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Sureshan SC, Tanavade RV, Ghosh S, Ghosh S, Sella RN, Mohideen HS. Complete mitochondrial genome sequencing of Oxycarenus laetus (Hemiptera: Lygaeidae) from two geographically distinct regions of India. Sci Rep 2021; 11:23738. [PMID: 34887433 PMCID: PMC8660866 DOI: 10.1038/s41598-021-02881-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 11/18/2021] [Indexed: 11/09/2022] Open
Abstract
Oxycarenus laetus is a seed-sap sucking pest affecting a variety of crops, including cotton plants. Rising incidence and pesticide resistance by O. laetus have been reported from India and neighbouring countries. In this study, O. laetus samples were collected from Bhatinda and Coimbatore (India). Pure mtDNA was isolated and sequenced using Illumina MiSeq. Both the samples were found to be identical species (99.9%), and the complete genome was circular (15,672 bp), consisting of 13 PCGs, 2 rRNA, 23 tRNA genes, and a 962 bp control region. The mitogenome is 74.1% AT-rich, 0.11 AT, and - 0.19 GC skewed. All the genes had ATN as the start codon except cox1 (TTG), and an additional trnT was predicted. Nearly all tRNAs folded into the clover-leaf structure, except trnS1 and trnV. The intergenic space between trnH and nad4, considered as a synapomorphy of Lygaeoidea, was displaced. Two 5 bp motifs AATGA and ACCTA, two tandem repeats, and a few microsatellite sequences, were also found. The phylogenetic tree was constructed using 36 mitogenomes from 7 super-families of Hemiptera by employing rigorous bootstrapping and ML. Ours is the first study to sequence the complete mitogenome of O. laetus or any Oxycarenus species. The findings from this study would further help in the evolutionary studies of Lygaeidae.
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Affiliation(s)
- Shruthi Chalil Sureshan
- grid.412742.60000 0004 0635 5080Bioinformatics and Entomoinformatics Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203 Tamil Nadu India
| | - Ruchi Vivekanand Tanavade
- grid.412742.60000 0004 0635 5080Bioinformatics and Entomoinformatics Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203 Tamil Nadu India
| | - Sewali Ghosh
- Department of Advanced Zoology and Biotechnology, Guru Nanak College, Chennai, 600042 Tamil Nadu India
| | - Saswati Ghosh
- grid.506009.aDepartment of Virology, King Institute of Preventive Medicine and Research, Chennai, 600032 Tamil Nadu India
| | - Raja Natesan Sella
- grid.412742.60000 0004 0635 5080Membrane Protein Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203 Tamil Nadu India
| | - Habeeb Shaik Mohideen
- Bioinformatics and Entomoinformatics Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Tamil Nadu, India.
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2
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Päckert M. No hybrid snowcocks in the Altai-Hyper-variable markers can be problematic for phylogenetic inference. Ecol Evol 2021; 11:16354-16364. [PMID: 34824832 PMCID: PMC8601899 DOI: 10.1002/ece3.8199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/24/2021] [Accepted: 09/10/2021] [Indexed: 11/10/2022] Open
Abstract
A recent article in Ecology and Evolution featured the discovery of hybrid snowcocks (Tetraogallus) and speculated on the hybrid origin of an extant species (T. altaicus). Comprehensive re-analyses of original data from the latter paper reliably refute the phylogenetic hypothesis taken as firm evidence of a past hybridization event in these birds. The new re-analyses showed that there is no evidence of hybridization in these snowcocks from the data available so far.
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Affiliation(s)
- Martin Päckert
- Senckenberg Natural History Collections Museum of Zoology Dresden Germany
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3
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Lee C, Day J, Goodman SM, Pedrono M, Besnard G, Frantz L, Taylor PJ, Herrera MJ, Gongora J. Genetic origins and diversity of bushpigs from Madagascar (Potamochoerus larvatus, family Suidae). Sci Rep 2020; 10:20629. [PMID: 33244111 PMCID: PMC7693328 DOI: 10.1038/s41598-020-77279-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/09/2020] [Indexed: 11/08/2022] Open
Abstract
The island of Madagascar, situated off the southeast coast of Africa, shows the first evidence of human presence ~ 10,000 years ago; however, other archaeological data indicates a settlement of the modern peoples of the island distinctly more recent, perhaps > 1500 years ago. Bushpigs of the genus Potamochoerus (family Suidae), are today widely distributed in Madagascar and presumed to have been introduced from Africa at some stage by human immigrants to the island. However, disparities about their origins in Madagascar have been presented in the literature, including the possibility of endemic subspecies, and few empirical data are available. Furthermore, the separation of bushpigs in Madagascar from their mainland relatives may have favoured the evolution of a different repertoire of immune genes first due to a founder effect and then as a response to distinct pathogens compared to their ancestors. Molecular analysis confirmed the species status of the bushpig in Madagascar as P. larvatus, likely introduced from the central region of southern Africa, with no genetic evidence for the recognition of eastern and western subspecies as suggested from previous cranial morphology examination. Investigation of the immunologically important SLA-DQB1 peptide-binding region showed a different immune repertoire of bushpigs in Madagascar compared to those on the African mainland, with seventeen exon-2 haplotypes unique to bushpigs in Madagascar (2/28 haplotypes shared). This suggests that the MHC diversity of the Madagascar populations may have enabled Malagasy bushpigs to adapt to new environments.
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Affiliation(s)
- Carol Lee
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jenna Day
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Steven M Goodman
- Field Museum of Natural History, Chicago, IL, 60605, USA
- Association Vahatra, 101, Antananarivo, Madagascar
| | - Miguel Pedrono
- UMR ASTRE, INRAE, CIRAD, Université de Montpellier, 34398, Montpellier Cedex 5, France
| | - Guillaume Besnard
- CNRS, UPS, IRD, Laboratoire Evolution et Diversité Biologique, UMR5174, Université Toulouse III Paul Sabatier, 31062, Toulouse, France
| | - Laurent Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Peter J Taylor
- School of Mathematical and Natural Sciences, University of Venda, Thohoyandou, Limpopo Province, South Africa
- Afromontane Research Unit and Zoology Department, University of the Free State, Qwa Qwa campus, Phuthaditjhaba, 9866, South Africa
| | - Michael J Herrera
- Archaeological Studies Program, University of the Philippines Diliman, 1101, Quezon City, Philippines
| | - Jaime Gongora
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW, 2006, Australia.
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4
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Hosner PA, Owens HL, Braun EL, Kimball RT. Phylogeny and diversification of the gallopheasants (Aves: Galliformes): Testing roles of sexual selection and environmental niche divergence. ZOOL SCR 2020. [DOI: 10.1111/zsc.12441] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter A. Hosner
- Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- Center for Macroecology, Evolution, and Climate Globe Institute University of Copenhagen Copenhagen Denmark
| | - Hannah L. Owens
- Center for Macroecology, Evolution, and Climate Globe Institute University of Copenhagen Copenhagen Denmark
| | - Edward L. Braun
- Department of Biology University of Florida Gainesville FL USA
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5
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Yiğit N, Çetintürk D, Çolak E. Phylogenetic assessment of voles of the Guentheri Group (Mammalia: Microtus) in Turkish Thrace and Western Anatolia. THE EUROPEAN ZOOLOGICAL JOURNAL 2017. [DOI: 10.1080/24750263.2017.1317041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- N. Yiğit
- Department of Biology, Faculty of Science, University of Ankara , Beşevler, Turkey
| | - D. Çetintürk
- Department of Biology, Faculty of Science, University of Ankara , Beşevler, Turkey
| | - E. Çolak
- Department of Biology, Faculty of Science, University of Ankara , Beşevler, Turkey
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6
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Kimball RT, Braun EL. Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix. PeerJ 2014; 2:e361. [PMID: 24795852 PMCID: PMC4006227 DOI: 10.7717/peerj.361] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 04/03/2014] [Indexed: 01/19/2023] Open
Abstract
The resolution of rapid evolutionary radiations or "bushes" in the tree of life has been one of the most difficult and interesting problems in phylogenetics. The avian order Galliformes appears to have undergone several rapid radiations that have limited the resolution of prior studies and obscured the position of taxa important both agriculturally and as model systems (chicken, turkey, Japanese quail). Here we present analyses of a multi-locus data matrix comprising over 15,000 sites, primarily from nuclear introns but also including three mitochondrial regions, from 46 galliform taxa with all gene regions sampled for all taxa. The increased sampling of unlinked nuclear genes provided strong bootstrap support for all but a small number of relationships. Coalescent-based methods to combine individual gene trees and analyses of datasets that are independent of published data indicated that this well-supported topology is likely to reflect the galliform species tree. The inclusion or exclusion of mitochondrial data had a limited impact upon analyses upon analyses using either concatenated data or multispecies coalescent methods. Some of the key phylogenetic findings include support for a second major clade within the core phasianids that includes the chicken and Japanese quail and clarification of the phylogenetic relationships of turkey. Jackknifed datasets suggested that there is an advantage to sampling many independent regions across the genome rather than obtaining long sequences for a small number of loci, possibly reflecting the differences among gene trees that differ due to incomplete lineage sorting. Despite the novel insights we obtained using this increased sampling of gene regions, some nodes remain unresolved, likely due to periods of rapid diversification. Resolving these remaining groups will likely require sequencing a very large number of gene regions, but our analyses now appear to support a robust backbone for this order.
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Affiliation(s)
- Rebecca T Kimball
- Department of Biology, University of Florida , Gainesville, FL , USA
| | - Edward L Braun
- Department of Biology, University of Florida , Gainesville, FL , USA
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7
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Phylogenetic and molecular dating analysis of Taiwan Blue Pheasant (Lophura swinhoii). Gene 2014; 539:21-9. [DOI: 10.1016/j.gene.2014.01.067] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 01/26/2014] [Accepted: 01/29/2014] [Indexed: 01/20/2023]
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8
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Liu F, Ma L, Yang C, Tu F, Xu Y, Ran J, Yue B, Zhang X. Taxonomic Status ofTetraophasis obscurusandTetraophasis szechenyii(Aves: Galliformes: Phasianidae) Based on the Complete Mitochondrial Genome. Zoolog Sci 2014; 31:160-7. [DOI: 10.2108/zsj.31.160] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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9
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Korrida A, Schweizer M. Diversification across the Palaearctic desert belt throughout the Pleistocene: phylogeographic history of the Houbara-Macqueen's bustard complex (Otididae: Chlamydotis
) as revealed by mitochondrial DNA. J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Amal Korrida
- Laboratoire des Substances Naturelles; Faculté des Sciences d'Agadir; B.P. 28/S. Université Ibnou Zohr; Agadir Royaume du Maroc
| | - Manuel Schweizer
- Naturhistorisches Museum der Burgergemeinde Bern; Bern Switzerland
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Dong L, Heckel G, Liang W, Zhang Y. Phylogeography of Silver Pheasant (Lophura nycthemera L.) across China: aggregate effects of refugia, introgression and riverine barriers. Mol Ecol 2013; 22:3376-90. [PMID: 23692215 DOI: 10.1111/mec.12315] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 03/12/2013] [Accepted: 03/14/2013] [Indexed: 11/27/2022]
Abstract
The role of Pleistocene glacial cycles in forming the contemporary genetic structure of organisms has been well studied in China with a particular focus on the Tibetan Plateau. However, China has a complex topography and diversity of local climates, and how glacial cycles may have shaped the subtropical and tropical biota of the region remains mostly unaddressed. To investigate the factors that affected the phylogeography and population history of a widely distributed and nondeciduous forest species, we analysed morphological characters, mitochondrial DNA sequences and nuclear microsatellite loci in the Silver Pheasant (Lophura nycthemera). In a pattern generally consistent with phenotypic clusters, but not nominal subspecies, deeply divergent mitochondrial lineages restricted to different geographic regions were detected. Coalescent simulations indicated that the time of main divergence events corresponded to major glacial periods in the Pleistocene and gene flow was only partially lowered by drainage barriers between some populations. Intraspecific cytonuclear discordance was revealed in mitochondrial lineages from Hainan Island and the Sichuan Basin with evidence of nuclear gene flow from neighbouring populations into the latter. Unexpectedly, hybridization was revealed in Yingjiang between the Silver Pheasant and Kalij Pheasant (Lophura leucomelanos) with wide genetic introgression at both the mtDNA and nuclear levels. Our results highlight a novel phylogeographic pattern in a subtropical area generated from the combined effects of climate oscillation, partial drainage barriers and interspecific hybridization. Cytonuclear discordance combined with morphological differentiation implies that complex historical factors shaped the divergence process in this biodiversity hot spot area of southern China.
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Affiliation(s)
- Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
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11
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Yu JN, Han SH, Kim BH, Kryukov AP, Kim S, Lee BY, Kwak M. Insights into Korean red fox (Vulpes vulpes) based on mitochondrial cytochrome b sequence variation in East Asia. Zoolog Sci 2013; 29:753-60. [PMID: 23106560 DOI: 10.2108/zsj.29.753] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The red fox (Vulpes vulpes) is the most widely distributed terrestrial carnivore in the world, occurring throughout most of North America, Europe, Asia, and North Africa. In South Korea, however, this species has been drastically reduced due to habitat loss and poaching. Consequently, it is classified as an endangered species in Korea. As a first step of a planned red fox restoration project, preserved red fox museum specimens were used to determine the genetic status of red foxes that had previously inhabited South Korea against red foxes from neighboring countries. Total eighty three mtDNA cytochrome b sequences, including 22 newly obtained East Asian red fox sequences and worldwide red fox sequences from NCBI, were clustered into three clades (i.e., I, II, and III) based on haplotype network and neighbor-joining trees. The mean genetic distance between clades was 2.0%. Clade III contained South Korean and other East Asian samples in addition to Eurasian and North Pacific individuals. In clade III, South Korean individuals were separated into two lineages of Eurasian and North Pacific groups, showing unclear phylogeographic structuring and admixture. This suggests that South Korean red fox populations may have been composed of individuals from these two different genetic lineages.
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Affiliation(s)
- Jeong-Nam Yu
- National Institute of Biological Resources, Environmental Research Complex, lncheon, Korea
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12
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Barker FK, Benesh MK, Vandergon AJ, Lanyon SM. Contrasting evolutionary dynamics and information content of the avian mitochondrial control region and ND2 gene. PLoS One 2012; 7:e46403. [PMID: 23071562 PMCID: PMC3465326 DOI: 10.1371/journal.pone.0046403] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 09/03/2012] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial DNA is an important tool for inference of population history in animals. A variety of mitochondrial loci have been sampled for this purpose, but many studies focus on the non-coding D-loop or control region (CR), which in at least some species appears hypermutable. Unfortunately, analyses of this region are sometimes complicated by segmental duplications, as well as by difficulties in sequencing through repeat expansions, driving many researchers to favor single-copy protein-coding or ribosomal RNA genes. Without systematic comparison, it is unclear if, how much, and what sort of information might be lost by focusing on coding regions, or conversely whether such regions might offer significant advantages over the CR. In this study, we compare the information content, both in terms of genealogy and tests of neutral equilibrium, of the mitochondrial CR and protein-coding ND2 gene of the red-winged blackbird (Agelaius phoeniceus) and its close relative the tricolored blackbird (A. tricolor). Both gene regions violate the standard infinite sites assumption central to moment-based population genetic inference, as well as exhibiting considerable among-site rate heterogeneity, obscuring significant departures from neutral equilibrium. Given the ubiquity of rate heterogeneity in mtDNA, use of more sophisticated tests that account for this should be obligatory. The two regions yield quite similar genealogical reconstructions, as well as indicating similar departures from neutral equilibrium assumptions for A. phoeniceus. However, individual Sanger-read-length fragments (~600 bases) of the CR have significantly higher information content than comparable fragments of ND2, suggesting that limited sampling of the mitochondrial genome should focus on the CR.
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Affiliation(s)
- F Keith Barker
- Bell Museum of Natural History, University of Minnesota, Saint Paul, Minnesota, United States of America.
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13
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Marine turtle mitogenome phylogenetics and evolution. Mol Phylogenet Evol 2012; 65:241-50. [PMID: 22750111 DOI: 10.1016/j.ympev.2012.06.010] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 06/11/2012] [Accepted: 06/13/2012] [Indexed: 11/21/2022]
Abstract
The sea turtles are a group of cretaceous origin containing seven recognized living species: leatherback, hawksbill, Kemp's ridley, olive ridley, loggerhead, green, and flatback. The leatherback is the single member of the Dermochelidae family, whereas all other sea turtles belong in Cheloniidae. Analyses of partial mitochondrial sequences and some nuclear markers have revealed phylogenetic inconsistencies within Cheloniidae, especially regarding the placement of the flatback. Population genetic studies based on D-Loop sequences have shown considerable structuring in species with broad geographic distributions, shedding light on complex migration patterns and possible geographic or climatic events as driving forces of sea-turtle distribution. We have sequenced complete mitogenomes for all sea-turtle species, including samples from their geographic range extremes, and performed phylogenetic analyses to assess sea-turtle evolution with a large molecular dataset. We found variation in the length of the ATP8 gene and a highly variable site in ND4 near a proton translocation channel in the resulting protein. Complete mitogenomes show strong support and resolution for phylogenetic relationships among all sea turtles, and reveal phylogeographic patterns within globally-distributed species. Although there was clear concordance between phylogenies and geographic origin of samples in most taxa, we found evidence of more recent dispersal events in the loggerhead and olive ridley turtles, suggesting more recent migrations (<1 Myr) in these species. Overall, our results demonstrate the complexity of sea-turtle diversity, and indicate the need for further research in phylogeography and molecular evolution.
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Werner J, Griebeler EM. Reproductive biology and its impact on body size: comparative analysis of mammalian, avian and dinosaurian reproduction. PLoS One 2011; 6:e28442. [PMID: 22194835 PMCID: PMC3237437 DOI: 10.1371/journal.pone.0028442] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 11/08/2011] [Indexed: 11/18/2022] Open
Abstract
Janis and Carrano (1992) suggested that large dinosaurs might have faced a lower risk of extinction under ecological changes than similar-sized mammals because large dinosaurs had a higher potential reproductive output than similar-sized mammals (JC hypothesis). First, we tested the assumption underlying the JC hypothesis. We therefore analysed the potential reproductive output (reflected in clutch/litter size and annual offspring number) of extant terrestrial mammals and birds (as "dinosaur analogs") and of extinct dinosaurs. With the exception of rodents, the differences in the reproductive output of similar-sized birds and mammals proposed by Janis and Carrano (1992) existed even at the level of single orders. Fossil dinosaur clutches were larger than litters of similar-sized mammals, and dinosaur clutch sizes were comparable to those of similar-sized birds. Because the extinction risk of extant species often correlates with a low reproductive output, the latter difference suggests a lower risk of population extinction in dinosaurs than in mammals. Second, we present a very simple, mathematical model that demonstrates the advantage of a high reproductive output underlying the JC hypothesis. It predicts that a species with a high reproductive output that usually faces very high juvenile mortalities will benefit more strongly in terms of population size from reduced juvenile mortalities (e.g., resulting from a stochastic reduction in population size) than a species with a low reproductive output that usually comprises low juvenile mortalities. Based on our results, we suggest that reproductive strategy could have contributed to the evolution of the exceptional gigantism seen in dinosaurs that does not exist in extant terrestrial mammals. Large dinosaurs, e.g., the sauropods, may have easily sustained populations of very large-bodied species over evolutionary time.
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Affiliation(s)
- Jan Werner
- Department of Ecology, Zoological Institute, University of Mainz, Mainz, Germany.
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15
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Kimball RT, Mary CMS, Braun EL. A macroevolutionary perspective on multiple sexual traits in the phasianidae (galliformes). INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2011; 2011:423938. [PMID: 21716735 PMCID: PMC3119463 DOI: 10.4061/2011/423938] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2010] [Accepted: 02/26/2011] [Indexed: 11/20/2022]
Abstract
Traits involved in sexual signaling are ubiquitous among animals. Although a single trait appears sufficient to convey information, many sexually dimorphic species exhibit multiple sexual signals, which may be costly to signalers and receivers. Given that one signal may be enough, there are many microevolutionary hypotheses to explain the evolution of multiple signals. Here we extend these hypotheses to a macroevolutionary scale and compare those predictions to the patterns of gains and losses of sexual dimorphism in pheasants and partridges. Among nine dimorphic characters, including six intersexual signals and three indicators of competitive ability, all exhibited both gains and losses of dimorphism within the group. Although theories of intersexual selection emphasize gain and elaboration, those six characters exhibited greater rates of loss than gain; in contrast, the competitive traits showed a slight bias towards gains. The available models, when examined in a macroevolutionary framework, did not yield unique predictions, making it difficult to distinguish among them. Even with this limitation, when the predictions of these alternative models were compared with the heterogeneous patterns of evolution of dimorphism in phasianids, it is clear that many different selective processes have been involved in the evolution of sexual signals in this group.
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Affiliation(s)
- Rebecca T. Kimball
- Department of Biology, University of Florida, P.O. Box 118525, Gainesville, FL 32611, USA
| | - Colette M. St. Mary
- Department of Biology, University of Florida, P.O. Box 118525, Gainesville, FL 32611, USA
| | - Edward L. Braun
- Department of Biology, University of Florida, P.O. Box 118525, Gainesville, FL 32611, USA
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16
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Ferchaud AL, Lyet A, Cheylan M, Arnal V, Baron JP, Montgelard C, Ursenbacher S. High Genetic Differentiation Among French Populations of the Orsini’s Viper (Vipera ursinii ursinii) Based on Mitochondrial and Microsatellite Data: Implications for Conservation Management. J Hered 2010; 102:67-78. [DOI: 10.1093/jhered/esq098] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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17
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Liu Y, Zhan X, Wang N, Chang J, Zhang Z. Effect of geological vicariance on mitochondrial DNA differentiation in Common Pheasant populations of the Loess Plateau and eastern China. Mol Phylogenet Evol 2010; 55:409-17. [DOI: 10.1016/j.ympev.2009.12.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Revised: 12/24/2009] [Accepted: 12/30/2009] [Indexed: 10/20/2022]
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18
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Bao XK, Liu NF, Qu JY, Wang XL, An B, Wen LY, Song S. The phylogenetic position and speciation dynamics of the genus Perdix (Phasianidae, Galliformes). Mol Phylogenet Evol 2010; 56:840-7. [PMID: 20363341 DOI: 10.1016/j.ympev.2010.03.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Revised: 03/24/2010] [Accepted: 03/29/2010] [Indexed: 10/19/2022]
Abstract
The nuclear gene (c-mos) and mitochondrial genes (CYT B and ND2) sequences, representing 44 phasianid species and 26 genera (mainly distributed in China), were used to study the phylogeny of the genus Perdix, which comprises three partridge species. Maximum parsimony and Bayesian methods were employed, and the analysis of mitochondrial sequence data and the combined dataset showed that Perdix is specifically related either to typical pheasants or to Ithaginis. Phylogenetic trees also indicated that: (1) Perdix is monophyletic; (2) the Tibetan partridge (Perdix hodgsoniae) has been consistently placed as basal to all other Perdix, and the Daurian partridge (Perdix dauuricae) is placed sister to gray partridge (Perdix perdix); (3) the Daurian partridge subspecies przewalskii and Tibetan partridge subspecies hodgsoniae are basal to other subspecies in their species clade, respectively. Speciation in Perdix was likely promoted by the late Pliocene/early Pleistocene intensive uplift of the Tibetan Plateau and by Pleistocene glaciations.
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Affiliation(s)
- Xin-kang Bao
- School of Life Science, Lanzhou University, Lanzhou 730000, China
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19
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Chang HW, Chou YC, Su YF, Cheng CA, Yao CT, Tsai CL, Lee HC, Wen CH, Cheng CC. Molecular phylogeny of the Pycnonotus sinensis and Pycnonotus taivanus in Taiwan based on sequence variations of nuclear CHD and mitochondrial cytochrome b genes. BIOCHEM SYST ECOL 2010. [DOI: 10.1016/j.bse.2009.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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A multi-gene estimate of phylogeny in the nightjars and nighthawks (Caprimulgidae). Mol Phylogenet Evol 2010; 55:443-53. [PMID: 20123032 DOI: 10.1016/j.ympev.2010.01.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 01/16/2010] [Accepted: 01/20/2010] [Indexed: 11/23/2022]
Abstract
Caprimulgidae is a cosmopolitan family of nocturnal and crepuscular insectivorous birds comprising the nightjars, nighthawks, and relatives. Sexual selection and convergence or parallelism in plumage and behavior have made it difficult to discern evolutionary relationships in this group. In order to provide a framework for comparative studies of this family, a molecular phylogeny was reconstructed using mitochondrial cytochrome b, and nuclear c-myc and growth hormone DNA sequences. Likelihood, parsimony and Bayesian analyses agree in placing Eurostopodus species and Caprimulgus enarratus, a Malagasy endemic, as the earliest branches of the tree. The remaining taxa are divided among four well-supported clades, three in the New World and one in the Old World. Insertion/deletion events, common in non-coding sequences, provide additional support in resolving the phylogeny. Neither of the traditional subfamilies, Caprimulginae (nightjars) and Chordeilinae (nighthawks), is monophyletic, suggesting that the morphological specializations characterizing "nighthawks" evolved multiple times and the "nightjar" body plan is an old and conservative one. The large genus Caprimulgus is polyphyletic with respect to many other genera in the family, which are often defined by derived plumage traits that likely reflect sexual selection or ecological specialization. A taxonomic revision of the family is proposed based on the combined tree, including naming a new genus for C. enarratus.
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Morgan K, O'Loughlin SM, Mun-Yik F, Linton YM, Somboon P, Min S, Htun PT, Nambanya S, Weerasinghe I, Sochantha T, Prakash A, Walton C. Molecular phylogenetics and biogeography of the Neocellia Series of Anopheles mosquitoes in the Oriental Region. Mol Phylogenet Evol 2009; 52:588-601. [PMID: 19603555 DOI: 10.1016/j.ympev.2009.01.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Molecular studies of population divergence and speciation across the Oriental Region are sparse, despite the region's high biodiversity and extensive Pliocene and Pleistocene environmental change. A molecular phylogenetic study of the Neocellia Series of Anopheles mosquitoes was undertaken to identify patterns of diversification across the Oriental Region and to infer the role of Pleistocene and Pliocene climatic change. A robust phylogeny was constructed using CO2 and ND5 mitochondrial genes and ITS2 and D3 nuclear ribosomal markers. Bayesian analysis of mitochondrial genes was used to date divergence events. The repeated contraction and expansion of forest habitat resulting from Pleistocene climatic fluctuations appears to have had a substantial impact on intraspecific diversification, but has not driven speciation within this group. Primarily early to mid Pliocene speciation was detected within the Annularis Group, whereas speciation within the Maculatus and Jamesii Groups occurred during the mid and late Pliocene. Both allopatric divergence driven by late Pliocene environmental changes and ecological adaptation, involving altitudinal replacement and seasonality, are likely to have influenced speciation in the Maculatus Group.
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Affiliation(s)
- Katy Morgan
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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22
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Kozyrenko MM, Fisenko PV, Zhuravlev YN. Genetic variation of Manchurian pheasant (Phasianus colchicus pallasi Rotshild, 1903) inferred from mitochondrial DNA control region sequences. RUSS J GENET+ 2009. [DOI: 10.1134/s1022795409040115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Ksepka DT. Broken gears in the avian molecular clock: new phylogenetic analyses support stem galliform status forGallinuloides wyomingensisand rallid affinities forAmitabha urbsinterdictensis. Cladistics 2009; 25:173-197. [DOI: 10.1111/j.1096-0031.2009.00250.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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24
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Meng Y, Dai B, Ran J, Li J, Yue B. Phylogenetic position of the genus Tetraophasis (Aves, Galliformes, Phasianidae) as inferred from mitochondrial and nuclear sequences. BIOCHEM SYST ECOL 2008. [DOI: 10.1016/j.bse.2008.01.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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25
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Li Y, Wu X, Ji X, Yan P, Amato G. The Complete Mitochondrial Genome of Salt-water Crocodile (Crocodylus porosus) and Phylogeny of Crocodilians. J Genet Genomics 2007; 34:119-28. [PMID: 17469784 DOI: 10.1016/s1673-8527(07)60013-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2006] [Accepted: 04/17/2006] [Indexed: 11/29/2022]
Abstract
The nucleotide sequence of the complete mitochondrial DNA (mtDNA) molecule of the salt-water crocodile (Crocodylus porosus) was determined in this article. The molecule is 16,917 base pairs (bp) in length, and codes for 22 tRNAs, 13 protein-coding genes, 2 rRNAs, as well as a control region (D-loop), as is characteristic for mitochondrial genomes of other metazoans. The gene order conforms to that of other crocodilians sequenced, but the arrangement of some tRNA genes differs from other vertebrates. It shows that the gene order of crocodilians is remarkably conserved. In this study, the relationships among crocodilians were examined in the phylogenetic analysis based on the control conserved regions of 17 crocodilians. The results suggest that the gharial (Gavialis gangeticus) joins the false gharial (Tomistoma schlegelii) on a common branch, and then constitutes a sister group to traditional Crocodylidae. Thus, the result supports that G. gangeticus belongs to Crocodylidae. The analyses also suggest that the African slender-snouted crocodile (Crocodylus cataphractus) can be treated as an isolated genus, and constitutes a sister group to Crocodylus.
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MESH Headings
- Alligators and Crocodiles/classification
- Alligators and Crocodiles/genetics
- Animals
- Base Sequence
- DNA, Mitochondrial/analysis
- DNA, Mitochondrial/chemistry
- Evolution, Molecular
- Genes, Mitochondrial
- Genome, Mitochondrial/drug effects
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phylogeny
- RNA, Ribosomal/analysis
- RNA, Ribosomal/chemistry
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- Reptiles
- Sequence Analysis, DNA
- Species Specificity
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Affiliation(s)
- Yan Li
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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26
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Crowe TM, Bowie RCK, Bloomer P, Mandiwana TG, Hedderson TAJ, Randi E, Pereira SL, Wakeling J. Phylogenetics, biogeography and classification of, and character evolution in, gamebirds (Aves: Galliformes): effects of character exclusion, data partitioning and missing data. Cladistics 2006; 22:495-532. [DOI: 10.1111/j.1096-0031.2006.00120.x] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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27
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Ursenbacher S, Carlsson M, Helfer V, Tegelström H, Fumagalli L. Phylogeography and Pleistocene refugia of the adder (Vipera berus) as inferred from mitochondrial DNA sequence data. Mol Ecol 2006; 15:3425-37. [PMID: 16968280 DOI: 10.1111/j.1365-294x.2006.03031.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In order to contribute to the debate about southern glacial refugia used by temperate species and more northern refugia used by boreal or cold-temperate species, we examined the phylogeography of a widespread snake species (Vipera berus) inhabiting Europe up to the Arctic Circle. The analysis of the mitochondrial DNA (mtDNA) sequence variation in 1043 bp of the cytochrome b gene and in 918 bp of the noncoding control region was performed with phylogenetic approaches. Our results suggest that both the duplicated control region and cytochrome b evolve at a similar rate in this species. Phylogenetic analysis showed that V. berus is divided into three major mitochondrial lineages, probably resulting from an Italian, a Balkan and a Northern (from France to Russia) refugial area in Eastern Europe, near the Carpathian Mountains. In addition, the Northern clade presents an important substructure, suggesting two sequential colonization events in Europe. First, the continent was colonized from the three main refugial areas mentioned above during the Lower-Mid Pleistocene. Second, recolonization of most of Europe most likely originated from several refugia located outside of the Mediterranean peninsulas (Carpathian region, east of the Carpathians, France and possibly Hungary) during the Mid-Late Pleistocene, while populations within the Italian and Balkan Peninsulas fluctuated only slightly in distribution range, with larger lowland populations during glacial times and with refugial mountain populations during interglacials, as in the present time. The phylogeographical structure revealed in our study suggests complex recolonization dynamics of the European continent by V. berus, characterized by latitudinal as well as altitudinal range shifts, driven by both climatic changes and competition with related species.
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Affiliation(s)
- S Ursenbacher
- Laboratoire de Biologie de la Conservation, Département d'Ecologie et Evolution, Biophore, Université de Lausanne, CH-1015 Lausanne, Switzerland.
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28
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Yang SJ, Yin ZH, Ma XM, Lei FM. Phylogeography of ground tit (Pseudopodoces humilis) based on mtDNA: evidence of past fragmentation on the Tibetan Plateau. Mol Phylogenet Evol 2006; 41:257-65. [PMID: 16843013 DOI: 10.1016/j.ympev.2006.06.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2005] [Revised: 05/27/2006] [Accepted: 06/01/2006] [Indexed: 11/20/2022]
Abstract
Pseudopodoces humilis, a long misclassified terrestrial tit, is the only species of parid whose distribution is limited to treeless terrain and endemic to the Tibetan Plateau. We revealed the phylogeographic structure of the species by using mitochondrial control region, as well as comparing morphological characters. The distinct geographic distributions of two major clades suggest spatial and temporal separations that coincide with important climatic and paleogeographic changes following the uplift of the Tibetan Plateau. Population expansion was inferred for the population at the platform of the Plateau 0.17 million years before present (Ma B.P.), and restricted gene flow with isolation by distance was detected within this region, congruent with expansion occurring after the extensive glacial period. A significant decrease in body size with decreasing altitude was found, possibly indicating selection for larger-sized birds at higher altitude.
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Affiliation(s)
- Shu-Juan Yang
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China
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29
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Zhan XJ, Zhang ZW. Molecular phylogeny of avian genus Syrmaticus based on the mitochondrial cytochrome B gene and control region. Zoolog Sci 2005; 22:427-35. [PMID: 15846051 DOI: 10.2108/zsj.22.427] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Mitochondrial DNA cytochrome b (cyt b) and control region (CR) nucleotide sequences were used to study the molecular phylogeny of the genus Syrmaticus. We found that the substitution rates among the three codon positions of cyt b were heterogeneous and the transition-transversion ratio was highly biased. As to CR sequences of the genus, most variable sites were in the peripheral domains. All molecular phylogenetic trees based on the two genes showed that: 1) the Syrmaticus was monophyletic and included five species with the following cladistic relationship: (S. reevesii, (S. soemmerringii, (S. mikado, (S. humiae and S. ellioti)))). Using the TN genetic distance of cyt b, we inferred the divergence time of the five species according to putative molecular clock and found that values were largely in agreement with the geological scenarios. The origin and speciation processes of the studied group were inferred by combining molecular and biogeographical evidences.
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Affiliation(s)
- Xiang-Jiang Zhan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, China
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A preliminary study on molecular phylogeny of giant flying squirrels, genus Petaurista (Rodentia, Sciuridae) based on mitochondrial cytochrome b gene sequences. RUSSIAN JOURNAL OF THERIOLOGY 2004. [DOI: 10.15298/rusjtheriol.03.1.04] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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HENNACHE ALAIN, RASMUSSEN PAMELA, LUCCHINI VITTORIO, RIMONDI SILVIA, RANDI ETTORE. Hybrid origin of the imperial pheasant Lophura imperialis (Delacour and Jabouille, 1924) demonstrated by morphology, hybrid experiments, and DNA analyses. Biol J Linn Soc Lond 2003. [DOI: 10.1111/j.1095-8312.2003.00251.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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DYKE GARETHJ, GULAS BONNIEE, CROWE TIMOTHYM. Suprageneric relationships of galliform birds (Aves, Galliformes): a cladistic analysis of morphological characters. Zool J Linn Soc 2003. [DOI: 10.1046/j.1096-3642.2003.00048.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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33
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Ray DA, Densmore L. The crocodilian mitochondrial control region: general structure, conserved sequences, and evolutionary implications. THE JOURNAL OF EXPERIMENTAL ZOOLOGY 2002; 294:334-45. [PMID: 12461813 DOI: 10.1002/jez.10198] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We present the first comprehensive analysis of the crocodilian control region. We have analyzed sequences from all three families of Crocodylia (Crocodylidae, Gavialidae, Alligatoridae), incorporating all genera except Paleosuchus and Melanosuchus. Within the control region of other vertebrates, several sequence motifs and their order appear to be conserved. Herein, we compare aligned crocodilian D-loop sequences to homologous sequences from other vertebrates ranging from fish to birds. Among other findings, we have discovered that while domain I tends to be shorter than the same region in mammals and birds, it contains sequences similar in structure to both the goose-hairpin and termination associated sequences (TAS). Domain II is highly conservative with regard to size among the taxa examined and contains several of the conserved sequence boxes characterized in other vertebrates. Domain III contains several interesting sequence motifs including tandemly repeated sequences, a long poly-A region in the Crocodylidae, and possible bidirection promoter sequences.
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Affiliation(s)
- David Alfred Ray
- Texas Tech University, Department of Biological Sciences, Lubbock, Texas 79409, USA.
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