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Liang M, Zhang L, Lai L, Li Z. Unraveling the role of Xist in X chromosome inactivation: insights from rabbit model and deletion analysis of exons and repeat A. Cell Mol Life Sci 2024; 81:156. [PMID: 38551746 PMCID: PMC10980640 DOI: 10.1007/s00018-024-05151-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 04/01/2024]
Abstract
X chromosome inactivation (XCI) is a process that equalizes the expression of X-linked genes between males and females. It relies on Xist, continuously expressed in somatic cells during XCI maintenance. However, how Xist impacts XCI maintenance and its functional motifs remain unclear. In this study, we conducted a comprehensive analysis of Xist, using rabbits as an ideal non-primate model. Homozygous knockout of exon 1, exon 6, and repeat A in female rabbits resulted in embryonic lethality. However, X∆ReAX females, with intact X chromosome expressing Xist, showed no abnormalities. Interestingly, there were no significant differences between females with homozygous knockout of exons 2-5 and wild-type rabbits, suggesting that exons 2, 3, 4, and 5 are less important for XCI. These findings provide evolutionary insights into Xist function.
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Affiliation(s)
- Mingming Liang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Lichao Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Liangxue Lai
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, 100039, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences, Guangzhou, 510530, China.
| | - Zhanjun Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
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2
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Černý D, Natale R. Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes). Mol Phylogenet Evol 2022; 177:107620. [PMID: 36038056 DOI: 10.1016/j.ympev.2022.107620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 06/03/2022] [Accepted: 08/17/2022] [Indexed: 01/20/2023]
Abstract
Shorebirds (Charadriiformes) are a globally distributed clade of modern birds and, due to their ecological and morphological disparity, a frequent subject of comparative studies. While molecular phylogenies have been key to establishing the suprafamilial backbone of the charadriiform tree, a number of relationships at both deep and shallow taxonomic levels remain poorly resolved. The timescale of shorebird evolution also remains uncertain as a result of extensive disagreements among the published divergence dating studies, stemming largely from different choices of fossil calibrations. Here, we present the most comprehensive non-supertree phylogeny of shorebirds to date, based on a total-evidence dataset comprising 353 ingroup taxa (90% of all extant or recently extinct species), 27 loci (15 mitochondrial and 12 nuclear), and 69 morphological characters. We further clarify the timeline of charadriiform evolution by time-scaling this phylogeny using a set of 14 up-to-date and thoroughly vetted fossil calibrations. In addition, we assemble a taxonomically restricted 100-locus dataset specifically designed to resolve outstanding problems in higher-level charadriiform phylogeny. In terms of tree topology, our results are largely congruent with previous studies but indicate that some of the conflicts among earlier analyses reflect a genuine signal of pervasive gene tree discordance. Monophyly of the plovers (Charadriidae), the position of the ibisbill (Ibidorhyncha), and the relationships among the five subfamilies of the gulls (Laridae) could not be resolved even with greatly increased locus and taxon sampling. Moreover, several localized regions of uncertainty persist in shallower parts of the tree, including the interrelationships of the true auks (Alcinae) and anarhynchine plovers. Our node-dating and macroevolutionary rate analyses find support for a Paleocene origin of crown-group shorebirds, as well as exceptionally rapid recent radiations of Old World oystercatchers (Haematopodidae) and select genera of gulls. Our study underscores the challenges involved in estimating a comprehensively sampled and carefully calibrated time tree for a diverse avian clade, and highlights areas in need of further research.
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Affiliation(s)
- David Černý
- Department of the Geophysical Sciences, University of Chicago, Chicago 60637, USA.
| | - Rossy Natale
- Department of Organismal Biology & Anatomy, University of Chicago, Chicago 60637, USA
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3
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Iotchev IB, Kubinyi E. Shared and unique features of mammalian sleep spindles - insights from new and old animal models. Biol Rev Camb Philos Soc 2021; 96:1021-1034. [PMID: 33533183 DOI: 10.1111/brv.12688] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 11/29/2022]
Abstract
Sleep spindles are phasic events observed in mammalian non-rapid eye movement sleep. They are relevant today in the study of memory consolidation, sleep quality, mental health and ageing. We argue that our advanced understanding of their mechanisms has not exhausted the utility and need for animal model work. This is both because some topics, like cognitive ageing, have not yet been addressed sufficiently in comparative efforts and because the evolutionary history of this oscillation is still poorly understood. Comparisons across species often are either limited to referencing the classical cat and rodent models, or are over-inclusive, uncritically including reports of sleep spindles in rarely studied animals. In this review, we discuss the emergence of new (dog and sheep) models for sleep spindles and compare the strengths and shortcomings of new and old models based on the three validation criteria for animal models - face, predictive, and construct validity. We conclude that an emphasis on cognitive ageing might dictate the future of comparative sleep spindle studies, a development that is already becoming visible in studies on dogs. Moreover, reconstructing the evolutionary history of sleep spindles will require more stringent criteria for their identification, across more species. In particular, a stronger emphasis on construct and predictive validity can help verify if spindle-like events in other species are actual sleep spindles. Work in accordance with such stricter validation suggests that sleep spindles display more universally shared features, like defining frequency, than previously thought.
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Affiliation(s)
- Ivaylo Borislavov Iotchev
- Department of Ethology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
| | - Eniko Kubinyi
- Department of Ethology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
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4
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Phillips MJ, Shazwani Zakaria S. Enhancing mitogenomic phylogeny and resolving the relationships of extinct megafaunal placental mammals. Mol Phylogenet Evol 2021; 158:107082. [PMID: 33482383 DOI: 10.1016/j.ympev.2021.107082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/21/2020] [Accepted: 01/11/2021] [Indexed: 10/22/2022]
Abstract
Mitochondrial genomes provided the first widely used sequences that were sufficiently informative to resolve relationships among animals across a wide taxonomic domain, from within species to between phyla. However, mitogenome studies supported several anomalous relationships and fell partly out of favour as sequencing multiple, independent nuclear loci proved to be highly effective. A tendency to blame mitochondrial DNA (mtDNA) has overshadowed efforts to understand and ameliorate underlying model misspecification. Here we find that influential assessments of the infidelity of mitogenome phylogenies have often been overstated, but nevertheless, substitution saturation and compositional non-stationarity substantially mislead reconstruction. We show that RY coding the mtDNA, excluding protein-coding 3rd codon sites, partitioning models based on amino acid hydrophobicity and enhanced taxon sampling improve the accuracy of mitogenomic phylogeny reconstruction for placental mammals, almost to the level of multi-gene nuclear datasets. Indeed, combined analysis of mtDNA with 3-fold longer nuclear sequence data either maintained or improved upon the nuclear support for all generally accepted clades, even those that mtDNA alone did not favour, thus indicating "hidden support". Confident mtDNA phylogeny reconstruction is especially important for understanding the evolutionary dynamics of mitochondria themselves, and for merging extinct taxa into the tree of life, with ancient DNA often only accessible as mtDNA. Our ancient mtDNA analyses lend confidence to the relationships of three extinct megafaunal taxa: glyptodonts are nested within armadillos, the South American ungulate, Macrauchenia is sister to horses and rhinoceroses, and sabre-toothed and scimitar cats are the monophyletic sister-group of modern cats.
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Affiliation(s)
- Matthew J Phillips
- School of Biology and Environmental Science, Queensland University of Technology, 2 George Street, Brisbane 4000, QLD, Australia.
| | - Sarah Shazwani Zakaria
- School of Biology and Environmental Science, Queensland University of Technology, 2 George Street, Brisbane 4000, QLD, Australia; School of Biology, Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM) Caw. Negeri Sembilan, Kuala Pilah 72000, Malaysia
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5
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Lv X, Hu J, Hu Y, Li Y, Xu D, Ryder OA, Irwin DM, Yu L. Diverse phylogenomic datasets uncover a concordant scenario of laurasiatherian interordinal relationships. Mol Phylogenet Evol 2020; 157:107065. [PMID: 33387649 DOI: 10.1016/j.ympev.2020.107065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 10/22/2022]
Abstract
Resolving the interordinal relationships in the mammalian superorder Laurasiatheria has been among the most intractable problems in higher-level mammalian systematics, with many conflicting hypotheses having been proposed. The present study collected three different sources of genome-scale data with comprehensive taxon sampling of laurasiatherian species, including two protein-coding datasets (4,186 protein-coding genes for an amino acid dataset comprising 2,761,247 amino acid residues and a nucleotide dataset comprising 5,516,340 nucleotides from 1st and 2nd codon positions), an intronic dataset (1,210 introns comprising 1,162,723 nucleotides) and an ultraconserved elements (UCEs) dataset (1,246 UCEs comprising 1,946,472 nucleotides) from 40 species representing all six laurasiatherian orders and 7 non-laurasiatherian outgroups. Remarkably, phylogenetic trees reconstructed with the four datasets using different tree-building methods (RAxML, FastTree, ASTRAL and MP-EST) all supported the relationship (Eulipotyphla, (Chiroptera, ((Carnivora, Pholidota), (Cetartiodactyla, Perissodactyla)))). We find a resolution of interordinal relationships of Laurasiatheria among all types of markers used in the present study, and the likelihood ratio tests for tree comparisons confirmed that the present tree topology is the optimal hypothesis compared to other examined hypotheses. Jackknifing subsampling analyses demonstrate that the results of laurasiatherian tree reconstruction varied with the number of loci and ordinal representatives used, which are likely the two main contributors to phylogenetic disagreements of Laurasiatheria seen in previous studies. Our study provides significant insight into laurasiatherian evolution, and moreover, an important methodological strategy and reference for resolving phylogenies of adaptive radiation, which have been a long-standing challenge in the field of phylogenetics.
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Affiliation(s)
- Xue Lv
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Jingyang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Yiwen Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Yitian Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Dongming Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, China
| | - Oliver A Ryder
- Institute for Conservation Research, San Diego Zoo Global, Escondido, CA, USA
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.
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Li G, Tian X, Lv D, Zhang L, Zhang Z, Wang J, Yang M, Tao J, Ma T, Wu H, Ji P, Wu Y, Lian Z, Cui W, Liu G. NLRP7 is expressed in the ovine ovary and associated with in vitro pre-implantation embryo development. Reproduction 2020; 158:415-427. [PMID: 31505467 PMCID: PMC6826174 DOI: 10.1530/rep-19-0081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 09/10/2019] [Indexed: 12/13/2022]
Abstract
NLRP (NACHT, LRR and PYD domain-containing proteins) family plays pivotal roles in mammalian reproduction. Mutation of NLRP7 is often associated with human recurrent hydatidiform moles. Few studies regarding the functions of NLRP7 have been performed in other mammalian species rather than humans. In the current study, for the first time, the function of NLRP7 has been explored in ovine ovary. NLRP7 protein was mainly located in ovarian follicles and in in vitro pre-implantation embryos. To identify its origin, 763 bp partial CDS of NLRP7 deriving from sheep cumulus oocyte complexes (COCs) was cloned, it showed a great homology with Homo sapiens. The high levels of mRNA and protein of NLRP7 were steadily expressed in oocytes, parthenogenetic embryos or IVF embryos. NLRP7 knockdown by the combination of siRNA and shRNA jeopardized both the parthenogenetic and IVF embryo development. These results strongly suggest that NLRP7 plays an important role in ovine reproduction. The potential mechanisms of NLRP7 will be fully investigated in the future.
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Affiliation(s)
- Guangdong Li
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiuzhi Tian
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dongying Lv
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lu Zhang
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhenzhen Zhang
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jing Wang
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Minghui Yang
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jingli Tao
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Teng Ma
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hao Wu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Pengyun Ji
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yingjie Wu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhengxing Lian
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wei Cui
- Department of Surgery and Cancer, Institute of Reproductive and Developmental Biology, Imperial College London, London, UK.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, China
| | - Guoshi Liu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
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7
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Two mitochondrial genomes in Alcedinidae (Ceryle rudis/Halcyon pileata) and the phylogenetic placement of Coraciiformes. Genetica 2017; 145:431-440. [PMID: 28791584 DOI: 10.1007/s10709-017-9978-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 08/03/2017] [Indexed: 10/19/2022]
Abstract
Coraciiformes comprises 209 species belonging to ten families with significant divergence on external morphologies and life styles. The phylogenetic placement of Coraciiformes was still in debate. Here, we determined the complete mitochondrial genomes (mitogenomes) of Crested Kingfisher (Ceryle rudis) and Black-capped Kingfisher (Halcyon pileata). The mitogenomes were 17,355 bp (C. rudis) and 17,612 bp (H. pileata) in length, and both of them contained 37 genes (two rRNA genes, 22 tRNA genes and 13 protein-coding genes) and one control region. The gene organizations and characters of two mitogenomes were similar with those of other mitogenomes in Coraciiformes, however the sizes and nucleotide composition of control regions in different mitogenomes were significantly different. Phylogenetic trees were constructed with both Bayesian and Maximum Likelihood methods based on mitogenome sequences from 11 families of six orders. The trees based on two different data sets supported the basal position of Psittacidae (Psittaciformes), the closest relationship between Cuculiformes (Cuculidae) and Trogoniformes (Trogonidae), and the close relationship between Coraciiformes and Piciformes. The phylogenetic placement of the clade including Cuculiformes and Trogoniformes has not been resolved in present study, which need further investigations with more molecular markers and species. The mitogenome sequences presented here provided valuable data for further taxonomic studies on Coraciiformes and other related groups.
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Two mitogenomes in Gruiformes (Amaurornis akool/A. phoenicurus) and the phylogenetic placement of Rallidae. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0562-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Zhou Y, Wang SR, Ma JZ. Comprehensive species set revealing the phylogeny and biogeography of Feliformia (Mammalia, Carnivora) based on mitochondrial DNA. PLoS One 2017; 12:e0174902. [PMID: 28358848 PMCID: PMC5373635 DOI: 10.1371/journal.pone.0174902] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 03/18/2017] [Indexed: 11/18/2022] Open
Abstract
Extant Feliformia species are one of the most diverse radiations of Carnivora (~123 species). Despite substantial recent interest in their conservation, diversification, and systematic study, no previous phylogeny contains a comprehensive species set, and no biogeography of this group is available. Here, we present a phylogenetic estimate for Feliformia with a comprehensive species set and establish a historical biogeography based on mitochondrial DNA. Both the Bayesian and maximum likelihood phylogeny for Feliformia are elucidated in our analyses and are strongly consistent with many groups recognized in previous studies. The mitochondrial phylogenetic relationships of Felidae were for the first time successfully reconstructed in our analyses with strong supported. When divergence times and dispersal/vicariance histories were compared with historical sea level changes, four dispersal and six vicariance events were identified. These vicariance events were closely related with global sea level changes. The transgression of sea into the lowland plains between Eurasia and Africa may have caused the vicariance in these regions. A fall in the sea level during late Miocene to Pliocene produced the Bering strait land bridge, which assisted the migration of American Feliformia ancestors from Asia to North America. In contrast with the ‘sweepstakes hypothesis’, our results suggest that the climate cooling during 30–27 Ma assisted Feliformia migration from the African mainland to Madagascar by creating a short-lived ice bridge across the Mozambique Channel. Lineages-through-time plots revealed a large increase in lineages since the Mid-Miocene. During the Mid-Miocene Climatic Optimum, the ecosystems and population of Feliformia rapidly expanded. Subsequent climate cooling catalyzed immigration, speciation, and the extinction of Feliformia.
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Affiliation(s)
- Yu Zhou
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
- Feline Research Center of Chinese State Forestry Administration, Northeast Forestry University, Harbin, China
| | - Si-Rui Wang
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Jian-Zhang Ma
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
- Feline Research Center of Chinese State Forestry Administration, Northeast Forestry University, Harbin, China
- * E-mail:
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Springer MS, Gatesy J. The gene tree delusion. Mol Phylogenet Evol 2016; 94:1-33. [DOI: 10.1016/j.ympev.2015.07.018] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/04/2015] [Accepted: 07/22/2015] [Indexed: 10/23/2022]
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Kawahara M, Koyama S, Iimura S, Yamazaki W, Tanaka A, Kohri N, Sasaki K, Takahashi M. Preimplantation death of xenomitochondrial mouse embryo harbouring bovine mitochondria. Sci Rep 2015; 5:14512. [PMID: 26416548 PMCID: PMC4586891 DOI: 10.1038/srep14512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 09/02/2015] [Indexed: 11/09/2022] Open
Abstract
Mitochondria, cellular organelles playing essential roles in eukaryotic cell metabolism, are thought to have evolved from bacteria. The organization of mtDNA is remarkably uniform across species, reflecting its vital and conserved role in oxidative phosphorylation (OXPHOS). Our objectives were to evaluate the compatibility of xenogeneic mitochondria in the development of preimplantation embryos in mammals. Mouse embryos harbouring bovine mitochondria (mtB-M embryos) were prepared by the cell-fusion technique employing the haemagglutinating virus of Japan (HVJ). The mtB-M embryos showed developmental delay at embryonic days (E) 3.5 after insemination. Furthermore, none of the mtB-M embryos could implant into the maternal uterus after embryo transfer, whereas control mouse embryos into which mitochondria from another mouse had been transferred developed as well as did non-manipulated embryos. When we performed quantitative PCR (qPCR) of mouse and bovine ND5, we found that the mtB-M embryos contained 8.3% of bovine mitochondria at the blastocyst stage. Thus, contamination with mitochondria from another species induces embryonic lethality prior to implantation into the maternal uterus. The heteroplasmic state of these xenogeneic mitochondria could have detrimental effects on preimplantation development, leading to preservation of species-specific mitochondrial integrity in mammals.
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Affiliation(s)
- Manabu Kawahara
- Laboratory of Animal Breeding and Reproduction, Research Faculty of Agriculture, Hokkaido University, Kita-ku Kita 9 Nishi 9, Sapporo 060-8589, Japan
| | - Shiori Koyama
- Laboratory of Animal Breeding and Reproduction, Research Faculty of Agriculture, Hokkaido University, Kita-ku Kita 9 Nishi 9, Sapporo 060-8589, Japan
| | - Satomi Iimura
- Laboratory of Animal Breeding and Reproduction, Research Faculty of Agriculture, Hokkaido University, Kita-ku Kita 9 Nishi 9, Sapporo 060-8589, Japan
| | - Wataru Yamazaki
- Laboratory of Animal Breeding and Reproduction, Research Faculty of Agriculture, Hokkaido University, Kita-ku Kita 9 Nishi 9, Sapporo 060-8589, Japan
| | - Aiko Tanaka
- Laboratory of Animal Breeding and Reproduction, Research Faculty of Agriculture, Hokkaido University, Kita-ku Kita 9 Nishi 9, Sapporo 060-8589, Japan
| | - Nanami Kohri
- Laboratory of Animal Breeding and Reproduction, Research Faculty of Agriculture, Hokkaido University, Kita-ku Kita 9 Nishi 9, Sapporo 060-8589, Japan
| | - Keisuke Sasaki
- Laboratory of Animal Breeding and Reproduction, Research Faculty of Agriculture, Hokkaido University, Kita-ku Kita 9 Nishi 9, Sapporo 060-8589, Japan
| | - Masashi Takahashi
- Laboratory of Animal Breeding and Reproduction, Research Faculty of Agriculture, Hokkaido University, Kita-ku Kita 9 Nishi 9, Sapporo 060-8589, Japan
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Zou Y, Jing MD, Bi XX, Zhang T, Huang L. The complete mitochondrial genome sequence of the little egret (Egretta garzetta). Genet Mol Biol 2015; 38:162-72. [PMID: 26273219 PMCID: PMC4530654 DOI: 10.1590/s1415-4757382220140203] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 12/02/2014] [Indexed: 11/22/2022] Open
Abstract
Many phylogenetic questions in the Ciconiiformes remain unresolved and complete mitogenome data are urgently needed for further molecular investigation. In this work, we determined the complete mitogenome sequence of the little egret (Egretta garzetta). The genome was 17,361 bp in length and the gene organization was typical of other avian mtDNA. In protein-coding genes (PCGs), a C insertion was found in ND3, and COIII and ND4 terminated with incomplete stop codons (T). tRNA-Val and tRNA-Ser (AGY) were unable to fold into canonical cloverleaf secondary structures because they had lost the DHU arms. Long repetitive sequences consisting of five types of tandem repeats were found at the 3' end of Domain III in the control region. A phylogenetic analysis of 11 species of Ciconiiformes was done using complete mitogenome data and 12 PCGs. The tree topologies obtained with these two strategies were identical, which strongly confirmed the monophyly of Ardeidae, Threskiorothidae and Ciconiidae. The phylogenetic analysis also revealed that Egretta was more closely related to Ardea than to Nycticorax in the Ardeidae, and Platalea was more closely related to Threskiornis than to Nipponia in the Threskiornithidae. These findings contribute to our understanding of the phylogenetic relationships of Ciconiiformes based on complete mitogenome data.
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Affiliation(s)
- Yi Zou
- College of Life Sciences, Ludong University, Yantai, Shandong, P.R. China
| | - Mei-Dong Jing
- College of Life Sciences, Ludong University, Yantai, Shandong, P.R. China
| | - Xiao-Xin Bi
- College of Life Sciences, Ludong University, Yantai, Shandong, P.R. China
| | - Ting Zhang
- College of Life Sciences, Ludong University, Yantai, Shandong, P.R. China
| | - Ling Huang
- College of Life Sciences, Ludong University, Yantai, Shandong, P.R. China
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13
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A Guide to Phylogenetic Reconstruction Using Heterogeneous Models—A Case Study from the Root of the Placental Mammal Tree. COMPUTATION 2015. [DOI: 10.3390/computation3020177] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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14
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Banguera-Hinestroza E, Hayano A, Crespo E, Hoelzel AR. Delphinid systematics and biogeography with a focus on the current genus Lagenorhynchus: multiple pathways for antitropical and trans-oceanic radiation. Mol Phylogenet Evol 2014; 80:217-30. [PMID: 25130419 DOI: 10.1016/j.ympev.2014.08.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 07/20/2014] [Accepted: 08/03/2014] [Indexed: 10/24/2022]
Abstract
The six species currently classified within the genus Lagenorhynchus exhibit a pattern of antitropical distribution common among marine taxa. In spite of their morphological similarities they are now considered an artificial grouping, and include both recent and the oldest representatives of the Delphinidae radiation. They are, therefore, a good model for studying questions about the evolutionary processes that have driven dolphin speciation, dispersion and distribution. Here we used two different approaches. First we constructed a multigenic phylogeny with a minimum amount of missing data (based on 9 genes, 11,030bp, using the 6 species of the genus and their closest relatives) to infer their relationships. Second, we built a supermatrix phylogeny (based on 33 species and 27 genes) to test the effect of taxon sampling on the phylogeny of the genus, to provide inference on biogeographic history, and provide inference on the main events shaping the dispersion and radiation of delphinids. Our analyses suggested an early evolutionary history of marine dolphins in the North Atlantic Ocean and revealed multiple pathways of migration and radiation, probably guided by paleoceanographic changes during the Miocene and Pliocene. L. acutus and L. albirostris likely shared a common ancestor that arose in the North Atlantic around the Middle Miocene, predating the radiation of subfamilies Delphininae, Globicephalinae and Lissodelphininae.
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Affiliation(s)
| | - Azusa Hayano
- Wildlife Research Center, Kyoto University, Sakyo, Kyoto 606-8203, Japan
| | - Enrique Crespo
- Centro Nacional Patagonico (CONICET), Blvd. Brown 3600 (9120), Puerto Madryn, Chubut, Argentina
| | - A Rus Hoelzel
- Department of Biological and Biomedical Sciences, University of Durham, South Road DH1 3LE, UK.
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15
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Wu J, Hasegawa M, Zhong Y, Yonezawa T. Importance of synonymous substitutions under dense taxon sampling and appropriate modeling in reconstructing the mitogenomic tree of Eutheria. Genes Genet Syst 2014; 89:237-51. [DOI: 10.1266/ggs.89.237] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Jiaqi Wu
- School of Life Sciences, Fudan University
| | - Masami Hasegawa
- The Institute of Statistical Mathematics
- School of Life Sciences, Fudan University
| | - Yang Zhong
- Institute of Biodiversity Science and Geobiology, Tibet University
- School of Life Sciences, Fudan University
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16
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Fabre PH, Jønsson KA, Douzery EJP. Jumping and gliding rodents: mitogenomic affinities of Pedetidae and Anomaluridae deduced from an RNA-Seq approach. Gene 2013; 531:388-97. [PMID: 23973722 DOI: 10.1016/j.gene.2013.07.059] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/10/2013] [Accepted: 07/16/2013] [Indexed: 10/26/2022]
Abstract
An RNA-Seq strategy was used to obtain the complete set of protein-coding mitochondrial genes from two rodent taxa. Thanks to the next generation sequencing (NGS) 454 approach, we determined the complete mitochondrial DNA genome from Graphiurus kelleni (Mammalia: Rodentia: Gliridae) and partial mitogenome from Pedetes capensis (Pedetidae), and compared them with published rodent and outgroup mitogenomes. We finished the mitogenome sequencing by a series of amplicons using conserved PCR primers to fill the gaps corresponding to tRNA, rRNA and control regions. Phylogenetic analyses of the mitogenomes suggest a well-supported rodent phylogeny in agreement with nuclear gene trees. Pedetes groups with Anomalurus into the clade Anomaluromorpha, while Graphiurus branches within the squirrel-related clade. Moreover, Pedetes+Anomalurus branch with Castor into the mouse-related clade. Our study demonstrates the utility of NGS for obtaining new mitochondrial genomes as well as the importance of choosing adequate models of sequence evolution to infer the phylogeny of rodents.
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Affiliation(s)
- Pierre-Henri Fabre
- Institut des Sciences de l'Evolution (ISEM, UMR 5554 UM2-CNRS-IRD), Université Montpellier II, Place Eugène Bataillon - CC 064 - 34095 Montpellier Cedex 5, France; Center for Macroecology Evolution and Climate at the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken, 15, DK-2100 Copenhagen Ø, Denmark
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17
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Hu JY, Zhang YP, Yu L. Summary of Laurasiatheria (mammalia) phylogeny. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2013; 33:E65-74. [PMID: 23266984 DOI: 10.3724/sp.j.1141.2012.e05-06e65] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Laurasiatheria is one of the richest and most diverse superorders of placental mammals. Because this group had a rapid evolutionary radiation, the phylogenetic relationships among the six orders of Laurasiatheria remain a subject of heated debate and several issues related to its phylogeny remain open. Reconstructing the true phylogenetic relationships of Laurasiatheria is a significant case study in evolutionary biology due to the diversity of this suborder and such research will have significant implications for biodiversity conservation. We review the higher-level (inter-ordinal) phylogenies of Laurasiatheria based on previous cytogenetic, morphological and molecular data, and discuss the controversies of its phylogenetic relationship. This review aims to outline future researches on Laurasiatheria phylogeny and adaptive evolution.
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18
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Liu Y. The complete mitochondrial genome sequence of Xenocypris davidi (Bleeker). ACTA ACUST UNITED AC 2013; 25:374-6. [DOI: 10.3109/19401736.2013.809429] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Yu Liu
- Aquatic Ecohealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences
XiamenPR China
- Graduate University of Chinese Academy of Sciences
BeijingPR China
- Xiamen Environmental Protection Research Institute
XiamenPR China
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19
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Tong GX, Kuang YY, Geng LW, Xu W, Yin JS. Mitochondrial DNA sequence of Mongolian redfin (Chanodichthys mongolicus). MITOCHONDRIAL DNA 2013; 25:407-9. [PMID: 23795832 DOI: 10.3109/19401736.2013.803539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Monglian redfin is a kind of freshwater aquaculture species which has an important economic value in China. In this study, we report the complete sequence of mitochondrial genome of Monglian redfin. The complete mitochondrial genome sequence is determined to be 16,621 base pairs (bp) in length and contain 13 protein-coding gene (PCGs), 22 transfer RNA genes, large (rrnL) and small (rrnS) ribosomal RNA, and the non-coding control region. Its total A+T content is 55.98%. We also analyzed the structure of control region, six conserved sequence blocks (CSBs) (CSB-1, CSB-2, CSB-3, CSB-D, CSB-E and CSB-F) and one potential termination-associated sequence were detected and the control region also included a 2-bp tandem repeat with eight repeat times.
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Affiliation(s)
- Guang-Xiang Tong
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Harbin , P. R. China
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20
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Zhang P, Liang D, Mao RL, Hillis DM, Wake DB, Cannatella DC. Efficient sequencing of Anuran mtDNAs and a mitogenomic exploration of the phylogeny and evolution of frogs. Mol Biol Evol 2013; 30:1899-915. [PMID: 23666244 DOI: 10.1093/molbev/mst091] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Anura (frogs and toads) constitute over 88% of living amphibian diversity but many important questions about their phylogeny and evolution remain unresolved. For this study, we developed an efficient method for sequencing anuran mitochondrial DNAs (mtDNAs) by amplifying the mitochondrial genome in 12 overlapping fragments using frog-specific universal primer sets. Based on this method, we generated 47 nearly complete, new anuran mitochondrial genomes and discovered nine novel gene arrangements. By combining the new data and published anuran mitochondrial genomes, we assembled a large mitogenomic data set (11,007 nt) including 90 frog species, representing 39 of 53 recognized anuran families, to investigate their phylogenetic relationships and evolutionary history. The resulting tree strongly supported a paraphyletic arrangement of archaeobatrachian (=nonneobatrachian) frogs, with Leiopelmatoidea branching first, followed by Discoglossoidea, Pipoidea, and Pelobatoidea. Within Neobatrachia, the South African Heleophrynidae is the sister-taxon to all other neobatrachian frogs and the Seychelles-endemic Sooglossidae is recovered as the sister-taxon to Ranoidea. These phylogenetic relationships agree with many nuclear gene studies. The chronogram derived from two Bayesian relaxed clock methods (MultiDivTime and BEAST) suggests that modern frogs (Anura) originated in the early Triassic about 244 Ma and the appearance of Neobatrachia took place in the late Jurassic about 163 Ma. The initial diversifications of two species-rich superfamilies Hyloidea and Ranoidea commenced 110 and 133 Ma, respectively. These times are older than some other estimates by approximately 30-40 My. Compared with nuclear data, mtDNA produces compatible time estimates for deep nodes (>150 Ma), but apparently older estimates for more shallow nodes. Our study shows that, although it evolves relatively rapidly and behaves much as a single locus, mtDNA performs well for both phylogenetic and divergence time inferences and will provide important reference hypotheses for the phylogeny and evolution of frogs.
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Affiliation(s)
- Peng Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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21
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Luo H, Arndt W, Zhang Y, Shi G, Alekseyev M, Tang J, Hughes AL, Friedman R. Phylogenetic analysis of genome rearrangements among five mammalian orders. Mol Phylogenet Evol 2012; 65:871-82. [PMID: 22929217 PMCID: PMC4425404 DOI: 10.1016/j.ympev.2012.08.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 08/11/2012] [Accepted: 08/13/2012] [Indexed: 01/16/2023]
Abstract
Evolutionary relationships among placental mammalian orders have been controversial. Whole genome sequencing and new computational methods offer opportunities to resolve the relationships among 10 genomes belonging to the mammalian orders Primates, Rodentia, Carnivora, Perissodactyla and Artiodactyla. By application of the double cut and join distance metric, where gene order is the phylogenetic character, we computed genomic distances among the sampled mammalian genomes. With a marsupial outgroup, the gene order tree supported a topology in which Rodentia fell outside the cluster of Primates, Carnivora, Perissodactyla, and Artiodactyla. Results of breakpoint reuse rate and synteny block length analyses were consistent with the prediction of random breakage model, which provided a diagnostic test to support use of gene order as an appropriate phylogenetic character in this study. We discussed the influence of rate differences among lineages and other factors that may contribute to different resolutions of mammalian ordinal relationships by different methods of phylogenetic reconstruction.
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Affiliation(s)
- Haiwei Luo
- Department of Biological Sciences, University of South Carolina, Columbia 29208, USA
| | - William Arndt
- Department of Computer Science and Engineering, University of South Carolina, Columbia 29208, USA
| | - Yiwei Zhang
- Department of Computer Science and Engineering, University of South Carolina, Columbia 29208, USA
| | - Guanqun Shi
- Department of Computer Science, University of California, Riverside, 92521, USA
| | - Max Alekseyev
- Department of Computer Science and Engineering, University of South Carolina, Columbia 29208, USA
| | - Jijun Tang
- Department of Computer Science and Engineering, University of South Carolina, Columbia 29208, USA
| | - Austin L. Hughes
- Department of Biological Sciences, University of South Carolina, Columbia 29208, USA
| | - Robert Friedman
- Department of Biological Sciences, University of South Carolina, Columbia 29208, USA
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22
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Resolution of the laurasiatherian phylogeny: Evidence from genomic data. Mol Phylogenet Evol 2012; 64:685-9. [DOI: 10.1016/j.ympev.2012.04.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 04/03/2012] [Accepted: 04/17/2012] [Indexed: 11/17/2022]
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23
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Sequencing of 21 varicella-zoster virus genomes reveals two novel genotypes and evidence of recombination. J Virol 2011; 86:1608-22. [PMID: 22130537 DOI: 10.1128/jvi.06233-11] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Genotyping of 21 varicella-zoster virus (VZV) strains using a scattered single nucleotide polymorphism (SNP) method revealed ambiguous SNPs and two nontypeable isolates. For a further genetic characterization, the genomes of all strains were sequenced using the 454 technology. Almost-complete genome sequences were assembled, and most remaining gaps were closed with Sanger sequencing. Phylogenetic analysis of 42 genomes revealed five established and two novel VZV genotypes, provisionally termed VIII and IX. Genotypes VIII and IX are distinct from the previously reported provisional genotypes VI and VII as judged from the SNP pattern. The alignments showed evidence of ancient recombination events in the phylogeny of clade 4 and recent recombinations within single strains: 3/2005 (clade 1), 11 and 405/2007 (clade 3), 8 and DR (clade 4), CA123 and 413/2000 (clade 5), and strains of the novel genotypes VIII and IX. Bayesian tree inference of the thymidine kinase and the polymerase genes of the VZV clades and other varicelloviruses revealed that VZV radiation began some 110,000 years ago, which correlates with the out-of-Africa dispersal of modern humans. The split of ancestral clades 2/4 and 1/3/5/VIII/IX shows the greatest node height.
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24
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Li WLS, Drummond AJ. Model averaging and Bayes factor calculation of relaxed molecular clocks in Bayesian phylogenetics. Mol Biol Evol 2011; 29:751-61. [PMID: 21940644 PMCID: PMC3258040 DOI: 10.1093/molbev/msr232] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We describe a procedure for model averaging of relaxed molecular clock models in Bayesian phylogenetics. Our approach allows us to model the distribution of rates of substitution across branches, averaged over a set of models, rather than conditioned on a single model. We implement this procedure and test it on simulated data to show that our method can accurately recover the true underlying distribution of rates. We applied the method to a set of alignments taken from a data set of 12 mammalian species and uncovered evidence that lognormally distributed rates better describe this data set than do exponentially distributed rates. Additionally, our implementation of model averaging permits accurate calculation of the Bayes factor(s) between two or more relaxed molecular clock models. Finally, we introduce a new computational approach for sampling rates of substitution across branches that improves the convergence of our Markov chain Monte Carlo algorithms in this context. Our methods are implemented under the BEAST 1.6 software package, available at http://beast-mcmc.googlecode.com.
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Affiliation(s)
- Wai Lok Sibon Li
- Computational Evolution Group, University of Auckland, Auckland, New Zealand
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25
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Modular organizations of novel cetacean papillomaviruses. Mol Phylogenet Evol 2011; 59:34-42. [DOI: 10.1016/j.ympev.2010.12.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 12/02/2010] [Accepted: 12/22/2010] [Indexed: 11/20/2022]
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26
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Campbell V, Lapointe FJ. Retrieving a mitogenomic mammal tree using composite taxa. Mol Phylogenet Evol 2011; 58:149-56. [DOI: 10.1016/j.ympev.2010.11.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Revised: 10/17/2010] [Accepted: 11/19/2010] [Indexed: 10/18/2022]
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27
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Gottschling M, Goker M, Stamatakis A, Bininda-Emonds ORP, Nindl I, Bravo IG. Quantifying the Phylodynamic Forces Driving Papillomavirus Evolution. Mol Biol Evol 2011; 28:2101-13. [DOI: 10.1093/molbev/msr030] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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28
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Pacheco MA, Battistuzzi FU, Lentino M, Aguilar RF, Kumar S, Escalante AA. Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders. Mol Biol Evol 2011; 28:1927-42. [PMID: 21242529 DOI: 10.1093/molbev/msr014] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial (mt) genes and genomes are among the major sources of data for evolutionary studies in birds. This places mitogenomic studies in birds at the core of intense debates in avian evolutionary biology. Indeed, complete mt genomes are actively been used to unveil the phylogenetic relationships among major orders, whereas single genes (e.g., cytochrome c oxidase I [COX1]) are considered standard for species identification and defining species boundaries (DNA barcoding). In this investigation, we study the time of origin and evolutionary relationships among Neoaves orders using complete mt genomes. First, we were able to solve polytomies previously observed at the deep nodes of the Neoaves phylogeny by analyzing 80 mt genomes, including 17 new sequences reported in this investigation. As an example, we found evidence indicating that columbiforms and charadriforms are sister groups. Overall, our analyses indicate that by improving the taxonomic sampling, complete mt genomes can solve the evolutionary relationships among major bird groups. Second, we used our phylogenetic hypotheses to estimate the time of origin of major avian orders as a way to test if their diversification took place prior to the Cretaceous/Tertiary (K/T) boundary. Such timetrees were estimated using several molecular dating approaches and conservative calibration points. Whereas we found time estimates slightly younger than those reported by others, most of the major orders originated prior to the K/T boundary. Finally, we used our timetrees to estimate the rate of evolution of each mt gene. We found great variation on the mutation rates among mt genes and within different bird groups. COX1 was the gene with less variation among Neoaves orders and the one with the least amount of rate heterogeneity across lineages. Such findings support the choice of COX 1 among mt genes as target for developing DNA barcoding approaches in birds.
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Affiliation(s)
- M Andreína Pacheco
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, AZ, USA
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29
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Hung CL, Lee C, Lin CY, Chang CH, Chung YC, Yi Tang C. Feature amplified voting algorithm for functional analysis of protein superfamily. BMC Genomics 2010; 11 Suppl 3:S14. [PMID: 21143781 PMCID: PMC2999344 DOI: 10.1186/1471-2164-11-s3-s14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Identifying the regions associated with protein function is a singularly important task in the post-genomic era. Biological studies often identify functional enzyme residues by amino acid sequences, particularly when related structural information is unavailable. In some cases of protein superfamilies, functional residues are difficult to detect by current alignment tools or evolutionary strategies when phylogenetic relationships do not parallel their protein functions. The solution proposed in this study is Feature Amplified Voting Algorithm with Three-profile alignment (FAVAT). The core concept of FAVAT is to reveal the desired features of a target enzyme or protein by voting on three different property groups aligned by three-profile alignment method. Functional residues of a target protein can then be retrieved by FAVAT analysis. In this study, the amidohydrolase superfamily was an interesting case for verifying the proposed approach because it contains divergent enzymes and proteins. RESULTS The FAVAT was used to identify critical residues of mammalian imidase, a member of the amidohydrolase superfamily. Members of this superfamily were first classified by their functional properties and sources of original organisms. After FAVAT analysis, candidate residues were identified and compared to a bacterial hydantoinase in which the crystal structure (1GKQ) has been fully elucidated. One modified lysine, three histidines and one aspartate were found to participate in the coordination of metal ions in the active site. The FAVAT analysis also redressed the misrecognition of metal coordinator Asp57 by the multiple sequence alignment (MSA) method. Several other amino acid residues known to be related to the function or structure of mammalian imidase were also identified. CONCLUSIONS The FAVAT is shown to predict functionally important amino acids in amidohydrolase superfamily. This strategy effectively identifies functionally important residues by analyzing the discrepancy between the sequence and functional properties of related proteins in a superfamily, and it should be applicable to other protein families.
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Affiliation(s)
- Che-Lun Hung
- Department of Computer Science, National Tsing Hua University, 101, Section 2 Kuang Fu Road, Hsinchu, Taiwan
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30
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Tobe SS, Kitchener AC, Linacre AMT. Reconstructing mammalian phylogenies: a detailed comparison of the cytochrome B and cytochrome oxidase subunit I mitochondrial genes. PLoS One 2010; 5:e14156. [PMID: 21152400 PMCID: PMC2994770 DOI: 10.1371/journal.pone.0014156] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 11/05/2010] [Indexed: 11/18/2022] Open
Abstract
The phylogeny and taxonomy of mammalian species were originally based upon shared or derived morphological characteristics. However, genetic analyses have more recently played an increasingly important role in confirming existing or establishing often radically different mammalian groupings and phylogenies. The two most commonly used genetic loci in species identification are the cytochrome oxidase I gene (COI) and the cytochrome b gene (cyt b). For the first time this study provides a detailed comparison of the effectiveness of these two loci in reconstructing the phylogeny of mammals at different levels of the taxonomic hierarchy in order to provide a basis for standardizing methodologies in the future. Interspecific and intraspecific variation is assessed and for the first time, to our knowledge, statistical confidence is applied to sequence comparisons. Comparison of the DNA sequences of 217 mammalian species reveals that cyt b more accurately reconstructs their phylogeny and known relationships between species based on other molecular and morphological analyses at Super Order, Order, Family and generic levels. Cyt b correctly assigned 95.85% of mammal species to Super Order, 94.31% to Order and 98.16% to Family compared to 78.34%, 93.36% and 96.93% respectively for COI. Cyt b also gives better resolution when separating species based on sequence data. Using a Kimura 2-parameter p-distance (x100) threshold of 1.5-2.5, cyt b gives a better resolution for separating species with a lower false positive rate and higher positive predictive value than those of COI.
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Affiliation(s)
- Shanan S Tobe
- Centre for Forensic Science, WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom.
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31
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Goremykin VV, Nikiforova SV, Bininda-Emonds ORP. Automated Removal of Noisy Data in Phylogenomic Analyses. J Mol Evol 2010; 71:319-31. [DOI: 10.1007/s00239-010-9398-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 10/06/2010] [Indexed: 10/18/2022]
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32
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A Phylogenetic Analysis of Human Syntenies Revealed by Chromosome Painting in Euarchontoglires Orders. J MAMM EVOL 2010. [DOI: 10.1007/s10914-010-9150-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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33
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Fink S, Fischer MC, Excoffier L, Heckel G. Genomic scans support repetitive continental colonization events during the rapid radiation of voles (Rodentia: Microtus): the utility of AFLPs versus mitochondrial and nuclear sequence markers. Syst Biol 2010; 59:548-72. [PMID: 20834011 DOI: 10.1093/sysbio/syq042] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Single locus studies might not resolve phylogenetic relationships and the evolutionary history of taxa. The analysis of multiple markers promises higher resolution, and congruence among loci may indicate that the phylogenies represent the underlying species history. Here, we examine the utility of a genome-wide approach based on amplified fragment length polymorphisms (AFLP) and several DNA sequence markers in resolving phylogenetic signals in the rapidly radiating rodent genus Microtus which produced about 70 vole species within the last 1.2-2 myr. The current Holarctic distribution of Microtus is assumed to have resulted from three independent colonization events out of Asia to North America, Europe, and northern Asia without subsequent colonization, which would have led to deep splits between species from different continents. We investigated this hypothesis of three single colonization events by reconstructing the phylogenetic relationships among species from all three continents based on data from the first exon of the nuclear arginine vasopressin receptor 1a gene (EXON1), an adjacent noncoding region and the mitochondrial cytochrome b gene. The phylogenetic patterns obtained from these sequence markers are contrasted to genome-wide data on more than 1800 amplified fragment length polymorphisms (AFLP) analyzed for the same samples. Our results show that the single sequence markers partially resolve the phylogenetic relationships within Microtus, but with some incongruence mostly between EXON1 and the other loci. However, deeper nodes of the radiation are only weakly supported and neither the combination of the markers nor additional nuclear sequences improved the resolution significantly. AFLPs provided much stronger support for major continent-specific clades, and show also that reciprocal monophyly of American and European voles is incomplete. Our results demonstrate that Microtus voles colonized the American and European continents each repeatedly in several independent events on similar colonization routes during their radiation. More generally, this study supports the suitability of AFLPs as an alternative to sequence markers to resolve the evolutionary history of rapidly radiating taxa.
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Affiliation(s)
- Sabine Fink
- Department of Biology, Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland
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34
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Wu W, Huang X, Cheng J, Li Z, de Folter S, Huang Z, Jiang X, Pang H, Tao S. Conservation and evolution in and among SRF- and MEF2-type MADS domains and their binding sites. Mol Biol Evol 2010; 28:501-11. [PMID: 20724380 DOI: 10.1093/molbev/msq214] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Serum response factor (SRF) and myocyte enhancer factor 2 (MEF2) represent two types of members of the MCM1, AGAMOUS, DEFICIENS, and SRF (MADS)-box transcription factor family present in animals and fungi. Each type has distinct biological functions, which are reflected by the distinct specificities of the proteins bound to their cognate DNA-binding sites and activated by their respective cofactors. However, little is known about the evolution of MADS domains and their DNA-binding sites. Here, we report on the conservation and evolution of the two types of MADS domains with their cognate DNA-binding sites by using phylogenetic analyses. First, there are great similarities between the two types of proteins with amino acid positions highly conserved, which are critical for binding to the DNA sequence and for the maintenance of the 3D structure. Second, in contrast to MEF2-type MADS domains, distinct conserved residues are present at some positions in SRF-type MADS domains, determining specificity and the configuration of the MADS domain bound to DNA sequences. Furthermore, the ancestor sequence of SRF- and MEF2-type MADS domains is more similar to MEF2-type MADS domains than to SRF-type MADS domains. In the case of DNA-binding sites, the MEF2 site has a T-rich core in one DNA sequence and an A-rich core in the reverse sequence as compared with the SRF site, no matter whether where either A or T is present in the two complementary sequences. In addition, comparing SRF sites in the human and the mouse genomes reveals that the evolution rate of CArG-boxes is faster in mouse than in human. Moreover, interestingly, a CArG-like sequence, which is probably functionless, could potentially mutate to a functional CArG-box that can be bound by SRF and vice versa. Together, these results significantly improve our knowledge on the conservation and evolution of the MADS domains and their binding sites to date and provide new insights to investigate the MADS family, which is not only on evolution of MADS factors but also on evolution of their binding sites and even on coevolution of MADS factors with their binding sites.
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Affiliation(s)
- Wenwu Wu
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
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Phylogenetic inference of Indian malaria vectors from multilocus DNA sequences. INFECTION GENETICS AND EVOLUTION 2010; 10:755-63. [DOI: 10.1016/j.meegid.2010.04.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 04/22/2010] [Accepted: 04/22/2010] [Indexed: 02/02/2023]
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Caravas J, Friedrich M. Of mites and millipedes: Recent progress in resolving the base of the arthropod tree. Bioessays 2010; 32:488-95. [DOI: 10.1002/bies.201000005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Campbell V, Lapointe FJ. An application of supertree methods to Mammalian mitogenomic sequences. Evol Bioinform Online 2010; 6:57-71. [PMID: 20535231 PMCID: PMC2880846 DOI: 10.4137/ebo.s4527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
TWO DIFFERENT APPROACHES CAN BE USED IN PHYLOGENOMICS: combined or separate analysis. In the first approach, different datasets are combined in a concatenated supermatrix. In the second, datasets are analyzed separately and the phylogenetic trees are then combined in a supertree. The supertree method is an interesting alternative to avoid missing data, since datasets that are analyzed separately do not need to represent identical taxa. However, the supertree approach and the corresponding consensus methods have been highly criticized for not providing valid phylogenetic hypotheses. In this study, congruence of trees estimated by consensus and supertree approaches were compared to model trees obtained from a combined analysis of complete mitochondrial sequences of 102 species representing 93 mammal families. The consensus methods produced poorly resolved consensus trees and did not perform well, except for the majority rule consensus with compatible groupings. The weighted supertree and matrix representation with parsimony methods performed equally well and were highly congruent with the model trees. The most similar supertree method was the least congruent with the model trees. We conclude that some of the methods tested are worth considering in a phylogenomic context.
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Affiliation(s)
- Véronique Campbell
- Université de Montréal, Département de Sciences Biologiques, C.P. 6128, Succ. Centre-ville, Montréal, Québec, H3C 3J7, Canada
| | - François-Joseph Lapointe
- Université de Montréal, Département de Sciences Biologiques, C.P. 6128, Succ. Centre-ville, Montréal, Québec, H3C 3J7, Canada
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Cloning and characterization of glutamate receptors in Californian sea lions (Zalophus californianus). Mar Drugs 2010; 8:1637-49. [PMID: 20559490 PMCID: PMC2885082 DOI: 10.3390/md8051637] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Revised: 04/16/2010] [Accepted: 04/29/2010] [Indexed: 11/23/2022] Open
Abstract
Domoic acid produced by marine algae has been shown to cause acute and chronic neurologic sequelae in Californian sea lions following acute or low-dose exposure. Histological findings in affected animals included a degenerative cardiomyopathy that was hypothesized to be caused by over-excitation of the glutamate receptors (GluRs) speculated to be present in the sea lion heart. Thus tissues from five sea lions without lesions associated with domoic acid toxicity and one animal with domoic acid-induced chronic neurologic sequelae and degenerative cardiomyopathy were examined for the presence of GluRs. Immunohistochemistry localized mGluR 2/3, mGluR 5, GluR 2/3 and NMDAR 1 in structures of the conducting system and blood vessels. NMDAR 1 and GluR 2/3 were the most widespread as immunoreactivity was observed within sea lion conducting system structures. PCR analysis, cloning and subsequent sequencing of the seal lion GluRs showed only 80% homology to those from rats, but more than 95% homologous to those from dogs. The cellular distribution and expression of subtypes of GluRs in the sea lion hearts suggests that exposure to domoic acid may induce cardiac damage and functional disturbances.
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Dobson FS, Way BM, Baudoin C. Spatial dynamics and the evolution of social monogamy in mammals. Behav Ecol 2010. [DOI: 10.1093/beheco/arq048] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Cooper WJ, Steppan SJ. Developmental constraint on the evolution of marsupial forelimb morphology. AUST J ZOOL 2010. [DOI: 10.1071/zo09102] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Compared with the placental mammals, marsupials are born at an almost embryonic stage, but nearly all of these neonates immediately climb or crawl to one of their mother’s teats using precociously developed forelimbs. Marsupial adults also exhibit limited forelimb shape diversity relative to the members of their sister group. That the functional requirements of this natal climb have imposed a developmental constraint on marsupial forelimb evolution represents a compelling and widely accepted hypothesis, yet its resulting predictions for the comparative patterns of mammal limb shape diversity have never been tested. In order to perform such tests we conducted extensive taxonomic sampling of mammal limb morphology (including fossil specimens), and then examined these data using morphometric methods, non-parametric analyses of anatomical disparity, and phylogenetic comparative analyses of evolutionary rates. Our results strongly support the constraint hypothesis, and indicate that the highly significant differences between marsupial and placental forelimb shape diversity has been strongly influenced by different rates of morphological evolution among the distal forelimb elements in these two important mammal lineages.
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Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny. Gene 2009; 441:132-40. [DOI: 10.1016/j.gene.2008.08.017] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Revised: 07/30/2008] [Accepted: 08/21/2008] [Indexed: 11/21/2022]
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Alekseyev MA, Pevzner PA. Breakpoint graphs and ancestral genome reconstructions. Genes Dev 2009; 19:943-57. [PMID: 19218533 PMCID: PMC2675983 DOI: 10.1101/gr.082784.108] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Accepted: 01/22/2009] [Indexed: 11/24/2022]
Abstract
Recently completed whole-genome sequencing projects marked the transition from gene-based phylogenetic studies to phylogenomics analysis of entire genomes. We developed an algorithm MGRA for reconstructing ancestral genomes and used it to study the rearrangement history of seven mammalian genomes: human, chimpanzee, macaque, mouse, rat, dog, and opossum. MGRA relies on the notion of the multiple breakpoint graphs to overcome some limitations of the existing approaches to ancestral genome reconstructions. MGRA also generates the rearrangement-based characters guiding the phylogenetic tree reconstruction when the phylogeny is unknown.
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Affiliation(s)
- Max A. Alekseyev
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, California 92093-0404, USA
| | - Pavel A. Pevzner
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, California 92093-0404, USA
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Blanga-Kanfi S, Miranda H, Penn O, Pupko T, DeBry RW, Huchon D. Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades. BMC Evol Biol 2009; 9:71. [PMID: 19341461 PMCID: PMC2674048 DOI: 10.1186/1471-2148-9-71] [Citation(s) in RCA: 185] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Accepted: 04/02/2009] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Rodentia is the most diverse order of placental mammals, with extant rodent species representing about half of all placental diversity. In spite of many morphological and molecular studies, the family-level relationships among rodents and the location of the rodent root are still debated. Although various datasets have already been analyzed to solve rodent phylogeny at the family level, these are difficult to combine because they involve different taxa and genes. RESULTS We present here the largest protein-coding dataset used to study rodent relationships. It comprises six nuclear genes, 41 rodent species, and eight outgroups. Our phylogenetic reconstructions strongly support the division of Rodentia into three clades: (1) a "squirrel-related clade", (2) a "mouse-related clade", and (3) Ctenohystrica. Almost all evolutionary relationships within these clades are also highly supported. The primary remaining uncertainty is the position of the root. The application of various models and techniques aimed to remove non-phylogenetic signal was unable to solve the basal rodent trifurcation. CONCLUSION Sequencing and analyzing a large sequence dataset enabled us to resolve most of the evolutionary relationships among Rodentia. Our findings suggest that the uncertainty regarding the position of the rodent root reflects the rapid rodent radiation that occurred in the Paleocene rather than the presence of conflicting phylogenetic and non-phylogenetic signals in the dataset.
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Affiliation(s)
- Shani Blanga-Kanfi
- Department of Zoology, George S, Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel.
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Roberts TE, Sargis EJ, Olson LE. Networks, trees, and treeshrews: assessing support and identifying conflict with multiple loci and a problematic root. Syst Biol 2009; 58:257-70. [PMID: 20525582 PMCID: PMC2715937 DOI: 10.1093/sysbio/syp025] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Revised: 12/09/2008] [Accepted: 02/18/2009] [Indexed: 11/13/2022] Open
Abstract
Multiple unlinked genetic loci often provide a more comprehensive picture of evolutionary history than any single gene can, but analyzing multigene data presents particular challenges. Differing rates and patterns of nucleotide substitution, combined with the limited information available in any data set, can make it difficult to specify a model of evolution. In addition, conflict among loci can be the result of real differences in evolutionary process or of stochastic variance and errors in reconstruction. We used 6 presumably unlinked nuclear loci to investigate relationships within the mammalian family Tupaiidae (Scandentia), containing all but one of the extant tupaiid genera. We used a phylogenetic mixture model to analyze the concatenated data and compared this with results using partitioned models. We found that more complex models were not necessarily preferred under tests using Bayes factors and that model complexity affected both tree length and parameter variance. We also compared the results of single-gene and multigene analyses and used splits networks to analyze the source and degree of conflict among genes. Networks can show specific relationships that are inconsistent with each other; these conflicting and minority relationships, which are implicitly ignored or collapsed by traditional consensus methods, can be useful in identifying the underlying causes of topological uncertainty. In our data, conflict is concentrated around particular relationships, not widespread throughout the tree. This pattern is further clarified by considering conflict surrounding the root separately from conflict within the ingroup. Uncertainty in rooting may be because of the apparent evolutionary distance separating these genera and our outgroup, the tupaiid genus Dendrogale. Unlike a previous mitochondrial study, these nuclear data strongly suggest that the genus Tupaia is not monophyletic with respect to the monotypic Urogale, even when uncertainty about rooting is taken into account. These data concur with mitochondrial DNA on other relationships, including the close affinity of Tupaia tana with the enigmatic Tupaia splendidula and of Tupaia belangeri with Tupaia glis. We also discuss the taxonomic and biogeographic implications of these results.
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Affiliation(s)
- Trina E Roberts
- University of Alaska Museum and Institute of Arctic Biology, University of Alaska-Fairbanks, Fairbanks, AK 99775, USA.
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Schulz E, Gottschling M, Bravo IG, Wittstatt U, Stockfleth E, Nindl I. Genomic characterization of the first insectivoran papillomavirus reveals an unusually long, second non-coding region and indicates a close relationship to Betapapillomavirus. J Gen Virol 2009; 90:626-633. [DOI: 10.1099/vir.0.008011-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Knowledge about biological diversity is the prerequisite to reliably reconstruct the evolution of pathogens such as papillomaviruses (PV). However, complete genomes of non-human PV have only been cloned and sequenced from 8 out of 18 orders within the Placentalia, although the host-specific variety of PV is considered much larger. We isolated and sequenced the complete genome of the first insectivoran PV type from hair follicle cells of the European hedgehog (Erinaceus europaeus), designated EHPV. We conducted phylogenetic analyses (maximum-likelihood criterion and Bayesian inference) with the genomic information of a systematically representative set of 67 PV types including EHPV. As inferred from amino acid sequence data of the separate genes E1, E2 and L1 as well as of the gene combination E6–E7–E1–E2–L1, EHPV clustered within the β-γ-π-Ξ-PV supertaxon and constituted the closest relative of genus Betapapillomavirus infecting primates. Beside the typical organization of the PV genome, EHPV exhibited a 1172 bp, non-coding region between the E2 and the L2 open reading frames. This trait has been previously described for the only distantly related Lambdapapillomavirus, but a common evolutionary origin of both non-coding regions is unlikely. Our results underscore the modular organization of the PV genome and the complex natural history of PV.
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Affiliation(s)
- Eric Schulz
- Clinic for Dermatology, Venereology and Allergology, Skin Cancer Center Charité (HTCC), Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Marc Gottschling
- Department of Biology, Systematic Botany, Ludwig-Maximilians-Universität München, Munich, Germany
- Clinic for Dermatology, Venereology and Allergology, Skin Cancer Center Charité (HTCC), Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Ignacio G. Bravo
- Experimental Molecular Evolution, Institute for Evolution and Biodiversity, Westfälische Wilhems Universität Münster, Munster, Germany
| | - Ullrich Wittstatt
- Institute für Lebensmittel, Arzneimittel und Tierseuchen, Zentrum für Infektionsdiagnostik (ZID), Berlin, Germany
| | - Eggert Stockfleth
- Clinic for Dermatology, Venereology and Allergology, Skin Cancer Center Charité (HTCC), Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Ingo Nindl
- DKFZ – Charité, Viral Skin Carcinogenesis, Viral Transformation Mechanisms, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Clinic for Dermatology, Venereology and Allergology, Skin Cancer Center Charité (HTCC), Charité – Universitätsmedizin Berlin, Berlin, Germany
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Guindon S, Delsuc F, Dufayard JF, Gascuel O. Estimating maximum likelihood phylogenies with PhyML. Methods Mol Biol 2009; 537:113-37. [PMID: 19378142 DOI: 10.1007/978-1-59745-251-9_6] [Citation(s) in RCA: 598] [Impact Index Per Article: 39.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Our understanding of the origins, the functions and/or the structures of biological sequences strongly depends on our ability to decipher the mechanisms of molecular evolution. These complex processes can be described through the comparison of homologous sequences in a phylogenetic framework. Moreover, phylogenetic inference provides sound statistical tools to exhibit the main features of molecular evolution from the analysis of actual sequences. This chapter focuses on phylogenetic tree estimation under the maximum likelihood (ML) principle. Phylogenies inferred under this probabilistic criterion are usually reliable and important biological hypotheses can be tested through the comparison of different models. Estimating ML phylogenies is computationally demanding, and careful examination of the results is warranted. This chapter focuses on PhyML, a software that implements recent ML phylogenetic methods and algorithms. We illustrate the strengths and pitfalls of this program through the analysis of a real data set. PhyML v3.0 is available from (http://atgc_montpellier.fr/phyml/).
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Affiliation(s)
- Stéphane Guindon
- Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM), UMR 5506-CNRS, Université Montpellier II, Montpellier, France
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Abstract
The remarkable high-frequency sensitivity and selectivity of the mammalian auditory system has been attributed to the evolution of mechanical amplification, in which sound waves are amplified by outer hair cells in the cochlea. This process is driven by the recently discovered protein prestin, encoded by the gene Prestin. Echolocating bats use ultrasound for orientation and hunting and possess the highest frequency hearing of all mammals. To test for the involvement of Prestin in the evolution of bat echolocation, we sequenced the coding region in echolocating and nonecholocating species. The resulting putative gene tree showed strong support for a monophyletic assemblage of echolocating species, conflicting with the species phylogeny in which echolocators are paraphyletic. We reject the possibilities that this conflict arises from either gene duplication and loss or relaxed selection in nonecholocating fruit bats. Instead, we hypothesize that the putative gene tree reflects convergence at stretches of functional importance. Convergence is supported by the recovery of the species tree from alignments of hydrophobic transmembrane domains, and the putative gene tree from the intra- and extracellular domains. We also found evidence that Prestin has undergone Darwinian selection associated with the evolution of specialized constant-frequency echolocation, which is characterized by sharp auditory tuning. Our study of a hearing gene in bats strongly implicates Prestin in the evolution of echolocation, and suggests independent evolution of high-frequency hearing in bats. These results highlight the potential problems of extracting phylogenetic signals from functional genes that may be prone to convergence.
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The phylogeny of Cetartiodactyla: The importance of dense taxon sampling, missing data, and the remarkable promise of cytochrome b to provide reliable species-level phylogenies. Mol Phylogenet Evol 2008; 48:964-85. [DOI: 10.1016/j.ympev.2008.05.046] [Citation(s) in RCA: 146] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Revised: 05/08/2008] [Accepted: 05/21/2008] [Indexed: 11/18/2022]
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Springer MS, Meredith RW, Eizirik E, Teeling E, Murphy WJ. Morphology and Placental Mammal Phylogeny. Syst Biol 2008; 57:499-503. [DOI: 10.1080/10635150802164504] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Mark S. Springer
- Department of Biology, University of California
Riverside, CA 92521, USA; E-mail: (M.S.S.)
| | - Robert W. Meredith
- Department of Biology, University of California
Riverside, CA 92521, USA; E-mail: (M.S.S.)
| | - Eduardo Eizirik
- Faculdade de Biociencias, PUCRS
Porto Alegre, RS 90619-900, Brazil
| | - Emma Teeling
- School of Biological and Environmental Sciences, University College Dublin Belfield
Dublin, 4, Ireland
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University
College Station, TX 77843-4458, USA
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da Fonseca RR, Johnson WE, O'Brien SJ, Ramos MJ, Antunes A. The adaptive evolution of the mammalian mitochondrial genome. BMC Genomics 2008; 9:119. [PMID: 18318906 PMCID: PMC2375446 DOI: 10.1186/1471-2164-9-119] [Citation(s) in RCA: 255] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2007] [Accepted: 03/04/2008] [Indexed: 11/18/2022] Open
Abstract
Background The mitochondria produce up to 95% of a eukaryotic cell's energy through oxidative phosphorylation. The proteins involved in this vital process are under high functional constraints. However, metabolic requirements vary across species, potentially modifying selective pressures. We evaluate the adaptive evolution of 12 protein-coding mitochondrial genes in 41 placental mammalian species by assessing amino acid sequence variation and exploring the functional implications of observed variation in secondary and tertiary protein structures. Results Wide variation in the properties of amino acids were observed at functionally important regions of cytochrome b in species with more-specialized metabolic requirements (such as adaptation to low energy diet or large body size, such as in elephant, dugong, sloth, and pangolin, and adaptation to unusual oxygen requirements, for example diving in cetaceans, flying in bats, and living at high altitudes in alpacas). Signatures of adaptive variation in the NADH dehydrogenase complex were restricted to the loop regions of the transmembrane units which likely function as protons pumps. Evidence of adaptive variation in the cytochrome c oxidase complex was observed mostly at the interface between the mitochondrial and nuclear-encoded subunits, perhaps evidence of co-evolution. The ATP8 subunit, which has an important role in the assembly of F0, exhibited the highest signal of adaptive variation. ATP6, which has an essential role in rotor performance, showed a high adaptive variation in predicted loop areas. Conclusion Our study provides insight into the adaptive evolution of the mtDNA genome in mammals and its implications for the molecular mechanism of oxidative phosphorylation. We present a framework for future experimental characterization of the impact of specific mutations in the function, physiology, and interactions of the mtDNA encoded proteins involved in oxidative phosphorylation.
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Affiliation(s)
- Rute R da Fonseca
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal.
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