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Pyron RA, Pirro S, Hains T, Colston TJ, Myers EA, O'Connell KA, Beamer DA. The Draft Genome Sequences of 50 Salamander species (Caudata, Amphibia). Biodivers Genomes 2024; 2024:10.56179/001c.116891. [PMID: 38725637 PMCID: PMC11081450 DOI: 10.56179/001c.116891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
We present partial genome sequences of 50 salamander species (Urodela) from 10 genera and 4 families. These span nearly the entire range of genome sizes in salamanders, from ~14-130GB, the latter of which is among the largest of all animal genomes. Only three salamander genomes were available to this point, from Ambystomatidae (one species) and Salamandridae (two species from two genera), to which we have added Amphiumidae (one species), Plethodontidae (45 species from 6 genera), Proteidae (one species), and Sirenidae (three species from two genera). These span ~140 million years of evolutionary divergence, leaving only Cryptobranchidae, Hynobiidae, and Rhyacotritonidae as salamander families without genome assemblies. These data should facilitate additional future work on speciation and genome evolution, both within Urodela and across Animalia.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, George Washington University
- Department of Vertebrate Zoology, Smithsonian Institution, National Museum of Natural History
| | | | - Taylor Hains
- Negaunee Integrative Research Center, Field Museum of Natural History
- Committee on Evolutionary Biology, University of Chicago
| | | | - Edward A Myers
- Department of Vertebrate Zoology, Smithsonian Institution, National Museum of Natural History
- Department of Herpetology, California Academy of Sciences
| | - Kyle A O'Connell
- Department of Biological Sciences, George Washington University
- Department of Vertebrate Zoology, Smithsonian Institution, National Museum of Natural History
- Health Data and AI, Deloitte Consulting LLP
| | - David A Beamer
- Office of Research, Economic Development and Engagement, East Carolina University
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Lyu B, Liu Q, Wu Y, Nguyen TQ, Che J, Nguyen SN, Myers EA, Burbrink FT, Guo P, Wang J. Genomic analysis reveals deep population divergence in the water snake Trimerodytes percarinatus (Serpentes, Natricidae). Ecol Evol 2024; 14:e11278. [PMID: 38628918 PMCID: PMC11019134 DOI: 10.1002/ece3.11278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 02/26/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
Although several phylogeographic studies of Asian snakes have been conducted, most have focused on pitvipers, with non-venomous snakes, such as colubrids or natricids, remaining poorly studied. The Chinese keelback water snake (Trimerodytes percarinatus Boulenger) is a widespread, semiaquatic, non-venomous species occurring in China and southeastern Asia. Based on mitochondrial DNA (mtDNA) and single nucleotide polymorphism (SNP) data, we explored the population genetic structure, genetic diversity, and evolutionary history of this species. MtDNA-based phylogenetic analysis showed that T. percarinatus was composed of five highly supported and geographically structured lineages. SNP-based phylogenetic analysis, principal component analysis, and population structure analysis consistently revealed four distinct, geographically non-overlapping lineages, which was different from the mtDNA-based analysis in topology. Estimation of divergence dates and ancestral area of origin suggest that T. percarinatus originated ~12.68 million years ago (95% highest posterior density: 10.36-15.96 Mya) in a region covering southwestern China and Vietnam. Intraspecific divergence may have been triggered by the Qinghai-Xizang Plateau uplift. Population demographics and ecological niche modeling indicated that the effective population size fluctuated during 0.5 Mya and 0.002 Mya. Based on the data collected here, we also comment on the intraspecific taxonomy of T. percarinatus and question the validity of the subspecies T. p. suriki.
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Affiliation(s)
- Bing Lyu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life SciencesHainan Normal UniversityHaikouChina
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinChina
| | - Qin Liu
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinChina
| | - Yayong Wu
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinChina
| | - Truong Q. Nguyen
- Institute of Ecology and Biological ResourcesVietnam Academy of Science and TechnologyHanoiVietnam
- Vietnam Academy of Science and TechnologyGraduate University of Science and TechnologyHanoiVietnam
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Sang N. Nguyen
- Institute of Tropical BiologyVietnam Academy of Science and TechnologyHo Chi Minh CityVietnam
| | - Edward A. Myers
- Department of HerpetologyCalifornia Academy of SciencesSan FranciscoCaliforniaUSA
| | - Frank T. Burbrink
- Department of HerpetologyAmerican Museum of Natural HistoryNew YorkNew YorkUSA
| | - Peng Guo
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinChina
| | - Jichao Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life SciencesHainan Normal UniversityHaikouChina
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3
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Burbrink FT, Harrington SM, Bobo D, Myers EA. Considering admixture when producing draft genomes: an example in North American ratsnakes (Pantherophis alleghaniensis/Pantherophis obsoletus). G3 (Bethesda) 2023; 13:jkad113. [PMID: 37228097 PMCID: PMC10411579 DOI: 10.1093/g3journal/jkad113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/24/2023] [Accepted: 05/04/2023] [Indexed: 05/27/2023]
Abstract
The number of reference genomes of snakes lags behind several other vertebrate groups (e.g. birds and mammals). However, in the last two years, a concerted effort by researchers from around the world has produced new genomes of snakes representing members from several new families. Here, we present a high-quality, annotated genome of the central ratsnake (Pantherophis alleghaniensis), a member of the most diverse snake lineage, Colubroidea. Pantherophis alleghaniensis is found in the central part of the Nearctic, east of the Mississippi River. This genome was sequenced using 10X Chromium synthetic long reads and polished using Illumina short reads. The final genome assembly had an N50 of 21.82 Mb and an L50 of 22 scaffolds with a maximum scaffold length of 82.078 Mb. The genome is composed of 49.24% repeat elements dominated by long interspersed elements. We annotated this genome using transcriptome assemblies from 14 tissue types and recovered 28,368 predicted proteins. Finally, we estimated admixture proportions between two species of ratsnakes and discovered that this specimen is an admixed individual containing genomes from the western (Pantherophis obsoletus) and central ratsnakes (P. alleghaniensis). We discuss the importance of considering interspecific admixture in downstream approaches for inferring demography and phylogeny.
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, New York, NY 10024, USA
| | - Sean M Harrington
- Department of Herpetology, American Museum of Natural History, New York, NY 10024, USA
- INBRE Data Science Core, University of Wyoming, Laramie, WY 82071, USA
| | - Dean Bobo
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Edward A Myers
- Department of Herpetology, American Museum of Natural History, New York, NY 10024, USA
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
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4
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Rosales-García RA, Rautsaw RM, Hofmann EP, Grünwald CI, Franz-Chavez H, Ahumada-Carrillo IT, Ramirez-Chaparro R, de la Torre-Loranca MA, Strickland JL, Mason AJ, Holding ML, Borja M, Castañeda-Gaytan G, Myers EA, Sasa M, Rokyta DR, Parkinson CL. Sequence Divergence in Venom Genes Within and Between Montane Pitviper (Viperidae: Crotalinae: Cerrophidion) Species is Driven by Mutation-Drift Equilibrium. J Mol Evol 2023; 91:514-535. [PMID: 37269364 PMCID: PMC10995822 DOI: 10.1007/s00239-023-10115-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 05/03/2023] [Indexed: 06/05/2023]
Abstract
Snake venom can vary both among and within species. While some groups of New World pitvipers-such as rattlesnakes-have been well studied, very little is known about the venom of montane pitvipers (Cerrophidion) found across the Mesoamerican highlands. Compared to most well-studied rattlesnakes, which are widely distributed, the isolated montane populations of Cerrophidion may facilitate unique evolutionary trajectories and venom differentiation. Here, we describe the venom gland transcriptomes for populations of C. petlalcalensis, C. tzotzilorum, and C. godmani from Mexico, and a single individual of C. sasai from Costa Rica. We explore gene expression variation in Cerrophidion and sequence evolution of toxins within C. godmani specifically. Cerrophidion venom gland transcriptomes are composed primarily of snake venom metalloproteinases, phospholipase A[Formula: see text]s (PLA[Formula: see text]s), and snake venom serine proteases. Cerrophidion petlalcalensis shows little intraspecific variation; however, C. godmani and C. tzotzilorum differ significantly between geographically isolated populations. Interestingly, intraspecific variation was mostly attributed to expression variation as we did not detect signals of selection within C. godmani toxins. Additionally, we found PLA[Formula: see text]-like myotoxins in all species except C. petlalcalensis, and crotoxin-like PLA[Formula: see text]s in the southern population of C. godmani. Our results demonstrate significant intraspecific venom variation within C. godmani and C. tzotzilorum. The toxins of C. godmani show little evidence of directional selection where variation in toxin sequence is consistent with evolution under a model of mutation-drift equilibrium. Cerrophidion godmani individuals from the southern population may exhibit neurotoxic venom activity given the presence of crotoxin-like PLA[Formula: see text]s; however, further research is required to confirm this hypothesis.
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Affiliation(s)
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
| | - Erich P Hofmann
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
- Science Department, Cape Fear Community College, Wilmington, NC, 28401, USA
| | | | - Hector Franz-Chavez
- Herp.mx A.C., Colima, Mexico
- Biodiversa A. C., Chapala, Jalisco, 45900, Mexico
| | | | | | | | - Jason L Strickland
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
- Department of Biology, University of South Alabama, Mobile, AL, 36688, USA
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Matthew L Holding
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Miguel Borja
- Facultad de Ciencias Biológicas, Universdad Juárez del Estado de Durango, Gómez Palacio, Durango, 35010, Mexico
| | - Gamaliel Castañeda-Gaytan
- Facultad de Ciencias Biológicas, Universdad Juárez del Estado de Durango, Gómez Palacio, Durango, 35010, Mexico
| | - Edward A Myers
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
| | - Mahmood Sasa
- Centro Investigaciones en Biodiversidad y Ecología Tropical and Instituto Clodomiro Picado, Universidad de Costa Rica, San José, Costa Rica
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA.
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Carvalho PS, Santana DJ, Zaher H, Myers EA. Effects of Environmental Variation in Structuring Population Genetic Variation in the False-Water Cobras (Xenodontinae: Hydrodynastes). Evol Biol 2023. [DOI: 10.1007/s11692-023-09601-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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Larkin IE, Myers EA, Carstens BC, Barrow LN. Predictors of genomic diversity within North American squamates. J Hered 2023; 114:131-142. [PMID: 36638275 PMCID: PMC10078173 DOI: 10.1093/jhered/esad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/13/2023] [Indexed: 01/15/2023] Open
Abstract
Comparisons of intraspecific genetic diversity across species can reveal the roles of geography, ecology, and life history in shaping biodiversity. The wide availability of mitochondrial DNA (mtDNA) sequences in open-access databases makes this marker practical for conducting analyses across several species in a common framework, but patterns may not be representative of overall species diversity. Here, we gather new and existing mtDNA sequences and genome-wide nuclear data (genotyping-by-sequencing; GBS) for 30 North American squamate species sampled in the Southeastern and Southwestern United States. We estimated mtDNA nucleotide diversity for two mtDNA genes, COI (22 species alignments; average 16 sequences) and cytb (22 species; average 58 sequences), as well as nuclear heterozygosity and nucleotide diversity from GBS data for 118 individuals (30 species; four individuals and 6,820-44,309 loci per species). We showed that nuclear genomic diversity estimates were highly consistent across individuals for some species, while other species showed large differences depending on the locality sampled. Range size was positively correlated with both cytb diversity (Phylogenetically Independent Contrasts: R 2 = 0.31, p = 0.007) and GBS diversity (R 2 = 0.21; p = 0.006), while other predictors differed across the top models for each dataset. Mitochondrial and nuclear diversity estimates were not correlated within species, although sampling differences in the data available made these datasets difficult to compare. Further study of mtDNA and nuclear diversity sampled across species' ranges is needed to evaluate the roles of geography and life history in structuring diversity across a variety of taxonomic groups.
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Affiliation(s)
- Ivy E Larkin
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 318 W. 12th Ave, Columbus, OH
| | - Edward A Myers
- Department of Biological Sciences, Clemson University, Clemson, SC
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 318 W. 12th Ave, Columbus, OH
| | - Lisa N Barrow
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 318 W. 12th Ave, Columbus, OH.,Current Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque NM
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Burbrink FT, Crother BI, Murray CM, Smith BT, Ruane S, Myers EA, Pyron RA. Empirical and philosophical problems with the subspecies rank. Ecol Evol 2022; 12:e9069. [PMID: 35845367 PMCID: PMC9271888 DOI: 10.1002/ece3.9069] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/01/2022] [Accepted: 06/10/2022] [Indexed: 11/12/2022] Open
Abstract
Species‐level taxonomy derives from empirical sources (data and techniques) that assess the existence of spatiotemporal evolutionary lineages via various species “concepts.” These concepts determine if observed lineages are independent given a particular methodology and ontology, which relates the metaphysical species concept to what “kind” of thing a species is in reality. Often, species concepts fail to link epistemology back to ontology. This lack of coherence is in part responsible for the persistence of the subspecies rank, which in modern usage often functions as a placeholder between the evolutionary events of divergence or collapse of incipient species. Thus, prospective events like lineages merging or diverging require information from unknowable future information. This is also conditioned on evidence that the lineage already has a detectably distinct evolutionary history. Ranking these lineages as subspecies can seem attractive given that many lineages do not exhibit intrinsic reproductive isolation. We argue that using subspecies is indefensible on philosophical and empirical grounds. Ontologically, the rank of subspecies is either identical to that of species or undefined in the context of evolutionary lineages representing spatiotemporally defined individuals. Some species concepts more inclined to consider subspecies, like the Biological Species Concept, are disconnected from evolutionary ontology and do not consider genealogy. Even if ontology is ignored, methods addressing reproductive isolation are often indirect and fail to capture the range of scenarios linking gene flow to species identity over space and time. The use of subspecies and reliance on reproductive isolation as a basis for an operational species concept can also conflict with ethical issues governing the protection of species. We provide a way forward for recognizing and naming species that links theoretical and operational species concepts regardless of the magnitude of reproductive isolation.
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology American Museum of Natural History New York New York USA
| | - Brian I Crother
- Department of Biological Sciences Southeastern Louisiana University Hammond Louisiana USA
| | - Christopher M Murray
- Department of Biological Sciences Southeastern Louisiana University Hammond Louisiana USA
| | - Brian Tilston Smith
- Department of Ornithology American Museum of Natural History New York New York USA
| | - Sara Ruane
- Life Sciences Section, Negaunee Integrative Research Center Field Museum of Natural History Chicago Illinois USA
| | - Edward A Myers
- Department of Herpetology American Museum of Natural History New York New York USA.,Department of Biological Sciences Clemson University Clemson South Carolina USA.,Department of Vertebrate Zoology Smithsonian Institution, National Museum of Natural History Washington District of Columbia USA
| | - Robert Alexander Pyron
- Department of Vertebrate Zoology Smithsonian Institution, National Museum of Natural History Washington District of Columbia USA.,Department of Biological Sciences The George Washington University Washington District of Columbia USA
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8
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Myers EA, Strickland JL, Rautsaw RM, Mason AJ, Schramer TD, Nystrom GS, Hogan MP, Yooseph S, Rokyta DR, Parkinson CL. De Novo Genome Assembly Highlights the Role of Lineage-Specific Duplications in the Evolution of Venom in Fea’s Viper. Genome Biol Evol 2022; 14:6603630. [PMID: 35670514 PMCID: PMC9256536 DOI: 10.1093/gbe/evac082] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/12/2022] Open
Abstract
Despite the medical significance to humans and important ecological roles filled by vipers, few high-quality genomic resources exist for these snakes outside of a few genera of pitvipers. Here we sequence, assemble, and annotate the genome of Fea’s Viper (Azemiops feae). This taxon is distributed in East Asia and belongs to a monotypic subfamily, sister to the pitvipers. The newly sequenced genome resulted in a 1.56 Gb assembly, a contig N50 of 1.59 Mb, with 97.6% of the genome assembly in contigs >50 Kb, and a BUSCO completeness of 92.4%. We found that A. feae venom is primarily composed of phospholipase A2 (PLA2) proteins expressed by genes that likely arose from lineage-specific PLA2 gene duplications. Additionally, we show that renin, an enzyme associated with blood pressure regulation in mammals and known from the venoms of two viper species including A. feae, is expressed in the venom gland at comparative levels to known toxins and is present in the venom proteome. The cooption of this gene as a toxin may be more widespread in viperids than currently known. To investigate the historical population demographics of A. feae, we performed coalescent-based analyses and determined that the effective population size has remained stable over the last 100 kyr. This suggests Quaternary glacial cycles likely had minimal influence on the demographic history of A. feae. This newly assembled genome will be an important resource for studying the genomic basis of phenotypic evolution and understanding the diversification of venom toxin gene families.
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Affiliation(s)
- Edward A. Myers
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
| | - Jason L. Strickland
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
- Department of Biology, University of South Alabama , Mobile, AL 36688, USA
| | - Rhett M. Rautsaw
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
| | - Andrew J. Mason
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University , Columbus, OH 43210, USA
| | - Tristan D. Schramer
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
| | - Gunnar S. Nystrom
- Department of Biological Science, Florida State University , Tallahassee, FL 32306, USA
| | - Michael P. Hogan
- Department of Biological Science, Florida State University , Tallahassee, FL 32306, USA
| | - Shibu Yooseph
- Department of Computer Science, Genomics and Bioinformatics Cluster, University of Central Florida, 4000 Central Florida Blvd , Orlando, FL, 32816, USA
| | - Darin R. Rokyta
- Department of Biological Science, Florida State University , Tallahassee, FL 32306, USA
| | - Christopher L. Parkinson
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
- Department of Forestry and Environmental Conservation, Clemson University , Clemson, SC 29634, USA
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Espindola S, Vázquez-Domínguez E, Nakamura M, Osorio-Olvera L, Martínez-Meyer E, Myers EA, Overcast I, Reid BN, Burbrink FT. Complex genetic patterns and distribution limits mediated by native congeners of the worldwide invasive red-eared slider turtle. Mol Ecol 2022; 31:1766-1782. [PMID: 35048442 DOI: 10.1111/mec.16356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/01/2021] [Accepted: 01/12/2022] [Indexed: 11/30/2022]
Abstract
Non-native (invasive) species offer a unique opportunity to study the geographic distribution and range limits of species, wherein the evolutionary change driven by interspecific interactions between native and non-native closely related species is a key component. The red-eared slider turtle, Trachemys scripta elegans (TSE), has been introduced and successfully established worldwide. It can coexist with its native congeners T. cataspila, T. venusta and T. taylori in Mexico. We performed comprehensive fieldwork, executed a battery of genetic analyses and applied a novel species distribution modeling approach to evaluate their historical lineage relationships and contemporary population genetic patterns. Our findings support the historical common ancestry between native TSE and non-native (TSEalien ), while also highlighting the genetic differentiation of the exotic lineage. Genetic patterns are associated with their range size/endemism gradient, the microendemic T. taylori showed significant reduced genetic diversity and high differentiation, whereas TSEalien showed the highest diversity and signals of population size expansion. Counter to our expectations, lower naturally occurring distribution overlap and little admixture patterns were found between TSE and its congeners, exhibiting reduced gene flow and clear genetic separation across neighboring species despite having zones of contact. We demonstrate that these native Trachemys species have distinct climatic niche suitability, likely preventing establishment of and displacement by the TSEalien . Moreover, we found major niche overlap between TSEalien and native species worldwide, supporting our prediction that sites with closer ecological optima to the invasive species have higher establishment risk than those that are closer to the niche-center of the native species.
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Affiliation(s)
- Sayra Espindola
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, 04510, México.,Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, 04510, México
| | - Ella Vázquez-Domínguez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, 04510, México.,American Museum of Natural History, Central Park West, 79th Street, New York, 10024, USA
| | - Miguel Nakamura
- Centro de Investigación en Matemáticas (CIMAT), Calle Jalisco S/N, Colonia Valenciana, 36023, Guanajuato, Guanajuato, México
| | - Luis Osorio-Olvera
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, 04510, México
| | - Enrique Martínez-Meyer
- Instituto de Biología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, 04510, México
| | - Edward A Myers
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA.,American Museum of Natural History, Central Park West, 79th Street, New York, 10024, USA
| | - Isaac Overcast
- Institut de Biologie de l'Ecole Normale Superieure, 75005, Paris, France
| | - Brendan N Reid
- Rutgers University, Department of Ecology, Evolution, and Natural Resources, 14 College Farm Road, New Brunswick, NJ, USA
| | - Frank T Burbrink
- American Museum of Natural History, Central Park West, 79th Street, New York, 10024, USA
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Myers EA, Mulcahy DG, Falk B, Johnson K, Carbi M, de Queiroz K. Interspecific Gene Flow and Mitochondrial Genome Capture During the Radiation of Jamaican Anolis Lizards (Squamata; Iguanidae). Syst Biol 2021; 71:501-511. [PMID: 34735007 DOI: 10.1093/sysbio/syab089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 11/12/2022] Open
Abstract
Gene flow and reticulation are increasingly recognized as important processes in the diversification of many taxonomic groups. With the increasing ease of collecting genomic data and the development of multispecies coalescent network approaches, such reticulations can be accounted for when inferring phylogeny and diversification. Caribbean Anolis lizards are a classic example of an adaptive radiation in which species have independently radiated on the islands of the Greater Antilles into the same ecomorph classes. Within the Jamaican radiation at least one species, A. opalinus, has been documented to be polyphyletic in its mitochondrial DNA, which could be the result of an ancient reticulation event or incomplete lineage sorting. Here we generate mtDNA and genotyping-by-sequencing (GBS) data and implement gene-tree, species-tree, and multispecies coalescent network methods to infer the diversification of this group. Our mtDNA gene-tree recovers the same relationships previously inferred for this group, which is strikingly different from the species-tree inferred from our GBS data. Posterior predictive simulations suggest that our genomic data violate commonly adopted assumptions of the multispecies coalescent model, so we use network approaches to infer phylogenetic relationships. The inferred network topology contains a reticulation event but does not explain the mtDNA polyphyly observed in this group, however coalescent simulations suggest that the observed mtDNA topology is likely the result of past introgression. How common a signature of gene flow and reticulation is across the radiation of Anolis is unknown; however, the reticulation events that we demonstrate here may have allowed for adaptive evolution, as has been suggested in other, more recent adaptive radiations.
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Affiliation(s)
- Edward A Myers
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Herpetology, The American Museum of Natural History, New York, NY, USA
| | - Daniel G Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Bryan Falk
- Division of Invertebrate Zoology, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Kiyomi Johnson
- Science Research Mentoring Program, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Marina Carbi
- Science Research Mentoring Program, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Kevin de Queiroz
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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11
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Myers EA. Genome-wide data reveal extensive gene flow during the diversification of the western rattlesnakes (Viperidae: Crotalinae: Crotalus). Mol Phylogenet Evol 2021; 165:107313. [PMID: 34537323 DOI: 10.1016/j.ympev.2021.107313] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 08/28/2021] [Accepted: 09/14/2021] [Indexed: 11/15/2022]
Abstract
Hybridization and introgression are important, but often overlooked processes when inferring phylogenies. When these processes are not accounted for and a strictly diverging phylogenetic model is applied to groups with a history of hybridization, phylogenetic inference and parameter estimation can be inaccurate. Recent developments in phylogenetic network approaches coupled with the increasing availability of genomic data allow inferences of reticulate evolutionary histories across the tree of life. The western rattlesnake species group (C. viridis species complex, C. mitchellii species complex, C. scutulutas, and C. tigris) is an iconic snake lineage that is widespread across western North America. This group is composed of several species complexes with unclear species limits, likely the result of ongoing gene flow among nascent lineages. Here I generate reduced representation genomic data and test for a history of reticulation within this group. I demonstrate that all species have undergone hybridization with at least one other lineage, suggesting introgression is widespread in this group. Topologies differ between phylogenies estimated under the multispecies coalescent and multispecies network coalescent methods, indicating that gene flow has obscured phylogenetic relationships within this group. These past introgression events are predominantly restricted to species that co-occur geographically. However, within species that have a history of introgression, this signature is detected regardless of specimen sampling across geography. Overall, my results suggest the accumulation of reproductive isolating barriers occurs slowly in rattlesnakes which likely leads to the difficulty in delimiting species, furthermore, the results of this study have implications for trait evolution in this group.
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Affiliation(s)
- Edward A Myers
- Department of Herpetology, American Museum of Natural History, New York, NY, USA; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
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12
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Jaynes KE, Myers EA, Gvoždík V, Blackburn DC, Portik DM, Greenbaum E, Jongsma GFM, Rödel MO, Badjedjea G, Bamba-Kaya A, Baptista NL, Akuboy JB, Ernst R, Kouete MT, Kusamba C, Masudi FM, McLaughlin PJ, Nneji LM, Onadeko AB, Penner J, Vaz Pinto P, Stuart BL, Tobi E, Zassi-Boulou AG, Leaché AD, Fujita MK, Bell RC. Giant Tree Frog diversification in West and Central Africa: Isolation by physical barriers, climate, and reproductive traits. Mol Ecol 2021; 31:3979-3998. [PMID: 34516675 DOI: 10.1111/mec.16169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/18/2021] [Accepted: 09/02/2021] [Indexed: 01/25/2023]
Abstract
Secondary sympatry amongst sister lineages is strongly associated with genetic and ecological divergence. This pattern suggests that for closely related species to coexist in secondary sympatry, they must accumulate differences in traits that mediate ecological and/or reproductive isolation. Here, we characterized inter- and intraspecific divergence in three giant tree frog species whose distributions stretch across West and Central Africa. Using genome-wide single-nucleotide polymorphism data, we demonstrated that species-level divergence coincides temporally and geographically with a period of large-scale forest fragmentation during the late Pliocene. Our environmental niche models further supported a dynamic history of climatic suitability and stability, and indicated that all three species occupy distinct environmental niches. We found modest morphological differentiation amongst the species with significant divergence in tympanum diameter and male advertisement call. In addition, we confirmed that two species occur in secondary sympatry in Central Africa but found no evidence of hybridization. These patterns support the hypothesis that cycles of genetic exchange and isolation across West and Central Africa have contributed to globally significant biodiversity. Furthermore, divergence in both ecology and reproductive traits appear to have played important roles in maintaining distinct lineages. At the intraspecific level, we found that climatic refugia, precipitation gradients, marine incursions, and potentially riverine barriers generated phylogeographic structure throughout the Pleistocene and into the Holocene. Further studies examining phenotypic divergence and secondary contact amongst these geographically structured populations may demonstrate how smaller scale and more recent biogeographic barriers contribute to regional diversification.
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Affiliation(s)
- Kyle E Jaynes
- Department of Biology, Adrian College, Michigan, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Integrative Biology, W.K. Kellogg Biological Station, Michigan State University, Michigan, USA.,Ecology, Evolution, and Behavior Program, Michigan State University, Michigan, USA
| | - Edward A Myers
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Václav Gvoždík
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.,Department of Zoology, National Museum, Prague, Czech Republic
| | - David C Blackburn
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | - Daniel M Portik
- Herpetology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, California, USA
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Gregory F M Jongsma
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA.,Department of Biology, University of Florida, Florida, USA
| | - Mark-Oliver Rödel
- Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
| | - Gabriel Badjedjea
- Département d'Ecologie et Biodiversité des Ressources Aquatiques, Centre de Surveillance de la Biodiversité, Université de Kisangani, Kisangani, République Démocratique du Congo
| | | | - Ninda L Baptista
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal.,Faculdade de Ciências da, Universidade do Porto, Porto, Portugal.,Instituto Superior de Ciências da Educação da Huíla (ISCED-Huíla), Rua Sarmento Rodrigues, Lubango, Angola
| | - Jeannot B Akuboy
- Département d'Ecologie et Biodiversité des Ressources Terrestres, Centre de Surveillance de la Biodiversité, Université de Kisangani, République Démocratique du Congo, Kisangani
| | - Raffael Ernst
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Dresden, Germany
| | - Marcel T Kouete
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA.,School of Natural Resources and Environment, University of Florida, Florida, USA
| | - Chifundera Kusamba
- Laboratoire d'Herpétologie, Département de Biologie, Centre de Recherche en Sciences Naturelles, République Démocratique du Congo, Lwiro
| | - Franck M Masudi
- Département d'Ecologie et Biodiversité des Ressources Terrestres, Centre de Surveillance de la Biodiversité, Université de Kisangani, République Démocratique du Congo, Kisangani
| | - Patrick J McLaughlin
- Bioko Biodiversity Protection Project, Drexel University, Philadelphia, Pennsylvania, USA.,Institute of Conservation Science and Learning, Bristol Zoological Society, Bristol, UK
| | - Lotanna M Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, New Jersey, USA
| | - Abiodun B Onadeko
- Department of Zoology, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Johannes Penner
- Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany.,Chair of Wildlife Ecology and Wildlife Management, University of Freiburg, Freiburg, Germany
| | - Pedro Vaz Pinto
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal.,Fundação Kissama, Luanda, Angola
| | - Bryan L Stuart
- Section of Research & Collections, North Carolina Museum of Natural Sciences, North Carolina, USA
| | - Elie Tobi
- Gabon Biodiversity Program, Smithsonian Conservation Biology Institute, Gamba, Gabon
| | | | - Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, USA
| | - Matthew K Fujita
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - Rayna C Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Herpetology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, California, USA
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13
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Myers EA, Folly H, Ragalzi E, Feio RN, Santana DJ. Late Pliocene population divergence and persistence despite Pleistocene climatic fluctuations in the Rio Doce snouted Treefrog ( Ololygon carnevallii). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Edward A. Myers
- Department of Vertebrate Zoology National Museum of Natural HistorySmithsonian Institution Washington DC USA
| | - Henrique Folly
- Departamento de Biologia Animal Museu de Zoologia João MoojenUniverisdade Federal de Viçosa Viçosa MG Brazil
- Instituto de Biociências Laboratório de Zoologia Universidade Federal de Mato Grosso do Sul Campo Grande MS Brazil
| | - Eric Ragalzi
- Instituto de Biociências Laboratório de Zoologia Universidade Federal de Mato Grosso do Sul Campo Grande MS Brazil
| | - Renato Neves Feio
- Departamento de Biologia Animal Museu de Zoologia João MoojenUniverisdade Federal de Viçosa Viçosa MG Brazil
| | - Diego José Santana
- Instituto de Biociências Laboratório de Zoologia Universidade Federal de Mato Grosso do Sul Campo Grande MS Brazil
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Burbrink FT, Gehara M, McKelvy AD, Myers EA. Resolving spatial complexities of hybridization in the context of the gray zone of speciation in North American ratsnakes (Pantherophis obsoletus complex). Evolution 2021; 75:260-277. [PMID: 33346918 DOI: 10.1111/evo.14141] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 10/01/2020] [Accepted: 11/17/2020] [Indexed: 01/04/2023]
Abstract
Inferring the history of divergence between species in a framework that permits the presence of gene flow has been crucial for characterizing the "gray zone" of speciation, which is the period of time where lineages have diverged but have not yet achieved strict reproductive isolation. However, estimates of both divergence times and rates of gene flow often ignore spatial information, for example when considering the location and width of hybrid zones with respect to changes in the environment between lineages. Using population genomic data from the North American ratsnake complex (Pantherophis obsoletus), we connected phylogeographic estimates of lineage structure, migration, historical demography, and timing of divergence with hybrid zone dynamics. We examined the spatial context of diversification by linking migration and timing of divergence to the location and widths of hybrid zones. Artificial neural network approaches were applied to understand how landscape features and past climate have influenced population genetic structure among these lineages. We found that rates of migration between lineages were associated with the overall width of hybrid zones. Timing of divergence was not related to migration rate or hybrid zone width across species pairs but may be related to the number of alleles weakly introgressing through hybrid zones. This research underscores how incomplete reproductive isolation can be better understood by considering differential allelic introgression and the effects of historical and contemporary landscape features on the formation of lineages as well as overall genomic estimates of migration rates through time.
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, Central Park West and 79th Street, New York, New York, 10024
| | - Marcelo Gehara
- Department of Biological Sciences, Rutgers University Newark, 195 University Ave, Newark, New Jersey, 07102
| | - Alexander D McKelvy
- Department of Biology, The Graduate School and Center, City University of New York, New York, New York, 10016
| | - Edward A Myers
- Department of Herpetology, The American Museum of Natural History, Central Park West and 79th Street, New York, New York, 10024.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC
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15
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Myers EA, Mulcahy DG. Six additional mitochondrial genomes for North American nightsnakes (Dipsadidae: Hypsiglena) and a novel gene feature for advanced snakes. Mitochondrial DNA B Resour 2020; 5:3056-3058. [PMID: 33458057 PMCID: PMC7781862 DOI: 10.1080/23802359.2020.1797573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The North American nightsnakes in the genus Hypsiglena is composed of nine named and at least two unnamed species. Here, we provide the first mt-genome of H. affinis, an additional mt-genome for H. sp. nov. 1, and four additional mt-genomes from the widespread H. jani. These mtDNA genomes were sequenced using both Illumina and Ion Torrent sequencing technologies. The resulting genomes contained the expected 13 protein coding genes, 22 tRNA genes, 2 rRNA genes, and 2 control regions typical of colubroid snakes. Two of the H. jani samples had partial tRNAIle genes upstream of CR2 which has not been previously documented in colubroid snakes. A maximum likelihood gene-tree based on these data combined with previously published sequence data recovers a well-supported phylogeny and is in concordance with previous estimates of evolutionary relationships in this group.
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Affiliation(s)
- Edward A. Myers
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Daniel G. Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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16
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Fausnacht AG, Myers EA, Hess EL, Davy BM, Hedrick VE. Update of the BEVQ-15, a beverage intake questionnaire for habitual beverage intake for adults: determining comparative validity and reproducibility. J Hum Nutr Diet 2020; 33:729-737. [PMID: 32283572 DOI: 10.1111/jhn.12749] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The BEVQ-15 is a beverage intake questionnaire that estimates the habitual average daily intake of 15 beverage categories (kcal and fl oz), as well as total sugar-sweetened beverages (SSB) and total beverages. However, subsequent to its initial validation in 2010, it has not been updated. The present study aimed to assess the convergent validity and reproducibility of the updated form of the BEVQ-15 to better reflect current beverage consumption trends. METHODS The study population included adults (n = 50) aged ≥18 years, recruited from a local university community. Participation consisted of three laboratory visits within a 4-week period in which the updated BEVQ-15 was administered during the first and last visit and four 24-h dietary recalls were collected. BEVQ-15 modifications included removing limits of 60 fl oz per beverage, adding a nut milk category, and providing creamer and sweetener preferences for coffee/tea categories. Convergent validity was assessed by comparing reported beverage intake between the BEVQ-15 and dietary recalls. Reproducibility was assessed by comparing both BEVQ-15 administrations. Analyses included descriptive statistics, Wilcoxon signed rank tests, Bland-Altman plots and Spearman's correlations. RESULTS For validity, Bland-Altman plot agreement between the BEVQ-15 and recalls was in the range 92-96% for total SSB and total beverage intake. For reproducibility, all beverage categories, total SSB, and total beverage intake were significantly correlated between the two BEVQ-15 administrations (r = 0.41-0.85; P ≤ 0.01). CONCLUSIONS This updated version of the BEVQ-15 demonstrated moderate convergent validity and reproducibility for total beverage consumption among well-educated southwest Virginia adults.
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Affiliation(s)
- A G Fausnacht
- Department of Human Nutrition, Foods, and Exercise, Virginia Tech, Blacksburg, VA, USA
| | - E A Myers
- Department of Human Nutrition, Foods, and Exercise, Virginia Tech, Blacksburg, VA, USA
| | - E L Hess
- Department of Human Nutrition, Foods, and Exercise, Virginia Tech, Blacksburg, VA, USA
| | - B M Davy
- Department of Human Nutrition, Foods, and Exercise, Virginia Tech, Blacksburg, VA, USA
| | - V E Hedrick
- Department of Human Nutrition, Foods, and Exercise, Virginia Tech, Blacksburg, VA, USA
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17
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Myers EA, McKelvy AD, Burbrink FT. Biogeographic barriers, Pleistocene refugia, and climatic gradients in the southeastern Nearctic drive diversification in cornsnakes (Pantherophis guttatus complex). Mol Ecol 2020; 29:797-811. [PMID: 31955477 DOI: 10.1111/mec.15358] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 12/21/2022]
Abstract
The southeastern Nearctic is a biodiversity hotspot that is also rich in cryptic species. Numerous hypotheses (e.g., vicariance, local adaptation, and Pleistocene speciation in glacial refugia) have been tested in an attempt to explain diversification and the observed pattern of extant biodiversity. However, previous phylogeographic studies have both supported and refuted these hypotheses. Therefore, while data support one or more of these diversification hypotheses, it is likely that taxa are forming within this region in species-specific ways. Here, we generate a genomic data set for the cornsnakes (Pantherophis guttatus complex), which are widespread across this region, spanning both biogeographic barriers and climatic gradients. We use phylogeographic model selection combined with hindcast ecological niche models to determine regions of habitat stability through time. This combined approach suggests that numerous drivers of population differentiation explain the current diversity of this group of snakes. The Mississippi River caused initial speciation in this species complex, with more recent divergence events linked to adaptations to ecological heterogeneity and allopatric Pleistocene refugia. Lastly, we discuss the taxonomy of this group and suggest there may be additional cryptic species in need of formal recognition.
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Affiliation(s)
- Edward A Myers
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Herpetology, The American Museum of Natural History, New York, NY, USA
| | - Alexander D McKelvy
- Department of Biology, The Graduate School and Center, City University of New York, New York, NY, USA
| | - Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, New York, NY, USA
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18
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Graham MR, Myers EA, Kaiser RC, Fet V. Cryptic species and co‐diversification in sand scorpions from the Karakum and Kyzylkum deserts of Central Asia. ZOOL SCR 2019. [DOI: 10.1111/zsc.12381] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Matthew R. Graham
- Department of Biology Eastern Connecticut State University Willimantic CT USA
| | - Edward A. Myers
- Department of Vertebrate Zoology National Museum of Natural History, Smithsonian Institution Washington DC USA
| | - Ronald C. Kaiser
- Department of Biology Eastern Connecticut State University Willimantic CT USA
| | - Victor Fet
- Department of Biological Sciences Marshall University Huntington WV USA
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19
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Myers EA, Xue AT, Gehara M, Cox CL, Davis Rabosky AR, Lemos‐Espinal J, Martínez‐Gómez JE, Burbrink FT. Environmental heterogeneity and not vicariant biogeographic barriers generate community‐wide population structure in desert‐adapted snakes. Mol Ecol 2019; 28:4535-4548. [DOI: 10.1111/mec.15182] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/23/2019] [Accepted: 07/08/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Edward A. Myers
- Department of Vertebrate Zoology Smithsonian Institution National Museum of Natural History Washington DC USA
- Department of Herpetology The American Museum of Natural History New York NY USA
| | | | - Marcelo Gehara
- Department of Herpetology The American Museum of Natural History New York NY USA
| | - Christian L. Cox
- Department of Biology Georgia Southern University Statesboro GA USA
| | - Alison R. Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor MI USA
| | - Julio Lemos‐Espinal
- Laboratorio de Ecología, UBIPRO, FES Iztacala Universidad Nacional Autónoma de México Tlalnepantla Mexico
| | | | - Frank T. Burbrink
- Department of Herpetology The American Museum of Natural History New York NY USA
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20
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Myers EA, Bryson RW, Hansen RW, Aardema ML, Lazcano D, Burbrink FT. Exploring Chihuahuan Desert diversification in the gray-banded kingsnake, Lampropeltis alterna (Serpentes: Colubridae). Mol Phylogenet Evol 2019; 131:211-218. [DOI: 10.1016/j.ympev.2018.10.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 10/23/2018] [Accepted: 10/23/2018] [Indexed: 12/20/2022]
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21
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Myers EA, Burgoon JL, Ray JM, Martínez-Gómez JE, Matías-Ferrer N, Mulcahy DG, Burbrink FT. Coalescent Species Tree Inference of Coluber and Masticophis. COPEIA 2017. [DOI: 10.1643/ch-16-552] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Ruane S, Myers EA, Lo K, Yuen S, Welt RS, Juman M, Futterman I, Nussbaum RA, Schneider G, Burbrink FT, Raxworthy CJ. Unrecognized species diversity and new insights into colour pattern polymorphism within the widespread Malagasy snake Mimophis (Serpentes: Lamprophiidae). SYST BIODIVERS 2017. [DOI: 10.1080/14772000.2017.1375046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Sara Ruane
- Department of Biological Sciences, 206 Boyden Hall, Rutgers University, 195 University Ave, Newark, NJ 07102, USA
- Department of Herpetology, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Edward A. Myers
- Department of Herpetology, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Kahmun Lo
- Science Research Mentoring Program, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Sara Yuen
- Science Research Mentoring Program, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Rachel S. Welt
- Department of Herpetology, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Maya Juman
- Science Research Mentoring Program, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - India Futterman
- Science Research Mentoring Program, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Ronald A. Nussbaum
- Division of Reptiles and Amphibians, Museum of Zoology, Research Museums Center, 3600 Varsity Drive, University of Michigan, Ann Arbor, MI 48108, USA
| | - Gregory Schneider
- Division of Reptiles and Amphibians, Museum of Zoology, Research Museums Center, 3600 Varsity Drive, University of Michigan, Ann Arbor, MI 48108, USA
| | - Frank T. Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Christopher J. Raxworthy
- Department of Herpetology, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
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Burbrink FT, Chan YL, Myers EA, Ruane S, Smith BT, Hickerson MJ. Asynchronous demographic responses to Pleistocene climate change in Eastern Nearctic vertebrates. Ecol Lett 2016; 19:1457-1467. [DOI: 10.1111/ele.12695] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 07/27/2016] [Accepted: 09/15/2016] [Indexed: 01/17/2023]
Affiliation(s)
- Frank T. Burbrink
- Department of Herpetology The American Museum of Natural History Central Park West and 79th Street New York NY10024 USA
| | - Yvonne L. Chan
- iDepartment ’Iolani School 563 Kamoku Street Honolulu HI96826 USA
| | - Edward A. Myers
- Department of Biology 6S‐143 College of Staten Island 2800 Victory Boulevard Staten Island NY10314 USA
- Department of Biology The Graduate School and University Center The City University of New York 365 Fifth Ave. NY10016 USA
| | - Sara Ruane
- Museum of Natural Science Louisiana State University 119 Foster Hall Baton Rouge LA70803 USA
| | - Brian Tilston Smith
- Department of Ornithology The American Museum of Natural History Central Park West and 79th Street New York NY10024 USA
| | - Michael J. Hickerson
- Department of Biology The Graduate School and University Center The City University of New York 365 Fifth Ave. NY10016 USA
- Biology Department City College of New York New York NY10016 USA
- Division of Invertebrate Zoology The American Museum of Natural History Central Park West and 79th Street New York NY10024 USA
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24
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Burbrink FT, McKelvy AD, Pyron RA, Myers EA. Predicting community structure in snakes on Eastern Nearctic islands using ecological neutral theory and phylogenetic methods. Proc Biol Sci 2016; 282:rspb.2015.1700. [PMID: 26609083 DOI: 10.1098/rspb.2015.1700] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Predicting species presence and richness on islands is important for understanding the origins of communities and how likely it is that species will disperse and resist extinction. The equilibrium theory of island biogeography (ETIB) and, as a simple model of sampling abundances, the unified neutral theory of biodiversity (UNTB), predict that in situations where mainland to island migration is high, species-abundance relationships explain the presence of taxa on islands. Thus, more abundant mainland species should have a higher probability of occurring on adjacent islands. In contrast to UNTB, if certain groups have traits that permit them to disperse to islands better than other taxa, then phylogeny may be more predictive of which taxa will occur on islands. Taking surveys of 54 island snake communities in the Eastern Nearctic along with mainland communities that have abundance data for each species, we use phylogenetic assembly methods and UNTB estimates to predict island communities. Species richness is predicted by island area, whereas turnover from the mainland to island communities is random with respect to phylogeny. Community structure appears to be ecologically neutral and abundance on the mainland is the best predictor of presence on islands. With regard to young and proximate islands, where allopatric or cladogenetic speciation is not a factor, we find that simple neutral models following UNTB and ETIB predict the structure of island communities.
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024-5192, USA Department of Biology, The Graduate Center, City University of New York, New York, NY 10016, USA Department of Biology, College of Staten Island, 2800 Victory Boulevard, 6S-143, Staten Island, New York, NY 10314, USA
| | - Alexander D McKelvy
- Department of Biology, The Graduate Center, City University of New York, New York, NY 10016, USA Department of Biology, College of Staten Island, 2800 Victory Boulevard, 6S-143, Staten Island, New York, NY 10314, USA
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, 2023 G Street NW, Washington, DC 20052, USA
| | - Edward A Myers
- Department of Biology, The Graduate Center, City University of New York, New York, NY 10016, USA Department of Biology, College of Staten Island, 2800 Victory Boulevard, 6S-143, Staten Island, New York, NY 10314, USA
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Guo P, Liu Q, Zhu F, Zhong GH, Chen X, Myers EA, Che J, Zhang L, Ziegler T, Nguyen TQ, Burbrink FT. Complex longitudinal diversification across South China and Vietnam in Stejneger's pit viper,Viridovipera stejnegeri(Schmidt, 1925) (Reptilia: Serpentes: Viperidae). Mol Ecol 2016; 25:2920-36. [DOI: 10.1111/mec.13658] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 03/16/2016] [Accepted: 03/29/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Peng Guo
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Qin Liu
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Fei Zhu
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Guang H. Zhong
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Xin Chen
- Department of Biological Sciences; Dartmouth College; Hanover NH 03755 USA
| | - Edward A. Myers
- Department of Biology; The Graduate School and University Center; The City University of New York; 365 5th Avenue New York NY 10016 USA
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals; Kunming Institute of Zoology; Chinese Academy of Sciences; Kunming 650223 China
- Southeast Asia Biodiversity Research Institute; Chinese Academy of Sciences; Menglun Mengla Yunnan 666303 China
| | - Liang Zhang
- South China Institute of Endangered Animals; Guangzhou 510260 China
| | - Thomas Ziegler
- AG Zoologischer Garten Köln; Riehler Strasse 173 D-50735 Cologne Germany
| | - Truong Q. Nguyen
- Institute of Ecology and Biological Resources; Vietnam Academy of Science and Technology; 18 Hoang Quoc Viet Street Hanoi Vietnam
| | - Frank T. Burbrink
- Department of Herpetology; American Museum of Natural History; Central Park West at 79th Street New York NY 10024-5192 USA
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Oliveira EF, Gehara M, São-Pedro VA, Chen X, Myers EA, Burbrink FT, Mesquita DO, Garda AA, Colli GR, Rodrigues MT, Arias FJ, Zaher H, Santos RML, Costa GC. Speciation with gene flow in whiptail lizards from a Neotropical xeric biome. Mol Ecol 2015; 24:5957-75. [PMID: 26502084 DOI: 10.1111/mec.13433] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/15/2015] [Accepted: 10/21/2015] [Indexed: 11/29/2022]
Abstract
Two main hypotheses have been proposed to explain the diversification of the Caatinga biota. The riverine barrier hypothesis (RBH) claims that the São Francisco River (SFR) is a major biogeographic barrier to gene flow. The Pleistocene climatic fluctuation hypothesis (PCH) states that gene flow, geographic genetic structure and demographic signatures on endemic Caatinga taxa were influenced by Quaternary climate fluctuation cycles. Herein, we analyse genetic diversity and structure, phylogeographic history, and diversification of a widespread Caatinga lizard (Cnemidophorus ocellifer) based on large geographical sampling for multiple loci to test the predictions derived from the RBH and PCH. We inferred two well-delimited lineages (Northeast and Southwest) that have diverged along the Cerrado-Caatinga border during the Mid-Late Miocene (6-14 Ma) despite the presence of gene flow. We reject both major hypotheses proposed to explain diversification in the Caatinga. Surprisingly, our results revealed a striking complex diversification pattern where the Northeast lineage originated as a founder effect from a few individuals located along the edge of the Southwest lineage that eventually expanded throughout the Caatinga. The Southwest lineage is more diverse, older and associated with the Cerrado-Caatinga boundaries. Finally, we suggest that C. ocellifer from the Caatinga is composed of two distinct species. Our data support speciation in the presence of gene flow and highlight the role of environmental gradients in the diversification process.
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Affiliation(s)
- Eliana F Oliveira
- Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Marcelo Gehara
- Pós-Graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Vinícius A São-Pedro
- Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Xin Chen
- Department of Biology, 6S-143, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, NY, 10314, USA.,Department of Biology, The Graduate School, City University of New York, New York, NY, 10016, USA
| | - Edward A Myers
- Department of Biology, 6S-143, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, NY, 10314, USA.,Department of Biology, The Graduate School, City University of New York, New York, NY, 10016, USA
| | - Frank T Burbrink
- Department of Biology, 6S-143, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, NY, 10314, USA.,Department of Biology, The Graduate School, City University of New York, New York, NY, 10016, USA.,Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024-5192, USA
| | - Daniel O Mesquita
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, PB, 58000-00, Brazil
| | - Adrian A Garda
- Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Miguel T Rodrigues
- Departamento de Zoologia, Universidade de São Paulo, São Paulo, SP, 05422-970, Brazil
| | - Federico J Arias
- Departamento de Zoologia, Universidade de São Paulo, São Paulo, SP, 05422-970, Brazil
| | - Hussam Zaher
- Museu de Zoologia, Universidade de São Paulo, São Paulo, SP, 04263-000, Brazil
| | - Rodrigo M L Santos
- Departamento de Zoologia, Universidade de São Paulo, São Paulo, SP, 05422-970, Brazil
| | - Gabriel C Costa
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
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Chen X, Jiang K, Guo P, Huang S, Rao D, Ding L, Takeuchi H, Che J, Zhang YP, Myers EA, Burbrink FT. Assessing species boundaries and the phylogenetic position of the rare Szechwan ratsnake, Euprepiophis perlaceus (Serpentes: Colubridae), using coalescent-based methods. Mol Phylogenet Evol 2014; 70:130-6. [DOI: 10.1016/j.ympev.2013.09.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 09/03/2013] [Accepted: 09/07/2013] [Indexed: 11/29/2022]
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Myers EA, Ruane S, Knight K, Knight JL, Ray JM. Distribution record of Tantilla alticola Boulenger, 1903 (Squamata: Colubridae) in Coclé Province, Republic of Panama. cl 2013. [DOI: 10.15560/9.1.151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
A single specimen of Tantilla alticola was collected from Parque Nacional G. D. Omar Torrijos Herrera of Coclé Province, Republic of Panama. This record fills in a gap in the distribution for this species within the cloud forests of Central America.
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Burbrink FT, Chen X, Myers EA, Brandley MC, Pyron RA. Evidence for determinism in species diversification and contingency in phenotypic evolution during adaptive radiation. Proc Biol Sci 2012; 279:4817-26. [PMID: 23034709 DOI: 10.1098/rspb.2012.1669] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Adaptive radiation (AR) theory predicts that groups sharing the same source of ecological opportunity (EO) will experience deterministic species diversification and morphological evolution. Thus, deterministic ecological and morphological evolution should be correlated with deterministic patterns in the tempo and mode of speciation for groups in similar habitats and time periods. We test this hypothesis using well-sampled phylogenies of four squamate groups that colonized the New World (NW) in the Late Oligocene. We use both standard and coalescent models to assess species diversification, as well as likelihood models to examine morphological evolution. All squamate groups show similar early pulses of speciation, as well as diversity-dependent ecological limits on clade size at a continental scale. In contrast, processes of morphological evolution are not easily predictable and do not show similar pulses of early and rapid change. Patterns of morphological and species diversification thus appear uncoupled across these groups. This indicates that the processes that drive diversification and disparification are not mechanistically linked, even among similar groups of taxa experiencing the same sources of EO. It also suggests that processes of phenotypic diversification cannot be predicted solely from the existence of an AR or knowledge of the process of diversification.
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Affiliation(s)
- Frank T Burbrink
- Department of Biology, The College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, NY 10314, USA.
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Osburne RC, Myers EA, Rodbard D, Burman KD, Georges LP, O'Brian JT. Adaptation to hypocaloric feeding: physiologic significance of the fall in serum T3 as measured by the pulse wave arrival time (QKd). Metabolism 1983; 32:9-13. [PMID: 6848901 DOI: 10.1016/0026-0495(83)90148-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We have investigated the physiologic significance of the decline in serum triiodothyronine (T3) occurring during hypocaloric feeding by measurement of changes in cardiovascular function. The QKd interval, the interval between the Q wave of the electrocardiogram and the onset of Korotkoff sounds at diastolic pressure at the brachial artery, is the sum of the preejection period and pulsetransmission time, and has proven to be a sensitive and effective measure of the effect of thyroid hormones on the cardiovascular system. Fifteen euthyroid obese volunteers underwent successive 2 wk periods of hypocaloric feeding (200-400 calories per day) interspersed with periods of at least 2 wk of re-feeding on a weight-maintaining diet (1500 calories). In a later phase subjects received oral supplementation of triiodothyronine (T3) in addition to the diet to prevent the fall in serum T3. In the last study phase, subjects on the diet received supplementation with oral thyroxine (T4), which prevented the fall in serum T3 and resulted in a slight increase in serum T4. During the first 2 wk period of hypocaloric feeding, there was a statistically significant increase in QKd, and a decrease in pulse rate, compatible with a hypothyroid state relative to initial measurements. When oral T3 supplementation was given, the rise in QKd and fall in pulse rate were prevented. Likewise, with oral T4 supplementation, the changes in QKd and pulse were prevented. Thus, the fall in serum T3 occurring during hypocaloric feeding is associated with changes in the cardiovascular system which are qualitatively similar to those observed during hypothyroidism. The present data, taken with other data in the literature, suggest that the decline in serum T3 during hypocaloric feeding may be an adaptive mechanism to conserve energy during caloric deprivation.
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Myers EA, Hardman JM, Worsham GF, Eil C. Adenocarcinoma of the lung causing ectopic adrenocorticotropic hormone syndrome. Arch Intern Med 1982; 142:1387-9. [PMID: 7092452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A patient with a left lower lung mass had muscle weakness, generalized hyperpigmentation, metabolic alkalosis, and profound hypokalemia. His elevated serum cortisol, corticosterone, and adrenocorticotropic hormone (ACTH) concentrations were not suppressed after midnight dexamethasone administration. Light and electron microscopic sections of the lung mass fitted the pathological criteria for adenocarcinoma. Immunocytochemical analysis of the tumor demonstrated specific staining with antibody to beta-endorphin, suggesting that the tumor cells made the common precursor molecule of ACTH, beta-lipotropin, and endorphin. This is, to the best of our knowledge, only the second case report of pulmonary adenocarcinoma associated with the syndrome of ectopic ACTH.
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