1
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Bhat MS, Cullen TM. Growth and life history of freshwater chelydrid turtles (Testudines: Cryptodira): A bone histological approach. J Anat 2024. [PMID: 39169639 DOI: 10.1111/joa.14130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/25/2024] [Accepted: 08/07/2024] [Indexed: 08/23/2024] Open
Abstract
The current study examines the growth pattern and lifestyle habits of the freshwater snapping turtles Chelydra and Macrochelys based on limb bone histology. Femora, humeri, and tibiae of 25 individuals selected from a range of ontogenetic stages were assessed to determine inter-element and intraskeletal histological variation. Osteohistological assessment of multiple elements is consistent with overall moderate growth rates as revealed by the dominance of parallel-fibered bone. However, the growth was cyclical as shown by deposition of multiple lines of arrested growths in the compacta. It appears that the bone tissue of C. serpentina is more variable through ontogeny with intermittent higher growth rates. M. temminckii appears to grow more slowly than C. serpentina possessing compact and thick cortices in accordance with their larger size. Overall, vascularization decreases through ontogeny with humeri and femora being well-vascularized in both species. Contrarily, epipodials are poorly vascularized, though simple longitudinal and radial canals are present, suggesting differences in growth patterns when compared with associated diaphyseal sections. The tibiae were found to be the least remodeled of the limb bones and therefore better suited for skeletochronology for snapping turtles. Intra-elementally, femora and humeri preserved higher cortical vascularity ventrally, suggestive of faster relative growth. We hypothesize that the differential growth pattern in limb bones of snapping turtles may relate to differential functional constraints, where forelimbs are operational in swimming while the hindlimbs provide stability.
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Affiliation(s)
- Mohd Shafi Bhat
- Department of Geosciences, Auburn University, Auburn, Alabama, USA
| | - Thomas M Cullen
- Department of Geosciences, Auburn University, Auburn, Alabama, USA
- Auburn University Museum of Natural History, Auburn, Alabama, USA
- Department of Earth Sciences, Carleton University, Ottawa, Ontario, Canada
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2
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Nuñez LP, Gray LN, Weisrock DW, Burbrink FT. The Phylogenomic and Biogeographic History of the Gartersnakes, Watersnakes, and Allies (Natricidae: Thamnophiini). Mol Phylogenet Evol 2023:107844. [PMID: 37301486 DOI: 10.1016/j.ympev.2023.107844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/01/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023]
Abstract
North American Thamnophiini (gartersnakes, watersnakes, brownsnakes, and swampsnakes) are an ecologically and phenotypically diverse temperate clade of snakes representing 61 species across 10 genera. In this study, we estimate phylogenetic trees using ∼3,700 ultraconserved elements (UCEs) for 76 specimens representing 75% of all Thamnophiini species. We infer phylogenies using multispecies coalescent methods and time calibrate them using the fossil record. We also conducted ancestral area estimation to identify how major biogeographic boundaries in North America affect broadscale diversification in the group. While most nodes exhibited strong statistical support, analysis of concordant data across gene trees reveals substantial heterogeneity. Ancestral area estimation demonstrated that the genus Thamnophis was the only taxon in this subfamily to cross the Western Continental Divide, even as other taxa dispersed southward toward the tropics. Additionally, levels of gene tree discordance are overall higher in transition zones between bioregions, including the Rocky Mountains. Therefore, the Western Continental Divide may be a significant transition zone structuring the diversification of Thamnophiini during the Neogene and Pleistocene. Here we show that despite high levels of discordance across gene trees, we were able to infer a highly resolved and well-supported phylogeny for Thamnophiini, which allows us to understand broadscale patterns of diversity and biogeography.
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Affiliation(s)
- Leroy P Nuñez
- Department of Herpetology, American Museum of Natural History, New York, NY, USA; Richard Gilder Graduate School, American Museum of Natural History, New York, NY, USA.
| | - Levi N Gray
- Fort Collins Science Center, United States Geological Survey, Guam, USA
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, New York, NY, USA
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3
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An Evaluation of Western Chicken Turtle (Deirochelys reticularia miaria) Survey and Capture Protocols. J HERPETOL 2022. [DOI: 10.1670/20-036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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4
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Bowers BC, Hibbitts RL, Hibbitts TJ, Walkup DK, Ryberg WA, Lopez RR, Crump PS. Fecundity, Female Maturation, and Nesting Season of Western Chicken Turtles (Deirochelys reticularia miaria) in Texas. CHELONIAN CONSERVATION AND BIOLOGY 2022. [DOI: 10.2744/ccb-1542.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Brandon C. Bowers
- Natural Resources Institute, Texas A&M University, College Station, Texas 77843 USA [; ; ; ]
| | - Rachel L. Hibbitts
- Wellborn Road Veterinary Medical Center, College Station, Texas 77845 USA []
| | - Toby J. Hibbitts
- Natural Resources Institute, Texas A&M University, College Station, Texas 77843 USA [; ; ; ]
| | - Danielle K. Walkup
- Natural Resources Institute, Texas A&M University, College Station, Texas 77843 USA [; ; ; ]
| | - Wade A. Ryberg
- Natural Resources Institute, Texas A&M University, College Station, Texas 77843 USA [; ; ; ]
| | - Roel R. Lopez
- Natural Resources Institute, Texas A&M University, College Station, Texas 77843 USA [; ; ; ]
| | - Paul S. Crump
- Texas Parks and Wildlife Department, Austin, Texas 78744 USA []
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5
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Nikolakis ZL, Orton RW, Crother BI. Fine‐scale population structure within an Eastern Nearctic snake complex (
Pituophis melanoleucus
). ZOOL SCR 2021. [DOI: 10.1111/zsc.12522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Zachary L. Nikolakis
- Department of Biology Southeastern Louisiana University Hammond Louisina USA
- Department of Biology University of Texas at Arlington Arlington Texas USA
| | - Richard W. Orton
- Department of Biology University of Texas at Arlington Arlington Texas USA
| | - Brian I. Crother
- Department of Biology Southeastern Louisiana University Hammond Louisina USA
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6
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Burbrink FT, Bernstein JM, Kuhn A, Gehara M, Ruane S. Ecological Divergence and the History of Gene Flow in the Nearctic Milksnakes (Lampropeltis triangulum Complex). Syst Biol 2021; 71:839-858. [PMID: 35043210 DOI: 10.1093/sysbio/syab093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Many phylogeographic studies on species with large ranges have found genetic-geographic structure associated with changes in habitat and physical barriers preventing or reducing gene flow. These interactions with geographic space, contemporary and historical climate, and biogeographic barriers have complex effects on contemporary population genetic structure and processes of speciation. While allopatric speciation at biogeographic barriers is considered the primary mechanism for generating species, more recently it has been shown that parapatric modes of divergence may be equally or even more common. With genomic data and better modeling capabilities, we can more clearly define causes of speciation in relation to biogeography and migration between lineages, the location of hybrid zones with respect to the ecology of parental lineages, and differential introgression of genes between taxa. Here, we examine the origins of three Nearctic milksnakes (Lampropeltis elapsoides, Lampropeltis triangulum and Lampropeltis gentilis) using genome-scale data to better understand species diversification. Results from artificial neural networks show that a mix of a strong biogeographic barrier, environmental changes, and physical space has affected genetic structure in these taxa. These results underscore conspicuous environmental changes that occur as the sister taxa L. triangulum and L. gentilis diverged near the Great Plains into the forested regions of the Eastern Nearctic. This area has been recognized as a region for turnover for many vertebrate species, but as we show here the contemporary boundary does not isolate these sister species. These two species likely formed in the mid-Pleistocene and have remained partially reproductively isolated over much of this time, showing differential introgression of loci. We also demonstrate that when L. triangulum and L. gentilis are each in contact with the much older L. elapsoides, some limited gene flow has occurred. Given the strong agreement between nuclear and mtDNA genomes, along with estimates of ecological niche, we suggest that all three lineages should continue to be recognized as unique species. Furthermore, this work emphasizes the importance of considering complex modes of divergence and differential allelic introgression over a complex landscape when testing mechanisms of speciation. [Cline; delimitation; Eastern Nearctic; Great Plains; hybrids; introgression; speciation.].
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Justin M Bernstein
- Department of Biological Sciences, Rutgers University Newark, 195 University Ave, Newark, NJ 07102, USA
| | - Arianna Kuhn
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University Newark, 195 University Ave, Newark, NJ 07102, USA
| | - Sara Ruane
- Department of Earth and Environmental Sciences, Rutgers University Newark, 195 University Ave, Newark, NJ 07102, USA.,Amphibian and Reptile Collection, Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Dr, Chicago, IL 60605, USA
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7
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Burbrink FT, Ruane S. Contemporary Philosophy and Methods for Studying Speciation and Delimiting Species. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/h2020073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Frank T. Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024; . Send reprint requests to this address
| | - Sara Ruane
- Earth and Environmental Sciences: Ecology and Evolution, Rutgers University–Newark, 195 University Avenue, Newark, New Jersey 07102
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8
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Whitaker M, Procter T, Fontanella FM. Phylogeography and demographic expansion in the widely distributed horned passalus beetle, Odontotaenius disjunctus (coleoptera: Passalidae). Mitochondrial DNA A DNA Mapp Seq Anal 2021; 32:85-97. [PMID: 33591237 DOI: 10.1080/24701394.2021.1882443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Dynamic climatic oscillations during the Pleistocene had profound effects on the distribution of species across North America. Although the role of historical climate change on speciation remains controversial, the impact on genetic variation within species has been well documented. Analyses of mtDNA sequences from the cytochrome oxidase I gene (911 bp) for 115 individuals of Odontotaenius disjunctus was combined with ecological niche modelling (ENM) to infer the demographic and population differentiation scenarios under present and past conditions. We inferred three lineages that diverged during the Pleistocene and replace each other geographically across the eastern United States. One of these lineages traverses previously identified genetic barriers for terrestrial animals including the Mississippi and Apalachicola Rivers and the Appalachian Mountains. We observed overlapping ranges between two haplotype groups as well as a region of secondary contact associated with ecological transition zone in northern Florida. The two continental lineages depict a genetic signature of a recent population increase associated with expanding niche envelope, whereas the clade restricted to peninsular Florida shows stable populations in a shrinking niche envelope. Given the lack of ecological separation, overlapping distribution of haplogroups and the presence of secondary contact zones, the taxonomic status of these lineages must await robust testing using multilocus DNA data to assess species boundaries.
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Affiliation(s)
- Megan Whitaker
- Department of Biology, University of West Georgia, Carrollton, GA, USA
| | - Taylor Procter
- Department of Biology, University of West Georgia, Carrollton, GA, USA
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9
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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] [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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10
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Walters AD, Cannizzaro AG, Trujillo DA, Berg DJ. Addressing the Linnean shortfall in a cryptic species complex. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Biodiversity is being lost at an alarming rate, but the rate of this loss is likely to be underestimated as a result of a deficit in taxonomic knowledge (i.e. the Linnean shortfall). This knowledge gap is more extensive for morphologically indistinct taxa. The advancement of molecular techniques and delimitation methods has facilitated the identification of such cryptic species, but a majority of these taxa remain undescribed. To investigate the effects of taxonomic uncertainty on understanding of biodiversity, we applied the general lineage concept of species to an amphipod species complex, the Gammaruslacustris lineage that occupies springs of the northern Chihuahuan Desert, which is emerging in contemporary times. We investigated species boundaries using a validation-based approach and examined genetic structure of the lineage using a suite of microsatellite markers to identify independently evolving metapopulations. Our results show that each spring contains a genetically distinct population that is geographically isolated from other springs, suggesting evolutionary independence and status as separate species. Additionally, we observed subtle interspecific morphological variation among the putative species. We used multiple lines of evidence to formally describe four new species (Gammarus langi sp. nov., G. percalacustris sp. nov., G. colei sp. nov. and G. malpaisensis sp. nov.) endemic to the northern Chihuahuan Desert. Cryptic speciation is likely to be high in other aquatic taxa within these ecosystems, and across arid landscapes throughout North America and elsewhere, suggesting that the magnitude of the Linnean shortfall is currently underestimated in desert springs worldwide.
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Affiliation(s)
| | | | | | - David J Berg
- Department of Biology, Miami University, Hamilton, OH USA
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11
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McKnight DT, Ligon DB. ESTIVATION SITE SELECTION OF WESTERN CHICKEN TURTLES (DEIROCHELYS RETICULARIA MIARIA). SOUTHWEST NAT 2020. [DOI: 10.1894/0038-4909-64.3-4.187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
| | - Day B. Ligon
- Department of Biology, Missouri State University, Springfield, MO 65897
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12
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Richardson DJ, Hammond CI, Moser WE, Phillips AJ, Lazo-Wasem EA, Barger MA. Molecular Variation and Biogeography of the Common North American Turtle Leech, Placobdella parasitica. BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY 2020. [DOI: 10.3374/014.061.0201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | | | - William E. Moser
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Suitland, MD 20746 USA
| | - Anna J. Phillips
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560-0163 USA
| | - Eric A. Lazo-Wasem
- Division of Invertebrate Zoology, Peabody Museum of Natural History, Yale University, New Haven, CT 06520 USA
| | - Michael A. Barger
- Department of Biology and Environmental Science, Westminster College, Fulton, MO 68251 USA
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13
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Eaton KR, Loxterman JL, Keeley ER. Connections and containers: Using genetic data to understand how watershed evolution and human activities influence cutthroat trout biogeography. PLoS One 2018; 13:e0202043. [PMID: 30096159 PMCID: PMC6086439 DOI: 10.1371/journal.pone.0202043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/26/2018] [Indexed: 11/19/2022] Open
Abstract
Species with large geographic distributions often exhibit complex patterns of diversity that can be further complicated by human activities. Cutthroat trout (Oncorhynchus clarkii) are one of the most widely distributed freshwater fish species in western North America exhibiting substantial phenotypic and genetic variability; however, fish stocking practices have translocated populations outside of their native range and may have obscured intraspecific boundaries. This study focuses on cutthroat trout populations representing three distinct evolutionary clades that are found intermixed within a contact zone between the Bonneville and upper Snake River watersheds in the western United States. We used mitochondrial and microsatellite genetic data, as well as historical stocking records, to evaluate whether populations of cutthroat trout in the contact zone are native or are introduced. We found significant genetic differentiation and fine-scale genetic population structure that was organized primarily by watershed boundaries. While we detected increased genetic diversity in some areas in close proximity to the greatest number of stocking events, the highly organized population structure both within and between areas of the contact zone indicates that the populations are native to the watersheds. Intermixing of distinct evolutionary lineages of cutthroat trout appears to be the result of historical connections between paleodrainages. Our analyses provide a context for understanding how genetic data can be used to assess the status of populations as native or introduced.
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Affiliation(s)
- Kendra R. Eaton
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, United States of America
| | - Janet L. Loxterman
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, United States of America
| | - Ernest R. Keeley
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, United States of America
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14
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Barrow LN, Lemmon AR, Lemmon EM. Targeted Sampling and Target Capture: Assessing Phylogeographic Concordance with Genome-wide Data. Syst Biol 2018; 67:979-996. [DOI: 10.1093/sysbio/syy021] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 03/15/2018] [Indexed: 01/09/2023] Open
Affiliation(s)
- Lisa N Barrow
- Department of Biology, Museum of Southwestern Biology, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131-0001, USA
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4120, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, USA
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15
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Vitek NS. Delineating modern variation from extinct morphology in the fossil record using shells of the Eastern Box Turtle (Terrapene carolina). PLoS One 2018; 13:e0193437. [PMID: 29513709 PMCID: PMC5841793 DOI: 10.1371/journal.pone.0193437] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/09/2018] [Indexed: 11/30/2022] Open
Abstract
Characterization of morphological variation in the shells of extant Eastern Box Turtles, Terrapene carolina, provides a baseline for comparison to fossil populations. It also provides an example of the difficulties inherent to recognizing intraspecific diversity in the fossil record. The degree to which variation in fossils of T. carolina can be accommodated by extant variation in the species has been disagreed upon for over eighty years. Using morphometric analyses of the carapace, I address the relationship between modern and fossil T. carolina in terms of sexual dimorphism, geographic and subspecific variation, and allometric variation. Modern T. carolina display weak male-biased sexual size dimorphism. Sexual shape dimorphism cannot be reliably detected in the fossil record. Rather than a four-part subspecific division, patterns of geographic variation are more consistent with clinal variation between various regions in the species distribution. Allometric patterns are qualitatively similar to those documented in other emydid turtles and explain a significant amount of shape variation. When allometric patterns are accounted for, Holocene specimens are not significantly different from modern specimens. In contrast, several geologically older specimens have significantly different carapace shape with no modern analogue. Those large, fossilized specimens represent extinct variation occupying novel portions of morphospace. This study highlights the need for additional documentation of modern osteological variation that can be used to test hypotheses of intraspecific evolution in the fossil record.
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Affiliation(s)
- Natasha S. Vitek
- Jackson School of Geosciences, The University of Texas at Austin, Austin, Texas, Florida Museum of Natural History and Department of Biology, the University of Florida, Gainesville, Florida, United States of America
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16
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Resolving taxonomic turbulence and uncovering cryptic diversity in the musk turtles (Sternotherus) using robust demographic modeling. Mol Phylogenet Evol 2018; 120:1-15. [DOI: 10.1016/j.ympev.2017.11.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/09/2017] [Accepted: 11/16/2017] [Indexed: 01/25/2023]
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17
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Carr JL, Tolson KM. Observations On Reproduction In the Western Chicken Turtle, Deirochelys reticularia miaria, In Louisiana. SOUTHWEST NAT 2017. [DOI: 10.1894/0038-4909-62.4.280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- John L. Carr
- Department of Biology and Museum of Natural History, University of Louisiana at Monroe, Monroe, LA 71209-0520
| | - Kim Marie Tolson
- Department of Biology and Museum of Natural History, University of Louisiana at Monroe, Monroe, LA 71209-0520
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18
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Ennen JR, Matamoros WA, Agha M, Lovich JE, Sweat SC, Hoagstrom CW. Hierarchical, Quantitative Biogeographic Provinces for All North American Turtles and Their Contribution to the Biogeography of Turtles and the Continent. HERPETOLOGICAL MONOGRAPHS 2017. [DOI: 10.1655/herpmonographs-d-16-00013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Joshua R. Ennen
- Tennessee Aquarium Conservation Institute, Tennessee Aquarium, 175 Baylor School Road, Chattanooga, TN 37405, USA
| | - Wilfredo A. Matamoros
- Facultad de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Museo de Zoología, Tuxtla Gutiérrez, Chiapas, México Apartado Postal 29000, México
| | - Mickey Agha
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Jeffrey E. Lovich
- U.S. Geological Survey, Southwest Biological Science Center, 2255 North Gemini Drive, Flagstaff, AZ 86001, USA
| | - Sarah C. Sweat
- Tennessee Aquarium Conservation Institute, Tennessee Aquarium, 175 Baylor School Road, Chattanooga, TN 37405, USA
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19
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Minton R, McGregor B, Hayes D, Paight C, Inoue K. Genetic structuring in the Pyramid Elimia, Elimia potosiensis (Gastropoda, Pleuroceridae), with implications for pleurocerid conservation. ZOOSYST EVOL 2017. [DOI: 10.3897/zse.93.14856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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20
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O'Connell KA, Streicher JW, Smith EN, Fujita MK. Geographical features are the predominant driver of molecular diversification in widely distributed North American whipsnakes. Mol Ecol 2017; 26:5729-5751. [PMID: 28802078 DOI: 10.1111/mec.14295] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 07/17/2017] [Accepted: 07/24/2017] [Indexed: 01/08/2023]
Abstract
Allopatric divergence following the formation of geographical features has been implicated as a major driver of evolutionary diversification. Widespread species complexes provide opportunities to examine allopatric divergence across varying degrees of isolation in both time and space. In North America, several geographical features may play such a role in diversification, including the Mississippi River, Pecos River, Rocky Mountains, Cochise Filter Barrier, Gulf of California and Isthmus of Tehuantepec. We used thousands of nuclear single nucleotide polymorphisms (SNPs) and mitochondrial DNA from several species of whipsnakes (genera Masticophis and Coluber) distributed across North and Central America to investigate the role that these geographical features have played on lineage divergence. We hypothesize that these features restrict gene flow and separate whipsnakes into diagnosable genomic clusters. We performed genomic clustering and phylogenetic reconstructions at the species and population levels using Bayesian and likelihood analyses and quantified migration levels across geographical features to assess the degree of genetic isolation due to allopatry. Our analyses suggest that (i) major genetic divisions are often consistent with isolation by geographical features, (ii) migration rates between clusters are asymmetrical across major geographical features, and (iii) areas that receive proportionally more migrants possess higher levels of genetic diversity. Collectively, our findings suggest that multiple features of the North American landscape contributed to allopatric divergence in this widely distributed snake group.
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Affiliation(s)
- Kyle A O'Connell
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
| | | | - Eric N Smith
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
| | - Matthew K Fujita
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
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21
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Selman W. Diagnostic Trait Variability in the Imperiled Freshwater Turtle, Graptemys flavimaculata. HERPETOLOGICA 2017. [DOI: 10.1655/herpetologica-d-16-00053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Will Selman
- Biology Department, Millsaps College, 1701 North State Street, Jackson, MS 39210, USA
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22
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Praschag P, Ihlow F, Flecks M, Vamberger M, Fritz U. Diversity of North American map and sawback turtles (Testudines: Emydidae: Graptemys
). ZOOL SCR 2017. [DOI: 10.1111/zsc.12249] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | - Flora Ihlow
- Herpetology Section; Zoologisches Forschungsmuseum Alexander Koenig (ZFMK); Bonn Germany
- Museum of Zoology; Senckenberg Dresden; Dresden Germany
| | - Morris Flecks
- Herpetology Section; Zoologisches Forschungsmuseum Alexander Koenig (ZFMK); Bonn Germany
| | | | - Uwe Fritz
- Museum of Zoology; Senckenberg Dresden; Dresden Germany
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23
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Ecological divergence in the yellow-bellied kingsnake (Lampropeltis calligaster) at two North American biodiversity hotspots. Mol Phylogenet Evol 2017; 106:61-72. [DOI: 10.1016/j.ympev.2016.09.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 08/25/2016] [Accepted: 09/12/2016] [Indexed: 11/22/2022]
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24
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Awadi A, Suchentrunk F, Makni M, Ben Slimen H. Variation of partial transferrin sequences and phylogenetic relationships among hares (Lepus capensis, Lagomorpha) from Tunisia. Genetica 2016; 144:497-512. [PMID: 27485731 DOI: 10.1007/s10709-016-9916-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 07/11/2016] [Indexed: 10/21/2022]
Abstract
North African hares are currently included in cape hares, Lepus capensis sensu lato, a taxon that may be considered a superspecies or a complex of closely related species. The existing molecular data, however, are not unequivocal, with mtDNA control region sequences suggesting a separate species status and nuclear loci (allozymes, microsatellites) revealing conspecificity of L. capensis and L. europaeus. Here, we study sequence variation in the intron 6 (468 bp) of the transferrin nuclear gene, of 105 hares with different coat colour from different regions in Tunisia with respect to genetic diversity and differentiation, as well as their phylogenetic status. Forty-six haplotypes (alleles) were revealed and compared phylogenetically to all available TF haplotypes of various Lepus species retrieved from GenBank. Maximum Likelihood, neighbor joining and median joining network analyses concordantly grouped all currently obtained haplotypes together with haplotypes belonging to six different Chinese hare species and the African scrub hare L. saxatilis. Moreover, two Tunisian haploypes were shared with L. capensis, L timidus, L. sinensis, L. yarkandensis, and L. hainanus from China. These results indicated the evolutionary complexity of the genus Lepus with the mixing of nuclear gene haplotypes resulting from introgressive hybridization or/and shared ancestral polymorphism. We report the presence of shared ancestral polymorphism between North African and Chinese hares. This has not been detected earlier in the mtDNA sequences of the same individuals. Genetic diversity of the TF sequences from the Tunisian populations was relatively high compared to other hare populations. However, genetic differentiation and gene flow analyses (AMOVA, FST, Nm) indicated little divergence with the absence of geographically meaningful phylogroups and lack of clustering with coat colour types. These results confirm the presence of a single hare species in Tunisia, but a sound inference on its phylogenetic position would require additional nuclear markers and numerous geographically meaningful samples from Africa and Eurasia.
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Affiliation(s)
- Asma Awadi
- Unité de recherche Génomique des Insectes ravageurs des Cultures d'intérêt agronomique, Université de Tunis El Manar, Tunis, Tunisia.
| | - Franz Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Mohamed Makni
- Unité de recherche Génomique des Insectes ravageurs des Cultures d'intérêt agronomique, Université de Tunis El Manar, Tunis, Tunisia
| | - Hichem Ben Slimen
- Unité de recherche Génomique des Insectes ravageurs des Cultures d'intérêt agronomique, Université de Tunis El Manar, Tunis, Tunisia
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25
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Williford D, Deyoung RW, Honeycutt RL, Brennan LA, Hernández F. Phylogeography of the bobwhite (Colinus) quails. WILDLIFE MONOGRAPHS 2015. [DOI: 10.1002/wmon.1017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Damon Williford
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; 700 University Boulevard MSC 218; Kingsville TX 78363 USA
| | - Randy W. Deyoung
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; 700 University Boulevard MSC 218; Kingsville TX 78363 USA
| | - Rodney L. Honeycutt
- Natural Science Division; Pepperdine University, 24255 Pacific Coast Highway; Malibu CA 90263 USA
| | - Leonard A. Brennan
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; 700 University Boulevard MSC 218; Kingsville TX 78363 USA
| | - Fidel Hernández
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; 700 University Boulevard MSC 218; Kingsville TX 78363 USA
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26
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McKnight DT, Harmon JR, McKnight JL, Ligon DB. The Spring–Summer Nesting and Activity Patterns of the Western Chicken Turtle (Deirochelys reticularia miaria). COPEIA 2015. [DOI: 10.1643/ce-15-262] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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27
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Godwin JC, Lovich JE, Ennen JR, Kreiser BR, Folt B, Lechowicz C. Hybridization of Two Megacephalic Map Turtles (Testudines: Emydidae:Graptemys) in the Choctawhatchee River Drainage of Alabama and Florida. COPEIA 2014. [DOI: 10.1643/ch-13-132] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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28
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A stable niche assumption-free test of ecological divergence. Mol Phylogenet Evol 2014; 76:211-26. [DOI: 10.1016/j.ympev.2014.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 02/26/2014] [Accepted: 03/04/2014] [Indexed: 11/23/2022]
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29
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Richter SC, O'Neill EM, Nunziata SO, Rumments A, Gustin ES, Young JE, Crother BI. Cryptic Diversity and Conservation of Gopher Frogs across the Southeastern United States. COPEIA 2014. [DOI: 10.1643/cg-13-040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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30
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Ennen JR, Kalis ME, Patterson AL, Kreiser BR, Lovich JE, Godwin J, Qualls CP. Clinal variation or validation of a subspecies? A case study of theGraptemys nigrinodacomplex (Testudines: Emydidae). Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12234] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Joshua R. Ennen
- Tennessee Aquarium Conservation Institute; 201 Chestnut St. Chattanooga TN 37402 USA
| | - Marley E. Kalis
- Department of Biology; Maryville College; 502 E. Lamar Alexander Parkway Maryville TN 37804 USA
| | - Adam L. Patterson
- Department of Biology; Maryville College; 502 E. Lamar Alexander Parkway Maryville TN 37804 USA
| | - Brian R. Kreiser
- Department of Biological Sciences; University of Southern Mississippi; 118 College Dr. #5018 Hattiesburg MS 39406 USA
| | - Jeffrey E. Lovich
- U.S. Geological Survey; Southwest Biological Science Center; Flagstaff AZ 86001 USA
| | - James Godwin
- Alabama Natural Heritage Program; Environmental Institute; Auburn University; Auburn AL 36849 USA
| | - Carl P. Qualls
- Department of Biological Sciences; University of Southern Mississippi; 118 College Dr. #5018 Hattiesburg MS 39406 USA
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31
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The Status of Louisiana's Diamondback Terrapin (Malaclemys terrapin) Populations in the Wake of the Deepwater Horizon Oil Spill: Insights from Population Genetic and Contaminant Analyses. J HERPETOL 2014. [DOI: 10.1670/12-186] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Todd EV, Blair D, Jerry DR. Influence of drainage divides versus arid corridors on genetic structure and demography of a widespread freshwater turtle, Emydura macquarii krefftii, from Australia. Ecol Evol 2014; 4:606-22. [PMID: 25035802 PMCID: PMC4098141 DOI: 10.1002/ece3.968] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 01/12/2014] [Accepted: 01/14/2014] [Indexed: 11/09/2022] Open
Abstract
The influence of Pleistocene climatic cycles on Southern Hemisphere biotas is not yet well understood. Australia's eastern coastal margin provides an ideal setting for examining the relative influence of landscape development, sea level fluctuation, and cyclic climatic aridity on the evolution of freshwater biodiversity. We examined the impact of climatic oscillations and physical biogeographic barriers on the evolutionary history of the wide-ranging Krefft's river turtle (Emydura macquarii krefftii), using range-wide sampling (649 individuals representing 18 locations across 11 drainages) and analysis of mitochondrial sequences (∼1.3-kb control region and ND4) and nuclear microsatellites (12 polymorphic loci). A range of phylogeographic (haplotype networks, molecular dating), demographic (neutrality tests, mismatch distributions), and population genetic analyses (pairwise F ST, analysis of molecular variance, Bayesian clustering analysis) were implemented to differentiate between competing demographic (local persistence vs. range expansion) and biogeographic (arid corridor vs. drainage divide) scenarios. Genetic data reveal population genetic structure in Krefft's river turtles primarily reflects isolation across drainage divides. Striking north-south regional divergence (2.2% ND4 p-distance; c. 4.73 Ma, 95% higher posterior density (HPD) 2.08-8.16 Ma) was consistent with long-term isolation across a major drainage divide, not an adjacent arid corridor. Ancient divergence among regional lineages implies persistence of northern Krefft's populations despite the recurrent phases of severe local aridity, but with very low contemporary genetic diversity. Stable demography and high levels of genetic diversity are inferred for southern populations, where aridity was less extreme. Range-wide genetic structure in Krefft's river turtles reflects contemporary and historical drainage architecture, although regional differences in the extent of Plio-Pleistocene climatic aridity may be reflected in current levels of genetic diversity.
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Affiliation(s)
- Erica V Todd
- School of Marine and Tropical Biology, James Cook University Townsville, Queensland, 4810, Australia ; Centre for Tropical Water and Aquatic Ecosystem Research, James Cook University Townsville, Queensland, 4810, Australia ; Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University Townsville, Queensland, 4810, Australia
| | - David Blair
- School of Marine and Tropical Biology, James Cook University Townsville, Queensland, 4810, Australia
| | - Dean R Jerry
- School of Marine and Tropical Biology, James Cook University Townsville, Queensland, 4810, Australia ; Centre for Tropical Water and Aquatic Ecosystem Research, James Cook University Townsville, Queensland, 4810, Australia ; Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University Townsville, Queensland, 4810, Australia
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33
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Lomonte B, Tsai WC, Ureña-Diaz JM, Sanz L, Mora-Obando D, Sánchez EE, Fry BG, Gutiérrez JM, Gibbs HL, Sovic MG, Calvete JJ. Venomics of New World pit vipers: genus-wide comparisons of venom proteomes across Agkistrodon. J Proteomics 2013; 96:103-16. [PMID: 24211403 DOI: 10.1016/j.jprot.2013.10.036] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 10/24/2013] [Accepted: 10/29/2013] [Indexed: 01/21/2023]
Abstract
UNLABELLED We report a genus-wide comparison of venom proteome variation across New World pit vipers in the genus Agkistrodon. Despite the wide variety of habitats occupied by this genus and that all its taxa feed on diverse species of vertebrates and invertebrate prey, the venom proteomes of copperheads, cottonmouths, and cantils are remarkably similar, both in the type and relative abundance of their different toxin families. The venoms from all the eleven species and subspecies sampled showed relatively similar proteolytic and PLA2 activities. In contrast, quantitative differences were observed in hemorrhagic and myotoxic activities in mice. The highest myotoxic activity was observed with the venoms of A. b. bilineatus, followed by A. p. piscivorus, whereas the venoms of A. c. contortrix and A. p. leucostoma induced the lowest myotoxic activity. The venoms of Agkistrodon bilineatus subspecies showed the highest hemorrhagic activity and A. c. contortrix the lowest. Compositional and toxicological analyses agree with clinical observations of envenomations by Agkistrodon in the USA and Central America. A comparative analysis of Agkistrodon shows that venom divergence tracks phylogeny of this genus to a greater extent than in Sistrurus rattlesnakes, suggesting that the distinct natural histories of Agkistrodon and Sistrurus clades may have played a key role in molding the patterns of evolution of their venom protein genes. BIOLOGICAL SIGNIFICANCE A deep understanding of the structural and functional profiles of venoms and of the principles governing the evolution of venomous systems is a goal of venomics. Isolated proteomics analyses have been conducted on venoms from many species of vipers and pit vipers. However, making sense of these large inventories of data requires the integration of this information across multiple species to identify evolutionary and ecological trends. Our genus-wide venomics study provides a comprehensive overview of the toxic arsenal across Agkistrodon and a ground for understanding the natural histories of, and clinical observations of envenomations by, species of this genus.
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Affiliation(s)
- Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica.
| | - Wan-Chih Tsai
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Juan Manuel Ureña-Diaz
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Libia Sanz
- Laboratorio de Venómica y Proteinómica Estructural, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Diana Mora-Obando
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Elda E Sánchez
- National Natural Toxins Research Center, Department of Chemistry, Texas A&M University-Kingsville, MSC 224, 975 West Avenue B, Kingsville, TX 78363, USA
| | - Bryan G Fry
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia, Qld 4072, Australia
| | - José María Gutiérrez
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - H Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43210, USA
| | - Michael G Sovic
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43210, USA
| | - Juan J Calvete
- Laboratorio de Venómica y Proteinómica Estructural, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.
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Rödder D, Lawing AM, Flecks M, Ahmadzadeh F, Dambach J, Engler JO, Habel JC, Hartmann T, Hörnes D, Ihlow F, Schidelko K, Stiels D, Polly PD. Evaluating the significance of paleophylogeographic species distribution models in reconstructing quaternary range-shifts of nearctic chelonians. PLoS One 2013; 8:e72855. [PMID: 24130664 PMCID: PMC3794015 DOI: 10.1371/journal.pone.0072855] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 07/14/2013] [Indexed: 12/27/2022] Open
Abstract
The climatic cycles of the Quaternary, during which global mean annual temperatures have regularly changed by 5-10°C, provide a special opportunity for studying the rate, magnitude, and effects of geographic responses to changing climates. During the Quaternary, high- and mid-latitude species were extirpated from regions that were covered by ice or otherwise became unsuitable, persisting in refugial retreats where the environment was compatible with their tolerances. In this study we combine modern geographic range data, phylogeny, Pleistocene paleoclimatic models, and isotopic records of changes in global mean annual temperature, to produce a temporally continuous model of geographic changes in potential habitat for 59 species of North American turtles over the past 320 Ka (three full glacial-interglacial cycles). These paleophylogeographic models indicate the areas where past climates were compatible with the modern ranges of the species and serve as hypotheses for how their geographic ranges would have changed in response to Quaternary climate cycles. We test these hypotheses against physiological, genetic, taxonomic and fossil evidence, and we then use them to measure the effects of Quaternary climate cycles on species distributions. Patterns of range expansion, contraction, and fragmentation in the models are strongly congruent with (i) phylogeographic differentiation; (ii) morphological variation; (iii) physiological tolerances; and (iv) intraspecific genetic variability. Modern species with significant interspecific differentiation have geographic ranges that strongly fluctuated and repeatedly fragmented throughout the Quaternary. Modern species with low genetic diversity have geographic distributions that were highly variable and at times exceedingly small in the past. Our results reveal the potential for paleophylogeographic models to (i) reconstruct past geographic range modifications, (ii) identify geographic processes that result in genetic bottlenecks; and (iii) predict threats due to anthropogenic climate change in the future.
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Affiliation(s)
- Dennis Rödder
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - A. Michelle Lawing
- National Institute for Mathematical and Biological Synthesis (NIMBioS), University of Tennessee, Knoxville, Tennessee, United States of America
| | - Morris Flecks
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | | | | | - Jan O. Engler
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
- Department of Biogeography, Trier University, Trier, Germany
| | | | - Timo Hartmann
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - David Hörnes
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Flora Ihlow
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | | | - Darius Stiels
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - P. David Polly
- Department of Geological Sciences, Indiana University, Bloomington, Indiana, United States of America
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Todd EV, Blair D, Farley S, Farrington L, FitzSimmons NN, Georges A, Limpus CJ, Jerry DR. Contemporary genetic structure reflects historical drainage isolation in an Australian snapping turtle,Elseya albagula. Zool J Linn Soc 2013. [DOI: 10.1111/zoj.12049] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Erica V. Todd
- School of Marine and Tropical Biology; James Cook University; Townsville; QLD; 4810; Australia
| | - David Blair
- School of Marine and Tropical Biology; James Cook University; Townsville; QLD; 4810; Australia
| | - Sharon Farley
- Institute for Applied Ecology; University of Canberra; Canberra; ACT; 2601; Australia
| | - Lachlan Farrington
- Institute for Applied Ecology; University of Canberra; Canberra; ACT; 2601; Australia
| | - Nancy N. FitzSimmons
- Institute for Applied Ecology; University of Canberra; Canberra; ACT; 2601; Australia
| | - Arthur Georges
- Institute for Applied Ecology; University of Canberra; Canberra; ACT; 2601; Australia
| | - Colin J. Limpus
- Aquatic Threatened Species Unit; Department of Environment and Heritage Protection; Brisbane; QLD; 4001; Australia
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36
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Khannoon ER, Lunt DH, Schulz S, Hardege JD. Divergence of Scent Pheromones in Allopatric Populations ofAcanthodactylus boskianus(Squamata: Lacertidae). Zoolog Sci 2013; 30:380-5. [DOI: 10.2108/zsj.30.380] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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37
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Li P, Li M, Shi Y, Zhao Y, Wan Y, Fu C, Cameron KM. Phylogeography of North American herbaceous Smilax (Smilacaceae): Combined AFLP and cpDNA data support a northern refugium in the Driftless Area. AMERICAN JOURNAL OF BOTANY 2013; 100:801-814. [PMID: 23538874 DOI: 10.3732/ajb.1200250] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
PREMISE OF THE STUDY The genetic structure of North American herbaceous Smilax, a clade of closely related understory herbs that has a wide and disjunct distribution, was investigated to test the hypothesis of whether a northern refugium in the upper Midwest may have existed for these plants during the last glaciation. METHODS We analyzed 33 populations sampled from California and throughout the eastern United States using AFLP and chloroplast DNA sequence data. KEY RESULTS Individuals of S. jamesii from northern California formed a clade sister to the eastern North American species, and they likely diverged from each other during the Pleistocene. Among the eastern species, two lineages were found on opposite sides of the Appalachian Mountains. The populations near the "Driftless Area" contained most of the chlorotypes found in the Midwest, including a unique one endemic to this area, and the AFLP data indicated that one population from this area has the highest frequency-down-weighted-marker value. CONCLUSIONS This study, and others that have focused on mammals, amphibians, and woody plants, provides further evidence for the debate over whether the upper Midwest's "Driftless Area" may have hosted a biologically diverse northern glacial refugium. Herbaceous species of Smilax from eastern North American exhibit an Appalachian discontinuity. They appear to have persisted in multiple refugia both east and west of the Appalachians, with several populations persisting in situ through the Last Glacial Maximum (LGM). We suggest that they experienced localized expansion after the LGM, possibly followed by subsequent contact between the Midwest and the East Coastal lineages.
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Affiliation(s)
- Pan Li
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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Bonett RM, Trujano-Alvarez AL, Williams MJ, Timpe EK. Biogeography and body size shuffling of aquatic salamander communities on a shifting refuge. Proc Biol Sci 2013; 280:20130200. [PMID: 23466988 DOI: 10.1098/rspb.2013.0200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Freshwater habitats of coastal plains are refugia for many divergent vertebrate lineages, yet these environments are highly vulnerable to sea-level fluctuations, which suggest that resident communities have endured dynamic histories. Using the fossil record and a multi-locus nuclear phylogeny, we examine divergence times, biogeography, body size evolution and patterns of community assembly of aquatic salamanders from North American coastal plains since the Late Cretaceous. At least five salamander families occurred on the extensive Western Interior Coastal Plain (WICP), which existed from the Late Cretaceous through the Eocene. Four of these families subsequently colonized the emergent Southeastern Coastal Plain (SECP) by the Early Oligocene to Late Miocene. Three families ultimately survived and underwent extensive body size evolution in situ on the SECP. This included at least two major size reversals in recent taxa that are convergent with confamilial WICP ancestors. Dynamics of the coastal plain, major lineage extinctions and frequent extreme changes in body size have resulted in significant shuffling of the size structure of aquatic salamander communities on this shifting refuge since the Cretaceous.
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Affiliation(s)
- Ronald M Bonett
- Department of Biological Science, University of Tulsa, Tulsa, OK 74104, USA.
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Qu Y, Zhang R, Quan Q, Song G, Li SH, Lei F. Incomplete lineage sorting or secondary admixture: disentangling historical divergence from recent gene flow in the Vinous-throated parrotbill (Paradoxornis webbianus). Mol Ecol 2012; 21:6117-33. [DOI: 10.1111/mec.12080] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 09/03/2012] [Accepted: 09/11/2012] [Indexed: 11/26/2022]
Affiliation(s)
- Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing; 100101; China
| | - Ruiying Zhang
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing; 100101; China
| | - Qing Quan
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing; 100101; China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing; 100101; China
| | - Shou Hsien Li
- Department of Life Science; National Taiwan Normal University; Taibei; Taiwan
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing; 100101; China
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40
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Clostio RW, Martinez AM, LeBlanc KE, Anthony NM. Population genetic structure of a threatened tortoise across the south-eastern United States: implications for conservation management. Anim Conserv 2012. [DOI: 10.1111/j.1469-1795.2012.00557.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- R. W. Clostio
- Department of Biological Sciences; University of New Orleans; New Orleans; LA; USA
| | - A. M. Martinez
- Department of Biological Sciences; University of New Orleans; New Orleans; LA; USA
| | - K. E. LeBlanc
- Life Sciences Department; Louisiana State University; Baton Rouge; LA; USA
| | - N. M. Anthony
- Department of Biological Sciences; University of New Orleans; New Orleans; LA; USA
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41
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Tollis M, Ausubel G, Ghimire D, Boissinot S. Multi-locus phylogeographic and population genetic analysis of Anolis carolinensis: historical demography of a genomic model species. PLoS One 2012; 7:e38474. [PMID: 22685573 PMCID: PMC3369884 DOI: 10.1371/journal.pone.0038474] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 05/07/2012] [Indexed: 11/19/2022] Open
Abstract
The green anole (Anolis carolinensis) has been widely used as an animal model in physiology and neurobiology but has recently emerged as an important genomic model. The recent sequencing of its genome has shed new light on the evolution of vertebrate genomes and on the process that govern species diversification. Surprisingly, the patterns of genetic diversity within natural populations of this widespread and abundant North American lizard remain relatively unknown. In the present study, we use 10 novel nuclear DNA sequence loci (N = 62 to 152) and one mitochondrial locus (N = 226) to delimit green anole populations and infer their historical demography. We uncovered four evolutionarily distinct and geographically restricted lineages of green anoles using phylogenetics, bayesian clustering, and genetic distance methods. Molecular dating indicates that these lineages last shared a common ancestor ∼2 million years ago. Summary statistics and analysis of the frequency distributions of DNA polymorphisms strongly suggest range-wide expansions in population size. Using Bayesian Skyline Plots, we inferred the timing of population size expansions, which differ across lineages, and found evidence for a relatively recent and rapid westward expansion of green anoles across the Gulf Coastal Plain during the mid-Pleistocene. One surprising result is that the distribution of genetic diversity is not consistent with a latitudinal shift caused by climatic oscillations as is observed for many co-distributed taxa. This suggests that the most recent Pleistocene glacial cycles had a limited impact on the geographic distribution of the green anole at the northern limits of its range.
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Affiliation(s)
- Marc Tollis
- Biology Department, Queens College, City University of New York, Flushing, New York, United States of America
- Biology Program: Ecology, Evolutionary Biology and Behavior, Graduate Center, City University of New York, New York, New York, United States of America
| | - Gavriel Ausubel
- Biology Department, Queens College, City University of New York, Flushing, New York, United States of America
| | - Dhruba Ghimire
- Biology Department, Queens College, City University of New York, Flushing, New York, United States of America
| | - Stéphane Boissinot
- Biology Department, Queens College, City University of New York, Flushing, New York, United States of America
- Biology Program: Ecology, Evolutionary Biology and Behavior, Graduate Center, City University of New York, New York, New York, United States of America
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42
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Pouyani ER, Noureini SK, Pouyani NR, Joger U, Wink M. Molecular phylogeny and intraspecific differentiation of the Eremias velox complex of the Iranian Plateau and Central Asia (Sauria, Lacertidae). J ZOOL SYST EVOL RES 2012. [DOI: 10.1111/j.1439-0469.2012.00662.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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43
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Ortego J, Riordan EC, Gugger PF, Sork VL. Influence of environmental heterogeneity on genetic diversity and structure in an endemic southern Californian oak. Mol Ecol 2012; 21:3210-23. [PMID: 22548448 DOI: 10.1111/j.1365-294x.2012.05591.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding how specific environmental factors shape gene flow while disentangling their importance relative to the effects of geographical isolation is a major question in evolutionary biology and a specific goal of landscape genetics. Here, we combine information from nuclear microsatellite markers and ecological niche modelling to study the association between climate and spatial genetic structure and variability in Engelmann oak (Quercus engelmannii), a wind-pollinated species with high potential for gene flow. We first test whether genetic diversity is associated with climatic niche suitability and stability since the Last Glacial Maximum (LGM). Second, we use causal modelling to analyse the potential influence of climatic factors (current and LGM niche suitability) and altitude in the observed patterns of genetic structure. We found that genetic diversity is negatively associated with local climatic stability since the LGM, which may be due to higher immigration rates in unstable patches during favourable climatic periods and/or temporally varying selection. Analyses of spatial genetic structure revealed the presence of three main genetic clusters, a pattern that is mainly driven by two highly differentiated populations located in the northern edge of the species distribution range. After controlling for geographic distance, causal modelling analyses showed that genetic relatedness decreases with the environmental divergence among sampling sites estimated as altitude and current and LGM niche suitability. Natural selection against nonlocal genotypes and/or asynchrony in reproductive phenology may explain this pattern. Overall, this study suggests that local environmental conditions can shape patterns of genetic structure and variability even in species with high potential for gene flow and relatively small distribution ranges.
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Affiliation(s)
- Joaquín Ortego
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Box 957239, Los Angeles, CA 90095-7239, USA.
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44
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FREEDBERG STEVEN, MYERS ERINM. Cytonuclear equilibrium following interspecific introgression in a turtle lacking sex chromosomes. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01862.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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45
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Comparative Historical Demography of Migratory and Nonmigratory Birds from the Caribbean Island of Hispaniola. Evol Biol 2012. [DOI: 10.1007/s11692-012-9164-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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46
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Ureña-Aranda CA, de los Monteros AE. The genetic crisis of the Mexican Bolson Tortoise (Gopherus flavomarginatus: Testudinidae). AMPHIBIA-REPTILIA 2012. [DOI: 10.1163/156853811x621508] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Gopherusflavomarginatus(Testudinidae) is endemic to a series of discontinuous, isolated basins collectively known as the Bolson de Mapimí in the Chihuahuan Desert. Its numbers declined after catastrophic levels of exploitation during the mid-20th century. However currently, the Bolson Tortoise appears to be on a path to recovery owing to intensive, sustained conservation efforts. We sequenced an 842-bp-long fragment of the D-loop from 76 individuals distributed throughout the species’ range. The results revealed only two haplotypes. An AMOVA showed that 95% of the variance occurred among populations, whereas the remaining 5% was explained by genetic differences within populations. Tectonic processes together with ecological transformation during the Pleistocene and Holocene may be responsible for the reduction in this species’ genetic variation. A bottleneck during which a significant percentage of the haplotype diversity was lost would result in genetic homogeneity. Although there is demographic growth, the lack of genetic diversity is indicative of the potential crisis that the Bolson Tortoise is facing, and awareness must be brought to this situation.
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Affiliation(s)
- Cinthya Alejandra Ureña-Aranda
- Laboratorio de Sistemática Filogenética, Departamento de Biología Evolutiva, Instituto de Ecología, A. C., Carretera antigua a Coatepec No. 351, Xalapa, Veracruz 91070, México
| | - Alejandro Espinosa de los Monteros
- Laboratorio de Sistemática Filogenética, Departamento de Biología Evolutiva, Instituto de Ecología, A. C., Carretera antigua a Coatepec No. 351, Xalapa, Veracruz 91070, México
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47
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KNOX MATTHEWA, HOGG IAND, PILDITCH CONRADA. The role of vicariance and dispersal on New Zealand's estuarine biodiversity: the case of Paracorophium (Crustacea: Amphipoda). Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01675.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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48
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Suzuki D, Hikida T. Mitochondrial phylogeography of the Japanese pond turtle, Mauremys japonica (Testudines, Geoemydidae). J ZOOL SYST EVOL RES 2011. [DOI: 10.1111/j.1439-0469.2010.00577.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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49
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BUTLER JASONM, DODD jr CKENNETH, ARESCO MATT, AUSTIN JAMESD. Morphological and molecular evidence indicates that the Gulf Coast box turtle (Terrapene carolina major) is not a distinct evolutionary lineage in the Florida Panhandle. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01625.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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50
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Hewitt GM. Quaternary phylogeography: the roots of hybrid zones. Genetica 2011; 139:617-38. [DOI: 10.1007/s10709-011-9547-3] [Citation(s) in RCA: 244] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 01/03/2011] [Indexed: 10/18/2022]
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