1
|
İbiş O, Yesari Selçuk A, Teber S, Baran M, Kaya A, Özcan S, Kefelioğlu H, Tez C. Complete mitogenomes of Turkish tree squirrels, Sciurus anomalus and S. vulgaris, (Sciuridae: Rodentia: Mammalia) and their phylogenetic status within the tribe Sciurini. Gene 2022; 841:146773. [PMID: 35905846 DOI: 10.1016/j.gene.2022.146773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/03/2022] [Accepted: 07/24/2022] [Indexed: 11/04/2022]
Abstract
The genus Sciurus, a member of the family Sciuridae, is widely distributed in the Holarctic region. To better understand mitogenomic characteristics and to reveal internal phylogenetic relationships of the genus, 20 complete mitogenomes of Turkish tree squirrels were successfully sequenced for the first time, including 19 for S. anomalus (from 16,505 bp to 16,510 bp) and one for S. vulgaris (16,511 bp). The mitogenomes of two species were AT-biased. All tRNAs for two species displayed a typical clover-leaf structure, except for tRNASer(AGY). The tRNA Serine1 (S1)-GCT structure lacked the dihydrouridine (DHU) loop and stem. Based on mitogenomic dataset for phylogeny of Sciurinae, phylogenetic analyses (Bayesian Inference and Maximum Likelihood) did not support monophyly of Sciurus and proposed that S. anomalus, the most basal taxa in the Sciurini tribe, had at least five mitogenome lineages, which were also supported by network analysis. The dissimilarities among the five linegaes of S. anomalus ranged from 0.0042 (0.42%) to 0.0062 (0.62%) using K2P sequence pairwise distances. In addition to this mitogenomic analysis result, phylogenetic analyses using the CYTB + D-loop dataset proposed the existence of at least nine lineages for S. anomalus, which was different than those of the previous studies. The current study proposed that the use of mitogenomic data for reconstructing the phylogeny of Turkey' Sciurus holds an important value for revealing evolutionary relationships.
Collapse
Affiliation(s)
- Osman İbiş
- Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey; Vectors and Vector-Born Diseases Research and Implementation Center, Erciyes University, Kayseri, Turkey.
| | - Ahmet Yesari Selçuk
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey; Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey.
| | - Saffet Teber
- Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey.
| | - Mehmet Baran
- Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey.
| | - Alaettin Kaya
- Department of Basic Sciences, Faculty of Veterinary Medicine, Dicle University, Diyarbakır, Turkey.
| | - Servet Özcan
- Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey; Department of Biology, Faculty of Sciences, Erciyes University, Kayseri, Turkey.
| | - Haluk Kefelioğlu
- Department of Biology, Faculty of Science and Letters, Ondokuz Mayıs University, Samsun, Turkey.
| | - Coşkun Tez
- Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey; Department of Biology, Faculty of Sciences, Erciyes University, Kayseri, Turkey.
| |
Collapse
|
2
|
Aledo JC. Phylogenies from unaligned proteomes using sequence environments of amino acid residues. Sci Rep 2022; 12:7497. [PMID: 35523825 PMCID: PMC9076898 DOI: 10.1038/s41598-022-11370-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 04/21/2022] [Indexed: 11/09/2022] Open
Abstract
Alignment-free methods for sequence comparison and phylogeny inference have attracted a great deal of attention in recent years. Several algorithms have been implemented in diverse software packages. Despite the great number of existing methods, most of them are based on word statistics. Although they propose different filtering and weighting strategies and explore different metrics, their performance may be limited by the phylogenetic signal preserved in these words. Herein, we present a different approach based on the species-specific amino acid neighborhood preferences. These differential preferences can be assessed in the context of vector spaces. In this way, a distance-based method to build phylogenies has been developed and implemented into an easy-to-use R package. Tests run on real-world datasets show that this method can reconstruct phylogenetic relationships with high accuracy, and often outperforms other alignment-free approaches. Furthermore, we present evidence that the new method can perform reliably on datasets formed by non-orthologous protein sequences, that is, the method not only does not require the identification of orthologous proteins, but also does not require their presence in the analyzed dataset. These results suggest that the neighborhood preference of amino acids conveys a phylogenetic signal that may be of great utility in phylogenomics.
Collapse
Affiliation(s)
- Juan Carlos Aledo
- Department of Molecular Biology and Biochemistry, University of Málaga, 29071, Málaga, Spain.
| |
Collapse
|
3
|
Schull JK, Turakhia Y, Hemker JA, Dally WJ, Bejerano G. OUP accepted manuscript. Genome Biol Evol 2022; 14:6529394. [PMID: 35171243 PMCID: PMC8920512 DOI: 10.1093/gbe/evac013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2022] [Indexed: 11/14/2022] Open
Abstract
We present Champagne, a whole-genome method for generating character matrices for phylogenomic analysis using large genomic indel events. By rigorously picking orthologous genes and locating large insertion and deletion events, Champagne delivers a character matrix that considerably reduces homoplasy compared with morphological and nucleotide-based matrices, on both established phylogenies and difficult-to-resolve nodes in the mammalian tree. Champagne provides ample evidence in the form of genomic structural variation to support incomplete lineage sorting and possible introgression in Paenungulata and human–chimp–gorilla which were previously inferred primarily through matrices composed of aligned single-nucleotide characters. Champagne also offers further evidence for Myomorpha as sister to Sciuridae and Hystricomorpha in the rodent tree. Champagne harbors distinct theoretical advantages as an automated method that produces nearly homoplasy-free character matrices on the whole-genome scale.
Collapse
Affiliation(s)
- James K Schull
- Department of Computer Science, Stanford University, USA
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California San Diego, USA
| | - James A Hemker
- Department of Computer Science, Stanford University, USA
| | - William J Dally
- Department of Computer Science, Stanford University, USA
- NVIDIA, Santa Clara, California, USA
- Department of Electrical Engineering, Stanford University, USA
| | - Gill Bejerano
- Department of Computer Science, Stanford University, USA
- Department of Developmental Biology, Stanford University, USA
- Department of Biomedical Data Science, Stanford University, USA
- Department of Pediatrics, Stanford University, USA
- Corresponding author: E-mail:
| |
Collapse
|
4
|
Zhao T, Zwaenepoel A, Xue JY, Kao SM, Li Z, Schranz ME, Van de Peer Y. Whole-genome microsynteny-based phylogeny of angiosperms. Nat Commun 2021; 12:3498. [PMID: 34108452 PMCID: PMC8190143 DOI: 10.1038/s41467-021-23665-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 05/10/2021] [Indexed: 02/05/2023] Open
Abstract
Plant genomes vary greatly in size, organization, and architecture. Such structural differences may be highly relevant for inference of genome evolution dynamics and phylogeny. Indeed, microsynteny-the conservation of local gene content and order-is recognized as a valuable source of phylogenetic information, but its use for the inference of large phylogenies has been limited. Here, by combining synteny network analysis, matrix representation, and maximum likelihood phylogenetic inference, we provide a way to reconstruct phylogenies based on microsynteny information. Both simulations and use of empirical data sets show our method to be accurate, consistent, and widely applicable. As an example, we focus on the analysis of a large-scale whole-genome data set for angiosperms, including more than 120 available high-quality genomes, representing more than 50 different plant families and 30 orders. Our 'microsynteny-based' tree is largely congruent with phylogenies proposed based on more traditional sequence alignment-based methods and current phylogenetic classifications but differs for some long-contested and controversial relationships. For instance, our synteny-based tree finds Vitales as early diverging eudicots, Saxifragales within superasterids, and magnoliids as sister to monocots. We discuss how synteny-based phylogenetic inference can complement traditional methods and could provide additional insights into some long-standing controversial phylogenetic relationships.
Collapse
Affiliation(s)
- Tao Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, China.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Arthur Zwaenepoel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Jia-Yu Xue
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Shu-Min Kao
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - M Eric Schranz
- Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- Center for Plant Systems Biology, VIB, Ghent, Belgium.
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China.
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
| |
Collapse
|
5
|
Fallah E, Strimbu CE, Olson ES. Nonlinearity of intracochlear motion and local cochlear microphonic: Comparison between guinea pig and gerbil. Hear Res 2021; 405:108234. [PMID: 33930834 DOI: 10.1016/j.heares.2021.108234] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/08/2021] [Accepted: 03/26/2021] [Indexed: 12/19/2022]
Abstract
Studying the in-vivo mechanical and electrophysiological cochlear responses in several species helps us to have a comprehensive view of the sensitivity and frequency selectivity of the cochlea. Different species might use different mechanisms to achieve the sharp frequency-place map. The outer hair cells (OHC) play an important role in mediating frequency tuning. In the present work, we measured the OHC-generated local cochlear microphonic (LCM) and the motion of different layers in the organ of Corti using optical coherence tomography (OCT) in the first turn of the cochlea in guinea pig. In the best frequency (BF) band, our observations were similar to our previous measurements in gerbil: a nonlinear peak in LCM responses and in the basilar membrane (BM) and OHC-region displacements, and higher motion in the OHC region than the BM. Sub-BF the responses in the two species were different. In both species the sub-BF displacement of the BM was linear and LCM was nonlinear. Sub-BF in the OHC-region, nonlinearity was only observed in a subset of healthy guinea pig cochleae while in gerbil, robust nonlinearity was observed in all healthy cochleae. The differences suggest that gerbils and guinea pigs employ different mechanisms for filtering sub-BF OHC activity from BM responses. However, it cannot be ruled out that the differences are due to technical measurement differences across the species.
Collapse
Affiliation(s)
- Elika Fallah
- Department of Biomedical Engineering, Columbia University, New York City, NY, United States
| | - C Elliott Strimbu
- Department of Otolaryngology-Head and Neck Surgery, Columbia University, New York City, NY, United States
| | - Elizabeth S Olson
- Department of Biomedical Engineering, Columbia University, New York City, NY, United States; Department of Otolaryngology-Head and Neck Surgery, Columbia University, New York City, NY, United States.
| |
Collapse
|
6
|
Abramson NI, Golenishchev FN, Bodrov SY, Bondareva OV, Genelt-Yanovskiy EA, Petrova TV. Phylogenetic relationships and taxonomic position of genus Hyperacrius (Rodentia: Arvicolinae) from Kashmir based on evidences from analysis of mitochondrial genome and study of skull morphology. PeerJ 2020; 8:e10364. [PMID: 33240667 PMCID: PMC7680025 DOI: 10.7717/peerj.10364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/24/2020] [Indexed: 11/24/2022] Open
Abstract
In this article, we present the nearly complete mitochondrial genome of the Subalpine Kashmir vole Hyperacrius fertilis (Arvicolinae, Cricetidae, Rodentia), assembled using data from Illumina next-generation sequencing (NGS) of the DNA from a century-old museum specimen. De novo assembly consisted of 16,341 bp and included all mitogenome protein-coding genes as well as 12S and 16S RNAs, tRNAs and D-loop. Using the alignment of protein-coding genes of 14 previously published Arvicolini tribe mitogenomes, seven Clethrionomyini mitogenomes, and also Ondatra and Dicrostonyx outgroups, we conducted phylogenetic reconstructions based on a dataset of 13 protein-coding genes (PCGs) under maximum likelihood and Bayesian inference. Phylogenetic analyses robustly supported the phylogenetic position of this species within the tribe Arvicolini. Among the Arvicolini, Hyperacrius represents one of the early-diverged lineages. This result of phylogenetic analysis altered the conventional view on phylogenetic relatedness between Hyperacrius and Alticola and prompted the revision of morphological characters underlying the former assumption. Morphological analysis performed here confirmed molecular data and provided additional evidence for taxonomic replacement of the genus Hyperacrius from the tribe Clethrionomyini to the tribe Arvicolini.
Collapse
Affiliation(s)
- Natalia I. Abramson
- Department of Molecular Systematics, Zoological Institute Russian Academy of Sciences, Saint-Petersburg, Russian Federation
| | - Fedor N. Golenishchev
- Department of Mammals, Zoological Institute Russian Academy of Sciences, Saint-Petersburg, Russian Federation
| | - Semen Yu. Bodrov
- Department of Molecular Systematics, Zoological Institute Russian Academy of Sciences, Saint-Petersburg, Russian Federation
| | - Olga V. Bondareva
- Department of Molecular Systematics, Zoological Institute Russian Academy of Sciences, Saint-Petersburg, Russian Federation
| | - Evgeny A. Genelt-Yanovskiy
- Department of Molecular Systematics, Zoological Institute Russian Academy of Sciences, Saint-Petersburg, Russian Federation
| | - Tatyana V. Petrova
- Department of Molecular Systematics, Zoological Institute Russian Academy of Sciences, Saint-Petersburg, Russian Federation
| |
Collapse
|
7
|
Springer MS, Foley NM, Brady PL, Gatesy J, Murphy WJ. Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary. Front Genet 2019; 10:1241. [PMID: 31850081 PMCID: PMC6896846 DOI: 10.3389/fgene.2019.01241] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/08/2019] [Indexed: 01/29/2023] Open
Abstract
Deciphering the timing of the placental mammal radiation is a longstanding problem in evolutionary biology, but consensus on the tempo and mode of placental diversification remains elusive. Nevertheless, an accurate timetree is essential for understanding the role of important events in Earth history (e.g., Cretaceous Terrestrial Revolution, KPg mass extinction) in promoting the taxonomic and ecomorphological diversification of Placentalia. Archibald and Deutschman described three competing models for the diversification of placental mammals, which are the Explosive, Long Fuse, and Short Fuse Models. More recently, the Soft Explosive Model and Trans-KPg Model have emerged as additional hypotheses for the placental radiation. Here, we review molecular and paleontological evidence for each of these five models including the identification of general problems that can negatively impact divergence time estimates. The Long Fuse Model has received more support from relaxed clock studies than any of the other models, but this model is not supported by morphological cladistic studies that position Cretaceous eutherians outside of crown Placentalia. At the same time, morphological cladistics has a poor track record of reconstructing higher-level relationships among the orders of placental mammals including the results of new pseudoextinction analyses that we performed on the largest available morphological data set for mammals (4,541 characters). We also examine the strengths and weaknesses of different timetree methods (node dating, tip dating, and fossilized birth-death dating) that may now be applied to estimate the timing of the placental radiation. While new methods such as tip dating are promising, they also have problems that must be addressed if these methods are to effectively discriminate among competing hypotheses for placental diversification. Finally, we discuss the complexities of timetree estimation when the signal of speciation times is impacted by incomplete lineage sorting (ILS) and hybridization. Not accounting for ILS results in dates that are older than speciation events. Hybridization, in turn, can result in dates than are younger or older than speciation dates. Disregarding this potential variation in "gene" history across the genome can distort phylogenetic branch lengths and divergence estimates when multiple unlinked genomic loci are combined together in a timetree analysis.
Collapse
Affiliation(s)
- Mark S. Springer
- Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, Riverside, CA, United States
| | - Nicole M. Foley
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Peggy L. Brady
- Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, Riverside, CA, United States
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, United States
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| |
Collapse
|
8
|
Lin J, Adjeroh DA, Jiang BH, Jiang Y. K2 and K2*: efficient alignment-free sequence similarity measurement based on Kendall statistics. Bioinformatics 2019; 34:1682-1689. [PMID: 29253072 DOI: 10.1093/bioinformatics/btx809] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/14/2017] [Indexed: 11/13/2022] Open
Abstract
Motivation Alignment-free sequence comparison methods can compute the pairwise similarity between a huge number of sequences much faster than sequence-alignment based methods. Results We propose a new non-parametric alignment-free sequence comparison method, called K2, based on the Kendall statistics. Comparing to the other state-of-the-art alignment-free comparison methods, K2 demonstrates competitive performance in generating the phylogenetic tree, in evaluating functionally related regulatory sequences, and in computing the edit distance (similarity/dissimilarity) between sequences. Furthermore, the K2 approach is much faster than the other methods. An improved method, K2*, is also proposed, which is able to determine the appropriate algorithmic parameter (length) automatically, without first considering different values. Comparative analysis with the state-of-the-art alignment-free sequence similarity methods demonstrates the superiority of the proposed approaches, especially with increasing sequence length, or increasing dataset sizes. Availability and implementation The K2 and K2* approaches are implemented in the R language as a package and is freely available for open access (http://community.wvu.edu/daadjeroh/projects/K2/K2_1.0.tar.gz). Contact yueljiang@163.com. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Jie Lin
- Department of Software engineering, College of Mathematics and Informatics, Fujian Normal University, Fuzhou 350108, China
| | - Donald A Adjeroh
- Department of Computer Science & Electrical Engineering, West Virginia University, Morgantown, WV 26506, USA
| | - Bing-Hua Jiang
- Department of Pathology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Yue Jiang
- Department of Software engineering, College of Mathematics and Informatics, Fujian Normal University, Fuzhou 350108, China
| |
Collapse
|
9
|
Kapustina SY, Adiya Y, Brandler OV. Genetic Differentiation of the Daurian Ground Squirrel Spermophilus dauricus Brandt, 1843 according to Variability of the Mitochondrial DNA Control Region. BIOL BULL+ 2018. [DOI: 10.1134/s1062359018050060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
10
|
Sarver BAJ, Demboski JR, Good JM, Forshee N, Hunter SS, Sullivan J. Comparative Phylogenomic Assessment of Mitochondrial Introgression among Several Species of Chipmunks (Tamias). Genome Biol Evol 2018; 9:7-19. [PMID: 28172670 PMCID: PMC5381575 DOI: 10.1093/gbe/evw254] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2016] [Indexed: 11/16/2022] Open
Abstract
Many species are not completely reproductively isolated, resulting in hybridization and genetic introgression. Organellar genomes, such as those derived from mitochondria (mtDNA) and chloroplasts, introgress frequently in natural systems; however, the forces shaping patterns of introgression are not always clear. Here, we investigate extensive mtDNA introgression in western chipmunks, focusing on species in the Tamias quadrivittatus group from the central and southern Rocky Mountains. Specifically, we investigate the role of selection in driving patterns of introgression. We sequenced 51 mtDNA genomes from six species and combine these sequences with other published genomic data to yield annotated mitochondrial reference genomes for nine species of chipmunks. Genomic characterization was performed using a series of molecular evolutionary and phylogenetic analyses to test protein-coding genes for positive selection. We fit a series of maximum likelihood models using a model-averaging approach, assessed deviations from neutral expectations, and performed additional tests to search for codons under the influence of selection. We found no evidence for positive selection among these genomes, suggesting that selection has not been the driving force of introgression in these species. Thus, extensive mtDNA introgression among several species of chipmunks likely reflects genetic drift of introgressed alleles in historically fluctuating populations.
Collapse
Affiliation(s)
- Brice A J Sarver
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO.,Department of Biological Sciences, University of Idaho, Moscow, ID.,Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - John R Demboski
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Nicholas Forshee
- Department of Biological Sciences, University of Idaho, Moscow, ID
| | - Samuel S Hunter
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, ID.,Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| |
Collapse
|
11
|
İbiş O, Kılıç M, Özcan S, Tez C. Genetic characterization of the Turkish gray hamster (Cricetulus migratorius) based on mitochondrial cytochrome b and 12S rRNA sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:819-830. [PMID: 28840764 DOI: 10.1080/24701394.2017.1365849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Although genetic diversity and phylogenetic status of the gray hamster (Cricetulus migratorius) have been investigated from different regions in previous studies, genetic data on this species from Turkey are still lacking, since previous data have been based on a limited number of gray hamsters sampled across the Anatolian part of Turkey. The aim of this study was to determine the genetic diversity of the Anatolian population and to reveal the phylogenetic relationships among the Anatolian population and conspecific populations of the gray hamster. The complete and partial fragments of mitochondrial Cyt b and 12S rRNA from the 20 Turkish samples were amplified and sequenced. Ten 12S rRNA (901 bp) and 15 Cyt b (1140 bp) haplotypes found in this work were not previously reported. Based on Bayesian, Maximum Likelihood, Neighbour-Joining and Median-Joining network analyses by using mitochondrial data under the name Cricetulus, the results of phylogenetic and network analyses indicated that there was a deep separation among the distinct lineages within the genus Cricetulus. When considering the position of the Turkish haplotypes in median joining network, the Anatolian part of Turkey may have hosted a source population of the gray hamster for expansion to adjacent regions in the past period. Additionally, the Anatolian population of gray hamster had relatively high haplotype diversity and the present study propounded the importance of data obtained from the Anatolian population of gray hamster to reveal the phylogenetic relationships among conspecific populations of the gray hamster.
Collapse
Affiliation(s)
- Osman İbiş
- a Department of Agricultural Biotechnology, Faculty of Agriculture , Erciyes University , Kayseri , Turkey.,b Genome and Stem Cell Center, GENKOK, Erciyes University , Kayseri , Turkey
| | - Metin Kılıç
- c Graduate School of Natural and Applied Sciences , Erciyes University , Kayseri , Turkey
| | - Servet Özcan
- b Genome and Stem Cell Center, GENKOK, Erciyes University , Kayseri , Turkey.,d Department of Biology, Faculty of Sciences , Erciyes University , Kayseri , Turkey
| | - Coşkun Tez
- b Genome and Stem Cell Center, GENKOK, Erciyes University , Kayseri , Turkey.,d Department of Biology, Faculty of Sciences , Erciyes University , Kayseri , Turkey
| |
Collapse
|
12
|
Moshtaghi S, Darvish J, Mirshamsi O, Mahmoudi A. Cryptic species diversity in the genusAllactaga(Rodentia: Dipodidae) at the edge of its distribution range. FOLIA ZOOLOGICA 2016. [DOI: 10.25225/fozo.v65.i2.a9.2016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Samira Moshtaghi
- Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Jamshid Darvish
- Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
- Rodentology Research Department, Institute of Applied Zoology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Omid Mirshamsi
- Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
- Zoological Innovations Research Department, Institute of Applied Zoology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ahmad Mahmoudi
- Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
| |
Collapse
|
13
|
Huang HH, Yu C. Clustering DNA sequences using the out-of-place measure with reduced n-grams. J Theor Biol 2016; 406:61-72. [PMID: 27375217 DOI: 10.1016/j.jtbi.2016.06.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 05/18/2016] [Accepted: 06/21/2016] [Indexed: 11/25/2022]
Abstract
The alignment-free n-gram based method with the out-of-place measures as the distance has been successfully applied to automatic text or natural languages categorization in real time. However, it is not clear about its performance and the selection of n for comparing genome sequences. Here we propose a symmetric version of the out-of-place measure and a new approach for finding the optimal range of n to construct a phylogenetic tree with the symmetric out-of-place measures. Our method is then applied to real genome sequence datasets. The resulting phylogenetic trees are matching with the standard biological classification. It shows that our proposed method is a very powerful tool for phylogenetic analysis in terms of both classification accuracy and computation efficiency.
Collapse
Affiliation(s)
- Hsin-Hsiung Huang
- Department of Statistics, University of Central Florida, Orlando, FL 32816, USA.
| | - Chenglong Yu
- Mind and Brain Theme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA 5000, Australia; School of Medicine, Flinders University, Adelaide, SA 5001, Australia
| |
Collapse
|
14
|
Li B, Yu D, Cheng H, Storey KB, Zhang J. The complete mitochondrial genomes of Cynomys leucurus and C. ludovicianus (Rodentia: Sciuridae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3295-6. [DOI: 10.3109/19401736.2015.1015010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Bingfei Li
- Institute of Ecology, Zhejiang Normal University, Jinhua, Zhejiang Province, P.R. China,
| | - Danna Yu
- College of Life Science and Chemistry, Zhejiang Normal University, Jinhua, Zhejiang Province, P.R. China, and
| | - Hongyi Cheng
- Institute of Ecology, Zhejiang Normal University, Jinhua, Zhejiang Province, P.R. China,
- College of Life Science and Chemistry, Zhejiang Normal University, Jinhua, Zhejiang Province, P.R. China, and
| | | | - Jiayong Zhang
- Institute of Ecology, Zhejiang Normal University, Jinhua, Zhejiang Province, P.R. China,
- College of Life Science and Chemistry, Zhejiang Normal University, Jinhua, Zhejiang Province, P.R. China, and
| |
Collapse
|
15
|
Pozzi L, Hodgson JA, Burrell AS, Sterner KN, Raaum RL, Disotell TR. Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes. Mol Phylogenet Evol 2014; 75:165-83. [PMID: 24583291 PMCID: PMC4059600 DOI: 10.1016/j.ympev.2014.02.023] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 02/17/2014] [Accepted: 02/19/2014] [Indexed: 01/23/2023]
Abstract
The origins and the divergence times of the most basal lineages within primates have been difficult to resolve mainly due to the incomplete sampling of early fossil taxa. The main source of contention is related to the discordance between molecular and fossil estimates: while there are no crown primate fossils older than 56Ma, most molecule-based estimates extend the origins of crown primates into the Cretaceous. Here we present a comprehensive mitogenomic study of primates. We assembled 87 mammalian mitochondrial genomes, including 62 primate species representing all the families of the order. We newly sequenced eleven mitochondrial genomes, including eight Old World monkeys and three strepsirrhines. Phylogenetic analyses support a strong topology, confirming the monophyly for all the major primate clades. In contrast to previous mitogenomic studies, the positions of tarsiers and colugos relative to strepsirrhines and anthropoids are well resolved. In order to improve our understanding of how fossil calibrations affect age estimates within primates, we explore the effect of seventeen fossil calibrations across primates and other mammalian groups and we select a subset of calibrations to date our mitogenomic tree. The divergence date estimates of the Strepsirrhine/Haplorhine split support an origin of crown primates in the Late Cretaceous, at around 74Ma. This result supports a short-fuse model of primate origins, whereby relatively little time passed between the origin of the order and the diversification of its major clades. It also suggests that the early primate fossil record is likely poorly sampled.
Collapse
Affiliation(s)
- Luca Pozzi
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, NY, United States; New York Consortium in Evolutionary Primatology, United States; Behavioral Ecology and Sociobiology Unit, German Primate Center, Göttingen, Germany.
| | - Jason A Hodgson
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, NY, United States; New York Consortium in Evolutionary Primatology, United States; Department of Life Sciences, Imperial College London, London, United Kingdom.
| | - Andrew S Burrell
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, NY, United States.
| | - Kirstin N Sterner
- Department of Anthropology, University of Oregon, Eugene, OR, United States.
| | - Ryan L Raaum
- New York Consortium in Evolutionary Primatology, United States; Department of Anthropology, Lehman College & The Graduate Center, City University of New York, Bronx, NY, United States.
| | - Todd R Disotell
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, NY, United States; New York Consortium in Evolutionary Primatology, United States.
| |
Collapse
|
16
|
Alignment free comparison: k word voting model and its applications. J Theor Biol 2013; 335:276-82. [DOI: 10.1016/j.jtbi.2013.06.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 04/25/2013] [Accepted: 06/26/2013] [Indexed: 02/06/2023]
|
17
|
Clustering based on median and closest string via rank distance with applications on DNA. Neural Comput Appl 2013. [DOI: 10.1007/s00521-013-1468-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Complete mitochondrial genome of the Eurasian flying squirrel Pteromys volans (Sciuromorpha, Sciuridae) and revision of rodent phylogeny. Mol Biol Rep 2012; 40:1917-26. [PMID: 23114915 DOI: 10.1007/s11033-012-2248-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 10/10/2012] [Indexed: 10/27/2022]
Abstract
In this study, the complete mitochondrial genome of the Eurasian flying squirrel Pteromys volans (Rodentia, Sciuromorpha, Sciuridae) was sequenced and characterized in detail. The entire mitochondrial genome of P. volans consisted of 16,513 bp and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions. Its gene arrangement pattern was consistent with the mammalian ground pattern. The overall base composition and AT contents were similar to those of other rodent mitochondrial genomes. The light-strand origin generally identified between tRNA ( Asn ) and tRNA ( Cys ) consisted of a secondary structure with an 11-bp stem and an 11-bp loop. The large control region was constructed of three characteristic domains, ETAS, CD, and CSB without any repeat sequences. Each domain contained ETAS1, subsequences A, B, and C, and CSB1, respectively. In order to examine phylogenetic contentious issues of the monophyly of rodents and phylogenetic relationships among five rodent suborders, here, phylogenetic analyses based on nucleotide sequence data of the 35 rodent and 3 lagomorph mitochondrial genomes were performed using the Bayesian inference and maximum likelihood method. The result strongly supported the rodent monophyly with high node confidence values (BP 100 % in ML and BPP 1.00 in BI) and also monophylies of four rodent suborders (BP 85-100 % in ML and BPP 1.00 in BI), except for Anomalumorpha in which only one species was examined here. Also, phylogenetic relationships among the five rodent suborders were suggested and discussed in detail.
Collapse
|
20
|
Using Markov model to improve word normalization algorithm for biological sequence comparison. Amino Acids 2011; 42:1867-77. [DOI: 10.1007/s00726-011-0906-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2010] [Accepted: 03/29/2011] [Indexed: 10/18/2022]
|
21
|
Tan T, Tang X, Zhang J, Niu Y, Chen H, Li B, Wei Q, Ji W. Generation of trophoblast stem cells from rabbit embryonic stem cells with BMP4. PLoS One 2011; 6:e17124. [PMID: 21359200 PMCID: PMC3040765 DOI: 10.1371/journal.pone.0017124] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 01/21/2011] [Indexed: 01/28/2023] Open
Abstract
Trophoblast stem (TS) cells are ideal models to investigate trophectoderm differentiation and placental development. Herein, we describe the derivation of rabbit trophoblast stem cells from embryonic stem (ES) cells. Rabbit ES cells generated in our laboratory were induced to differentiate in the presence of BMP4 and TS-like cell colonies were isolated and expanded. These cells expressed the molecular markers of mouse TS cells, were able to invade, give rise to derivatives of TS cells, and chimerize placental tissues when injected into blastocysts. The rabbit TS-like cells maintained self-renewal in culture medium with serum but without growth factors or feeder cells, whilst their proliferation and identity were compromised by inhibitors of FGFs and TGF-β receptors. Taken together, our study demonstrated the derivation of rabbit TS cells and suggested the essential roles of FGF and TGF-β signalings in maintenance of rabbit TS cell self-renewal.
Collapse
Affiliation(s)
- Tao Tan
- Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Graduate School of Chinese Academy of Sciences, Beijing, China
- Yunnan Key Laboratory of Animal Reproductive Biology, Kunming, Yunnan, China
| | - Xianghui Tang
- Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Animal Reproductive Biology, Kunming, Yunnan, China
| | - Jing Zhang
- Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Graduate School of Chinese Academy of Sciences, Beijing, China
- Yunnan Key Laboratory of Animal Reproductive Biology, Kunming, Yunnan, China
| | - Yuyu Niu
- Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Animal Reproductive Biology, Kunming, Yunnan, China
| | - Hongwei Chen
- Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Graduate School of Chinese Academy of Sciences, Beijing, China
- Yunnan Key Laboratory of Animal Reproductive Biology, Kunming, Yunnan, China
| | - Bin Li
- Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Graduate School of Chinese Academy of Sciences, Beijing, China
- Yunnan Key Laboratory of Animal Reproductive Biology, Kunming, Yunnan, China
| | - Qiang Wei
- Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Graduate School of Chinese Academy of Sciences, Beijing, China
- Yunnan Key Laboratory of Animal Reproductive Biology, Kunming, Yunnan, China
| | - Weizhi Ji
- Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Animal Reproductive Biology, Kunming, Yunnan, China
- Kunming Biomed International, Kunming, Yunnan, China
- * E-mail:
| |
Collapse
|
22
|
Liu X, Dai Q, Li L, He Z. An efficient binomial model-based measure for sequence comparison and its application. J Biomol Struct Dyn 2011; 28:833-43. [PMID: 21294594 DOI: 10.1080/07391102.2011.10508611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Sequence comparison is one of the major tasks in bioinformatics, which could serve as evidence of structural and functional conservation, as well as of evolutionary relations. There are several similarity/dissimilarity measures for sequence comparison, but challenges remains. This paper presented a binomial model-based measure to analyze biological sequences. With help of a random indicator, the occurrence of a word at any position of sequence can be regarded as a random Bernoulli variable, and the distribution of a sum of the word occurrence is well known to be a binomial one. By using a recursive formula, we computed the binomial probability of the word count and proposed a binomial model-based measure based on the relative entropy. The proposed measure was tested by extensive experiments including classification of HEV genotypes and phylogenetic analysis, and further compared with alignment-based and alignment-free measures. The results demonstrate that the proposed measure based on binomial model is more efficient.
Collapse
Affiliation(s)
- Xiaoqing Liu
- School of Science, Hangzhou Dianzi Unviersity, Hangzhou 310018, People's Republic of China
| | | | | | | |
Collapse
|
23
|
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]
|
24
|
Speciation dynamics in the SE Asian tropics: Putting a time perspective on the phylogeny and biogeography of Sundaland tree squirrels, Sundasciurus. Mol Phylogenet Evol 2010; 55:711-20. [DOI: 10.1016/j.ympev.2009.12.023] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Revised: 12/17/2009] [Accepted: 12/21/2009] [Indexed: 11/18/2022]
|
25
|
Dynamic refolding of IFN-gamma mRNA enables it to function as PKR activator and translation template. Nat Chem Biol 2009; 5:896-903. [PMID: 19801993 DOI: 10.1038/nchembio.234] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Accepted: 08/03/2009] [Indexed: 12/16/2022]
Abstract
Interferon-gamma mRNA activates the RNA-dependent protein kinase PKR, which in turn strongly attenuates translation of interferon-gamma mRNA. Unlike riboswitches restricted to noncoding regions, the interferon-gamma RNA domain that activates PKR comprises the 5' UTR and 26 translated codons. Extensive interferon-gamma coding sequence is thus dedicated to activating PKR and blocking interferon-gamma synthesis. This implies that the PKR activator is disrupted by ribosomes during translation initiation and must refold promptly to restore PKR activation. The activator structure harbors an essential kink-turn, probably to allow formation of a pseudoknot that is critical for PKR activation. Three indispensable short helices, bordered by orientation-sensitive base pairs, align with the pseudoknot stem, generating RNA helix of sufficient length to activate PKR. Through gain-of-function mutations, we show that the RNA activator can adopt alternative conformations that activate PKR. This flexibility promotes efficient refolding of interferon-gamma mRNA, which is necessary for its dual function as translation template and activator of PKR, and which thus prevents overexpression of this inflammatory cytokine.
Collapse
|
26
|
Lee SJ, Liu T, Chattoraj A, Zhang SL, Wang L, Lee TM, Wang MM, Borjigin J. Posttranscriptional regulation of pineal melatonin synthesis in Octodon degus. J Pineal Res 2009; 47:75-81. [PMID: 19538336 PMCID: PMC2837936 DOI: 10.1111/j.1600-079x.2009.00690.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Small laboratory animals have provided significant information about melatonin regulation, yet most of these organisms are nocturnal and regulate melatonin synthesis by mechanisms that diverge from those of humans. For example, in all rodents examined, melatonin secretion occurs with a time lag of several hours after the onset of darkness; in addition, arylalkylamine N-acetyltransferase (AANAT), the key enzyme in melatonin synthesis, displays dynamic transcriptional activation specifically at night in all rodents studied to date. In ungulates and primates including humans, on the other hand, melatonin secretion occurs immediately during the early night and is controlled by circadian posttranscriptional regulation of AANAT. We hypothesize that the diurnal Octodon degus (an Hystricognath rodent) could serve as an improved experimental model for studies of human melatonin regulation. To test this, we monitored melatonin production in degus using pineal microdialysis and characterized the regulation of melatonin synthesis by analyzing degu Aanat. Degu pineal melatonin rises with little latency at night, as in ungulates and primates. In addition, degu Aanat mRNA expression displays no detectable diurnal variation, suggesting that, like ungulates and primates, melatonin in this species is regulated by a posttranscriptional mechanism. Compared with AANAT from all rodents examined to date, the predicted amino acid sequence of degu AANAT is phylogenetically more closely related to ungulate and primate AANAT. These data suggest that Octodon degus may provide an ideal model system for laboratory investigation of mechanisms of melatonin synthesis and secretion in diurnal mammals.
Collapse
Affiliation(s)
- Soo Jung Lee
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Tiecheng Liu
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Asamanja Chattoraj
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Samantha L. Zhang
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Department of Neuroscience Program, University of Michigan, Ann Arbor, MI, USA
| | - Lijun Wang
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Theresa M. Lee
- Department of Neuroscience Program, University of Michigan, Ann Arbor, MI, USA
- Department of Psychology, University of Michigan, Ann Arbor, MI, USA
| | - Michael M. Wang
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Department of Neuroscience Program, University of Michigan, Ann Arbor, MI, USA
| | - Jimo Borjigin
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Department of Neuroscience Program, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
27
|
GRILL ANDREA, AMORI GIOVANNI, ALOISE GAETANO, LISI IRENE, TOSI GUIDO, WAUTERS LUCASA, RANDI ETTORE. Molecular phylogeography of EuropeanSciurus vulgaris: refuge within refugia? Mol Ecol 2009; 18:2687-99. [DOI: 10.1111/j.1365-294x.2009.04215.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
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.
Collapse
Affiliation(s)
- Shani Blanga-Kanfi
- Department of Zoology, George S, Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel.
| | | | | | | | | | | |
Collapse
|
30
|
Zheng X, Dou Y, Wang J. Phylogenetic inference from binary sequences reduced by primary DNA sequences. JOURNAL OF MATHEMATICAL CHEMISTRY 2008; 46:1137-1148. [PMID: 32214589 PMCID: PMC7088321 DOI: 10.1007/s10910-008-9504-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2008] [Accepted: 10/31/2008] [Indexed: 06/10/2023]
Abstract
Given a bi-classification of nucleotides, we can obtain a reduced binary sequence of a primary DNA sequence. This binary sequence will undoubtedly retain some biological information and lose the rest. Here we want to know what kind of and how much biological information an individual binary sequence carries. Three classifications of nucleotides are explored in the present article. Phylogenetic trees are built from these binary sequences by the Neighbor-Joining (NJ) method, with evolutionary distance evaluated on the basis of a symbolic sequence complexity. We find that, for all data sets studied, binary sequences reduced by the purine/pyrimidine classification give reliable phylogeny (almost the same as that from the primary sequences), while the other two result in discrepancies at different levels. Some possible reasons and a simple model of sequence evolutionary are introduced to interpret this phenomenon.
Collapse
Affiliation(s)
- Xiaoqi Zheng
- Department of Applied Mathematics, Dalian University of Technology, Dalian, 116024 People’s Republic of China
- College of Advanced Science and Technology, Dalian University of Technology, Dalian, 116024 People’s Republic of China
| | - Yongchao Dou
- Department of Applied Mathematics, Dalian University of Technology, Dalian, 116024 People’s Republic of China
| | - Jun Wang
- Department of Mathematics, Shanghai Normal University, Shanghai, 200234 People’s Republic of China
- Scientific Computing Key Laboratory of Shanghai Universities, Shanghai, 200234 People’s Republic of China
| |
Collapse
|
31
|
Zheng X, Qin Y, Wang J. A Poisson model of sequence comparison and its application to coronavirus phylogeny. Math Biosci 2008; 217:159-66. [PMID: 19073197 PMCID: PMC7094598 DOI: 10.1016/j.mbs.2008.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 09/30/2008] [Accepted: 11/14/2008] [Indexed: 11/18/2022]
Abstract
In this paper, we propose two metrics to compare DNA and protein sequences based on a Poisson model of word occurrences. Instead of comparing the frequencies of all fixed-length words in two sequences, we consider (1) the probability of ‘generating’ one sequence under the Poisson model estimated from the other; (2) their different expression levels of words. Phylogenetic trees of 25 viruses including SARS-CoVs are constructed to illustrate our approach.
Collapse
Affiliation(s)
- Xiaoqi Zheng
- Department of Applied Mathematics, Dalian University of Technology, Dalian 116024, PR China
- College of Advanced Science and Technology, Dalian University of Technology, Dalian 116024, PR China
| | - Yufang Qin
- Department of Applied Mathematics, Dalian University of Technology, Dalian 116024, PR China
| | - Jun Wang
- Department of Mathematics, Shanghai Normal University, Shanghai 200034, PR China
- Corresponding author. Tel.: +86 411 8470 6101; fax: +86 411 8470 6100.
| |
Collapse
|
32
|
Dai Q, Yang Y, Wang T. Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison. ACTA ACUST UNITED AC 2008; 24:2296-302. [PMID: 18710871 DOI: 10.1093/bioinformatics/btn436] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
MOTIVATION Many proposed statistical measures can efficiently compare biological sequences to further infer their structures, functions and evolutionary information. They are related in spirit because all the ideas for sequence comparison try to use the information on the k-word distributions, Markov model or both. Motivated by adding k-word distributions to Markov model directly, we investigated two novel statistical measures for sequence comparison, called wre.k.r and S2.k.r. RESULTS The proposed measures were tested by similarity search, evaluation on functionally related regulatory sequences and phylogenetic analysis. This offers the systematic and quantitative experimental assessment of our measures. Moreover, we compared our achievements with these based on alignment or alignment-free. We grouped our experiments into two sets. The first one, performed via ROC (receiver operating curve) analysis, aims at assessing the intrinsic ability of our statistical measures to search for similar sequences from a database and discriminate functionally related regulatory sequences from unrelated sequences. The second one aims at assessing how well our statistical measure is used for phylogenetic analysis. The experimental assessment demonstrates that our similarity measures intending to incorporate k-word distributions into Markov model are more efficient.
Collapse
Affiliation(s)
- Qi Dai
- Department of Applied Mathematics, Dalian University of Technology, Dalian 116024, China.
| | | | | |
Collapse
|
33
|
Xin L, Ma B, Zhang K. A New Quartet Approach for Reconstructing Phylogenetic Trees: Quartet Joining Method. LECTURE NOTES IN COMPUTER SCIENCE 2007. [DOI: 10.1007/978-3-540-73545-8_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
|
34
|
Analysis of septins across kingdoms reveals orthology and new motifs. BMC Evol Biol 2007; 7:103. [PMID: 17601340 PMCID: PMC1931588 DOI: 10.1186/1471-2148-7-103] [Citation(s) in RCA: 203] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Accepted: 07/01/2007] [Indexed: 11/10/2022] Open
Abstract
Background Septins are cytoskeletal GTPase proteins first discovered in the fungus Saccharomyces cerevisiae where they organize the septum and link nuclear division with cell division. More recently septins have been found in animals where they are important in processes ranging from actin and microtubule organization to embryonic patterning and where defects in septins have been implicated in human disease. Previous studies suggested that many animal septins fell into independent evolutionary groups, confounding cross-kingdom comparison. Results In the current work, we identified 162 septins from fungi, microsporidia and animals and analyzed their phylogenetic relationships. There was support for five groups of septins with orthology between kingdoms. Group 1 (which includes S. cerevisiae Cdc10p and human Sept9) and Group 2 (which includes S. cerevisiae Cdc3p and human Sept7) contain sequences from fungi and animals. Group 3 (which includes S. cerevisiae Cdc11p) and Group 4 (which includes S. cerevisiae Cdc12p) contain sequences from fungi and microsporidia. Group 5 (which includes Aspergillus nidulans AspE) contains sequences from filamentous fungi. We suggest a modified nomenclature based on these phylogenetic relationships. Comparative sequence alignments revealed septin derivatives of already known G1, G3 and G4 GTPase motifs, four new motifs from two to twelve amino acids long and six conserved single amino acid positions. One of these new motifs is septin-specific and several are group specific. Conclusion Our studies provide an evolutionary history for this important family of proteins and a framework and consistent nomenclature for comparison of septin orthologs across kingdoms.
Collapse
|
35
|
Kjer KM, Honeycutt RL. Site specific rates of mitochondrial genomes and the phylogeny of eutheria. BMC Evol Biol 2007; 7:8. [PMID: 17254354 PMCID: PMC1796853 DOI: 10.1186/1471-2148-7-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Accepted: 01/25/2007] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Traditionally, most studies employing data from whole mitochondrial genomes to diagnose relationships among the major lineages of mammals have attempted to exclude regions that potentially complicate phylogenetic analysis. Components generally excluded are 3rd codon positions of protein-encoding genes, the control region, rRNAs, tRNAs, and the ND6 gene (encoded on the opposite strand). We present an approach that includes all the data, with the exception of the control region. This approach is based on a site-specific rate model that accommodates excessive homoplasy and that utilizes secondary structure as a reference for proper alignment of rRNAs and tRNAs. RESULTS Mitochondrial genomic data for 78 eutherian mammals, 8 metatherians, and 3 monotremes were analyzed with a Bayesian analysis and our site specific rate model. The resultant phylogeny revealed strong support for most nodes and was highly congruent with more recent phylogenies based on nuclear DNA sequences. In addition, many of the conflicting relationships observed by earlier mitochondrial-based analyses were resolved without need for the exclusion of large subsets of the data. CONCLUSION Rather than exclusion of data to minimize presumed noise associated with non-protein encoding genes in the mitochondrial genome, our results indicate that selection of an appropriate model that accommodates rate heterogeneity across data partitions and proper treatment of RNA genes can result in a mitochondrial genome-based phylogeny of eutherian mammals that is reasonably congruent with recent phylogenies derived from nuclear genes.
Collapse
Affiliation(s)
- Karl M Kjer
- Rutgers University, Department of Ecology, Evolution, and Natural Resources, Blake Hall, 93 Lipman Drive, New Brunswick, New Jersey 08901-8524, USA
| | - Rodney L Honeycutt
- Pepperdine University, Natural Science Division, 24255 Pacific Coast Hwy, Malibu, California 90263-4321, USA
| |
Collapse
|
36
|
Cannarozzi G, Schneider A, Gonnet G. A phylogenomic study of human, dog, and mouse. PLoS Comput Biol 2007; 3:e2. [PMID: 17206860 PMCID: PMC1761043 DOI: 10.1371/journal.pcbi.0030002] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2006] [Accepted: 11/20/2006] [Indexed: 11/19/2022] Open
Abstract
In recent years the phylogenetic relationship of mammalian orders has been addressed in a number of molecular studies. These analyses have frequently yielded inconsistent results with respect to some basal ordinal relationships. For example, the relative placement of primates, rodents, and carnivores has differed in various studies. Here, we attempt to resolve this phylogenetic problem by using data from completely sequenced nuclear genomes to base the analyses on the largest possible amount of data. To minimize the risk of reconstruction artifacts, the trees were reconstructed under different criteria-distance, parsimony, and likelihood. For the distance trees, distance metrics that measure independent phenomena (amino acid replacement, synonymous substitution, and gene reordering) were used, as it is highly improbable that all of the trees would be affected the same way by any reconstruction artifact. In contradiction to the currently favored classification, our results based on full-genome analysis of the phylogenetic relationship between human, dog, and mouse yielded overwhelming support for a primate-carnivore clade with the exclusion of rodents.
Collapse
Affiliation(s)
- Gina Cannarozzi
- Institute of Computational Science, ETH Zurich, Zurich, Switzerland
| | - Adrian Schneider
- Institute of Computational Science, ETH Zurich, Zurich, Switzerland
| | - Gaston Gonnet
- Institute of Computational Science, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
37
|
Five-year study of the genetic structure and demography of two subpopulations of the Japanese squirrel (Sciurus lis) in a continuous forest and an isolated woodlot. Ecol Res 2006. [DOI: 10.1007/s11284-006-0019-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
38
|
Deng R, Huang M, Wang J, Huang Y, Yang J, Feng J, Wang X. PTreeRec: Phylogenetic Tree Reconstruction based on genome BLAST distance. Comput Biol Chem 2006; 30:300-2. [PMID: 16797236 DOI: 10.1016/j.compbiolchem.2006.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2005] [Revised: 04/19/2006] [Accepted: 04/24/2006] [Indexed: 11/24/2022]
Abstract
Phylogenetic Tree Reconstruction (PTreeRec) is a web-based tool for automatic phylogeny inferences from whole-genome sequences, which accepts files of DNA sequences in the FASTA format and allows users to save the output tree file, and displays the inferred tree through an applet in a web browser. PTreeRec involves three basic steps. First, regions of maximal segment pairs (MSPs) based on an all-against-all pairwise comparison of genomes are located. Second, a distance matrix is calculated from MSP scores or coverage. Finally, a phylogenetic tree is reconstructed by the neighbor-joining method.
Collapse
Affiliation(s)
- Riqiang Deng
- State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen (Zhongshan) University, Guangzhou 510275, People's Republic of China
| | | | | | | | | | | | | |
Collapse
|
39
|
Li B, Li YB, He HB. LZ complexity distance of DNA sequences and its application in phylogenetic tree reconstruction. GENOMICS PROTEOMICS & BIOINFORMATICS 2006; 3:206-12. [PMID: 16689687 PMCID: PMC5172548 DOI: 10.1016/s1672-0229(05)03028-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
DNA sequences can be treated as finite-length symbol strings over a four-letter alphabet (A, C, T, G). As a universal and computable complexity measure, LZ complexity is valid to describe the complexity of DNA sequences. In this study, a concept of conditional LZ complexity between two sequences is proposed according to the principle of LZ complexity measure. An LZ complexity distance metric between two nonnull sequences is defined by utilizing conditional LZ complexity. Based on LZ complexity distance, a phylogenetic tree of 26 species of placental mammals (Eutheria) with three outgroup species was reconstructed from their complete mitochondrial genomes. On the debate that which two of the three main groups of placental mammals, namely Primates, Ferungulates, and Rodents, are more closely related, the phylogenetic tree reconstructed based on LZ complexity distance supports the suggestion that Primates and Ferungulates are more closely related.
Collapse
Affiliation(s)
- Bin Li
- School of Information Science and Engineering, Central South University, Changsha 410083, China.
| | | | | |
Collapse
|
40
|
Kriegs JO, Churakov G, Kiefmann M, Jordan U, Brosius J, Schmitz J. Retroposed elements as archives for the evolutionary history of placental mammals. PLoS Biol 2006; 4:e91. [PMID: 16515367 PMCID: PMC1395351 DOI: 10.1371/journal.pbio.0040091] [Citation(s) in RCA: 220] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2005] [Accepted: 01/23/2006] [Indexed: 11/30/2022] Open
Abstract
Reconstruction of the placental mammalian (eutherian) evolutionary tree has undergone diverse revisions, and numerous aspects remain hotly debated. Initial hierarchical divisions based on morphology contained many misgroupings due to features that evolved independently by similar selection processes. Molecular analyses corrected many of these misgroupings and the superordinal hierarchy of placental mammals was recently assembled into four clades. However, long or rapid evolutionary periods, as well as directional mutation pressure, can produce molecular homoplasies, similar characteristics lacking common ancestors. Retroposed elements, by contrast, integrate randomly into genomes with negligible probabilities of the same element integrating independently into orthologous positions in different species. Thus, presence/absence analyses of these elements are a superior strategy for molecular systematics. By computationally scanning more than 160,000 chromosomal loci and judiciously selecting from only phylogenetically informative retroposons for experimental high-throughput PCR applications, we recovered 28 clear, independent monophyly markers that conclusively verify the earliest divergences in placental mammalian evolution. Using tests that take into account ancestral polymorphisms, multiple long interspersed elements and long terminal repeat element insertions provide highly significant evidence for the monophyletic clades Boreotheria (synonymous with Boreoeutheria), Supraprimates (synonymous with Euarchontoglires), and Laurasiatheria. More importantly, two retropositions provide new support for a prior scenario of early mammalian evolution that places the basal placental divergence between Xenarthra and Epitheria, the latter comprising all remaining placentals. Due to its virtually homoplasy-free nature, the analysis of retroposon presence/absence patterns avoids the pitfalls of other molecular methodologies and provides a rapid, unequivocal means for revealing the evolutionary history of organisms. The authors identified and sequenced retroposons in mammalian genomes. The presence and absence of these retroposons provided evolutionary markers from which the authors reconstructed the phylogenetic history of placental mammals.
Collapse
Affiliation(s)
- Jan Ole Kriegs
- 1Institute of Experimental Pathology, Center for Molecular Biology of Inflammation, University of Münster, Münster, Germany
| | - Gennady Churakov
- 1Institute of Experimental Pathology, Center for Molecular Biology of Inflammation, University of Münster, Münster, Germany
| | - Martin Kiefmann
- 1Institute of Experimental Pathology, Center for Molecular Biology of Inflammation, University of Münster, Münster, Germany
| | - Ursula Jordan
- 1Institute of Experimental Pathology, Center for Molecular Biology of Inflammation, University of Münster, Münster, Germany
| | - Jürgen Brosius
- 1Institute of Experimental Pathology, Center for Molecular Biology of Inflammation, University of Münster, Münster, Germany
| | - Jürgen Schmitz
- 1Institute of Experimental Pathology, Center for Molecular Biology of Inflammation, University of Münster, Münster, Germany
| |
Collapse
|
41
|
Ulitsky I, Burstein D, Tuller T, Chor B. The Average Common Substring Approach to Phylogenomic Reconstruction. J Comput Biol 2006; 13:336-50. [PMID: 16597244 DOI: 10.1089/cmb.2006.13.336] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We describe a novel method for efficient reconstruction of phylogenetic trees, based on sequences of whole genomes or proteomes, whose lengths may greatly vary. The core of our method is a new measure of pairwise distances between sequences. This measure is based on computing the average lengths of maximum common substrings, which is intrinsically related to information theoretic tools (Kullback-Leibler relative entropy). We present an algorithm for efficiently computing these distances. In principle, the distance of two l long sequences can be calculated in O(l) time. We implemented the algorithm using suffix arrays our implementation is fast enough to enable the construction of the proteome phylogenomic tree for hundreds of species and the genome phylogenomic forest for almost two thousand viruses. An initial analysis of the results exhibits a remarkable agreement with "acceptable phylogenetic and taxonomic truth." To assess our approach, our results were compared to the traditional (single-gene or protein-based) maximum likelihood method. The obtained trees were compared to implementations of a number of alternative approaches, including two that were previously published in the literature, and to the published results of a third approach. Comparing their outcome and running time to ours, using a "traditional" trees and a standard tree comparison method, our algorithm improved upon the "competition" by a substantial margin. The simplicity and speed of our method allows for a whole genome analysis with the greatest scope attempted so far. We describe here five different applications of the method, which not only show the validity of the method, but also suggest a number of novel phylogenetic insights.
Collapse
Affiliation(s)
- Igor Ulitsky
- School of Computer Science, Tel Aviv University, Ramat Aviv, Israel
| | | | | | | |
Collapse
|
42
|
Trizio I, Crestanello B, Galbusera P, Wauters LA, Tosi G, Matthysen E, Hauffe HC. Geographical distance and physical barriers shape the genetic structure of Eurasian red squirrels (Sciurus vulgaris) in the Italian Alps. Mol Ecol 2005; 14:469-81. [PMID: 15660938 DOI: 10.1111/j.1365-294x.2005.02428.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Red squirrels (Sciurus vulgaris) are widely distributed throughout Eurasia, occurring in many types of coniferous and mixed-deciduous forests. In fragmented landscapes, small and partly isolated populations with low immigration rates show reduced genetic diversity, but reforestation can increase gene flow and restore levels of genetic variation in a few decades. No studies have so far investigated the genetic structure of red squirrel in large, continuous forests. The Italian Alps are presently characterized by almost continuous, recently reconnected forest habitats, that were affected by deep landscape changes during last glaciations but remained mostly unchanged between 10 000 and 200 years bp, when forest cover was heavily reduced. In this study we analyse patterns of genetic variability of red squirrels in and between seven sites distributed over 250 km of Alpine habitat, using mitochondrial DNA (mtDNA) and microsatellites. We use isolation-by-distance (IBD) models to investigate the relative importance that past (Pleistocene glaciations) and recent (fragmentation, bottlenecks) events had on the present genetic situation. Both nuclear and mtDNA data indicate a significant differentiation among study sites and a significant correlation between genetic and geographical distance only over a large scale. No recent bottlenecks are recorded through microsatellites and demographic models strongly support equilibrium between gene flow and drift; however, mtDNA suggests that there may have been local demographic crashes, probably in correspondence with the 19th-century forest fragmentation. These findings indicate that local landscape factors other than geographical distance per se, such as barriers of unsuitable habitat, affect gene flow and determine differentiation.
Collapse
Affiliation(s)
- I Trizio
- Department Environment-Health-Security, University of Insubria, Varese, Via J.H. Dunant 3, I-21100 Varese, Italy
| | | | | | | | | | | | | |
Collapse
|
43
|
|
44
|
MARIVAUX LAURENT, VIANEY-LIAUD MONIQUE, JAEGER JEANJACQUES. High-level phylogeny of early Tertiary rodents: dental evidence. Zool J Linn Soc 2004. [DOI: 10.1111/j.1096-3642.2004.00131.x] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
45
|
Oshida T, Shafique CM, Barkati S, Yasuda M, Hussein NA, Endo H, Yanagawa H, Masuda R. Phylogenetic position of the small Kashmir flying squirrel, Hylopetes fimbriatus (≡ Eoglaucomys fimbriatus), in the subfamily Pteromyinae. CAN J ZOOL 2004. [DOI: 10.1139/z04-108] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The phylogenetic relationships of flying squirrels (Pteromyinae) were studied by obtaining complete sequence data from the mitochondrial cytochrome b gene of eight Old World and two New World flying squirrel species, with special reference to the systematic and phylogenetic status among Hylopetes fimbriatus (Gray, 1837) (≡ Eoglaucomys fimbriatus (Gray, 1837)) from Pakistan, two Glaucomys Thomas, 1908 species from North America, and two Hylopetes Thomas, 1908 species from Southeast Asia. Phylogenetic trees supported clustering of (i) Belomys pearsonii (Gray, 1842), (ii) H. fimbriatus, the Glaucomys species, Hylopetes lepidus (Horsfield, 1823), and Hylopetes phayrei (Blyth, 1859), (iii) species of Pteromys G. Cuvier, 1800, and (iv) species of Petaurista Link, 1795. Early polytomic divergence among the flying squirrel genera could have taken place in the northern part of the Eurasian continent. The unclear divergence between the Old and New World flying squirrels shows that divergence among flying squirrel genera could have occurred before the formation of the Bering Strait. Hylopetes fimbriatus was more closely related to the two Glaucomys species than to H. lepidus or H. phayrei, supporting placement of the species fimbriatus in the monotypic genus Eoglaucomys Howell, 1915.
Collapse
|
46
|
Maloney B, Ge YW, Greig N, Lahiri DK. Presence of a “CAGA box” in the
APP
gene unique to amyloid plaque‐forming species and absent in all
APLP
‐1/2 genes: implications in Alzheimer's disease. FASEB J 2004; 18:1288-90. [PMID: 15208260 DOI: 10.1096/fj.03-1703fje] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Potentially toxic amyloid beta-peptide (Abeta) in Alzheimer's disease (AD) is generated from a family of Abeta-containing precursor proteins (APP), which is regulated via the 5'-untranslated region (5'-UTR) of its mRNA. We analyzed 5'-UTRs of the APP superfamily, including amyloid plaque-forming and non-amyloid plaque-forming species, and of prions (27 different DNA sequences). A "CAGA" sequence proximal to the "ATG" start codon was present in a location unique to APP genes of amyloid plaque-forming species and absent in all other genes surveyed. This CAGA box is immediately upstream of an interleukin-1-responsive element (acute box). In addition, the proximal CAGA box is predicted to appear on a stem-loop structure in both human and guinea pig APP mRNA. This stem-loop is part of a predicted bulge-loop that encompasses a known iron regulatory element (IRE). Electrophoretic mobility shift with segments of the APP 5'-UTR showed that a region with the proximal CAGA sequence binds nuclear proteins, and this UTR fragment is active in a reporter gene functional assay. Thus, the 5'-UTR in the human APP but not those of APP-like proteins contains a specific region that may participate in APP regulation and may determine a more general model for amyloid generation as seen in AD. The 5'-UTR of human APP contains several interesting control elements, such as an acute box element, a CAGA box, an IRE, and a transforming growth factor-beta-responsive element, that could control APP expression and provide suitable and specific drug targets for AD.
Collapse
Affiliation(s)
- Bryan Maloney
- Departments of Psychiatry, Institute of Psychiatric Research, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | | | | | | |
Collapse
|
47
|
Pikov V, McCreery DB. Mapping of spinal cord circuits controlling the bladder and external urethral sphincter functions in the rabbit. Neurourol Urodyn 2004; 23:172-9. [PMID: 14983431 DOI: 10.1002/nau.20008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
AIMS A primary purpose of this study was to evaluate the rabbit as a model for studying the spinal circuitry controlling the bladder emptying. We aimed to map the locations of the neuronal circuitry controlling the external urethral sphincter (EUS) and the detrusor by stimulating at different spinal cord locations with a microelectrode, while recording the responses from these muscles. METHODS Spinal cord microstimulation was performed in the intermediate zone of the gray matter at the L7-S4 spinal cord levels in eight rabbits with empty and full bladders. Bladder activity was measured as intravesical pressure (IVP) changes and EUS activity was measured via electromyographic (EMG) electrodes positioned within the urethra. RESULTS Under both bladder conditions, EUS activation was produced from similar locations in the spinal cord comprising a continuous area in the intermediate zone of the S2-S3 spinal cord. This region extended 25 mm in the rostrocaudal dimension, at least 1 mm lateral to the midline, and 0.5-1 mm in the dorsoventral dimension at a depth of 2-3 mm beneath the dorsal surface. No locations in the intermediate zone produced EUS inhibition. The S2-S3 spinal region, stimulation of which produced the strongest EUS activation, also produced modest bladder contractions. CONCLUSIONS Overall, the results indicate that spinal cord networks controlling bladder and EUS activation in the rabbit are overlapping and clustered into columns extending rostrocaudally. The lack of spinal locations producing EUS inhibition and large bladder contractions make the rabbit an unattractive model for studies of neuroprosthetic spinal control of micturition.
Collapse
Affiliation(s)
- Victor Pikov
- Neural Engineering Program, Huntington Medical Research Institutes, Fairmount Avenue, Pasadena, California 91105, USA.
| | | |
Collapse
|
48
|
Cotta C, Moscato P. A memetic-aided approach to hierarchical clustering from distance matrices: application to gene expression clustering and phylogeny. Biosystems 2003; 72:75-97. [PMID: 14642660 DOI: 10.1016/s0303-2647(03)00136-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We propose a heuristic approach to hierarchical clustering from distance matrices based on the use of memetic algorithms (MAs). By using MAs to solve some variants of the Minimum Weight Hamiltonian Path Problem on the input matrix, a sequence of the individual elements to be clustered (referred to as patterns) is first obtained. While this problem is also NP-hard, a probably optimal sequence is easy to find with the current advances for this problem and helps to prune the space of possible solutions and/or to guide the search performed by an actual clustering algorithm. This technique has been successfully applied to both a Branch-and-Bound algorithm, and to evolutionary algorithms and MAs. Experimental results are given in the context of phylogenetic inference and in the hierarchical clustering of gene expression data.
Collapse
Affiliation(s)
- Carlos Cotta
- Dept. Lenguajes y Ciencias de la Computación, Universidad de Málaga ETSI Informática (3.2.49), Campus de Teatinos, 29071 Malaga, Spain.
| | | |
Collapse
|
49
|
Van Hooser SD, Heimel JAF, Nelson SB. Receptive field properties and laminar organization of lateral geniculate nucleus in the gray squirrel (Sciurus carolinensis). J Neurophysiol 2003; 90:3398-418. [PMID: 12840084 DOI: 10.1152/jn.00474.2003] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Physiological studies of the lateral geniculate nucleus (LGN) have revealed three classes of relay neurons, called X, Y, and W cells in carnivores and parvocellular (P), magnocellular (M), and koniocellular (K) in primates. The homological relationships among these cell classes and how receptive field (RF) properties of these cells compare with LGN cells in other mammals are poorly understood. To address these questions, we have characterized RF properties and laminar organization in LGN of a highly visual diurnal rodent, the gray squirrel, under isoflurane anesthesia. We identified three classes of LGN cells. One class found in layers 1 and 2 showed sustained, reliable firing, center-surround organization, and was almost exclusively linear in spatial summation. Another class, found in layer 3, showed short response latencies, transient and reliable firing, center-surround organization, and could show either linear (76%) or nonlinear (24%) spatial summation. A third, heterogeneous class found throughout the LGN but primarily in layer 3 showed highly variable responses, a variety of response latencies and could show either center-surround or noncenter-surround receptive field organization and either linear (77%) or nonlinear (23%) spatial summation. RF sizes of all cell classes showed little dependency on eccentricity, and all of these classes showed low contrast gains. When compared with LGN cells in other mammals, our data are consistent with the idea that all mammals contain three basic classes of LGN neurons, one showing reliable, sustained responses, and center-surround organization (X or P); another showing transient but reliable responses, short latencies, and center-surround organization (Y or M); and a third, highly variable and heterogeneous class of cells (W or K). Other properties such as dependency of receptive field size on eccentricity, linearity of spatial summation, and contrast gain appear to vary from species to species.
Collapse
|
50
|
Nikaido M, Cao Y, Harada M, Okada N, Hasegawa M. Mitochondrial phylogeny of hedgehogs and monophyly of Eulipotyphla. Mol Phylogenet Evol 2003; 28:276-84. [PMID: 12878464 DOI: 10.1016/s1055-7903(03)00120-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We sequenced the complete mitochondrial (mt) genomes of three insectivores: the long-eared hedgehog Hemiechinus auritus, the Japanese mole Mogera wogura, and the greater Japanese shrew-mole Urotrichus talpoides. These mtDNA data together with other previously sequenced mtDNAs were analyzed using a maximum likelihood method to infer their phylogenetic relationships among eutherians. Previous mitochondrial protein analyses used a simple model that did not consider site-heterogeneity, and Erinaceoidea (hedgehogs and moonrats) was placed at the basal eutherian position that is separated from Soricoidea (shrews) and Talpoidea (moles), suggesting the exclusion of the Erinaceoidea-Eulipotyphla tree. By including the new mtDNA sequences and introducing site-heterogeneity into the model, the Erinaceoidea-Eulipotyphla tree emerges as the best tree or as a tree with a log-likelihood score indistinguishable from that of the best tree. However, this conclusion depends on species sampling in Erinaceoidea, demonstrating the importance of both species sampling and use of an appropriate substitution model when inferring phylogenetic relationships.
Collapse
Affiliation(s)
- Masato Nikaido
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | | | | | | | | |
Collapse
|