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Wilenzik IV, Barger BB, Pyron RA. Fossil-informed biogeographic analysis suggests Eurasian regionalization in crown Squamata during the early Jurassic. PeerJ 2024; 12:e17277. [PMID: 38708352 PMCID: PMC11067913 DOI: 10.7717/peerj.17277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/01/2024] [Indexed: 05/07/2024] Open
Abstract
Background Squamata (lizards, snakes, and amphisbaenians) is a Triassic lineage with an extensive and complex biogeographic history, yet no large-scale study has reconstructed the ancestral range of early squamate lineages. The fossil record indicates a broadly Pangaean distribution by the end- Cretaceous, though many lineages (e.g., Paramacellodidae, Mosasauria, Polyglyphanodontia) subsequently went extinct. Thus, the origin and occupancy of extant radiations is unclear and may have been localized within Pangaea to specific plates, with potential regionalization to distinct Laurasian and Gondwanan landmasses during the Mesozoic in some groups. Methods We used recent tectonic models to code extant and fossil squamate distributions occurring on nine discrete plates for 9,755 species, with Jurassic and Cretaceous fossil constraints from three extinct lineages. We modeled ancestral ranges for crown Squamata from an extant-only molecular phylogeny using a suite of biogeographic models accommodating different evolutionary processes and fossil-based node constraints from known Jurassic and Cretaceous localities. We hypothesized that the best-fit models would not support a full Pangaean distribution (i.e., including all areas) for the origin of crown Squamata, but would instead show regionalization to specific areas within the fragmenting supercontinent, likely in the Northern Hemisphere where most early squamate fossils have been found. Results Incorporating fossil data reconstructs a localized origin within Pangaea, with early regionalization of extant lineages to Eurasia and Laurasia, while Gondwanan regionalization did not occur until the middle Cretaceous for Alethinophidia, Scolecophidia, and some crown Gekkotan lineages. While the Mesozoic history of extant squamate biogeography can be summarized as a Eurasian origin with dispersal out of Laurasia into Gondwana, their Cenozoic history is complex with multiple events (including secondary and tertiary recolonizations) in several directions. As noted by previous authors, squamates have likely utilized over-land range expansion, land-bridge colonization, and trans-oceanic dispersal. Tropical Gondwana and Eurasia hold more ancient lineages than the Holarctic (Rhineuridae being a major exception), and some asymmetries in colonization (e.g., to North America from Eurasia during the Cenozoic through Beringia) deserve additional study. Future studies that incorporate fossil branches, rather than as node constraints, into the reconstruction can be used to explore this history further.
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Affiliation(s)
- Ian V. Wilenzik
- Department of Biology, George Washington University, Washington D.C., United States of America
| | - Benjamin B. Barger
- Department of Biology, George Washington University, Washington D.C., United States of America
| | - R. Alexander Pyron
- Department of Biology, George Washington University, Washington D.C., United States of America
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2
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Malik S, Rashid M, Javid A, Hussain A, Bukhari SM, Suleman S, Noor R, Husaain S, Ismat N, Hussain M, Ghafoor S, Mustafa G, Ali W. Genetic variations and phylogenetic relationship of genus Uromastyx from Punjab Pakistan. BRAZ J BIOL 2021; 84:e254253. [PMID: 34816973 DOI: 10.1590/1519-6984.254253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/24/2021] [Indexed: 11/22/2022] Open
Abstract
During the present study, specimens were collected from selected sites of Cholistan desert and Kalabagh Game Reserve, Punjab province, Pakistan. Each captured specimen was tagged with voucher number and morphometric measurements were taken. The average snout to vent length was 172.559±1.40 mm and average weight was 92.1±1.30 g. The DNA of Uromastyx hardwickii was amplified and sequenced using 16S rRNA primer set. The obtained DNA sequence has shown reliable and clear species identification. After trimming ambiguous bases, the obtained 16S rRNA fragment was 520 bp while 16S rRNA fragments aligned with closely matched sequence from NCBI comprised of 510 bp. Closely matched sequences of genus Uromastyx were retrieved from NCBI in blast searches. Neighbour-joining tree of genus Uromastyx was constructed based on p-distance using MEGA X. The mean intraspecific variation was 0.095±0.01 while intraspecific variation was ranging from 0-1%. Similarly, interspecific variation of Uromastyx hardwikii with Saara asmussi, Uromastyx alfredschmidti, Uromastyx geyri, Uromastyx thomasi, Uromastyx alfredschmidti was 0-12%, 0-19%, 0-19%, 0-20%, 12-19% respectively. The newly produced DNA was submitted to NCBI and accession number was obtained (MW052563.1). Results of current study provided information about the molecular and morphological identification of Genus Uromastyx. In our recommendation, comprehensive molecular based identification of Pakistan's reptiles is required to report any new or subspecies from country.
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Affiliation(s)
- S Malik
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - M Rashid
- University of Veterinary and Animal Sciences, Faculty of Fisheries and Wildlife, Lahore, Pakistan
| | - A Javid
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - A Hussain
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - S M Bukhari
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - S Suleman
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - R Noor
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - S Husaain
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - N Ismat
- The University of Lahore, Institue of Molecular Biology and Biotechnology - IMBB, Pakistan
| | - M Hussain
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - S Ghafoor
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - G Mustafa
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - W Ali
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
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3
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Brennan IG, Lemmon AR, Lemmon EM, Portik DM, Weijola V, Welton L, Donnellan SC, Keogh JS. Phylogenomics of Monitor Lizards and the Role of Competition in Dictating Body Size Disparity. Syst Biol 2020; 70:120-132. [PMID: 32521014 DOI: 10.1093/sysbio/syaa046] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/22/2020] [Accepted: 05/27/2020] [Indexed: 12/13/2022] Open
Abstract
Organismal interactions drive the accumulation of diversity by influencing species ranges, morphology, and behavior. Interactions vary from agonistic to cooperative and should result in predictable patterns in trait and range evolution. However, despite a conceptual understanding of these processes, they have been difficult to model, particularly on macroevolutionary timescales and across broad geographic spaces. Here, we investigate the influence of biotic interactions on trait evolution and community assembly in monitor lizards (Varanus). Monitors are an iconic radiation with a cosmopolitan distribution and the greatest size disparity of any living terrestrial vertebrate genus. Between the colossal Komodo dragon Varanus komodoensis and the smallest Australian dwarf goannas, Varanus length and mass vary by multiple orders of magnitude. To test the hypothesis that size variation in this genus was driven by character displacement, we extended existing phylogenetic comparative methods which consider lineage interactions to account for dynamic biogeographic history and apply these methods to Australian monitors and marsupial predators. Incorporating both exon-capture molecular and morphological data sets we use a combined evidence approach to estimate the relationships among living and extinct varaniform lizards. Our results suggest that communities of Australian Varanus show high functional diversity as a result of continent-wide interspecific competition among monitors but not with faunivorous marsupials. We demonstrate that patterns of trait evolution resulting from character displacement on continental scales are recoverable from comparative data and highlight that these macroevolutionary patterns may develop in parallel across widely distributed sympatric groups.[Character displacement; comparative methods; phylogenetics; trait evolution; Varanus.].
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Affiliation(s)
- Ian G Brennan
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Alan R Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Daniel M Portik
- Department of Ecology and Evolution, University of Arizona, Biosciences West Rm 310, 1041 E. Lowell St, Tucson, AZ 85745 USA
| | - Valter Weijola
- Zoological Museum, Biodiversity Unit, FI-20014 University of Turku, Finland
| | - Luke Welton
- Univeristy of Kansas Biodiversity Institute & Natural History Museum, 1345 Jayhawk Blvd, Lawrence, KS 66045, USA
| | - Stephen C Donnellan
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia.,South Australian Museum, North Terrace, Adelaide SA 5000 Australia
| | - J Scott Keogh
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
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Hong S, Gim JS, Kim HG, Cowan PE, Joo GJ. A molecular approach to identifying the relationship between resource use and availability in Eurasian otters (Lutra lutra). CAN J ZOOL 2019. [DOI: 10.1139/cjz-2018-0289] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In South Korea, the Eurasian otter (Lutra lutra (Linnaeus, 1758)), a semi-aquatic carnivore, is found mainly in lower order streams that tend to have a low abundance of preferred prey fish species. To investigate the relationship between resource use and availability, we used DNA barcoding to identify otter diet items in 24 otter spraints (faeces) from 16 sites along the Nakdong River basin from 4 to 6 June 2014. At these sites fish availability was assessed using scoop nets and casting nets. Fish formed the bulk of otter diet, which included also frogs, mammals, and reptiles. By DNA barcoding (success rate: 72.38%), we identified 79 prey items from 105 bone remains. The diet comprised mostly fish, but frogs, mammals, and reptiles were also identified. The fish fauna and otter diet composition differed significantly. Across the study sites, members of the Cyprinidae dominated in netted samples, but occurred less frequently in otter diet. Because most Cyprinidae are fast swimmers, otters also fed on benthic fishes and frogs, suggesting limited foraging flexibility in otters and specialization on more slowly moving prey.
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Affiliation(s)
- Sungwon Hong
- Department of Biological Sciences, Pusan National University, Jangjeon-dong, Gumjeong-gu, Busan 46241, Republic of Korea
| | - Jeong-Soo Gim
- Department of Biological Sciences, Pusan National University, Jangjeon-dong, Gumjeong-gu, Busan 46241, Republic of Korea
| | - Hyo Gyeom Kim
- Department of Biological Sciences, Pusan National University, Jangjeon-dong, Gumjeong-gu, Busan 46241, Republic of Korea
| | - Phil E. Cowan
- Manaaki Whenua Landcare Research, Lincoln 7640, New Zealand
| | - Gea-Jae Joo
- Department of Biological Sciences, Pusan National University, Jangjeon-dong, Gumjeong-gu, Busan 46241, Republic of Korea
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Villa A, Abella J, Alba DM, Almécija S, Bolet A, Koufos GD, Knoll F, Luján ÀH, Morales J, Robles JM, Sánchez IM, Delfino M. Revision of Varanus marathonensis (Squamata, Varanidae) based on historical and new material: morphology, systematics, and paleobiogeography of the European monitor lizards. PLoS One 2018; 13:e0207719. [PMID: 30517172 PMCID: PMC6281198 DOI: 10.1371/journal.pone.0207719] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/05/2018] [Indexed: 11/20/2022] Open
Abstract
Monitor lizards (genus Varanus) inhabited Europe at least from the early Miocene to the Pleistocene. Their fossil record is limited to about 40 localities that have provided mostly isolated vertebrae. Due to the poor diagnostic value of these fossils, it was recently claimed that all the European species described prior to the 21st century are not taxonomically valid and a new species, Varanus amnhophilis, was erected on the basis of fragmentary material including cranial elements, from the late Miocene of Samos (Greece). We re-examined the type material of Varanus marathonensis Weithofer, 1888, based on material from the late Miocene of Pikermi (Greece), and concluded that it is a valid, diagnosable species. Previously unpublished Iberian material from the Aragonian (middle Miocene) of Abocador de Can Mata (Vallès-Penedès Basin, Barcelona) and the Vallesian (late Miocene) of Batallones (Madrid Basin) is clearly referable to the same species on a morphological basis, further enabling to provide an emended diagnosis for this species. Varanus amnhophilis appears to be a junior subjective synonym of V. marathonensis. On the basis of the most complete fossil Varanus skeleton ever described, it has been possible to further resolve the internal phylogeny of this genus by cladistically analyzing 80 taxa coded for 495 morphological and 5729 molecular characters. Varanus marathonensis was a large-sized species distributed at relatively low latitudes in both southwestern and southeastern Europe from at least MN7+8 to MN12. Our cladistic analysis nests V. marathonensis into an eastern clade of Varanus instead of the African clade comprising Varanus griseus, to which it had been related in the past. At least two different Varanus lineages were present in Europe during the Neogene, represented by Varanus mokrensis (early Miocene) and V. marathonensis (middle to late Miocene), respectively.
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Affiliation(s)
- Andrea Villa
- Dipartimento di Scienze della Terra, Università di Torino, Torino, Italy
| | - Juan Abella
- Universidad Estatal de la Peninsula de Santa Elena, La Libertad, Santa Elena, Ecuador
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - David M. Alba
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Sergio Almécija
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
- Division of Anthropology, American Museum of Natural History, New York, United States of America
- New York Consortium in Evolutionary Primatology, New York, United States of America
| | - Arnau Bolet
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom
| | - George D. Koufos
- Laboratory of Geology and Paleontology, Department of Geology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Fabien Knoll
- Departamento de Paleobiología, Museo Nacional de Ciencias Naturales–Consejo Superior de Investigaciones Cientificas, Madrid, Spain
- ARAID–Fundación Conjunto Paleontológico de Teruel-Dinópolis, Teruel, Spain
- School of Earth & Environmental Sciences, University of Manchester, Manchester, United Kingdom
| | - Àngel H. Luján
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
- Department of Geological Sciences, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jorge Morales
- Departamento de Paleobiología, Museo Nacional de Ciencias Naturales–Consejo Superior de Investigaciones Cientificas, Madrid, Spain
| | - Josep M. Robles
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Israel M. Sánchez
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Massimo Delfino
- Dipartimento di Scienze della Terra, Università di Torino, Torino, Italy
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
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Pinch K, Madsen T, Ujvari B. No signs of Na +
/K +
-ATPase adaptations to an invasive exotic toxic prey in native squamate predators. AUSTRAL ECOL 2017. [DOI: 10.1111/aec.12520] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Kimberly Pinch
- Centre for Integrative Ecology; School of Life and Environmental Sciences; Deakin University; Geelong Victoria 3218 Australia
| | - Thomas Madsen
- Centre for Integrative Ecology; School of Life and Environmental Sciences; Deakin University; Geelong Victoria 3218 Australia
- School of Biological Sciences; University of Wollongong; Wollongong New South Wales Australia
| | - Beata Ujvari
- Centre for Integrative Ecology; School of Life and Environmental Sciences; Deakin University; Geelong Victoria 3218 Australia
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Arida E. Genetic Divergence and Phylogenetic Relationships Among Indonesian Species of Monitor Lizards of the Genus Varanus Based on Cytochrome Oxidase I Sequences. HAYATI JOURNAL OF BIOSCIENCES 2017. [DOI: 10.1016/j.hjb.2017.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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8
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Rajpoot A, Kumar VP, Bahuguna A, Kumar D. Forensically informative nucleotide sequencing (FINS) for the first time authentication of Indian Varanus species: implication in wildlife forensics and conservation. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:892-900. [PMID: 27838947 DOI: 10.1080/24701394.2016.1202943] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Monitor lizards are Varanus species widely distributed, endangered reptile in the IUCN red data list. In India, based on the morphological and ecological characteristic, it is divided into four species viz. Bengal monitor lizard, Yellow monitor lizard, Desert monitor lizard and Water monitor lizard. These four species listed as Schedule I species in Indian Wildlife (Protection) Act 1972. This paper first attempt to present Forensically Informative Nucleotide Sequencing (FINS) for the Indian Varanus based on three mitochondrial genes. The molecular framework will be useful for the identification of Indian Varanus species and trade products derived from monitors and as such, have important applications for wildlife management and conservation. Here, we used known 14 individual skin pieces of four species of monitor lizards; the partial fragment of three mitochondrial genes (Cyt b, 12S rRNA, and 16S rRNA) were amplified for genetic study. In Cyt b, 12S rRNA and 16s rRNA, we observed, 5, 5 and 4 Haplotypes; 71, 69, and 43 Variables sites; 90, 89, and 50 Parsimony Informative sites within four species of Indian monitor lizards, respectively. Despite it, the nucleotide composition was T 26.4, C 32.8, A 29.2 and G11.6; T 18.8, C 29.7, A 34.0 and G 17.5; T 21.7, C 27.3, A 32.5 and G 18.5 in Cyt b, 12S rRNA and 16S rRNA, respectively. The neighbor joining phylogenetic tree and maximum parsimony tree of three mitochondrial genes, showed similar results and reveal that, there are two major clades are present in Indian monitor lizards.
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Affiliation(s)
- Ankita Rajpoot
- a Molecular Systematic Laboratory , Zoological Survey of India, NRC , Dehradun , Uttarakhand , India
| | - Ved Prakash Kumar
- b Forensic and Conservation Genetic Cell , Wildlife Institute of India , Dehradun , Uttarakhand , India.,c Department of Zoology , Veer Kunwar Singh University , Arrah , Bihar , India
| | - Archana Bahuguna
- a Molecular Systematic Laboratory , Zoological Survey of India, NRC , Dehradun , Uttarakhand , India
| | - Dhyanendra Kumar
- c Department of Zoology , Veer Kunwar Singh University , Arrah , Bihar , India
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Piggott MP. Evaluating the effects of laboratory protocols on eDNA detection probability for an endangered freshwater fish. Ecol Evol 2016; 6:2739-50. [PMID: 27066248 PMCID: PMC4798829 DOI: 10.1002/ece3.2083] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/11/2016] [Accepted: 02/22/2016] [Indexed: 11/07/2022] Open
Abstract
The effectiveness and accuracy of detection using environmental DNA (eDNA) is dependent on understanding the influence laboratory methods such as DNA extraction and PCR strategies have on detection probability. Ideally choice of sampling and extraction method will maximize eDNA yield and detection probability. Determining the survey effort required to reach a satisfactory detection probability (via increased PCR replicates or more sampling) could compensate for a lower eDNA yield if the sampling and extraction method has other advantages for a study, species or system. I analysed the effect of three different sampling and extraction methods on eDNA yield, detection probability and PCR replication for detecting the endangered freshwater fish Macquaria australasica from water samples. The impact of eDNA concentration, PCR strategy, target amplicon size and two marker regions: 12S (a mitochondrial gene) and 18S (a nuclear gene) was also assessed. The choice of sampling and extraction method and PCR strategy, rather than amplicon size and marker region, had the biggest effect on detection probability and PCR replication. The PCR replication effort required to achieve a detection probability of 0.95, ranged from 2 to 6 PCR replicates depending on the laboratory method used. As all methods yielded eDNA from which M. australasica was detected using the three target amplicons, differences in eDNA yield and detection probability between the three methods could be mitigated by determining the appropriate PCR replication effort. Evaluating the effect sampling and extraction methods will have on the detection probability and determining the laboratory protocols and PCR replication required to maximize detection and minimize false positives and negatives is a useful first step for eDNA occupancy studies.
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Affiliation(s)
- Maxine P. Piggott
- Division of EcologyEvolution & GeneticsResearch School of BiologyThe Australian National University44 Daley Rd Acton ACT2601Australia
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10
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Furlan EM, Gleeson D. Environmental DNA detection of redfin perch, Perca fluviatilis. CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0523-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Chilton NB, Huby-Chilton F, Koehler AV, Gasser RB, Beveridge I. The phylogenetic relationships of endemic Australasian trichostrongylin families (Nematoda: Strongylida) parasitic in marsupials and monotremes. Parasitol Res 2015; 114:3665-73. [PMID: 26156243 DOI: 10.1007/s00436-015-4594-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 06/17/2015] [Indexed: 10/23/2022]
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12
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Chaiprasertsri N, Uno Y, Peyachoknagul S, Prakhongcheep O, Baicharoen S, Charernsuk S, Nishida C, Matsuda Y, Koga A, Srikulnath K. Highly species-specific centromeric repetitive DNA sequences in lizards: molecular cytogenetic characterization of a novel family of satellite DNA sequences isolated from the water monitor lizard (Varanus salvator macromaculatus, Platynota). J Hered 2014; 104:798-806. [PMID: 24129994 DOI: 10.1093/jhered/est061] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Two novel repetitive DNA sequences, VSAREP1 and VSAREP2, were isolated from the water monitor lizard (Varanus salvator macromaculatus, Platynota) and characterized using molecular cytogenetics. The respective lengths and guanine-cytosine (GC) contents of the sequences were 190 bp and 57.5% for VSAREP1 and 185 bp and 59.7% for VSAREP2, and both elements were tandemly arrayed as satellite DNA in the genome. VSAREP1 and VSAREP2 were each located at the C-positive heterochromatin in the pericentromeric region of chromosome 2q, the centromeric region of chromosome 5, and 3 pairs of microchromosomes. This suggests that genomic compartmentalization between macro- and microchromosomes might not have occurred in the centromeric repetitive sequences of V. salvator macromaculatus. These 2 sequences did only hybridize to genomic DNA of V. salvator macromaculatus, but no signal was observed even for other squamate reptiles, including Varanus exanthematicus, which is a closely related species of V. salvator macromaculatus. These results suggest that these sequences were differentiated rapidly or were specifically amplified in the V. salvator macromaculatus genome.
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Affiliation(s)
- Nampech Chaiprasertsri
- the Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
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13
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Matsubara K, Sarre SD, Georges A, Matsuda Y, Marshall Graves JA, Ezaz T. Highly differentiated ZW sex microchromosomes in the Australian Varanus species evolved through rapid amplification of repetitive sequences. PLoS One 2014; 9:e95226. [PMID: 24743344 PMCID: PMC3990592 DOI: 10.1371/journal.pone.0095226] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 03/24/2014] [Indexed: 11/20/2022] Open
Abstract
Transitions between sex determination systems have occurred in many lineages of squamates and it follows that novel sex chromosomes will also have arisen multiple times. The formation of sex chromosomes may be reinforced by inhibition of recombination and the accumulation of repetitive DNA sequences. The karyotypes of monitor lizards are known to be highly conserved yet the sex chromosomes in this family have not been fully investigated. Here, we compare male and female karyotypes of three Australian monitor lizards, Varanus acanthurus, V. gouldii and V. rosenbergi, from two different clades. V. acanthurus belongs to the acanthurus clade and the other two belong to the gouldii clade. We applied C-banding and comparative genomic hybridization to reveal that these species have ZZ/ZW sex micro-chromosomes in which the W chromosome is highly differentiated from the Z chromosome. In combination with previous reports, all six Varanus species in which sex chromosomes have been identified have ZZ/ZW sex chromosomes, spanning several clades on the varanid phylogeny, making it likely that the ZZ/ZW sex chromosome is ancestral for this family. However, repetitive sequences of these ZW chromosome pairs differed among species. In particular, an (AAT)n microsatellite repeat motif mapped by fluorescence in situ hybridization on part of W chromosome in V. acanthurus only, whereas a (CGG)n motif mapped onto the W chromosomes of V. gouldii and V. rosenbergi. Furthermore, the W chromosome probe for V. acanthurus produced hybridization signals only on the centromeric regions of W chromosomes of the other two species. These results suggest that the W chromosome sequences were not conserved between gouldii and acanthurus clades and that these repetitive sequences have been amplified rapidly and independently on the W chromosome of the two clades after their divergence.
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Affiliation(s)
- Kazumi Matsubara
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, Australia
| | - Stephen D. Sarre
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, Australia
| | - Yoichi Matsuda
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | | | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, Australia
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Monod L, Prendini L. Evidence for Eurogondwana: the roles of dispersal, extinction and vicariance in the evolution and biogeography of Indo-Pacific Hormuridae (Scorpiones: Scorpionoidea). Cladistics 2014; 31:71-111. [DOI: 10.1111/cla.12067] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Lionel Monod
- Département des arthropodes et d'entomologie I; Muséum d'histoire naturelle; Route de Malagnou 1 1208 Genève Switzerland
- Division of Invertebrate Zoology; American Museum of Natural History; Central Park West at 79th Street New York NY 10024-5192 USA
| | - Lorenzo Prendini
- Division of Invertebrate Zoology; American Museum of Natural History; Central Park West at 79th Street New York NY 10024-5192 USA
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Welton LJ, Wood PL, Oaks JR, Siler CD, Brown RM. Fossil-calibrated phylogeny and historical biogeography of Southeast Asian water monitors (Varanus salvator Complex). Mol Phylogenet Evol 2014; 74:29-37. [PMID: 24486878 DOI: 10.1016/j.ympev.2014.01.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 01/11/2014] [Accepted: 01/17/2014] [Indexed: 11/25/2022]
Abstract
We utilize robust geographical genetic sampling, a multilocus dataset, a new synthesis of numerous fossil calibration points, a time-calibrated phylogeny, and the Dispersal-Extinction-Cladogenesis model to test the prediction that widespread Southeast Asian water monitor species initially diversified on the Asian mainland and subsequently invaded the island archipelagos of the Philippines, Sundaland, and Wallacea. Our results strongly contradict these expectations and instead infer an initial water monitor radiation of range-restricted but highly divergent evolutionary lineages (now recognized as endemic species) in one archipelago around 3.6 mya, followed by an out-of-the-Philippines reinvasion of the mainland (2.2 mya), resulting in a few, widespread species that now inhabit most the islands of the Sunda Shelf and the Southeast Asian mainland as far north as Myanmar, as well as an out-of-the-Philippines invasion of Sulawesi (2.1 mya). Our analyses both confirm the importance of island archipelagos as drivers of diversification for mainland biodiversity and emphasize the global evolutionary significance and conservation priority of the Philippines for understanding processes of diversification in island archipelagos.
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Affiliation(s)
- Luke J Welton
- Department of Biology, Brigham Young University, Provo, UT 84602, USA; Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7561, USA.
| | - Perry L Wood
- Department of Biology, Brigham Young University, Provo, UT 84602, USA.
| | - Jamie R Oaks
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7561, USA.
| | - Cameron D Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK 73072-7029, USA.
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7561, USA.
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Jensen B, Moorman AFM, Wang T. Structure and function of the hearts of lizards and snakes. Biol Rev Camb Philos Soc 2013; 89:302-36. [DOI: 10.1111/brv.12056] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 06/26/2013] [Accepted: 07/30/2013] [Indexed: 12/20/2022]
Affiliation(s)
- Bjarke Jensen
- Department of Bioscience, Zoophysiology; Aarhus University; Aarhus C 8000 Denmark
- Department of Anatomy, Embryology & Physiology, Academic Medical Center; University of Amsterdam; Amsterdam 1105 The Netherlands
| | - Antoon F. M. Moorman
- Department of Anatomy, Embryology & Physiology, Academic Medical Center; University of Amsterdam; Amsterdam 1105 The Netherlands
| | - Tobias Wang
- Department of Bioscience, Zoophysiology; Aarhus University; Aarhus C 8000 Denmark
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Welton LJ, Siler CD, Oaks JR, Diesmos AC, Brown RM. Multilocus phylogeny and Bayesian estimates of species boundaries reveal hidden evolutionary relationships and cryptic diversity in Southeast Asian monitor lizards. Mol Ecol 2013; 22:3495-510. [DOI: 10.1111/mec.12324] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 03/17/2013] [Accepted: 03/19/2013] [Indexed: 11/28/2022]
Affiliation(s)
- L. J. Welton
- Department of Biology; Brigham Young University; Provo UT 84602 USA
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045-7561 USA
| | - C. D. Siler
- Department of Biology; University of South Dakota; Vermillion SD 57069 USA
| | - J. R. Oaks
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045-7561 USA
| | - A. C. Diesmos
- Herpetology Section; Zoology Division; Philippine National Museum; Rizal Park, Burgos Street Manila Philippines
| | - R. M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045-7561 USA
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18
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Grechko VV. The problems of molecular phylogenetics with the example of squamate reptiles: Mitochondrial DNA markers. Mol Biol 2013. [DOI: 10.1134/s0026893313010056] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Vidal N, Marin J, Sassi J, Battistuzzi FU, Donnellan S, Fitch AJ, Fry BG, Vonk FJ, Rodriguez de la Vega RC, Couloux A, Hedges SB. Molecular evidence for an Asian origin of monitor lizards followed by Tertiary dispersals to Africa and Australasia. Biol Lett 2012; 8:853-5. [PMID: 22809723 PMCID: PMC3441001 DOI: 10.1098/rsbl.2012.0460] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 06/26/2012] [Indexed: 11/12/2022] Open
Abstract
Monitor lizards are emblematic reptiles that are widely distributed in the Old World. Although relatively well studied in vertebrate research, their biogeographic history is still controversial. We constructed a molecular dataset for 54 anguimorph species, including representatives of all families with detailed sampling of the Varanidae (38 species). Our results are consistent with an Asian origin of the Varanidae followed by a dispersal to Africa 41 (49-33) Ma, possibly via an Iranian route. Another major event was the dispersal of monitors to Australia in the Late Eocene-Oligocene 32 (39-26) Ma. This divergence estimate adds to the suggestion that Australia was colonized by several squamate lineages prior to the collision of the Australian plate with the Asian plate starting 25 Ma.
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Affiliation(s)
- Nicolas Vidal
- Département Systématique et Evolution, UMR 7138, C.P. 26, Muséum National d'Histoire Naturelle, 57 Rue Cuvier, 75231 Paris Cedex 05, France.
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Kupriyanova N, Shibalev D, Voronov A, Netchvolodov K, Kurako T, Ryskov A. Vertebrate evolution reflected in the evolution of nuclear ribosomal internal transcribed spacer 2. Gene 2012; 508:85-91. [DOI: 10.1016/j.gene.2012.07.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Revised: 07/10/2012] [Accepted: 07/17/2012] [Indexed: 10/28/2022]
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Ujvari B, Mun HC, Conigrave AD, Bray A, Osterkamp J, Halling P, Madsen T. ISOLATION BREEDS NAIVETY: ISLAND LIVING ROBS AUSTRALIAN VARANID LIZARDS OF TOAD-TOXIN IMMUNITY VIA FOUR-BASE-PAIR MUTATION. Evolution 2012; 67:289-94. [DOI: 10.1111/j.1558-5646.2012.01751.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Conrad JL, Balcarcel AM, Mehling CM. Earliest example of a giant monitor lizard (Varanus, Varanidae, Squamata). PLoS One 2012; 7:e41767. [PMID: 22900001 PMCID: PMC3416840 DOI: 10.1371/journal.pone.0041767] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Accepted: 06/27/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Varanidae is a clade of tiny (<20 mm pre-caudal length [PCL]) to giant (>600 mm PCL) lizards first appearing in the Cretaceous. True monitor lizards (Varanus) are known from diagnostic remains beginning in the early Miocene (Varanus rusingensis), although extremely fragmentary remains have been suggested as indicating earlier Varanus. The paleobiogeographic history of Varanus and timing for origin of its gigantism remain uncertain. METHODOLOGY/PRINCIPAL FINDINGS A new Varanus from the Mytilini Formation (Turolian, Miocene) of Samos, Greece is described. The holotype consists of a partial skull roof, right side of a braincase, partial posterior mandible, fragment of clavicle, and parts of six vertebrae. A cladistic analysis including 83 taxa coded for 5733 molecular and 489 morphological characters (71 previously unincluded) demonstrates that the new fossil is a nested member of an otherwise exclusively East Asian Varanus clade. The new species is the earliest-known giant (>600 mm PCL) terrestrial lizard. Importantly, this species co-existed with a diverse continental mammalian fauna. CONCLUSIONS/SIGNIFICANCE The new monitor is larger (longer) than 99% of known fossil and living lizards. Varanus includes, by far, the largest limbed squamates today. The only extant non-snake squamates that approach monitors in maximum size are the glass-snake Pseudopus and the worm-lizard Amphisbaena. Mosasauroids were larger, but exclusively marine, and occurred only during the Late Cretaceous. Large, extant, non-Varanus, lizards are limbless and/or largely isolated from mammalian competitors. By contrast, our new Varanus achieved gigantism in a continental environment populated by diverse eutherian mammal competitors.
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Affiliation(s)
- Jack L Conrad
- Anatomy Department, New York College of Osteopathic Medicine, Old Westbury, New York, United States of America.
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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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Abstract
Abstract
The forces acting on the vertebral column of varanid lizards differ greatly during swimming and walking. To examine the long-term impact of these forces, the dorsal vertebrae of terrestrial and aquatic species of Varanus were compared using 3-D laser scanning and morphometric analysis. There were significant differences between the two groups in vertebral anatomical features, particularly in the articular surfaces. Further analysis demonstrated that the dorsal vertebrae could be significantly divided into three groups of nearly equal size: the sternal group (dorsal vertebrae 1–7), the middle group (dorsal vertebrae 8–14), and the pelvic group (dorsal vertebrae 15–22). Within each of these groups there was significant differences between the terrestrial and aquatic species; these differences were least in the more conserved sternal region and greatest in the highly variable pelvic region. The results suggest that vertebral morphometrics can be used as a tool to further delineate the habitat preferences of extinct varanoid lizards, and could serve to highlight the functional transitions between terrestrial and aquatic species.
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Affiliation(s)
- Amy Burnell
- Department of Physical Therapy, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Sean Collins
- Department of Physical Therapy, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Bruce A. Young
- Department of Physical Therapy, University of Massachusetts Lowell, Lowell, MA, 01854, USA
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25
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The Power and Utility Of Morphological Characters In Systematics: A Fully Resolved Phylogeny of Xenosaurus and Its Fossil Relatives (Squamata: Anguimorpha). ACTA ACUST UNITED AC 2011. [DOI: 10.3099/0027-4100-160.3.65] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Gilbert C, Hernandez SS, Flores-Benabib J, Smith EN, Feschotte C. Rampant horizontal transfer of SPIN transposons in squamate reptiles. Mol Biol Evol 2011; 29:503-15. [PMID: 21771716 DOI: 10.1093/molbev/msr181] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Transposable elements (TEs) are highly abundant in the genome and capable of mobility, two properties that make them particularly prone to transfer horizontally between organisms. Although the impact of horizontal transfer (HT) of TEs is well recognized in prokaryotes, the frequency of this phenomenon and its contribution to genome evolution in eukaryotes remain poorly appreciated. Here, we provide evidence that a DNA transposon called SPIN has colonized the genome of 17 species of reptiles representing nearly every major lineage of squamates, including 14 families of lizards, snakes, and amphisbaenians. Slot blot analyses indicate that SPIN has amplified to high copy numbers in most of these species, ranging from 2,000-28,000 copies per haploid genome. In contrast, we could not detect the presence of SPIN in any of the turtles (seven species from seven families) and crocodiles (four species) examined. Genetic distances between SPIN sequences from species belonging to different squamate families are consistently very low (average = 0.1), considering the deep evolutionary divergence of the families investigated (most are >100 My diverged). Furthermore, these distances fall below interfamilial distances calculated for two genes known to have evolved under strong functional constraint in vertebrates (RAG1, average = 0.24 and C-mos, average = 0.27). These data, combined with phylogenetic analyses, indicate that the widespread distribution of SPIN among squamates is the result of at least 13 independent events of HTs. Molecular dating and paleobiogeographical data suggest that these transfers took place during the last 50 My on at least three different continents (North America, South America and, Africa). Together, these results triple the number of known SPIN transfer events among tetrapods, provide evidence for a previously hypothesized transoceanic movement of SPIN transposons during the Cenozoic, and further underscore the role of HT in the evolution of vertebrate genomes.
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Voronov AS, Shibalev DV, Kupriyanova NS. Evolutionary relationships between reptiles inferred from the comparison of their ITS2 sequences. RUSS J GENET+ 2011. [DOI: 10.1134/s1022795411060160] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Conrad JL, Ast JC, Montanari S, Norell MA. A combined evidence phylogenetic analysis of Anguimorpha (Reptilia: Squamata). Cladistics 2010; 27:230-277. [DOI: 10.1111/j.1096-0031.2010.00330.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Hardy CM, Krull ES, Hartley DM, Oliver RL. Carbon source accounting for fish using combined DNA and stable isotope analyses in a regulated lowland river weir pool. Mol Ecol 2009; 19:197-212. [PMID: 19912537 DOI: 10.1111/j.1365-294x.2009.04411.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Determining the source and flow of carbon, energy and nutrients through food webs is essential for understanding ecological connectivity and thus determining the impact of management practices on biodiversity. We combined DNA sequencing, microarrays and stable isotope analyses to test whether this approach would allow us to resolve the carbon flows through food webs in a weir pool on the lower Murray River, a highly impacted, complex and regulated ecosystem in southern Australia. We demonstrate that small fish in the Murray River consume a wide range of food items, but that a significant component of carbon and nitrogen entering the food web during dry periods in summer, but not spring, is derived from nonconventional sources other than in-channel primary producers. This study also showed that isotopic analyses alone cannot distinguish food sources and that a combined approach is better able to elucidate food-consumer dynamics. Our results highlight that a major river ecosystem, stressed by reduced environmental flows, can rapidly undergo significant and previously undetected changes that impact on the ecology of the system as a whole.
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Affiliation(s)
- Christopher M Hardy
- CSIRO Water for a Healthy Country National Research Flagship, GPO Box 1700, Canberra, ACT 2601, Australia.
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Hocknull SA, Piper PJ, van den Bergh GD, Due RA, Morwood MJ, Kurniawan I. Dragon's paradise lost: palaeobiogeography, evolution and extinction of the largest-ever terrestrial lizards (Varanidae). PLoS One 2009; 4:e7241. [PMID: 19789642 PMCID: PMC2748693 DOI: 10.1371/journal.pone.0007241] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Accepted: 08/24/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The largest living lizard species, Varanus komodoensis Ouwens 1912, is vulnerable to extinction, being restricted to a few isolated islands in eastern Indonesia, between Java and Australia, where it is the dominant terrestrial carnivore. Understanding how large-bodied varanids responded to past environmental change underpins long-term management of V. komodoensis populations. METHODOLOGY/PRINCIPAL FINDINGS We reconstruct the palaeobiogeography of Neogene giant varanids and identify a new (unnamed) species from the island of Timor. Our data reject the long-held perception that V. komodoensis became a giant because of insular evolution or as a specialist hunter of pygmy Stegodon. Phyletic giantism, coupled with a westward dispersal from mainland Australia, provides the most parsimonious explanation for the palaeodistribution of V. komodoensis and the newly identified species of giant varanid from Timor. Pliocene giant varanid fossils from Australia are morphologically referable to V. komodoensis suggesting an ultimate origin for V. komodoensis on mainland Australia (>3.8 million years ago). Varanus komodoensis body size has remained stable over the last 900,000 years (ka) on Flores, a time marked by major faunal turnovers, extinction of the island's megafauna, the arrival of early hominids by 880 ka, co-existence with Homo floresiensis, and the arrival of modern humans by 10 ka. Within the last 2000 years their populations have contracted severely. CONCLUSIONS/SIGNIFICANCE Giant varanids were once a ubiquitous part of Subcontinental Eurasian and Australasian faunas during the Neogene. Extinction played a pivotal role in the reduction of their ranges and diversity throughout the late Quaternary, leaving only V. komodoensis as an isolated long-term survivor. The events over the last two millennia now threaten its future survival.
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Affiliation(s)
- Scott A Hocknull
- Geosciences, Queensland Museum, Brisbane, Queensland, Australia.
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Böhme W, Ziegler T. A review of iguanian and anguimorph lizard genitalia (Squamata: Chamaeleonidae; Varanoidea, Shinisauridae, Xenosauridae, Anguidae) and their phylogenetic significance: comparisons with molecular data sets. J ZOOL SYST EVOL RES 2009. [DOI: 10.1111/j.1439-0469.2008.00495.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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The Liang Bua faunal remains: a 95k.yr. sequence from Flores, East Indonesia. J Hum Evol 2008; 57:527-37. [PMID: 19058833 DOI: 10.1016/j.jhevol.2008.08.015] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Revised: 05/27/2008] [Accepted: 08/20/2008] [Indexed: 11/20/2022]
Abstract
Excavations at Liang Bua, a limestone cave on the island of Flores, East Indonesia, have yielded a well-dated archaeological and faunal sequence spanning the last 95k.yr., major climatic fluctuations, and two human species -H. floresiensis from 95 to 17k.yr.(1), and modern humans from 11k.yr. to the present. The faunal assemblage comprises well-preserved mammal, bird, reptile and mollusc remains, including examples of island gigantism in small mammals and the dwarfing of large taxa. Together with evidence from Early-Middle Pleistocene sites in the Soa Basin, it confirms the long-term isolation, impoverishment, and phylogenetic continuity of the Flores faunal community. The accumulation of Stegodon and Komodo dragon remains at the site in the Pleistocene is attributed to Homo floresiensis, while predatory birds, including an extinct species of owl, were largely responsible for the accumulation of the small vertebrates. The disappearance from the sequence of the two large-bodied, endemic mammals, Stegodon florensis insularis and Homo floresiensis, was associated with a volcanic eruption at 17 ka and precedes the earliest evidence for modern humans, who initiated use of mollusc and shell working, and began to introduce a range of exotic animals to the island. Faunal introductions during the Holocene included the Sulawesi warty pig (Sus celebensis) at about 7ka, followed by the Eurasian pig (Sus scrofa), Long-tailed macaque, Javanese porcupine, and Masked palm civet at about 4ka, and cattle, deer, and horse - possibly by the Portuguese within historic times. The Holocene sequence at the site also documents local faunal extinctions - a result of accelerating human population growth, habitat loss, and over-exploitation.
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Kosushkin SA, Borodulina OR, Solovyeva EN, Grechko VV. A family of short retroposons (Squam1) from squamate reptiles (Reptilia: Squamata): Structure, evolution, and correlation with phylogeny. Mol Biol 2008. [DOI: 10.1134/s002689330806006x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Conrad JL. Phylogeny And Systematics Of Squamata (Reptilia) Based On Morphology. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2008. [DOI: 10.1206/310.1] [Citation(s) in RCA: 318] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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RAWLINGS LESLEYH, RABOSKY DANIELL, DONNELLAN STEPHENC, HUTCHINSON MARKN. Python phylogenetics: inference from morphology and mitochondrial DNA. Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.2007.00904.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Thompson GG, Clemente CJ, Withers PC, Fry BG, Norman JA. Is body shape of varanid lizards linked with retreat choice? AUST J ZOOL 2008. [DOI: 10.1071/zo08030] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In our earlier analysis of Varanus body shape, size was a dominating factor with some qualitative phylogenetic patterns and grouping of species into ecological categories. With a phylogeny and an improved capacity to account for the effects of size, we have reanalysed our morphometric data for male Australian goannas (Varanus spp.) using an increased number of specimens and species to examine whether variations in body shape can be accounted for by retreat choice, as it can for Western Australian Ctenophorus dragon lizards. After accounting for body size in the current analysis, four ecotypes based on retreat choice (i.e. those that retreat to oblique crevices between large rocks or rock faces, those that retreat to burrows dug into the ground, those that retreat to spaces under rocks or in tree hollows, and those that retreat to trees but not tree hollows) accounted for much of the variation in body shape. There is a phylogenetic pattern to the ecotypes, but accounting for phylogenetic effects did not weaken the link between body shape and ecotype based on retreat choice. This suggests that there are large differences in body shape among ecotypes, and shape is relatively independent of phylogeny. The strong link between shape and choice of retreat site in Varanus spp. is consistent with that for Ctenophorus spp. We speculate on why there might be a strong link between retreat choice and body shape for both Varanus and Ctenophorus.
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Amer SAM, Kumazawa Y. Timing of a mtDNA gene rearrangement and intercontinental dispersal of varanid lizards. Genes Genet Syst 2008; 83:275-80. [DOI: 10.1266/ggs.83.275] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Sayed A. M. Amer
- Zoology Department, Faculty of Science, Cairo University
- Graduate School of Science, Nagoya University
| | - Yoshinori Kumazawa
- Graduate School of Science, Nagoya University
- Graduate School of Natural Sciences, Nagoya City University
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Molecular phylogeography of Rosenberg's goanna (Reptilia: Varanidae:Varanus rosen bergi) and its conservation status in New South Wales. SYST BIODIVERS 2007. [DOI: 10.1017/s1477200007002460] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Piskurek O, Austin CC, Okada N. Sauria SINEs: Novel short interspersed retroposable elements that are widespread in reptile genomes. J Mol Evol 2006; 62:630-44. [PMID: 16612539 DOI: 10.1007/s00239-005-0201-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2005] [Accepted: 12/16/2005] [Indexed: 10/24/2022]
Abstract
SINEs are short interspersed retrotransposable elements that invade new genomic sites. Their retrotransposition depends on reverse transcriptase and endonuclease activities encoded by partner LINEs (long interspersed elements). Recent genomic research has demonstrated that retroposons account for at least 40% of the human genome. Hitherto, more than 30 families of SINEs have been characterized in mammalian genomes, comprising approximately 4600 extant species; the distribution and extent of SINEs in reptilian genomes, however, are poorly documented. With more than 7400 species of lizards and snakes, Squamata constitutes the largest and most diverse group of living reptiles. We have discovered and characterized a novel SINE family, Sauria SINEs, whose members are widely distributed among genomes of lizards, snakes, and tuataras. Sauria SINEs comprise a 5' tRNA-related region, a tRNA-unrelated region, and a 3' tail region (containing short tandem repeats) derived from LINEs. We distinguished eight Sauria SINE subfamilies in genomes of four major squamate lineages and investigated their evolutionary relationships. Our data illustrate the overall efficacy of Sauria SINEs as novel retrotransposable markers for elucidation of squamate evolutionary history. We show that all Sauria SINEs share an identical 3' sequence with Bov-B LINEs and propose that they utilize the enzymatic machinery of Bov-B LINEs for their own retrotransposition. This finding, along with the ubiquity of Bov-B LINEs previously demonstrated in squamate genomes, suggests that these LINEs have been an active partner of Sauria SINEs since this SINE family was generated more than 200 million years ago.
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Affiliation(s)
- Oliver Piskurek
- Faculty of Bioscience and Biotechnology, Department of Biological Sciences, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Yokohama, 226-8501, Japan
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Fitch AJ, Goodman AE, Donnellan SC. A molecular phylogeny of the Australian monitor lizards (Squamata:Varanidae) inferred from mitochondrial DNA sequences. AUST J ZOOL 2006. [DOI: 10.1071/zo05038] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
To date no complete phylogeny of all of the currently recognised Indo-Australian varanid species and subspecies has been published. This paper presents a comprehensive mitochondrial gene phylogeny of these lizards. A portion of the mitochondrial genome comprising part of the ND4 gene and three adjacent tRNA genes (hereafter referred to as ND4) was analysed alone and, for a subset of the taxa, combined with previously published mitochondrial data. Similar tree topologies were produced by both datasets although combining the data helped resolve some of the unresolved or weakly supported nodes in the ND4 analyses. The monophyly of the Indo-Australian group was strongly supported in all analyses. This group comprised three major lineages: the gouldii group, the Odatria group and the varius group. Mitochondrial ND4 nucleotide sequences were successfully amplified from all of the Indo-Australian monitor species and subspecies currently recognised and, as such, is the first comprehensive phylogenetic study of the Australian monitor lizards published. Analysis of the tempo of diversification and evolution of preferred habitat use identified six episodes of increased net speciation rate, with two closely adjacent episodes showing the highest rates of diversification and correlating with the appearance of all preferred habitat types. The comprehensive molecular phylogenetic framework will also be useful for the identification of varanid species and traded products derived from monitors and, as such, has important applications for wildlife management and conservation.
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HANLEY TC, CACCONE A. Development of primers to characterize the mitochondrial control region of Galápagos land and marine iguanas (ConolophusandAmblyrhynchus). ACTA ACUST UNITED AC 2005. [DOI: 10.1111/j.1471-8286.2005.01004.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Amer SAM, Kumazawa Y. Mitochondrial genome of Pogona vitticepes (Reptilia; Agamidae): control region duplication and the origin of Australasian agamids. Gene 2005; 346:249-56. [PMID: 15716001 DOI: 10.1016/j.gene.2004.11.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Revised: 10/30/2004] [Accepted: 11/17/2004] [Indexed: 10/25/2022]
Abstract
The complete mitochondrial DNA sequence for an Australian agamid Pogona vitticepes was determined. Twenty-two tRNA genes, two rRNA genes, thirteen protein-coding genes, and two control regions were identified in this mitochondrial genome. The second control region was inserted between NADH dehydrogenase subunits 5 and 6 genes. The duplication of the control region was found in all Australasian agamids examined and was not found in other Asian or African taxa. The two control regions had nearly identical sequences within species but they were divergent among species, suggesting their concerted sequence evolution. Phylogenetic analyses including divergence time estimation without assuming the molecular clock suggested that the duplication of the control region occurred on a lineage leading to the Australasian agamids 25-45 million years ago after their divergence from a Southeast Asian Physignathus cocincinus. Our finding thus supports the recent dispersal origin of Australasian agamids in connection with plate tectonic movement of Australia to the proximity of Southeast Asia.
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Affiliation(s)
- Sayed A M Amer
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.
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GOULD GINAC, MacFADDEN BRUCEJ. Chapter 17: Gigantism, Dwarfism, and Cope's Rule: “Nothing in Evolution Makes Sense without a Phylogeny”. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2004. [DOI: 10.1206/0003-0090(2004)285<0219:c>2.0.co;2] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Cox RM, Skelly SL, John-Alder HB. A comparative test of adaptive hypotheses for sexual size dimorphism in lizards. Evolution 2003; 57:1653-69. [PMID: 12940368 DOI: 10.1111/j.0014-3820.2003.tb00371.x] [Citation(s) in RCA: 198] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It is commonly argued that sexual size dimorphism (SSD) in lizards has evolved in response to two primary, nonexclusive processes: (1) sexual selection for large male size, which confers an advantage in intrasexual mate competition (intrasexual selection hypothesis), and (2) natural selection for large female size, which confers a fecundity advantage (fecundity advantage hypothesis). However, outside of several well-studied lizard genera, the empirical support for these hypotheses has not been examined with appropriate phylogenetic control. We conducted a comparative phylogenetic analysis to test these hypotheses using literature data from 497 lizard populations representing 302 species and 18 families. As predicted by the intrasexual selection hypothesis, male aggression and territoriality are correlated with SSD, but evolutionary shifts in these categorical variables each explain less than 2% of the inferred evolutionary change in SSD. We found stronger correlations between SSD and continuous estimates of intrasexual selection such as male to female home range ratio and female home range size. These results are consistent with the criticism that categorical variables may obscure much of the actual variation in intrasexual selection intensity needed to explain patterns in SSD. In accordance with the fecundity advantage hypothesis, SSD is correlated with clutch size, reproductive frequency, and reproductive mode (but not fecundity slope, reduced major axis estimator of fecundity slope, length of reproductive season, or latitude). However, evolutionary shifts in clutch size explain less than 8% of the associated change in SSD, which also varies significantly in the absence of evolutionary shifts in reproductive frequency and mode. A multiple regression model retained territoriality and clutch size as significant predictors of SSD, but only 16% of the variation in SSD is explained using these variables. Intrasexual selection for large male size and fecundity selection for large female size have undoubtedly helped to shape patterns of SSD across lizards, but the comparative data at present provide only weak support for these hypotheses as general explanations for SSD in this group. Future work would benefit from the consideration of alternatives to these traditional evolutionary hypotheses, and the elucidation of proximate mechanisms influencing growth and SSD within populations.
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Affiliation(s)
- Robert M Cox
- Program in Ecology and Evolution, Rutgers University, New Brunswick, New Jersey 08901, USA.
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Honda M, Ota H, Köhler G, Ineich I, Chirio L, Chen SL, Hikida T. Phylogeny of the lizard subfamily Lygosominae (Reptilia: Scincidae), with special reference to the origin of the new world taxa. Genes Genet Syst 2003; 78:71-80. [PMID: 12655139 DOI: 10.1266/ggs.78.71] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Phylogenetic relationships of the three lygosomine skink genera occurring both in the Old World and the New World (Mabuya, Scincella and Sphenomorphus) were inferred from mitochondrial DNA sequence of 12S and 16S rRNA genes. Results strongly suggested the non-monophyly for any of these three genera. Within the Mabuya group, Asian members appear to have diverged first, leaving the Neotropical and the Afro-Malagasy Mabuya as sister groups. These relationships, together with the absence of extant or fossil representatives of the Mabuya group from North America, strongly suggest the trans-Atlantic dispersals of Mabuya from Africa to Neotropics. Our results also indicated a closer affinity of the New World Scincella with the New World Sphenomorphus than with the Old World Scincella. Such relationships suggest the trans-Beringian dispersal of the common ancestor from Asia and its subsequent divergence into the North American Scincella and the Neotropical Sphenomorphus.
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Affiliation(s)
- Masanao Honda
- School of Allied Medical Sciences, Shinshu University, Asahi, Matsumoto, Nagano, Japan.
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Cox RM, Skelly SL, John-Alder HB. A COMPARATIVE TEST OF ADAPTIVE HYPOTHESES FOR SEXUAL SIZE DIMORPHISM IN LIZARDS. Evolution 2003. [DOI: 10.1554/02-227] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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OTA HIDETOSHI, HONDA MASANAO, CHEN SZULUNG, HIKIDA TSUTOMU, PANHA SOMSAK, OH HONGSHIK, MATSUI MASAFUMI. Phylogenetic relationships, taxonomy, character evolution and biogeography of the lacertid lizards of the genus Takydromus (Reptilia: Squamata): a molecular perspective. Biol J Linn Soc Lond 2002. [DOI: 10.1046/j.1095-8312.2002.00084.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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