1
|
Makarchenko EA, Semenchenko AA. Two new chironomid species of the genus Pseudokiefferiella Zavel (Diptera: Chironomidae: Diamesinae) from the Amur River basin of Russia. Zootaxa 2023; 5339:481-491. [PMID: 38221403 DOI: 10.11646/zootaxa.5339.5.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Indexed: 01/16/2024]
Abstract
The adult male, pupa, larva with DNA barcoding of Ps. matafonovi sp. nov. and the adult male of Ps. silinka sp. nov. from Amur River basin of Russia are described and illustrated. Ps. matafonovi sp. nov. is genetically distant from other Pseudokiefferiella showing uncorrected p-distances of >6.8 %. The results of species delimitation show that genus Pseudokiefferiella includes 10 (mPTP), 13 (ASAP, GMYC) or 14 (BOLD) distinct molecular taxonomic units (mOTUs) that requires a revision of this genus using both morphological and molecular approaches.
Collapse
Affiliation(s)
- Eugenyi A Makarchenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity; Far East Branch of the Russian Academy of Sciences.
| | - Alexander A Semenchenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity; Far East Branch of the Russian Academy of Sciences.
| |
Collapse
|
2
|
Niwa K, Nishikawa K, Matsui M, Kanamori S, Kuro-O M. Taxonomic reassessment of salamanders (genus Hynobius) from Tsushima Islands, Japan, with a resurrection of Hynobius tagoi Dunn, 1923 (Amphibia: Caudata). Zootaxa 2023; 5339:201-236. [PMID: 38221056 DOI: 10.11646/zootaxa.5339.3.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Indexed: 01/16/2024]
Abstract
To clarify the taxonomic status of salamanders from Tsushima Islands, Japan, we examined two species of salamanders, Hynobius tsuensis and Hynobius sp. from Tsushima Islands, and compared them with H. nebulosus from Kyushu. We found that the three taxa differ from each other in nuclear DNA, adult morphology, and egg-sac shape, and consider them to be independent species. Based on the investigation of type specimens of the synonyms, we identified Hynobius sp. as H. tagoi Dunn, 1923 and redescribe it herein. Also, we designate a neotype for H. tsuensis and redescribe H. tsuensis. The distribution areas of the two species partly overlap but they were distinguishable by their body colorations: H. tsuensis has uniformly blackish tail sides and a distinct yellow stripe on the upper tail edge; whereas H. tagoi has brown tail sides with numerous dark stippling and without a distinct yellow stripe on the upper tail edge.
Collapse
Affiliation(s)
- Keita Niwa
- 1Graduate School of Human and Environmental Studies; Kyoto University; Yoshida Nihonmatsu; Sakyo-ku; Kyoto 606-8501; JAPAN. Present affiliation: Akita Prefectural Office; Sanno 4-1-1; Akita 010-8570; JAPAN..
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies; Kyoto University; Yoshida Nihonmatsu; Sakyo-ku; Kyoto 606-8501; JAPAN. Graduate School of Global Environmental Studies; Kyoto University; Yoshida Honmachi; Sakyo-ku; Kyoto 606-8501; JAPAN..
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies; Kyoto University; Yoshida Nihonmatsu; Sakyo-ku; Kyoto 606-8501; JAPAN..
| | - Sally Kanamori
- Graduate School of Global Environmental Studies; Kyoto University; Yoshida Honmachi; Sakyo-ku; Kyoto 606-8501; JAPAN..
| | - Masaki Kuro-O
- Faculty of Agriculture and Life Science; Hirosaki University; Bunkyo-cho 3; Hirosaki; Aomori 036-8561; JAPAN..
| |
Collapse
|
3
|
Makarchenko EA, Semenchenko AA. Review of subfamily Prodiamesinae (Diptera: Chironomidae) from the Russian Far East and bordering territory. Zootaxa 2023; 5323:1-26. [PMID: 37518203 DOI: 10.11646/zootaxa.5323.1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 08/01/2023]
Abstract
Based on material from the Russian Far East and Eastern Siberia, a revision of the chironomids of the subfamily Prodiamesinae was carried out. A new species Monodiamesa fontinalis sp. nov., is here described, ten species from four genera-Monodiamesa bathyphila Kieffer, M. kamora Makarchenko et Yavorskaya, M. improvisa Makarchenko, M. nitida Kieffer, Odontomesa fulva Kieffer, Prodiamesa levanidovae Makarchenko, Propsilocerus amurensis Makarchenko, P. jacuticus (Zvereva), P. paradoxus Lundström and P. taimyrus Zelentzov are redescribed with varying degrees of completeness. Propsilocerus taimyrus Zelentzov, 2000 is proposed as senior synonym of P. saetheri Wang, Liu et Paasivirta, 2007. DNA barcoding of four species, M. fontinalis sp. nov., M. bathyphila, P. olivacea Meigen and P. akamusi (Tokunaga) was provided. Species delimitation and phylogenetic relationships using COI DNA barcodes confirms the species validity of M. fontinalis sp. nov.
Collapse
Affiliation(s)
- Eugenyi A Makarchenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity; Far East Branch of the Russian Academy of Sciences.
| | - Alexander A Semenchenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity; Far East Branch of the Russian Academy of Sciences.
| |
Collapse
|
4
|
Tomimori Y, Matsui M, Okawa H, Nishikawa K, Tanabe S, Kamasaka R. Reassessment of species delimitation using nuclear markers in three lentic-breeding salamanders from the Chugoku District of Japan (Amphibia: Caudata: Hynobiidae). Zootaxa 2023; 5293:145-160. [PMID: 37518493 DOI: 10.11646/zootaxa.5293.1.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Indexed: 08/01/2023]
Abstract
Hynobius akiensis sensu lato has recently been split into three species based on short sequence analyses of cyt-b gene of mtDNA and without data of nuclear DNA, and strange sympatric distribution in some areas has been indicated in two species. We analyzed nuclear DNA marker (SNPs) and complete sequence of cyt-b in H. akiensis sensu lato to reassess species delimitation and genetic introgression among species. As a result, we found two lineages with discordant mitochondrial and nuclear DNA in some areas. Of H. akiensis sensu lato, each of the two contains the type locality of two species recently reported (H. sumidai and H. geiyoensis), and the use of these names has been previously advocated. However, their sympatric distribution was rejected based on nuclear DNA data, which we consider is more reliable than mtDNA. We thus clarify geographic boundary of these two species and revise the species delimitations.
Collapse
Affiliation(s)
- Yusuke Tomimori
- Graduate School of Human and Environmental Studies; Kyoto University; Yoshida Nihonmatsu-cho; Sakyo-ku; Kyoto 606-8501; JAPAN; Graduate School of Global Environmental Studies; Kyoto University; Yoshida Honmachi; Sakyo-ku; Kyoto 606-8501; JAPAN.
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies; Kyoto University; Yoshida Nihonmatsu-cho; Sakyo-ku; Kyoto 606-8501; JAPAN.
| | | | - Kanto Nishikawa
- Graduate School of Global Environmental Studies; Kyoto University; Yoshida Honmachi; Sakyo-ku; Kyoto 606-8501; JAPAN.
| | - Shingo Tanabe
- Graduate School of Global Environmental Studies; Kyoto University; Yoshida Honmachi; Sakyo-ku; Kyoto 606-8501; JAPAN.
| | - Ryo Kamasaka
- Kuta 435-19-103; Izuhara-Machi; Tsushima; Nagasaki 817-0032; JAPAN.
| |
Collapse
|
5
|
Makarchenko EA, Semenchenko AA, Palatov DM. Fauna and taxonomy of Diamesinae (Diptera, Chironomidae) from the Caucasus, with a morphological description and DNA barcoding of new taxa and a discussion of diagnostic problems for Diamesa Meigen and Pseudodiamesa Goetghebuer. Zootaxa 2023; 5271:313-328. [PMID: 37518126 DOI: 10.11646/zootaxa.5271.2.6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Indexed: 08/01/2023]
Abstract
As a result of the revision of adult males as well as available literature data, 26 species of the subfamily Diamesinae are registered for the Caucasus, belonging to 5 genera. Four species are recorded for the first time for this region, one species, D. elbrusica sp. nov., and one subspecies, D. sakartvella gidanica subsp. nov., are new to science and are described. Six species are classified as endemics of the Caucasus. Distribution of other species of Caucasian Diamesinae is discussed. DNA barcodes of 102 specimens and 20 species of four genera, Boreoheptagyia Brundin, Diamesa Meigen, Pseudodiamesa Goetghebuer and Syndiamesa Kieffer were obtained in this study. Of these, 12 species were deposed in the GenBank and BOLD systems for the first time. We have established that D. cinerella group includes D. kasymovi and probably D. lavillei whereas D. zernyi group includes D. vaillanti and D. valentinae. Highly supported phylogeny and results of species delimitation suggest the description of D. elbrusica sp. nov. and D. sakartvella gidanica subsp. nov. Ps. aff. branickii and Ps. aff. nivosa are new species based on DNA barcoding. The results of species delimitation show that genus Pseudodiamesa includes 10 (ASAP, GMYC), 14 (mPTP) or 21 (BOLD) distinct molecular taxonomic units (mOTUs) among which only Ps. stackelbergi have an undoubted species status that requires a large revision using both morphological and molecular approaches.
Collapse
Affiliation(s)
- Eugenyi A Makarchenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity; Far East Branch of the Russian Academy of Sciences; 100 let Vladi- vostoku 159; 690022 Vladivostok; Russia.
| | - Alexander A Semenchenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity; Far East Branch of the Russian Academy of Sciences; 100 let Vladi- vostoku 159; 690022 Vladivostok; Russia.
| | - Dmitry M Palatov
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences; Leninskij prosp. 33; 119071 Moscow; Russia.
| |
Collapse
|
6
|
Oh M, Kim S, Lee S. Revisiting the phylogeny of the family Miridae (Heteroptera: Cimicomorpha), with updated insights into its origin and life history evolution. Mol Phylogenet Evol 2023; 184:107796. [PMID: 37086912 DOI: 10.1016/j.ympev.2023.107796] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 04/15/2023] [Accepted: 04/17/2023] [Indexed: 04/24/2023]
Abstract
Heteroptera is one of the most successfully adapted groups on Earth and can be observed in almost every environment. Within the evolution of heteropteran insects, Miridae show remarkable diversity (>11,700 spp.), accounting for a quarter of all Heteroptera. However, their phylogeny is still unclear, and no plausible theory for the driving force of their diversification has been established. In this work, we provide new suggestions for the phylogeny of Miridae using a larger dataset than previous studies. In addition, we suggest an alternative evolutionary history based on newly calibrated divergence dates for Miridae and its subordinate groups, and present probable factors of the family's success in terms of species diversity. The entire dataset comprises 16 outgroups and 188 ingroup taxa including all seven known subfamilies and 37 out of 45 known tribes. Each species is aligned as 3,577bp with six molecular loci (COI, 16S rRNA, 18S rRNA, 28S rRNA D3 region, H2A, and H3A). Among the molecular markers, we are the first to test histone genes (H2A, H3A) in Miridae. Our results raise the following points about phylogenetic relationships: i) The earliest group to diverge from Miridae was Monaloniini (Bryocorinae). ii) Bryocorinae and Cylapinae are polyphyletic, Deraeocorinae and Orthotylinae also rendered as non-monophyletic group. iii) Termatophylini and Coridromiini separated from Deraeocorinae and Orthotylinae respectively. iv) Four large tribes, Orthotylini, Phylini, Deraeocorini and Mirini are non-monophyletic. The results from our ancestral state reconstruction and divergence date estimation suggest the following: i) Miridae first diverged during the Late Jurassic (approx. 163.4 Mya), and the divergence dates of most subfamilies and tribes overlap with angiosperm radiation, which perhaps synergized their diversification. ii) Ancestral reconstruction results for Miridae reveal it to be predominantly phytophagous and diverge to oligophagy mainly in plant-tissue habitats, which could have allowed the mirids to select optimal tactics as plant-dwellers. iii) The common ancestor of Miridae originated among plant-dwellers mainly on Eudicots, and that tendency was largely maintained, but sporadic host shifts also occurred.
Collapse
Affiliation(s)
- Minsuk Oh
- Insect Biosystematics Laboratory, Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Sora Kim
- Insect Phylogenetics and Evolution Laboratory, Department of Plant Protection & Quarantine, Jeonbuk National University, Jeonju, 54896, Republic of Korea; Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Seunghwan Lee
- Insect Biosystematics Laboratory, Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea; Research Institute of Agricultural and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
| |
Collapse
|
7
|
González-Toral C, Nava HS, Fernández Prieto JA, Cires E. What Hides in the Heights? The Case of the Iberian Endemism Bromus picoeuropeanus. PLANTS (BASEL, SWITZERLAND) 2023; 12:1531. [PMID: 37050157 PMCID: PMC10096826 DOI: 10.3390/plants12071531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/28/2023] [Accepted: 03/30/2023] [Indexed: 06/19/2023]
Abstract
Bromus picoeuropeanus is a recently described species belonging to a complex genus of grasses. It inhabits stony soils at heights ranging from 1600 to 2200 m in Picos de Europa (Cantabrian Mountains, northern Spain). This species is morphologically very similar to B. erectus, partially sharing its presumed distribution range. We aim to determine the relationship between these species and their altitudinal ranges in Picos de Europa and the Cantabrian Mountains by conducting phylogenetic analyses based on nuclear (ETS and ITS) and chloroplastic (trnL) markers. Phylogenetic trees were inferred by Maximum Likelihood and Bayesian Inference. Haplotype networks were estimated based on the plastid marker. Although the ITS topologies could not generate exclusive clades for these species, the ETS analyses generated highly supported B. picoeuropeanus exclusive clades, which included locations outside its altitudinal putative range. The ETS-ITS and ETS-ITS-trnL topologies generated B. picoeuropeanus exclusive clades, whereas the trnL-based trees and haplotype networks were unable to discriminate B. erectus and B. picoeuropeanus. This evidence suggests that B. picoeuropeanus is a separate species with a larger distribution than previously thought, opening new questions regarding the evolution of B. erectus and other similar species in European mountainous systems. However, more information is needed regarding B. picoeuropeanus susceptibility to temperature rises.
Collapse
Affiliation(s)
- Claudia González-Toral
- Department of Organisms and Systems Biology, University of Oviedo, C/Catedrático Rodrigo Uría s/n, 33071 Oviedo, Spain
| | - Herminio S. Nava
- Department of Organisms and Systems Biology, University of Oviedo, C/Catedrático Rodrigo Uría s/n, 33071 Oviedo, Spain
| | - José Antonio Fernández Prieto
- Department of Organisms and Systems Biology, University of Oviedo, C/Catedrático Rodrigo Uría s/n, 33071 Oviedo, Spain
- Institute of Natural Resources and Territorial Planning (INDUROT), Campus de Mieres, C/Gonzalo Gutiérrez Quirós s/n, 33600 Mieres, Spain
| | - Eduardo Cires
- Department of Organisms and Systems Biology, University of Oviedo, C/Catedrático Rodrigo Uría s/n, 33071 Oviedo, Spain
- Institute of Natural Resources and Territorial Planning (INDUROT), Campus de Mieres, C/Gonzalo Gutiérrez Quirós s/n, 33600 Mieres, Spain
| |
Collapse
|
8
|
Bohnsack KS, Kaden M, Abel J, Villmann T. Alignment-Free Sequence Comparison: A Systematic Survey From a Machine Learning Perspective. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:119-135. [PMID: 34990369 DOI: 10.1109/tcbb.2022.3140873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The encounter of large amounts of biological sequence data generated during the last decades and the algorithmic and hardware improvements have offered the possibility to apply machine learning techniques in bioinformatics. While the machine learning community is aware of the necessity to rigorously distinguish data transformation from data comparison and adopt reasonable combinations thereof, this awareness is often lacking in the field of comparative sequence analysis. With realization of the disadvantages of alignments for sequence comparison, some typical applications use more and more so-called alignment-free approaches. In light of this development, we present a conceptual framework for alignment-free sequence comparison, which highlights the delineation of: 1) the sequence data transformation comprising of adequate mathematical sequence coding and feature generation, from 2) the subsequent (dis-)similarity evaluation of the transformed data by means of problem-specific but mathematically consistent proximity measures. We consider coding to be an information-loss free data transformation in order to get an appropriate representation, whereas feature generation is inevitably information-lossy with the intention to extract just the task-relevant information. This distinction sheds light on the plethora of methods available and assists in identifying suitable methods in machine learning and data analysis to compare the sequences under these premises.
Collapse
|
9
|
Kanamori S, Nishikawa K, Matsui M, Tanabe S. A new species of lotic breeding salamander (Amphibia, Caudata, Hynobiidae) from Shikoku, Japan. PeerJ 2022; 10:e13891. [PMID: 36046503 PMCID: PMC9422979 DOI: 10.7717/peerj.13891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/21/2022] [Indexed: 01/19/2023] Open
Abstract
Background Hynobius hirosei is a lotic-breeding salamander endemic to Shikoku Island in western Japan. Significant allozymic and morphological differences have been found among the populations of this species; however, the degree and pattern of intraspecific variation have not been surveyed using a sufficient number of samples. Methods For the taxonomic revision of H. hirosei, we conducted genetic and morphological surveys using samples collected throughout the distribution. Phylogenetic analysis using the cytochrome b region of mitochondrial DNA and population structure analysis using single nucleotide polymorphisms were conducted to evaluate the population structure within the species and the degree of genetic differentiation. Subsequently, a morphological survey based on multivariate and univariate analyses was performed to assess the morphological variation. Results Genetic analyses revealed three genetic groups (Tsurugi, Central, and Nanyo) within H. hirosei, with the Nanyo group distributed allopatrically from the others, and the Tsurugi and Central groups distributed parapatrically with the formation of a hybrid zone between them. The Nanyo group was morphologically distinguishable from the remaining samples, including the topotype of H. hirosei, based on a smaller body size and several ratio values of characters to snout-vent length, longer axilla-groin distance, shorter tail length, shorter internarial distance, longer upper eyelid length, and larger medial tail width. These results support the notion that the Nanyo group is an undescribed species. However, the remaining genetically differentiated groups could not be divided in the present study. Herein, we described the Nanyo group as a new species.
Collapse
Affiliation(s)
- Sally Kanamori
- Graduate School of Global and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Kanto Nishikawa
- Graduate School of Global and Environmental Studies, Kyoto University, Kyoto, Japan,Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Shingo Tanabe
- Graduate School of Global and Environmental Studies, Kyoto University, Kyoto, Japan
| |
Collapse
|
10
|
Fan X, Wang C, Bunker DE. Population Structure of German Cockroaches (Blattodea: Ectobiidae) in an Urban Environment Based on Single Nucleotide Polymorphisms. JOURNAL OF MEDICAL ENTOMOLOGY 2022; 59:1319-1327. [PMID: 35462399 DOI: 10.1093/jme/tjac036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Indexed: 06/14/2023]
Abstract
German cockroaches (Blattella germanica L.) harbor and disperse medically important pathogens and are a source of allergens that impact human health and wellbeing. Management of this pest requires an understanding of their distribution and dispersal. In this study, we collected German cockroaches from three apartment buildings in New Jersey, USA. We identified single-nucleotide polymorphisms (SNPs) from DNA extractions using next generation sequencing. We analyzed the SNPs and characterized cockroach population genetic structure using Fst, principal component, phylogenetic, and STRUCTURE analyses. We found significant differences in German cockroach population structure among the buildings. Within buildings, we found variable population structure that may be evidence for multiple colonization events. This study shows that SNPs derived from next generation sequencing provide a powerful tool for analyzing the genetic population structure of these medically important pests.
Collapse
Affiliation(s)
- X Fan
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - C Wang
- Department of Entomology, Rutgers, The State University of New Jersey, 96 Lipman Drive, New Brunswick, NJ, 08901, USA
| | - D E Bunker
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| |
Collapse
|
11
|
Ledda A, Cummins M, Shaw LP, Jauneikaite E, Cole K, Lasalle F, Barry D, Turton J, Rosmarin C, Anaraki S, Wareham D, Stoesser N, Paul J, Manuel R, Cherian BP, Didelot X. Hospital outbreak of carbapenem-resistant Enterobacterales associated with a blaOXA-48 plasmid carried mostly by Escherichia coli ST399. Microb Genom 2022; 8:000675. [PMID: 35442183 PMCID: PMC9453065 DOI: 10.1099/mgen.0.000675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A hospital outbreak of carbapenem-resistant Enterobacterales was detected by routine surveillance. Whole genome sequencing and subsequent analysis revealed a conserved promiscuous blaOXA-48 carrying plasmid as the defining factor within this outbreak. Four different species of Enterobacterales were involved in the outbreak. Escherichia coli ST399 accounted for 35 of all the 55 isolates. Comparative genomics analysis using publicly available E. coli ST399 genomes showed that the outbreak E. coli ST399 isolates formed a unique clade. We developed a mathematical model of pOXA-48-like plasmid transmission between host lineages and used it to estimate its conjugation rate, giving a lower bound of 0.23 conjugation events per lineage per year. Our analysis suggests that co-evolution between the pOXA-48-like plasmid and E. coli ST399 could have played a role in the outbreak. This is the first study to report carbapenem-resistant E. coli ST399 carrying blaOXA-48 as the main cause of a plasmid-borne outbreak within a hospital setting. Our findings suggest complementary roles for both plasmid conjugation and clonal expansion in the emergence of this outbreak.
Collapse
Affiliation(s)
- Alice Ledda
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, UK
- Healthcare Associated Infections and Antimicrobial Resistance Division, National Infection Service, Public Health England, London, UK
- *Correspondence: Alice Ledda,
| | - Martina Cummins
- Department of Microbiology and Infection Control, Barts Health NHS Trust, London, UK
| | - Liam P. Shaw
- Department of Zoology, University of Oxford, Oxford, UK
| | - Elita Jauneikaite
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, UK
- NHIR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious disease, Imperial College London, Hammersmith Campus, London, UK
| | | | - Florent Lasalle
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, UK
- Microbes and Pathogens Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Deborah Barry
- Department of Microbiology and Infection Control, Barts Health NHS Trust, London, UK
| | - Jane Turton
- Healthcare Associated Infections and Antimicrobial Resistance Division, National Infection Service, Public Health England, London, UK
| | - Caryn Rosmarin
- Department of Microbiology and Infection Control, Barts Health NHS Trust, London, UK
| | - Sudy Anaraki
- North East and North Central London Health Protection Team, Public Health England, London, UK
| | - David Wareham
- Department of Microbiology and Infection Control, Barts Health NHS Trust, London, UK
| | - Nicole Stoesser
- Modernising Medical Microbiology, Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - John Paul
- Brighton and Sussex Medical school, Department of Global health and Infection, University of Sussex, Falmer, Brighton, UK
| | - Rohini Manuel
- Public Health Laboratory London, National Infection Service, Public Health England, London, UK
| | - Benny P. Cherian
- Department of Microbiology and Infection Control, Barts Health NHS Trust, London, UK
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK
| |
Collapse
|
12
|
Mahar JE, Jenckel M, Huang N, Smertina E, Holmes EC, Strive T, Hall RN. Frequent intergenotypic recombination between the non-structural and structural genes is a major driver of epidemiological fitness in caliciviruses. Virus Evol 2021; 7:veab080. [PMID: 34754513 PMCID: PMC8570162 DOI: 10.1093/ve/veab080] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/14/2021] [Accepted: 09/15/2021] [Indexed: 12/21/2022] Open
Abstract
The diversity of lagoviruses (Caliciviridae) in Australia has increased considerably in recent years. By the end of 2017, five variants from three viral genotypes were present in populations of Australian rabbits, while prior to 2014 only two variants were known. To understand the evolutionary interactions among these lagovirus variants, we monitored their geographical distribution and relative incidence over time in a continental-scale competition study. Within 3 years of the incursion of rabbit haemorrhagic disease virus 2 (RHDV2, denoted genotype GI.1bP-GI.2 [polymerase genotype]P-[capsid genotype]) into Australia, two novel recombinant lagovirus variants emerged: RHDV2-4e (genotype GI.4eP-GI.2) in New South Wales and RHDV2-4c (genotype GI.4cP-GI.2) in Victoria. Although both novel recombinants contain non-structural genes related to those from benign, rabbit-specific, enterotropic viruses, these variants were recovered from the livers of both rabbits and hares that had died acutely. This suggests that the determinants of host and tissue tropism for lagoviruses are associated with the structural genes, and that tropism is intricately connected with pathogenicity. Phylogenetic analyses demonstrated that the RHDV2-4c recombinant emerged independently on multiple occasions, with five distinct lineages observed. Both the new RHDV2-4e and -4c recombinant variants replaced the previous dominant parental RHDV2 (genotype GI.1bP-GI.2) in their respective geographical areas, despite sharing an identical or near-identical (i.e. single amino acid change) VP60 major capsid protein with the parental virus. This suggests that the observed replacement by these recombinants was not driven by antigenic variation in VP60, implicating the non-structural genes as key drivers of epidemiological fitness. Molecular clock estimates place the RHDV2-4e recombination event in early to mid-2015, while the five RHDV2-4c recombination events occurred from late 2015 through to early 2017. The emergence of at least six viable recombinant variants within a 2-year period highlights the high frequency of these events, detectable only through intensive surveillance, and demonstrates the importance of recombination in lagovirus evolution.
Collapse
Affiliation(s)
- Jackie E Mahar
- Marie Bashir Institute for Infectious Disease and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Maria Jenckel
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Black Mountain, ACT 2601, Australia
| | - Nina Huang
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Black Mountain, ACT 2601, Australia
| | - Elena Smertina
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Black Mountain, ACT 2601, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Disease and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Tanja Strive
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Black Mountain, ACT 2601, Australia
| | - Robyn N Hall
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Black Mountain, ACT 2601, Australia
| |
Collapse
|
13
|
Wang Y, Zhao Y, Pan Q. Advances, challenges and opportunities of phylogenetic and social network analysis using COVID-19 data. Brief Bioinform 2021; 23:6380452. [PMID: 34601563 DOI: 10.1093/bib/bbab406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/04/2021] [Accepted: 09/03/2021] [Indexed: 11/15/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) has attracted research interests from all fields. Phylogenetic and social network analyses based on connectivity between either COVID-19 patients or geographic regions and similarity between syndrome coronavirus 2 (SARS-CoV-2) sequences provide unique angles to answer public health and pharmaco-biological questions such as relationships between various SARS-CoV-2 mutants, the transmission pathways in a community and the effectiveness of prevention policies. This paper serves as a systematic review of current phylogenetic and social network analyses with applications in COVID-19 research. Challenges in current phylogenetic network analysis on SARS-CoV-2 such as unreliable inferences, sampling bias and batch effects are discussed as well as potential solutions. Social network analysis combined with epidemiology models helps to identify key transmission characteristics and measure the effectiveness of prevention and control strategies. Finally, future new directions of network analysis motivated by COVID-19 data are summarized.
Collapse
Affiliation(s)
- Yue Wang
- School of Mathematical and Natural Science, Arizona State University, 4701 W Thunderbird Rd, 85306, Arizona, USA
| | - Yunpeng Zhao
- School of Mathematical and Natural Science, Arizona State University, 4701 W Thunderbird Rd, 85306, Arizona, USA
| | - Qing Pan
- Department of Statistics, George Washington University, 801 22nd St. NW, 20052, Washington DC, USA
| |
Collapse
|
14
|
Kuhl H, Frankl-Vilches C, Bakker A, Mayr G, Nikolaus G, Boerno ST, Klages S, Timmermann B, Gahr M. An Unbiased Molecular Approach Using 3'-UTRs Resolves the Avian Family-Level Tree of Life. Mol Biol Evol 2021; 38:108-127. [PMID: 32781465 PMCID: PMC7783168 DOI: 10.1093/molbev/msaa191] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Presumably, due to a rapid early diversification, major parts of the higher-level phylogeny of birds are still resolved controversially in different analyses or are considered unresolvable. To address this problem, we produced an avian tree of life, which includes molecular sequences of one or several species of ∼90% of the currently recognized family-level taxa (429 species, 379 genera) including all 106 family-level taxa of the nonpasserines and 115 of the passerines (Passeriformes). The unconstrained analyses of noncoding 3-prime untranslated region (3′-UTR) sequences and those of coding sequences yielded different trees. In contrast to the coding sequences, the 3′-UTR sequences resulted in a well-resolved and stable tree topology. The 3′-UTR contained, unexpectedly, transcription factor binding motifs that were specific for different higher-level taxa. In this tree, grebes and flamingos are the sister clade of all other Neoaves, which are subdivided into five major clades. All nonpasserine taxa were placed with robust statistical support including the long-time enigmatic hoatzin (Opisthocomiformes), which was found being the sister taxon of the Caprimulgiformes. The comparatively late radiation of family-level clades of the songbirds (oscine Passeriformes) contrasts with the attenuated diversification of nonpasseriform taxa since the early Miocene. This correlates with the evolution of vocal production learning, an important speciation factor, which is ancestral for songbirds and evolved convergent only in hummingbirds and parrots. As 3′-UTR-based phylotranscriptomics resolved the avian family-level tree of life, we suggest that this procedure will also resolve the all-species avian tree of life
Collapse
Affiliation(s)
- Heiner Kuhl
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany.,Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany.,Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Carolina Frankl-Vilches
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Antje Bakker
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Gerald Mayr
- Ornithological Section, Senckenberg Research Institute, Frankfurt am Main, Germany
| | - Gerhard Nikolaus
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Stefan T Boerno
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany
| | - Sven Klages
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany
| | - Manfred Gahr
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| |
Collapse
|
15
|
Niwa K, Kuro-O M, Nishikawa K. Discovery of Two Lineages of Hynobius tsuensis (Amphibia, Caudata) Endemic to Tsushima Island, Japan. Zoolog Sci 2021; 38:259-266. [PMID: 34057351 DOI: 10.2108/zs200149] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/03/2020] [Indexed: 11/17/2022]
Abstract
The Tsushima salamander, Hynobius tsuensis, is a lotic-breeding species endemic to Tsushima Island, Japan. We investigated genetic variation in this species using samples covering all known localities on the island. Phylogenetic analyses based on mitochondrial cytochrome b gene sequences divided H. tsuensis populations into two genetic groups: true H. tsuensis and an unknown species (Hynobius sp.) showing a closer relationship to Hynobius nebulosus than to H. tsuensis. The genetic distance between the two groups was greater than the genetic distances between different species of Hynobius. Both groups were found to breed in mountain streams, sometimes in the same streams syntopically. Population structure analysis based on several nuclear microsatellite loci strongly indicated reproductive isolation between the two groups in the syntopic localities. This is the first report confirming the syntopic occurrence of two lotic salamanders of Hynobius on a small island. We propose that the lotic breeding habits of the two salamanders were independently acquired.
Collapse
Affiliation(s)
- Keita Niwa
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan.,Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-Nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masaki Kuro-O
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-Nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan,
| |
Collapse
|
16
|
Abadi S, Avram O, Rosset S, Pupko T, Mayrose I. ModelTeller: Model Selection for Optimal Phylogenetic Reconstruction Using Machine Learning. Mol Biol Evol 2021; 37:3338-3352. [PMID: 32585030 DOI: 10.1093/molbev/msaa154] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Statistical criteria have long been the standard for selecting the best model for phylogenetic reconstruction and downstream statistical inference. Although model selection is regarded as a fundamental step in phylogenetics, existing methods for this task consume computational resources for long processing time, they are not always feasible, and sometimes depend on preliminary assumptions which do not hold for sequence data. Moreover, although these methods are dedicated to revealing the processes that underlie the sequence data, they do not always produce the most accurate trees. Notably, phylogeny reconstruction consists of two related tasks, topology reconstruction and branch-length estimation. It was previously shown that in many cases the most complex model, GTR+I+G, leads to topologies that are as accurate as using existing model selection criteria, but overestimates branch lengths. Here, we present ModelTeller, a computational methodology for phylogenetic model selection, devised within the machine-learning framework, optimized to predict the most accurate nucleotide substitution model for branch-length estimation. We demonstrate that ModelTeller leads to more accurate branch-length inference than current model selection criteria on data sets simulated under realistic processes. ModelTeller relies on a readily implemented machine-learning model and thus the prediction according to features extracted from the sequence data results in a substantial decrease in running time compared with existing strategies. By harnessing the machine-learning framework, we distinguish between features that mostly contribute to branch-length optimization, concerning the extent of sequence divergence, and features that are related to estimates of the model parameters that are important for the selection made by current criteria.
Collapse
Affiliation(s)
- Shiran Abadi
- School of Plant Sciences and Food security, Tel-Aviv University, Tel-Aviv, Israel
| | - Oren Avram
- School of Molecular Cell Biology & Biotechnology, Tel-Aviv University, Tel-Aviv, Israel
| | - Saharon Rosset
- Department of Statistics and Operations Research, School of Mathematical Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Tal Pupko
- School of Molecular Cell Biology & Biotechnology, Tel-Aviv University, Tel-Aviv, Israel
| | - Itay Mayrose
- School of Plant Sciences and Food security, Tel-Aviv University, Tel-Aviv, Israel
| |
Collapse
|
17
|
Irwin NAT, Twynstra CS, Mathur V, Keeling PJ. The molecular phylogeny of Chionaster nivalis reveals a novel order of psychrophilic and globally distributed Tremellomycetes (Fungi, Basidiomycota). PLoS One 2021; 16:e0247594. [PMID: 33760841 PMCID: PMC7990227 DOI: 10.1371/journal.pone.0247594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/09/2021] [Indexed: 12/04/2022] Open
Abstract
Snow and ice present challenging substrates for cellular growth, yet microbial snow communities not only exist, but are diverse and ecologically impactful. These communities are dominated by green algae, but additional organisms, such as fungi, are also abundant and may be important for nutrient cycling, syntrophic interactions, and community structure in general. However, little is known about these non-algal community members, including their taxonomic affiliations. An example of this is Chionaster nivalis, a unicellular fungus that is morphologically enigmatic and frequently observed in snow communities globally. Despite being described over one hundred years ago, the phylogeny and higher-level taxonomic classifications of C. nivalis remain unknown. Here, we isolated and sequenced the internal transcribed spacer (ITS) and the D1-D2 region of the large subunit ribosomal RNA gene of C. nivalis, providing a molecular barcode for future studies. Phylogenetic analyses using the ITS and D1-D2 region revealed that C. nivalis is part of a novel lineage in the class Tremellomycetes (Basidiomycota, Agaricomycotina) for which a new order Chionasterales ord. nov. (MB838717) and family Chionasteraceae fam. nov. (MB838718) are proposed. Comparisons between C. nivalis and sequences generated from environmental surveys revealed that the Chionasterales are globally distributed and probably psychrophilic, as they appear to be limited to the high alpine and arctic regions. These results highlight the unexplored diversity that exists within these extreme habitats and emphasize the utility of single-cell approaches in characterizing these complex algal-dominated communities.
Collapse
Affiliation(s)
- Nicholas A. T. Irwin
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Merton College, University of Oxford, Oxford, United Kingdom
- * E-mail:
| | - Chantelle S. Twynstra
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick J. Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
18
|
Tougard C, Vukić J, Ahnelt H, Buj I, Kovačić M, Moro GA, Tutman P, Šanda R. Quaternary climatic cycles promoted (re)colonization and diversification events in Adriatic sand gobies. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Jasna Vukić
- Department of Ecology Faculty of Science Charles University Prague Czech Republic
| | - Harald Ahnelt
- Department of Evolutionary Biology Faculty of Life Sciences University of Vienna Vienna Austria
- First Zoological Department Natural History Museum in Vienna Vienna Austria
| | - Ivana Buj
- Department of Zoology Faculty of Science University of Zagreb Zagreb Croatia
| | | | | | - Pero Tutman
- Laboratory for Ichthyology and Coastal Fisheries Institute of Oceanography and Fisheries Split Croatia
| | - Radek Šanda
- Department of Zoology National Museum Prague Czech Republic
| |
Collapse
|
19
|
Villanueva-Corrales S, García-Botero C, Garcés-Cardona F, Ramírez-Ríos V, Villanueva-Mejía DF, Álvarez JC. The Complete Chloroplast Genome of Plukenetia volubilis Provides Insights Into the Organelle Inheritance. FRONTIERS IN PLANT SCIENCE 2021; 12:667060. [PMID: 33968119 PMCID: PMC8103035 DOI: 10.3389/fpls.2021.667060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/24/2021] [Indexed: 05/04/2023]
Abstract
Plukenetia volubilis L. (Malpighiales: Euphorbiaceae), also known as Sacha inchi, is considered a promising crop due to its high seed content of unsaturated fatty acids (UFAs), all of them highly valuable for food and cosmetic industries, but the genetic basis of oil biosynthesis of this non-model plant is still insufficient. Here, we sequenced the total DNA of Sacha inchi by using Illumina and Nanopore technologies and approached a de novo reconstruction of the whole nucleotide sequence and the organization of its 164,111 bp length of the chloroplast genome, displaying two copies of an inverted repeat sequence [inverted repeat A (IRA) and inverted repeat B (IRB)] of 28,209 bp, each one separating a small single copy (SSC) region of 17,860 bp and a large single copy (LSC) region of 89,833 bp. We detected two large inversions on the chloroplast genome that were not presented in the previously reported sequence and studied a promising cpDNA marker, useful in phylogenetic approaches. This chloroplast DNA (cpDNA) marker was used on a set of five distinct Colombian cultivars of P. volubilis from different geographical locations to reveal their phylogenetic relationships. Thus, we evaluated if it has enough resolution to genotype cultivars, intending to crossbreed parents and following marker's trace down to the F1 generation. We finally elucidated, by using molecular and cytological methods on cut flower buds, that the inheritance mode of P. volubilis cpDNA is maternally transmitted and proposed that it occurs as long as it is physically excluded during pollen development. This de novo chloroplast genome will provide a valuable resource for studying this promising crop, allowing the determination of the organellar inheritance mechanism of some critical phenotypic traits and enabling the use of genetic engineering in breeding programs to develop new varieties.
Collapse
Affiliation(s)
| | - Camilo García-Botero
- CIBIOP Research Group, Biological Sciences Department, EAFIT University, Medellín, Colombia
| | - Froilán Garcés-Cardona
- CIBIOP Research Group, Biological Sciences Department, EAFIT University, Medellín, Colombia
| | - Viviana Ramírez-Ríos
- CIBIOP Research Group, Biological Sciences Department, EAFIT University, Medellín, Colombia
| | | | - Javier C. Álvarez
- BEC Research Group, Biological Sciences Department, EAFIT University, Medellín, Colombia
- CIBIOP Research Group, Biological Sciences Department, EAFIT University, Medellín, Colombia
- *Correspondence: Javier C. Álvarez,
| |
Collapse
|
20
|
Verma NK, Kumar S, Basotra SD, Jain A, Vij M, Prasad G, Bhattacharyya MS. Biocatalytic reduction of prochiral ketones to enantiopure alcohols by novel yeast isolates from unique biodiversity. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2020.101547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
21
|
Matsui M, Yoshikawa N, Aoki G, Sasamori K, Matsui M, Tanabe S, Misawa Y, Nishikawa K. Wide Distribution but Low Differentiation: Phylogenetic Relationships and Phylogeography of Hynobius nigrescens (Amphibia: Caudata). Zoolog Sci 2020; 37:529-537. [PMID: 33269868 DOI: 10.2108/zs200099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/02/2020] [Indexed: 11/17/2022]
Abstract
We surveyed the genetic structure of Hynobius nigrescens Stejneger, 1907, a lentic breeding salamander widespread throughout montane and lowland regions of northeastern Japan. We performed a mitochondrial DNA analysis to explore intraspecific genetic variation and infer the evolutionary population history of H. nigrescens. Complete 1141 bp sequences of the mitochondrial cytochrome b gene were studied for 134 adult and larval individuals collected from 62 localities, encompassing the known range of the species. Hynobius nigrescens proved to be monophyletic, including two major clades (Clade II from southwestern Hokuriku and Clade I from all other localities). The latter clade comprises four well-supported and geographically structured subclades, which show genetic distances smaller than those seen in the widely sympatric species Hynobius lichenatus. Results of population statistical analyses indicated that Clade II of the westernmost range of H. nigrescens seems to have maintained a constant population size, while Clade I from most of the northeastern species range shows a tendency of recent population expansion, which is evident in Subclades I-A from the northernmost range and I-B from southern Tohoku to northern Kanto and eastern Chubu. In contrast, Subclades I-C from northeastern Chubu and Sado Is. and I-D from northwestern Chubu to Hokuriku seem to have been relatively stable in population size. Hynobius nigrescens differs greatly from other salamander species from northeastern Japan in its much more recent periods of genetic differentiation and its pattern thereof, and is suggested to be a young faunal element in this region.
Collapse
Affiliation(s)
- Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Natsuhiko Yoshikawa
- Department of Biology, Keio University, 4-1-1 Hiyoshi, Kohoku-Ku, Yokohama, Kanagawa 223-8521, Japan,
| | - Gen Aoki
- Hokuetsu High School, 5-12-1 Yoneyama, Chuo-ku, Niigata 950-0916, Japan
| | | | | | - Shingo Tanabe
- Kamikatsura-Higashi-no-Kuchi-cho 6-10, Nishikyo-ku, Kyoto 615-8221, Japan
| | - Yasuchika Misawa
- Civil Engineering and Eco-Technology Consultants, Osaka Branch, Minami-senba 1-15-14, Chuo-ku, Osaka 542-0081, Japan
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.,Graduate School of Global Environmental Studies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| |
Collapse
|
22
|
Sohpal VK. Computational analysis of SARS-CoV-2, SARS-CoV, and MERS-CoV genome using MEGA. Genomics Inform 2020; 18:e30. [PMID: 33017874 PMCID: PMC7560444 DOI: 10.5808/gi.2020.18.3.e30] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/05/2020] [Accepted: 09/22/2020] [Indexed: 11/29/2022] Open
Abstract
The novel coronavirus pandemic that has originated from China and spread throughout the world in three months. Genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) predecessor, severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) play an important role in understanding the concept of genetic variation. In this paper, the genomic data accessed from National Center for Biotechnology Information (NCBI) through Molecular Evolutionary Genetic Analysis (MEGA) for statistical analysis. Firstly, the Bayesian information criterion (BIC) and Akaike information criterion (AICc) are used to evaluate the best substitution pattern. Secondly, the maximum likelihood method used to estimate of transition/transversions (R) through Kimura-2, Tamura-3, Hasegawa-Kishino-Yano, and Tamura-Nei nucleotide substitutions model. Thirdly and finally nucleotide frequencies computed based on genomic data of NCBI. The results indicate that general times reversible model has the lowest BIC and AICc score 347,394 and 347,287, respectively. The transition/transversions bias for nucleotide substitutions models varies from 0.56 to 0.59 in MEGA output. The average nitrogenous bases frequency of U, C, A, and G are 31.74, 19.48, 28.04, and 20.74, respectively in percentages. Overall the genomic data analysis of SARS-CoV-2, SARS-CoV, and MERS-CoV highlights the close genetic relationship.
Collapse
Affiliation(s)
- Vipan Kumar Sohpal
- Department of Chemical & Bio Engineering, Beant
College of Engineering & Technology, Gurdaspur 143521,
India
| |
Collapse
|
23
|
Nascimento FF, Baral S, Geidelberg L, Mukandavire C, Schwartz SR, Turpin G, Turpin N, Diouf D, Diouf NL, Coly K, Kane CT, Ndour C, Vickerman P, Boily MC, Volz EM. Phylodynamic analysis of HIV-1 subtypes B, C and CRF 02_AG in Senegal. Epidemics 2019; 30:100376. [PMID: 31767497 PMCID: PMC10066795 DOI: 10.1016/j.epidem.2019.100376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 01/12/2023] Open
Abstract
Surveillance of HIV epidemics in key populations and in developing countries is often challenging due to sparse, incomplete, or low-quality data. Analysis of HIV sequence data can provide an alternative source of information about epidemic history, population structure, and transmission patterns. To understand HIV-1 dynamics and transmission patterns in Senegal, we carried out model-based phylodynamic analyses using the structured-coalescent approach using HIV-1 sequence data from three different subgroups: reproductive aged males and females from the adult Senegalese population and men who have sex with other men (MSM). We fitted these phylodynamic analyses to time-scaled phylogenetic trees individually for subtypes C and CRF 02_AG, and for the combined data for subtypes B, C and CRF 02_AG. In general, the combined analysis showed a decreasing proportion of effective number of infections among all reproductive aged adults relative to MSM. However, we observed a nearly time-invariant distribution for subtype CRF 02_AG and an increasing trend for subtype C on the proportion of effective number of infections. The population attributable fraction also differed between analyses: subtype CRF 02_AG showed little contribution from MSM, while for subtype C and combined analyses this contribution was much higher. Despite observed differences, results suggested that the combination of high assortativity among MSM and the unmet HIV prevention and treatment needs represent a significant component of the HIV epidemic in Senegal.
Collapse
Affiliation(s)
- Fabrícia F Nascimento
- Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place W2 1PG, UK
| | - Stefan Baral
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Lily Geidelberg
- Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place W2 1PG, UK
| | - Christinah Mukandavire
- Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place W2 1PG, UK
| | - Sheree R Schwartz
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Gnilane Turpin
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD, USA
| | | | | | - Nafissatou Leye Diouf
- Institut de Recherche en Santé, de Surveillance Epidemiologique et de Formations, Dakar, Senegal
| | - Karleen Coly
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Coumba Toure Kane
- Institut de Recherche en Santé, de Surveillance Epidemiologique et de Formations, Dakar, Senegal
| | - Cheikh Ndour
- Division de La Lutte Contre Le Sida et Les IST, Ministry of Health, Dakar, Senegal
| | - Peter Vickerman
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Marie-Claude Boily
- Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place W2 1PG, UK
| | - Erik M Volz
- Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place W2 1PG, UK; MRC Centre for Global Infectious Disease Analysis, Imperial College London, UK.
| |
Collapse
|
24
|
Chen W, Kenney T, Bielawski J, Gu H. Testing adequacy for DNA substitution models. BMC Bioinformatics 2019; 20:349. [PMID: 31221105 PMCID: PMC6585133 DOI: 10.1186/s12859-019-2905-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 05/17/2019] [Indexed: 12/22/2022] Open
Abstract
Background Testing model adequacy is important before a DNA substitution model is chosen for phylogenetic inference. Using a mis-specified model can negatively impact phylogenetic inference, for example, the maximum likelihood method can be inconsistent when the DNA sequences are generated under a tree topology which is in the Felsentein Zone and analyzed with a mis-specified or inadequate model. However, model adequacy testing in phylogenetics is underdeveloped. Results Here we develop a simple, general, powerful and robust model test based on Pearson’s goodness-of-fit test and binning of site patterns. We demonstrate through simulation that this test is robust in its high power to reject the inadequate models for a large range of different ways of binning site patterns while the Type I error is controlled well. In the real data analysis we discovered many cases where models chosen by another method can be rejected by this new test, in particular, our proposed test rejects the most complex DNA model (GTR+I+ Γ) while the Goldman-Cox test fails to reject the commonly used simple models. Conclusions Model adequacy testing and bootstrap should be used together to assess reliability of conclusions after model selection and model fitting have already been applied to choose the model and fit it. The new goodness-of-fit test proposed in this paper is a simple and powerful model adequacy testing method serving such a regular model checking purpose. We caution against deriving strong conclusions from analyses based on inadequate models. At a minimum, those results derived from inadequate models can now be readly flagged using the new test, and reported as such.
Collapse
Affiliation(s)
- Wei Chen
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Canada
| | - Toby Kenney
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Canada
| | - Joseph Bielawski
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Canada.,Department of Biology, Dalhousie University, Halifax, Canada
| | - Hong Gu
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Canada.
| |
Collapse
|
25
|
Gladstone NS, Niemiller ML, Pieper EB, Dooley K, McKinney ML. Morphometrics and phylogeography of the cave-obligate land snail Helicodiscus barri (Gastropoda, Stylommatophora, Helicodiscidae). SUBTERRANEAN BIOLOGY 2019. [DOI: 10.3897/subtbiol.30.35321] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Molecular studies have recently led to the detection of many cryptic species complexes within morphologically ambiguous species formerly undescribed by the scientific community. Organisms such as land snails are at a particularly higher risk of species misidentification and misinterpretation, in that gastropod systematics are based almost entirely on external shell morphology. Subterranean ecosystems are associated with especially high degrees of cryptic speciation, largely owing to the abiotic similarities of these systems. In this study, we attempt to diagnose the potential cryptic diversity in the troglobitic land snail Helicodiscusbarri. Land snails are generally associated with having low vagility, and as such this species’ broad, mosaic distribution indicates the misdiagnosis of this organism as a single species. We analyze both mitochondrial (16S, CO1) and nuclear (28S, H3) genetic data for 23 populations. Phylogeny for H.barri was reconstructed using both maximum-likelihood and Bayesian approaches to assess relationships among populations, and two species delimitation methods (mPTP and ABGD) were used to detect the presence of unique molecular operational taxonomic units (MOTUs). Species delimitation results revealed seven and sixteen MOTUs respectively, suggesting the presence of several cryptic lineages within H.barri. To assess how external shell morphology corresponds with patterns of genetic and environmental variation, two morphometric approaches were used incorporating 115 shells from 31 populations. Both morphometric approaches reveal a significant environmental influence on shell morphology, and one approach showed the significance of MOTU groups. We discuss the delimitation and morphometric results and additionally provide discussion on the taxonomic and conservation implications of this study.
Collapse
|
26
|
Genome-wide analysis of the ovodefensin gene family: Monophyletic origin, independent gene duplication and presence of different selection patterns. INFECTION GENETICS AND EVOLUTION 2019; 68:265-272. [DOI: 10.1016/j.meegid.2019.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/28/2018] [Accepted: 01/02/2019] [Indexed: 11/15/2022]
|
27
|
Abadi S, Azouri D, Pupko T, Mayrose I. Model selection may not be a mandatory step for phylogeny reconstruction. Nat Commun 2019; 10:934. [PMID: 30804347 PMCID: PMC6389923 DOI: 10.1038/s41467-019-08822-w] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 01/29/2019] [Indexed: 11/29/2022] Open
Abstract
Determining the most suitable model for phylogeny reconstruction constitutes a fundamental step in numerous evolutionary studies. Over the years, various criteria for model selection have been proposed, leading to debate over which criterion is preferable. However, the necessity of this procedure has not been questioned to date. Here, we demonstrate that although incongruency regarding the selected model is frequent over empirical and simulated data, all criteria lead to very similar inferences. When topologies and ancestral sequence reconstruction are the desired output, choosing one criterion over another is not crucial. Moreover, skipping model selection and using instead the most parameter-rich model, GTR+I+G, leads to similar inferences, thus rendering this time-consuming step nonessential, at least under current strategies of model selection.
Collapse
Affiliation(s)
- Shiran Abadi
- School of Plant Sciences and Food Security, Tel Aviv University, Ramat Aviv, Tel-Aviv, 69978, Israel
| | - Dana Azouri
- School of Plant Sciences and Food Security, Tel Aviv University, Ramat Aviv, Tel-Aviv, 69978, Israel
- School of Molecular Cell Biology & Biotechnology, Tel Aviv University, Ramat Aviv, Tel-Aviv, 69978, Israel
| | - Tal Pupko
- School of Molecular Cell Biology & Biotechnology, Tel Aviv University, Ramat Aviv, Tel-Aviv, 69978, Israel.
| | - Itay Mayrose
- School of Plant Sciences and Food Security, Tel Aviv University, Ramat Aviv, Tel-Aviv, 69978, Israel.
| |
Collapse
|
28
|
Matsui M, Okawa H, Nishikawa K, Aoki G, Eto K, Yoshikawa N, Tanabe S, Misawa Y, Tominaga A. Systematics of the Widely Distributed Japanese Clouded Salamander, Hynobius nebulosus (Amphibia: Caudata: Hynobiidae), and Its Closest Relatives. CURRENT HERPETOLOGY 2019. [DOI: 10.5358/hsj.38.32] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Masafumi Matsui
- 1Graduate School of Human and Environmental Studies, Kyoto University, Sakyo, Kyoto 606–8501, JAPAN
| | | | - Kanto Nishikawa
- 1Graduate School of Human and Environmental Studies, Kyoto University, Sakyo, Kyoto 606–8501, JAPAN
| | - Gen Aoki
- 3Doshisha International Junior/Senior High School, 60–1 Tatara-Miyakodani, Kyotanabe, Kyoto 610–0321
| | - Koshiro Eto
- 4Kitakyushu Museum of Natural History & Human History, Higashida 2–4–1, Yahatahigashi-ku, Kitakyushu
| | - Natsuhiko Yoshikawa
- 5Center for Molecular Biodiversity Research, National Museum of Nature and Science, 4–1–1 Amakubo, T
| | - Shingo Tanabe
- 6Kamikatsura-Higashi-no-Kuchi-Cho, Nishikyo-ku, Kyoto 615–8221, JAPAN
| | - Yasuchika Misawa
- 7Civil Engineering and Eco-Technology Consultants, Minamisenba 1–15–14, Chuo-ku, Osaka 542–0081, JAP
| | - Atsushi Tominaga
- 8Faculty of Education, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa 903–0213, JAPAN
| |
Collapse
|
29
|
|
30
|
Abstract
Codon usage depends on mutation bias, tRNA-mediated selection, and the need for high efficiency and accuracy in translation. One codon in a synonymous codon family is often strongly over-used, especially in highly expressed genes, which often leads to a high dN/dS ratio because dS is very small. Many different codon usage indices have been proposed to measure codon usage and codon adaptation. Sense codon could be misread by release factors and stop codons misread by tRNAs, which also contribute to codon usage in rare cases. This chapter outlines the conceptual framework on codon evolution, illustrates codon-specific and gene-specific codon usage indices, and presents their applications. A new index for codon adaptation that accounts for background mutation bias (Index of Translation Elongation) is presented and contrasted with codon adaptation index (CAI) which does not consider background mutation bias. They are used to re-analyze data from a recent paper claiming that translation elongation efficiency matters little in protein production. The reanalysis disproves the claim.
Collapse
|
31
|
Morgan EJ, Sutton TL, Darwell CT, Cook JM. Restructuring of a mutualism following introduction of Australian fig trees and pollinating wasps to Europe and the USA. Biol Invasions 2018. [DOI: 10.1007/s10530-018-1775-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
32
|
Abeyratne SAE, Amarasekera SSC, Ranaweera LT, Salpadoru TB, Thilakarathne SMNK, Knowles NJ, Wadsworth J, Puvanendiran S, Kothalawala H, Jayathilake BK, Wijithasiri HA, Chandrasena MMPSK, Sooriyapathirana SDSS. The phylogenetic analysis of VP1 genomic region in foot-and-mouth disease virus serotype O isolates in Sri Lanka reveals the existence of 'Srl-97', a newly named endemic lineage. PLoS One 2018; 13:e0194077. [PMID: 29570746 PMCID: PMC5865751 DOI: 10.1371/journal.pone.0194077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 02/23/2018] [Indexed: 11/25/2022] Open
Abstract
Foot and mouth disease (FMD) has devastated the cattle industry in Sri Lanka many times in the past. Despite its seriousness, limited attempts have been made to understand the disease to ameliorate its effects–current recommendation for vaccines being based solely on immunological assessments rather than on molecular identification. The general belief is that the cattle population in Sri Lanka acquired the FMD virus (FMDV) strains via introductions from India. However, there could be endemic FMDV lineages circulating in Sri Lanka. To infer the phylogenetic relationships of the FMDV strains in the island, we sequenced the VP1 genomic region of the virus isolates collected during the 2014 outbreak together with a few reported cases in 2012 and 1997 and compared them to VP1 sequences from South Asia. The FMDV strains collected in the 2014 outbreak belonged to the lineage, Ind-2001d, of the topotype, ME-SA. The strains collected in 2012 and 1997 belonged to another lineage called 'unnamed' by the World Reference Laboratory for Foot and Mouth Disease (WRLFMD). Based on the present analysis, we designate the lineage 'unnamed' as Srl-97 which we found endemic to Sri Lanka. The evolutionary rates of Srl-97 and Ind-2001d in Sri Lanka were estimated to be 0.0004 and 0.0046 substitutions/site/year, respectively, suggesting that Srl-97 evolves slowly.
Collapse
Affiliation(s)
- S. A. E. Abeyratne
- Animal Virus Laboratory, Veterinary Research Institute, Polgolla, Kandy, Sri Lanka
- Postgraduate Institute of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - S. S. C. Amarasekera
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - L. T. Ranaweera
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - T. B. Salpadoru
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - S. M. N. K. Thilakarathne
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - N. J. Knowles
- The Pirbright Institute, Pirbright, Woking, Surrey, United Kingdom
| | - J. Wadsworth
- The Pirbright Institute, Pirbright, Woking, Surrey, United Kingdom
| | - S. Puvanendiran
- Animal Virus Laboratory, Veterinary Research Institute, Polgolla, Kandy, Sri Lanka
| | - H. Kothalawala
- Animal Virus Laboratory, Veterinary Research Institute, Polgolla, Kandy, Sri Lanka
| | - B. K. Jayathilake
- Animal Virus Laboratory, Veterinary Research Institute, Polgolla, Kandy, Sri Lanka
| | - H. A. Wijithasiri
- Animal Virus Laboratory, Veterinary Research Institute, Polgolla, Kandy, Sri Lanka
| | | | - S. D. S. S. Sooriyapathirana
- Postgraduate Institute of Science, University of Peradeniya, Peradeniya, Sri Lanka
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
- * E-mail:
| |
Collapse
|
33
|
Roelke CE, Maldonado JA, Pope BW, Firneno TJ, Laduc TJ, Hibbitts TJ, Ryberg WA, Rains ND, Fujita MK. Mitochondrial genetic variation within and between Holbrookia lacerata lacerata and Holbrookia lacerata subcaudalis, the spot-tailed earless lizards of Texas. J NAT HIST 2018. [DOI: 10.1080/00222933.2018.1436726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Corey E. Roelke
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
| | - Jose A. Maldonado
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
| | - Blake W. Pope
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA
| | - Thomas J. Firneno
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
| | - Travis J. Laduc
- Biodiversity Collections, Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Toby J. Hibbitts
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA
| | - Wade A. Ryberg
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA
| | | | - Matthew K. Fujita
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
| |
Collapse
|
34
|
Comparing evolutionary distances via adaptive distance functions. J Theor Biol 2018; 440:88-99. [PMID: 29277603 DOI: 10.1016/j.jtbi.2017.12.022] [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: 06/22/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 11/23/2022]
Abstract
Distance-based methods for phylogenetic reconstruction are based on a two-step approach: first, pairwise distances are computed from DNA sequences associated with a given set of taxa, and then these distances are used to reconstruct the phylogenetic relationships between taxa. Because the estimated distances are based on finite sequences, they are inherently noisy, and this noise may result in reconstruction errors. Previous attempts to improve reconstruction accuracy focused either on improving the robustness of reconstruction algorithms to this stochastic noise, or on improving the accuracy of the distance estimates. Here, we aim to further improve reconstruction accuracy by utilizing the basic observation that reconstruction algorithms are based on a series of comparisons between distances (or linear combinations of distances). We start by examining the relationship between the stochastic noise in the sequence data and the accuracy of the comparisons between pairwise distance estimates. This examination results in improved methods for distance comparison, which are shown to be as accurate as likelihood-based methods, while being much simpler and more efficient to compute. We then extend these methods to improve reconstruction accuracy of quartet trees, and examine some of the challenges moving forward.
Collapse
|
35
|
Cardinal S, Buchmann SL, Russell AL. The evolution of floral sonication, a pollen foraging behavior used by bees (Anthophila). Evolution 2018; 72:590-600. [PMID: 29392714 PMCID: PMC5873439 DOI: 10.1111/evo.13446] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 01/25/2018] [Accepted: 01/26/2018] [Indexed: 02/03/2023]
Abstract
Over 22,000 species of biotically pollinated flowering plants, including some major agricultural crops, depend primarily on bees capable of floral sonication for pollination services. The ability to sonicate ("buzz") flowers is widespread in bees but not ubiquitous. Despite the prevalence of this pollinator behavior and its importance to natural and agricultural systems, the evolutionary history of floral sonication in bees has not been previously studied. Here, we reconstruct the evolutionary history of floral sonication in bees by generating a time-calibrated phylogeny and reconstructing ancestral states for this pollen extraction behavior. We also test the hypothesis that the ability to sonicate flowers and thereby efficiently access pollen from a diverse assemblage of plant species, led to increased diversification among sonicating bee taxa. We find that floral sonication evolved on average 45 times within bees, possibly first during the Early Cretaceous (100-145 million years ago) in the common ancestor of bees. We find that sonicating lineages are significantly more species rich than nonsonicating sister lineages when comparing sister clades, but a probabilistic structured rate permutation on phylogenies approach failed to support the hypothesis that floral sonication is a key driver of bee diversification. This study provides the evolutionary framework needed to further study how floral sonication by bees may have facilitated the spread and common evolution of angiosperm species with poricidal floral morphology.
Collapse
Affiliation(s)
- Sophie Cardinal
- Canadian National Collection of Insects, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada
| | - Stephen L Buchmann
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721
| | - Avery L Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| |
Collapse
|
36
|
Arcangeli J, Light JE, Cervantes FA. Molecular and morphological evidence of the diversification in the gray mouse opossum, Tlacuatzin canescens (Didelphimorphia), with description of a new species. J Mammal 2018. [DOI: 10.1093/jmammal/gyx173] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
37
|
Javidkar M, Cooper SJB, Humphreys WF, King RA, Judd S, Austin AD. Biogeographic history of subterranean isopods from groundwater calcrete islands in Western Australia. ZOOL SCR 2017. [DOI: 10.1111/zsc.12265] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Mohammad Javidkar
- Australian Centre for Evolutionary Biology and Biodiversity and School of Biological Sciences the University of Adelaide Adelaide SA Australia
- Department of Biodiversity and Ecosystem Management Environmental Sciences Research Institute Shahid Beheshti University Tehran Iran
| | - Steven J. B. Cooper
- Australian Centre for Evolutionary Biology and Biodiversity and School of Biological Sciences the University of Adelaide Adelaide SA Australia
- Evolutionary Biology Unit South Australian Museum Adelaide SA Australia
| | - William F. Humphreys
- Western Australian Museum Welshpool WA Australia
- School of Animal Biology University of Western Australia Crawley WA Australia
| | - Rachael A. King
- Australian Centre for Evolutionary Biology and Biodiversity and School of Biological Sciences the University of Adelaide Adelaide SA Australia
- South Australian Museum Adelaide SA Australia
| | - Simon Judd
- Phoenix Environmental Sciences Balcatta WA Australia
| | - Andrew D. Austin
- Australian Centre for Evolutionary Biology and Biodiversity and School of Biological Sciences the University of Adelaide Adelaide SA Australia
| |
Collapse
|
38
|
Copetti D, Búrquez A, Bustamante E, Charboneau JLM, Childs KL, Eguiarte LE, Lee S, Liu TL, McMahon MM, Whiteman NK, Wing RA, Wojciechowski MF, Sanderson MJ. Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti. Proc Natl Acad Sci U S A 2017; 114:12003-12008. [PMID: 29078296 PMCID: PMC5692538 DOI: 10.1073/pnas.1706367114] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus (Carnegiea gigantea) of the Sonoran Desert. We assembled a high-coverage draft genome for saguaro and lower coverage genomes for three other genera of tribe Pachycereeae (Pachycereus, Lophocereus, and Stenocereus) and a more distant outgroup cactus, Pereskia We used these to construct 4,436 orthologous gene alignments. Species tree inference consistently returned the same phylogeny, but gene tree discordance was high: 37% of gene trees having at least 90% bootstrap support conflicted with the species tree. Evidently, discordance is a product of long generation times and moderately large effective population sizes, leading to extensive incomplete lineage sorting (ILS). In the best supported gene trees, 58% of apparent homoplasy at amino sites in the species tree is due to gene tree-species tree discordance rather than parallel substitutions in the gene trees themselves, a phenomenon termed "hemiplasy." The high rate of genomic hemiplasy may contribute to apparent parallelisms in phenotypic traits, which could confound understanding of species relationships and character evolution in cacti.
Collapse
Affiliation(s)
- Dario Copetti
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Alberto Búrquez
- Instituto de Ecología, Unidad Hermosillo, Universidad Nacional Autónoma de México, Hermosillo, Sonora, Mexico
| | - Enriquena Bustamante
- Instituto de Ecología, Unidad Hermosillo, Universidad Nacional Autónoma de México, Hermosillo, Sonora, Mexico
| | - Joseph L M Charboneau
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Seunghee Lee
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721
| | - Tiffany L Liu
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824
| | | | - Noah K Whiteman
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | | | - Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721;
| |
Collapse
|
39
|
Nascimento FF, Reis MD, Yang Z. A biologist's guide to Bayesian phylogenetic analysis. Nat Ecol Evol 2017; 1:1446-1454. [PMID: 28983516 PMCID: PMC5624502 DOI: 10.1038/s41559-017-0280-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 07/17/2017] [Indexed: 11/09/2022]
Abstract
Bayesian methods have become very popular in molecular phylogenetics due to the availability of user-friendly software implementing sophisticated models of evolution. However, Bayesian phylogenetic models are complex, and analyses are often carried out using default settings, which may not be appropriate. Here, we summarize the major features of Bayesian phylogenetic inference and discuss Bayesian computation using Markov chain Monte Carlo (MCMC), the diagnosis of an MCMC run, and ways of summarising the MCMC sample. We discuss the specification of the prior, the choice of the substitution model, and partitioning of the data. Finally, we provide a list of common Bayesian phylogenetic software and provide recommendations as to their use.
Collapse
Affiliation(s)
- Fabrícia F Nascimento
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
- Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK.
| | - Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK.
| |
Collapse
|
40
|
Matsui M, Misawa Y, Nishikawa K, Shimada T. A New Species of Lentic Breeding Salamander (Amphibia, Caudata) from Central Japan. CURRENT HERPETOLOGY 2017. [DOI: 10.5358/hsj.36.116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-Nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, JAPAN
| | - Yasuchika Misawa
- Civil Engineering and Eco-Technology Consultants, Minamisenba 1-15-14, Chuo-ku, Osaka 542-0081, JAPAN
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-Nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, JAPAN
| | | |
Collapse
|
41
|
Chernick A, van der Meer F. Evolution of Bovine viral diarrhea virus in Canada from 1997 to 2013. Virology 2017; 509:232-238. [PMID: 28668732 DOI: 10.1016/j.virol.2017.06.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 06/20/2017] [Accepted: 06/21/2017] [Indexed: 10/19/2022]
Abstract
Bovine viral diarrhea virus (BVDV) is a rapidly evolving, single-stranded RNA virus and a production limiting pathogen of cattle worldwide. 79 viral isolates collected between 1997 and 2013 in Canada were subjected to next-generation sequencing. Bayesian phylogenetics was used to assess the evolution of this virus. A mean substitution rate of 1.4×10-3 substitutions/site/year was found across both BVDV1 and BVDV2. Evolutionary rates in the E2 gene were slightly faster than other regions. We also identified population structures below the sub-genotype level that likely have phenotypic implications. Two distinct clusters within BVDV2a are present and can be differentiated, in part, by a tyrosine to isoleucine mutation at position 963 in the E2 protein, a position implicated in the antigenicity of BVDV1 isolates. Distinct clustering within all sub-genotypes, particularly BVDV2a, is apparent and could lead to new levels of genotypic classification. Continuous monitoring of emerging variants is therefore necessary.
Collapse
Affiliation(s)
- Adam Chernick
- Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB T2N 1N4, Canada.
| | - Frank van der Meer
- Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB T2N 1N4, Canada.
| |
Collapse
|
42
|
Hauquier F, Leliaert F, Rigaux A, Derycke S, Vanreusel A. Distinct genetic differentiation and species diversification within two marine nematodes with different habitat preference in Antarctic sediments. BMC Evol Biol 2017; 17:120. [PMID: 28558672 PMCID: PMC5450352 DOI: 10.1186/s12862-017-0968-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 05/12/2017] [Indexed: 11/20/2022] Open
Abstract
Background Dispersal ability, population genetic structure and species divergence in marine nematodes are still poorly understood, especially in remote areas such as the Southern Ocean. We investigated genetic differentiation of species and populations of the free-living endobenthic nematode genera Sabatieria and Desmodora using nuclear 18S rDNA, internal transcribed spacer (ITS) rDNA, and mitochondrial cytochrome oxidase I (COI) gene sequences. Specimens were collected at continental shelf depths (200–500 m) near the Antarctic Peninsula, Scotia Arc and eastern side of the Weddell Sea. The two nematode genera co-occurred at all sampled locations, but with different vertical distribution in the sediment. A combination of phylogenetic (GMYC, Bayesian Inference, Maximum Likelihood) and population genetic (AMOVA) analyses were used for species delimitation and assessment of gene flow between sampling locations. Results Sequence analyses resulted in the delimitation of four divergent species lineages in Sabatieria, two of which could not be discriminated morphologically and most likely constitute cryptic species. Two species were recognised in Desmodora, one of which showed large intraspecific morphological variation. Both genera comprised species that were restricted to one side of the Weddell Sea and species that were widely spread across it. Population genetic structuring was highly significant and more pronounced in the deeper sediment-dwelling Sabatieria species, which are generally less prone to resuspension and passive dispersal in the water column than surface Desmodora species. Conclusions Our results indicate that gene flow is restricted at large geographic distance in the Southern Ocean, which casts doubt on the efficiency of the Weddell gyre and Antarctic Circumpolar Current in facilitating circum-Antarctic nematode species distributions. We also show that genetic structuring and cryptic speciation can be very different in nematode species isolated from the same geographic area, but with different habitat preferences (surface versus deeper sediment layers). Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0968-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Freija Hauquier
- Marine Biology Research Group, Biology Department, Ghent University, Krijgslaan 281, 9000, Ghent, Belgium.
| | - Frederik Leliaert
- Marine Biology Research Group, Biology Department, Ghent University, Krijgslaan 281, 9000, Ghent, Belgium.,Botanic Garden Meise, Nieuwelaan 38, 1860, Meise, Belgium
| | - Annelien Rigaux
- Marine Biology Research Group, Biology Department, Ghent University, Krijgslaan 281, 9000, Ghent, Belgium
| | - Sofie Derycke
- Marine Biology Research Group, Biology Department, Ghent University, Krijgslaan 281, 9000, Ghent, Belgium.,Operational Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences (RBINS), Rue Vautier 29, 1000, Brussels, Belgium
| | - Ann Vanreusel
- Marine Biology Research Group, Biology Department, Ghent University, Krijgslaan 281, 9000, Ghent, Belgium
| |
Collapse
|
43
|
Huhndorf SM, Miller AN, Fernández FA. Molecular systematics of the Sordariales: the order and the family Lasiosphaeriaceae redefined. Mycologia 2017. [DOI: 10.1080/15572536.2005.11832982] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Sabine M. Huhndorf
- Botany Department, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois 60605-2496
| | - Andrew N. Miller
- Botany Department, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois 60605-2496 University of Illinois at Chicago, Department of Biological Sciences, Chicago, Illinois 60607-7060
| | - Fernando A. Fernández
- Botany Department, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois 60605-2496
| |
Collapse
|
44
|
Blaha J, Grube M. The new speciesLecanora bicinctoidea, its position and considerations about phenotypic evolution in theLecanora rupicolagroup. Mycologia 2017. [DOI: 10.1080/15572536.2007.11832600] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Martin Grube
- Institute of Plant Sciences, Holteigasse 6, Karl-Franzens-University Graz, A-8010 Graz, Austria
| |
Collapse
|
45
|
Sánchez R, Miller A, Bianchinotti M. A new species of Acanthostigma (Tubeufiaceae, Dothideomycetes) from the southern hemisphere. Mycologia 2017; 104:223-31. [DOI: 10.3852/11-105] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- R.M. Sánchez
- Laboratorio de Estudios Básicos y Biotecnológicos de Algas y Hongos, CERZOS-CCT-CONICET y U.N.S., Camino La Carrindanga Km7, B8000FWB Bahía Blanca, Buenos Aires, Argentina
| | - A.N. Miller
- University of Illinois, Illinois Natural History Survey, 1816 South Oak Street, Champaign, Illinois 61820-6970, USA
| | - M.V. Bianchinotti
- Laboratorio de Estudios Básicos y Biotecnológicos de Algas y Hongos, CERZOS-CCT-CONICET y U.N.S., Camino La Carrindanga Km7, B8000FWB Bahía Blanca, Buenos Aires, Argentina
| |
Collapse
|
46
|
Javidkar M, Cooper SJ, King RA, Humphreys WF, Bertozzi T, Stevens MI, Austin AD. Molecular systematics and biodiversity of oniscidean isopods in the groundwater calcretes of central Western Australia. Mol Phylogenet Evol 2016; 104:83-98. [DOI: 10.1016/j.ympev.2016.07.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 10/21/2022]
|
47
|
Abstract
We report genomes of two species of cactophilic Drosophila: Drosophila arizonae and D. navojoa These two are the closest relatives of D. mojavensis, forming the D. mojavensis cluster. D. mojavensis and D. arizonae diverged from D. navojoa ∼5.8 Mya, while the split between D. arizonae and D. mojavensis is more recent, at 1.5 Mya. Together the three genomes provide opportunities to examine genomic changes associated with speciation and host shifts in this ecologically defined group of flies. The three species are also separated by fixed inversion differences in three of their six chromosomes. While the levels of nucleotide divergence in the colinear chromosomes are significantly lower than in the inverted chromosomes, consistent with a past role of the inversions in preventing gene flow, the patterns differ among the inverted chromosomes when the locations of nucleotides inside or outside of the inversions are considered. For Muller element E, there is greater divergence external to the inversion breakpoints. For Muller A, the divergence is slightly higher inside the inversions, while for Muller B, the breakpoints and hence the difference in substitutions in relation to the inversions could not be determined. The differences among the inverted chromosomes, especially once the breakpoints are clearly established, could aid in dating the origins of the inversions.
Collapse
|
48
|
Nakashima C, Motohashi K, Chen CY, Groenewald JZ, Crous PW. Species diversity of Pseudocercospora from Far East Asia. Mycol Prog 2016. [DOI: 10.1007/s11557-016-1231-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
49
|
Nascimento FF, Rodrigo AG. Computational Evaluation of the Strict Master and Random Template Models of Endogenous Retrovirus Evolution. PLoS One 2016; 11:e0162454. [PMID: 27649303 PMCID: PMC5029938 DOI: 10.1371/journal.pone.0162454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 08/02/2016] [Indexed: 02/05/2023] Open
Abstract
Transposable elements (TEs) are DNA sequences that are able to replicate and move within and between host genomes. Their mechanism of replication is also shared with endogenous retroviruses (ERVs), which are also a type of TE that represent an ancient retroviral infection within animal genomes. Two models have been proposed to explain TE proliferation in host genomes: the strict master model (SMM), and the random template (or transposon) model (TM). In SMM only a single copy of a given TE lineage is able to replicate, and all other genomic copies of TEs are derived from that master copy. In TM, any element of a given family is able to replicate in the host genome. In this paper, we simulated ERV phylogenetic trees under variations of SMM and TM. To test whether current phylogenetic programs can recover the simulated ERV phylogenies, DNA sequence alignments were simulated and maximum likelihood trees were reconstructed and compared to the simulated phylogenies. Results indicate that visual inspection of phylogenetic trees alone can be misleading. However, if a set of statistical summaries is calculated, we are able to distinguish between models with high accuracy by using a data mining algorithm that we introduce here. We also demonstrate the use of our data mining algorithm with empirical data for the porcine endogenous retrovirus (PERV), an ERV that is able to replicate in human and pig cells in vitro.
Collapse
Affiliation(s)
| | - Allen G. Rodrigo
- National Evolutionary Synthesis Center, Durham, NC, United States of America
| |
Collapse
|
50
|
|