1
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Webster TH, Vannan A, Pinto BJ, Denbrock G, Morales M, Dolby GA, Fiddes IT, DeNardo DF, Wilson MA. Lack of Dosage Balance and Incomplete Dosage Compensation in the ZZ/ZW Gila Monster (Heloderma suspectum) Revealed by De Novo Genome Assembly. Genome Biol Evol 2024; 16:evae018. [PMID: 38319079 PMCID: PMC10950046 DOI: 10.1093/gbe/evae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/07/2024] Open
Abstract
Reptiles exhibit a variety of modes of sex determination, including both temperature-dependent and genetic mechanisms. Among those species with genetic sex determination, sex chromosomes of varying heterogamety (XX/XY and ZZ/ZW) have been observed with different degrees of differentiation. Karyotype studies have demonstrated that Gila monsters (Heloderma suspectum) have ZZ/ZW sex determination and this system is likely homologous to the ZZ/ZW system in the Komodo dragon (Varanus komodoensis), but little else is known about their sex chromosomes. Here, we report the assembly and analysis of the Gila monster genome. We generated a de novo draft genome assembly for a male using 10X Genomics technology. We further generated and analyzed short-read whole genome sequencing and whole transcriptome sequencing data for three males and three females. By comparing female and male genomic data, we identified four putative Z chromosome scaffolds. These putative Z chromosome scaffolds are homologous to Z-linked scaffolds identified in the Komodo dragon. Further, by analyzing RNAseq data, we observed evidence of incomplete dosage compensation between the Gila monster Z chromosome and autosomes and a lack of balance in Z-linked expression between the sexes. In particular, we observe lower expression of the Z in females (ZW) than males (ZZ) on a global basis, though we find evidence suggesting local gene-by-gene compensation. This pattern has been observed in most other ZZ/ZW systems studied to date and may represent a general pattern for female heterogamety in vertebrates.
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Affiliation(s)
- Timothy H Webster
- Department of Anthropology, University of Utah, Salt Lake City, UT, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Annika Vannan
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Brendan J Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
| | - Grant Denbrock
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Matheo Morales
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Genetics, Yale University, New Haven, CT, USA
| | - Greer A Dolby
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Dale F DeNardo
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ, USA
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2
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Elmer KR. Evolutionary paths to new phenotypes. Science 2024; 383:27-28. [PMID: 38175891 DOI: 10.1126/science.adm9239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Ecological model systems inform on innovative traits in plants and animals.
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Affiliation(s)
- Kathryn R Elmer
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
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3
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Webster TH, Vannan A, Pinto BJ, Denbrock G, Morales M, Dolby GA, Fiddes IT, DeNardo DF, Wilson MA. Incomplete dosage balance and dosage compensation in the ZZ/ZW Gila monster ( Heloderma suspectum) revealed by de novo genome assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538436. [PMID: 37163099 PMCID: PMC10168389 DOI: 10.1101/2023.04.26.538436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Reptiles exhibit a variety of modes of sex determination, including both temperature-dependent and genetic mechanisms. Among those species with genetic sex determination, sex chromosomes of varying heterogamety (XX/XY and ZZ/ZW) have been observed with different degrees of differentiation. Karyotype studies have demonstrated that Gila monsters (Heloderma suspectum) have ZZ/ZW sex determination and this system is likely homologous to the ZZ/ZW system in the Komodo dragon (Varanus komodoensis), but little else is known about their sex chromosomes. Here, we report the assembly and analysis of the Gila monster genome. We generated a de novo draft genome assembly for a male using 10X Genomics technology. We further generated and analyzed short-read whole genome sequencing and whole transcriptome sequencing data for three males and three females. By comparing female and male genomic data, we identified four putative Z-chromosome scaffolds. These putative Z-chromosome scaffolds are homologous to Z-linked scaffolds identified in the Komodo dragon. Further, by analyzing RNAseq data, we observed evidence of incomplete dosage compensation between the Gila monster Z chromosome and autosomes and a lack of balance in Z-linked expression between the sexes. In particular, we observe lower expression of the Z in females (ZW) than males (ZZ) on a global basis, though we find evidence suggesting local gene-by-gene compensation. This pattern has been observed in most other ZZ/ZW systems studied to date and may represent a general pattern for female heterogamety in vertebrates.
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Affiliation(s)
- Timothy H. Webster
- Department of Anthropology, University of Utah, Salt Lake City, UT
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Annika Vannan
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Brendan J. Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
| | - Grant Denbrock
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Matheo Morales
- School of Life Sciences, Arizona State University, Tempe, AZ
- Department of Genetics, Yale University, New Haven, CT
| | - Greer A. Dolby
- School of Life Sciences, Arizona State University, Tempe, AZ
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ
| | | | - Dale F. DeNardo
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Melissa A. Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ
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4
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Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles. Animals (Basel) 2023; 13:ani13030471. [PMID: 36766360 PMCID: PMC9913427 DOI: 10.3390/ani13030471] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 02/01/2023] Open
Abstract
Non-avian reptiles comprise a large proportion of amniote vertebrate diversity, with squamate reptiles-lizards and snakes-recently overtaking birds as the most species-rich tetrapod radiation. Despite displaying an extraordinary diversity of phenotypic and genomic traits, genomic resources in non-avian reptiles have accumulated more slowly than they have in mammals and birds, the remaining amniotes. Here we review the remarkable natural history of non-avian reptiles, with a focus on the physical traits, genomic characteristics, and sequence compositional patterns that comprise key axes of variation across amniotes. We argue that the high evolutionary diversity of non-avian reptiles can fuel a new generation of whole-genome phylogenomic analyses. A survey of phylogenetic investigations in non-avian reptiles shows that sequence capture-based approaches are the most commonly used, with studies of markers known as ultraconserved elements (UCEs) especially well represented. However, many other types of markers exist and are increasingly being mined from genome assemblies in silico, including some with greater information potential than UCEs for certain investigations. We discuss the importance of high-quality genomic resources and methods for bioinformatically extracting a range of marker sets from genome assemblies. Finally, we encourage herpetologists working in genomics, genetics, evolutionary biology, and other fields to work collectively towards building genomic resources for non-avian reptiles, especially squamates, that rival those already in place for mammals and birds. Overall, the development of this cross-amniote phylogenomic tree of life will contribute to illuminate interesting dimensions of biodiversity across non-avian reptiles and broader amniotes.
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5
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Card DC, Van Camp AG, Santonastaso T, Jensen-Seaman MI, Anthony NM, Edwards SV. Structure and evolution of the squamate major histocompatibility complex as revealed by two Anolis lizard genomes. Front Genet 2022; 13:979746. [PMID: 36425073 PMCID: PMC9679377 DOI: 10.3389/fgene.2022.979746] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/20/2022] [Indexed: 11/10/2022] Open
Abstract
The major histocompatibility complex (MHC) is an important genomic region for adaptive immunity and has long been studied in ecological and evolutionary contexts, such as disease resistance and mate and kin selection. The MHC has been investigated extensively in mammals and birds but far less so in squamate reptiles, the third major radiation of amniotes. We localized the core MHC genomic region in two squamate species, the green anole (Anolis carolinensis) and brown anole (A. sagrei), and provide the first detailed characterization of the squamate MHC, including the presence and ordering of known MHC genes in these species and comparative assessments of genomic structure and composition in MHC regions. We find that the Anolis MHC, located on chromosome 2 in both species, contains homologs of many previously-identified mammalian MHC genes in a single core MHC region. The repetitive element composition in anole MHC regions was similar to those observed in mammals but had important distinctions, such as higher proportions of DNA transposons. Moreover, longer introns and intergenic regions result in a much larger squamate MHC region (11.7 Mb and 24.6 Mb in the green and brown anole, respectively). Evolutionary analyses of MHC homologs of anoles and other representative amniotes uncovered generally monophyletic relationships between species-specific homologs and a loss of the peptide-binding domain exon 2 in one of two mhc2β gene homologs of each anole species. Signals of diversifying selection in each anole species was evident across codons of mhc1, many of which appear functionally relevant given known structures of this protein from the green anole, chicken, and human. Altogether, our investigation fills a major gap in understanding of amniote MHC diversity and evolution and provides an important foundation for future squamate-specific or vertebrate-wide investigations of the MHC.
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Affiliation(s)
- Daren C. Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States
- *Correspondence: Daren C. Card,
| | - Andrew G. Van Camp
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States
| | - Trenten Santonastaso
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States
| | | | - Nicola M. Anthony
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States
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6
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Sidharthan C, Roy P, Narayanan S, Karanth KP. A widespread commensal loses its identity: suggested taxonomic revision for Indotyphlops braminus (Scolecophidia: Typhlopidae) based on molecular data. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00577-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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7
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Coordinating tiny limbs and long bodies: Geometric mechanics of lizard terrestrial swimming. Proc Natl Acad Sci U S A 2022; 119:e2118456119. [PMID: 35759665 PMCID: PMC9271186 DOI: 10.1073/pnas.2118456119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Although typically possessing four limbs and short bodies, lizards have evolved diverse morphologies, including elongate trunks with tiny limbs. Such forms are hypothesized to aid locomotion in cluttered/fossorial environments but propulsion mechanisms (e.g., the use of body and/or limbs to interact with substrates) and potential body/limb coordination remain unstudied. Here, we use biological experiments, a geometric theory of locomotion, and robophysical models to investigate body-limb coordination in diverse lizards. Locomotor field studies in short-limbed, elongate lizards (Brachymeles and Lerista) and laboratory studies of fully limbed lizards (Uma scoparia and Sceloporus olivaceus) and a snake (Chionactis occipitalis) reveal that body-wave dynamics can be described by a combination of standing and traveling waves; the ratio of the amplitudes of these components is inversely related to the degree of limb reduction and body elongation. The geometric theory (which replaces laborious calculation with diagrams) helps explain our observations, predicting that the advantage of traveling-wave body undulations (compared with a standing wave) emerges when the dominant thrust-generation mechanism arises from the body rather than the limbs and reveals that such soil-dwelling lizards propel via "terrestrial swimming" like sand-swimming lizards and snakes. We test our hypothesis by inducing the use of traveling waves in stereotyped lizards via modulating the ground-penetration resistance. Study of a limbed/undulatory robophysical model demonstrates that a traveling wave is beneficial when propulsion is generated by body-environment interaction. Our models could be valuable in understanding functional constraints on the evolutionary processes of elongation and limb reduction as well as advancing robot designs.
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8
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Loebens L, Theis TF, Almeida-Santos SM, Cechin SZ. Reproductive Biology, Sperm storage, and Sexual Maturity of Thamnodynastes strigatus (Serpentes: Dipsadidae). AN ACAD BRAS CIENC 2022; 94:e20211087. [PMID: 35703696 DOI: 10.1590/0001-3765202220211087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/03/2021] [Indexed: 11/21/2022] Open
Abstract
Life history strategies determine and influence many aspects of species fitness. In this study, we describe the reproductive biology - reproductive cycle, sperm storage, and sexual maturity - of Thamnodynastes strigatus in South Brazil. We analyzed 49 individuals (25 males and 24 females) from herpetological collections. The reproductive cycle of males and females was described considering the morpho-anatomical and histological changes in the testes, ductus deferens, and kidney, as well in the ovary and oviduct. The age at the onset of sexual maturity was determined by skeletochronology of the caudal vertebra. The reproductive cycle is seasonal semi-synchronous and most individuals have a reproductive peak in spring and summer. The seasonal biennial reproductive cycle and viviparity are two phylogenetically conserved characters in Tachymenini snakes. Thamnodynastes Strigatus females store sperm in the utero-vaginal junction furrows during autumn. There were no differences between the ages of sexual maturity of males (4-11y) and females (4-12y). Females reach sexual maturity at larger body sizes, and this may confer an adaptive advantage due to a higher fecundity potential. Herein, we confirmed the previously described seasonal biennial reproductive cycle of T. strigatus through histological analysis.
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Affiliation(s)
- Luiza Loebens
- Universidade Federal de Santa Maria, Departamento de Ecologia e Evolução, Laboratório de Herpetologia, Avenida Roraima, 1000, Camobi, 97105-900 Santa Maria, RS, Brazil
| | - Tiago F Theis
- Universidade Federal de Santa Maria, Departamento de Ecologia e Evolução, Laboratório de Herpetologia, Avenida Roraima, 1000, Camobi, 97105-900 Santa Maria, RS, Brazil
| | - Selma M Almeida-Santos
- Instituto Butantan, Laboratório de Ecologia e Evolução, Avenida Vital Brazil, 1500, 05503-900 São Paulo, SP, Brazil
| | - Sonia Z Cechin
- Universidade Federal de Santa Maria, Departamento de Ecologia e Evolução, Laboratório de Herpetologia, Avenida Roraima, 1000, Camobi, 97105-900 Santa Maria, RS, Brazil
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9
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Nicolau GK, Jackson EA, Jordaan A, Alexander GJ. Tropidosaura essexi Hewitt, 1927 (Reptilia: Lacertidae) is live bearing: the only viviparous African lacertid. AFR J HERPETOL 2022. [DOI: 10.1080/21564574.2021.2019839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Gary K Nicolau
- Department of Zoology and Entomology, Rhodes University, Makhanda, South Africa
| | - Emily A Jackson
- Department of Zoology and Entomology, Rhodes University, Makhanda, South Africa
| | - Adriaan Jordaan
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Cape Town, South Africa
- South African National Biodiversity Institute, Pretoria, South Africa
| | - Graham J Alexander
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
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10
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Recknagel H, Trontelj P. From Cave Dragons to Genomics: Advancements in the Study of Subterranean Tetrapods. Bioscience 2021; 72:254-266. [PMID: 35241972 PMCID: PMC8888124 DOI: 10.1093/biosci/biab117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Throughout most of the kingdom Animalia, evolutionary transitions from surface life to a life permanently bound to caves and other subterranean habitats have occurred innumerous times. Not so in tetrapods, where a mere 14 cave-obligate species—all plethodontid and proteid salamanders—are known. We discuss why cave tetrapods are so exceptional and why only salamanders have made the transition. Their evolution follows predictable and convergent, albeit independent pathways. Among the many known changes associated with transitions to subterranean life, eye degeneration, starvation resistance, and longevity are especially relevant to human biomedical research. Recently, sequences of salamander genomes have become available opening up genomic research for cave tetrapods. We discuss new genomic methods that can spur our understanding of the evolutionary mechanisms behind convergent phenotypic change, the relative roles of selective and neutral evolution, cryptic species diversity, and data relevant for conservation such as effective population size and demography.
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Affiliation(s)
- Hans Recknagel
- University of Ljubljana, Slovenia, working, Biotechnical Faculty, Dept. of Biology, Subterranean Biology Lab
| | - Peter Trontelj
- University of Ljubljana, Slovenia, working, Biotechnical Faculty, Dept. of Biology, Subterranean Biology Lab
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11
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Cornejo-Páramo P, Dissanayake DSB, Lira-Noriega A, Martínez-Pacheco ML, Acosta A, Ramírez-Suástegui C, Méndez-de-la-Cruz FR, Székely T, Urrutia AO, Georges A, Cortez D. Viviparous Reptile Regarded to Have Temperature-Dependent Sex Determination Has Old XY Chromosomes. Genome Biol Evol 2021; 12:924-930. [PMID: 32433751 PMCID: PMC7313667 DOI: 10.1093/gbe/evaa104] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2020] [Indexed: 01/27/2023] Open
Abstract
The water skinks Eulamprus tympanum and Eulamprus heatwolei show thermally induced sex determination where elevated temperatures give rise to male offspring. Paradoxically, Eulamprus species reproduce in temperatures of 12–15 °C making them outliers when compared with reptiles that use temperature as a cue for sex determination. Moreover, these two species are among the very few viviparous reptiles reported to have thermally induced sex determination. Thus, we tested whether these skinks possess undetected sex chromosomes with thermal override. We produced transcriptome and genome data for E. heatwolei. We found that E. heatwolei presents XY chromosomes that include 14 gametologs with regulatory functions. The Y chromosomal region is 79–116 Myr old and shared between water and spotted skinks. Our work provides clear evidence that climate could be useful to predict the type of sex determination systems in reptiles and it also indicates that viviparity is strictly associated with sex chromosomes.
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Affiliation(s)
- Paola Cornejo-Páramo
- Center for Genome Sciences, UNAM, Cuernavaca, México.,Department of Biology and Biochemistry, Milner Centre for Evolution, University of Bath, United Kingdom
| | - Duminda S B Dissanayake
- Institute for Applied Ecology, University of Canberra, Australia.,CSIRO, Australian National Wildlife Collection, Canberra, Australia
| | - Andrés Lira-Noriega
- CONACYT Research Fellow, Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C. Carretera antigua a Coatepec 351, Xalapa, Veracruz, México
| | | | | | - Ciro Ramírez-Suástegui
- Center for Genome Sciences, UNAM, Cuernavaca, México.,Department of Biology and Biochemistry, Milner Centre for Evolution, University of Bath, United Kingdom
| | | | - Tamás Székely
- Department of Biology and Biochemistry, Milner Centre for Evolution, University of Bath, United Kingdom.,Department of Evolutionary Zoology and Human Biology, University of Debrecen, Hungary
| | - Araxi O Urrutia
- Department of Biology and Biochemistry, Milner Centre for Evolution, University of Bath, United Kingdom.,Institute of Ecology, UNAM, Mexico City, Mexico
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Australia
| | - Diego Cortez
- Center for Genome Sciences, UNAM, Cuernavaca, México
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12
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Recknagel H, Kamenos NA, Elmer KR. Evolutionary origins of viviparity consistent with palaeoclimate and lineage diversification. J Evol Biol 2021; 34:1167-1176. [PMID: 34107111 DOI: 10.1111/jeb.13886] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 04/28/2021] [Accepted: 05/14/2021] [Indexed: 12/28/2022]
Abstract
It is of fundamental importance for the field of evolutionary biology to understand when and why major evolutionary transitions occur. Live-bearing young (viviparity) is a major evolutionary change and has evolved from egg-laying (oviparity) independently in many vertebrate lineages and most abundantly in lizards and snakes. Although contemporary viviparous squamate species generally occupy cold climatic regions across the globe, it is not known whether viviparity evolved as a response to cold climate in the first place. Here, we used available published time-calibrated squamate phylogenies and parity data on 3,498 taxa. We compared the accumulation of transitions from oviparity to viviparity relative to background diversification and a simulated binary trait. Extracting the date of each transition in the phylogenies and informed by 65 my of global palaeoclimatic data, we tested the nonexclusive hypotheses that viviparity evolved under the following: (a) cold, (b) long-term stable climatic conditions and (c) with background diversification rate. We show that stable and long-lasting cold climatic conditions are correlated with transitions to viviparity across squamates. This correlation of parity mode and palaeoclimate is mirrored by background diversification in squamates, and simulations of a binary trait also showed a similar association with palaeoclimate, meaning that trait evolution cannot be separated from squamate lineage diversification. We suggest that parity mode transitions depend on environmental and intrinsic effects and that background diversification rate may be a factor in trait diversification more generally.
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Affiliation(s)
- Hans Recknagel
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Nicholas A Kamenos
- School of Geographical and Earth Sciences, University of Glasgow, Glasgow, UK
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
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13
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Cleuren SGC, Hocking DP, Evans AR. Fang evolution in venomous snakes: Adaptation of 3D tooth shape to the biomechanical properties of their prey. Evolution 2021; 75:1377-1394. [PMID: 33904594 DOI: 10.1111/evo.14239] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 11/27/2022]
Abstract
Venomous snakes are among the world's most specialized predators. During feeding, they use fangs to penetrate the body tissues of their prey, but the success of this penetration depends on the shape of these highly specialized teeth. Here, we examined the evolution of fang shape in a wide range of snakes using 3D geometric morphometrics (3DGM) and cross-sectional tooth sharpness measurements. We investigated the relationship of these variables with six diet categories based on the prey's biomechanical properties, and tested for evolutionary convergence using two methods. Our results show that slender elongate fangs with sharp tips are used by snakes that target soft-skinned prey (e.g., mammals), whereas fangs become more robust and blunter as the target's skin becomes scaly (e.g., fish and reptiles) and eventually hard-shelled (e.g., crustaceans), both with and without correction for evolutionary allometry. Convergence in fang shape is present, indicating that fangs of snakes with the same diet are more similar than those of closely related species with different diets. Establishing the relationship between fang morphology and diet helps to explain how snakes became adapted to different lifestyles, while also providing a proxy to infer diet in lesser known species or extinct snakes from the fossil record.
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Affiliation(s)
- Silke G C Cleuren
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | - David P Hocking
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | - Alistair R Evans
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia.,Geosciences, Museums Victoria, Melbourne, Victoria, 3001, Australia
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14
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Ancestral Reconstruction of Diet and Fang Condition in the Lamprophiidae: Implications for the Evolution of Venom Systems in Snakes. J HERPETOL 2021. [DOI: 10.1670/19-071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Swimming through the sands of the Sahara and Arabian deserts: Phylogeny of sandfish skinks (Scincidae, Scincus) reveals a recent and rapid diversification. Mol Phylogenet Evol 2020; 155:107012. [PMID: 33217580 DOI: 10.1016/j.ympev.2020.107012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 11/18/2022]
Abstract
Large parts of the Sahara Desert and Arabia are covered by sand seas and sand dunes, which are inhabited by specialized animal communities. For example, many lizards have developed adaptations to life in loose sand, including sand-swimming behavior. The best-known sand swimmers of the Saharo-Arabia are the sandfish skinks (genus Scincus). Although there are currently only four Scincus species recognized, their phylogenetic relationships have not yet been addressed in detail. We use eight genetic markers (three mitochondrial, five nuclear) and a complete sampling of species to infer the relationships within the genus. We employ multiple phylogenetic approaches to reconstruct the evolutionary history of these skinks and to assess the level of reticulation at the onset of their radiation. Our results indicate the presence of five strongly supported species-level lineages, four represented by the currently recognized species and the fifth by S. scincus conirostris, which does not form a clade with S. scincus. Based on these results we elevate the Iranian and northern Arabian S. conirostris to the species level. The two Saharan species, S. albifasciatus and S. scincus, are sister in all analyses. Deeper relationships within the genus, however, remained largely unresolved despite the extensive genetic data set. This basal polytomy, together with the fact that we detected no sign of hybridization in the history of the genus, indicates that the diversification of the five Scincus species was rapid, burst-like, and not followed by secondary hybridization events. Divergence time estimations show a Middle Pliocene crown radiation of the genus (3.3 Mya). We hypothesize that the aridification of the Saharo-Arabia that began in the Late Miocene triggered the initial diversification of Scincus, and that the subsequent expansion of sand deserts enabled their dispersal over the large Saharan and Arabian range. We discuss the evolution of body form in sand swimming lizards and ponder how Scincus retained their fully limbed morphology despite being sand swimmers that are typically limbless.
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16
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Fujita MK, Singhal S, Brunes TO, Maldonado JA. Evolutionary Dynamics and Consequences of Parthenogenesis in Vertebrates. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-011720-114900] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Parthenogenesis is asexual reproduction without any required participation from males and, as such, is a null model for sexual reproduction. In a comparative context, we can expand our understanding of the evolution and ecology of sex by investigating the consequences of parthenogenesis. In this review, we examine the theoretical predictions of and empirical results on the evolution of asexual reproduction in vertebrates, focusing on recent studies addressing the origins and geographic spread of parthenogenetic lineages and the genomic consequences of an asexual life history. With advances in computational methods and genome technologies, researchers are poised to make rapid and significant progress in studying the origin and evolution of parthenogenesis in vertebrates, thus providing an important perspective on understanding biodiversity patterns of both asexual and sexual populations.
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Affiliation(s)
- Matthew K. Fujita
- Amphibian and Reptile Diversity Research Center and Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Sonal Singhal
- Department of Biology, California State University, Dominguez Hills, Carson, California 90747, USA
| | - Tuliana O. Brunes
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Jose A. Maldonado
- Amphibian and Reptile Diversity Research Center and Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
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17
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Yurchenko AA, Recknagel H, Elmer KR. Chromosome-Level Assembly of the Common Lizard (Zootoca vivipara) Genome. Genome Biol Evol 2020; 12:1953-1960. [PMID: 32835354 PMCID: PMC7643610 DOI: 10.1093/gbe/evaa161] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2020] [Indexed: 01/01/2023] Open
Abstract
Squamate reptiles exhibit high variation in their phenotypic traits and geographical distributions and are therefore fascinating taxa for evolutionary and ecological research. However, genomic resources are very limited for this group of species, consequently inhibiting research efforts. To address this gap, we assembled a high-quality genome of the common lizard, Zootoca vivipara (Lacertidae), using a combination of high coverage Illumina (shotgun and mate-pair) and PacBio sequencing data, coupled with RNAseq data and genetic linkage map generation. The 1.46-Gb genome assembly has a scaffold N50 of 11.52 Mb with N50 contig size of 220.4 kb and only 2.96% gaps. A BUSCO analysis indicates that 97.7% of the single-copy Tetrapoda orthologs were recovered in the assembly. In total, 19,829 gene models were annotated to the genome using a combination of ab initio and homology-based methods. To improve the chromosome-level assembly, we generated a high-density linkage map from wild-caught families and developed a novel analytical pipeline to accommodate multiple paternity and unknown father genotypes. We successfully anchored and oriented almost 90% of the genome on 19 linkage groups. This annotated and oriented chromosome-level reference genome represents a valuable resource to facilitate evolutionary studies in squamate reptiles.
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Affiliation(s)
- Andrey A Yurchenko
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Hans Recknagel
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
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18
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DeLorenzo L, Vander Linden A, Bergmann PJ, Wagner GP, Siler CD, Irschick DJ. Using 3D-digital photogrammetry to examine scaling of the body axis in burrowing skinks. J Morphol 2020; 281:1382-1390. [PMID: 32815588 DOI: 10.1002/jmor.21253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 07/02/2020] [Accepted: 07/28/2020] [Indexed: 11/10/2022]
Abstract
Three-dimensional (3D) modeling techniques have been increasingly utilized across disciplines for the visualization and analysis of complex structures. We employ 3D-digital photogrammetry for understanding the scaling of the body axis of 12 species of scincid lizards in the genus Brachymeles. These skinks represent a diverse radiation which shows tremendous variation in body size and degree of axial elongation. Because of the complex nature of the body axis, 3D-methods are important for understanding how the body axis evolves. 3D-digital photogrammetry presents a flexible, inexpensive, and portable system for the reconstruction of biological forms. As body size increased among species, the cross-sectional area and circumference of the head and other portions of the body axis increased isometrically, which indicates that species of differing sizes possess proportionally similar head and body shapes. These results suggest that there are no substantial head and body shape changes with body size among the sampled species, but further comparative studies with larger sample sizes and functional studies of size and morphology effects on burrowing or above-ground locomotion are needed.
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Affiliation(s)
- Leah DeLorenzo
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Abby Vander Linden
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Philip J Bergmann
- Department of Biology, Clark University, Worcester, Massachusetts, USA
| | - Gunter P Wagner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Cameron D Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Duncan J Irschick
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
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19
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Westeen EP, Durso AM, Grundler MC, Rabosky DL, Davis Rabosky AR. What makes a fang? Phylogenetic and ecological controls on tooth evolution in rear-fanged snakes. BMC Evol Biol 2020; 20:80. [PMID: 32646372 PMCID: PMC7346461 DOI: 10.1186/s12862-020-01645-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 06/22/2020] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Fangs are a putative key innovation that revolutionized prey capture and feeding in snakes, and - along with their associated venom phenotypes - have made snakes perhaps the most medically-significant vertebrate animals. Three snake clades are known for their forward-positioned fangs, and these clades (Elapidae, Viperidae, and Atractaspidinae) contain the majority of snakes that are traditionally considered venomous. However, many other snakes are "rear-fanged": they possess potentially venom-delivering teeth situated at the rear end of the upper jaw. Quantification of fang phenotypes - and especially those of rear-fanged species - has proved challenging or impossible owing to the small size and relative rarity of many such snakes. Consequently, it has been difficult to understand the evolutionary history of both venom and prey-capture strategies across extant snakes. We quantified variation in the dentition of 145 colubriform ("advanced") snake species using microCT scanning and compared dental characters with ecological data on species' diet and prey capture method(s) to understand broader patterns in snake fang evolution. RESULTS Dental traits such as maxilla length, tooth number, and fang size show strong phylogenetic signal across Colubriformes. We find extreme heterogeneity and evolutionary lability in the rear-fanged phenotype in colubrid (colubrine, dipsadine, and natricine lineages) and lamprophiid snakes, in contrast to relative uniformity in the front fanged phenotypes of other groups (vipers and, to a lesser extent, elapids). Fang size and position are correlated with venom-use in vipers, elapids, and colubrid snakes, with the latter group shifting fangs anteriorly by shortening the entire maxillary bone. We find that maxilla length and tooth number may also be correlated with the evolution of dietary specialization. Finally, an ancestral state reconstruction suggests that fang loss is a recurring phenomenon in colubrid snakes, likely accompanied by shifts in diet and prey capture mode. CONCLUSIONS Our study provides a framework for quantifying the complex morphologies associated with venom use in snakes. Our results suggest that fang phenotypes, and particularly the rear-fanged phenotype, in snakes are both diverse and labile, facilitating a wide range of ecological strategies and contributing to spectacular radiations of these organisms in tropical and subtropical biomes worldwide.
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Affiliation(s)
- Erin P Westeen
- Department of Environmental Science, Policy, and Management & Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.
- Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan, Ann Arbor, MI, USA.
| | - Andrew M Durso
- Department of Biological Sciences, Florida Gulf Coast University, Ft. Myers, FL, USA
| | - Michael C Grundler
- Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Alison R Davis Rabosky
- Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
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20
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Horreo JL, Suarez T, Fitze PS. Reversals in complex traits uncovered as reticulation events: Lessons from the evolution of parity-mode, chromosome morphology, and maternal resource transfer. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2019; 334:5-13. [PMID: 31650690 DOI: 10.1002/jez.b.22912] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 05/18/2019] [Accepted: 10/02/2019] [Indexed: 11/08/2022]
Abstract
Complex traits include, among many others, the evolution of eyes, wings, body forms, reproductive modes, human intelligence, social behavior, diseases, and chromosome morphology. Dollo's law states that the evolution of complex traits is irreversible. However, potential exceptions have been proposed. Here, we investigated whether reticulation, a simple and elegant means by which complex characters may be reacquired, could account for suggested reversals in the evolution of complex characters using two datasets with sufficient genetic coverage and a total of five potential reversals. Our analyses uncovered a potential reversal in the evolution of parity mode and a potential reversal in the evolution of placentotrophy of fish (Cyprinodontiformes) as reticulation events. Moreover, in a reptile that exhibits a potential reversal from viviparity to oviparity (Zootoca vivipara), reticulation provided the most parsimonious explanation for sex chromosome evolution. Therefore, three of the five studied potential reversals were unraveled as reticulation events. This constitutes the first evidence that accounting for reticulation can fundamentally influence the interpretation of the evolution of complex traits, that testing for reticulation is crucial for obtaining robust phylogenies, and that complex ancestral characters may be reacquired through hybridization with a lineage that still exhibits the trait. Hybridization, rather than reappearance of ancestral traits by means of small evolutionary steps, may thus account for suggested exceptions to Dollo's law. Consequently, ruling out reticulation is required to claim the evolutionary reversal of complex characters and potential exceptions to Dollo's rule.
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Affiliation(s)
- Jose L Horreo
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,UMIB Research Unit of Biodiversity (UO, CSIC, PA), Oviedo University-Campus Mieres, Spain
| | - Teresa Suarez
- Department of Molecular Biomedicine, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain
| | - Patrick S Fitze
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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21
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McLennan D, Recknagel H, Elmer KR, Monaghan P. Distinct telomere differences within a reproductively bimodal common lizard population. Funct Ecol 2019; 33:1917-1927. [PMID: 31762528 PMCID: PMC6853248 DOI: 10.1111/1365-2435.13408] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 06/18/2019] [Accepted: 07/03/2019] [Indexed: 12/21/2022]
Abstract
Different strategies of reproductive mode, either oviparity (egg-laying) or viviparity (live-bearing), will be associated with a range of other life-history differences that are expected to affect patterns of ageing and longevity. It is usually difficult to compare the effects of alternative reproductive modes because of evolutionary and ecological divergence. However, the very rare exemplars of reproductive bimodality, in which different modes exist within a single species, offer an opportunity for robust and controlled comparisons.One trait of interest that could be associated with life history, ageing and longevity is the length of the telomeres, which form protective caps at the chromosome ends and are generally considered a good indicator of cellular health. The shortening of these telomeres has been linked to stressful conditions; therefore, it is possible that differing reproductive costs will influence patterns of telomere loss. This is important because a number of studies have linked a shorter telomere length to reduced survival.Here, we have studied maternal and offspring telomere dynamics in the common lizard (Zootoca vivipara). Our study has focused on a population where oviparous and viviparous individuals co-occur in the same habitat and occasionally interbreed to form admixed individuals.While viviparity confers many advantages for offspring, it might also incur substantial costs for the mother, for example require more energy. Therefore, we predicted that viviparous mothers would have relatively shorter telomeres than oviparous mothers, with admixed mothers having intermediate telomere lengths. There is thought to be a heritable component to telomere length; therefore, we also hypothesized that offspring would follow the same pattern as the mothers.Contrary to our predictions, the viviparous mothers and offspring had the longest telomeres, and the oviparous mothers and offspring had the shortest telomeres. The differing telomere lengths may have evolved as an effect of the life-history divergence between the reproductive modes, for example due to the increased growth rate that viviparous individuals may undergo to reach a similar size at reproduction. A free http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.13408/suppinfo can be found within the Supporting Information of this article.
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Affiliation(s)
- Darryl McLennan
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
- Department of Fish Ecology and EvolutionEAWAGKastanienbaumSwitzerland
| | - Hans Recknagel
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
| | - Kathryn R. Elmer
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
| | - Pat Monaghan
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
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22
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Recknagel H, Elmer KR. Differential reproductive investment in co-occurring oviparous and viviparous common lizards (Zootoca vivipara) and implications for life-history trade-offs with viviparity. Oecologia 2019; 190:85-98. [PMID: 31062164 PMCID: PMC6535419 DOI: 10.1007/s00442-019-04398-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 04/02/2019] [Indexed: 01/31/2023]
Abstract
Live-bearing reproduction (viviparity) has evolved from egg-laying (oviparity) independently many times and most abundantly in squamate reptiles. Studying life-history trade-offs between the two reproductive modes is an inherently difficult task, as most transitions to viviparity are evolutionarily old and/or are confounded by environmental effects. The common lizard (Zootoca vivipara) is one of very few known reproductively bimodal species, in which some populations are oviparous and others viviparous. Oviparous and viviparous populations can occur in sympatry in the same environment, making this a unique system for investigating alternative life-history trade-offs between oviparous and viviparous reproduction. We find that viviparous females exhibit larger body size, smaller clutch sizes, a larger reproductive investment, and a higher hatching success rate than oviparous females. We find that offspring size and weight from viviparous females was lower compared to offspring from oviparous females, which may reflect space constraints during pregnancy. We suggest that viviparity in common lizards is associated with increased reproductive burden for viviparous females and speculate that this promoted the evolution of larger body size to create more physical space for developing embryos. In the context of life-history trade-offs in the evolution of viviparity, we suggest that the extent of correlation between reproductive traits, or differences between reproductive modes, may also depend on the time since the transition occurred.
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Affiliation(s)
- Hans Recknagel
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
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23
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Snake diversity in floodplains of central South America: Is flood pulse the principal driver? ACTA OECOLOGICA 2019. [DOI: 10.1016/j.actao.2019.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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Alternative reproductive adaptations predict asymmetric responses to climate change in lizards. Sci Rep 2019; 9:5093. [PMID: 30911069 PMCID: PMC6433898 DOI: 10.1038/s41598-019-41670-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/15/2019] [Indexed: 11/28/2022] Open
Abstract
Anthropogenic climate change ranks among the major global-scale threats to modern biodiversity. Extinction risks are known to increase via the interactions between rapid climatic alterations and environmentally-sensitive species traits that fail to adapt to those changes. Accumulating evidence reveals the influence of ecophysiological, ecological and phenological factors as drivers underlying demographic collapses that lead to population extinctions. However, the extent to which life-history traits influence population responses to climate change remains largely unexplored. The emerging ‘cul-de-sac hypothesis’ predicts that reptilian viviparity (‘live-bearing’ reproduction), a ‘key innovation’ facilitating historical invasions of cold climates, increases extinction risks under progressively warming climates compared to oviparous reproduction – as warming advances polewards/mountainwards, historically cold-climates shrink, leading viviparous species to face demographic collapses. We present the first large-scale test of this prediction based on multiple lizard radiations and on future projections of climate-based ecological niche models. Viviparous species were found to experience stronger elevational range shifts (and potentially increased extinctions) in coming decades, compared to oviparous lizards. Therefore, our analyses support the hypothesis’s fundamental prediction that elevational shifts are more severe in viviparous species, and highlight the role that life-history adaptations play in the responses of biodiversity to ongoing climate change.
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25
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Esquerré D, Brennan IG, Catullo RA, Torres‐Pérez F, Keogh JS. How mountains shape biodiversity: The role of the Andes in biogeography, diversification, and reproductive biology in South America's most species‐rich lizard radiation (Squamata: Liolaemidae). Evolution 2018; 73:214-230. [DOI: 10.1111/evo.13657] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 11/04/2018] [Accepted: 11/19/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University 0200 Canberra Australian Capital Territory Australia
| | - Ian G. Brennan
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University 0200 Canberra Australian Capital Territory Australia
| | - Renee A. Catullo
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University 0200 Canberra Australian Capital Territory Australia
- School of Science & Health and Hawkesbury Institute for the EnvironmentWestern Sydney University 2751 Perth New South Wales Australia
| | - Fernando Torres‐Pérez
- Instituto de BiologíaPontificia Universidad Católica de Valparaíso 2950 Valparaíso Chile
| | - J. Scott Keogh
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University 0200 Canberra Australian Capital Territory Australia
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26
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Recknagel H, Kamenos NA, Elmer KR. Common lizards break Dollo’s law of irreversibility: Genome-wide phylogenomics support a single origin of viviparity and re-evolution of oviparity. Mol Phylogenet Evol 2018; 127:579-588. [DOI: 10.1016/j.ympev.2018.05.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 04/12/2018] [Accepted: 05/22/2018] [Indexed: 01/03/2023]
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27
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Mongiardino Koch N, Gauthier JA. Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata. PLoS One 2018; 13:e0202729. [PMID: 30133514 PMCID: PMC6105018 DOI: 10.1371/journal.pone.0202729] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/08/2018] [Indexed: 12/23/2022] Open
Abstract
Squamate reptiles are a major component of vertebrate biodiversity whose crown-clade traces its origin to a narrow window of time in the Mesozoic during which the main subclades diverged in rapid succession. Deciphering phylogenetic relationships among these lineages has proven challenging given the conflicting signals provided by genomic and phenomic data. Most notably, the placement of Iguania has routinely differed between data sources, with morphological evidence supporting a sister relationship to the remaining squamates (Scleroglossa hypothesis) and molecular data favoring a highly nested position alongside snakes and anguimorphs (Toxicofera hypothesis). We provide novel insights by generating an expanded morphological dataset and exploring the presence of phylogenetic signal, noise, and biases in molecular data. Our analyses confirm the presence of strong conflicting signals for the position of Iguania between morphological and molecular datasets. However, we also find that molecular data behave highly erratically when inferring the deepest branches of the squamate tree, a consequence of limited phylogenetic signal to resolve this ancient radiation with confidence. This, in turn, seems to result from a rate of evolution that is too high for historical signals to survive to the present. Finally, we detect significant systematic biases, with iguanians and snakes sharing faster rates of molecular evolution and a similarly biased nucleotide composition. A combination of scant phylogenetic signal, high levels of noise, and the presence of systematic biases could result in the misplacement of Iguania. We regard this explanation to be at least as plausible as the complex scenario of convergence and reversals required for morphological data to be misleading. We further evaluate and discuss the utility of morphological data to resolve ancient radiations, as well as its impact in combined-evidence phylogenomic analyses, with results relevant for the assessment of evidence and conflict across the Tree of Life.
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Affiliation(s)
- Nicolás Mongiardino Koch
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut, United States of America
| | - Jacques A. Gauthier
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut, United States of America
- Yale Peabody Museum of Natural History, New Haven, Connecticut, United States of America
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28
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Streicher JW, Wiens JJ. Phylogenomic analyses of more than 4000 nuclear loci resolve the origin of snakes among lizard families. Biol Lett 2017; 13:rsbl.2017.0393. [PMID: 28904179 DOI: 10.1098/rsbl.2017.0393] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 08/18/2017] [Indexed: 01/02/2023] Open
Abstract
Squamate reptiles (lizards and snakes) are the most diverse group of terrestrial vertebrates, with more than 10 000 species. Despite considerable effort to resolve relationships among major squamates clades, some branches have remained difficult. Among the most vexing has been the placement of snakes among lizard families, with most studies yielding only weak support for the position of snakes. Furthermore, the placement of iguanian lizards has remained controversial. Here we used targeted sequence capture to obtain data from 4178 nuclear loci from ultraconserved elements from 32 squamate taxa (and five outgroups) including representatives of all major squamate groups. Using both concatenated and species-tree methods, we recover strong support for a sister relationship between iguanian and anguimorph lizards, with snakes strongly supported as the sister group of these two clades. These analyses strongly resolve the difficult placement of snakes within squamates and show overwhelming support for the contentious position of iguanians. More generally, we provide a strongly supported hypothesis of higher-level relationships in the most species-rich tetrapod clade using coalescent-based species-tree methods and approximately 100 times more loci than previous estimates.
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Affiliation(s)
- Jeffrey W Streicher
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0088, USA .,Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0088, USA
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29
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Infante CR, Rasys AM, Menke DB. Appendages and gene regulatory networks: Lessons from the limbless. Genesis 2017; 56. [PMID: 29076617 DOI: 10.1002/dvg.23078] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/06/2017] [Accepted: 10/06/2017] [Indexed: 01/19/2023]
Abstract
Among squamate reptiles, dozens of lineages have independently evolved complete or partial limb reduction. This remarkable convergence of limbless and limb-reduced phenotypes provides multiple natural replicates of different ages to explore the evolution and development of the vertebrate limb and the gene regulatory network that controls its formation. The most successful and best known of the limb-reduced squamates are snakes, which evolved a limb-reduced body form more than 100 million years ago. Recent studies have revealed the unexpected finding that many ancient limb enhancers are conserved in the genomes of snakes. Analyses in limbed animals show that many of these limb enhancers are also active during development of the phallus, suggesting that these enhancers may have been retained in snakes due their importance in regulating transcription in the external genitalia. This hypothesis is substantiated by functional tests of snake enhancers, which demonstrate that snake enhancer elements have lost limb function while retaining genital enhancer function. The large degree of overlap in the gene regulatory networks deployed during limb and phallus development may act to constrain the divergence of shared gene network components and the evolution of appendage morphology. Future studies will reveal whether limb regulatory elements have undergone similar functional changes in other lineages of limb-reduced squamates.
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Affiliation(s)
- Carlos R Infante
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, 85721
| | - Ashley M Rasys
- Department of Cellular Biology, University of Georgia, Athens, Georgia, 30602.,Department of Genetics, University of Georgia, Athens, Georgia, 30602
| | - Douglas B Menke
- Department of Genetics, University of Georgia, Athens, Georgia, 30602
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30
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Lima VF, Brito SV, Araujo Filho JA, Teles DA, Ribeiro SC, Teixeira AAM, Pereira AMA, Almeida WO. Helminth parasites of Phyllodactylidae and Gekkonidae lizards in a Caatinga ecological station, northeastern Brazil. BIOTA NEOTROPICA 2017. [DOI: 10.1590/1676-0611-bn-2016-0263] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract We investigated the parasites of five lizard species belonging to Phyllodactylidae (Phyllopezus pollicaris and Gymnodactylus geckoides) and Gekkonidae (Hemidactylus agrius, Lygodactylus klugei and Hemidactylus brasilianus) families in a semiarid region of Brazil. Six nematode species were identified: Parapharyngodon alvarengai and Spauligodon oxkutzcabiensis (Pharyngodonidae), Physaloptera lutzi (Physalopteridae), Skrjabinelazia intermedia (Seuratidae), Trichospirura sp. (Rhabdochonidae) and Piratuba sp. (Onchocercidae), and a cestode species, Oochoristica sp. (Linstowiidae). The most prevalent species were Spauligodon oxkutzcabiensis, which infected P. pollicaris (75%), and Parapharyngodon alvarengai, which infected G. geckoides (29%). South American lizards were identified as being new hosts for the Trichospirura genus (a usual parasite of mammals), and there were 16 new occurrences of parasite species in the five lizard species studied herein.
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31
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Koludarov I, Jackson TN, Brouw BOD, Dobson J, Dashevsky D, Arbuckle K, Clemente CJ, Stockdale EJ, Cochran C, Debono J, Stephens C, Panagides N, Li B, Manchadi MLR, Violette A, Fourmy R, Hendrikx I, Nouwens A, Clements J, Martelli P, Kwok HF, Fry BG. Enter the Dragon: The Dynamic and Multifunctional Evolution of Anguimorpha Lizard Venoms. Toxins (Basel) 2017; 9:E242. [PMID: 28783084 PMCID: PMC5577576 DOI: 10.3390/toxins9080242] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/04/2017] [Accepted: 08/04/2017] [Indexed: 01/08/2023] Open
Abstract
While snake venoms have been the subject of intense study, comparatively little work has been done on lizard venoms. In this study, we have examined the structural and functional diversification of anguimorph lizard venoms and associated toxins, and related these results to dentition and predatory ecology. Venom composition was shown to be highly variable across the 20 species of Heloderma, Lanthanotus, and Varanus included in our study. While kallikrein enzymes were ubiquitous, they were also a particularly multifunctional toxin type, with differential activities on enzyme substrates and also ability to degrade alpha or beta chains of fibrinogen that reflects structural variability. Examination of other toxin types also revealed similar variability in their presence and activity levels. The high level of venom chemistry variation in varanid lizards compared to that of helodermatid lizards suggests that venom may be subject to different selection pressures in these two families. These results not only contribute to our understanding of venom evolution but also reveal anguimorph lizard venoms to be rich sources of novel bioactive molecules with potential as drug design and development lead compounds.
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Affiliation(s)
- Ivan Koludarov
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia QLD 4072, Australia.
| | - Timothy Nw Jackson
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia QLD 4072, Australia.
- Australian Venom Research Unit, School of Biomedical Sciences, Level 2 Medical Building, University of Melbourne, Victoria 3010, Australia.
| | - Bianca Op den Brouw
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia QLD 4072, Australia.
| | - James Dobson
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia QLD 4072, Australia.
| | - Daniel Dashevsky
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia QLD 4072, Australia.
| | - Kevin Arbuckle
- Department of Biosciences, College of Science, Swansea University, Swansea SA2 8PP, UK.
| | - Christofer J Clemente
- University of the Sunshine Coast, School of Science and Engineering, Sippy Downs, Queensland 4558, Australia.
| | | | - Chip Cochran
- Department of Earth and Biological Sciences, Loma Linda University, Loma Linda, CA 92350, USA.
| | - Jordan Debono
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia QLD 4072, Australia.
| | - Carson Stephens
- School of Biomedical Sciences, Queensland University of Technology, Brisbane QLD 4001, Australia.
| | - Nadya Panagides
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia QLD 4072, Australia.
| | - Bin Li
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau.
| | | | - Aude Violette
- Alphabiotoxine Laboratory sprl, Barberie 15, 7911 Montroeul-au-bois, Belgium.
| | - Rudy Fourmy
- Alphabiotoxine Laboratory sprl, Barberie 15, 7911 Montroeul-au-bois, Belgium.
| | - Iwan Hendrikx
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia QLD 4072, Australia.
| | - Amanda Nouwens
- School of Chemistry and Molecular Biology, University of Queenslnd, St. Lucia QLD 4072, Australia.
| | - Judith Clements
- School of Biomedical Sciences, Queensland University of Technology, Brisbane QLD 4001, Australia.
| | | | - Hang Fai Kwok
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau.
| | - Bryan G Fry
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia QLD 4072, Australia.
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32
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Morinaga G, Bergmann PJ. Convergent body shapes have evolved via deterministic and historically contingent pathways in Lerista lizards. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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33
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Hernández-Díaz N, Torres R, Ramírez-Pinilla MP. Proteomic Profile of Mabuya sp. (Squamata: Scincidae) Ovary and Placenta During Gestation. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017; 328:371-389. [PMID: 28397398 DOI: 10.1002/jez.b.22739] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/28/2017] [Accepted: 03/02/2017] [Indexed: 02/07/2023]
Abstract
Reptiles are one of the most diverse groups of vertebrates, providing an integrated system for comparative studies on metabolic, animal physiology, and developmental biology. However, the molecular data available are limited and only recently have started to call attention in the "omics" sciences. Mabuya sp. is a viviparous placentrotrophic skink with particular reproductive features, including microlecithal eggs, early luteolysis, prolonged gestation, and development of a highly specialized placenta. This placenta is responsible for respiratory exchange and the transference of all nutrients necessary for embryonic development. Our aim was to identify differentially expressed proteins in the ovary and placenta of Mabuya sp. during early, mid, and late gestation; their possible metabolic pathways; and biological processes. We carried out a comparative proteomic analysis during gestation in both tissues by sodium dodecyl sulfate polyacrylamide gel electrophoresis, two-dimensional gel electrophoresis, and matrix-assisted laser desorption/ionization. Differential protein expression in both tissues (Student's t-test P < 0.05) was related to several processes such as cell structure, cell movement, and energy. Proteins found in ovary are mainly associated with follicular development and its regulation. In the placenta, particularly during mid and late gestation, protein expression is involved in nutrient metabolism, transport, protein synthesis, and embryonic development. This work provides new insights about the proteins expressed and their physiological mechanisms in Mabuya sp. placenta and ovary during gestation.
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Affiliation(s)
- Nathaly Hernández-Díaz
- Laboratorio de Biología Reproductiva de Vertebrados, Escuela de Biología, Facultad de Ciencias, Universidad Industrial de Santander, Bucaramanga, Santander, Colombia.,Grupo de Investigación en Bioquímica y Microbiología, GIBIM, Escuela de Química, Universidad Industrial de Santander, Bucaramanga, Santander, Colombia
| | - Rodrigo Torres
- Grupo de Investigación en Bioquímica y Microbiología, GIBIM, Escuela de Química, Universidad Industrial de Santander, Bucaramanga, Santander, Colombia.,Laboratorio de Biotecnología-CEO, Instituto Colombiano del Petróleo, ECOPETROL, Piedecuesta, Santander, Colombia
| | - Martha Patricia Ramírez-Pinilla
- Laboratorio de Biología Reproductiva de Vertebrados, Escuela de Biología, Facultad de Ciencias, Universidad Industrial de Santander, Bucaramanga, Santander, Colombia
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34
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Pan AD, Williams KA, Wilson JS. Are diurnal iguanian lizards the evolutionary drivers of New World female velvet ant (Hymenoptera: Mutillidae) Müllerian mimicry rings? Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Aaron D. Pan
- Don Harrington Discovery Center; 1200 Streit Drive Amarillo TX 79106 USA
| | - Kevin A. Williams
- Plant Pest Diagnostics Branch; California Department of Food & Agriculture; 3294 meadowview road Sacramento CA 95832 USA
| | - Joseph S. Wilson
- Department of Biology; Utah State University; 1021 West Vine Street Tooele UT 84074 USA
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35
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Origin of origami cockroach reveals long-lasting (11 Ma) phenotype instability following viviparity. Naturwissenschaften 2016; 103:78. [DOI: 10.1007/s00114-016-1398-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/14/2016] [Accepted: 08/17/2016] [Indexed: 10/21/2022]
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36
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Colston TJ, Jackson CR. Microbiome evolution along divergent branches of the vertebrate tree of life: what is known and unknown. Mol Ecol 2016; 25:3776-800. [DOI: 10.1111/mec.13730] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/25/2016] [Accepted: 05/30/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Timothy J. Colston
- Department of Biology The University of Mississippi University MS 38677 USA
| | - Colin R. Jackson
- Department of Biology The University of Mississippi University MS 38677 USA
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37
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The Primary Structure of β(I)-Chain of Hemoglobin from Snake Sindhi Krait (Bungarus sindanus sindanus). Protein J 2016; 35:193-201. [PMID: 27118198 DOI: 10.1007/s10930-016-9661-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The amino acid sequence of β(I)-globin chain from Sindhi Krait (Bungarus sindanus sindanus) was determined to study the molecular evolution among snakes. The hemoglobin was isolated from the red blood cells and was analyzed by ion-exchange chromatography (IEX). The crude globin was subjected to reversed phased-high performance liquid chromatography (RP-HPLC) using C4 column. The N-terminal sequences of intact globin chains and tryptic peptides were determined by Edman degradation in a pulsed liquid gas phase sequencer using an online Phenylthiohydantoin analyzer. Sindhi Krait is expected to express three hemoglobin components that are composed of β(II), β(I), α(D) and α(A)-globin chains, as apparent by IEX, RP-HPLC and N-terminal sequence analyses. Sequence alignment and phylogenetic analyses of β(I) globin chain from Sindhi Krait showed closest relationship with β(I) globin chain from Rattlesnake, Water snake and Indigo snake. Interestingly, comparison of primary sequence of β(I) globin chain of Sindhi Krait with human β chain revealed 63 % similarity along with the retention of all heme contact points. Variations among the two sequences were prominent at αβ contact points and in regions directly not important for function.
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38
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Booth W, Schuett GW. The emerging phylogenetic pattern of parthenogenesis in snakes. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12744] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Warren Booth
- Department of Biological Sciences; The University of Tulsa; Tulsa OK 74104 USA
- The Copperhead Institute; PO Box 6755 Spartanburg SC 29304 USA
- Chiricahua Desert Museum; PO Box 376 Rodeo NM 88056 USA
| | - Gordon W. Schuett
- The Copperhead Institute; PO Box 6755 Spartanburg SC 29304 USA
- Chiricahua Desert Museum; PO Box 376 Rodeo NM 88056 USA
- Department of Biology and Neuroscience Institute; Georgia State University; Atlanta GA 30303 USA
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39
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40
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Streicher JW, Schulte JA, Wiens JJ. How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards. Syst Biol 2015; 65:128-45. [PMID: 26330450 DOI: 10.1093/sysbio/syv058] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 08/04/2015] [Indexed: 11/12/2022] Open
Abstract
Targeted sequence capture is becoming a widespread tool for generating large phylogenomic data sets to address difficult phylogenetic problems. However, this methodology often generates data sets in which increasing the number of taxa and loci increases amounts of missing data. Thus, a fundamental (but still unresolved) question is whether sampling should be designed to maximize sampling of taxa or genes, or to minimize the inclusion of missing data cells. Here, we explore this question for an ancient, rapid radiation of lizards, the pleurodont iguanians. Pleurodonts include many well-known clades (e.g., anoles, basilisks, iguanas, and spiny lizards) but relationships among families have proven difficult to resolve strongly and consistently using traditional sequencing approaches. We generated up to 4921 ultraconserved elements with sampling strategies including 16, 29, and 44 taxa, from 1179 to approximately 2.4 million characters per matrix and approximately 30% to 60% total missing data. We then compared mean branch support for interfamilial relationships under these 15 different sampling strategies for both concatenated (maximum likelihood) and species tree (NJst) approaches (after showing that mean branch support appears to be related to accuracy). We found that both approaches had the highest support when including loci with up to 50% missing taxa (matrices with ~40-55% missing data overall). Thus, our results show that simply excluding all missing data may be highly problematic as the primary guiding principle for the inclusion or exclusion of taxa and genes. The optimal strategy was somewhat different for each approach, a pattern that has not been shown previously. For concatenated analyses, branch support was maximized when including many taxa (44) but fewer characters (1.1 million). For species-tree analyses, branch support was maximized with minimal taxon sampling (16) but many loci (4789 of 4921). We also show that the choice of these sampling strategies can be critically important for phylogenomic analyses, since some strategies lead to demonstrably incorrect inferences (using the same method) that have strong statistical support. Our preferred estimate provides strong support for most interfamilial relationships in this important but phylogenetically challenging group.
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Affiliation(s)
- Jeffrey W Streicher
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA; Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK and
| | - James A Schulte
- Department of Biology, Clarkson University, Potsdam, NY 13699, USA
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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41
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Stewart JR. Placental specializations in lecithotrophic viviparous squamate reptiles. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:549-61. [DOI: 10.1002/jez.b.22632] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/29/2015] [Indexed: 12/19/2022]
Affiliation(s)
- James R. Stewart
- Department of Biological Sciences; East Tennessee State University; Johnson City Tennessee 37614
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42
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Gardner MG, Pearson SK, Johnston GR, Schwarz MP. Group living in squamate reptiles: a review of evidence for stable aggregations. Biol Rev Camb Philos Soc 2015; 91:925-936. [PMID: 26052742 DOI: 10.1111/brv.12201] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 05/06/2015] [Accepted: 05/15/2015] [Indexed: 01/19/2023]
Abstract
How sociality evolves and is maintained remains a key question in evolutionary biology. Most studies to date have focused on insects, birds, and mammals but data from a wider range of taxonomic groups are essential to identify general patterns and processes. The extent of social behaviour among squamate reptiles is under-appreciated, yet they are a promising group for further studies. Living in aggregations is posited as an important step in the evolution of more complex sociality. We review data on aggregations among squamates and find evidence for some form of aggregations in 94 species across 22 families. Of these, 18 species across 7 families exhibited 'stable' aggregations that entail overlapping home ranges and stable membership in long-term (years) or seasonal aggregations. Phylogenetic analysis suggests that stable aggregations have evolved multiple times in squamates. We: (i) identify significant gaps in our understanding; (ii) outline key traits which should be the focus of future research; and (iii) outline the potential for utilising reproductive skew theory to provide insights into squamate sociality.
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Affiliation(s)
- Michael G Gardner
- School of Biological Sciences, Flinders University of South Australia, GPO Box 2100, Adelaide, 5001, Australia. .,South Australian Museum, North Terrace, Adelaide, 5000, Australia.
| | - Sarah K Pearson
- School of Biological Sciences, Flinders University of South Australia, GPO Box 2100, Adelaide, 5001, Australia
| | - Gregory R Johnston
- School of Biological Sciences, Flinders University of South Australia, GPO Box 2100, Adelaide, 5001, Australia.,South Australian Museum, North Terrace, Adelaide, 5000, Australia
| | - Michael P Schwarz
- School of Biological Sciences, Flinders University of South Australia, GPO Box 2100, Adelaide, 5001, Australia
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43
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Miralles A, Hipsley CA, Erens J, Gehara M, Rakotoarison A, Glaw F, Müller J, Vences M. Distinct patterns of desynchronized limb regression in malagasy scincine lizards (squamata, scincidae). PLoS One 2015; 10:e0126074. [PMID: 26042667 PMCID: PMC4456255 DOI: 10.1371/journal.pone.0126074] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 03/28/2015] [Indexed: 12/27/2022] Open
Abstract
Scincine lizards in Madagascar form an endemic clade of about 60 species exhibiting a variety of ecomorphological adaptations. Several subclades have adapted to burrowing and convergently regressed their limbs and eyes, resulting in a variety of partial and completely limbless morphologies among extant taxa. However, patterns of limb regression in these taxa have not been studied in detail. Here we fill this gap in knowledge by providing a phylogenetic analysis of DNA sequences of three mitochondrial and four nuclear gene fragments in an extended sampling of Malagasy skinks, and microtomographic analyses of osteology of various burrowing taxa adapted to sand substrate. Based on our data we propose to (i) consider Sirenoscincus Sakata & Hikida, 2003, as junior synonym of Voeltzkowia Boettger, 1893; (ii) resurrect the genus name Grandidierina Mocquard, 1894, for four species previously included in Voeltzkowia; and (iii) consider Androngo Brygoo, 1982, as junior synonym of Pygomeles Grandidier, 1867. By supporting the clade consisting of the limbless Voeltzkowia mira and the forelimb-only taxa V. mobydick and V. yamagishii, our data indicate that full regression of limbs and eyes occurred in parallel twice in the genus Voeltzkowia (as hitherto defined) that we consider as a sand-swimming ecomorph: in the Voeltzkowia clade sensu stricto the regression first affected the hindlimbs and subsequently the forelimbs, whereas the Grandidierina clade first regressed the forelimbs and subsequently the hindlimbs following the pattern prevalent in squamates. Timetree reconstructions for the Malagasy Scincidae contain a substantial amount of uncertainty due to the absence of suitable primary fossil calibrations. However, our preliminary reconstructions suggest rapid limb regression in Malagasy scincids with an estimated maximal duration of 6 MYr for a complete regression in Paracontias, and 4 and 8 MYr respectively for complete regression of forelimbs in Grandidierina and hindlimbs in Voeltzkowia.
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Affiliation(s)
- Aurélien Miralles
- Centre d’Ecologie Fonctionnelle et Evolutive, Centre National de la Recherche Scientifique, Montpellier, France
- Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany
- * E-mail:
| | - Christy A. Hipsley
- Museum für Naturkunde, Leibniz-Institut für Evolutions und Biodiversitätsforschung, Berlin, Germany
- University of Melbourne, School of BioSciences, Melbourne, Victoria, Australia
| | - Jesse Erens
- Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany
- Biosystematics Group, Wageningen University, Droevendaalsesteeg, Wageningen, The Netherlands
| | - Marcelo Gehara
- Centro de Biociencias, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Andolalao Rakotoarison
- Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany
- Département de Biologie Animale, Université d’Antananarivo, Antananarivo, Madagascar
| | - Frank Glaw
- Zoologische Staatssammlung München, München, Germany
| | - Johannes Müller
- Museum für Naturkunde, Leibniz-Institut für Evolutions und Biodiversitätsforschung, Berlin, Germany
| | - Miguel Vences
- Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany
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44
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Gibson S, Penniket S, Cree A. Are viviparous lizards from cool climates ever exclusively nocturnal? Evidence for extensive basking in a New Zealand gecko. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12533] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sophie Gibson
- Department of Zoology; University of Otago; P.O. Box 56 Dunedin New Zealand
| | - Sophie Penniket
- Department of Zoology; University of Otago; P.O. Box 56 Dunedin New Zealand
| | - Alison Cree
- Department of Zoology; University of Otago; P.O. Box 56 Dunedin New Zealand
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45
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Reeder TW, Townsend TM, Mulcahy DG, Noonan BP, Wood PL, Sites JW, Wiens JJ. Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa. PLoS One 2015; 10:e0118199. [PMID: 25803280 PMCID: PMC4372529 DOI: 10.1371/journal.pone.0118199] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 01/08/2015] [Indexed: 11/18/2022] Open
Abstract
Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement.
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Affiliation(s)
- Tod W. Reeder
- Department of Biology, San Diego State University, San Diego, California, 92182, United States of America
| | - Ted M. Townsend
- Department of Biology, San Diego State University, San Diego, California, 92182, United States of America
| | - Daniel G. Mulcahy
- Laboratories of Analytical Biology, Smithsonian Institution, 10th & Constitution Aves. NW, Washington, D.C., 20560, United States of America
| | - Brice P. Noonan
- Department of Biology, University of Mississippi, Box 1848, Mississippi, 38677, United States of America
| | - Perry L. Wood
- Department of Biology and Bean Life Science Museum, Brigham Young University, Provo, Utah, 84602, United States of America
| | - Jack W. Sites
- Department of Biology and Bean Life Science Museum, Brigham Young University, Provo, Utah, 84602, United States of America
| | - John J. Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721, United States of America
- * E-mail:
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46
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Pyron RA, Burbrink FT. Contrasting models of parity-mode evolution in squamate reptiles. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:467-72. [DOI: 10.1002/jez.b.22593] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 08/20/2014] [Indexed: 12/31/2022]
Affiliation(s)
- R. Alexander Pyron
- Department of Biological Sciences; The George Washington University; Washington DC
| | - Frank T. Burbrink
- Department of Biology; The Graduate School and University Center; The City University of New York; New York New York
- Department of Biology; The College of Staten Island; The City University of New York; New York New York
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47
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Aspden JW, Armstrong CL, Gutierrez-Ibanez CI, Hawkes R, Iwaniuk AN, Kohl T, Graham DJ, Wylie DR. Zebrin II / aldolase C expression in the cerebellum of the western diamondback rattlesnake (Crotalus atrox). PLoS One 2015; 10:e0117539. [PMID: 25692946 PMCID: PMC4334253 DOI: 10.1371/journal.pone.0117539] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/27/2014] [Indexed: 11/19/2022] Open
Abstract
Aldolase C, also known as Zebrin II (ZII), is a glycolytic enzyme that is expressed in cerebellar Purkinje cells of the vertebrate cerebellum. In both mammals and birds, ZII is expressed heterogeneously, such that there are sagittal stripes of Purkinje cells with high ZII expression (ZII+), alternating with stripes of Purkinje cells with little or no expression (ZII-). The patterns of ZII+ and ZII- stripes in the cerebellum of birds and mammals are strikingly similar, suggesting that it may have first evolved in the stem reptiles. In this study, we examined the expression of ZII in the cerebellum of the western diamondback rattlesnake (Crotalus atrox). In contrast to birds and mammals, the cerebellum of the rattlesnake is much smaller and simpler, consisting of a small, unfoliated dome of cells. A pattern of alternating ZII+ and ZII- sagittal stripes cells was not observed: rather all Purkinje cells were ZII+. This suggests that ZII stripes have either been lost in snakes or that they evolved convergently in birds and mammals.
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Affiliation(s)
- Joel W. Aspden
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Alberta, Canada, T6G 2E9
| | - Carol L. Armstrong
- Department of Biology, Mount Royal University, 4825 Mount Royal Gate SW, Calgary, Alberta, Canada, T3E 6K6
| | - Cristian I. Gutierrez-Ibanez
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Alberta, Canada, T6G 2E9
- Lehrstuhl für Zoologie, Technische Universität München, Liesel-Beckmann Straße 4, 85354, Freising-Weihenstephan, Germany
| | - Richard Hawkes
- Department of Cell Biology & Anatomy, Genes and Development Research Group, and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada, T2N 4N1
| | - Andrew N. Iwaniuk
- Department of Neuroscience, Canadian Centre for Behavioural Neuroscience, University of Lethbridge, Lethbridge, Alberta, Canada, T1K 3M4
| | - Tobias Kohl
- Lehrstuhl für Zoologie, Technische Universität München, Liesel-Beckmann Straße 4, 85354, Freising-Weihenstephan, Germany
| | - David J. Graham
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Alberta, Canada, T6G 2E9
| | - Douglas R. Wylie
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Alberta, Canada, T6G 2E9
- * E-mail:
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King B, Lee MSY. Ancestral State Reconstruction, Rate Heterogeneity, and the Evolution of Reptile Viviparity. Syst Biol 2015; 64:532-44. [DOI: 10.1093/sysbio/syv005] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/14/2015] [Indexed: 11/13/2022] Open
Affiliation(s)
- Benedict King
- School of Biological Sciences, Flinders University, PO Box 2100, Adelaide, South Australia 5001; 2School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005; and 3Earth Sciences Section, South Australian Museum, North Terrace, Adelaide 5000, Australia
| | - Michael S. Y. Lee
- School of Biological Sciences, Flinders University, PO Box 2100, Adelaide, South Australia 5001; 2School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005; and 3Earth Sciences Section, South Australian Museum, North Terrace, Adelaide 5000, Australia
- School of Biological Sciences, Flinders University, PO Box 2100, Adelaide, South Australia 5001; 2School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005; and 3Earth Sciences Section, South Australian Museum, North Terrace, Adelaide 5000, Australia
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Cornetti L, Belluardo F, Ghielmi S, Giovine G, Ficetola GF, Bertorelle G, Vernesi C, Hauffe HC. Reproductive isolation between oviparous and viviparous lineages of the Eurasian common lizardZootoca viviparain a contact zone. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12478] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luca Cornetti
- Department of Biodiversity and Molecular Ecology; Research and Innovation Centre; Fondazione Edmund Mach; Via E. Mach 1 38010 San Michele all'Adige Trento Italy
- Dipartimento di Scienze della Vita e Biotecnologie; University of Ferrara; Via Borsari 46 44121 Ferrara Italy
| | - Francesco Belluardo
- Department of Biodiversity and Molecular Ecology; Research and Innovation Centre; Fondazione Edmund Mach; Via E. Mach 1 38010 San Michele all'Adige Trento Italy
- Dipartimento di Bioscienze; University of Milan; Via Festa del Perdono 7 20122 Milan Italy
| | - Samuele Ghielmi
- Museo Insubrico di Storia Naturale di Clivio e Induno Olona; Via Manzoni 215 21050 Clivio Varese Italy
| | - Giovanni Giovine
- Stazione sperimentale regionale per lo studio e la conservazione degli anfibi in Lombardia - Lago di Endine; Via del Cantiere 4 24065 Lovere Bergamo Italy
| | - Gentile F. Ficetola
- Dipartimento di Scienze dell'Ambiente e del Territorio e di Scienze della Terra; University of Milano-Bicocca; Piazza dell'Ateneo Nuovo 1 20126 Milan Italy
- Laboratoire d'Ecologie Alpine (LECA); Université Grenoble-Alpes; 2233 Rue de la Piscine 38041 Grenoble Cedex 9 France
| | - Giorgio Bertorelle
- Dipartimento di Scienze della Vita e Biotecnologie; University of Ferrara; Via Borsari 46 44121 Ferrara Italy
| | - Cristiano Vernesi
- Department of Biodiversity and Molecular Ecology; Research and Innovation Centre; Fondazione Edmund Mach; Via E. Mach 1 38010 San Michele all'Adige Trento Italy
| | - Heidi C. Hauffe
- Department of Biodiversity and Molecular Ecology; Research and Innovation Centre; Fondazione Edmund Mach; Via E. Mach 1 38010 San Michele all'Adige Trento Italy
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Sharpe SS, Koehler SA, Kuckuk RM, Serrano M, Vela PA, Mendelson J, Goldman DI. Locomotor benefits of being a slender and slick sand swimmer. ACTA ACUST UNITED AC 2014; 218:440-50. [PMID: 25524983 DOI: 10.1242/jeb.108357] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Squamates classified as 'subarenaceous' possess the ability to move long distances within dry sand; body elongation among sand and soil burrowers has been hypothesized to enhance subsurface performance. Using X-ray imaging, we performed the first kinematic investigation of the subsurface locomotion of the long, slender shovel-nosed snake (Chionactis occipitalis) and compared its biomechanics with those of the shorter, limbed sandfish lizard (Scincus scincus). The sandfish was previously shown to maximize swimming speed and minimize the mechanical cost of transport during burial. Our measurements revealed that the snake also swims through sand by propagating traveling waves down the body, head to tail. Unlike the sandfish, the snake nearly followed its own tracks, thus swimming in an approximate tube of self-fluidized granular media. We measured deviations from tube movement by introducing a parameter, the local slip angle, βs, which measures the angle between the direction of movement of each segment and body orientation. The average βs was smaller for the snake than for the sandfish; granular resistive force theory (RFT) revealed that the curvature utilized by each animal optimized its performance. The snake benefits from its slender body shape (and increased vertebral number), which allows propagation of a higher number of optimal curvature body undulations. The snake's low skin friction also increases performance. The agreement between experiment and RFT combined with the relatively simple properties of the granular 'frictional fluid' make subarenaceous swimming an attractive system to study functional morphology and bauplan evolution.
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Affiliation(s)
- Sarah S Sharpe
- Interdisciplinary Bioengineering Program, Georgia Tech, Atlanta, GA 30332-0363, USA Department of Biomedical Engineering, Georgia Tech, Atlanta, GA 30332-0363, USA
| | - Stephan A Koehler
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Robyn M Kuckuk
- Department of Biomedical Engineering, Georgia Tech, Atlanta, GA 30332-0363, USA
| | - Miguel Serrano
- Department of Electrical and Computer Engineering, Georgia Tech, Atlanta, GA 30332-0363, USA
| | - Patricio A Vela
- Department of Electrical and Computer Engineering, Georgia Tech, Atlanta, GA 30332-0363, USA
| | - Joseph Mendelson
- Zoo Atlanta and School of Biology, Georgia Tech, Atlanta, GA 30332-0363, USA
| | - Daniel I Goldman
- Interdisciplinary Bioengineering Program, Georgia Tech, Atlanta, GA 30332-0363, USA School of Physics, Georgia Tech, Atlanta, GA 30332-0363, USA
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