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Xu L, Wa Sin SY, Grayson P, Edwards SV, Sackton TB. Evolutionary Dynamics of Sex Chromosomes of Paleognathous Birds. Genome Biol Evol 2020; 11:2376-2390. [PMID: 31329234 PMCID: PMC6735826 DOI: 10.1093/gbe/evz154] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2019] [Indexed: 12/20/2022] Open
Abstract
Standard models of sex chromosome evolution propose that recombination suppression leads to the degeneration of the heterogametic chromosome, as is seen for the Y chromosome in mammals and the W chromosome in most birds. Unlike other birds, paleognaths (ratites and tinamous) possess large nondegenerate regions on their sex chromosomes (PARs or pseudoautosomal regions). It remains unclear why these large PARs are retained over >100 Myr, and how this retention impacts the evolution of sex chromosomes within this system. To address this puzzle, we analyzed Z chromosome evolution and gene expression across 12 paleognaths, several of whose genomes have recently been sequenced. We confirm at the genomic level that most paleognaths retain large PARs. As in other birds, we find that all paleognaths have incomplete dosage compensation on the regions of the Z chromosome homologous to degenerated portions of the W (differentiated regions), but we find no evidence for enrichments of male-biased genes in PARs. We find limited evidence for increased evolutionary rates (faster-Z) either across the chromosome or in differentiated regions for most paleognaths with large PARs, but do recover signals of faster-Z evolution in tinamou species with mostly degenerated W chromosomes, similar to the pattern seen in neognaths. Unexpectedly, in some species, PAR-linked genes evolve faster on average than genes on autosomes, suggested by diverse genomic features to be due to reduced efficacy of selection in paleognath PARs. Our analysis shows that paleognath Z chromosomes are atypical at the genomic level, but the evolutionary forces maintaining largely homomorphic sex chromosomes in these species remain elusive.
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Affiliation(s)
- Luohao Xu
- Department of Molecular Evolution and Development, University of Vienna, Austria
| | - Simon Yung Wa Sin
- Department of Organismic and Evolutionary Biology, Harvard University
- Museum of Comparative Zoology, Harvard University
- School of Biological Sciences, The University of Hong Kong, Hong Kong
| | - Phil Grayson
- Department of Organismic and Evolutionary Biology, Harvard University
- Museum of Comparative Zoology, Harvard University
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University
- Museum of Comparative Zoology, Harvard University
| | - Timothy B Sackton
- Informatics Group, Division of Science, Harvard University
- Corresponding author: E-mail:
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52
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Nielsen SV, Pinto BJ, Guzmán-Méndez IA, Gamble T. First Report of Sex Chromosomes in Night Lizards (Scincoidea: Xantusiidae). J Hered 2020; 111:307-317. [DOI: 10.1093/jhered/esaa007] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 02/18/2020] [Indexed: 12/31/2022] Open
Abstract
Abstract
Squamate reptiles (lizards, snakes, and amphibians) are an outstanding group for studying sex chromosome evolution—they are old, speciose, geographically widespread, and exhibit myriad sex-determining modes. Yet, the vast majority of squamate species lack heteromorphic sex chromosomes. Cataloging the sex chromosome systems of species lacking easily identifiable, heteromorphic sex chromosomes, therefore, is essential before we are to fully understand the evolution of vertebrate sex chromosomes. Here, we use restriction site-associated DNA sequencing (RADseq) to classify the sex chromosome system of the granite night lizard, Xantusia henshawi. RADseq is an effective alternative to traditional cytogenetic methods for determining a species’ sex chromosome system (i.e., XX/XY or ZZ/ZW), particularly in taxa with non-differentiated sex chromosomes. Although many xantusiid lineages have been karyotyped, none possess heteromorphic sex chromosomes. We identified a ZZ/ZW sex chromosome system in X. henshawi—the first such data for this family. Furthermore, we report that the X. henshawi sex chromosome contains fragments of genes found on Gallus gallus chromosomes 7, 12, and 18 (which are homologous to Anolis carolinensis chromosome 2), the first vertebrate sex chromosomes to utilize this linkage group.
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Affiliation(s)
- Stuart V Nielsen
- Florida Museum of Natural History, University of Florida, Gainesville, FL
- Department of Biological Sciences, Marquette University, Milwaukee, WI
| | - Brendan J Pinto
- Department of Biological Sciences, Marquette University, Milwaukee, WI
- Milwaukee Public Museum, Milwaukee, WI
| | | | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI
- Bell Museum of Natural History, University of Minnesota, Saint Paul, MN
- Milwaukee Public Museum, Milwaukee, WI
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53
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Sidhom M, Said K, Chatti N, Guarino FM, Odierna G, Petraccioli A, Picariello O, Mezzasalma M. Karyological characterization of the common chameleon (Chamaeleo chamaeleon) provides insights on the evolution and diversification of sex chromosomes in Chamaeleonidae. ZOOLOGY 2020; 141:125738. [PMID: 32291142 DOI: 10.1016/j.zool.2019.125738] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 01/01/2023]
Abstract
Chameleons display high karyological diversity in chromosome number (from 2n = 20 to 62), morphology, heterochromatin distribution and location of specific chromosomal markers, making them unique study models in evolutionary cytogenetics. However, most available cytogenetic data are limited to the description of the chromosome number and morphology. Concerning sex chromosomes, our knowledge is limited to ZZ/ZW and Z1Z1Z2Z2/Z1Z2W systems in the genus Furcifer and the isolation of sex-linked, male-specific, sequences in Chamaeleo calyptratus, but the putative XY chromosomes have still to be identified in Chamaeleo and the conservation of male heterogamety in the genus needs confirmation from other species. In this study we performed a molecular and a cytogenetic analysis on C. chamaeleon, using standard, banding methods and molecular cytogenetics to provide a throughout karyological characterization of the species and to identify and locate the putative XY chromosomes. We confirm that the chromosome formula of the species is 2n = 24, with 12 metacentric macrochromosomes, 12 microchromosomes and NORs on the second chromosome pair. Heterochromatin was detected as weak C-bands on centromeric regions, differently from what was previously reported for C. calyptratus. Fluorescence in situ hybridization (FISH) showed the occurrence of interspersed telomeric signals on most macrochromosomes, suggesting that ancient chromosome fusions may have led to a reduction of the chromosome number. Using a combination of molecular and FISH analyses, we proved that male specific Restriction site-Associated DNA sequences (RADseq) isolated in C. calyptratus are conserved in C. chamaeleon and located the putative XY chromosomes on the second chromosome pair. We also identified different transposable elements in the focal taxa, which are highly interspersed on most chromosome pairs.
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Affiliation(s)
- Marwa Sidhom
- Laboratoire de Génétique, Biodiversité et Valorisation des Bioressources, Institut Supérieur de Biotechnologie de Monastir, Université de Monastir, Avenue Taher Hadded (B.P 74), Monastir, 5000, Tunisia
| | - Khaled Said
- Laboratoire de Génétique, Biodiversité et Valorisation des Bioressources, Institut Supérieur de Biotechnologie de Monastir, Université de Monastir, Avenue Taher Hadded (B.P 74), Monastir, 5000, Tunisia
| | - Noureddine Chatti
- Laboratoire de Génétique, Biodiversité et Valorisation des Bioressources, Institut Supérieur de Biotechnologie de Monastir, Université de Monastir, Avenue Taher Hadded (B.P 74), Monastir, 5000, Tunisia
| | - Fabio M Guarino
- Dipartimento di Biologia, Università di Napoli Federico II, Via Cinthia 26, 80126, Napoli, Italy.
| | - Gaetano Odierna
- Dipartimento di Biologia, Università di Napoli Federico II, Via Cinthia 26, 80126, Napoli, Italy
| | - Agnese Petraccioli
- Dipartimento di Biologia, Università di Napoli Federico II, Via Cinthia 26, 80126, Napoli, Italy
| | - Orfeo Picariello
- Dipartimento di Biologia, Università di Napoli Federico II, Via Cinthia 26, 80126, Napoli, Italy
| | - Marcello Mezzasalma
- Dipartimento di Biologia, Università di Napoli Federico II, Via Cinthia 26, 80126, Napoli, Italy; Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK.
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54
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Rovatsos M, Altmanová M, Augstenová B, Mazzoleni S, Velenský P, Kratochvíl L. ZZ/ZW Sex Determination with Multiple Neo-Sex Chromosomes is Common in Madagascan Chameleons of the Genus Furcifer (Reptilia: Chamaeleonidae). Genes (Basel) 2019; 10:genes10121020. [PMID: 31817782 PMCID: PMC6947276 DOI: 10.3390/genes10121020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 01/24/2023] Open
Abstract
Chameleons are well-known, highly distinctive lizards characterized by unique morphological and physiological traits, but their karyotypes and sex determination system have remained poorly studied. We studied karyotypes in six species of Madagascan chameleons of the genus Furcifer by classical (conventional stain, C-banding) and molecular (comparative genomic hybridization, in situ hybridization with rDNA, microsatellite, and telomeric sequences) cytogenetic approaches. In contrast to most sauropsid lineages, the chameleons of the genus Furcifer show chromosomal variability even among closely related species, with diploid chromosome numbers varying from 2n = 22 to 2n = 28. We identified female heterogamety with cytogenetically distinct Z and W sex chromosomes in all studied species. Notably, multiple neo-sex chromosomes in the form Z1Z1Z2Z2/Z1Z2W were uncovered in four species of the genus (F. bifidus, F. verrucosus, F. willsii, and previously studied F. pardalis). Phylogenetic distribution and morphology of sex chromosomes suggest that multiple sex chromosomes, which are generally very rare among vertebrates with female heterogamety, possibly evolved several times within the genus Furcifer. Although acrodontan lizards (chameleons and dragon lizards) demonstrate otherwise notable variability in sex determination, it seems that female heterogamety with differentiated sex chromosomes remained stable in the chameleons of the genus Furcifer for about 30 million years.
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Affiliation(s)
- Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, 12800 Prague, Czech Republic; (M.A.); (B.A.); (S.M.); (L.K.)
- Correspondence:
| | - Marie Altmanová
- Department of Ecology, Faculty of Science, Charles University, 12800 Prague, Czech Republic; (M.A.); (B.A.); (S.M.); (L.K.)
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic
| | - Barbora Augstenová
- Department of Ecology, Faculty of Science, Charles University, 12800 Prague, Czech Republic; (M.A.); (B.A.); (S.M.); (L.K.)
| | - Sofia Mazzoleni
- Department of Ecology, Faculty of Science, Charles University, 12800 Prague, Czech Republic; (M.A.); (B.A.); (S.M.); (L.K.)
| | - Petr Velenský
- Prague Zoological Garden, 17100 Prague, Czech Republic;
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, 12800 Prague, Czech Republic; (M.A.); (B.A.); (S.M.); (L.K.)
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55
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Cytogenetic Analysis Did Not Reveal Differentiated Sex Chromosomes in Ten Species of Boas and Pythons (Reptilia: Serpentes). Genes (Basel) 2019; 10:genes10110934. [PMID: 31731798 PMCID: PMC6896069 DOI: 10.3390/genes10110934] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/11/2019] [Accepted: 11/12/2019] [Indexed: 01/16/2023] Open
Abstract
Homologous and differentiated ZZ/ZW sex chromosomes (or derived multiple neo-sex chromosomes) were often described in caenophidian snakes, but sex chromosomes were unknown until recently in non-caenophidian snakes. Previous studies revealed that two species of boas (Boa imperator, B. constrictor) and one species of python (Python bivittatus) independently evolved XX/XY sex chromosomes. In addition, heteromorphic ZZ/ZW sex chromosomes were recently revealed in the Madagascar boa (Acrantophis sp. cf. dumerili) and putatively also in the blind snake Myriopholis macrorhyncha. Since the evolution of sex chromosomes in non-caenophidian snakes seems to be more complex than previously thought, we examined ten species of pythons and boas representing the families Boidae, Calabariidae, Candoiidae, Charinidae, Pythonidae, and Sanziniidae by conventional and molecular cytogenetic methods, aiming to reveal their sex chromosomes. Our results show that all examined species do not possess sex-specific differences in their genomes detectable by the applied cytogenetic methods, indicating the presence of poorly differentiated sex chromosomes or even the absence of sex chromosomes. Interestingly, fluorescence in situ hybridization with telomeric repeats revealed extensive distribution of interstitial telomeric repeats in eight species, which are likely a consequence of intra-chromosomal rearrangements.
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56
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Diversity of PBI-DdeI satellite DNA in snakes correlates with rapid independent evolution and different functional roles. Sci Rep 2019; 9:15459. [PMID: 31664097 PMCID: PMC6820872 DOI: 10.1038/s41598-019-51863-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 10/09/2019] [Indexed: 11/24/2022] Open
Abstract
To better understand PBI-DdeI satellite DNA located in the centromeric region of python, molecular evolution analysis was conducted on 40 snake species. A ladder-like pattern of DNA bands with repetition of the 194–210 bp monomer was observed in 15 species using PCR. Molecular cloning was performed to obtain 97 AT-rich monomer sequences. Phylogenetic and network analyses showed three PBI-DdeI subfamilies with sequences grouped in species-specific clusters, suggesting rapid evolution. Slow evolution was found in eight species with shared PBI-DdeI sequences, suggesting recent species diversification, allowing PBI-DdeI no time to diverge, with limited homogenization and fixation processes. Quantitative real-time PCR showed large differences in copy number between Python bivittatus and other snakes, consistent with repeat scanning of whole genome sequences. Copy numbers were significantly higher in female Naja kaouthia than in males, concurring with chromosomal distribution of PBI-DdeI specifically localized to female W chromosomes. PBI-DdeI might act as an evolutionary driver with several repeats to promote W chromosome differentiation and heterochromatinization in N. kaouthia. Analysis revealed PBI-DdeI with a reduced copy number, compared to P. bivittatus, in most snakes studied, and it is possible that it subsequently dispersed and amplified on W chromosomes with different functional roles in N. kaouthia.
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57
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Lind AL, Lai YYY, Mostovoy Y, Holloway AK, Iannucci A, Mak ACY, Fondi M, Orlandini V, Eckalbar WL, Milan M, Rovatsos M, Kichigin IG, Makunin AI, Johnson Pokorná M, Altmanová M, Trifonov VA, Schijlen E, Kratochvíl L, Fani R, Velenský P, Rehák I, Patarnello T, Jessop TS, Hicks JW, Ryder OA, Mendelson JR, Ciofi C, Kwok PY, Pollard KS, Bruneau BG. Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards. Nat Ecol Evol 2019; 3:1241-1252. [PMID: 31358948 PMCID: PMC6668926 DOI: 10.1038/s41559-019-0945-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 06/13/2019] [Indexed: 01/24/2023]
Abstract
Monitor lizards are unique among ectothermic reptiles in that they have high aerobic capacity and distinctive cardiovascular physiology resembling that of endothermic mammals. Here, we sequence the genome of the Komodo dragon Varanus komodoensis, the largest extant monitor lizard, and generate a high-resolution de novo chromosome-assigned genome assembly for V. komodoensis using a hybrid approach of long-range sequencing and single-molecule optical mapping. Comparing the genome of V. komodoensis with those of related species, we find evidence of positive selection in pathways related to energy metabolism, cardiovascular homoeostasis, and haemostasis. We also show species-specific expansions of a chemoreceptor gene family related to pheromone and kairomone sensing in V. komodoensis and other lizard lineages. Together, these evolutionary signatures of adaptation reveal the genetic underpinnings of the unique Komodo dragon sensory and cardiovascular systems, and suggest that selective pressure altered haemostasis genes to help Komodo dragons evade the anticoagulant effects of their own saliva. The Komodo dragon genome is an important resource for understanding the biology of monitor lizards and reptiles worldwide.
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Affiliation(s)
| | - Yvonne Y Y Lai
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Yulia Mostovoy
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | | | - Alessio Iannucci
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Angel C Y Mak
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Marco Fondi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Valerio Orlandini
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Walter L Eckalbar
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Massimo Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | - Michail Rovatsos
- Department of Ecology, Charles University, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Liběchov, Czech Republic
| | - Ilya G Kichigin
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Alex I Makunin
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Martina Johnson Pokorná
- Department of Ecology, Charles University, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Liběchov, Czech Republic
| | - Marie Altmanová
- Department of Ecology, Charles University, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Liběchov, Czech Republic
| | | | - Elio Schijlen
- B.U. Bioscience, Wageningen University, Wageningen, The Netherlands
| | - Lukáš Kratochvíl
- Department of Ecology, Charles University, Prague, Czech Republic
| | - Renato Fani
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | | | - Ivan Rehák
- Prague Zoological Garden, Prague, Czech Republic
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | - Tim S Jessop
- Centre for Integrative Ecology, Deakin University, Waurn Ponds, Victoria, Australia
| | - James W Hicks
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine, CA, USA
| | - Oliver A Ryder
- Institute for Conservation Research, San Diego Zoo, Escondido, CA, USA
| | - Joseph R Mendelson
- Zoo Atlanta, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Claudio Ciofi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Department of Dermatology, University of California, San Francisco, CA, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, CA, USA.
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA.
- Institute for Computational Health Sciences, University of California, San Francisco, CA, USA.
- Chan-Zuckerberg BioHub, San Francisco, CA, USA.
| | - Benoit G Bruneau
- Gladstone Institutes, San Francisco, CA, USA.
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA.
- Department of Pediatrics, University of California, San Francisco, CA, USA.
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58
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Kaundun SS, Marchegiani E, Hutchings SJ, Baker K. Derived Polymorphic Amplified Cleaved Sequence (dPACS): A Novel PCR-RFLP Procedure for Detecting Known Single Nucleotide and Deletion-Insertion Polymorphisms. Int J Mol Sci 2019; 20:E3193. [PMID: 31261867 PMCID: PMC6651057 DOI: 10.3390/ijms20133193] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/21/2019] [Accepted: 06/27/2019] [Indexed: 12/21/2022] Open
Abstract
Most methods developed for detecting known single nucleotide polymorphisms (SNP) and deletion-insertion polymorphisms (DIP) are dependent on sequence conservation around the SNP/DIP and are therefore not suitable for application to heterogeneous organisms. Here we describe a novel, versatile and simple PCR-RFLP procedure baptised 'derived Polymorphic Amplified Cleaved Sequence' (dPACS) for genotyping individual samples. The notable advantage of the method is that it employs a pair of primers that cover the entire fragment to be amplified except for one or few diagnostic bases around the SNP/DIP being investigated. As such, it provides greater opportunities to introduce mismatches in one or both of the 35-55 bp primers for creating a restriction site that unambiguously differentiates wild from mutant sequences following PCR-RFLP and horizontal MetaPhorTM gel electrophoresis. Selection of effective restriction enzymes and primers is aided by the newly developed dPACS 1.0 software. The highly transferable dPACS procedure is exemplified here with the positive detection (in up to 24 grass and broadleaf species tested) of wild type proline106 of 5-enolpyruvylshikimate-3-phosphate synthase and its serine, threonine and alanine variants that confer resistance to glyphosate, and serine264 and isoleucine2041 which are key target-site determinants for weed sensitivities to some photosystem II and acetyl-CoA carboxylase inhibiting herbicides, respectively.
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Affiliation(s)
- Shiv Shankhar Kaundun
- Herbicide Bioscience, Syngenta Ltd., Jealott's Hill International Research Centre, RG42 6EY Bracknell, UK.
| | - Elisabetta Marchegiani
- Herbicide Bioscience, Syngenta Ltd., Jealott's Hill International Research Centre, RG42 6EY Bracknell, UK
| | - Sarah-Jane Hutchings
- Herbicide Bioscience, Syngenta Ltd., Jealott's Hill International Research Centre, RG42 6EY Bracknell, UK
| | - Ken Baker
- General Bioinformatics, Jealott's Hill International Research Centre, RG42 6EY Bracknell, UK
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59
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Rovatsos M, Farkačová K, Altmanová M, Johnson Pokorná M, Kratochvíl L. The rise and fall of differentiated sex chromosomes in geckos. Mol Ecol 2019; 28:3042-3052. [DOI: 10.1111/mec.15126] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/02/2019] [Accepted: 05/02/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Michail Rovatsos
- Department of Ecology, Faculty of Science Charles University Prague Czech Republic
| | - Klára Farkačová
- Department of Ecology, Faculty of Science Charles University Prague Czech Republic
| | - Marie Altmanová
- Department of Ecology, Faculty of Science Charles University Prague Czech Republic
- Institute of Animal Physiology and Genetics The Czech Academy of Sciences Liběchov Czech Republic
| | - Martina Johnson Pokorná
- Department of Ecology, Faculty of Science Charles University Prague Czech Republic
- Institute of Animal Physiology and Genetics The Czech Academy of Sciences Liběchov Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science Charles University Prague Czech Republic
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60
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Evolutionary Insights of the ZW Sex Chromosomesin Snakes: A New Chapter Added by the AmazonianPuffing Snakes of the Genus Spilotes. Genes (Basel) 2019; 10:genes10040288. [PMID: 30970650 PMCID: PMC6523457 DOI: 10.3390/genes10040288] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/12/2019] [Accepted: 03/31/2019] [Indexed: 01/16/2023] Open
Abstract
Amazonian puffing snakes (Spilotes; Colubridae) are snakes widely distributed in the Neotropical region. However, chromosomal data are scarce in this group and, when available, are only limited to karyotype description using conventional staining. In this paper, we focused on the process of karyotype evolution and trends for sex chromosomes in two Amazonian Puffer Snakes (S. pulllatus and S. sulphureus). We performed an extensive karyotype characterization using conventional and molecular cytogenetic approaches. The karyotype of S. sulphureus (presented here for the first time) exhibits a 2n = 36, similar to that previously described in S. pullatus. Both species have highly differentiated ZZ/ZW sex chromosomes, where the W chromosome is highly heterochromatic in S. pullatus but euchromatic in S. sulphureus. Both W chromosomes are homologous between these species as revealed by cross-species comparative genomic hybridization, even with heterogeneous distributions of several repetitive sequences across their genomes, including on the Z and on the W chromosomes. Our study provides evidence that W chromosomes in these two species have shared ancestry.
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61
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Schield DR, Card DC, Hales NR, Perry BW, Pasquesi GM, Blackmon H, Adams RH, Corbin AB, Smith CF, Ramesh B, Demuth JP, Betrán E, Tollis M, Meik JM, Mackessy SP, Castoe TA. The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes. Genome Res 2019; 29:590-601. [PMID: 30898880 PMCID: PMC6442385 DOI: 10.1101/gr.240952.118] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 02/15/2019] [Indexed: 01/28/2023]
Abstract
Here we use a chromosome-level genome assembly of a prairie rattlesnake (Crotalus viridis), together with Hi-C, RNA-seq, and whole-genome resequencing data, to study key features of genome biology and evolution in reptiles. We identify the rattlesnake Z Chromosome, including the recombining pseudoautosomal region, and find evidence for partial dosage compensation driven by an evolutionary accumulation of a female-biased up-regulation mechanism. Comparative analyses with other amniotes provide new insight into the origins, structure, and function of reptile microchromosomes, which we demonstrate have markedly different structure and function compared to macrochromosomes. Snake microchromosomes are also enriched for venom genes, which we show have evolved through multiple tandem duplication events in multiple gene families. By overlaying chromatin structure information and gene expression data, we find evidence for venom gene-specific chromatin contact domains and identify how chromatin structure guides precise expression of multiple venom gene families. Further, we find evidence for venom gland-specific transcription factor activity and characterize a complement of mechanisms underlying venom production and regulation. Our findings reveal novel and fundamental features of reptile genome biology, provide insight into the regulation of snake venom, and broadly highlight the biological insight enabled by chromosome-level genome assemblies.
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Affiliation(s)
- Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Daren C Card
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Nicole R Hales
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Giulia M Pasquesi
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Richard H Adams
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Andrew B Corbin
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Cara F Smith
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado 80639, USA
| | - Balan Ramesh
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Jeffery P Demuth
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Esther Betrán
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Marc Tollis
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Jesse M Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas 76402, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado 80639, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
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62
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Abstract
The evolution of heteromorphic sex chromosomes has occurred independently many times in different lineages. The differentiation of sex chromosomes leads to dramatic changes in sequence composition and function and guides the evolutionary trajectory and utilization of genes in pivotal sex determination and reproduction roles. In addition, meiotic recombination and pairing mechanisms are key in orchestrating the resultant impact, retention and maintenance of heteromorphic sex chromosomes, as the resulting exposure of unpaired DNA at meiosis triggers ancient repair and checkpoint pathways. In this review, we summarize the different ways in which sex chromosome systems are organized at meiosis, how pairing is affected, and differences in unpaired DNA responses. We hypothesize that lineage specific differences in meiotic organization is not only a consequence of sex chromosome evolution, but that the establishment of epigenetic changes on sex chromosomes contributes toward their evolutionary conservation.
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Affiliation(s)
- Tasman Daish
- Comparative Genome Biology Laboratory, Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Frank Grützner
- Comparative Genome Biology Laboratory, Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia.
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63
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Singchat W, O'Connor RE, Tawichasri P, Suntronpong A, Sillapaprayoon S, Suntrarachun S, Muangmai N, Baicharoen S, Peyachoknagul S, Chanhome L, Griffin D, Srikulnath K. Chromosome map of the Siamese cobra: did partial synteny of sex chromosomes in the amniote represent "a hypothetical ancestral super-sex chromosome" or random distribution? BMC Genomics 2018; 19:939. [PMID: 30558533 PMCID: PMC6296137 DOI: 10.1186/s12864-018-5293-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/21/2018] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Unlike the chromosome constitution of most snakes (2n=36), the cobra karyotype shows a diploid chromosome number of 38 with a highly heterochromatic W chromosome and a large morphologically different chromosome 2. To investigate the process of sex chromosome differentiation and evolution between cobras, most snakes, and other amniotes, we constructed a chromosome map of the Siamese cobra (Naja kaouthia) with 43 bacterial artificial chromosomes (BACs) derived from the chicken and zebra finch libraries using the fluorescence in situ hybridization (FISH) technique, and compared it with those of the chicken, the zebra finch, and other amniotes. RESULTS We produced a detailed chromosome map of the Siamese cobra genome, focusing on chromosome 2 and sex chromosomes. Synteny of the Siamese cobra chromosome 2 (NKA2) and NKAZ were highly conserved among snakes and other squamate reptiles, except for intrachromosomal rearrangements occurring in NKA2. Interestingly, twelve BACs that had partial homology with sex chromosomes of several amniotes were mapped on the heterochromatic NKAW as hybridization signals such as repeat sequences. Sequence analysis showed that most of these BACs contained high proportions of transposable elements. In addition, hybridization signals of telomeric repeat (TTAGGG)n and six microsatellite repeat motifs ((AAGG)8, (AGAT)8, (AAAC)8, (ACAG)8, (AATC)8, and (AAAAT)6) were observed on NKAW, and most of these were also found on other amniote sex chromosomes. CONCLUSIONS The frequent amplification of repeats might involve heterochromatinization and promote sex chromosome differentiation in the Siamese cobra W sex chromosome. Repeat sequences are also shared among amniote sex chromosomes, which supports the hypothesis of an ancestral super-sex chromosome with overlaps of partial syntenies. Alternatively, amplification of microsatellite repeat motifs could have occurred independently in each lineage, representing convergent sex chromosomal differentiation among amniote sex chromosomes.
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Affiliation(s)
- Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Bangkok, 10900, Thailand
| | - Rebecca E O'Connor
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom
| | - Panupong Tawichasri
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Bangkok, 10900, Thailand
| | - Aorarat Suntronpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Bangkok, 10900, Thailand
| | - Siwapech Sillapaprayoon
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Bangkok, 10900, Thailand
| | - Sunutcha Suntrarachun
- Department of Research and Development, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Narongrit Muangmai
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Bangkok, 10900, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand
| | - Sudarath Baicharoen
- Bureau of Conservation and Research, Zoological Park Organization under the Royal Patronage of His Majesty the King, Bangkok, Thailand
| | - Surin Peyachoknagul
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Lawan Chanhome
- Snake Farm, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Darren Griffin
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Bangkok, 10900, Thailand.
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok, 10900, Thailand.
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok, 10900, Thailand.
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64
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Pennell MW, Mank JE, Peichel CL. Transitions in sex determination and sex chromosomes across vertebrate species. Mol Ecol 2018; 27:3950-3963. [PMID: 29451715 PMCID: PMC6095824 DOI: 10.1111/mec.14540] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 01/30/2018] [Accepted: 02/06/2018] [Indexed: 12/14/2022]
Abstract
Despite the prevalence of sexual reproduction across eukaryotes, there is a remarkable diversity of sex-determination mechanisms. The underlying causes of this diversity remain unclear, and it is unknown whether there are convergent trends in the directionality of turnover in sex-determination mechanisms. We used the recently assembled Tree of Sex database to assess patterns in the evolution of sex-determination systems in the remarkably diverse vertebrate clades of teleost fish, squamate reptiles and amphibians. Contrary to theoretical predictions, we find no evidence that the evolution of separate sexes is irreversible, as transitions from separate sexes to hermaphroditism occur at higher rates than the reverse in fish. We also find that transitions from environmental sex determination to genetic sex determination occur at higher rates than the reverse in both squamates and fish, suggesting that genetic sex determination is more stable. However, our data are not consistent with the hypothesis that heteromorphic sex chromosomes are an "evolutionary trap." Rather, we find similar transition rates between homomorphic and heteromorphic sex chromosomes in both fish and amphibians, and to environmental sex determination from heteromorphic vs. homomorphic sex chromosome systems in fish. Finally, we find that transitions between male and female heterogamety occur at similar rates in amphibians and squamates, while transitions to male heterogamety occur at higher rates in fish. Together, these results provide the most comprehensive view to date of the evolution of vertebrate sex determination in a phylogenetic context, providing new insight into long-standing questions about the evolution of sexual reproduction.
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Affiliation(s)
- Matthew W. Pennell
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Judith E. Mank
- Department of Genetics, Evolution and Environment, University College London, London, UK
- Department of Organismal Biology, Uppsala University, Sweden
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65
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Calvete JJ, Casewell NR, Hernández-Guzmán U, Quesada-Bernat S, Sanz L, Rokyta DR, Storey D, Albulescu LO, Wüster W, Smith CF, Schuett GW, Booth W. Venom Complexity in a Pitviper Produced by Facultative Parthenogenesis. Sci Rep 2018; 8:11539. [PMID: 30068934 PMCID: PMC6070573 DOI: 10.1038/s41598-018-29791-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 07/12/2018] [Indexed: 11/25/2022] Open
Abstract
Facultative parthenogenesis (FP) is asexual reproduction in plant and animal species that would otherwise reproduce sexually. This process in vertebrates typically results from automictic development (likely terminal fusion) and is phylogenetically widespread. In squamate reptiles and chondrichthyan fishes, FP has been reported to occur in nature and can result in the production of reproductively viable offspring; suggesting that it is of ecological and evolutionary significance. However, terminal fusion automixis is believed to result in near genome-wide reductions in heterozygosity; thus, FP seems likely to affect key phenotypic characters, yet this remains almost completely unstudied. Snake venom is a complex phenotypic character primarily used to subjugate prey and is thus tightly linked to individual fitness. Surprisingly, the composition and function of venom produced by a parthenogenetic pitviper exhibits a high degree of similarity to that of its mother and conspecifics from the same population. Therefore, the apparent loss of allelic diversity caused by FP appears unlikely to have a significant impact on the prey-capturing ability of this snake. Accordingly, the pitviper offspring produced by FP retained complex phenotypic characteristics associated with fitness. This result reinforces the potential ecological and evolutionary importance of FP and questions our understanding of the inheritance of venom-associated genes.
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Affiliation(s)
- J J Calvete
- Evolutionary and Translational Venomics Laboratory, CSIC, Valencia, Spain.
| | - N R Casewell
- Alistair Reid Venom Research Unit, Parasitology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
| | - U Hernández-Guzmán
- Evolutionary and Translational Venomics Laboratory, CSIC, Valencia, Spain
- Laboratorio de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Delegación Coyoacán C.P, 04510, Ciudad de México, Mexico
| | - S Quesada-Bernat
- Evolutionary and Translational Venomics Laboratory, CSIC, Valencia, Spain
| | - L Sanz
- Evolutionary and Translational Venomics Laboratory, CSIC, Valencia, Spain
| | - D R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - D Storey
- Alistair Reid Venom Research Unit, Parasitology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales, Bangor University, Bangor, LL57 2UW, UK
| | - L-O Albulescu
- Alistair Reid Venom Research Unit, Parasitology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - W Wüster
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales, Bangor University, Bangor, LL57 2UW, UK
- Chiricahua Desert Museum, P.O. Box 376, Rodeo, NM, USA
| | - C F Smith
- Chiricahua Desert Museum, P.O. Box 376, Rodeo, NM, USA
- The Copperhead Institute, P.O. Box 6755, Spartanburg, SC, USA
- Department of Biology, Wofford College, 429 North Church Street, Spartanburg, SC, USA
| | - G W Schuett
- Chiricahua Desert Museum, P.O. Box 376, Rodeo, NM, USA
- The Copperhead Institute, P.O. Box 6755, Spartanburg, SC, USA
- Department of Biology and Neuroscience Institute, Georgia State University, Atlanta, GA, USA
| | - W Booth
- Chiricahua Desert Museum, P.O. Box 376, Rodeo, NM, USA
- The Copperhead Institute, P.O. Box 6755, Spartanburg, SC, USA
- Department of Biological Science, The University of Tulsa, Tulsa, OK, USA
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66
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Perry BW, Card DC, McGlothlin JW, Pasquesi GIM, Adams RH, Schield DR, Hales NR, Corbin AB, Demuth JP, Hoffmann FG, Vandewege MW, Schott RK, Bhattacharyya N, Chang BSW, Casewell NR, Whiteley G, Reyes-Velasco J, Mackessy SP, Gamble T, Storey KB, Biggar KK, Passow CN, Kuo CH, McGaugh SE, Bronikowski AM, de Koning APJ, Edwards SV, Pfrender ME, Minx P, Brodie ED, Brodie ED, Warren WC, Castoe TA. Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome. Genome Biol Evol 2018; 10:2110-2129. [PMID: 30060036 PMCID: PMC6110522 DOI: 10.1093/gbe/evy157] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2018] [Indexed: 12/26/2022] Open
Abstract
Colubridae represents the most phenotypically diverse and speciose family of snakes, yet no well-assembled and annotated genome exists for this lineage. Here, we report and analyze the genome of the garter snake, Thamnophis sirtalis, a colubrid snake that is an important model species for research in evolutionary biology, physiology, genomics, behavior, and the evolution of toxin resistance. Using the garter snake genome, we show how snakes have evolved numerous adaptations for sensing and securing prey, and identify features of snake genome structure that provide insight into the evolution of amniote genomes. Analyses of the garter snake and other squamate reptile genomes highlight shifts in repeat element abundance and expansion within snakes, uncover evidence of genes under positive selection, and provide revised neutral substitution rate estimates for squamates. Our identification of Z and W sex chromosome-specific scaffolds provides evidence for multiple origins of sex chromosome systems in snakes and demonstrates the value of this genome for studying sex chromosome evolution. Analysis of gene duplication and loss in visual and olfactory gene families supports a dim-light ancestral condition in snakes and indicates that olfactory receptor repertoires underwent an expansion early in snake evolution. Additionally, we provide some of the first links between secreted venom proteins, the genes that encode them, and their evolutionary origins in a rear-fanged colubrid snake, together with new genomic insight into the coevolutionary arms race between garter snakes and highly toxic newt prey that led to toxin resistance in garter snakes.
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Affiliation(s)
- Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington
| | - Daren C Card
- Department of Biology, University of Texas at Arlington, Arlington
| | - Joel W McGlothlin
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia
| | | | - Richard H Adams
- Department of Biology, University of Texas at Arlington, Arlington
| | - Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington
| | - Nicole R Hales
- Department of Biology, University of Texas at Arlington, Arlington
| | - Andrew B Corbin
- Department of Biology, University of Texas at Arlington, Arlington
| | - Jeffery P Demuth
- Department of Biology, University of Texas at Arlington, Arlington
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville
| | - Michael W Vandewege
- Department of Biology, Institute for Genomics and Evolutionary Medicine, Temple University
| | - Ryan K Schott
- Department of Ecology and Evolutionary Biology, Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution & Function, University of Toronto, Ontario, Canada.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia
| | - Nihar Bhattacharyya
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada
| | - Belinda S W Chang
- Department of Ecology and Evolutionary Biology, Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution & Function, University of Toronto, Ontario, Canada
| | - Nicholas R Casewell
- Alistair Reid Venom Research Unit, Parasitology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom
| | - Gareth Whiteley
- Alistair Reid Venom Research Unit, Parasitology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom
| | - Jacobo Reyes-Velasco
- Department of Biology, University of Texas at Arlington, Arlington.,Department of Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | | | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA.,Bell Museum of Natural History, University of Minnesota, Saint Paul, MN, USA
| | - Kenneth B Storey
- Institute of Biochemistry, Carleton University, Ottawa, Ontario, Canada
| | - Kyle K Biggar
- Institute of Biochemistry, Carleton University, Ottawa, Ontario, Canada
| | | | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | | | - Anne M Bronikowski
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
| | - A P Jason de Koning
- Department of Biochemistry and Molecular Biology, Department of Medical Genetics, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University
| | - Michael E Pfrender
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame
| | - Patrick Minx
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis
| | | | | | - Wesley C Warren
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington
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67
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Augstenová B, Johnson Pokorná M, Altmanová M, Frynta D, Rovatsos M, Kratochvíl L. ZW, XY, and yet ZW: Sex chromosome evolution in snakes even more complicated. Evolution 2018; 72:1701-1707. [PMID: 29972583 DOI: 10.1111/evo.13543] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/26/2018] [Indexed: 01/07/2023]
Abstract
Snakes are historically important in the formulation of several central concepts on the evolution of sex chromosomes. For over 50 years, it was believed that all snakes shared the same ZZ/ZW sex chromosomes, which are homomorphic and poorly differentiated in "basal" snakes such as pythons and boas, while heteromorphic and well differentiated in "advanced" (caenophidian) snakes. Recent molecular studies revealed that differentiated sex chromosomes are indeed shared among all families of caenophidian snakes, but that boas and pythons evolved likely independently male heterogamety (XX/XY sex chromosomes). The historical report of heteromorphic ZZ/ZW sex chromosomes in a boid snake was previously regarded as ambiguous. In the current study, we document heteromorphic ZZ/ZW sex chromosomes in a boid snake. A comparative approach suggests that these heteromorphic sex chromosomes evolved very recently and that they are poorly differentiated at the sequence level. Interestingly, two snake lineages with confirmed male heterogamety possess homomorphic sex chromosomes, but heteromorphic sex chromosomes are present in both snake lineages with female heterogamety. We point out that this phenomenon is more common across squamates. The presence of female heterogamety in non-caenophidian snakes indicates that the evolution of sex chromosomes in this lineage is much more complex than previously thought, making snakes an even better model system for the evolution of sex chromosomes.
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Affiliation(s)
- Barbora Augstenová
- Department of Ecology, Faculty of Science, Charles University, Prague, 128 44, Czech Republic
| | - Martina Johnson Pokorná
- Department of Ecology, Faculty of Science, Charles University, Prague, 128 44, Czech Republic
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Liběchov, 277 21, Czech Republic
| | - Marie Altmanová
- Department of Ecology, Faculty of Science, Charles University, Prague, 128 44, Czech Republic
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Liběchov, 277 21, Czech Republic
| | - Daniel Frynta
- Department of Zoology, Faculty of Science, Charles University, Prague, 128 44, Czech Republic
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Prague, 128 44, Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Prague, 128 44, Czech Republic
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68
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Rovatsos M, Augstenová B, Altmanová M, Sloboda M, Kodym P, Kratochvíl L. Triploid Colubrid Snake Provides Insight into the Mechanism of Sex Determination in Advanced Snakes. Sex Dev 2018; 12:251-255. [PMID: 29913458 DOI: 10.1159/000490124] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2018] [Indexed: 01/14/2023] Open
Abstract
The advanced snakes (Caenophidia), the important amniote lineage encompassing more than 3,000 living species, possess highly conserved female heterogamety across all families. However, we still lack any knowledge on the gene(s) and the molecular mechanism controlling sex determination. Triploid individuals spontaneously appear in populations of diploid species and can provide an important insight into the evolution of sex determination. Here, we report a case of spontaneous triploidy in a male of the twin-spotted ratsnake (Elaphe bimaculata) with ZZW sex chromosomes. We speculate that as both ZZ and ZZW individuals develop male gonads, the ratio between the number of Z chromosomes and autosomes, and not the presence of the W chromosome in the genome, drives sex determination in the advanced snakes.
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69
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Scott MF, Osmond MM, Otto SP. Haploid selection, sex ratio bias, and transitions between sex-determining systems. PLoS Biol 2018; 16:e2005609. [PMID: 29940019 PMCID: PMC6042799 DOI: 10.1371/journal.pbio.2005609] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 07/12/2018] [Accepted: 06/06/2018] [Indexed: 12/20/2022] Open
Abstract
Sex determination is remarkably dynamic; many taxa display shifts in the location of sex-determining loci or the evolution of entirely new sex-determining systems. Predominant theories for why we observe such transitions generally conclude that novel sex-determining systems are favoured by selection if they equalise the sex ratio or increase linkage with a locus that experiences different selection in males versus females. We use population genetic models to extend these theories in two ways: (1) We consider the dynamics of loci very tightly linked to the ancestral sex-determining loci, e.g., within the nonrecombining region of the ancestral sex chromosomes. Variation at such loci can favour the spread of new sex-determining systems in which the heterogametic sex changes (XY to ZW or ZW to XY) and the new sex-determining region is less closely linked (or even unlinked) to the locus under selection. (2) We consider selection upon haploid genotypes either during gametic competition (e.g., pollen competition) or meiosis (i.e., nonmendelian segregation), which can cause the zygotic sex ratio to become biased. Haploid selection can drive transitions between sex-determining systems without requiring selection to act differently in diploid males versus females. With haploid selection, we find that transitions between male and female heterogamety can evolve so that linkage with the sex-determining locus is either strengthened or weakened. Furthermore, we find that sex ratio biases may increase or decrease with the spread of new sex chromosomes, which implies that transitions between sex-determining systems cannot be simply predicted by selection to equalise the sex ratio. In fact, under many conditions, we find that transitions in sex determination are favoured equally strongly in cases in which the sex ratio bias increases or decreases. Overall, our models predict that sex determination systems should be highly dynamic, particularly when haploid selection is present, consistent with the evolutionary lability of this trait in many taxa.
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Affiliation(s)
- Michael Francis Scott
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Matthew Miles Osmond
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sarah Perin Otto
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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70
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Nielsen SV, Banks JL, Diaz RE, Trainor PA, Gamble T. Dynamic sex chromosomes in Old World chameleons (Squamata: Chamaeleonidae). J Evol Biol 2018; 31:484-490. [DOI: 10.1111/jeb.13242] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/04/2018] [Accepted: 01/05/2018] [Indexed: 01/04/2023]
Affiliation(s)
- S. V. Nielsen
- Department of Biological Sciences; Marquette University; Milwaukee WI USA
| | - J. L. Banks
- Department of Biological Sciences; Marquette University; Milwaukee WI USA
| | - R. E. Diaz
- Department of Biological Sciences; Southeastern Louisiana University; Hammond LA USA
- Natural History Museum of Los Angeles County; Los Angeles CA USA
| | - P. A. Trainor
- Stowers Institute for Medical Research; Kansas City MO USA
- Department of Anatomy and Cell Biology; Medical Center; University of Kansas; Kansas City KS USA
| | - T. Gamble
- Department of Biological Sciences; Marquette University; Milwaukee WI USA
- Bell Museum of Natural History; University of Minnesota; Saint Paul MN USA
- Milwaukee Public Museum; Milwaukee WI USA
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71
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Allen L, Sanders KL, Thomson VA. Molecular evidence for the first records of facultative parthenogenesis in elapid snakes. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171901. [PMID: 29515892 PMCID: PMC5830781 DOI: 10.1098/rsos.171901] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 01/18/2018] [Indexed: 09/29/2023]
Abstract
Parthenogenesis is a form of asexual reproduction by which embryos develop from unfertilized eggs. Parthenogenesis occurs in reptiles; however, it is not yet known to occur in the widespread elapid snakes (Elapidae), which include well-known taxa such as cobras, mambas, taipans and sea snakes. Here, we describe the production of viable parthenogens in two species of Australo-Papuan elapids with divergent reproductive modes: the oviparous coastal/Papuan taipan (Oxyuranus scutellatus) and the viviparous southern death adder (Acanthophis antarcticus). Analyses of nuclear SNP data excluded paternity for putative fathers and convincingly demonstrated asexual reproduction, thus representing the first evidence of facultative parthenogenesis in Elapidae. Our finding has broad implications for understanding the evolution of reproductive diversity in snakes, as well as managing the conservation of genetic diversity in wild and captive populations.
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Affiliation(s)
- L. Allen
- Venom Supplies, PO Box 547, Tanunda, South Australia 5352, Australia
- School of Biological Sciences, and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - K. L. Sanders
- School of Biological Sciences, and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - V. A. Thomson
- School of Biological Sciences, and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
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72
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Evolutionary Dynamics of the W Chromosome in Caenophidian Snakes. Genes (Basel) 2017; 9:genes9010005. [PMID: 29283388 PMCID: PMC5793158 DOI: 10.3390/genes9010005] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/15/2017] [Accepted: 12/20/2017] [Indexed: 11/18/2022] Open
Abstract
The caenophidian (assigned also as “advanced”) snakes are traditionally viewed as a group of reptiles with a limited karyotypic variation and stable ZZ/ZW sex chromosomes. The W chromosomes of the caenophidian snakes are heterochromatic, and pioneering studies demonstrated that they are rich in repetitive elements. However, a comparative study of the evolutionary dynamics of the repetitive content of the W chromosome across the whole lineage is missing. Using molecular-cytogenetic techniques, we explored the distribution of four repetitive motifs (microsatellites GATA, GACA, AG and telomeric-like sequences), which are frequently accumulated in differentiated sex chromosomes in vertebrates, in the genomes of 13 species of the caenophidian snakes covering a wide phylogenetic spectrum of the lineage. The results demonstrate a striking variability in the morphology and the repetitive content of the W chromosomes even between closely-related species, which is in contrast to the homology and long-term stability of the gene content of the caenophidian Z chromosome. We uncovered that the tested microsatellite motifs are accumulated on the degenerated, heterochromatic W chromosomes in all tested species of the caenophidian snakes with the exception of the Javan file snake representing a basal clade. On the other hand, the presence of the accumulation of the telomeric-like sequences on the caenophidian W chromosome is evolutionary much less stable. Moreover, we demonstrated that large accumulations of telomeric-like motifs on the W chromosome contribute to sexual differences in the number of copies of the telomeric and telomeric-like repeats estimated by quantitative PCR, which might be confusing and incorrectly interpreted as sexual differences in telomere length.
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Gamble T, McKenna E, Meyer W, Nielsen SV, Pinto BJ, Scantlebury DP, Higham TE. XX/XY Sex Chromosomes in the South American Dwarf Gecko (Gonatodes humeralis). J Hered 2017; 109:462-468. [DOI: 10.1093/jhered/esx112] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/19/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI
- Bell Museum of Natural History, University of Minnesota, Saint Paul, MN
- Milwaukee Public Museum, Milwaukee, WI
| | | | - Wyatt Meyer
- Department of Biological Sciences, Marquette University, Milwaukee, WI
| | - Stuart V Nielsen
- Department of Biological Sciences, Marquette University, Milwaukee, WI
| | - Brendan J Pinto
- Department of Biological Sciences, Marquette University, Milwaukee, WI
| | | | - Timothy E Higham
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA
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Shibata H, Sakata S, Hirano Y, Nitasaka E, Sakabe A. Facultative parthenogenesis validated by DNA analyses in the green anaconda (Eunectes murinus). PLoS One 2017; 12:e0189654. [PMID: 29236745 PMCID: PMC5728508 DOI: 10.1371/journal.pone.0189654] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/29/2017] [Indexed: 11/19/2022] Open
Abstract
In reptiles, the mode of reproduction is typically sexual. However, facultative parthenogenesis occurs in some Squamata, such as Komodo dragon (Varanus komodoensis) and Burmese python (Python bivittatus). Here, we report facultative parthenogenesis in the green anaconda (Eunectes murinus). We found two fully developed female neonates and 17 undeveloped eggs in the oviduct of a female anaconda isolated from other individuals for eight years and two months at Ueno Zoo, Japan. To clarify the zygosity of the neonates, we analyzed 18 microsatellite markers of which 16 were informative. We observed only maternal alleles and no paternal alleles for all 16 markers. To examine the possibility of the long-term sperm storage, we estimated allele frequencies in a putative parental stock by genotyping five unrelated founders. If all founders, including the mother, are originated from a single Mendelian population, then the probability that the neonates were produced by sexual reproduction with an unrelated male via long-term sperm storage was infinitesimally small (2.31E-32 per clutch). We also examined samples from two additional offspring that the mother delivered eight years before her death. We consistently observed paternal alleles in these elder offspring, indicating that the mother had switched from sexual reproduction to asexual reproduction during the eight years of isolation. This is the first case of parthenogenesis in Eunectes to be validated by DNA analysis, and suggests that facultative parthenogenesis is widespread in the Boidae.
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Affiliation(s)
- Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | | | - Yuzo Hirano
- Ueno Zoo, 9-83, Ueno Park, Taito-ku, Tokyo, Japan
| | - Eiji Nitasaka
- Graduate School of Science, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Ai Sakabe
- Ueno Zoo, 9-83, Ueno Park, Taito-ku, Tokyo, Japan
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Whiteley SL, Holleley CE, Ruscoe WA, Castelli M, Whitehead DL, Lei J, Georges A, Weisbecker V. Sex determination mode does not affect body or genital development of the central bearded dragon ( Pogona vitticeps). EvoDevo 2017; 8:25. [PMID: 29225770 PMCID: PMC5716226 DOI: 10.1186/s13227-017-0087-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 11/21/2017] [Indexed: 11/10/2022] Open
Abstract
Background The development of male- or female-specific phenotypes in squamates is typically controlled by either temperature-dependent sex determination (TSD) or chromosome-based genetic sex determination (GSD). However, while sex determination is a major switch in individual phenotypic development, it is unknownhow evolutionary transitions between GSD and TSD might impact on the evolution of squamate phenotypes, particularly the fast-evolving and diverse genitalia. Here, we take the unique opportunity of studying the impact of both sex determination mechanisms on the embryological development of the central bearded dragon (Pogona vitticeps). This is possible because of the transitional sex determination system of this species, in which genetically male individuals reverse sex at high incubation temperatures. This can trigger the evolutionary transition of GSD to TSD in a single generation, making P. vitticeps an ideal model organism for comparing the effects of both sex determination processes in the same species. Results We conducted four incubation experiments on 265 P. vitticeps eggs, covering two temperature regimes ("normal" at 28 °C and "sex reversing" at 36 °C) and the two maternal sexual genotypes (concordant ZW females or sex-reversed ZZ females). From this, we provide the first detailed staging system for the species, with a focus on genital and limb development. This was augmented by a new sex chromosome identification methodology for P. vitticeps that is non-destructive to the embryo. We found a strong correlation between embryo age and embryo stage. Aside from faster growth in 36 °C treatments, body and external genital development was entirely unperturbed by temperature, sex reversal or maternal sexual genotype. Unexpectedly, all females developed hemipenes (the genital phenotype of adult male P. vitticeps), which regress close to hatching. Conclusions The tight correlation between embryo age and embryo stage allows the precise targeting of specific developmental periods in the emerging field of molecular research on P. vitticeps. The stability of genital development in all treatments suggests that the two sex-determining mechanisms have little impact on genital evolution, despite their known role in triggering genital development. Hemipenis retention in developing female P. vitticeps, together with frequent occurrences of hemipenis-like structures during development in other squamate species, raises the possibility of a bias towards hemipenis formation in the ancestral developmental programme for squamate genitalia.
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Affiliation(s)
- Sarah L Whiteley
- School of Biological Sciences, University of Queensland, Brisbane, QLD Australia.,Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, ACT Australia.,Institute for Applied Ecology, University of Canberra, Canberra, ACT Australia
| | - Clare E Holleley
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, ACT Australia.,Institute for Applied Ecology, University of Canberra, Canberra, ACT Australia
| | - Wendy A Ruscoe
- Institute for Applied Ecology, University of Canberra, Canberra, ACT Australia
| | - Meghan Castelli
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, ACT Australia.,Institute for Applied Ecology, University of Canberra, Canberra, ACT Australia
| | - Darryl L Whitehead
- School of Biomedical Science, University of Queensland, Brisbane, QLD Australia
| | - Juan Lei
- School of Biological Sciences, University of Queensland, Brisbane, QLD Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT Australia
| | - Vera Weisbecker
- School of Biological Sciences, University of Queensland, Brisbane, QLD Australia
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Using blood and non-invasive shed skin samples to identify sex of caenophidian snakes based on multiplex PCR assay. ZOOL ANZ 2017. [DOI: 10.1016/j.jcz.2017.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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