homologue of mammalian COX-2, show a closer relationship between homologues of CyCMV Mauritius and the RhCMVs than between homologues of CyCMV Mauritius and CyCMV Ottawa. A broader phylogenetic analysis of 12 CMV strains from eight species recovers evolutionary relationships among viral strains that mirror those amongst the host species, further demonstrating co-evolution of host and virus. Conclusions Phylogenetic analyses of rhesus and cynomolgus macaque CMV genome sequences demonstrate co-speciation of the virus and host. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2588-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Angie K Marsh
- Department of Immunology, University of Toronto, Toronto, M5S 1A8, ON, Canada
| | - David O Willer
- Department of Medicine, University of Toronto, Toronto, M5S 1A8, ON, Canada.,Department of Microbiology, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada
| | - Aruna P N Ambagala
- Department of Medicine, University of Toronto, Toronto, M5S 1A8, ON, Canada.,Department of Microbiology, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada.,Present Address: Canadian Science Centre for Human and Animal Health, National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, R3E 3M4, MB, Canada
| | - Misko Dzamba
- Department of Computer Science, University of Toronto, Toronto, M5S 1A8, ON, Canada
| | - Jacqueline K Chan
- Department of Medicine, University of Toronto, Toronto, M5S 1A8, ON, Canada.,Department of Microbiology, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada
| | - Richard Pilon
- National HIV & Retrovirology Laboratories, Public Health Agency of Canada, Ottawa, K1A 0K9, ON, Canada
| | - Jocelyn Fournier
- Scientific Services Division, Health Products & Food Branch, Health Canada, Ottawa, K1A 0L2, ON, Canada
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, M5S 1A8, ON, Canada
| | - Joseph M Antony
- Department of Medicine, University of Toronto, Toronto, M5S 1A8, ON, Canada.,Department of Microbiology, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada
| | - Paul Sandstrom
- National HIV & Retrovirology Laboratories, Public Health Agency of Canada, Ottawa, K1A 0K9, ON, Canada
| | - Ben J Evans
- Biology Department, McMaster University, Life Sciences Building, 1280 Main Street West, Hamilton, L8S 4K1, ON, Canada
| | - Kelly S MacDonald
- Department of Immunology, University of Toronto, Toronto, M5S 1A8, ON, Canada. .,Department of Medicine, University of Toronto, Toronto, M5S 1A8, ON, Canada. .,Department of Microbiology, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada. .,Section of Infectious Diseases, Department of Internal Medicine, University of Manitoba, 745 Bannatyne Ave, Winnipeg, R3E 0J9, MB, Canada. .,Present Address: University of Manitoba, Basic Medical Sciences Building, Room 501, 745 Bannatyne Ave., Winnipeg, R3E 0J9, MB, Canada.
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Ghenu AH, Bolker BM, Melnick DJ, Evans BJ. Multicopy gene family evolution on primate Y chromosomes. BMC Genomics 2016; 17:157. [PMID: 26925773 PMCID: PMC4772468 DOI: 10.1186/s12864-015-2187-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 11/02/2015] [Indexed: 12/12/2022] Open
Abstract
Background The primate Y chromosome is distinguished by a lack of inter-chromosomal recombination along most of its length, extensive gene loss, and a prevalence of repetitive elements. A group of genes on the male-specific portion of the Y chromosome known as the “ampliconic genes” are present in multiple copies that are sometimes part of palindromes, and that undergo a form of intra-chromosomal recombination called gene conversion, wherein the nucleotides of one copy are homogenized by those of another. With the aim of further understanding gene family evolution of these genes, we collected nucleotide sequence and gene copy number information for several species of papionin monkey. We then tested for evidence of gene conversion, and developed a novel statistical framework to evaluate alternative models of gene family evolution using our data combined with other information from a human, a chimpanzee, and a rhesus macaque. Results Our results (i) recovered evidence for several novel examples of gene conversion in papionin monkeys and indicate that (ii) ampliconic gene families evolve faster than autosomal gene families and than single-copy genes on the Y chromosome and that (iii) Y-linked singleton and autosomal gene families evolved faster in humans and chimps than they do in the other Old World Monkey lineages we studied. Conclusions Rapid evolution of ampliconic genes cannot be attributed solely to residence on the Y chromosome, nor to variation between primate lineages in the rate of gene family evolution. Instead other factors, such as natural selection and gene conversion, appear to play a role in driving temporal and genomic evolutionary heterogeneity in primate gene families. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2187-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana-Hermina Ghenu
- Biology Department, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada.
| | - Benjamin M Bolker
- Biology Department, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada.,Department of Mathematics & Statistics, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Don J Melnick
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 10th Floor Schermerhorn Extension, New York, 10027, USA
| | - Ben J Evans
- Biology Department, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada.
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Evans BJ, Carter TF, Greenbaum E, Gvoždík V, Kelley DB, McLaughlin PJ, Pauwels OSG, Portik DM, Stanley EL, Tinsley RC, Tobias ML, Blackburn DC. Genetics, Morphology, Advertisement Calls, and Historical Records Distinguish Six New Polyploid Species of African Clawed Frog (Xenopus, Pipidae) from West and Central Africa. PLoS One 2015; 10:e0142823. [PMID: 26672747 PMCID: PMC4682732 DOI: 10.1371/journal.pone.0142823] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 10/27/2015] [Indexed: 01/08/2023] Open
Abstract
African clawed frogs, genus Xenopus, are extraordinary among vertebrates in the diversity of their polyploid species and the high number of independent polyploidization events that occurred during their diversification. Here we update current understanding of the evolutionary history of this group and describe six new species from west and central sub-Saharan Africa, including four tetraploids and two dodecaploids. We provide information on molecular variation, morphology, karyotypes, vocalizations, and estimated geographic ranges, which support the distinctiveness of these new species. We resurrect Xenopus calcaratus from synonymy of Xenopus tropicalis and refer populations from Bioko Island and coastal Cameroon (near Mt. Cameroon) to this species. To facilitate comparisons to the new species, we also provide comments on the type specimens, morphology, and distributions of X. epitropicalis, X. tropicalis, and X. fraseri. This includes significantly restricted application of the names X. fraseri and X. epitropicalis, the first of which we argue is known definitively only from type specimens and possibly one other specimen. Inferring the evolutionary histories of these new species allows refinement of species groups within Xenopus and leads to our recognition of two subgenera (Xenopus and Silurana) and three species groups within the subgenus Xenopus (amieti, laevis, and muelleri species groups).
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Affiliation(s)
- Ben J. Evans
- Department of Biology, Life Sciences Building Room 328 McMaster University, Hamilton, Ontario, Canada
- * E-mail:
| | - Timothy F. Carter
- Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, United States of America
| | - Václav Gvoždík
- Institute of Vertebrate Biology, Czech Academy of Sciences, Kvetna 8, Brno, Czech Republic
- Department of Zoology, National Museum, Prague, Czech Republic
| | - Darcy B. Kelley
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Patrick J. McLaughlin
- Department of Biology, Papadakis Integrated Sciences Building, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Olivier S. G. Pauwels
- Département des Vertébrés Récents, Instítut Royal des Sciences Naturelles de Belgique, Brussels, Belgium
| | - Daniel M. Portik
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
| | - Edward L. Stanley
- California Academy of Sciences, San Francisco, California, United States of America
| | - Richard C. Tinsley
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | | | - David C. Blackburn
- California Academy of Sciences, San Francisco, California, United States of America
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Evans BJ, Schmid M. Preface. Cytogenet Genome Res 2015. [PMID: 26202694 DOI: 10.1159/000437176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Abstract
This review summarizes the current status of the known extant genuine polyploid anuran and urodelan species, as well as spontaneously originated and/or experimentally produced amphibian polyploids. The mechanisms by which polyploids can originate, the meiotic pairing configurations, the diploidization processes operating in polyploid genomes, the phenomenon of hybridogenesis, and the relationship between polyploidization and sex chromosome evolution are discussed. The polyploid systems in some important amphibian taxa are described in more detail.
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Evans BJ, Kwon T. Molecular Polymorphism and Divergence of Duplicated Genes in Tetraploid African Clawed Frogs (Xenopus). Cytogenet Genome Res 2015; 145:243-52. [PMID: 26066830 DOI: 10.1159/000431108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Genome duplication creates redundancy in proteins and their interaction networks, and subsequent smaller-scale gene duplication can further amplify genetic redundancy. Mutations then lead to the loss, maintenance or functional divergence of duplicated genes. Genome duplication occurred many times in African clawed frogs (genus Xenopus), and almost all extant species in this group evolved from a polyploid ancestor. To better understand the nature of selective constraints in a polyploid genome, we examined molecular polymorphism and divergence of duplicates and single-copy genes in 2 tetraploid African clawed frog species, Xenopus laevis and X. victorianus. We found that molecular polymorphism in the coding regions of putative duplicated genes was higher than in singletons, but not significantly so. Our findings also suggest that transcriptome evolution in polyploids is influenced by variation in the genome-wide mutation rate, and do not reject the hypothesis that gene dosage balance is also important.
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Affiliation(s)
- Ben J Evans
- Department of Biology, McMaster University, Hamilton, Ont., Canada
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Furman BLS, Bewick AJ, Harrison TL, Greenbaum E, Gvoždík V, Kusamba C, Evans BJ. Pan-African phylogeography of a model organism, the African clawed frog 'Xenopus laevis'. Mol Ecol 2015; 24:909-25. [PMID: 25583226 DOI: 10.1111/mec.13076] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [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: 06/20/2014] [Revised: 01/06/2015] [Accepted: 01/08/2015] [Indexed: 11/30/2022]
Abstract
The African clawed frog Xenopus laevis has a large native distribution over much of sub-Saharan Africa and is a model organism for research, a proposed disease vector, and an invasive species. Despite its prominent role in research and abundance in nature, surprisingly little is known about the phylogeography and evolutionary history of this group. Here, we report an analysis of molecular variation of this clade based on 17 loci (one mitochondrial, 16 nuclear) in up to 159 individuals sampled throughout its native distribution. Phylogenetic relationships among mitochondrial DNA haplotypes were incongruent with those among alleles of the putatively female-specific sex-determining gene DM-W, in contrast to the expectation of strict matrilineal inheritance of both loci. Population structure and evolutionarily diverged lineages were evidenced by analyses of molecular variation in these data. These results further contextualize the chronology, and evolutionary relationships within this group, support the recognition of X. laevis sensu stricto, X. petersii, X. victorianus and herein revalidated X. poweri as separate species. We also propose that portions of the currently recognized distributions of X. laevis (north of the Congo Basin) and X. petersii (south of the Congo Basin) be reassigned to X. poweri.
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Affiliation(s)
- Benjamin L S Furman
- Biology Department, McMaster University, Life Sciences Building, 1280 Main Street West, Hamilton, Ontario, Canada, L8S 4K1
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Iskandar DT, Evans BJ, McGuire JA. A novel reproductive mode in frogs: a new species of fanged frog with internal fertilization and birth of tadpoles. PLoS One 2014; 9:e115884. [PMID: 25551466 PMCID: PMC4281041 DOI: 10.1371/journal.pone.0115884] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 11/23/2014] [Indexed: 11/18/2022] Open
Abstract
We describe a new species of fanged frog (Limnonectes larvaepartus) that is unique among anurans in having both internal fertilization and birth of tadpoles. The new species is endemic to Sulawesi Island, Indonesia. This is the fourth valid species of Limnonectes described from Sulawesi despite that the radiation includes at least 15 species and possibly many more. Fewer than a dozen of the 6455 species of frogs in the world are known to have internal fertilization, and of these, all but the new species either deposit fertilized eggs or give birth to froglets.
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Affiliation(s)
- Djoko T. Iskandar
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
| | - Ben J. Evans
- Center for Environmental Genomics, Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Jimmy A. McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California, United States of America
- * E-mail:
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Evans BJ, Zeng K, Esselstyn JA, Charlesworth B, Melnick DJ. Reduced representation genome sequencing suggests low diversity on the sex chromosomes of tonkean macaque monkeys. Mol Biol Evol 2014; 31:2425-40. [PMID: 24987106 DOI: 10.1093/molbev/msu197] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In species with separate sexes, social systems can differ in the relative variances of male versus female reproductive success. Papionin monkeys (macaques, mangabeys, mandrills, drills, baboons, and geladas) exhibit hallmarks of a high variance in male reproductive success, including a female-biased adult sex ratio and prominent sexual dimorphism. To explore the potential genomic consequences of such sex differences, we used a reduced representation genome sequencing approach to quantifying polymorphism at sites on autosomes and sex chromosomes of the tonkean macaque (Macaca tonkeana), a species endemic to the Indonesian island of Sulawesi. The ratio of nucleotide diversity of the X chromosome to that of the autosomes was less than the value (0.75) expected with a 1:1 sex ratio and no sex differences in the variance in reproductive success. However, the significance of this difference was dependent on which outgroup was used to standardize diversity levels. Using a new model that includes the effects of varying population size, sex differences in mutation rate between the autosomes and X chromosome, and GC-biased gene conversion (gBGC) or selection on GC content, we found that the maximum-likelihood estimate of the ratio of effective population size of the X chromosome to that of the autosomes was 0.68, which did not differ significantly from 0.75. We also found evidence for 1) a higher level of purifying selection on genic than nongenic regions, 2) gBGC or natural selection favoring increased GC content, 3) a dynamic demography characterized by population growth and contraction, 4) a higher mutation rate in males than females, and 5) a very low polymorphism level on the Y chromosome. These findings shed light on the population genomic consequences of sex differences in the variance in reproductive success, which appear to be modest in the tonkean macaque; they also suggest the occurrence of hitchhiking on the Y chromosome.
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Affiliation(s)
- Ben J Evans
- Biology Department, McMaster University, Hamilton, ON, Canada
| | - Kai Zeng
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Sheffield, United Kingdom
| | - Jacob A Esselstyn
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University
| | - Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Don J Melnick
- Department of Ecology, Evolution, and Environmental Biology, Columbia University
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Bewick AJ, Chain FJJ, Zimmerman LB, Sesay A, Gilchrist MJ, Owens NDL, Seifertova E, Krylov V, Macha J, Tlapakova T, Kubickova S, Cernohorska H, Zarsky V, Evans BJ. A large pseudoautosomal region on the sex chromosomes of the frog Silurana tropicalis. Genome Biol Evol 2013; 5:1087-98. [PMID: 23666865 PMCID: PMC3698919 DOI: 10.1093/gbe/evt073] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [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] [Indexed: 12/26/2022] Open
Abstract
Sex chromosome divergence has been documented across phylogenetically diverse species, with amphibians typically having cytologically nondiverged (“homomorphic”) sex chromosomes. With an aim of further characterizing sex chromosome divergence of an amphibian, we used “RAD-tags” and Sanger sequencing to examine sex specificity and heterozygosity in the Western clawed frog Silurana tropicalis (also known as Xenopus tropicalis). Our findings based on approximately 20 million genotype calls and approximately 200 polymerase chain reaction-amplified regions across multiple male and female genomes failed to identify a substantially sized genomic region with genotypic hallmarks of sex chromosome divergence, including in regions known to be tightly linked to the sex-determining region. We also found that expression and molecular evolution of genes linked to the sex-determining region did not differ substantially from genes in other parts of the genome. This suggests that the pseudoautosomal region, where recombination occurs, comprises a large portion of the sex chromosomes of S. tropicalis. These results may in part explain why African clawed frogs have such a high incidence of polyploidization, shed light on why amphibians have a high rate of sex chromosome turnover, and raise questions about why homomorphic sex chromosomes are so prevalent in amphibians.
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Affiliation(s)
- Adam J Bewick
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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Esselstyn JA, Maharadatunkamsi, Achmadi AS, Siler CD, Evans BJ. Carving out turf in a biodiversity hotspot: multiple, previously unrecognized shrew species co-occur on Java Island, Indonesia. Mol Ecol 2013; 22:4972-87. [PMID: 24010862 DOI: 10.1111/mec.12450] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [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: 04/15/2013] [Revised: 07/06/2013] [Accepted: 07/08/2013] [Indexed: 11/28/2022]
Abstract
In theory, competition among species in a shared habitat results in niche separation. In the case of small recondite mammals such as shrews, little is known about their autecologies, leaving open questions regarding the degree to which closely related species co-occur and how or whether ecological niches are partitioned. The extent to which species are able to coexist may depend on the degree to which they exploit different features of their habitat, which may in turn influence our ability to recognize them as species. We explored these issues in a biodiversity hotspot, by surveying shrew (genus Crocidura) diversity on the Indonesian island of Java. We sequenced portions of nine unlinked genes in 100-117 specimens of Javan shrews and incorporated homologous data from most known Crocidura species from other parts of island South-East Asia. Current taxonomy recognizes four Crocidura species on Java, including two endemics. However, our phylogenetic, population genetic and species delimitation analyses identify five species on the island, and all are endemic to Java. While the individual ranges of these species may not overlap in their entirety, we found up to four species living syntopically and all five species co-occurring on one mountain. Differences in species' body size, use of above ground-level habitats by one species and habitat partitioning along ecological gradients may have facilitated species diversification and coexistence.
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Affiliation(s)
- Jacob A Esselstyn
- Biology Department, McMaster University, Hamilton, Ontario, Canada L8S 4K1
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Mechkarska M, Prajeep M, Leprince J, Vaudry H, Meetani MA, Evans BJ, Conlon JM. A comparison of host-defense peptides in skin secretions of female Xenopus laevis × Xenopus borealis and X. borealis × X. laevis F1 hybrids. Peptides 2013; 45:1-8. [PMID: 23624316 DOI: 10.1016/j.peptides.2013.04.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/15/2013] [Accepted: 04/17/2013] [Indexed: 12/30/2022]
Abstract
Peptidomic analysis was used to compare the diversity of host-defense peptides in norepinephrine-stimulated skin secretions from laboratory-generated female F1 hybrids of Xenopus laevis and Xenopus borealis (Pipidae). Skin secretions of hybrids with maternal X. laevis (XLB) contained 12 antimicrobial peptides (AMPs), comprising 8 from X. laevis and 4 from X. borealis. Magainin-B1, XPF-B1, PGLa-B1 CPF-B2, CPF-B3 and CPF-B4 from X. borealis and XPF-1, XPF-2, and CPF-6 from X. laevis were not detected and CPF-1 and CPF-7 were present in low concentration. The secretions contained caerulein and caerulein-B1 derived from both parents but lacked X. laevis xenopsin and X. borealis caerulein-B2. Skin secretions of hybrids with maternal X. borealis (XBL) contained 14 AMPs comprising 6 from X. borealis and 8 from X. laevis. Magainin-B1, XPF-B1, PGLa-B1, CPF-B2, XPF-1, CPF-5, and CPF-7 were absent and CPF-B3, CPF-B4, CPF-1 and CPF-6 were present only in low concentration. Xenopsin and caerulein were identified in the secretions but caerulein-B2 was absent and caerulein-B1 was present in low concentration. No peptides were identified in secretions of either XLB or XBL hybrids that were not present in the parental species. The data indicate that hybridization between X. laevis and X. borealis results in increased diversity of host-defense peptides in skin secretions but point to extensive AMP gene silencing compared with previously studied female X. laevis×X. muelleri F1 hybrids and no novel peptide expression.
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Affiliation(s)
- Milena Mechkarska
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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Shen JJ, Dushoff J, Bewick AJ, Chain FJ, Evans BJ. Genomic dynamics of transposable elements in the western clawed frog (Silurana tropicalis). Genome Biol Evol 2013; 5:998-1009. [PMID: 23645600 PMCID: PMC3673623 DOI: 10.1093/gbe/evt065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [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] [Accepted: 04/18/2013] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs) are repetitive DNA sequences that can make new copies of themselves that are inserted elsewhere in a host genome. The abundance and distributions of TEs vary considerably among phylogenetically diverse hosts. With the aim of exploring the basis of this variation, we evaluated correlations between several genomic variables and the presence of TEs and non-TE repeats in the complete genome sequence of the Western clawed frog (Silurana tropicalis). This analysis reveals patterns of TE insertion consistent with gene disruption but not with the insertional preference model. Analysis of non-TE repeats recovered unique features of their genome-wide distribution when compared with TE repeats, including no strong correlation with exons and a particularly strong negative correlation with GC content. We also collected polymorphism data from 25 TE insertion sites in 19 wild-caught S. tropicalis individuals. DNA transposon insertions were fixed at eight of nine sites and at a high frequency at one of nine, whereas insertions of long terminal repeat (LTR) and non-LTR retrotransposons were fixed at only 4 of 16 sites and at low frequency at 12 of 16. A maximum likelihood model failed to attribute these differences in insertion frequencies to variation in selection pressure on different classes of TE, opening the possibility that other phenomena such as variation in rates of replication or duration of residence in the genome could play a role. Taken together, these results identify factors that sculpt heterogeneity in TE distribution in S. tropicalis and illustrate that genomic dynamics differ markedly among TE classes and between TE and non-TE repeats.
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Affiliation(s)
- Jiangshan J. Shen
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
- Present address: Department of Pathology, The University of Hong Kong, Hong Kong, China
| | - Jonathan Dushoff
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Adam J. Bewick
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Frédéric J.J. Chain
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Ben J. Evans
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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Esselstyn JA, Evans BJ, Sedlock JL, Anwarali Khan FA, Heaney LR. Single-locus species delimitation: a test of the mixed Yule-coalescent model, with an empirical application to Philippine round-leaf bats. Proc Biol Sci 2012; 279:3678-86. [PMID: 22764163 DOI: 10.1098/rspb.2012.0705] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Prospects for a comprehensive inventory of global biodiversity would be greatly improved by automating methods of species delimitation. The general mixed Yule-coalescent (GMYC) was recently proposed as a potential means of increasing the rate of biodiversity exploration. We tested this method with simulated data and applied it to a group of poorly known bats (Hipposideros) from the Philippines. We then used echolocation call characteristics to evaluate the plausibility of species boundaries suggested by GMYC. In our simulations, GMYC performed relatively well (errors in estimated species diversity less than 25%) when the product of the haploid effective population size (N(e)) and speciation rate (SR; per lineage per million years) was less than or equal to 10(5), while interspecific variation in N(e) was twofold or less. However, at higher but also biologically relevant values of N(e) × SR and when N(e) varied tenfold among species, performance was very poor. GMYC analyses of mitochondrial DNA sequences from Philippine Hipposideros suggest actual diversity may be approximately twice the current estimate, and available echolocation call data are mostly consistent with GMYC delimitations. In conclusion, we consider the GMYC model useful under some conditions, but additional information on N(e), SR and/or corroboration from independent character data are needed to allow meaningful interpretation of results.
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Affiliation(s)
- Jacob A Esselstyn
- Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA.
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Affiliation(s)
- Adam J. Bewick
- Department of Biology, Life Sciences Building Room 328, McMaster University, 1280 Main Street West Hamilton, ON L8S 4K1, Canada
| | - Frédéric J. J. Chain
- Department of Biology, Life Sciences Building Room 328, McMaster University, 1280 Main Street West Hamilton, ON L8S 4K1, Canada
- Present address: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
| | - Joseph Heled
- Department of Computer Science, University of Auckland, Auckland 1142, New Zealand
| | - Ben J. Evans
- Department of Biology, Life Sciences Building Room 328, McMaster University, 1280 Main Street West Hamilton, ON L8S 4K1, Canada
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Abstract
Background Gene duplication is an important biological phenomenon associated with genomic redundancy, degeneration, specialization, innovation, and speciation. After duplication, both copies continue functioning when natural selection favors duplicated protein function or expression, or when mutations make them functionally distinct before one copy is silenced. Results Here we quantify the degree to which genetic parameters related to gene expression, molecular evolution, and gene structure in a diploid frog - Silurana tropicalis - influence the odds of functional persistence of orthologous duplicate genes in a closely related tetraploid species - Xenopus laevis. Using public databases and 454 pyrosequencing, we obtained genetic and expression data from S. tropicalis orthologs of 3,387 X. laevis paralogs and 4,746 X. laevis singletons - the most comprehensive dataset for African clawed frogs yet analyzed. Using logistic regression, we demonstrate that the most important predictors of the odds of duplicate gene persistence in the tetraploid species are the total gene expression level and evenness of expression across tissues and development in the diploid species. Slow protein evolution and information density (fewer exons, shorter introns) in the diploid are also positively correlated with duplicate gene persistence in the tetraploid. Conclusions Our findings suggest that a combination of factors contribute to duplicate gene persistence following whole genome duplication, but that the total expression level and evenness of expression across tissues and through development before duplication are most important. We speculate that these parameters are useful predictors of duplicate gene longevity after whole genome duplication in other taxa.
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Affiliation(s)
- Frédéric J J Chain
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada.
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Setiadi MI, McGuire JA, Brown RM, Zubairi M, Iskandar DT, Andayani N, Supriatna J, Evans BJ. Adaptive radiation and ecological opportunity in Sulawesi and Philippine fanged frog (Limnonectes) communities. Am Nat 2011; 178:221-40. [PMID: 21750386 DOI: 10.1086/660830] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Because island communities are derived from mainland communities, they are often less diverse by comparison. However, reduced complexity of island communities can also present ecological opportunities. For example, amphibian diversity on Sulawesi Island is lower than it is in the Philippines, but Sulawesi supports a surprising diversity of Sulawesi fanged frogs (Limnonectes). Here we examine molecular, morphological, and geographical variation of fanged frogs from these two regions. Using genealogical concordance, morphology, and a Bayesian approach to species delimitation, we identified 13 species on Sulawesi, only four of which have been previously described. After evolutionary history is accounted for, a model with multiple body size optima in sympatric species is favored over a "random-walk" model of body size evolution. Additionally, morphological variation is higher among sympatric than nonsympatric species on Sulawesi but not in the Philippines. These findings suggest that adaptive radiation of fanged frogs on Sulawesi was driven by natural selection to infiltrate ecological niches occupied by other frog lineages in the Philippines. This supports a role of ecological opportunity in community assembly: diversification in mature communities, such as the Philippines, is limited by a dearth of unoccupied ecological niches. On Sulawesi, evolutionary novelties originated in a predictable and replicated fashion in response to opportunities presented by a depauperate ancestral community.
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Affiliation(s)
- Mohammad I Setiadi
- Center for Environmental Genomics, Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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Abstract
Indirect tests have detected recombination in mitochondrial DNA (mtDNA) from many animal lineages, including mammals. However, it is possible that features of the molecular evolutionary process without recombination could be incorrectly inferred by indirect tests as being due to recombination. We have identified one such example, which we call "patchy-tachy" (PT), where different partitions of sequences evolve at different rates, that leads to an excess of false positives for recombination inferred by indirect tests. To explore this phenomena, we characterized the false positive rates of six widely used indirect tests for recombination using simulations of general models for mtDNA evolution with PT but without recombination. All tests produced 30-99% false positives for recombination, although the conditions that produced the maximal level of false positives differed between the tests. To evaluate the degree to which conditions that exacerbate false positives are found in published sequence data, we turned to 20 animal mtDNA data sets in which recombination is suggested by indirect tests. Using a model where different regions of the sequences were free to evolve at different rates in different lineages, we demonstrated that PT is prevalent in many data sets in which recombination was previously inferred using indirect tests. Taken together, our results argue that PT without recombination is a viable alternative explanation for detection of widespread recombination in animal mtDNA using indirect tests.
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Affiliation(s)
- Stephanie Sun
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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Abstract
For most frogs, advertisement calls are essential for reproductive success, conveying information on species identity, male quality, sexual state and location. While the evolutionary divergence of call characters has been examined in a number of species, the relative impacts of genetic drift or natural and sexual selection remain unclear. Insights into the evolutionary trajectory of vocal signals can be gained by examining how advertisement calls vary in a phylogenetic context. Evolution by genetic drift would be supported if more closely related species express more similar songs. Conversely, a poor correlation between evolutionary history and song expression would suggest evolution shaped by natural or sexual selection. Here, we measure seven song characters in 20 described and two undescribed species of African clawed frogs (genera Xenopus and Silurana) and four populations of X. laevis. We identify three call types - click, burst and trill - that can be distinguished by click number, call rate and intensity modulation. A fourth type is biphasic, consisting of two of the above. Call types vary in complexity from the simplest, a click, to the most complex, a biphasic call. Maximum parsimony analysis of variation in call type suggests that the ancestral type was of intermediate complexity. Each call type evolved independently more than once and call type is typically not shared by closely related species. These results indicate that call type is homoplasious and has low phylogenetic signal. We conclude that the evolution of call type is not due to genetic drift, but is under selective pressure.
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Affiliation(s)
- Martha L. Tobias
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Ben J. Evans
- Department of Ecology, Evolutionary and Environmental Biology, Columbia University, New York, NY, USA
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Darcy B. Kelley
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Ecology, Evolutionary and Environmental Biology, Columbia University, New York, NY, USA
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Evans BJ, Greenbaum E, Kusamba C, Carter TF, Tobias ML, Mendel SA, Kelley DB. Description of a new octoploid frog species (Anura: Pipidae: Xenopus) from the Democratic Republic of the Congo, with a discussion of the biogeography of African clawed frogs in the Albertine Rift. J Zool (1987) 2010; 283:276-290. [PMID: 21546992 DOI: 10.1111/j.1469-7998.2010.00769.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We describe a new octoploid species of African clawed frog (Xenopus) from the Lendu Plateau in the northern Albertine Rift of eastern Democratic Republic of the Congo. This species is the sister taxon of Xenopus vestitus (another octoploid), but is distinguished by a unique morphology, vocalization and molecular divergence in mitochondrial and autosomal DNA. Using a comprehensive genetic sample, we provide new information on the species ranges and intra-specific diversity of African clawed frogs from the Albertine Rift, including the details of a small range extension for the critically endangered Xenopus itombwensis and previously uncharacterized variation in Xenopus laevis. We also detail a new method for generating cytogenetic preparations in the field that can be stored at room temperature for up to 3 weeks. While extending our understanding of the extant diversity in the Albertine Rift, this new species highlights components of species diversity in ancestral African clawed frogs that are not represented by known extant descendants.
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Affiliation(s)
- B J Evans
- Department of Biology, Center for Environmental Genomics, McMaster University, Hamilton, ON, Canada
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