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Zhan L, Chen Y, He J, Guo Z, Wu L, Storey KB, Zhang J, Yu D. The Phylogenetic Relationships of Major Lizard Families Using Mitochondrial Genomes and Selection Pressure Analyses in Anguimorpha. Int J Mol Sci 2024; 25:8464. [PMID: 39126033 PMCID: PMC11312734 DOI: 10.3390/ijms25158464] [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: 06/11/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024] Open
Abstract
Anguimorpha, within the order Squamata, represents a group with distinct morphological and behavioral characteristics in different ecological niches among lizards. Within Anguimorpha, there is a group characterized by limb loss, occupying lower ecological niches, concentrated within the subfamily Anguinae. Lizards with limbs and those without exhibit distinct locomotor abilities when adapting to their habitats, which in turn necessitate varying degrees of energy expenditure. Mitochondria, known as the metabolic powerhouses of cells, play a crucial role in providing approximately 95% of an organism's energy. Functionally, mitogenomes (mitochondrial genomes) can serve as a valuable tool for investigating potential adaptive evolutionary selection behind limb loss in reptiles. Due to the variation of mitogenome structures among each species, as well as its simple genetic structure, maternal inheritance, and high evolutionary rate, the mitogenome is increasingly utilized to reconstruct phylogenetic relationships of squamate animals. In this study, we sequenced the mitogenomes of two species within Anguimorpha as well as the mitogenomes of two species in Gekkota and four species in Scincoidea. We compared these data with the mitogenome content and evolutionary history of related species. Within Anguimorpha, between the mitogenomes of limbless and limbed lizards, a branch-site model analysis supported the presence of 10 positively selected sites: Cytb protein (at sites 183 and 187), ND2 protein (at sites 90, 155, and 198), ND3 protein (at site 21), ND5 protein (at sites 12 and 267), and ND6 protein (at sites 72 and 119). These findings suggested that positive selection of mitogenome in limbless lizards may be associated with the energy requirements for their locomotion. Additionally, we acquired data from 205 mitogenomes from the NCBI database. Bayesian inference (BI) and Maximum Likelihood (ML) trees were constructed using the 13 mitochondrial protein-coding genes (PCGs) and two rRNAs (12S rRNA and 16S rRNA) from 213 mitogenomes. Our phylogenetic tree and the divergence time estimates for Squamata based on mitogenome data are consistent with results from previous studies. Gekkota was placed at the root of Squamata in both BI and ML trees. However, within the Toxicofera clade, due to long-branch attraction, Anguimorpha and (Pleurodonta + (Serpentes + Acrodonta)) were closely related groupings, which might indicate errors and also demonstrate that mitogenome-based phylogenetic trees may not effectively resolve long-branch attraction issues. Additionally, we reviewed the origin and diversification of Squamata throughout the Mesozoic era, suggesting that Squamata originated in the Late Triassic (206.05 Mya), with the diversification of various superfamilies occurring during the Cretaceous period. Future improvements in constructing squamate phylogenetic relationships using mitogenomes will rely on identifying snake and acrodont species with slower evolutionary rates, ensuring comprehensive taxonomic coverage of squamate diversity, and increasing the number of genes analyzed.
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Affiliation(s)
- Lemei Zhan
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Yuxin Chen
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Jingyi He
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Zhiqiang Guo
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Lian Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Jiayong Zhang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Laboratory of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Danna Yu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Laboratory of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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Chen BZ, Li DW, Luo KY, Jiu ST, Dong X, Wang WB, Li XZ, Hao TT, Lei YH, Guo DZ, Liu XT, Duan SC, Zhu YF, Chen W, Dong Y, Yu WB. Chromosome-level assembly of Lindenbergia philippensis and comparative genomic analyses shed light on genome evolution in Lamiales. FRONTIERS IN PLANT SCIENCE 2024; 15:1444234. [PMID: 39157518 PMCID: PMC11327160 DOI: 10.3389/fpls.2024.1444234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 07/16/2024] [Indexed: 08/20/2024]
Abstract
Lamiales, comprising over 23,755 species across 24 families, stands as a highly diverse and prolific plant group, playing a significant role in the cultivation of horticultural, ornamental, and medicinal plant varieties. Whole-genome duplication (WGD) and its subsequent post-polyploid diploidization (PPD) process represent the most drastic type of karyotype evolution, injecting significant potential for promoting the diversity of this lineage. However, polyploidization histories, as well as genome and subgenome fractionation following WGD events in Lamiales species, are still not well investigated. In this study, we constructed a chromosome-level genome assembly of Lindenbergia philippensis (Orobanchaceae) and conducted comparative genomic analyses with 14 other Lamiales species. L. philippensis is positioned closest to the parasitic lineage within Orobanchaceae and has a conserved karyotype. Through a combination of Ks analysis and syntenic depth analysis, we reconstructed and validated polyploidization histories of Lamiales species. Our results indicated that Primulina huaijiensis underwent three rounds of diploidization events following the γ-WGT event, rather than two rounds as reported. Besides, we reconfirmed that most Lamiales species shared a common diploidization event (L-WGD). Subsequently, we constructed the Lamiales Ancestral Karyotype (LAK), comprising 11 proto-chromosomes, and elucidated its evolutionary trajectory, highlighting the highly flexible reshuffling of the Lamiales paleogenome. We identified biased fractionation of subgenomes following the L-WGD event across eight species, and highlighted the positive impacts of non-WGD genes on gene family expansion. This study provides novel genomic resources and insights into polyploidy and karyotype remodeling of Lamiales species, essential for advancing our understanding of species diversification and genome evolution.
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Affiliation(s)
- Bao-Zheng Chen
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Da-Wei Li
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Kai-Yong Luo
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Song-Tao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao Dong
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Wei-Bin Wang
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xu-Zhen Li
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Ting-Ting Hao
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Ya-Hui Lei
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Da-Zhong Guo
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xu-Tao Liu
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Sheng-Chang Duan
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yi-Fan Zhu
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Wei Chen
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yang Dong
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Wen-Bin Yu
- Center for Integrative Conservation and Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla, Yunnan, China
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3
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Brennan IG, Singhal S, Al Bkhetan Z. pipesnake: generalized software for the assembly and analysis of phylogenomic datasets from conserved genomic loci. Bioinformatics 2024; 40:btae195. [PMID: 38597877 PMCID: PMC11082421 DOI: 10.1093/bioinformatics/btae195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 03/18/2024] [Accepted: 04/08/2024] [Indexed: 04/11/2024] Open
Abstract
MOTIVATION Phylogenetics has moved into the era of genomics, incorporating enormous volumes of data to study questions at both shallow and deep scales. With this increase in information, phylogeneticists need new tools and skills to manipulate and analyze these data. To facilitate these tasks and encourage reproducibility, the community is increasingly moving toward automated workflows. RESULTS Here we present pipesnake, a phylogenomics pipeline written in Nextflow for the processing, assembly, and phylogenetic estimation of genomic data from short-read sequences. pipesnake is an easy to use and efficient software package designed for this next era in phylogenetics. AVAILABILITY AND IMPLEMENTATION pipesnake is publicly available on GitHub at https://github.com/AusARG/pipesnake and accompanied by documentation and a wiki/tutorial.
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Affiliation(s)
- Ian G Brennan
- Natural History Museum, London, SW7 5BD, United Kingdom
- Division of Ecology & Evolution, The Australian National University, Canberra, ACT 2601, Australia
| | - Sonal Singhal
- Department of Biology, California State University, Dominguez Hills, Carson, CA 90747, United States
| | - Ziad Al Bkhetan
- Australian BioCommons, The University of Melbourne, Melbourne, VIC 3010, Australia
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Bernstein JM, Voris HK, Stuart BL, Karns DR, McGuire JA, Iskandar DT, Riyanto A, Calderón-Acevedo CA, Brown RM, Gehara M, Soto-Centeno JA, Ruane S. Integrative methods reveal multiple drivers of diversification in rice paddy snakes. Sci Rep 2024; 14:4727. [PMID: 38472264 DOI: 10.1038/s41598-024-54744-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
Divergence dating analyses in systematics provide a framework to develop and test biogeographic hypotheses regarding speciation. However, as molecular datasets grow from multilocus to genomic, sample sizes decrease due to computational burdens, and the testing of fine-scale biogeographic hypotheses becomes difficult. In this study, we use coalescent demographic models to investigate the diversification of poorly known rice paddy snakes from Southeast Asia (Homalopsidae: Hypsiscopus), which have conflicting dates of origin based on previous studies. We use coalescent modeling to test the hypothesis that Hypsiscopus diversified 2.5 mya during the Khorat Plateau uplift in Thailand. Additionally, we use ecological niche analyses to identify potential differences in the niche space of the two most widely distributed species in the past and present. Our results suggest Hypsiscopus diversified ~ 2.4 mya, supporting that the Khorat Plateau may have initiated the diversification of rice paddy snakes. We also find significant niche differentiation and shifts between species of Hypsiscopus, indicating that environmental differences may have sustained differentiation of this genus after the Khorat Plateau uplift. Our study expands on the diversification history of snakes in Southeast Asia, and highlights how results from smaller multilocus datasets can be useful in developing and testing biogeographic hypotheses alongside genomic datasets.
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Affiliation(s)
- Justin M Bernstein
- Center for Genomics, University of Kansas, Dyche Hall, 1345 Jayhawk Blvd, Lawrence, KS, 66045, USA.
| | - Harold K Voris
- Life Sciences Section, Negaunee Integrative Research Center, Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA
| | - Bryan L Stuart
- Section of Research and Collections, North Carolina Museum of Natural Sciences, Raleigh, NC, 27601, USA
| | - Daryl R Karns
- Biology Department, Hanover College, Hanover, IN, 47243, USA
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Djoko T Iskandar
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
| | - Awal Riyanto
- Museum Zoologicum Bogoriense, Research Center for Biology, National Research and Innovation Agency of Indonesia (BRIN), Cibinong, 16911, Indonesia
| | - Camilo A Calderón-Acevedo
- State University of New York: College of Environmental Science and Forestry, Syracuse, NY, 13210, USA
| | - Rafe M Brown
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, 66045, USA
| | - Marcelo Gehara
- Department of Earth and Environmental Science, Rutgers University-Newark, Newark, NJ, 07102, USA
| | - J Angel Soto-Centeno
- Department of Earth and Environmental Science, Rutgers University-Newark, Newark, NJ, 07102, USA
- Department of Mammalogy, American Museum of Natural History, New York, NY, 10024, USA
| | - Sara Ruane
- Life Sciences Section, Negaunee Integrative Research Center, Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA
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Title PO, Singhal S, Grundler MC, Costa GC, Pyron RA, Colston TJ, Grundler MR, Prates I, Stepanova N, Jones MEH, Cavalcanti LBQ, Colli GR, Di-Poï N, Donnellan SC, Moritz C, Mesquita DO, Pianka ER, Smith SA, Vitt LJ, Rabosky DL. The macroevolutionary singularity of snakes. Science 2024; 383:918-923. [PMID: 38386744 DOI: 10.1126/science.adh2449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 01/02/2024] [Indexed: 02/24/2024]
Abstract
Snakes and lizards (Squamata) represent a third of terrestrial vertebrates and exhibit spectacular innovations in locomotion, feeding, and sensory processing. However, the evolutionary drivers of this radiation remain poorly known. We infer potential causes and ultimate consequences of squamate macroevolution by combining individual-based natural history observations (>60,000 animals) with a comprehensive time-calibrated phylogeny that we anchored with genomic data (5400 loci) from 1018 species. Due to shifts in the dynamics of speciation and phenotypic evolution, snakes have transformed the trophic structure of animal communities through the recurrent origin and diversification of specialized predatory strategies. Squamate biodiversity reflects a legacy of singular events that occurred during the early history of snakes and reveals the impact of historical contingency on vertebrate biodiversity.
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Affiliation(s)
- Pascal O Title
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
- Environmental Resilience Institute, Indiana University, Bloomington, IN 47408, USA
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sonal Singhal
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology, California State University, Dominguez Hills, Carson, CA 90747, USA
| | - Michael C Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gabriel C Costa
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology and Environmental Sciences, Auburn University at Montgomery, Montgomery, AL 36117, USA
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
| | - Timothy J Colston
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00680, Puerto Rico
| | - Maggie R Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ivan Prates
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Natasha Stepanova
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marc E H Jones
- Science Group: Fossil Reptiles, Amphibians and Birds Section, Natural History Museum, London SW7 5BD, UK
- Research Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
- Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Lucas B Q Cavalcanti
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba 58051-900, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Distrito Federal 70910-900, Brazil
| | - Nicolas Di-Poï
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | | | - Craig Moritz
- Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
| | - Daniel O Mesquita
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba 58051-900, Brazil
| | - Eric R Pianka
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laurie J Vitt
- Sam Noble Museum and Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Meyer D, Brownstein CD, Jenkins KM, Gauthier JA. A Morrison stem gekkotan reveals gecko evolution and Jurassic biogeography. Proc Biol Sci 2023; 290:20232284. [PMID: 38018104 PMCID: PMC10685121 DOI: 10.1098/rspb.2023.2284] [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: 10/09/2023] [Accepted: 10/30/2023] [Indexed: 11/30/2023] Open
Abstract
Geckos are a speciose and globally distributed clade of Squamata (lizards, including snakes and amphisbaenians) that are characterized by a host of modifications for nocturnal, scansorial and insectivorous ecologies. They are among the oldest divergences in the lizard crown, so understanding the origin of geckoes (Gekkota) is essential to understanding the origin of Squamata, the most species-rich extant tetrapod clade. However, the poor fossil record of gekkotans has obscured the sequence and timing of the assembly of their distinctive morphology. Here, we describe the first North American stem gekkotan based on a three-dimensionally preserved skull from the Morrison Formation of western North America. Despite its Late Jurassic age, the new species already possesses several key characteristics of the gekkotan skull along with retained ancestral features. We show that this new stem gekkotan, and several previously named species of uncertain phylogenetic relationships, comprise a widespread clade of early crown lizards, substantiating faunal homogeneity in Laurasia during the Late Jurassic that extended across disparate ecological, body-size and physiological classes.
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Affiliation(s)
- Dalton Meyer
- Department of Earth and Planetary Sciences, Yale University, New Haven, CT 06506520-8109, USA
| | - Chase D. Brownstein
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520-8106, USA
- Stamford Museum and Nature Center, Stamford, CT 06903, USA
| | - Kelsey M. Jenkins
- Department of Earth and Planetary Sciences, Yale University, New Haven, CT 06506520-8109, USA
- Yale Peabody Museum, New Haven, CT 06520-8118, USA
| | - Jacques A. Gauthier
- Department of Earth and Planetary Sciences, Yale University, New Haven, CT 06506520-8109, USA
- Yale Peabody Museum, New Haven, CT 06520-8118, USA
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Capaldo A. The Adrenal Gland of Squamata (Reptilia): A Comparative Overview. Animals (Basel) 2023; 13:2686. [PMID: 37684950 PMCID: PMC10486442 DOI: 10.3390/ani13172686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023] Open
Abstract
The adrenal gland is a complex endocrine organ composed of two components: a steroidogenic tissue, which produces steroid hormones, and a chromaffin tissue, which mainly produces norepinephrine and epinephrine. Through evolution, their relationships with each other changed. They begin as isolated chromaffin and steroidogenic cell aggregates, typical of fish, and end with the advanced compact gland, typical of mammals, which consists of an external steroidogenic cortical zone and an internal chromaffin medullary zone. The adrenal gland of reptiles is unique because, with few exceptions, it is near the gonads and genital ducts, and the chromaffin and steroidogenic tissues are closely associated. However, the degree of mixing is variable. For example, in Squamata, the mixing degree of chromaffin and steroidogenic tissues, their reciprocal position in the gland, and the relative quantities of norepinephrine and epinephrine secreted by the chromaffin cells are extremely variable. This variability could be related to the phylogenetic history of the species. After a brief discussion of the adrenal gland and its main functions in vertebrates, this overview will examine the general characteristics of the adrenal gland of squamates, the differences in morphology of the gland, and the possible relationships with the phylogeny of the different species.
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Affiliation(s)
- Anna Capaldo
- Department of Biology, University of Naples Federico II, Via Cinthia, Edificio 7, 80126 Naples, Italy
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8
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Rezaei Orimi J, Eskandarzadeh N, Amrollahi-Sharifabadi M, Miri V, Aghabeiglooei Z, Rezghi M. Analyzing the biological traits of snakes in Avicenna's Canon of medicine and making a comparison with contemporary serpentology. Toxicon 2023; 231:107198. [PMID: 37331525 DOI: 10.1016/j.toxicon.2023.107198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 06/20/2023]
Abstract
Snakes are a group of reptiles in the order of squamata that have been the subject of scientific research for years. This study aimed to determine the biological characteristics of snakes that were mentioned in Avicenna's Canon of Medicine to compare with modern serpentology. Data were obtained from the Canon of Medicine using keywords concerning snakes and also appropriate literature in PubMed, Scopus, Web of Science, Scientific Information Database (SID), and IranDoc. Our results revealed that Avicenna divided snakes into three classes including highly, moderately, and slightly venomous snakes that are comparable to modern serpontology. Moreover, Avicenna clarified physiological factors such as age, gender, size, psychological state, hunger state, physical features, the type of living climate, habitat, and the time of snakebite. Considering the snake features presented in the Canon of Medicine, even though is not feasible to make a full comparison between Avicenna's snake knowledge and modern serpentology but some characteristics can be still applicable. Conclusively, the present study suggested that the criteria used for the identification and classification of snakes have changed from the medieval ages to the nowadays.
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Affiliation(s)
- Jamal Rezaei Orimi
- Traditional Medicine and History of Medical Sciences Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
| | | | | | - Vajihe Miri
- Department of Research Sciences, Faculty of Theology, Law and Political Sciences, Azad University, Tehran, Iran.
| | - Zahra Aghabeiglooei
- Traditional Medicine Clinical Trial Research Center, Shahed University, Tehran, Iran.
| | - Maedeh Rezghi
- Traditional Medicine and History of Medical Sciences Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran; Department of Traditional Medicine, School of Traditional Medicine, Babol University of Medical Sciences, Babol, Iran.
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9
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Kahnt B, Theodorou P, Grimm-Seyfarth A, Onstein RE. When lizards try out a more plant-based lifestyle: The macroevolution of mutualistic lizard-plant-interactions (Squamata: Sauria/Lacertilia). Mol Phylogenet Evol 2023:107839. [PMID: 37290582 DOI: 10.1016/j.ympev.2023.107839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 05/12/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Pollination and seed dispersal of plants by animals are key mutualistic processes for the conservation of plant diversity and ecosystem functioning. Although different animals frequently act as pollinators or seed dispersers, some species can provide both functions, so-called 'double mutualists', suggesting that the evolution of pollination and seed dispersal may be linked. Here, we assess the macroevolution of mutualistic behaviours in lizards (Lacertilia) by applying comparative methods to a phylogeny comprising 2,838 species. We found that both flower visitation (potential pollination) (recorded in 64 species [2.3% of total] across 9 families) and seed dispersal (recorded in 382 species [13,5% of total] across 26 families) have evolved repeatedly in Lacertilia. Furthermore, we found that seed dispersal activity pre-dated flower visitation and that the evolution of seed dispersal activity and flower visitation was correlated, illustrating a potential evolutionary mechanism behind the emergence of double mutualisms. Finally, we provide evidence that lineages with flower visitation or seed dispersal activity have higher diversification rates than lineages lacking these behaviours. Our study illustrates the repeated innovation of (double) mutualisms across Lacertilia and we argue that island settings may provide the ecological conditions under which (double) mutualisms persist over macroevolutionary timescales.
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Affiliation(s)
- Belinda Kahnt
- General Zoology, Institute of Biology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany.
| | - Panagiotis Theodorou
- General Zoology, Institute of Biology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
| | - Annegret Grimm-Seyfarth
- Department of Conservation Biology and Social-Ecological Systems, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Renske E Onstein
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Naturalis Biodiversity Center, Darwinweg, 2 2333CR Leiden, the Netherlands
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10
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Zhao Z, Conradie W, Pietersen DW, Jordaan A, Nicolau G, Edwards S, Riekert S, Heideman N. Diversification of the African legless skinks in the subfamily Acontinae (Family Scincidae). Mol Phylogenet Evol 2023; 182:107747. [PMID: 36849095 DOI: 10.1016/j.ympev.2023.107747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
Cladogenic diversification is often explained by referring to climatic oscillations and geomorphic shifts that cause allopatric speciation. In this regard, southern Africa retains a high level of landscape heterogeneity in vegetation, geology, and rainfall patterns. The legless skink subfamily Acontinae occurs broadly across the southern African subcontinent and therefore provides an ideal model group for investigating biogeographic patterns associated with the region. A robust phylogenetic study of the Acontinae with comprehensive coverage and adequate sampling of each taxon has been lacking up until now, resulting in unresolved questions regarding the subfamily's biogeography and evolution. In this study, we used multi-locus genetic markers (three mitochondrial and two nuclear) with comprehensive taxon coverage (all currently recognized Acontinae species) and adequate sampling (multiple specimens for most taxa) of each taxon to infer a phylogeny for the subfamily. The phylogeny retrieved four well-supported clades in Acontias and supported the monophyly of Typhlosaurus. Following the General Lineage Concept (GLC), many long-standing phylogenetic enigmas within Acontias occidentalis and the A. kgalagadi, A. lineatus and A. meleagris species complexes, and within Typhlosaurus were resolved. Our species delimitation analyses suggest the existence of hidden taxa in the A. occidentalis, A. cregoi and A. meleagris species groups, but also suggest that some currently recognized species in the A. lineatus and A. meleagris species groups, and within Typhlosaurus, should be synonymised. We also possibly encountered "ghost introgression" in A. occidentalis. Our inferred species tree revealed a signal of gene flow, which implies possible cross-over in some groups. Fossil evidence calibration dating results showed that the divergence between Typhlosaurus and Acontias was likely influenced by cooling and increasing aridity along the southwest coast in the mid-Oligocene caused by the opening of the Drake Passage. Further cladogenesis observed in Typhlosaurus and Acontias was likely influenced by Miocene cooling, expansion of open habitat, uplifting of the eastern Great Escarpment (GE), and variation in rainfall patterns, together with the effect of the warm Agulhas Current since the early Miocene, the development of the cold Benguela Current since the late Miocene, and their co-effects. The biogeographic pattern of the Acontinae bears close resemblance to that of other herpetofauna (e.g., rain frogs and African vipers) in southern Africa.
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Affiliation(s)
- Zhongning Zhao
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa; Department of Genetics, University of the Free State, Bloemfontein, South Africa.
| | - Werner Conradie
- Port Elizabeth Museum (Bayworld), P.O. Box 13147, Humewood, Port Elizabeth 6013, South Africa; Department of Nature Conservation Management, Natural Resource Science and Management Cluster, Faculty of Science, George Campus, Nelson Mandela University, George, South Africa
| | - Darren W Pietersen
- Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - Adriaan Jordaan
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa
| | - Gary Nicolau
- Zoology & Entomology Molecular Lab, Department of Zoology and Entomology, Rhodes University, Makhanda, South Africa
| | - Shelley Edwards
- Zoology & Entomology Molecular Lab, Department of Zoology and Entomology, Rhodes University, Makhanda, South Africa
| | - Stephanus Riekert
- Department of Information and Communication Technology Services, University of the Free State, Bloemfontein, South Africa
| | - Neil Heideman
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa
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11
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Costa FP, Schrago CG, Mello B. Assessing the relative performance of fast molecular dating methods for phylogenomic data. BMC Genomics 2022; 23:798. [PMID: 36460948 PMCID: PMC9719170 DOI: 10.1186/s12864-022-09030-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022] Open
Abstract
Advances in genome sequencing techniques produced a significant growth of phylogenomic datasets. This massive amount of data represents a computational challenge for molecular dating with Bayesian approaches. Rapid molecular dating methods have been proposed over the last few decades to overcome these issues. However, a comparative evaluation of their relative performance on empirical data sets is lacking. We analyzed 23 empirical phylogenomic datasets to investigate the performance of two commonly employed fast dating methodologies: penalized likelihood (PL), implemented in treePL, and the relative rate framework (RRF), implemented in RelTime. They were compared to Bayesian analyses using the closest possible substitution models and calibration settings. We found that RRF was computationally faster and generally provided node age estimates statistically equivalent to Bayesian divergence times. PL time estimates consistently exhibited low levels of uncertainty. Overall, to approximate Bayesian approaches, RelTime is an efficient method with significantly lower computational demand, being more than 100 times faster than treePL. Thus, to alleviate the computational burden of Bayesian divergence time inference in the era of massive genomic data, molecular dating can be facilitated using the RRF, allowing evolutionary hypotheses to be tested more quickly and efficiently.
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Affiliation(s)
- Fernanda P. Costa
- grid.8536.80000 0001 2294 473XDepartment of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-617 Brazil
| | - Carlos G. Schrago
- grid.8536.80000 0001 2294 473XDepartment of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-617 Brazil
| | - Beatriz Mello
- grid.8536.80000 0001 2294 473XDepartment of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-617 Brazil
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12
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Maldonado JA, Firneno TJ, Hall AS, Fujita MK. Parthenogenesis doubles the rate of amino acid substitution in whiptail mitochondria. Evolution 2022; 76:1434-1442. [PMID: 35580923 DOI: 10.1111/evo.14509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 03/10/2022] [Accepted: 03/21/2022] [Indexed: 01/21/2023]
Abstract
Sexual reproduction is ubiquitous in the natural world, suggesting that sex must have extensive benefits to overcome the cost of males compared to asexual reproduction. One hypothesized advantage of sex with strong theoretical support is that sex plays a role in removing deleterious mutations from the genome. Theory predicts that transitions to asexuality should lead to the suppression of recombination and segregation and, in turn, weakened natural selection, allowing for the accumulation of slightly deleterious mutations. We tested this prediction by estimating the dN/dS ratios in asexual vertebrate lineages in the genus Aspidoscelis using whole mitochondrial genomes from seven asexual and five sexual species. We found higher dN/dS ratios in asexual Aspidoscelis species, indicating that asexual whiptails accumulate nonsynonymous substitutions due to weaker purifying selection. Additionally, we estimated nucleotide diversity and found that asexuals harbor significantly less diversity. Thus, despite their recent origins, slightly deleterious mutations accumulated rapidly enough in asexual lineages to be detected. We provide empirical evidence to corroborate the connection between asexuality and increased amino acid substitutions in asexual vertebrate lineages.
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Affiliation(s)
- Jose A Maldonado
- Amphibian and Reptile Diversity Research Center, Department of Biology, The University of Texas, Arlington, Texas, USA
| | - Thomas J Firneno
- Amphibian and Reptile Diversity Research Center, Department of Biology, The University of Texas, Arlington, Texas, USA
| | - Alexander S Hall
- Amphibian and Reptile Diversity Research Center, Department of Biology, The University of Texas, Arlington, Texas, USA
| | - Matthew K Fujita
- Amphibian and Reptile Diversity Research Center, Department of Biology, The University of Texas, Arlington, Texas, USA
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13
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Bolet A, Stubbs TL, Herrera-Flores JA, Benton MJ. The Jurassic rise of squamates as supported by lepidosaur disparity and evolutionary rates. eLife 2022; 11:e66511. [PMID: 35502582 PMCID: PMC9064307 DOI: 10.7554/elife.66511] [Citation(s) in RCA: 5] [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: 01/13/2021] [Accepted: 03/24/2022] [Indexed: 12/30/2022] Open
Abstract
The squamates (lizards, snakes, and relatives) today comprise more than 10,000 species, and yet their sister group, the Rhynchocephalia, is represented by a single species today, the tuatara. The explosion in squamate diversity has been tracked back to the Cretaceous Terrestrial Revolution, 100 million years ago (Ma), the time when flowering plants began their takeover of terrestrial ecosystems, associated with diversification of coevolving insects and insect-eating predators such as lizards, birds, and mammals. Squamates arose much earlier, but their long pre-Cretaceous history of some 150 million years (Myr) is documented by sparse fossils. Here, we provide evidence for an initial radiation of squamate morphology in the Middle and Late Jurassic (174-145 Ma), and show that they established their key ecological roles much earlier than had been assumed, and they have not changed them much since.
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Affiliation(s)
- Arnau Bolet
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de BarcelonaCerdanyola del VallèsSpain
- School of Earth Sciences, University of BristolBristolUnited Kingdom
| | - Thomas L Stubbs
- School of Earth Sciences, University of BristolBristolUnited Kingdom
| | | | - Michael J Benton
- School of Earth Sciences, University of BristolBristolUnited Kingdom
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14
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Vernygora OV, Campbell EO, Grishin NV, Sperling FA, Dupuis JR. Gauging ages of tiger swallowtail butterflies using alternate SNP analyses. Mol Phylogenet Evol 2022; 171:107465. [DOI: 10.1016/j.ympev.2022.107465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/26/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022]
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15
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Blais BR, Smith BE, Placyk JS, Casper GS, Spellman GM. Phylogeography of the smooth greensnake, Opheodrys vernalis (Squamata: Colubridae): divergent lineages and variable demographics in a widely distributed yet enigmatic species. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Abstract
Phylogeographic studies can uncover robust details about the population structure, demographics, and diversity of species. The smooth greensnake, Opheodrys vernalis, is a small, cryptic snake occupying mesic grassland and sparsely wooded habitats. Although O. vernalis has a wide geographical range, many metapopulations are patchy and some are declining. We used mitochondrial DNA and double digest restriction-site associated DNA sequencing to construct the first phylogeographic assessment of O. vernalis. Genomic analysis of 119 individuals (mitochondrial DNA) and a subset of another 45 smooth greensnakes (nuclear DNA; N = 3031 single nucleotide polymorphisms) strongly supports two longitudinally separated lineages, with admixture in the Great Lakes region. Post-Pleistocene secondary contact best explains admixture from populations advancing northwards. Overall, populations expressed low heterozygosity, variable inbreeding rates, and moderate to high differentiation. Disjunct populations in the Rocky Mountains and central Great Plains regions might be contracting relicts, whereas northerly populations in more continuous mesic habitats (e.g., Prairie Pothole region, southern Canada) had signals of population expansion. Broadly, conservation management efforts should be focused on local populations, because habitat connectivity may facilitate gene flow and genetic diversity.
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Affiliation(s)
- Brian R Blais
- School of Natural Sciences, Black Hills State University, Spearfish, SD, USA
| | - Brian E Smith
- School of Natural Sciences, Black Hills State University, Spearfish, SD, USA
| | - John S Placyk
- Department of Biology, University of Texas at Tyler, 3900 University Boulevard, Tyler, TX, USA
| | - Gary S Casper
- University of Wisconsin-Milwaukee Field Station, Saukville, WI, USA
| | - Garth M Spellman
- Department of Zoology, Denver Museum of Nature & Science, 2001 Colorado Boulevard, Denver, CO, USA
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16
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Salvi D, Pinho C, Mendes J, Harris DJ. Fossil-calibrated time tree of Podarcis wall lizards provides limited support for biogeographic calibration models. Mol Phylogenet Evol 2021; 161:107169. [PMID: 33798673 DOI: 10.1016/j.ympev.2021.107169] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/17/2021] [Accepted: 03/25/2021] [Indexed: 11/15/2022]
Abstract
Podarcis wall lizards are endemic to the Mediterranean Basin where they represent the predominant reptile group. Despite being extensively used as model organisms in evolutionary and ecological studies their phylogeny and historical biogeography are still incompletely resolved. Moreover, molecular clock calibrations used in wall lizard phylogeography are based on the assumption of vicariant speciation triggered by the abrupt Mediterranean Sea level rise at the end of the Messinian salinity crisis (MSC). However, the validity of this biogeographic calibration remains untested. In this study we inferred a robust time tree based on multilocus data and fossil calibrations using both gene concatenation and species-tree approaches and including models with gene-flow. We found five deeply divergent, geographically coherent, and well-supported clades comprising species from i) Iberian Peninsula and North Africa; ii) Western Mediterranean islands, iii) Sicilian and Maltese islands; and iv-v) Balkan region and Aegean islands. The mitochondrial tree shows some inconsistencies with the species tree that warrant future investigation. Diversification of main clades is estimated in a short time frame during the Middle Miocene and might have been associated with a period of global climate cooling with the establishment of a marked climatic zonation in Europe. Cladogenetic events within the main clades are scattered throughout the time tree, from the Late Miocene to the Early Pleistocene, suggesting that speciation events in wall lizards reflect a complex interplay between regional topography, climate and geological history rather than a shared major climatic or paleogeographic event. Our absolute time estimates, as well as a relative dating approach, demonstrate that the assumption of a causal link between sea-level rise at the end of the MSC and the diversification of many island endemics is not justified. This study reinforces the notion that multiple dispersal and vicariant events, at different time frames, are required to explain current allopatric distributions and to account for the historical assembly of Mediterranean biota, and cautions against the use of biogeographic calibrations based on the assumption of vicariance.
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Affiliation(s)
- Daniele Salvi
- University of L'Aquila, Department of Health, Life and Environmental Sciences, 67100 Coppito, L'Aquila, Italy; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
| | - Catarina Pinho
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
| | - Joana Mendes
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - D James Harris
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
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17
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Sidharthan C, Karanth KP. India's biogeographic history through the eyes of blindsnakes- filling the gaps in the global typhlopoid phylogeny. Mol Phylogenet Evol 2020; 157:107064. [PMID: 33387646 DOI: 10.1016/j.ympev.2020.107064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 12/05/2020] [Accepted: 12/24/2020] [Indexed: 11/25/2022]
Abstract
The Indian subcontinent's unique geological history is reflected in the diverse assemblage of its biota. The blindsnake superfamily Typhlopoidea, with its unique mix of ancient as well as younger lineages in Asia, provides an opportunity to understand the various biotic exchange scenarios proposed for the Indian landmass. In this study, we aim to understand the biogeographic origins of the four genera of typhlopoids found in India and to decipher their times and modes of arrival in the subcontinent. Five nuclear markers were sequenced for 12 samples collected from across India, encompassing all four genera under study. Published sequences of typhlopoid genera were compiled and combined with Indian sequences to generate a global dataset. Phylogenetic relationships were reconstructed using maximum likelihood and Bayesian inference methods. Divergence times were estimated using BEAST 1.8.2. Ancestral geographical ranges were estimated using DEC + J, implemented in BioGeoBEARS. Divergence time estimates suggest that Gerrhopilus is an ancient lineage, and the lineage leading to it was present on the Indian landmass since the last 100 million years. The other three genera are more recent dispersals into India, possibly trans-oceanic. Biogeographic reconstructions suggest an East Gondwanan origin for Typhlopoidea, an African origin for Grypotyphlops and an Asian origin for Indotyphlops and Argyrophis. It appears that India harbours a combination of ancient and more recently dispersed lineages of typhlopoids. The genus Gerrhopilus is of Gondwanan origin that likely dispersed out of India into Southeast Asia. The other genera are intrusive elements that dispersed into India from Africa (Grypotyphlops) and Asia (Indotyphlops and possibly Argyrophis) post break-up of Gondwana. Thus, our study provides further evidence on the ability of blindsnakes to undergo long distance trans-oceanic dispersal. Results also suggest an Asian origin for typhlopoids from Australasia, Philippines and Wallacea.
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Affiliation(s)
- Chinta Sidharthan
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560012, India.
| | - K Praveen Karanth
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560012, India
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18
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Kundu S, Lalremsanga HT, Biakzuala L, Chandra K, Kumar V. DNA barcoding reveals distinct population of Dopasia gracilis (Squamata: Anguidae) in Mizoram, Northeast India. Mitochondrial DNA B Resour 2020; 5:3229-3233. [PMID: 33458121 PMCID: PMC7782129 DOI: 10.1080/23802359.2020.1810147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/11/2020] [Indexed: 10/29/2022] Open
Abstract
The DNA barcode data of Asian Glass Lizard, Dopasia gracilis, is limited in the global database, especially from India. The present study aimed to generate a barcode sequence of morphologically identified D. gracilis from the Mizoram state in northeast India and compared with other Anguidae species. The studied species showed monophyletic clustering in the Bayesian analysis (BA) phylogeny with strong posterior probability support and also discriminated sufficient Kimura 2 parameter genetic distances. The barcode data of D. gracilis revealed high intra-species genetic variability and formed two clusters in BA phylogeny. The Templeton, Crandall, and Sing network also depicted four different haplotypes within the barcode sequences of D. gracilis. The DNA sequences generated from northeast India showed 6.5-6.6% and 7.3% genetic distances with the sequences generated from Yunnan Province and Tibetan Plateau, respectively. Considering the high genetic distances, multiple clustering, and distinct haplotypes, the present study assumed the presence of possible cryptic diversity of D. gracilis in the Indochina sub-region and a distinct population in northeast India. We recommended the generation of more DNA information from different localities to elucidate the actual diversity of D. gracilis within the known range distribution.
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Affiliation(s)
- Shantanu Kundu
- Molecular Systematics Division, Zoological Survey of India, Centre for DNA Taxonomy, Kolkata, India
| | - Hmar Tlawmte Lalremsanga
- Developmental Biology and Herpetology Laboratory, Department of Zoology, Mizoram University, Aizawl, India
| | - Lal Biakzuala
- Developmental Biology and Herpetology Laboratory, Department of Zoology, Mizoram University, Aizawl, India
| | - Kailash Chandra
- Molecular Systematics Division, Zoological Survey of India, Centre for DNA Taxonomy, Kolkata, India
| | - Vikas Kumar
- Molecular Systematics Division, Zoological Survey of India, Centre for DNA Taxonomy, Kolkata, India
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19
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Recoder R, Prates I, Marques-Souza S, Camacho A, Nunes PMS, Dal Vechio F, Ghellere JM, McDiarmid RW, Rodrigues MT. Lizards from the Lost World: two new species and evolutionary relationships of the Pantepui highland Riolama (Gymnophthalmidae). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlz168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The Pantepui region of northern South America harbours an endemic fauna that differs dramatically from those of the surrounding lowland rainforests and savannas. A component of this unique fauna is Riolama, a poorly known genus of microteiid lizards with four described and two undescribed species restricted to tepui mountains. We here implement an integrative approach to formally describe the two unnamed species and investigate the phylogenetic relationships and timing of diversification in Riolama using a fossil-calibrated molecular approach. Our results suggest that diversification initiated in Riolama during the Oligocene (c. 28 Mya), thereby characterizing the genus as an ancient lineage. This supports the Plateau biogeographic hypothesis to explain the diversification of the Pantepui fauna. Our divergence time estimation analysis also provides an updated temporal framework for the diversification of the highly diverse Gymnophthalmidae clade.
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Affiliation(s)
- Renato Recoder
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Ivan Prates
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Sergio Marques-Souza
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Agustín Camacho
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Pedro M Sales Nunes
- Departamento de Zoologia, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Francisco Dal Vechio
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - José Mario Ghellere
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Roy W McDiarmid
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Miguel Trefaut Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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20
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Huang W, Xie X, Peng F, Liang X, Wang X, Chen X. Optimizing the widely used nuclear protein-coding gene primers in beetle phylogenies and their application in the genus Sasajiscymnus Vandenberg (Coleoptera: Coccinellidae). Ecol Evol 2020; 10:7731-7738. [PMID: 32760560 PMCID: PMC7391345 DOI: 10.1002/ece3.6497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/10/2020] [Accepted: 06/02/2020] [Indexed: 11/26/2022] Open
Abstract
Advances in genomic biology and the increasing availability of genomic resources allow developing hundreds of nuclear protein-coding (NPC) markers, which can be used in phylogenetic research. However, for low taxonomic levels, it may be more practical to select a handful of suitable molecular loci for phylogenetic inference. Unfortunately, the presence of degenerate primers of NPC markers can be a major impediment, as the amplification success rate is low and they tend to amplify nontargeted regions. In this study, we optimized five NPC fragments widely used in beetle phylogenetics (i.e., two parts of carbamoyl-phosphate synthetase: CADXM and CADMC, Topoisomerase, Wingless and Pepck) by reducing the degenerate site of primers and the length of target genes slightly. These five NPC fragments and 6 other molecular loci were amplified to test the monophyly of the coccinellid genus Sasajiscymnus Vandenberg. The analysis of our molecular data set clearly supported the genus Sasajiscymnus may be monophyletic but confirmation with an extended sampling is required. A fossil-calibrated chronogram was generated by BEAST, indicating an origin of the genus at the end of the Cretaceous (77.87 Myr). Furthermore, a phylogenetic informativeness profile was generated to compare the phylogenetic properties of each gene more explicitly. The results showed that COI provides the strongest phylogenetic signal among all the genes, but Pepck, Topoisomerase, CADXM and CADMC are also relatively informative. Our results provide insight into the evolution of the genus Sasajiscymnus, and also enrich the molecular data resources for further study.
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Affiliation(s)
- Weidong Huang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmDepartment of Forest ProtectionCollege of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Bio‐Pesticide Innovation and Application, Guangdong ProvinceEngineering Research Center of BiocontrolMinistry of Education and Guangdong ProvinceGuangzhouChina
| | - Xiufeng Xie
- Guangdong Agriculture Industry Business Polytechnic CollegeGuangzhouChina
| | - Feng Peng
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmDepartment of Forest ProtectionCollege of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
| | - Xinyue Liang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmDepartment of Forest ProtectionCollege of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Bio‐Pesticide Innovation and Application, Guangdong ProvinceEngineering Research Center of BiocontrolMinistry of Education and Guangdong ProvinceGuangzhouChina
| | - Xingmin Wang
- Key Laboratory of Bio‐Pesticide Innovation and Application, Guangdong ProvinceEngineering Research Center of BiocontrolMinistry of Education and Guangdong ProvinceGuangzhouChina
| | - Xiaosheng Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmDepartment of Forest ProtectionCollege of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Bio‐Pesticide Innovation and Application, Guangdong ProvinceEngineering Research Center of BiocontrolMinistry of Education and Guangdong ProvinceGuangzhouChina
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21
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Soto Gomez M, Lin Q, Silva Leal E, Gallaher TJ, Scherberich D, Mennes CB, Smith SY, Graham SW. A bi‐organellar phylogenomic study of Pandanales: inference of higher‐order relationships and unusual rate‐variation patterns. Cladistics 2020; 36:481-504. [DOI: 10.1111/cla.12417] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/21/2022] Open
Affiliation(s)
- Marybel Soto Gomez
- Department of Botany University of British Columbia 6270 University Boulevard Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research University of British Columbia 6804 Marine Drive SW Vancouver BC V6T 1Z4 Canada
| | - Qianshi Lin
- Department of Botany University of British Columbia 6270 University Boulevard Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research University of British Columbia 6804 Marine Drive SW Vancouver BC V6T 1Z4 Canada
| | - Eduardo Silva Leal
- Universidade Federal Rural da Amazônia, Campus Capanema Avenida Barão de Capanema s/n Capanema68700-665 PA Brazil
| | | | - David Scherberich
- Jardin Botanique de la Ville de Lyon Mairie de Lyon69205 Lyon Cedex 01 France
| | | | - Selena Y. Smith
- Department of Earth & Environmental Sciences and Museum of Paleontology University of Michigan Ann Arbor MI 48109 USA
| | - Sean W. Graham
- Department of Botany University of British Columbia 6270 University Boulevard Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research University of British Columbia 6804 Marine Drive SW Vancouver BC V6T 1Z4 Canada
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22
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Song N, Geng Y, Li X. The Mitochondrial Genome of the Phytopathogenic Fungus Bipolaris sorokiniana and the Utility of Mitochondrial Genome to Infer Phylogeny of Dothideomycetes. Front Microbiol 2020; 11:863. [PMID: 32457727 PMCID: PMC7225605 DOI: 10.3389/fmicb.2020.00863] [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] [Received: 01/27/2020] [Accepted: 04/09/2020] [Indexed: 12/01/2022] Open
Abstract
A number of species in Bipolaris are important plant pathogens. Due to a limited number of synapomorphic characters, it is difficult to perform species identification and to estimate phylogeny of Bipolaris based solely on morphology. In this study, we sequenced the complete mitochondrial genome of Bipolaris sorokiniana, and presented the detailed annotation of the genome. The B. sorokiniana mitochondrial genome is 137,775 bp long, and contains two ribosomal RNA genes, 12 core protein-coding genes, 38 tRNA genes. In addition, two ribosomal protein genes (rps3 gene and rps5 gene) and the fungal mitochondrial RNase P gene (rnpB) are identified. The large genome size is mostly determined by the presence of numerous intronic and intergenic regions. A total of 28 introns are inserted in eight core protein-coding genes. Together with the published mitochondrial genome sequences, we conducted a preliminary phylogenetic inference of Dothideomycetes under various datasets and substitution models. The monophyly of Capnodiales, Botryosphaeriales and Pleosporales are consistently supported in all analyses. The Venturiaceae forms an independent lineage, with a distant phylogenetic relationship to Pleosporales. At the family level, the Mycosphaerellaceae, Botryosphaeriaceae. Phaeosphaeriaceae, and Pleosporaceae are recognized in the majority of trees.
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Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yuehua Geng
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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23
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Varadharajan S, Rastas P, Löytynoja A, Matschiner M, Calboli FCF, Guo B, Nederbragt AJ, Jakobsen KS, Merilä J. A High-Quality Assembly of the Nine-Spined Stickleback (Pungitius pungitius) Genome. Genome Biol Evol 2019; 11:3291-3308. [PMID: 31687752 PMCID: PMC7145574 DOI: 10.1093/gbe/evz240] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2019] [Indexed: 12/22/2022] Open
Abstract
The Gasterosteidae fish family hosts several species that are important models for eco-evolutionary, genetic, and genomic research. In particular, a wealth of genetic and genomic data has been generated for the three-spined stickleback (Gasterosteus aculeatus), the "ecology's supermodel," whereas the genomic resources for the nine-spined stickleback (Pungitius pungitius) have remained relatively scarce. Here, we report a high-quality chromosome-level genome assembly of P. pungitius consisting of 5,303 contigs (N50 = 1.2 Mbp) with a total size of 521 Mbp. These contigs were mapped to 21 linkage groups using a high-density linkage map, yielding a final assembly with 98.5% BUSCO completeness. A total of 25,062 protein-coding genes were annotated, and about 23% of the assembly was found to consist of repetitive elements. A comprehensive analysis of repetitive elements uncovered centromere-specific tandem repeats and provided insights into the evolution of retrotransposons. A multigene phylogenetic analysis inferred a divergence time of about 26 million years ago (Ma) between nine- and three-spined sticklebacks, which is far older than the commonly assumed estimate of 13 Ma. Compared with the three-spined stickleback, we identified an additional duplication of several genes in the hemoglobin cluster. Sequencing data from populations adapted to different environments indicated potential copy number variations in hemoglobin genes. Furthermore, genome-wide synteny comparisons between three- and nine-spined sticklebacks identified chromosomal rearrangements underlying the karyotypic differences between the two species. The high-quality chromosome-scale assembly of the nine-spined stickleback genome obtained with long-read sequencing technology provides a crucial resource for comparative and population genomic investigations of stickleback fishes and teleosts.
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Affiliation(s)
- Srinidhi Varadharajan
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
| | - Pasi Rastas
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
| | - Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, Finland
| | - Michael Matschiner
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
- Department of Paleontology and Museum, University of Zurich, Switzerland
| | - Federico C F Calboli
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Baocheng Guo
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences, Beijing, China
| | - Alexander J Nederbragt
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
- Biomedical Informatics Research Group, Department of Informatics, University of Oslo, Norway
| | - Kjetill S Jakobsen
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
| | - Juha Merilä
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
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24
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Varadharajan S, Rastas P, Löytynoja A, Matschiner M, Calboli FCF, Guo B, Nederbragt AJ, Jakobsen KS, Merilä J. A High-Quality Assembly of the Nine-Spined Stickleback (Pungitius pungitius) Genome. Genome Biol Evol 2019. [PMID: 31687752 DOI: 10.1101/741751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
The Gasterosteidae fish family hosts several species that are important models for eco-evolutionary, genetic, and genomic research. In particular, a wealth of genetic and genomic data has been generated for the three-spined stickleback (Gasterosteus aculeatus), the "ecology's supermodel," whereas the genomic resources for the nine-spined stickleback (Pungitius pungitius) have remained relatively scarce. Here, we report a high-quality chromosome-level genome assembly of P. pungitius consisting of 5,303 contigs (N50 = 1.2 Mbp) with a total size of 521 Mbp. These contigs were mapped to 21 linkage groups using a high-density linkage map, yielding a final assembly with 98.5% BUSCO completeness. A total of 25,062 protein-coding genes were annotated, and about 23% of the assembly was found to consist of repetitive elements. A comprehensive analysis of repetitive elements uncovered centromere-specific tandem repeats and provided insights into the evolution of retrotransposons. A multigene phylogenetic analysis inferred a divergence time of about 26 million years ago (Ma) between nine- and three-spined sticklebacks, which is far older than the commonly assumed estimate of 13 Ma. Compared with the three-spined stickleback, we identified an additional duplication of several genes in the hemoglobin cluster. Sequencing data from populations adapted to different environments indicated potential copy number variations in hemoglobin genes. Furthermore, genome-wide synteny comparisons between three- and nine-spined sticklebacks identified chromosomal rearrangements underlying the karyotypic differences between the two species. The high-quality chromosome-scale assembly of the nine-spined stickleback genome obtained with long-read sequencing technology provides a crucial resource for comparative and population genomic investigations of stickleback fishes and teleosts.
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Affiliation(s)
- Srinidhi Varadharajan
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
| | - Pasi Rastas
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
| | - Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, Finland
| | - Michael Matschiner
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
- Department of Paleontology and Museum, University of Zurich, Switzerland
| | - Federico C F Calboli
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Baocheng Guo
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences, Beijing, China
| | - Alexander J Nederbragt
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
- Biomedical Informatics Research Group, Department of Informatics, University of Oslo, Norway
| | - Kjetill S Jakobsen
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
| | - Juha Merilä
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
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25
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Burbrink FT, Grazziotin FG, Pyron RA, Cundall D, Donnellan S, Irish F, Keogh JS, Kraus F, Murphy RW, Noonan B, Raxworthy CJ, Ruane S, Lemmon AR, Lemmon EM, Zaher H. Interrogating Genomic-Scale Data for Squamata (Lizards, Snakes, and Amphisbaenians) Shows no Support for Key Traditional Morphological Relationships. Syst Biol 2019; 69:502-520. [DOI: 10.1093/sysbio/syz062] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 09/05/2019] [Accepted: 09/10/2019] [Indexed: 12/15/2022] Open
Abstract
Abstract
Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards, snakes, and amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a consensus on the relationships among them has been highly problematic. In this study, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome-scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites (PIS), phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously well-supported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a few undesirable gene properties, such as an insufficient number of PIS), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata. We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; among the three toxicoferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families).
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
| | - Felipe G Grazziotin
- Laboratório de Coleções Zoológicas, Instituto Butantan, Av. Vital Brasil, 1500—Butantã, São Paulo—SP 05503-900, Brazil
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - David Cundall
- Department of Biological Sciences, 1 W. Packer Avenue, Lehigh University, Bethlehem, PA 18015, USA
| | - Steve Donnellan
- South Australian Museum, North Terrace, Adelaide SA 5000, Australia
- School of Biological Sciences, University of Adelaide, SA 5005 Australia
| | - Frances Irish
- Department of Biological Sciences, Moravian College, 1200 Main St, Bethlehem, PA 18018, US
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Fred Kraus
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robert W Murphy
- Department of Natural History, Royal Ontario Museum, 100 Queens Park, Toronto, ON M5S 2C6, Canada
| | - Brice Noonan
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
| | - Christopher J Raxworthy
- Department of Herpetology, The American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
| | - Sara Ruane
- Department of Biological Sciences, 206 Boyden Hall, Rutgers University, 195 University Avenue, Newark, NJ 07102, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4102, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306-4295, USA
| | - Hussam Zaher
- Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil CEP 04263-000, Brazil
- Centre de Recherche sur la Paléobiodiversité et les Paléoenvironnements (CR2P), UMR 7207 CNRS/MNHN/Sorbonne Université, Muséum national d’Histoire naturelle, 8 rue Buffon, CP 38, 75005 Paris, France
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26
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Evolution, Diversity, and Development of the Craniocervical System in Turtles with Special Reference to Jaw Musculature. HEADS, JAWS, AND MUSCLES 2019. [DOI: 10.1007/978-3-319-93560-7_8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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27
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Lavin BR, Girman DJ. Phylogenetic relationships and divergence dating in the Glass Lizards (Anguinae). Mol Phylogenet Evol 2018; 133:128-140. [PMID: 30584918 DOI: 10.1016/j.ympev.2018.12.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 12/14/2018] [Accepted: 12/17/2018] [Indexed: 11/19/2022]
Abstract
The Glass Lizards are a subfamily (Anguinae) of Anguid Lizards with an elongated limbless body plan that occur throughout the Northern Hemisphere primarily in North America, Europe, and Asia, but also have a presence in North Africa and Indonesia. We used twenty-five nuclear loci (15,191 bp) and 2090 bp of the mtDNA genome to generate a phylogeny containing all known species groups to explore species relationships within the group as well as divergence dating. We also examined the group in the context of a coalescent species tree analysis and species delimitation. All major lineages were found to be monophyletic with potential cryptic diversity in some. The Anguinae first appeared in the Eocene and most lineages were present by the beginning of the Miocene. The Anguinae originated in Europe from an Anguidae ancestor that crossed the Thulean land bridge, spreading to Asia after the drying of the Turgai Sea, then across Beringia as the climate permitted. A species tree analyses found support for the major Anguinae lineages and species delimitation supported accepted species.
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Affiliation(s)
- Brian R Lavin
- Department of Biology, Sonoma State University, 1801 East Cotati Ave, Rohnert Park, CA 94928, USA.
| | - Derek J Girman
- Department of Biology, Sonoma State University, 1801 East Cotati Ave, Rohnert Park, CA 94928, USA.
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28
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Zhang QL, Zhang GL, Yuan ML, Dong ZX, Li HW, Guo J, Wang F, Deng XY, Chen JY, Lin LB. A Phylogenomic Framework and Divergence History of Cephalochordata Amphioxus. Front Physiol 2018; 9:1833. [PMID: 30618839 PMCID: PMC6305399 DOI: 10.3389/fphys.2018.01833] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 12/06/2018] [Indexed: 11/21/2022] Open
Abstract
Amphioxus, or cephalochordates, are often used as the living invertebrate proxy of vertebrate ancestors and are widely used as evolutionary biology models of chordates. However, their phylogeny, divergence history, and speciation characteristics remain poorly understood, and phylogenomic studies to explore these problems lacking entirely from the literature. Here, we determined a new transcriptome of Branchiostoma japonicum. Combined with mass sequences of all other 18 species, a 19-way phylogeny was constructed via multiple methods (ML, BI, PhyloBayes, and ASTRAL), consistently supporting a phylogeny of [(B. belcheri + B. japonicum) + (B. lanceolatum + B. floridae) + Asymmetron lucayanum] in amphioxus. Congruent phylogenetic signals were found across mitochondrial genes, 12S RNA, and complete mitochondrial genomes according to previous reports, indicating that 12S RNA may have potential as a molecular marker for phylogenetic analysis in amphioxus. Molecular dating analysis indicated a radiation of the cephalochordates during the Cretaceous (∼104-61 million years ago), supporting an association between the diversification and speciation of cephalochordates with continental drift and associated changes in their respective habitats during this time. The identified functional enrichment analysis for species-specific domains indicated that their function mainly involves immune response, apoptosis, and lipid metabolism and utilization, signaling that pathogens and changes of energy requirements are an important driving force for amphioxus speciation. This study represents the first large-scale phylogenomic analysis of most major amphioxus genera based on phylogenomic data, providing a new perspective on both phylogeny and divergence speciation of cephalochordates.
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Affiliation(s)
- Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.,Evo-Devo Institute, School of Life Sciences, Nanjing University, Nanjing, China
| | - Guan-Ling Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhi-Xiang Dong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Hong-Wei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jun Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xian-Yu Deng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jun-Yuan Chen
- Evo-Devo Institute, School of Life Sciences, Nanjing University, Nanjing, China.,State Key Laboratory of Palaeobiology and Stratigraphy (LPS), Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
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29
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Hofmann EP, Rautsaw RM, Strickland JL, Holding ML, Hogan MP, Mason AJ, Rokyta DR, Parkinson CL. Comparative venom-gland transcriptomics and venom proteomics of four Sidewinder Rattlesnake (Crotalus cerastes) lineages reveal little differential expression despite individual variation. Sci Rep 2018; 8:15534. [PMID: 30341342 PMCID: PMC6195556 DOI: 10.1038/s41598-018-33943-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/03/2018] [Indexed: 11/24/2022] Open
Abstract
Changes in gene expression can rapidly influence adaptive traits in the early stages of lineage diversification. Venom is an adaptive trait comprised of numerous toxins used for prey capture and defense. Snake venoms can vary widely between conspecific populations, but the influence of lineage diversification on such compositional differences are unknown. To explore venom differentiation in the early stages of lineage diversification, we used RNA-seq and mass spectrometry to characterize Sidewinder Rattlesnake (Crotalus cerastes) venom. We generated the first venom-gland transcriptomes and complementary venom proteomes for eight individuals collected across the United States and tested for expression differences across life history traits and between subspecific, mitochondrial, and phylotranscriptomic hypotheses. Sidewinder venom was comprised primarily of hemorrhagic toxins, with few cases of differential expression attributable to life history or lineage hypotheses. However, phylotranscriptomic lineage comparisons more than doubled instances of significant expression differences compared to all other factors. Nevertheless, only 6.4% of toxins were differentially expressed overall, suggesting that shallow divergence has not led to major changes in Sidewinder venom composition. Our results demonstrate the need for consensus venom-gland transcriptomes based on multiple individuals and highlight the potential for discrepancies in differential expression between different phylogenetic hypotheses.
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Affiliation(s)
- Erich P Hofmann
- Clemson University, Department of Biological Sciences, Clemson, SC, 29634, USA
| | - Rhett M Rautsaw
- Clemson University, Department of Biological Sciences, Clemson, SC, 29634, USA
| | - Jason L Strickland
- Clemson University, Department of Biological Sciences, Clemson, SC, 29634, USA
- University of Central Florida, Department of Biology, Orlando, FL, 32816, USA
| | - Matthew L Holding
- Clemson University, Department of Biological Sciences, Clemson, SC, 29634, USA
- Florida State University, Department of Biological Science, Tallahassee, FL, 32306, USA
| | - Michael P Hogan
- Florida State University, Department of Biological Science, Tallahassee, FL, 32306, USA
| | - Andrew J Mason
- Clemson University, Department of Biological Sciences, Clemson, SC, 29634, USA
| | - Darin R Rokyta
- Florida State University, Department of Biological Science, Tallahassee, FL, 32306, USA
| | - Christopher L Parkinson
- Clemson University, Department of Biological Sciences, Clemson, SC, 29634, USA.
- Clemson University, Department of Forestry and Environmental Conservation, Clemson, SC, 29634, USA.
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30
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Bloom DD, Egan JP. Systematics of Clupeiformes and testing for ecological limits on species richness in a trans-marine/freshwater clade. NEOTROPICAL ICHTHYOLOGY 2018. [DOI: 10.1590/1982-0224-20180095] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
ABSTRACT Clupeiformes (herring, sardines, shad, anchovies and allies) are a globally distributed clade with nearly 400 marine, freshwater, and diadromous species. Although best known as filter feeding fishes that form large schools, this group occupies a diverse array of trophic guilds and habitats. Theory suggests that species richness in clades is modulated by ecological limits, which results in diversity-dependent clade growth, a pattern that most clades exhibit. As a trans-marine/freshwater clade that has undergone repeated transitions between marine and freshwaters, Clupeiformes are an excellent system for investigating the interplay between ecological diversity and macroevolutionary dynamics. In this study we review the systematics of Clupeiformes and explore discordance in phylogenetic relationships and divergence times between mitochondrial and nuclear loci. We then use comparative methods to test whether ecological limits regulate diversity in Clupeiformes. We find discordance in phylogenetic relationships at various taxonomic scales, but also considerable agreement between genomes. Our results suggest that trans-marine/freshwater clades are able to circumvent ecological limits on clade growth at regional, but not on local scales. Our study demonstrates that phylogenies are a critical link between ecology and macroevolutionary dynamics, and suggests habitat transitions can play a key role in shaping diversity patterns, particularly in the neotropics.
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Affiliation(s)
- Devin D. Bloom
- Western Michigan University, USA; Western Michigan University, USA
| | - Joshua P. Egan
- University of Minnesota, USA; University of Minnesota, USA
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31
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When did anoles diverge? An analysis of multiple dating strategies. Mol Phylogenet Evol 2018; 127:655-668. [DOI: 10.1016/j.ympev.2018.06.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 04/27/2018] [Accepted: 06/06/2018] [Indexed: 11/17/2022]
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32
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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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33
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Laopichienpong N, Muangmai N, Chanhome L, Suntrarachun S, Twilprawat P, Peyachoknagul S, Srikulnath K. Evolutionary Dynamics of the Gametologous CTNNB1 Gene on the Z and W Chromosomes of Snakes. J Hered 2018; 108:142-151. [PMID: 28175328 DOI: 10.1093/jhered/esw074] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 10/13/2016] [Indexed: 12/29/2022] Open
Abstract
Snakes exhibit genotypic sex determination with female heterogamety (ZZ males and ZW females), and the state of sex chromosome differentiation also varies among lineages. To investigate the evolutionary history of homologous genes located in the nonrecombining region of differentiated sex chromosomes in snakes, partial sequences of the gametologous CTNNB1 gene were analyzed for 12 species belonging to henophid (Cylindrophiidae, Xenopeltidae, and Pythonidae) and caenophid snakes (Viperidae, Elapidae, and Colubridae). Nonsynonymous/synonymous substitution ratios (Ka/Ks) in coding sequences were low (Ka/Ks < 1) between CTNNB1Z and CTNNB1W, suggesting that these 2 genes may have similar functional properties. However, frequencies of intron sequence substitutions and insertion–deletions were higher in CTNNB1Z than CTNNB1W, suggesting that Z-linked sequences evolved faster than W-linked sequences. Molecular phylogeny based on both intron and exon sequences showed the presence of 2 major clades: 1) Z-linked sequences of Caenophidia and 2) W-linked sequences of Caenophidia clustered with Z-linked sequences of Henophidia, which suggests that the sequence divergence between CTNNB1Z and CTNNB1W in Caenophidia may have occurred by the cessation of recombination after the split from Henophidia.
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Affiliation(s)
- Nararat Laopichienpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Lawan Chanhome
- Snake Farm, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok, Thailand
| | - Sunutcha Suntrarachun
- Department of Research and Development, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok, Thailand
| | - Panupon Twilprawat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok, Thailand
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, Thailand.,Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok, Thailand
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Underground cryptic speciation within the Maghreb: Multilocus phylogeography sheds light on the diversification of the checkerboard worm lizard Trogonophis wiegmanni. Mol Phylogenet Evol 2018; 120:118-128. [DOI: 10.1016/j.ympev.2017.11.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 11/02/2017] [Accepted: 11/27/2017] [Indexed: 11/21/2022]
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35
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Cleary TJ, Benson RBJ, Evans SE, Barrett PM. Lepidosaurian diversity in the Mesozoic-Palaeogene: the potential roles of sampling biases and environmental drivers. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171830. [PMID: 29657788 PMCID: PMC5882712 DOI: 10.1098/rsos.171830] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/13/2018] [Indexed: 05/27/2023]
Abstract
Lepidosauria is a speciose clade with a long evolutionary history, but there have been few attempts to explore its taxon richness through time. Here we estimate patterns of terrestrial lepidosaur genus diversity for the Triassic-Palaeogene (252-23 Ma), and compare observed and sampling-corrected richness curves generated using Shareholder Quorum Subsampling and classical rarefaction. Generalized least-squares regression (GLS) is used to investigate the relationships between richness, sampling and environmental proxies. We found low levels of richness from the Triassic until the Late Cretaceous (except in the Kimmeridgian-Tithonian of Europe). High richness is recovered for the Late Cretaceous of North America, which declined across the K-Pg boundary but remained relatively high throughout the Palaeogene. Richness decreased following the Eocene-Oligocene Grande Coupure in North America and Europe, but remained high in North America and very high in Europe compared to the Late Cretaceous; elsewhere data are lacking. GLS analyses indicate that sampling biases (particularly, the number of fossil collections per interval) are the best explanation for long-term face-value genus richness trends. The lepidosaur fossil record presents many problems when attempting to reconstruct past diversity, with geographical sampling biases being of particular concern, especially in the Southern Hemisphere.
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Affiliation(s)
- Terri J. Cleary
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Roger B. J. Benson
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Susan E. Evans
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Paul M. Barrett
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
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36
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Systematics and phylogeography of the widely distributed African skink Trachylepis varia species complex. Mol Phylogenet Evol 2018; 120:103-117. [DOI: 10.1016/j.ympev.2017.11.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 10/23/2017] [Accepted: 11/27/2017] [Indexed: 11/23/2022]
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37
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Pyron RA. Novel Approaches for Phylogenetic Inference from Morphological Data and Total-Evidence Dating in Squamate Reptiles (Lizards, Snakes, and Amphisbaenians). Syst Biol 2018; 66:38-56. [PMID: 28173602 DOI: 10.1093/sysbio/syw068] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 07/12/2016] [Accepted: 07/20/2016] [Indexed: 02/04/2023] Open
Abstract
Here, I combine previously underutilized models and priors to perform more biologically realistic phylogenetic inference from morphological data, with an example from squamate reptiles. When coding morphological characters, it is often possible to denote ordered states with explicit reference to observed or hypothetical ancestral conditions. Using this logic, we can integrate across character-state labels and estimate meaningful rates of forward and backward transitions from plesiomorphy to apomorphy. I refer to this approach as MkA, for “asymmetric.” The MkA model incorporates the biological reality of limited reversal for many phylogenetically informative characters, and significantly increases likelihoods in the empirical data sets. Despite this, the phylogeny of Squamata remains contentious. Total-evidence analyses using combined morphological and molecular data and the MkA approach tend toward recent consensus estimates supporting a nested Iguania. However, support for this topology is not unambiguous across data sets or analyses, and no mechanism has been proposed to explain the widespread incongruence between partitions, or the hidden support for various topologies in those partitions. Furthermore, different morphological data sets produced by different authors contain both different characters and different states for the same or similar characters, resulting in drastically different placements for many important fossil lineages. Effort is needed to standardize ontology for morphology, resolve incongruence, and estimate a robust phylogeny. The MkA approach provides a preliminary avenue for investigating morphological evolution while accounting for temporal evidence and asymmetry in character-state changes.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC, USA
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38
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Title PO, Rabosky DL. Do Macrophylogenies Yield Stable Macroevolutionary Inferences? An Example from Squamate Reptiles. Syst Biol 2018; 66:843-856. [PMID: 27821703 DOI: 10.1093/sysbio/syw102] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 10/27/2016] [Indexed: 01/03/2023] Open
Abstract
Advances in the generation, retrieval, and analysis of phylogenetic data have enabled researchers to create phylogenies that contain many thousands of taxa. These "macrophylogenies"-large trees that typically derive from megaphylogeny, supermatrix, or supertree approaches-provide researchers with an unprecedented ability to conduct evolutionary analyses across broad phylogenetic scales. Many studies have now used these phylogenies to explore the dynamics of speciation, extinction, and phenotypic evolution across large swaths of the tree of life. These trees are characterized by substantial phylogenetic uncertainty on multiple levels, and the stability of macroevolutionary inferences from these data sets has not been rigorously explored. As a case study, we tested whether five recently published phylogenies for squamate reptiles-each consisting of more than 4000 species-yield congruent inferences about the processes that underlie variation in species richness across replicate evolutionary radiations of Australian snakes and lizards. We find discordance across the five focal phylogenies with respect to clade age and several diversification rate metrics, and in the effects of clade age on species richness. We also find that crown clade ages reported in the literature on these Australian groups are in conflict with all of the large phylogenies examined. Macrophylogenies offer an unprecedented opportunity to address evolutionary and ecological questions at broad phylogenetic scales, but accurately representing the uncertainty that is inherent to such analyses remains a critical challenge to our field. [Australia; macroevolution; macrophylogeny; squamates; time calibration.].
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Affiliation(s)
- Pascal O Title
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
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39
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Jin Y, Brown RP. Partition number, rate priors and unreliable divergence times in Bayesian phylogenetic dating. Cladistics 2017; 34:568-573. [DOI: 10.1111/cla.12223] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 11/30/2022] Open
Affiliation(s)
- Yuanting Jin
- College of Life Sciences; China Jiliang University; Hangzhou 310018 PR China
| | - Richard P. Brown
- School of Natural Sciences and Psychology; Liverpool John Moores University; Liverpool L3 3AF UK
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40
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Tucker DB, Hedges SB, Colli GR, Pyron RA, Sites JW. Genomic timetree and historical biogeography of Caribbean island ameiva lizards ( Pholidoscelis: Teiidae). Ecol Evol 2017; 7:7080-7090. [PMID: 28904785 PMCID: PMC5587475 DOI: 10.1002/ece3.3157] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/08/2017] [Accepted: 05/21/2017] [Indexed: 01/07/2023] Open
Abstract
The phylogenetic relationships and biogeographic history of Caribbean island ameivas (Pholidoscelis) are not well-known because of incomplete sampling, conflicting datasets, and poor support for many clades. Here, we use phylogenomic and mitochondrial DNA datasets to reconstruct a well-supported phylogeny and assess historical colonization patterns in the group. We obtained sequence data from 316 nuclear loci and one mitochondrial marker for 16 of 19 extant species of the Caribbean endemic genus Pholidoscelis. Phylogenetic analyses were carried out using both concatenation and species tree approaches. To estimate divergence times, we used fossil teiids to calibrate a timetree which was used to elucidate the historical biogeography of these lizards. All phylogenetic analyses recovered four well-supported species groups (clades) recognized previously and supported novel relationships of those groups, including a (P. auberi + P. lineolatus) clade (western + central Caribbean), and a (P. exsul + P. plei) clade (eastern Caribbean). Divergence between Pholidoscelis and its sister clade was estimated to have occurred ~25 Ma, with subsequent diversification on Caribbean islands occurring over the last 11 Myr. Of the six models compared in the biogeographic analyses, the scenario which considered the distance among islands and allowed dispersal in all directions best fit the data. These reconstructions suggest that the ancestor of this group colonized either Hispaniola or Puerto Rico from Middle America. We provide a well-supported phylogeny of Pholidoscelis with novel relationships not reported in previous studies that were based on significantly smaller datasets. We propose that Pholidoscelis colonized the eastern Greater Antilles from Middle America based on our biogeographic analysis, phylogeny, and divergence time estimates. The closing of the Central American Seaway and subsequent formation of the modern Atlantic meridional overturning circulation may have promoted dispersal in this group.
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Affiliation(s)
- Derek B. Tucker
- Biology DepartmentUniversity of West FloridaPensacolaFLUSA
- Department of Biology LSB 4102Brigham Young UniversityProvoUTUSA
| | | | - Guarino R. Colli
- Departamento de ZoologiaUniversidade de BrasíliaBrasíliaDFBrazil
| | | | - Jack W. Sites
- Department of Biology LSB 4102Brigham Young UniversityProvoUTUSA
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Shaffer HB, McCartney-Melstad E, Near TJ, Mount GG, Spinks PQ. Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines). Mol Phylogenet Evol 2017; 115:7-15. [PMID: 28711671 DOI: 10.1016/j.ympev.2017.07.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 05/30/2017] [Accepted: 07/10/2017] [Indexed: 10/19/2022]
Abstract
Accurate time-calibrated phylogenies are the centerpiece of many macroevolutionary studies, and the relationship between the size and scale of molecular data sets and the density and accuracy of fossil calibrations is a key element of time tree studies. Here, we develop a target capture array specifically for living turtles, compare its efficiency to an ultraconserved element (UCE) dataset, and present a time-calibrated molecular phylogeny based on 539 nuclear loci sequenced from 26 species representing the breadth of living turtle diversity plus outgroups. Our gene array, based on three fully sequenced turtle genomes, is 2.4 times more variable across turtles than a recently published UCE data set for an identical subset of 13 species, confirming that taxon-specific arrays return more informative data per sequencing effort than UCEs. We used our genomic data to estimate the ages of living turtle clades including a mid-late Triassic origin for crown turtles and a mid-Carboniferous split of turtles from their sister group, Archosauria. By specifically excluding several of the earliest potential crown turtle fossils and limiting the age of fossil calibration points to the unambiguous crown lineage Caribemys oxfordiensis from the Late Jurassic (Oxfordian, 163.5-157.3Ma) we corroborate a relatively ancient age for living turtles. We also provide novel age estimates for five of the ten testudine families containing more than a single species, as well as several intrafamilial clades. Most of the diversity of crown turtles appears to date to the Paleogene, well after the Cretaceous-Paleogene mass extinction 66mya.
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Affiliation(s)
- H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.
| | - Evan McCartney-Melstad
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Genevieve G Mount
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA; Department of Biological Sciences, Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Phillip Q Spinks
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
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42
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Pereira AG, Schrago CG. Arrival and diversification of mabuyine skinks (Squamata: Scincidae) in the Neotropics based on a fossil-calibrated timetree. PeerJ 2017; 5:e3194. [PMID: 28439466 PMCID: PMC5398276 DOI: 10.7717/peerj.3194] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/16/2017] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The evolution of South American Mabuyinae skinks holds significant biogeographic interest because its sister lineage is distributed across the African continent and adjacent islands. Moreover, at least one insular species, Trachylepis atlantica, has independently reached the New World through transoceanic dispersal. To clarify the evolutionary history of both Neotropical lineages, this study aimed to infer an updated timescale using the largest species and gene sampling dataset ever assembled for this group. By extending the analysis to the Scincidae family, we could employ fossil information to estimate mabuyinae divergence times and carried out a formal statistical biogeography analysis. To unveil macroevolutionary patterns, we also inferred diversification rates for this lineage and evaluated whether the colonization of South American continent significantly altered the mode of Mabuyinae evolution. METHODS A time-calibrated phylogeny was inferred under the Bayesian framework employing fossil information. This timetree was used to (i) evaluate the historical biogeography of mabuiyines using the statistical approach implemented in BioGeoBEARS; (ii) estimate macroevolutionary diversification rates of the South American Mabuyinae lineages and the patterns of evolution of selected traits, namely, the mode of reproduction, body mass and snout-vent length; (iii) test the hypothesis of differential macroevolutionary patterns in South American lineages in BAMM and GeoSSE; and (iv) re-evaluate the ancestral state of the mode of reproduction of mabuyines. RESULTS Our results corroborated the hypothesis that the occupation of the South American continent by Mabuyinae consisted of two independent dispersion events that occurred between the Oligocene and the Miocene. We found significant differences in speciation rates between the New World and the remaining Mabuyinae clades only in GeoSSE. The influence of phenotypic traits on diversification rates was not supported by any method. Ancestral state reconstruction suggested that the ancestor of South American mabuyine was likely viviparous. DISCUSSION Our analyses further corroborated the existence of a transoceanic connection between Africa and South America in the Eocene/Oligocene period (Atlantogea). Following colonization of the isolated South America and subsequent dispersal through the continent by the ancestral mabuyine stock, we detected no difference in macroevolutionary regimes of New World clades. This finding argued against the ecological opportunity model as an explanation for the diversity of living mabuyines.
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Affiliation(s)
- Anieli Guirro Pereira
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Carlos G. Schrago
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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43
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Poe S, Nieto-montes de oca A, Torres-carvajal O, De Queiroz K, Velasco JA, Truett B, Gray LN, Ryan MJ, Köhler G, Ayala-varela F, Latella I. A Phylogenetic, Biogeographic, and Taxonomic study of all Extant Species of Anolis (Squamata; Iguanidae). Syst Biol 2017; 66:663-697. [DOI: 10.1093/sysbio/syx029] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 01/21/2017] [Indexed: 11/13/2022] Open
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44
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Harrington SM, Reeder TW. Phylogenetic inference and divergence dating of snakes using molecules, morphology and fossils: new insights into convergent evolution of feeding morphology and limb reduction. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw039] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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45
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Rovatsos M, Vukić J, Lymberakis P, Kratochvíl L. Evolutionary stability of sex chromosomes in snakes. Proc Biol Sci 2017; 282:20151992. [PMID: 26702042 DOI: 10.1098/rspb.2015.1992] [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] [Indexed: 11/12/2022] Open
Abstract
Amniote vertebrates possess various mechanisms of sex determination, but their variability is not equally distributed. The large evolutionary stability of sex chromosomes in viviparous mammals and birds was believed to be connected with their endothermy. However, some ectotherm lineages seem to be comparably conserved in sex determination, but previously there was a lack of molecular evidence to confirm this. Here, we document a stability of sex chromosomes in advanced snakes based on the testing of Z-specificity of genes using quantitative PCR (qPCR) across 37 snake species (our qPCR technique is suitable for molecular sexing in potentially all advanced snakes). We discovered that at least part of sex chromosomes is homologous across all families of caenophidian snakes (Acrochordidae, Xenodermatidae, Pareatidae, Viperidae, Homalopsidae, Colubridae, Elapidae and Lamprophiidae). The emergence of differentiated sex chromosomes can be dated back to about 60 Ma and preceded the extensive diversification of advanced snakes, the group with more than 3000 species. The Z-specific genes of caenophidian snakes are (pseudo)autosomal in the members of the snake families Pythonidae, Xenopeltidae, Boidae, Erycidae and Sanziniidae, as well as in outgroups with differentiated sex chromosomes such as monitor lizards, iguanas and chameleons. Along with iguanas, advanced snakes are therefore another example of ectothermic amniotes with a long-term stability of sex chromosomes comparable with endotherms.
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Affiliation(s)
- Michail Rovatsos
- Faculty of Science, Department of Ecology, Charles University in Prague, Viničná 7, 12844 Praha 2, Czech Republic
| | - Jasna Vukić
- Faculty of Science, Department of Ecology, Charles University in Prague, Viničná 7, 12844 Praha 2, Czech Republic
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Knossou Avenue, 71409 Irakleio, Crete, Greece
| | - Lukáš Kratochvíl
- Faculty of Science, Department of Ecology, Charles University in Prague, Viničná 7, 12844 Praha 2, Czech Republic
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46
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Simões TR, Caldwell MW, Nydam RL, Jiménez-Huidobro P. Osteology, phylogeny, and functional morphology of two Jurassic lizard species and the early evolution of scansoriality in geckoes. Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Tiago R. Simões
- Department of Biological Sciences; University of Alberta; Edmonton AB T6G 2E9 Canada
| | - Michael W. Caldwell
- Department of Biological Sciences; University of Alberta; Edmonton AB T6G 2E9 Canada
- Department of Earth and Atmospheric Sciences; University of Alberta; Edmonton AB T6G 2E9 Canada
| | - Randall L. Nydam
- Department of Anatomy; Arizona College of Osteopathic Medicine; Midwestern University; 19555 North 59th Drive Glendale AZ 85383 USA
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47
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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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48
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Cattin L, Schuerch J, Salamin N, Dubey S. Why are some species older than others? A large-scale study of vertebrates. BMC Evol Biol 2016; 16:90. [PMID: 27142042 PMCID: PMC4855795 DOI: 10.1186/s12862-016-0646-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 03/30/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Strong variations are observed between and within taxonomic groups in the age of extant species and these differences can clarify factors that render species more vulnerable to extinction. Understanding the factors that influence the resilience of species is thus a key component of evolutionary biology, but it is also of prime importance in a context of climate change and for conservation in general. We explored the effect of extrinsic and intrinsic factors on the timing of the oldest diversification event in over 600 vertebrate species distributed worldwide. We used phylogenetic comparative methods to show that color polymorphism, latitude and reproduction (the latter through its interaction with latitude) affected the timing of the oldest diversification event within a species. RESULTS Species from higher latitudes tended to be younger, and colour-polymorphic species were older than monomorphic species. Mode of reproduction was important also, in that the age of oviparous species decreased with latitude, whereas no pattern was apparent for viviparous species. Organisms which have already persisted for a long time may be more likely to deal with future modifications of their environment. CONCLUSIONS Species that are colour polymorphic, viviparous, and/or live at low latitudes have exhibited resilience to past environmental changes, and hence may be better able to deal with current climate change.
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Affiliation(s)
- Laure Cattin
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland
| | - Johan Schuerch
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015, Lausanne, Switzerland
| | - Sylvain Dubey
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland.
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49
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Linkem CW, Minin VN, Leaché AD. Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae). Syst Biol 2016; 65:465-77. [PMID: 26738927 PMCID: PMC6383586 DOI: 10.1093/sysbio/syw001] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 12/29/2015] [Indexed: 01/28/2023] Open
Abstract
The anomaly zone, defined by the presence of gene tree topologies that are more probable than the true species tree, presents a major challenge to the accurate resolution of many parts of the Tree of Life. This discrepancy can result from consecutive rapid speciation events in the species tree. Similar to the problem of long-branch attraction, including more data via loci concatenation will only reinforce the support for the incorrect species tree. Empirical phylogenetic studies often employ coalescent-based species tree methods to avoid the anomaly zone, but to this point these studies have not had a method for providing any direct evidence that the species tree is actually in the anomaly zone. In this study, we use 16 species of lizards in the family Scincidae to investigate whether nodes that are difficult to resolve place the species tree within the anomaly zone. We analyze new phylogenomic data (429 loci), using both concatenation and coalescent-based species tree estimation, to locate conflicting topological signal. We then use the unifying principle of the anomaly zone, together with estimates of ancestral population sizes and species persistence times, to determine whether the observed phylogenetic conflict is a result of the anomaly zone. We identify at least three regions of the Scincidae phylogeny that provide demographic signatures consistent with the anomaly zone, and this new information helps reconcile the phylogenetic conflict in previously published studies on these lizards. The anomaly zone presents a real problem in phylogenetics, and our new framework for identifying anomalous relationships will help empiricists leverage their resources appropriately for investigating and overcoming this challenge.
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Affiliation(s)
| | - Vladimir N Minin
- Department of Biology, University of Washington, Seattle WA; Department of Statistics, University of Washington, Seattle WA
| | - Adam D Leaché
- Department of Biology, University of Washington, Seattle WA; Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, 98195, USA
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50
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Up high and down low: Molecular systematics and insight into the diversification of the ground beetle genus Rhadine LeConte. Mol Phylogenet Evol 2016; 98:161-75. [DOI: 10.1016/j.ympev.2016.01.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 12/10/2015] [Accepted: 01/14/2016] [Indexed: 11/24/2022]
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