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Gvoždík V, Dolinay M, Zassi-Boulou AG, Lemmon AR, Lemmon EM, Procházka M. Central African dwarf crocodiles found in syntopy are comparably divergent to South American dwarf caimans. Biol Lett 2024; 20:20230448. [PMID: 38716586 PMCID: PMC11135362 DOI: 10.1098/rsbl.2023.0448] [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: 09/25/2023] [Revised: 12/18/2023] [Accepted: 03/04/2024] [Indexed: 05/31/2024] Open
Abstract
Recent molecular taxonomic advancements have expanded our understanding of crocodylian diversity, revealing the existence of previously overlooked species, including the Congo dwarf crocodile (Osteolaemus osborni) in the central Congo Basin rainforests. This study explores the genomic divergence between O. osborni and its better-known relative, the true dwarf crocodile (Osteolaemus tetraspis), shedding light on their evolutionary history. Field research conducted in the northwestern Republic of the Congo uncovered a locality where both species coexist in sympatry/syntopy. Genomic analysis of sympatric individuals reveals a level of divergence comparable to that between ecologically similar South American dwarf caimans (Paleosuchus palpebrosus and Paleosuchus trigonatus), suggesting parallel speciation in the Afrotropics and Neotropics during the Middle to Late Miocene, 10-12 Ma. Comparison of the sympatric and allopatric dwarf crocodiles indicates no gene flow between the analysed sympatric individuals of O. osborni and O. tetraspis. However, a larger sample will be required to answer the question of whether or to what extent these species hybridize. This study emphasizes the need for further research on the biology and conservation status of the Congo dwarf crocodile, highlighting its significance in the unique biodiversity of the Congolian rainforests and thus its potential as a flagship species.
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Affiliation(s)
- Václav Gvoždík
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Zoology, National Museum of the Czech Republic, Prague, Czech Republic
| | - Matej Dolinay
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Ange-Ghislain Zassi-Boulou
- Department of Biology, National Institute for Research in Exact and Natural Sciences (IRSEN), Brazzaville, Republic of the Congo
| | - Alan R. Lemmon
- Department of Scientific Computing, Dirac Science Library, Florida State University, Tallahassee, FL, USA
| | - Emily M. Lemmon
- Department of Biological Sciences, Florida State University, Tallahassee, FL, 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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3
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Martins LF, Choueri EL, Oliveira AFS, Domingos FMCB, Caetano GHO, Cavalcante VHGL, Leite RN, Fouquet A, Rodrigues MT, Carnaval AC, Colli GR, Werneck FP. Whiptail lizard lineage delimitation and population expansion as windows into the history of Amazonian open ecosystems. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1953185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Lidia F. Martins
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Erik L. Choueri
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Alan F. S. Oliveira
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | | | - Gabriel H. O. Caetano
- Mitrani Department of Desert Ecology, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 849900 Midreshet Ben-Gurion, Israel
| | | | - Rafael N. Leite
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Antoine Fouquet
- Laboratoire Evolution et Diversité Biologique (EDB), UMR5174, Bâtiment 4R1, 118 Route de Narbonne 31077, Toulouse, France
| | - Miguel T. Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ana C. Carnaval
- City College of New York and Biology Ph.D. Program, The Graduate Center City University of New York, New York, NY 10031, USA
| | - Guarino R. Colli
- Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Fernanda P. Werneck
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
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4
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Mikula O, Nicolas V, Šumbera R, Konečný A, Denys C, Verheyen E, Bryjová A, Lemmon AR, Moriarty Lemmon E, Bryja J. Nuclear phylogenomics, but not mitogenomics, resolves the most successful Late Miocene radiation of African mammals (Rodentia: Muridae: Arvicanthini). Mol Phylogenet Evol 2021; 157:107069. [PMID: 33421615 DOI: 10.1016/j.ympev.2021.107069] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 12/17/2020] [Accepted: 01/04/2021] [Indexed: 01/09/2023]
Abstract
The tribe Arvicanthini (Muridae: Murinae) is a highly diversified group of rodents (ca. 100 species) and with 18 African genera (plus one Asiatic) represents probably the most successful adaptive radiation of extant mammals in Africa. They colonized a broad spectrum of habitats (from rainforests to semi-deserts) in whole sub-Saharan Africa and their members often belong to most abundant parts of mammal communities. Despite intensive efforts, the phylogenetic relationships among major lineages (i.e. genera) remained obscured, which was likely caused by the intensive radiation of the group, dated to the Late Miocene. Here we used genomic scale data (377 nuclear loci; 581,030 bp) and produced the first fully resolved species tree containing all currently delimited genera of the tribe. Mitogenomes were also extracted, and while the results were largely congruent, there was less resolution at basal nodes of the mitochondrial phylogeny. Results of a fossil-based divergence dating analysis suggest that the African radiation started early after the colonization of Africa by a single arvicanthine ancestor from Asia during the Messinian stage (ca. 7 Ma), and was likely linked with a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forest, while many others successfully colonized broad spectrum of new open habitats (e.g. savannas, wetlands or montane moorlands) that appeared at the beginning of Pliocene. One lineage even evolved partially arboricolous life style in savanna woodlands, which allowed them to re-colonize equatorial forests. We also discuss delimitation of genera in Arvicanthini and propose corresponding taxonomic changes.
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Affiliation(s)
- Ondřej Mikula
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, 602 00 Brno, Czech Republic
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - Radim Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Adam Konečný
- Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - Erik Verheyen
- Royal Belgian Institute for Natural Sciences, Operational Direction Taxonomy and Phylogeny, 1000 Brussels, Belgium; Evolutionary Ecology Group, Biology Department, University of Antwerp, 2020 Antwerp, Belgium
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4295, United States
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, United States
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic.
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5
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Scarpetta SG. Unusual lizard fossil from the Miocene of Nebraska and a minimum age for cnemidophorine teiids. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200317. [PMID: 32968509 PMCID: PMC7481707 DOI: 10.1098/rsos.200317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
Teiid lizards are well represented in the fossil record and are common components of modern ecosystems in North and South America. Many fossils were referred to the cnemidophorine teiid group (whiptails, racerunners and relatives), particularly from North America. However, systematic interpretations of morphological features in cnemidophorines were hampered by the historically problematic taxonomy of the clade, and the biogeography and chronology of cnemidophorine evolution in North America is poorly understood from the fossil record. Few fossil cnemidophorines were identified with an apomorphy-based diagnosis, and there are almost no fossil cnemidophorines that could be used to anchor node calibrations. Here, I describe a cnemidophorine from the Miocene Ogallala Group of Nebraska and diagnose the fossil using apomorphies. In that process, I clarify the systematic utility of several morphological features of cnemidophorine lizards. I refer the fossil to the least inclusive clade containing Aspidoscelis, Holcosus and Pholidoscelis. The most conservative minimum age of the locality of the fossil is a fission-track date of 6.3 Ma, but mammal biochronology provides a more refined age of 9.4 Ma, which can be used as a minimum age for the crown cnemidophorine clade in divergence time analyses. The fossil indicates that a cnemidophorine lineage that does not live in Nebraska today inhabited the area during the Miocene. I refrain from naming a new taxon pending discovery of additional fossil material of the lineage to which the fossil belonged.
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Affiliation(s)
- Simon G. Scarpetta
- Department of Geological Sciences, Jackson School of Geosciences, The University of Texas at Austin, Austin, TX, USA
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6
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Granados-González G, Pérez-Almazán C, Gómez-Benitez A, Walker JM, Hernández-Gallegos O. Aspidoscelis costatus costatus (Squamata, Teiidae): high elevation clutch production for a population of whiptail lizards. HERPETOZOA 2020. [DOI: 10.3897/herpetozoa.33.e54901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Clutch size and number of clutches per reproductive cycle are important life history traits that can be influenced by anatomical, physiological, evolutionary, and ecological factors. This report on the clutch size and number of clutches of an endemic Mexican whiptail lizard, Aspidoscelis costatus costatus (Cope, 1878), is based on a study of population at an unusually high elevation for a member of this genus. The study site is located in Ixtapan de la Sal, southeastern Estado de México, Central Mexico, at 2090 m a.s.l. Lizards were sampled in June 2006, and from May to July 2007, where females of Aspidoscelis costatus costatus were collected by hand along a drift fence. Female reproductive condition was evaluated based on abdominal palpation for presence of developing eggs; clutch size was determined by actual counts of either vitellogenic follicles or oviductal eggs. The smallest reproductive female was 77 mm snout-vent length; females produced a minimum of two clutches during the breeding season, the mean clutch size of 6.5 eggs (n = 33) was one of the largest reported for the genus. However, both length and width of its eggs, and the relative clutch mass have not been diminished by development of a large clutch. Additionally, comparisons of clutch size were undertaken within the polytypic A. costatus complex, within the genus Aspidoscelis, and between certain genera of whiptail lizards. This apparently represents the first study of whiptail lizards (genus Aspidoscelis), assessing the aforementioned reproductive characteristics, in a population above 2000 m.
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Cole CJ, Dessauer HC, Paulissen MA, Walker JM. Hybridization between Whiptail Lizards in Texas: Aspidoscelis laredoensis and A. Gularis, with Notes on Reproduction of a Hybrid. AMERICAN MUSEUM NOVITATES 2020. [DOI: 10.1206/3947.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Charles J. Cole
- Division of Vertebrate Zoology (Herpetology), American Museum of Natural History
| | - Herbert C. Dessauer
- Deceased. Department of Biochemistry and Molecular Biology, Louisiana State University Health Science Center, New Orleans, LA
| | - Mark A. Paulissen
- Department of Natural Sciences, Northeastern State University, Tahlequah, OK
| | - James M. Walker
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR
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Karin BR, Gamble T, Jackman TR. Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements. Mol Biol Evol 2020; 37:904-922. [PMID: 31710677 PMCID: PMC7038749 DOI: 10.1093/molbev/msz263] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutionary rate among other factors. The most commonly used reduced representation data sets for phylogenomics are ultraconserved elements (UCEs) and Anchored Hybrid Enrichment (AHE). Here, we introduce Rapidly Evolving Long Exon Capture (RELEC), a new set of loci that targets single exons that are both rapidly evolving (evolutionary rate faster than RAG1) and relatively long in length (>1,500 bp), while at the same time avoiding paralogy issues across amniotes. We compare the RELEC data set to UCEs and AHE in squamate reptiles by aligning and analyzing orthologous sequences from 17 squamate genomes, composed of 10 snakes and 7 lizards. The RELEC data set (179 loci) outperforms AHE and UCEs by maximizing per-locus genetic variation while maintaining presence and orthology across a range of evolutionary scales. RELEC markers show higher phylogenetic informativeness than UCE and AHE loci, and RELEC gene trees show greater similarity to the species tree than AHE or UCE gene trees. Furthermore, with fewer loci, RELEC remains computationally tractable for full Bayesian coalescent species tree analyses. We contrast RELEC to and discuss important aspects of comparable methods, and demonstrate how RELEC may be the most effective set of loci for resolving difficult nodes and rapid radiations. We provide several resources for capturing or extracting RELEC loci from other amniote groups.
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Affiliation(s)
- Benjamin R Karin
- Department of Biology, Villanova University, Villanova, PA
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI
- Milwaukee Public Museum, Milwaukee, WI
- Bell Museum of Natural History, University of Minnesota, St. Paul, MN
| | - Todd R Jackman
- Department of Biology, Villanova University, Villanova, PA
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Hudson SB, Kluever BM, Webb AC, French SS. Steroid hormones, energetic state, and immunocompetence vary across reproductive contexts in a parthenogenetic lizard. Gen Comp Endocrinol 2020; 288:113372. [PMID: 31866306 DOI: 10.1016/j.ygcen.2019.113372] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 01/22/2023]
Abstract
Reproduction is energetically expensive and investing in this life history trait is likely accompanied by significant changes in physiological activity. Investment strategy necessary for achieving reproductive success in reptiles can vary with reproductive form and pattern, potentiating different consequences for competing fitness-related traits such as those key to survival. The goal of this study was to assess if and how energetic state (i.e., energy metabolites) and self-maintenance (i.e., immunocompetence) are hormonally modulated across reproductive contexts in an oviparous, parthenogenetic lizard, the Colorado Checkered Whiptail Aspidoscelis neotesselata. Here blood plasma samples were collected from lizards within the US Army Fort Carson Military Installation near Colorado Springs, CO, USA, during seasons of reproductive activity (i.e., June) and inactivity (i.e., August). Measures of reproductive (i.e., estradiol) and energy-mobilizing (i.e., corticosterone) hormones, energy metabolites (i.e., glucose, triglycerides, and free glycerol), and innate immunity (i.e., bactericidal ability) were compared by season and reproductive stage. Levels of energy metabolites and bactericidal ability were compared to levels of E2 and CORT. Bactericidal ability was also compared to levels of energy metabolites. Corticosterone and glucose levels were lower during the reproductive season while triglyceride levels and bactericidal ability were higher, but both estradiol and free glycerol levels did not differ between seasons. Throughout vitellogenesis, corticosterone and glucose levels as well as bactericidal ability did not differ, but estradiol levels were higher during early and mid-stage and both triglyceride and free glycerol levels were lower during gravidity. Corticosterone levels were negatively associated with circulating triglycerides and bactericidal ability, but were not related to glucose nor free glycerol levels. Estradiol levels were positively associated with free glycerol levels and bactericidal ability, but were not related to glucose nor triglyceride levels. Finally, bactericidal ability was negatively associated with glucose, but positively associated with triglycerides. Differences in energetic state and immunocompetence are thus reflected by shifts in hormone secretion across reproductive investment. These findings provide partial support for the hypothesis that energetic state is differentially regulated by steroid hormones to afford reproduction, potentially at the cost of future survival.
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Affiliation(s)
- S B Hudson
- Department of Biology, Utah State University, Logan, UT 84322-5205, USA; Ecology Center, Utah State University, Logan, UT 84322‑5205, USA.
| | - B M Kluever
- United States Department of Defense, Department of the Army, Directorate of Public Works, Environmental Division, Conservation Branch, Fort Carson, CO 80913, USA; United States Department of Agriculture, Wildlife Services, National Wildlife Research Center, Florida Field Station, Gainesville, FL 32641-6033, USA
| | - A C Webb
- Department of Biology, Utah State University, Logan, UT 84322-5205, USA; Ecology Center, Utah State University, Logan, UT 84322‑5205, USA
| | - S S French
- Department of Biology, Utah State University, Logan, UT 84322-5205, USA; Ecology Center, Utah State University, Logan, UT 84322‑5205, USA
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10
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Sheu Y, Zurano JP, Ribeiro‐Junior MA, Ávila‐Pires TC, Rodrigues MT, Colli GR, Werneck FP. The combined role of dispersal and niche evolution in the diversification of Neotropical lizards. Ecol Evol 2020; 10:2608-2625. [PMID: 32185006 PMCID: PMC7069304 DOI: 10.1002/ece3.6091] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 01/23/2023] Open
Abstract
Ecological requirements and environmental conditions can influence diversification across temporal and spatial scales. Understanding the role of ecological niche evolution under phylogenetic contexts provides insights on speciation mechanisms and possible responses to future climatic change. Large-scale phyloclimatic studies on the megadiverse Neotropics, where biomes with contrasting vegetation types occur in narrow contact, are rare. We integrate ecological and biogeographic data with phylogenetic comparative methods, to investigate the relative roles of biogeographic events and niche divergence and conservatism on the diversification of the lizard genus Kentropyx Spix, 1825 (Squamata: Teiidae), distributed in South American rainforests and savannas. Using five molecular markers, we estimated a dated species tree, which recovered three clades coincident with previously proposed species groups diverging during the mid-Miocene. Biogeography reconstruction indicates a role of successive dispersal events from an ancestral range in the Brazilian Shield and western Amazonia. Ancestral reconstruction of climatic tolerances and niche overlap metrics indicates a trend of conservatism during the diversification of groups from the Amazon Basin and Guiana Shield, and a strong signal of niche divergence in the Brazilian Shield savannas. Our results suggest that climatic-driven divergence at dynamic forest-savanna borders might have resulted in adaptation to new environmental niches, promoting habitat shifts and shaping speciation patterns of Neotropical lizards. Dispersal and ecological divergence could have a more important role in Neotropical diversification than previously thought.
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Affiliation(s)
- Yumi Sheu
- Programa de Pós‐Graduação em GenéticaConservação e Biologia EvolutivaInstituto Nacional de Pesquisas do AmazôniaManausBrasil
- Programa de Pós‐Graduação em Genética e MelhoramentoUniversidade Federal do Espírito SantoEspírito SantoBrasil
| | - Juan P. Zurano
- Departamento de Sistemática e EcologiaUniversidade Federal da ParaíbaJoão PessoaBrasil
| | | | | | - Miguel T. Rodrigues
- Departamento de ZoologiaInstituto de BiociênciasUniversidade de São PauloSão PauloBrasil
| | - Guarino R. Colli
- Departamento de ZoologiaInstituto de Ciências BiológicasUniversidade de BrasíliaBrasíliaBrasil
| | - Fernanda P. Werneck
- Programa de Coleções Científicas BiológicasCoordenação de BiodiversidadeInstituto Nacional de Pesquisas da AmazôniaManausBrasil
- Department of Organismic and Evolutionary BiologyMuseum of Comparative BiologyHarvard UniversityCambridgeMAUSA
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11
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da Silva MJ, de Araújo Vieira AP, Galvão Cipriano FM, Dos Santos Cândido MR, de Oliveira EHC, Gimenez Pinheiro T, da Silva EL. The Karyotype of Salvator merianae (Squamata, Teiidae): Analyses by Classical and Molecular Cytogenetic Techniques. Cytogenet Genome Res 2020; 160:94-99. [PMID: 32062647 DOI: 10.1159/000506140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2020] [Indexed: 12/28/2022] Open
Abstract
In this study, we analyzed the karyotype of Salvator merianae (Teiidae) from the Brazilian semiarid region using different cytogenetic markers. Chromosomes were examined by classical (Giemsa and AgNOR staining) and molecular (FISH with ribosomal, telomeric, and microsatellite probes) cytogenetic approaches. S. merianae showed a diploid chromosome number of 2n = 38 (10 biarmed macrochromosomes + 28 microchromosomes). No sex-linked chromosome heteromorphisms were observed. Clusters of 18S/28S rDNA were localized in the terminal region of the long arm of pair 2. In addition to the typical telomeric signals, (TTAGGG)n repeats were detected in the pericentromeric region of some macrochromosome pairs, which might indicate the occurrence of chromosomal rearrangements via chromosome fusions. Hybridization signals of the microsatellite probes (GA)n, (GAA)n, and (GAG)n were uniformly distributed across all chromosomes, while (CA)n, (CAA)n, and (CAC)n produced brighter signals in the telomeric and pericentromeric regions of specific chromosome pairs. The comparison with previous studies demonstrates that, despite the wide distribution of S. merianae, the macrostructure organization of the karyotype remained unchanged, showing stability in diploid number and chromosome morphology.
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12
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Esquivel‐Ramírez A, Hornung‐Leoni CT, Manríquez‐Morán NL. Morphological variation and sexual dimorphism in the
Aspidoscelis gularis
complex (Squamata: Teiidae) from Mexico. ACTA ZOOL-STOCKHOLM 2020. [DOI: 10.1111/azo.12322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anahí Esquivel‐Ramírez
- Centro de Investigaciones Biológicas Universidad Autónoma del Estado de Hidalgo Mineral de la Reforma Hidalgo México
| | - Claudia T. Hornung‐Leoni
- Centro de Investigaciones Biológicas Universidad Autónoma del Estado de Hidalgo Mineral de la Reforma Hidalgo México
| | - Norma L. Manríquez‐Morán
- Centro de Investigaciones Biológicas Universidad Autónoma del Estado de Hidalgo Mineral de la Reforma Hidalgo México
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13
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Natusch DJ, Esquerré D, Lyons JA, Hamidy A, Lemmon AR, Moriarty Lemmon E, Riyanto A, Keogh JS, Donnellan S. Species delimitation and systematics of the green pythons (Morelia viridis complex) of melanesia and Australia. Mol Phylogenet Evol 2020; 142:106640. [DOI: 10.1016/j.ympev.2019.106640] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/30/2019] [Accepted: 10/05/2019] [Indexed: 02/01/2023]
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14
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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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15
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Garcia-Porta J, Irisarri I, Kirchner M, Rodríguez A, Kirchhof S, Brown JL, MacLeod A, Turner AP, Ahmadzadeh F, Albaladejo G, Crnobrnja-Isailovic J, De la Riva I, Fawzi A, Galán P, Göçmen B, Harris DJ, Jiménez-Robles O, Joger U, Jovanović Glavaš O, Karış M, Koziel G, Künzel S, Lyra M, Miles D, Nogales M, Oğuz MA, Pafilis P, Rancilhac L, Rodríguez N, Rodríguez Concepción B, Sanchez E, Salvi D, Slimani T, S'khifa A, Qashqaei AT, Žagar A, Lemmon A, Moriarty Lemmon E, Carretero MA, Carranza S, Philippe H, Sinervo B, Müller J, Vences M, Wollenberg Valero KC. Environmental temperatures shape thermal physiology as well as diversification and genome-wide substitution rates in lizards. Nat Commun 2019; 10:4077. [PMID: 31501432 PMCID: PMC6733905 DOI: 10.1038/s41467-019-11943-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 08/13/2019] [Indexed: 11/09/2022] Open
Abstract
Climatic conditions changing over time and space shape the evolution of organisms at multiple levels, including temperate lizards in the family Lacertidae. Here we reconstruct a dated phylogenetic tree of 262 lacertid species based on a supermatrix relying on novel phylogenomic datasets and fossil calibrations. Diversification of lacertids was accompanied by an increasing disparity among occupied bioclimatic niches, especially in the last 10 Ma, during a period of progressive global cooling. Temperate species also underwent a genome-wide slowdown in molecular substitution rates compared to tropical and desert-adapted lacertids. Evaporative water loss and preferred temperature are correlated with bioclimatic parameters, indicating physiological adaptations to climate. Tropical, but also some populations of cool-adapted species experience maximum temperatures close to their preferred temperatures. We hypothesize these species-specific physiological preferences may constitute a handicap to prevail under rapid global warming, and contribute to explaining local lizard extinctions in cool and humid climates.
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Affiliation(s)
- Joan Garcia-Porta
- CREAF, 08193, Cerdanyola del Vallès, Spain
- Department of Biology, Washington University in Saint Louis, St. Louis, MO, 63130, USA
| | - Iker Irisarri
- Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Martin Kirchner
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Ariel Rodríguez
- Institute of Zoology, Tierärztliche Hochschule Hannover, Bünteweg 17, 30559, Hannover, Germany
| | - Sebastian Kirchhof
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Jason L Brown
- Department of Zoology, Southern Illinois University, Carbondale, IL, USA
| | - Amy MacLeod
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Alexander P Turner
- School of Engineering and Computer Science, University of Hull, Cottingham Road, HU6 7RX, Kingston-Upon-Hull, UK
| | - Faraham Ahmadzadeh
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C, Tehran, Iran
| | - Gonzalo Albaladejo
- Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas (CSIC), c/Astrofísico Francisco Sánchez, 38206, Tenerife, Canary Islands, Spain
| | - Jelka Crnobrnja-Isailovic
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18000 Niš, Institute for Biological Research "S. Stanković" University of Belgrade, Despota Stefana 142, Belgrade, 11000, Serbia
| | - Ignacio De la Riva
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, C/José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Adnane Fawzi
- Faculty of Sciences, Biodiversity and Ecosystem Dynamics Laboratory, Cadi Ayyad University, Marrakech, Morocco
| | - Pedro Galán
- Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, Grupo de Investigación en Biología Evolutiva (GIBE), 15071, A Coruña, Spain
| | - Bayram Göçmen
- Zoology Section, Biology Department, Faculty of Science, Ege University, 35100, Bornova, Izmir, Turkey
| | - D James Harris
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, University of Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Octavio Jiménez-Robles
- Department of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Ulrich Joger
- Staatliches Naturhistorisches Museum, Braunschweig, Germany
| | | | - Mert Karış
- Department of Chemistry and Chemical Process Technologies, Acıgöl Vocational High School of Technical Sciences, Nevşehir Hacı Bektaş Veli University, 50300, Nevşehir, Turkey
| | - Giannina Koziel
- Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106, Braunschweig, Germany
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Mariana Lyra
- Departamento de Zoologia, Instituto de Biociências, UNESP - Universidade Estadual Paulista, Rio Claro, Brazil
| | - Donald Miles
- Department of Biological Sciences, Ohio University, Athens, OH, 45701, USA
| | - Manuel Nogales
- Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas (CSIC), c/Astrofísico Francisco Sánchez, 38206, Tenerife, Canary Islands, Spain
| | - Mehmet Anıl Oğuz
- Zoology Section, Biology Department, Faculty of Science, Ege University, 35100, Bornova, Izmir, Turkey
| | - Panayiotis Pafilis
- Section of Zoology and Marine Biology, Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, Ilissia, Athens, 157-84, Greece
| | - Loïs Rancilhac
- Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106, Braunschweig, Germany
| | - Noemí Rodríguez
- Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas (CSIC), c/Astrofísico Francisco Sánchez, 38206, Tenerife, Canary Islands, Spain
| | - Benza Rodríguez Concepción
- Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas (CSIC), c/Astrofísico Francisco Sánchez, 38206, Tenerife, Canary Islands, Spain
| | - Eugenia Sanchez
- Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106, Braunschweig, Germany
| | - Daniele Salvi
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, University of Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
- Department of Health, Life and Environmental Sciences, University of L'Aquila, 67100, Coppito, L'Aquila, Italy
| | - Tahar Slimani
- Faculty of Sciences, Biodiversity and Ecosystem Dynamics Laboratory, Cadi Ayyad University, Marrakech, Morocco
| | - Abderrahim S'khifa
- Faculty of Sciences, Biodiversity and Ecosystem Dynamics Laboratory, Cadi Ayyad University, Marrakech, Morocco
| | - Ali Turk Qashqaei
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C, Tehran, Iran
| | - Anamarija Žagar
- National Institute of Biology NIB, Department of Organisms and Ecosystems Research, Vecna pot 111, 1000, Ljubljana, Slovenia
| | - Alan Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, USA
| | | | - Miguel Angel Carretero
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, University of Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat, Pompeu Fabra), Passeig Marítim de la Barceloneta 37-,49, 08003, Barcelona, Spain
| | - Hervé Philippe
- Centre for Biodiversity Theory and Modelling, UMR CNRS 5321, Station of Theoretical and Experimental Ecology, 09200, Moulis, France
| | - Barry Sinervo
- Department of Ecology and Evolutionary Biology, and Institute for the Study of the Ecological and Evolutionary Climate Impacts, University of California, 130 McAllister Way, Coastal Biology Building, Santa Cruz, CA, 95064, USA
| | - Johannes Müller
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Miguel Vences
- Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106, Braunschweig, Germany.
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16
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Cole CJ, Cordes JE, Walker JM. Karyotypes of the North American Parthenogenetic Whiptail Lizard Aspidoscelis velox, and Return of Aspidoscelis innotatus to the Synonymy of A. velox (Reptilia: Squamata: Teiidae). AMERICAN MUSEUM NOVITATES 2019. [DOI: 10.1206/3936.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Charles J. Cole
- Division of Vertebrate Zoology (Herpetology), American Museum of Natural History
| | - James E. Cordes
- Division of Sciences and Mathematics, Louisiana State University Eunice, LA
| | - James M. Walker
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR
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17
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Lemos-Espinal JA, Smith GR, Rorabaugh JC. A conservation checklist of the amphibians and reptiles of Sonora, Mexico, with updated species lists. Zookeys 2019; 829:131-160. [PMID: 30914839 PMCID: PMC6422993 DOI: 10.3897/zookeys.829.32146] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 01/28/2019] [Indexed: 11/12/2022] Open
Abstract
Sonora has a rich natural diversity, including reptiles and amphibians. Sonora's location on the United States-Mexico border creates some unique conservation challenges for its wildlife. We compiled a list of the amphibian and reptile species currently known for Sonora, summarized the conservation status of these species, and compared our list of species with known species lists for adjacent states. The herpetofauna of Sonora comprises 200 species of amphibians and reptiles (38 amphibians and 162 reptiles). Overall, Sonora shares the most species with Chihuahua, Sinaloa, and Arizona. Approximately 11% of the amphibian and reptile species are IUCN listed, but 35.5% are placed in a protected category by SEMARNAT, and 32.6% are categorized as high risk by the Environmental Vulnerability Score.
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Affiliation(s)
- Julio A Lemos-Espinal
- Laboratorio de Ecología-UBIPRO, FES Iztacala UNAM, Avenida los Barrios 1, Los Reyes Iztacala, Tlalnepantla, edo. de Mexico, 54090, Mexico Universidad Nacional Autónoma de México Tlalnepantla Mexico
| | - Geoffrey R Smith
- Department of Biology, Denison University, Granville, Ohio 43023, USA Denison University Granville United States of America
| | - James C Rorabaugh
- P.O. Box 31, Saint David, Arizona 85630, USA Unaffilaited Phoenix United States of America
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18
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Borczyk B, Skawiński T. Tracking down the lizards from Gravenhorst's collection at the University of Wrocław: type specimens of Callopistes maculatus Gravenhorst, 1838 and three Liolaemus species rediscovered. PeerJ 2019; 7:e6525. [PMID: 30809465 PMCID: PMC6388667 DOI: 10.7717/peerj.6525] [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: 10/10/2018] [Accepted: 01/26/2019] [Indexed: 11/30/2022] Open
Abstract
Johann Ludwig Christian Gravenhorst's herpetological collection at the Museum of Natural History, University of Wrocław included numerous important specimens of amphibians and reptiles. The majority, if not the entirety, of this collection has long been thought to be lost. However, we were able to rediscover some type specimens of lizards. The rediscovered specimens include the holotypes of Liolaemus conspersus and L. hieroglyphicus, one syntype of Callopistes maculatus (here designated as the lectotype) and two syntypes of L. lineatus (one of which is herein designated as the lectotype). Reexamination of these specimens indicates that previous synonymies proposed for L. conspersus and two syntypes of L. hieroglyphicus are problematic; furthermore, more complex taxonomic work is needed to resolve this issue. Two rediscovered syntypes of L. lineatus differ in several scalation traits and are possibly not conspecific. The type specimens of several other species of lizards from Gravenhorst's collection (Liolaemus marmoratus, L. unicolor and two other syntypes of L. lineatus, Leiocephalus schreibersii and Chalcides viridanus) were not found and are probably lost.
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Affiliation(s)
- Bartosz Borczyk
- Department of Evolutionary Biology and Conservation of Vertebrates, University of Wrocław, Wrocław, Poland
| | - Tomasz Skawiński
- Department of Evolutionary Biology and Conservation of Vertebrates, University of Wrocław, Wrocław, Poland
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19
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Laskowski KL, Doran C, Bierbach D, Krause J, Wolf M. Naturally clonal vertebrates are an untapped resource in ecology and evolution research. Nat Ecol Evol 2019; 3:161-169. [PMID: 30692622 DOI: 10.1038/s41559-018-0775-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 11/29/2018] [Indexed: 11/09/2022]
Abstract
Science requires replication. The development of many cloned or isogenic model organisms is a testament to this. But researchers are reluctant to use these traditional animal model systems for certain questions in evolution or ecology research, because of concerns over relevance or inbreeding. It has largely been overlooked that there are a substantial number of vertebrate species that reproduce clonally in nature. Here we highlight how use of these naturally evolved, phenotypically complex animals can push the boundaries of traditional experimental design and contribute to answering fundamental questions in the fields of ecology and evolution.
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Affiliation(s)
- Kate L Laskowski
- Department of Biology & Ecology of Fishes, Leibniz-Institute of Freshwater Ecology & Inland Fisheries, Berlin, Germany.
| | - Carolina Doran
- Department of Biology & Ecology of Fishes, Leibniz-Institute of Freshwater Ecology & Inland Fisheries, Berlin, Germany
| | - David Bierbach
- Department of Biology & Ecology of Fishes, Leibniz-Institute of Freshwater Ecology & Inland Fisheries, Berlin, Germany
| | - Jens Krause
- Department of Biology & Ecology of Fishes, Leibniz-Institute of Freshwater Ecology & Inland Fisheries, Berlin, Germany.,Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Max Wolf
- Department of Biology & Ecology of Fishes, Leibniz-Institute of Freshwater Ecology & Inland Fisheries, Berlin, Germany
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20
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Bradshaw WS, Phillips AJ, Bybee SM, Gill RA, Peck SL, Jensen JL. A longitudinal study of attitudes toward evolution among undergraduates who are members of the Church of Jesus Christ of Latter-day Saints. PLoS One 2018; 13:e0205798. [PMID: 30403685 PMCID: PMC6221276 DOI: 10.1371/journal.pone.0205798] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 10/02/2018] [Indexed: 11/18/2022] Open
Abstract
Polling data reveal a decades-long residual rejection of evolution in the United States, based on perceived religious conflict. Similarly, a strong creationist movement has been documented internationally, including in the Muslim world. Members of the Church of Jesus Christ of Latter-day Saints (LDS, Mormon), a generally conservative denomination, have historically harbored strong anti-evolution sentiments. We report here a significant shift toward acceptance, compared to attitudes 30 years earlier, by students at Brigham Young University, which is owned and operated by the LDS church. This change appears to have multiple explanations. Students currently entering the university have been exposed to a much-improved introduction to evolution during high school. More importantly, there has been a significant decrease in negative messaging from Church authorities and in its religious education system. There is also evidence that current students have been positively influenced toward evolution by their parents, a large percentage of whom were BYU students, who earlier were given a strong science education deemed compatible with the maintenance of religious belief. A pre-post comparison demonstrates that a majority of current students become knowledgeable and accepting following a course experience focused on evolutionary principles delivered in a faith-friendly atmosphere. Elements of that classroom pedagogy, intended to promote reconciliation, are presented. Our experience may serve as a case-study for prompting changes in acceptance of evolution in other conservative religious groups.
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Affiliation(s)
- William S. Bradshaw
- Department of Microbiology & Molecular Biology, Brigham Young University, LSB, Provo, UT, United States of America
| | - Andrea J. Phillips
- Department of Biology, Brigham Young University, LSB, Provo, UT, United States of America
| | - Seth M. Bybee
- Department of Biology, Brigham Young University, LSB, Provo, UT, United States of America
| | - Richard A. Gill
- Department of Biology, Brigham Young University, LSB, Provo, UT, United States of America
| | - Steven L. Peck
- Department of Biology, Brigham Young University, LSB, Provo, UT, United States of America
| | - Jamie L. Jensen
- Department of Biology, Brigham Young University, LSB, Provo, UT, United States of America
- * E-mail:
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21
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Taucce PPG, Canedo C, Haddad CFB, Lemmon AR, Lemmon EM, Vences M, Lyra M. The mitochondrial genomes of five frog species of the Neotropical genus Ischnocnema (Anura: Brachycephaloidea: Brachycephalidae). Mitochondrial DNA B Resour 2018; 3:915-917. [PMID: 33474365 PMCID: PMC7800048 DOI: 10.1080/23802359.2018.1501312] [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: 06/15/2018] [Accepted: 07/08/2018] [Indexed: 11/30/2022] Open
Abstract
We report the mitogenomes for five species of the Ischnocnema guentheri series, being the first described for this genus of brachycephalid frogs. We assembled mitogenomes from anchored hybrid enrichment data and recovered the 13 protein-coding genes, 22 tRNA genes, and two rRNA genes for all species. The general structure agrees with most previously sequenced neobatrachians, with two exceptions: the origin of replication of L-strand (OL) was found between tRNA-A and tRNA-N, and the position of tRNA-L and tRNA-T, which are dispersed in the control region. We provide a phylogenetic tree with outgroups, which is consistent with previous phylogenetic hypotheses.
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Affiliation(s)
- Pedro P. G. Taucce
- Department of Zoology and Aquaculture Center (CAUNESP), Biosciences Institute, São Paulo State University – UNESP, Rio Claro, Brazil
| | - Clarissa Canedo
- Department of Zoology, Instituto de Biologia Roberto Alcântara Gomes, Rio de Janeiro State University – UERJ, Rio de Janeiro, Brazil
| | - Célio F. B. Haddad
- Department of Zoology and Aquaculture Center (CAUNESP), Biosciences Institute, São Paulo State University – UNESP, Rio Claro, Brazil
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, USA
| | | | - Miguel Vences
- Zoological Institute Technical University of Braunschweig, Braunschweig, Germany
| | - Mariana Lyra
- Department of Zoology and Aquaculture Center (CAUNESP), Biosciences Institute, São Paulo State University – UNESP, Rio Claro, Brazil
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Toussaint EFA, Breinholt JW, Earl C, Warren AD, Brower AVZ, Yago M, Dexter KM, Espeland M, Pierce NE, Lohman DJ, Kawahara AY. Anchored phylogenomics illuminates the skipper butterfly tree of life. BMC Evol Biol 2018; 18:101. [PMID: 29921227 PMCID: PMC6011192 DOI: 10.1186/s12862-018-1216-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 06/07/2018] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Butterflies (Papilionoidea) are perhaps the most charismatic insect lineage, yet phylogenetic relationships among them remain incompletely studied and controversial. This is especially true for skippers (Hesperiidae), one of the most species-rich and poorly studied butterfly families. METHODS To infer a robust phylogenomic hypothesis for Hesperiidae, we sequenced nearly 400 loci using Anchored Hybrid Enrichment and sampled all tribes and more than 120 genera of skippers. Molecular datasets were analyzed using maximum-likelihood, parsimony and coalescent multi-species phylogenetic methods. RESULTS All analyses converged on a novel, robust phylogenetic hypothesis for skippers. Different optimality criteria and methodologies recovered almost identical phylogenetic trees with strong nodal support at nearly all nodes and all taxonomic levels. Our results support Coeliadinae as the sister group to the remaining skippers, the monotypic Euschemoninae as the sister group to all other subfamilies but Coeliadinae, and the monophyly of Eudaminae plus Pyrginae. Within Pyrginae, Celaenorrhinini and Tagiadini are sister groups, the Neotropical firetips, Pyrrhopygini, are sister to all other tribes but Celaenorrhinini and Tagiadini. Achlyodini is recovered as the sister group to Carcharodini, and Erynnini as sister group to Pyrgini. Within the grass skippers (Hesperiinae), there is strong support for the monophyly of Aeromachini plus remaining Hesperiinae. The giant skippers (Agathymus and Megathymus) once classified as a subfamily, are recovered as monophyletic with strong support, but are deeply nested within Hesperiinae. CONCLUSIONS Anchored Hybrid Enrichment sequencing resulted in a large amount of data that built the foundation for a new, robust evolutionary tree of skippers. The newly inferred phylogenetic tree resolves long-standing systematic issues and changes our understanding of the skipper tree of life. These resultsenhance understanding of the evolution of one of the most species-rich butterfly families.
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Affiliation(s)
- Emmanuel F A Toussaint
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA.
| | - Jesse W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
- , RAPiD Genomics 747 SW 2nd Avenue IMB#14, Gainesville, FL, 32601, USA
| | - Chandra Earl
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - Andrew D Warren
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - Andrew V Z Brower
- Evolution and Ecology Group, Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Masaya Yago
- The University Museum, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kelly M Dexter
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - Marianne Espeland
- Arthropoda Department, Zoological Research Museum Alexander Koenig, Adenauer Allee 160, 53113, Bonn, Germany
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - David J Lohman
- Biology Department, City College of New York, City University of New York, New York, NY, 10031, USA
- Ph.D. Program in Biology, Graduate Center, City University of New York, New York, NY, 10016, USA
- Entomology Section, National Museum of the Philippines, 1000, Manila, Philippines
| | - Akito Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
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23
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Lemos-Espinal JA, Smith GR, Gadsden-Esparza H, Rosaura Valdez-Lares, Woolrich-Piña GA. Amphibians and reptiles of the state of Durango, Mexico, with comparisons with adjoining states. Zookeys 2018:65-87. [PMID: 29674915 PMCID: PMC5904398 DOI: 10.3897/zookeys.748.22768] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/09/2018] [Indexed: 12/14/2022] Open
Abstract
A summary of the species of amphibians and reptiles of Durango, as well as their geographic distributions, habitat, and conservation status have been compiled. The herpetofauna of Durango consists of 36 species of amphibians and 120 species of reptiles. Durango shares the most species with Chihuahua (74.0%), and shares fewer species with Sinaloa (48.0%), Nayarit (48.7%), and Coahuila (48.0%). Arid-semiarid and Sierras habitat types have the most species, with valleys and Quebradas habitat types having fewer species. In Durango, there are several taxa of particular conservation concern including eleutherodactylid frogs, eublepharid, iguanid, phrynosomatid, and xantusid lizards, boid, colubrid, and natricid snakes, and emydid and testudinid turtles.
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Affiliation(s)
- Julio A Lemos-Espinal
- Laboratorio de Ecología-UBIPRO, FES Iztacala UNAM, Avenida los Barrios 1, Los Reyes Iztacala, Tlalnepantla, edo. de México, Mexico - 54090
| | | | - Hector Gadsden-Esparza
- Instituto de Ecología, A.C.-Centro Regional del Bajío, Av. Lázaro Cárdenas No 253 A.P. 386 C.P. 61600 Pátzcuaro, Michoacán, Mexico
| | - Rosaura Valdez-Lares
- Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Instituto Politécnico Nacional, Unidad Durango. Sigma 119, Fracc. 20 de Noviembre II, C.P. 34220. Durango, Durango, Mexico
| | - Guillermo A Woolrich-Piña
- Laboratorio de Zoología. División de Biología. Subdirección de Investigación y Posgrado. Instituto Tecnológico Superior de Zacapoaxtla. Carretera Acuaco Zacapoaxtla Km. 8, Col. Totoltepec, Zacapoaxtla, Puebla 73680, México
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24
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Arias FJ, Recoder R, Álvarez BB, Ethcepare E, Quipildor M, Lobo F, Rodrigues MT. Diversity of teiid lizards from Gran Chaco and Western Cerrado (Squamata: Teiidae). ZOOL SCR 2018. [DOI: 10.1111/zsc.12277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Federico José Arias
- Laboratório de Herpetologia; Departamento de Zoologia; Instituto de Biociências; Universidade de São Paulo; São Paulo Brazil
- Museo de Ciencias Naturales; Universidad Nacional de Salta; Salta Argentina
- IBIGEO; Rosario de lerma, Salta Argentina
| | - Renato Recoder
- Laboratório de Herpetologia; Departamento de Zoologia; Instituto de Biociências; Universidade de São Paulo; São Paulo Brazil
| | - Blanca Beatriz Álvarez
- Laboratorio de Herpetología; Facultad de Ciencias Exactas y Naturales y Agrimensura; Universidad Nacional del Nordeste; Corrientes Argentina
| | - Eduardo Ethcepare
- Laboratorio de Herpetología; Facultad de Ciencias Exactas y Naturales y Agrimensura; Universidad Nacional del Nordeste; Corrientes Argentina
| | - Matias Quipildor
- Museo de Ciencias Naturales; Universidad Nacional de Salta; Salta Argentina
- IBIGEO; Rosario de lerma, Salta Argentina
| | - Fernando Lobo
- Museo de Ciencias Naturales; Universidad Nacional de Salta; Salta Argentina
- IBIGEO; Rosario de lerma, Salta Argentina
| | - Miguel Trefaut Rodrigues
- Laboratório de Herpetologia; Departamento de Zoologia; Instituto de Biociências; Universidade de São Paulo; São Paulo Brazil
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25
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Heinicke MP, Lemmon AR, Lemmon EM, McGrath K, Hedges SB. Phylogenomic support for evolutionary relationships of New World direct-developing frogs (Anura: Terraranae). Mol Phylogenet Evol 2018; 118:145-155. [DOI: 10.1016/j.ympev.2017.09.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 09/15/2017] [Accepted: 09/25/2017] [Indexed: 10/18/2022]
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26
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Oliveira EF, Martinez PA, São-Pedro VA, Gehara M, Burbrink FT, Mesquita DO, Garda AA, Colli GR, Costa GC. Climatic suitability, isolation by distance and river resistance explain genetic variation in a Brazilian whiptail lizard. Heredity (Edinb) 2017; 120:251-265. [PMID: 29238076 DOI: 10.1038/s41437-017-0017-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/30/2017] [Accepted: 10/03/2017] [Indexed: 11/09/2022] Open
Abstract
Spatial patterns of genetic variation can help understand how environmental factors either permit or restrict gene flow and create opportunities for regional adaptations. Organisms from harsh environments such as the Brazilian semiarid Caatinga biome may reveal how severe climate conditions may affect patterns of genetic variation. Herein we combine information from mitochondrial DNA with physical and environmental features to study the association between different aspects of the Caatinga landscape and spatial genetic variation in the whiptail lizard Ameivula ocellifera. We investigated which of the climatic, environmental, geographical and/or historical components best predict: (1) the spatial distribution of genetic diversity, and (2) the genetic differentiation among populations. We found that genetic variation in A. ocellifera has been influenced mainly by temperature variability, which modulates connectivity among populations. Past climate conditions were important for shaping current genetic diversity, suggesting a time lag in genetic responses. Population structure in A. ocellifera was best explained by both isolation by distance and isolation by resistance (main rivers). Our findings indicate that both physical and climatic features are important for explaining the observed patterns of genetic variation across the xeric Caatinga biome.
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Affiliation(s)
- Eliana Faria Oliveira
- Pós-Graduação em Ecologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil. .,Universidade Federal de Mato Grosso do Sul, Centro de Ciências Biológicas e da Saúde, Laboratório de Zoologia, Campo Grande, MS, Brazil.
| | - Pablo Ariel Martinez
- Universidade Federal de Sergipe, Laboratório de Pesquisas Integrativas em Biodiversidade (PIBi Lab), Pós-Graduação em Ecologia e Conservação, São Cristovão, SE, Brazil
| | - Vinícius Avelar São-Pedro
- Universidade Federal de São Carlos, Campus Lagoa do Sino, Centro de Ciências da Natureza, Buri, SP, Brazil
| | - Marcelo Gehara
- Department of Herpetology, American Museum of Natural History, New York, NY, USA
| | | | - Daniel Oliveira Mesquita
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, PB, Brazil
| | - Adrian Antonio Garda
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Centro de Biociências, Natal, RN, Brazil
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27
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Wanke S, Granados Mendoza C, Müller S, Paizanni Guillén A, Neinhuis C, Lemmon AR, Lemmon EM, Samain MS. Recalcitrant deep and shallow nodes in Aristolochia (Aristolochiaceae) illuminated using anchored hybrid enrichment. Mol Phylogenet Evol 2017; 117:111-123. [DOI: 10.1016/j.ympev.2017.05.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 01/05/2023]
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28
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Jones MEH, Gröning F, Dutel H, Sharp A, Fagan MJ, Evans SE. The biomechanical role of the chondrocranium and sutures in a lizard cranium. J R Soc Interface 2017; 14:20170637. [PMID: 29263126 PMCID: PMC5746569 DOI: 10.1098/rsif.2017.0637] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/28/2017] [Indexed: 11/30/2022] Open
Abstract
The role of soft tissues in skull biomechanics remains poorly understood. Not least, the chondrocranium, the portion of the braincase which persists as cartilage with varying degrees of mineralization. It also remains commonplace to overlook the biomechanical role of sutures despite evidence that they alter strain distribution. Here, we examine the role of both the sutures and the chondrocranium in the South American tegu lizard Salvator merianae We use multi-body dynamics analysis (MDA) to provide realistic loading conditions for anterior and posterior unilateral biting and a detailed finite element model to examine strain magnitude and distribution. We find that strains within the chondrocranium are greatest during anterior biting and are primarily tensile; also that strain within the cranium is not greatly reduced by the presence of the chondrocranium unless it is given the same material properties as bone. This result contradicts previous suggestions that the anterior portion (the nasal septum) acts as a supporting structure. Inclusion of sutures to the cranium model not only increases overall strain magnitudes but also leads to a more complex distribution of tension and compression rather than that of a beam under sagittal bending.
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Affiliation(s)
- Marc E H Jones
- School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
- South Australian Museum, North Terrace, Adelaide, South Australia 5001, Australia
| | - Flora Gröning
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Hugo Dutel
- School of Engineering and Computer Science, Medical and Biological Engineering Research Group, University of Hull, Hull HU6 7RX, UK
| | - Alana Sharp
- Research Department of Cell and Developmental Biology, UCL, University College London, Anatomy Building, Gower Street, London WCIE 6BT, UK
| | - Michael J Fagan
- School of Engineering and Computer Science, Medical and Biological Engineering Research Group, University of Hull, Hull HU6 7RX, UK
| | - Susan E Evans
- Research Department of Cell and Developmental Biology, UCL, University College London, Anatomy Building, Gower Street, London WCIE 6BT, UK
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29
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The Second Known Tetraploid Species of Parthenogenetic Tetrapod (Reptilia: Squamata: Teiidae): Description, Reproduction, Comparisons With Ancestral Taxa, And Origins Of Multiple Clones. ACTA ACUST UNITED AC 2017. [DOI: 10.3099/mcz37.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Inferring the shallow phylogeny of true salamanders (Salamandra) by multiple phylogenomic approaches. Mol Phylogenet Evol 2017; 115:16-26. [DOI: 10.1016/j.ympev.2017.07.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 05/31/2017] [Accepted: 07/13/2017] [Indexed: 01/31/2023]
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31
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Redescription of the Extinct SpeciesCallopistes bicuspidatusChani, 1976 (Squamata, Teiidae). J HERPETOL 2017. [DOI: 10.1670/16-121] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Taylor HL, Wilmes AJ, Montgomery CE, Livo LJ, Walker JM. Recent northward range expansion of the parthenogenetic lizard Aspidoscelis tesselatusin Colorado and the distributional enigma posed by pattern-classes C and D at the northern range periphery. SOUTHWEST NAT 2017. [DOI: 10.1894/0038-4909-62.3.179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Harry L. Taylor
- Department of Biology, Regis University, Denver, CO 80221 (HLT)
| | - Anthony J. Wilmes
- Biology Department, Truman State University, Kirksville, MO 63501 (AJW, CEM)
- Present address of AJW: Department of Basic Sciences, St. Louis College of Pharmacy, St. Louis, MO 63110
| | - Chad E. Montgomery
- Biology Department, Truman State University, Kirksville, MO 63501 (AJW, CEM)
| | | | - James M. Walker
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701 (JMW)
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33
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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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Genome-wide data delimits multiple climate-determined species ranges in a widespread Australian fish, the golden perch (Macquaria ambigua). Mol Phylogenet Evol 2017; 111:65-75. [DOI: 10.1016/j.ympev.2017.03.021] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 03/14/2017] [Accepted: 03/23/2017] [Indexed: 01/08/2023]
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35
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Baca SM, Toussaint EF, Miller KB, Short AE. Molecular phylogeny of the aquatic beetle family Noteridae (Coleoptera: Adephaga) with an emphasis on data partitioning strategies. Mol Phylogenet Evol 2017; 107:282-292. [DOI: 10.1016/j.ympev.2016.10.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 10/11/2016] [Accepted: 10/22/2016] [Indexed: 01/06/2023]
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36
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In the shadows: Phylogenomics and coalescent species delimitation unveil cryptic diversity in a Cerrado endemic lizard (Squamata: Tropidurus). Mol Phylogenet Evol 2017; 107:455-465. [DOI: 10.1016/j.ympev.2016.12.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 11/07/2016] [Accepted: 12/07/2016] [Indexed: 11/18/2022]
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37
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Lyra ML, Joger U, Schulte U, Slimani T, El Mouden EH, Bouazza A, Künzel S, Lemmon AR, Lemmon EM, Vences M. The mitochondrial genomes of Atlas Geckos ( Quedenfeldtia): mitogenome assembly from transcriptomes and anchored hybrid enrichment datasets. Mitochondrial DNA B Resour 2017; 2:356-358. [PMID: 33473826 PMCID: PMC7800026 DOI: 10.1080/23802359.2017.1339212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The nearly complete mitogenomes of the two species of North African Atlas geckos, Quedenfeldtia moerens and Q. trachyblepharus were assembled from anchored hybrid enrichment data and RNAseq data. Congruent assemblies were obtained for four samples included in both datasets. We recovered the 13 protein-coding genes, 22 tRNA genes, and two rRNA genes for both species, including partial control region. The order of genes agrees with that of other geckos.
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Affiliation(s)
- Mariana L. Lyra
- Departamento de Zoologia, Instituto de Biociências, UNESP – Universidade Estadual Paulista, Rio Claro, Brazil
| | - Ulrich Joger
- Staatliches Naturhistorisches Museum, Braunschweig, Germany
| | - Ulrich Schulte
- Büro für Faunistische Gutachten, Borgholzhausen, Germany
| | - Tahar Slimani
- Faculty of Sciences, Biodiversity and Ecosystem Dynamics Laboratory, Cadi Ayyad University, Marrakech, Morocco
| | - El Hassan El Mouden
- Faculty of Sciences, Biodiversity and Ecosystem Dynamics Laboratory, Cadi Ayyad University, Marrakech, Morocco
| | - Abdellah Bouazza
- Faculty of Sciences, Biodiversity and Ecosystem Dynamics Laboratory, Cadi Ayyad University, Marrakech, Morocco
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, USA
| | | | - Miguel Vences
- Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany
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