1
|
Zhao Z, Conradie W, Pietersen DW, Jordaan A, Nicolau G, Edwards S, Riekert S, Heideman N. Diversification of the African legless skinks in the subfamily Acontinae (Family Scincidae). Mol Phylogenet Evol 2023; 182:107747. [PMID: 36849095 DOI: 10.1016/j.ympev.2023.107747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
Cladogenic diversification is often explained by referring to climatic oscillations and geomorphic shifts that cause allopatric speciation. In this regard, southern Africa retains a high level of landscape heterogeneity in vegetation, geology, and rainfall patterns. The legless skink subfamily Acontinae occurs broadly across the southern African subcontinent and therefore provides an ideal model group for investigating biogeographic patterns associated with the region. A robust phylogenetic study of the Acontinae with comprehensive coverage and adequate sampling of each taxon has been lacking up until now, resulting in unresolved questions regarding the subfamily's biogeography and evolution. In this study, we used multi-locus genetic markers (three mitochondrial and two nuclear) with comprehensive taxon coverage (all currently recognized Acontinae species) and adequate sampling (multiple specimens for most taxa) of each taxon to infer a phylogeny for the subfamily. The phylogeny retrieved four well-supported clades in Acontias and supported the monophyly of Typhlosaurus. Following the General Lineage Concept (GLC), many long-standing phylogenetic enigmas within Acontias occidentalis and the A. kgalagadi, A. lineatus and A. meleagris species complexes, and within Typhlosaurus were resolved. Our species delimitation analyses suggest the existence of hidden taxa in the A. occidentalis, A. cregoi and A. meleagris species groups, but also suggest that some currently recognized species in the A. lineatus and A. meleagris species groups, and within Typhlosaurus, should be synonymised. We also possibly encountered "ghost introgression" in A. occidentalis. Our inferred species tree revealed a signal of gene flow, which implies possible cross-over in some groups. Fossil evidence calibration dating results showed that the divergence between Typhlosaurus and Acontias was likely influenced by cooling and increasing aridity along the southwest coast in the mid-Oligocene caused by the opening of the Drake Passage. Further cladogenesis observed in Typhlosaurus and Acontias was likely influenced by Miocene cooling, expansion of open habitat, uplifting of the eastern Great Escarpment (GE), and variation in rainfall patterns, together with the effect of the warm Agulhas Current since the early Miocene, the development of the cold Benguela Current since the late Miocene, and their co-effects. The biogeographic pattern of the Acontinae bears close resemblance to that of other herpetofauna (e.g., rain frogs and African vipers) in southern Africa.
Collapse
Affiliation(s)
- Zhongning Zhao
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa; Department of Genetics, University of the Free State, Bloemfontein, South Africa.
| | - Werner Conradie
- Port Elizabeth Museum (Bayworld), P.O. Box 13147, Humewood, Port Elizabeth 6013, South Africa; Department of Nature Conservation Management, Natural Resource Science and Management Cluster, Faculty of Science, George Campus, Nelson Mandela University, George, South Africa
| | - Darren W Pietersen
- Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - Adriaan Jordaan
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa
| | - Gary Nicolau
- Zoology & Entomology Molecular Lab, Department of Zoology and Entomology, Rhodes University, Makhanda, South Africa
| | - Shelley Edwards
- Zoology & Entomology Molecular Lab, Department of Zoology and Entomology, Rhodes University, Makhanda, South Africa
| | - Stephanus Riekert
- Department of Information and Communication Technology Services, University of the Free State, Bloemfontein, South Africa
| | - Neil Heideman
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa
| |
Collapse
|
2
|
dos Santos MV, Prudente ALC, Rodrigues MT, Sturaro MJ. The Role of Vicariance and Paleoclimatic Shifts in the Diversification of Uranoscodon superciliosus (Squamata, Tropiduridae) of the Amazonian Floodplains. Evol Biol 2022. [DOI: 10.1007/s11692-022-09583-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
3
|
Chromosome-level genome assembly of the bar-headed goose (Anser indicus). Sci Data 2022; 9:668. [PMID: 36329062 PMCID: PMC9633837 DOI: 10.1038/s41597-022-01801-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
Bar-headed geese (Anser indicus) are adaptable to plateau environments. In this study, we sequenced and assembled a high-quality chromosome-level genome of the bar-headed goose using PacBio long reads and Hi-C technique, and generated 115.73 Gb of Illumina short-reads and 95.89 Gb of PacBio long-reads. The assembled bar-headed goose genome, with a contig N50 of 5.734 Mb and a scaffold N50 of 65.77 Mb, is 1.129 Gb in length and includes 33 chromosomes and 451 fragments. BUSCO assessment yielded a completeness score of 94.4%. In total, 15,376 protein-coding genes were predicted, of which 94.95% had homologs in protein databases. We identified 78 positively selected genes (PSGs) in the bar-headed goose genome, which were mainly enriched in calcium ion and ATP-binding. This bar-headed goose genome will be an important resource for increasing our understanding regarding the genetic basis of adaptation to life at a high altitude.
Collapse
|
4
|
Cannibalism in Microlophus Lizards. J HERPETOL 2022. [DOI: 10.1670/20-132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
5
|
Que T, Wang H, Yang W, Wu J, Hou C, Pei S, Wu Q, Li LM, Wei S, Xie X, Huang H, Chen P, Huang Y, Wu A, He M, Nong D, Wei X, Wu J, Nong R, Huang N, Zhou Q, Lin Y, Lu T, Wei Y, Li S, Yao J, Zhong Y, Qin H, Tan L, Li Y, Li W, Liu T, Liu S, Yu Y, Qiu H, Jiang Y, Li Y, Liu Z, Huang CM, Hu Y. The reference genome and transcriptome of the limestone langur, Trachypithecus leucocephalus, reveal expansion of genes related to alkali tolerance. BMC Biol 2021; 19:67. [PMID: 33832502 PMCID: PMC8034193 DOI: 10.1186/s12915-021-00998-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/05/2021] [Indexed: 01/13/2023] Open
Abstract
Background Trachypithecus leucocephalus, the white-headed langur, is a critically endangered primate that is endemic to the karst mountains in the southern Guangxi province of China. Studying the genomic and transcriptomic mechanisms underlying its local adaptation could help explain its persistence within a highly specialized ecological niche. Results In this study, we used PacBio sequencing and optical assembly and Hi-C analysis to create a high-quality de novo assembly of the T. leucocephalus genome. Annotation and functional enrichment revealed many genes involved in metabolism, transport, and homeostasis, and almost all of the positively selected genes were related to mineral ion binding. The transcriptomes of 12 tissues from three T. leucocephalus individuals showed that the great majority of genes involved in mineral absorption and calcium signaling were expressed, and their gene families were significantly expanded. For example, FTH1 primarily functions in iron storage and had 20 expanded copies. Conclusions These results increase our understanding of the evolution of alkali tolerance and other traits necessary for the persistence of T. leucocephalus within an ecologically unique limestone karst environment.
Collapse
Affiliation(s)
- Tengcheng Que
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Huifeng Wang
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Weifei Yang
- Annoroad Gene Technology, Beijing, 100176, China
| | - Jianbao Wu
- Guangxi Chongzuo white headed langur national nature reserve, Chongzuo, Guangxi, 532200, China
| | - Chenyang Hou
- School of Information and Management, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Surui Pei
- Annoroad Gene Technology, Beijing, 100176, China
| | - Qunying Wu
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Liu Ming Li
- Guangxi Reproductive Medical Research Center, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Shilu Wei
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Xing Xie
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Hongli Huang
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Panyu Chen
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Yiming Huang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Aiqiong Wu
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Meihong He
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Dengpan Nong
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Xiao Wei
- Guangxi Chongzuo white headed langur national nature reserve, Chongzuo, Guangxi, 532200, China
| | - Junyi Wu
- Nanning Animal Zoo, Nanning, Guangxi, 530021, China
| | - Ru Nong
- Nanning Animal Zoo, Nanning, Guangxi, 530021, China
| | - Ning Huang
- Nanning Animal Zoo, Nanning, Guangxi, 530021, China
| | - Qingniao Zhou
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Yaowang Lin
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Tingxi Lu
- School of Information and Management, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Yongjie Wei
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Shousheng Li
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Jianglong Yao
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Yanli Zhong
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Huayong Qin
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Luohao Tan
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Yingjiao Li
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, 530003, China
| | - Weidong Li
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Tao Liu
- Annoroad Gene Technology, Beijing, 100176, China
| | - Sanyang Liu
- Annoroad Gene Technology, Beijing, 100176, China
| | - Yongyi Yu
- Annoroad Gene Technology, Beijing, 100176, China
| | - Hong Qiu
- Annoroad Gene Technology, Beijing, 100176, China
| | - Yonghua Jiang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Youcheng Li
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Zhijin Liu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Cheng Ming Huang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China.
| | - Yanling Hu
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China. .,Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, 530021, China. .,Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China.
| |
Collapse
|
6
|
Carvalho AL. Resolving the Obscure Identity of Steironotus arenarius Tschudi, 1845 and Tropidurus tschudii Roux, 1907 (Squamata: Tropiduridae). SOUTH AMERICAN JOURNAL OF HERPETOLOGY 2021. [DOI: 10.2994/sajh-d-19-00094.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- André L.G. Carvalho
- Department of Herpetology, Division of Vertebrate Zoology, American Museum of Natural History. Central Park West at 79th Street, New York, New York, 10024, USA
| |
Collapse
|
7
|
Poulakakis N, Miller JM, Jensen EL, Beheregaray LB, Russello MA, Glaberman S, Boore J, Caccone A. Colonization history of Galapagos giant tortoises: Insights from mitogenomes support the progression rule. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12387] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Nikos Poulakakis
- Department of Biology School of Sciences and Engineering University of Crete Heraklio Greece
- Natural History Museum of Crete School of Sciences and Engineering University of Crete Heraklio Greece
| | - Joshua M. Miller
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
| | - Evelyn L. Jensen
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
| | | | | | - Scott Glaberman
- Department of Environmental Science and Policy George Mason University Fairfax VA USA
| | - Jeffrey Boore
- Providence St. Joseph Health and Institute for Systems Biology Seattle WA USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
| |
Collapse
|
8
|
Toyama KS, Junes K, Ruiz J, Mendoza A, Pérez JM. Ontogenetic Changes in the Diet and Head Morphology of an Omnivorous Tropidurid Lizard (Microlophus thoracicus). ZOOLOGY 2018; 129:45-53. [DOI: 10.1016/j.zool.2018.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 06/14/2018] [Accepted: 06/18/2018] [Indexed: 11/26/2022]
|
9
|
Carvalho AL, Rivas LR, Céspedes R, Rodrigues MT. A New Collared Lizard (Tropidurus: Tropiduridae) Endemic to the Western Bolivian Andes and Its Implications for Seasonally Dry Tropical Forests. AMERICAN MUSEUM NOVITATES 2018. [DOI: 10.1206/3896.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- André L.G. Carvalho
- Division of Vertebrate Zoology (Herpetology), American Museum of Natural History
- Richard Gilder Graduate School, American Museum of Natural History
- Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Luis Rolando Rivas
- Museo de Historia Natural Alcide d'Orbigny, Cochabamba, Bolivia
- Universidad Autónoma del Beni “Mcal. José Ballivián,” Trinidad, Beni, Bolivia
| | | | | |
Collapse
|
10
|
Interaction Between Morphology and Habitat Use: A Large-Scale Approach in Tropidurinae Lizards. ACTA ACUST UNITED AC 2017. [DOI: 10.3099/0006-9698-554.1.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
11
|
Carvalho AL, Sena MA, Peloso PL, Machado FA, Montesinos R, Silva HR, Campbell G, Rodrigues MT. A NewTropidurus(Tropiduridae) from the Semiarid Brazilian Caatinga: Evidence for Conflicting Signal between Mitochondrial and Nuclear Loci Affecting the Phylogenetic Reconstruction of South American Collared Lizards. AMERICAN MUSEUM NOVITATES 2016. [DOI: 10.1206/3852.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
12
|
Geometric morphometric analysis of the head of Microlophus atacamensis (Tropiduridae) in a latitudinal gradient. Zool Stud 2015; 54:e24. [PMID: 31966111 DOI: 10.1186/s40555-014-0099-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 12/25/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND Clinal variation is defined as gradual variation in a character associated with geographic distance among sites. Microlophus atacamensis is a medium large lizard species which inhabits the intertidal zone of northern Chile, distributed from Antofagasta (23° 39' S) to Arrayán, La Serena (29° 41' S) in a gradient which could show clinal variation. Geometric morphometrics analyzes differences in shape independent of size; information about shape allows a more complete biological interpretation than information on morphological variation. This studyevaluated clinal variation in the head shape of M.atacamensis fromfive localities (Antofagasta, Paposo, Pan de Azúcar, Caldera, and Tres Playitas) using dorsal and lateral views, comparing form variation with latitudinal distribution. The heads of adults collected were photographed in lateral and dorsal views. RESULTS The analysis did not find significant differences in form among the five localities, in contrast to the proposal of earlier studies, and no differences were recorded between the sexes. Possible reasons why these populations are not differentiated in the latitudinal gradient are discussed. CONCLUSIONS Our results show that there are no differences between the studied, among the explanations are that populationsof this species are subjected to similar environments that promote convergence of the structures analyzed.
Collapse
|
13
|
Geist DJ, Snell H, Snell H, Goddard C, Kurz MD. A Paleogeographic Model of the Galápagos Islands and Biogeographical and Evolutionary Implications. THE GALÁPAGOS 2014. [DOI: 10.1002/9781118852538.ch8] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
|
14
|
Noonan BP, Pramuk JB, Bezy RL, Sinclair EA, Queiroz KD, Sites JW. Phylogenetic relationships within the lizard clade Xantusiidae: Using trees and divergence times to address evolutionary questions at multiple levels. Mol Phylogenet Evol 2013; 69:109-22. [DOI: 10.1016/j.ympev.2013.05.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 05/15/2013] [Accepted: 05/21/2013] [Indexed: 11/25/2022]
|
15
|
Barley AJ, White J, Diesmos AC, Brown RM. THE CHALLENGE OF SPECIES DELIMITATION AT THE EXTREMES: DIVERSIFICATION WITHOUT MORPHOLOGICAL CHANGE IN PHILIPPINE SUN SKINKS. Evolution 2013; 67:3556-72. [DOI: 10.1111/evo.12219] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 07/08/2013] [Indexed: 12/01/2022]
Affiliation(s)
- Anthony J. Barley
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence Kansas 66045
| | - Jordan White
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence Kansas 66045
| | | | - Rafe M. Brown
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence Kansas 66045
| |
Collapse
|
16
|
Kwun HJ, Kim JK. Molecular phylogeny and new classification of the genera Eulophias and Zoarchias (PISCES, Zoarcoidei). Mol Phylogenet Evol 2013; 69:787-95. [PMID: 23845463 DOI: 10.1016/j.ympev.2013.06.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Revised: 06/22/2013] [Accepted: 06/28/2013] [Indexed: 12/12/2022]
Abstract
Morphological and osteological studies of the Zoarcoidei group have previously been undertaken, but the group (especially the genera Eulophias and Zoarchias) still remains enigmatic. Therefore, we conducted molecular phylogenetic studies on the two genera Eulophias and Zoarchias using two mitochondrial (16S rRNA and COI) and two nuclear genes (RAG2 and RNF213). Our phylogenetic analysis supported the monophyly of the suborder level of the Zoarcoidei, but rejected the previous morphology- and osteology-based classification hypotheses regarding the two genera. Conflict between mtDNA and nDNA phylogenies within the genus Eulophias implies that the genus shows a complicated relationship such as hybridization in the process of the evolutionary history. The genetic distances between the Eulophias (or Zoarchias) and other Zoarcoidei spp. were the greatest, showing different family-level affiliations. In addition, the mtDNA topology showed the two genera were clearly separated from each other as well as from the families Stichaeidae and Zoarcidae. Considering the new molecular phylogeny, we suggest a new classification for the two genera: (1) Eulophias belongs to a new family named as the Eulophiidae; (2) Zoarchias belongs to the family Neozoarcidae (sensu Radchenko et al., 2012b) rather than to Stichaeidae and Zoarcidae.
Collapse
Affiliation(s)
- Hyuck Joon Kwun
- Department of Marine Biology, Pukyong National University, 599-1 Daeyeon 3-Dong, Nam-gu, Busan 608-737, Republic of Korea.
| | | |
Collapse
|
17
|
Yuri T, Kimball RT, Harshman J, Bowie RCK, Braun MJ, Chojnowski JL, Han KL, Hackett SJ, Huddleston CJ, Moore WS, Reddy S, Sheldon FH, Steadman DW, Witt CC, Braun EL. Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals. BIOLOGY 2013; 2:419-44. [PMID: 24832669 PMCID: PMC4009869 DOI: 10.3390/biology2010419] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 02/21/2013] [Accepted: 02/22/2013] [Indexed: 11/19/2022]
Abstract
Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions.
Collapse
Affiliation(s)
- Tamaki Yuri
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072, USA
| | - Rebecca T. Kimball
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| | - John Harshman
- 4869 Pepperwood Way, San Jose, CA 95124, USA; E-Mail:
| | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA; E-Mail:
| | - Michael J. Braun
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA; E-Mails: (M.J.B.); (C.J.H.)
- Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, MD 20742, USA
| | - Jena L. Chojnowski
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| | - Kin-Lan Han
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| | - Shannon J. Hackett
- Zoology Department, Field Museum of Natural History, 1400 South Lakeshore Drive, Chicago, IL 60605, USA; E-Mail:
| | - Christopher J. Huddleston
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA; E-Mails: (M.J.B.); (C.J.H.)
| | - William S. Moore
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA; E-Mail:
| | - Sushma Reddy
- Biology Department, Loyola University Chicago, Chicago, IL 60660, USA; E-Mail:
| | - Frederick H. Sheldon
- Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA; E-Mail:
| | - David W. Steadman
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; E-Mail:
| | - Christopher C. Witt
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA; E-Mail:
| | - Edward L. Braun
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| |
Collapse
|
18
|
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]
|
19
|
Tóth A, Hausknecht A, Krisai-Greilhuber I, Papp T, Vágvölgyi C, Nagy LG. Iteratively refined guide trees help improving alignment and phylogenetic inference in the mushroom family Bolbitiaceae. PLoS One 2013; 8:e56143. [PMID: 23418526 PMCID: PMC3572013 DOI: 10.1371/journal.pone.0056143] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 01/07/2013] [Indexed: 11/19/2022] Open
Abstract
Reconciling traditional classifications, morphology, and the phylogenetic relationships of brown-spored agaric mushrooms has proven difficult in many groups, due to extensive convergence in morphological features. Here, we address the monophyly of the Bolbitiaceae, a family with over 700 described species and examine the higher-level relationships within the family using a newly constructed multilocus dataset (ITS, nrLSU rDNA and EF1-alpha). We tested whether the fast-evolving Internal Transcribed Spacer (ITS) sequences can be accurately aligned across the family, by comparing the outcome of two iterative alignment refining approaches (an automated and a manual) and various indel-treatment strategies. We used PRANK to align sequences in both cases. Our results suggest that--although PRANK successfully evades overmatching of gapped sites, referred previously to as alignment overmatching--it infers an unrealistically high number of indel events with natively generated guide-trees. This 'alignment undermatching' could be avoided by using more rigorous (e.g. ML) guide trees. The trees inferred in this study support the monophyly of the core Bolbitiaceae, with the exclusion of Panaeolus, Agrocybe, and some of the genera formerly placed in the family. Bolbitius and Conocybe were found monophyletic, however, Pholiotina and Galerella require redefinition. The phylogeny revealed that stipe coverage type is a poor predictor of phylogenetic relationships, indicating the need for a revision of the intrageneric relationships within Conocybe.
Collapse
Affiliation(s)
- Annamária Tóth
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Anton Hausknecht
- Department of Systematic and Evolutionary Botany, Faculty Centre of Biodiversity, University of Vienna, Wien, Austria
| | - Irmgard Krisai-Greilhuber
- Department of Systematic and Evolutionary Botany, Faculty Centre of Biodiversity, University of Vienna, Wien, Austria
| | - Tamás Papp
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - László G. Nagy
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| |
Collapse
|
20
|
Venzal JM, Nava S, González-Acuña D, Mangold AJ, Muñoz-Leal S, Lado P, Guglielmone AA. A new species of Ornithodoros (Acari: Argasidae), parasite of Microlophus spp. (Reptilia: Tropiduridae) from northern Chile. Ticks Tick Borne Dis 2013; 4:128-32. [DOI: 10.1016/j.ttbdis.2012.10.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 10/02/2012] [Accepted: 10/15/2012] [Indexed: 10/27/2022]
|
21
|
Nagy LG, Kocsubé S, Csanádi Z, Kovács GM, Petkovits T, Vágvölgyi C, Papp T. Re-mind the gap! Insertion - deletion data reveal neglected phylogenetic potential of the nuclear ribosomal internal transcribed spacer (ITS) of fungi. PLoS One 2012; 7:e49794. [PMID: 23185439 PMCID: PMC3501463 DOI: 10.1371/journal.pone.0049794] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/12/2012] [Indexed: 01/09/2023] Open
Abstract
Rapidly evolving, indel-rich phylogenetic markers play a pivotal role in our understanding of the relationships at multiple levels of the tree of life. There is extensive evidence that indels provide conserved phylogenetic signal, however, the range of phylogenetic depths for which gaps retain tree signal has not been investigated in detail. Here we address this question using the fungal internal transcribed spacer (ITS), which is central in many phylogenetic studies, molecular ecology, detection and identification of pathogenic and non-pathogenic species. ITS is repeatedly criticized for indel-induced alignment problems and the lack of phylogenetic resolution above species level, although these have not been critically investigated. In this study, we examined whether the inclusion of gap characters in the analyses shifts the phylogenetic utility of ITS alignments towards earlier divergences. By re-analyzing 115 published fungal ITS alignments, we found that indels are slightly more conserved than nucleotide substitutions, and when included in phylogenetic analyses, improved the resolution and branch support of phylogenies across an array of taxonomic ranges and extended the resolving power of ITS towards earlier nodes of phylogenetic trees. Our results reconcile previous contradicting evidence for the effects of data exclusion: in the case of more sophisticated indel placement, the exclusion of indel-rich regions from the analyses results in a loss of tree resolution, whereas in the case of simpler alignment methods, the exclusion of gapped sites improves it. Although the empirical datasets do not provide to measure alignment accuracy objectively, our results for the ITS region are consistent with previous simulations studies alignment algorithms. We suggest that sophisticated alignment algorithms and the inclusion of indels make the ITS region and potentially other rapidly evolving indel-rich loci valuable sources of phylogenetic information, which can be exploited at multiple taxonomic levels.
Collapse
Affiliation(s)
- László G Nagy
- University of Szeged, Faculty of Science and Informatics, Department of Microbiology, Szeged, Hungary.
| | | | | | | | | | | | | |
Collapse
|
22
|
Luan PT, Ryder OA, Davis H, Zhang YP, Yu L. Incorporating indels as phylogenetic characters: impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora). Mol Phylogenet Evol 2012; 66:748-56. [PMID: 23147269 DOI: 10.1016/j.ympev.2012.10.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 10/27/2012] [Accepted: 10/29/2012] [Indexed: 10/27/2022]
Abstract
Insertion and deletion events (indels) provide a suite of markers with enormous potential for molecular phylogenetics. Using many more indel characters than those in previous studies, we here for the first time address the impact of indel inclusion on the phylogenetic inferences of Arctoidea (Mammalia: Carnivora). Based on 6843 indel characters from 22 nuclear intron loci of 16 species of Arctoidea, our analyses demonstrate that when the indels were not taken into consideration, the monophyly of Ursidae and Pinnipedia tree and the monophyly of Pinnipedia and Musteloidea tree were both recovered, whereas inclusion of indels by using three different indel coding schemes give identical phylogenetic tree topologies supporting the monophyly of Ursidae and Pinnipedia. Our work brings new perspectives on the previously controversial placements among Arctoidea families, and provides another example demonstrating the importance of identifying and incorporating indels in the phylogenetic analyses of introns. In addition, comparison of indel incorporation methods revealed that the three indel coding methods are all advantageous over treating indels as missing data, given that incorporating indels produces consistent results across methods. This is the first report of the impact of different indel coding schemes on phylogenetic reconstruction at the family level in Carnivora, which indicates that indels should be taken into account in the future phylogenetic analyses.
Collapse
Affiliation(s)
- Peng-Tao Luan
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | | | | | | | | |
Collapse
|
23
|
Wang XP, Yu L, Roos C, Ting N, Chen CP, Wang J, Zhang YP. Phylogenetic relationships among the colobine monkeys revisited: new insights from analyses of complete mt genomes and 44 nuclear non-coding markers. PLoS One 2012; 7:e36274. [PMID: 22558416 PMCID: PMC3338693 DOI: 10.1371/journal.pone.0036274] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 04/03/2012] [Indexed: 01/05/2023] Open
Abstract
Background Phylogenetic relationships among Asian and African colobine genera have been disputed and are not yet well established. In the present study, we revisit the contentious relationships within the Asian and African Colobinae by analyzing 44 nuclear non-coding genes (>23 kb) and mitochondrial (mt) genome sequences from 14 colobine and 4 non-colobine primates. Principal Findings The combined nuclear gene and the mt genome as well as the combined nuclear and mt gene analyses yielded different phylogenetic relationships among colobine genera with the exception of a monophyletic ‘odd-nosed’ group consisting of Rhinopithecus, Pygathrix and Nasalis, and a monophyletic African group consisting of Colobus and Piliocolobus. The combined nuclear data analyses supported a sister-grouping between Semnopithecus and Trachypithecus, and between Presbytis and the odd-nosed monkey group, as well as a sister-taxon association of Pygathrix and Rhinopithecus within the odd-nosed monkey group. In contrast, mt genome data analyses revealed that Semnopithecus diverged earliest among the Asian colobines and that the odd-nosed monkey group is sister to a Presbytis and Trachypithecus clade, as well as a close association of Pygathrix with Nasalis. The relationships among these genera inferred from the analyses of combined nuclear and mt genes, however, varied with the tree-building methods used. Another remarkable finding of the present study is that all of our analyses rejected the recently proposed African colobine paraphyly and hybridization hypothesis and supported reciprocal monophyly of the African and Asian groups. Significance The phylogenetic utility of large-scale new non-coding genes was assessed using the Colobinae as a model, We found that these markers were useful for distinguishing nodes resulting from rapid radiation episodes such as the Asian colobine radiation. None of these markers here have previously been used for colobine phylogenetic reconstruction, increasing the spectrum of molecular markers available to mammalian systematics.
Collapse
Affiliation(s)
- Xiao Ping Wang
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, Yunnan, China
| | - Li Yu
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, Yunnan, China
- * E-mail: (LY); (YPZ)
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Göttingen, Germany
| | - Nelson Ting
- Department of Anthropology, University of Oregon, Eugene, Oregon, United States of America
| | - Cui Ping Chen
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, Yunnan, China
| | - Jing Wang
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, Yunnan, China
| | - Ya Ping Zhang
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, Yunnan, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- * E-mail: (LY); (YPZ)
| |
Collapse
|
24
|
Poulakakis N, Russello M, Geist D, Caccone A. Unravelling the peculiarities of island life: vicariance, dispersal and the diversification of the extinct and extant giant Galápagos tortoises. Mol Ecol 2011; 21:160-73. [PMID: 22098061 DOI: 10.1111/j.1365-294x.2011.05370.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
In isolated oceanic islands, colonization patterns are often interpreted as resulting from dispersal rather than vicariant events. Such inferences may not be appropriate when island associations change over time and new islands do not form in a simple linear trend. Further complexity in the phylogeography of ocean islands arises when dealing with endangered taxa as extinctions, uncertainty on the number of evolutionary 'units', and human activities can obscure the progression of colonization events. Here, we address these issues through a reconstruction of the evolutionary history of giant Galápagos tortoises, integrating DNA data from extinct and extant species with information on recent human activities and newly available geological data. Our results show that only three of the five extinct or nearly extinct species should be considered independent evolutionary units. Dispersal from mainland South America started at approximately 3.2 Ma after the emergence of the two oldest islands of San Cristobal and Española. Dispersal from older to younger islands began approximately 1.74 Ma and was followed by multiple colonizations from different sources within the archipelago. Vicariant events, spurred by island formation, coalescence, and separation, contributed to lineage diversifications on Pinzón and Floreana dating from 1.26 and 0.85 Ma. This work provides an example of how to reconstruct the history of endangered taxa in spite of extinctions and human-mediated dispersal events and highlights the need to take into account both vicariance and dispersal when dealing with organisms from islands whose associations are not simply explained by a linear emergence model.
Collapse
Affiliation(s)
- Nikos Poulakakis
- Molecular Systematics Lab, Natural History Museum of Crete, University of Crete, Iraklion, Crete.
| | | | | | | |
Collapse
|
25
|
Yu L, Peng D, Liu J, Luan P, Liang L, Lee H, Lee M, Ryder OA, Zhang Y. On the phylogeny of Mustelidae subfamilies: analysis of seventeen nuclear non-coding loci and mitochondrial complete genomes. BMC Evol Biol 2011; 11:92. [PMID: 21477367 PMCID: PMC3088541 DOI: 10.1186/1471-2148-11-92] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2011] [Accepted: 04/10/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Mustelidae, as the largest and most-diverse family of order Carnivora, comprises eight subfamilies. Phylogenetic relationships among these Mustelidae subfamilies remain argumentative subjects in recent years. One of the main reasons is that the mustelids represent a typical example of rapid evolutionary radiation and recent speciation event. Prior investigation has been concentrated on the application of different mitochondrial (mt) sequence and nuclear protein-coding data, herein we employ 17 nuclear non-coding loci (>15 kb), in conjunction with mt complete genome data (>16 kb), to clarify these enigmatic problems. RESULTS The combined nuclear intron and mt genome analyses both robustly support that Taxidiinae diverged first, followed by Melinae. Lutrinae and Mustelinae are grouped together in all analyses with strong supports. The position of Helictidinae, however, is enigmatic because the mt genome analysis places it to the clade uniting Lutrinae and Mustelinae, whereas the nuclear intron analysis favors a novel view supporting a closer relationship of Helictidinae to Martinae. This finding emphasizes a need to add more data and include more taxa to resolve this problem. In addition, the molecular dating provides insights into the time scale of the origin and diversification of the Mustelidae subfamilies. Finally, the phylogenetic performances and limits of nuclear introns and mt genes are discussed in the context of Mustelidae phylogeny. CONCLUSION Our study not only brings new perspectives on the previously obscured phylogenetic relationships among Mustelidae subfamilies, but also provides another example demonstrating the effectiveness of nuclear non-coding loci for reconstructing evolutionary histories in a group that has undergone rapid bursts of speciation.
Collapse
Affiliation(s)
- Li Yu
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, PR, China
| | - Dan Peng
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, PR, China
| | - Jiang Liu
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, PR, China
| | - Pengtao Luan
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, PR, China
| | - Lu Liang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
| | - Hang Lee
- Conservation Genome Resource Bank for Korean Wildlife, Research Institute for Veterinary Science and Coll. of Vet. Med., Seoul National Univ., Seoul 151-742, South Korea
| | - Muyeong Lee
- Conservation Genome Resource Bank for Korean Wildlife, Research Institute for Veterinary Science and Coll. of Vet. Med., Seoul National Univ., Seoul 151-742, South Korea
| | - Oliver A Ryder
- San Diego Zoo's Institute for Conservation Research, Escondido, CA, USA 92027-7000
| | - Yaping Zhang
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, PR, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
| |
Collapse
|
26
|
Yu L, Luan PT, Jin W, Ryder OA, Chemnick LG, Davis HA, Zhang YP. Phylogenetic Utility of Nuclear Introns in Interfamilial Relationships of Caniformia (Order Carnivora). Syst Biol 2011; 60:175-87. [DOI: 10.1093/sysbio/syq090] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Li Yu
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
| | - Peng-Tao Luan
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
| | - Wei Jin
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
| | - Oliver A. Ryder
- San Diego Zoo Conservation Research, PO Box 120551, San Diego, CA 92112, USA
| | - Leona G. Chemnick
- San Diego Zoo Conservation Research, PO Box 120551, San Diego, CA 92112, USA
| | - Heidi A. Davis
- San Diego Zoo Conservation Research, PO Box 120551, San Diego, CA 92112, USA
| | - Ya-ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
| |
Collapse
|
27
|
Jacobsen F, Friedman NR, Omland KE. Congruence between nuclear and mitochondrial DNA: Combination of multiple nuclear introns resolves a well-supported phylogeny of New World orioles (Icterus). Mol Phylogenet Evol 2010; 56:419-27. [PMID: 20363347 DOI: 10.1016/j.ympev.2010.03.035] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Revised: 03/25/2010] [Accepted: 03/29/2010] [Indexed: 02/03/2023]
|
28
|
Steinfartz S, Glaberman S, Lanterbecq D, Russello MA, Rosa S, Hanley TC, Marquez C, Snell HL, Snell HM, Gentile G, Dell'Olmo G, Powell AM, Caccone A. Progressive colonization and restricted gene flow shape island-dependent population structure in Galápagos marine iguanas (Amblyrhynchus cristatus). BMC Evol Biol 2009; 9:297. [PMID: 20028547 PMCID: PMC2807874 DOI: 10.1186/1471-2148-9-297] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Accepted: 12/22/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Marine iguanas (Amblyrhynchus cristatus) inhabit the coastlines of large and small islands throughout the Galápagos archipelago, providing a rich system to study the spatial and temporal factors influencing the phylogeographic distribution and population structure of a species. Here, we analyze the microevolution of marine iguanas using the complete mitochondrial control region (CR) as well as 13 microsatellite loci representing more than 1200 individuals from 13 islands. RESULTS CR data show that marine iguanas occupy three general clades: one that is widely distributed across the northern archipelago, and likely spread from east to west by way of the South Equatorial current, a second that is found mostly on the older eastern and central islands, and a third that is limited to the younger northern and western islands. Generally, the CR haplotype distribution pattern supports the colonization of the archipelago from the older, eastern islands to the younger, western islands. However, there are also signatures of recurrent, historical gene flow between islands after population establishment. Bayesian cluster analysis of microsatellite genotypes indicates the existence of twenty distinct genetic clusters generally following a one-cluster-per-island pattern. However, two well-differentiated clusters were found on the easternmost island of San Cristóbal, while nine distinct and highly intermixed clusters were found on youngest, westernmost islands of Isabela and Fernandina. High mtDNA and microsatellite genetic diversity were observed for populations on Isabela and Fernandina that may be the result of a recent population expansion and founder events from multiple sources. CONCLUSIONS While a past genetic study based on pure FST analysis suggested that marine iguana populations display high levels of nuclear (but not mitochondrial) gene flow due to male-biased dispersal, the results of our sex-biased dispersal tests and the finding of strong genetic differentiation between islands do not support this view. Therefore, our study is a nice example of how recently developed analytical tools such as Bayesian clustering analysis and DNA sequence-based demographic analyses can overcome potential biases introduced by simply relying on FST estimates from markers with different inheritance patterns.
Collapse
Affiliation(s)
- Sebastian Steinfartz
- Department of Ecology and Evolutionary Biology and Yale Institute for Biospheric Studies - Molecular Systematics and Conservation Genetics Laboratory, New Haven, Connecticut 06511, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Hayashi F, Shima A, Horikoshi K, Kawakami K, Segawa RD, Aotsuka T, Suzuki T. Limited Overwater Dispersal and Genetic Differentiation of the Snake-Eyed Skink (Cryptoblepharus nigropunctatus) in the Oceanic Ogasawara Islands, Japan. Zoolog Sci 2009; 26:543-9. [DOI: 10.2108/zsj.26.543] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
30
|
Morrison DA. Why Would Phylogeneticists Ignore Computerized Sequence Alignment? Syst Biol 2009; 58:150-8. [DOI: 10.1093/sysbio/syp009] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
31
|
Benavides E, Baum R, Snell HM, Snell HL, Sites JW. Island biogeography of Galápagos lava lizards (Tropiduridae: Microlophus): species diversity and colonization of the archipelago. Evolution 2009; 63:1606-26. [PMID: 19154379 DOI: 10.1111/j.1558-5646.2009.00617.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The "lava lizards" (Microlophus) are distributed throughout the Galápagos Archipelago, and consist of radiations derived from two independent colonizations. The "Eastern Radiation" includes M. bivittatus and M. habeli endemic to San Cristobal and Marchena Islands. The "Western Radiation" includes five to seven historically recognized species distributed across almost the entire Archipelago. We combine dense geographic sampling and multilocus sequence data to estimate a phylogenetic hypothesis for the Western Radiation, to delimit species boundaries in this radiation, and to estimate a time frame for colonization events. Our phylogenetic hypothesis rejects two earlier topologies for the Western Radiation and paraphyly of M. albemarlensis, while providing strong support for single colonizations on each island. The colonization history implied by our phylogeny is consistent with general expectations of an east-to-west route predicted by the putative age of island groups, and prevailing ocean currents in the Archipelago. Additionally, combined evidence suggests that M. indefatigabilis from Santa Fe should be recognized as a full species. Finally, molecular divergence estimates suggest that the two colonization events likely occurred on the oldest existing islands, and the Western Radiation represents a recent radiation that, in most cases, has produced species that are considerably younger than the islands they inhabit.
Collapse
Affiliation(s)
- Edgar Benavides
- Department of Biology, Brigham Young University, Provo, Utah 84602, USA.
| | | | | | | | | |
Collapse
|
32
|
Kutty SN, Pape T, Pont A, Wiegmann BM, Meier R. The Muscoidea (Diptera: Calyptratae) are paraphyletic: Evidence from four mitochondrial and four nuclear genes. Mol Phylogenet Evol 2008; 49:639-52. [DOI: 10.1016/j.ympev.2008.08.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Revised: 08/20/2008] [Accepted: 08/21/2008] [Indexed: 10/21/2022]
|
33
|
Parent CE, Caccone A, Petren K. Colonization and diversification of Galápagos terrestrial fauna: a phylogenetic and biogeographical synthesis. Philos Trans R Soc Lond B Biol Sci 2008; 363:3347-61. [PMID: 18782729 PMCID: PMC2607378 DOI: 10.1098/rstb.2008.0118] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Remote oceanic islands have long been recognized as natural models for the study of evolutionary processes involved in diversification. Their remoteness provides opportunities for isolation and divergence of populations, which make islands remarkable settings for the study of diversification. Groups of islands may share a relatively similar geological history and comparable climate, but their inhabitants experience subtly different environments and have distinct evolutionary histories, offering the potential for comparative studies. A range of organisms have colonized the Galápagos Islands, and various lineages have radiated throughout the archipelago to form unique assemblages. This review pays particular attention to molecular phylogenetic studies of Galápagos terrestrial fauna. We find that most of the Galápagos terrestrial fauna have diversified in parallel to the geological formation of the islands. Lineages have occasionally diversified within islands, and the clearest cases occur in taxa with very low vagility and on large islands with diverse habitats. Ecology and habitat specialization appear to be critical in speciation both within and between islands. Although the number of phylogenetic studies is continuously increasing, studies of natural history, ecology, evolution and behaviour are essential to completely reveal how diversification proceeded on these islands.
Collapse
Affiliation(s)
- Christine E Parent
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, Canada.
| | | | | |
Collapse
|
34
|
Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica 2008; 135:439-55. [DOI: 10.1007/s10709-008-9293-3] [Citation(s) in RCA: 218] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Accepted: 06/28/2008] [Indexed: 10/21/2022]
|
35
|
JORDAN MA, SNELL HL. Historical fragmentation of islands and genetic drift in populations of Galápagos lava lizards (Microlophus albemarlensis complex). Mol Ecol 2008; 17:1224-37. [DOI: 10.1111/j.1365-294x.2007.03658.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|