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de Souza Oliveira L, de Araújo Bitencourt J, Galdino JH, Sampaio I, Souza Carneiro PL, Antunes de Mello Affonso PR. Genetic Diversity in Natural Populations of the Near-Threatened Species Lignobrycon myersi (Characiformes, Triportheidae): Implications for Species Conservation. Zebrafish 2023; 20:271-279. [PMID: 38011710 DOI: 10.1089/zeb.2023.0036] [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] [Indexed: 11/29/2023] Open
Abstract
The river basins of Brazil contain a highly diverse ichthyofauna of remarkable endemism, including several threatened species. Accordingly, Lignobrycon myersi is a fish species distributed only in a few rivers from the state of Bahia, northeastern Brazil. Since this species is classified as Near Threatened and is poorly studied, efforts to understand the genetic structure of populations and putative cryptic forms should help define efficient strategies of management and conservation. Herein, the molecular identification and the population genetic diversity of specimens of L. myersi across their range (Almada, Contas, and Cachoeira river basins) were assessed using mitochondrial markers (16S rDNA and D-Loop, respectively). The inferences based on phylogenetics, genetic distance, and species delimitation methods invariably identified all samples as L. myersi. In addition, sequencing of D-loop fragments revealed significant haplotype diversity and a considerable level of population genetic structure. Despite their geographic isolation, these data suggested that populations from Almada and Contas rivers represent a single evolutionary lineage that could be managed as a whole. In contrast, the population from Cachoeira River was highly differentiated from the others and should be managed separately as a unique and endemic unit, particularly focused on the conservation of native habitats.
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Affiliation(s)
| | | | - José Henrique Galdino
- Department of Biological Sciences, State University of Southwestern Bahia, Jequié, Brazil
| | - Iracilda Sampaio
- Department of Coastal Studies, Federal University of Pará, Bragança, Brazil
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2
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De Prins J, Taylor DBJ, Gonzalez GF, Dobson J, Hereward JP, Shi B, Rahman MM, Dhileepan K. Taxonomic Delineation of the Old World Species Stomphastis thraustica (Lepidoptera: Gracillariidae) Feeding on Jatropha gossypiifolia (Euphorbiaceae) that Was Collected in the New World and Imported as a Biocontrol Agent to Australia. NEOTROPICAL ENTOMOLOGY 2023; 52:380-406. [PMID: 36251214 DOI: 10.1007/s13744-022-00994-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/29/2022] [Indexed: 05/13/2023]
Abstract
We provide the identification and species delineation of this biocontrol agent as Stomphastis thraustica (Meyrick in Trans Ent Soc Lond 80(1):107-120, 1908) belonging to the family Gracillariidae. We clarify the distribution pattern of S. thraustica, its host plant preferences, and present taxonomic and molecular diagnoses based on original morphological and genetic data as well as data retrieved from historic literature and genetic databases. Following our own collecting efforts in three continents Africa, South America, and Australia as well as our study of historic museum collection material, we present many new distribution records of S. thraustica for countries and territories in the world including the new discovery of this species in the Neotropical region and we report its introduction in Australia as a biocontrol agent. Using mitogenomic and COI gene data, we clarified that the closest relative of S. thraustica is Stomphastis sp. that occurs in Madagascar and Australia and feeds on the same host plant as S. thraustica - Jatropha gossypiifolia L. (Euphorbiaceae). The molecular sequence divergence in the mitochondrial DNA barcode fragment between these two closely related species S. thraustica and Stomphastis sp. is over 5.7% supporting that they are different species.
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Affiliation(s)
- Jurate De Prins
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium.
| | - Dianne B J Taylor
- Dept of Agriculture and Fisheries, Biosecurity Queensland, Ecosciences Precinct, Dutton Park, QLD, Australia
| | | | - Jeremy Dobson
- Lepidopterists' Society of Africa, Pretoria, South Africa
| | - James P Hereward
- School of Biological Sciences, The Univ of Queensland, Brisbane, QLD, Australia
| | - Boyang Shi
- Dept of Agriculture and Fisheries, Biosecurity Queensland, Ecosciences Precinct, Dutton Park, QLD, Australia
| | - Md Mahbubur Rahman
- Dept of Agriculture and Fisheries, Biosecurity Queensland, Ecosciences Precinct, Dutton Park, QLD, Australia
| | - Kunjithapatham Dhileepan
- Dept of Agriculture and Fisheries, Biosecurity Queensland, Ecosciences Precinct, Dutton Park, QLD, Australia
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3
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Pedersen MW, De Sanctis B, Saremi NF, Sikora M, Puckett EE, Gu Z, Moon KL, Kapp JD, Vinner L, Vardanyan Z, Ardelean CF, Arroyo-Cabrales J, Cahill JA, Heintzman PD, Zazula G, MacPhee RDE, Shapiro B, Durbin R, Willerslev E. Environmental genomics of Late Pleistocene black bears and giant short-faced bears. Curr Biol 2021; 31:2728-2736.e8. [PMID: 33878301 DOI: 10.1016/j.cub.2021.04.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/31/2021] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time,1-3 by allowing for parallel sequencing of DNA from all trophic levels.4-8 However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species,9 the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies.5,6,10,11 This is in contrast to data from fossils12,13 where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable.14-16 Here, we report the retrieval of three low-coverage (0.03×) environmental genomes from American black bear (Ursus americanus) and a 0.04× environmental genome of the extinct giant short-faced bear (Arctodus simus) from cave sediment samples from northern Mexico dated to 16-14 thousand calibrated years before present (cal kyr BP), which we contextualize with a new high-coverage (26×) and two lower-coverage giant short-faced bear genomes obtained from fossils recovered from Yukon Territory, Canada, which date to ∼22-50 cal kyr BP. We show that the Late Pleistocene black bear population in Mexico is ancestrally related to the present-day Eastern American black bear population, and that the extinct giant short-faced bears present in Mexico were deeply divergent from the earlier Beringian population. Our findings demonstrate the ability to separately analyze genomic-scale DNA sequences of closely related species co-preserved in environmental samples, which brings the use of ancient eDNA into the era of population genomics and phylogenetics.
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Affiliation(s)
- Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Bianca De Sanctis
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Nedda F Saremi
- Department of Biomolecular Engineering and Bioinformatics, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Emily E Puckett
- Department of Biological Sciences, University of Memphis, 3770 Walker Avenue, Ellington Hall, Memphis, TN 38152, USA
| | - Zhenquan Gu
- State Key Laboratory of Tibetan Plateau Earth System Science (LATPES), Beijing 100101, China
| | - Katherine L Moon
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Joshua D Kapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Zaruhi Vardanyan
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ciprian F Ardelean
- Unidad Académica de Antropología, Universidad Autónoma de Zacatecas, Campus II, Col. Progreso, 98066 Zacatecas, Mexico; The Archaeology Centre, Department of Anthropology, University of Toronto, 19 Ursula Franklin Street, Toronto, ON M5S 2S2, Canada
| | - Joaquin Arroyo-Cabrales
- Laboratorio de Arqueozoologia, Subdireccion de Laboratorios y Apoyo Academico, Instituto Nacional de Antropologia e Historia, Moneda 16, Col. Centro, 06060 Mexico, CdMx, Mexico
| | - James A Cahill
- Laboratory of the Neurogenetics of Language, Rockefeller University, New York, NY, USA
| | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, PO Box 6050, Langnes, N-9037 Tromsø, Norway
| | - Grant Zazula
- Yukon Palaeontology Program, Department of Tourism & Culture, Government of Yukon, Whitehorse, YT Y1A 2C6, Canada
| | - Ross D E MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, NY 12484, USA; American Museum of Natural History, New York, NY, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Wellcome Sanger Institute, Cambridge CB10 1SA, UK; MARUM, University of Bremen, Bremen, Germany.
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4
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Abreu EF, Jung DMH, Christoff AU, Valiati VH, Jansa SA, Percequillo AR. Systematics of Brucepattersonius Hershkovitz, 1998 (Rodentia, Sigmodontinae): molecular species delimitation and morphological analyses suggest an overestimation in species diversity. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1890270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Edson Fiedler Abreu
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, 13418900, SP, Brazil
| | - Diego Marques Henriques Jung
- Laboratório de Genética e Biologia Molecular, Universidade do Vale do Rio dos Sinos, São Leopoldo, 93022750, RS, Brazil
| | - Alexandre Uarth Christoff
- Laboratório de Genética e Biologia Molecular, Universidade do Vale do Rio dos Sinos, São Leopoldo, 93022750, RS, Brazil
| | - Victor Hugo Valiati
- Laboratório de Genética e Biologia Molecular, Universidade do Vale do Rio dos Sinos, São Leopoldo, 93022750, RS, Brazil
| | - Sharon A. Jansa
- Department of Ecology, Evolution, and Behavior and Bell Museum of Natural History, University of Minnesota, St Paul, 55108, MN, USA
| | - Alexandre Reis Percequillo
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, 13418900, SP, Brazil
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Henningsson R, Moratorio G, Bordería AV, Vignuzzi M, Fontes M. DISSEQT-DIStribution-based modeling of SEQuence space Time dynamics. Virus Evol 2019; 5:vez028. [PMID: 31392032 PMCID: PMC6680062 DOI: 10.1093/ve/vez028] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Rapidly evolving microbes are a challenge to model because of the volatile, complex, and dynamic nature of their populations. We developed the DISSEQT pipeline (DIStribution-based SEQuence space Time dynamics) for analyzing, visualizing, and predicting the evolution of heterogeneous biological populations in multidimensional genetic space, suited for population-based modeling of deep sequencing and high-throughput data. The pipeline is openly available on GitHub (https://github.com/rasmushenningsson/DISSEQT.jl, accessed 23 June 2019) and Synapse (https://www.synapse.org/#!Synapse: syn11425758, accessed 23 June 2019), covering the entire workflow from read alignment to visualization of results. Our pipeline is centered around robust dimension and model reduction algorithms for analysis of genotypic data with additional capabilities for including phenotypic features to explore dynamic genotype-phenotype maps. We illustrate its utility and capacity with examples from evolving RNA virus populations, which present one of the highest degrees of genetic heterogeneity within a given population found in nature. Using our pipeline, we empirically reconstruct the evolutionary trajectories of evolving populations in sequence space and genotype-phenotype fitness landscapes. We show that while sequence space is vastly multidimensional, the relevant genetic space of evolving microbial populations is of intrinsically low dimension. In addition, evolutionary trajectories of these populations can be faithfully monitored to identify the key minority genotypes contributing most to evolution. Finally, we show that empirical fitness landscapes, when reconstructed to include minority variants, can predict phenotype from genotype with high accuracy.
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Affiliation(s)
- R Henningsson
- The Centre for Mathematical Sciences, Lund University, Sweden
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Paris, France
- The International Group for Data Analysis, Institut Pasteur, Paris, France
- Division of Clinical Genetics, Lund University, Sweden
| | - G Moratorio
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Paris, France
- Laboratorio de Virología Molecular, Universidad de la República, Montevideo, Uruguay
| | - A V Bordería
- The International Group for Data Analysis, Institut Pasteur, Paris, France
| | - M Vignuzzi
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Paris, France
| | - M Fontes
- The International Group for Data Analysis, Institut Pasteur, Paris, France
- Department of Cancer Immunology, Genentech, South San Francisco, CA, USA
- The Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
- Persimune, The Centre of Excellence for Personalized Medicine, Copenhagen, Denmark
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6
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Molecular Data Reveal Multiple Lineages in Piranhas of the Genus Pygocentrus (Teleostei, Characiformes). Genes (Basel) 2019; 10:genes10050371. [PMID: 31096658 PMCID: PMC6562675 DOI: 10.3390/genes10050371] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/09/2019] [Accepted: 05/13/2019] [Indexed: 11/26/2022] Open
Abstract
Carnivorous piranhas are distributed in four serrasalmid genera including Pygocentrus, which inhabit major river basins of South America. While P. cariba and P. piraya are endemics of the Orinoco and São Francisco basins, respectively, P. nattereri is widely distributed across the Amazonas, Essequibo, lower Paraná, Paraguay, and coastal rivers of northeastern Brazil, with recent records of introductions in Asia. Few studies have focused on the genetic diversity and systematics of Pygocentrus and the putative presence of additional species within P. nattereri has never been the subject of a detailed molecular study. Here we aimed to delimit species of Pygocentrus, test the phylogeographic structure of P. nattereri, and access the origin of introduced specimens of P. nattereri in Asia. Phylogenetic analyses based on a mitochondrial dataset involving maximum-likelihood tree reconstruction, genetic distances, Bayesian analysis, three delimitation approaches, and haplotype analysis corroborate the morphological hypothesis of the occurrence of three species of Pygocentrus. However, we provide here strong evidence that P. nattereri contains at least five phylogeographically-structured lineages in the Amazonas, Guaporé (type locality), Itapecuru, Paraná/Paraguay, and Tocantins/Araguaia river basins. We finally found that the introduced specimens in Asia consistently descend from the lineage of P. nattereri from the main Rio Amazonas. These results contribute to future research aimed to detect morphological variation that may occur in those genetic lineages of Pygocentrus.
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Shastri AA, Ahuja K, Ratnaparkhe MB, Shah A, Gagrani A, Lal A. Vector Quantized Spectral Clustering Applied to Whole Genome Sequences of Plants. Evol Bioinform Online 2019; 15:1176934319836997. [PMID: 30936678 PMCID: PMC6435876 DOI: 10.1177/1176934319836997] [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: 09/30/2018] [Accepted: 02/07/2019] [Indexed: 11/16/2022] Open
Abstract
We develop a Vector Quantized Spectral Clustering (VQSC) algorithm that is a combination of spectral clustering (SC) and vector quantization (VQ) sampling for grouping genome sequences of plants. The inspiration here is to use SC for its accuracy and VQ to make the algorithm computationally cheap (the complexity of SC is cubic in terms of the input size). Although the combination of SC and VQ is not new, the novelty of our work is in developing the crucial similarity matrix in SC as well as use of k-medoids in VQ, both adapted for the plant genome data. For Soybean, we compare our approach with commonly used techniques like Un-weighted Pair Graph Method with Arithmetic mean (UPGMA) and Neighbor Joining (NJ). Experimental results show that our VQSC outperforms both these techniques significantly in terms of cluster quality (average improvement of 21% over UPGMA and 24% over NJ) as well as time complexity (order of magnitude faster than both UPGMA and NJ).
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Affiliation(s)
- Aditya A Shastri
- Computer Science and Engineering, Indian Institute of Technology Indore, Indore, India
| | - Kapil Ahuja
- Computer Science and Engineering, Indian Institute of Technology Indore, Indore, India
| | | | - Aditya Shah
- Computer Science and Engineering, Indian Institute of Technology Indore, Indore, India
| | - Aishwary Gagrani
- Computer Science and Engineering, Indian Institute of Technology Indore, Indore, India
| | - Anant Lal
- Computer Science and Engineering, Indian Institute of Technology Indore, Indore, India
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8
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Belaiba E, Marrone F, Vecchioni L, Bahri-Sfar L, Arculeo M. An exhaustive phylogeny of the combtooth blenny genus Salaria (Pisces, Blenniidae) shows introgressive hybridization and lack of reciprocal mtDNA monophyly between the marine species Salaria basilisca and Salaria pavo. Mol Phylogenet Evol 2019; 135:210-221. [PMID: 30831270 DOI: 10.1016/j.ympev.2019.02.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 02/28/2019] [Accepted: 02/28/2019] [Indexed: 12/18/2022]
Abstract
A comprehensive phylogeny of the genus Salaria based on mitochondrial and nuclear markers grouped the extant species of the genus in well-characterised marine and freshwater clades, thus rejecting the hypothesis of a polytypic origin of the freshwater Salaria populations and supporting the occurrence of a single invasion event of the inland waters by the genus. Based on both mitochondrial and nuclear DNA datasets, the Salaria species of the freshwater clade proved to be vicariant taxa originating from a common ancestor which could possibly spread throughout the circum-Mediterranean inland waters during the late Miocene Messinian salinity crisis, then experiencing a process of allopatric differentiation after the re-flooding of the Mediterranean basin. Within the marine clade, although the nuDNA datasets showed the existence of well-supported subclades in accordance to the morphological identification of the studied specimens, one of the two subclades obtained in the phylogenetic tree based on the mtDNA dataset included both S. basilisca and S. pavo specimens, thus failing to find the two species as reciprocally monophyletic. Such a mito-nuclear discordance is here ascribed to multiple mtDNA unidirectional introgression events from S. basilisca to S. pavo, and the molecular diversity pattern of the marine Salaria species is here ascribed to a Pleistocene speciation event nowadays partly concealed by the occurrence of introgressive hybridization phenomena between the two taxa. Our results urge for prudence when implementing DNA barcoding approaches since, in the presence of mito-nuclear discordance phenomena, single-marker mtDNA-only analyses might lead to significant misidentifications.
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Affiliation(s)
- E Belaiba
- University of Palermo, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), via Archirafi 18, 90123 Palermo, Italy; Université de Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Biodiversité, Parasitologie et Ecologie des Ecosystèmes Aquatiques, 2092 Tunis, Tunisia.
| | - F Marrone
- University of Palermo, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), via Archirafi 18, 90123 Palermo, Italy.
| | - L Vecchioni
- University of Palermo, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), via Archirafi 18, 90123 Palermo, Italy.
| | - L Bahri-Sfar
- Université de Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Biodiversité, Parasitologie et Ecologie des Ecosystèmes Aquatiques, 2092 Tunis, Tunisia.
| | - M Arculeo
- University of Palermo, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), via Archirafi 18, 90123 Palermo, Italy.
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9
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Araújo NP, Dias CAR, Stumpp R, Svartman M. Cytogenetic analyses in Trinomys (Echimyidae, Rodentia), with description of new karyotypes. PeerJ 2018; 6:e5316. [PMID: 30083457 PMCID: PMC6074804 DOI: 10.7717/peerj.5316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 07/05/2018] [Indexed: 11/24/2022] Open
Abstract
Trinomys Thomas (1921) is a terrestrial genus of spiny rats endemic to the Brazilian areas of Atlantic Forest and the transitional areas of Cerrado and Caatinga. Although most species have been already karyotyped, the available cytogenetic information is mostly restricted to diploid and fundamental numbers. We analyzed the chromosomes of two Trinomys species: Trinomys moojeni (2n = 56, FN = 106) and Trinomys setosus setosus (2n = 56, FN = 106 and 2n = 56, FN = 108). Our analyses included GTG- and CBG-banding, silver-staining of the nucleolar organizer regions, and chromosome mapping of telomeres and 45S rDNA by fluorescent in situ hybridization (FISH). Comparative GTG- and CBG-banding suggested that the interspecific variation may be due to rearrangements such as pericentric inversions, centromere repositioning, and heterochromatin variation. We report two new karyotypes for T. s. setosus and describe for the first time the banding patterns of the two Trinomys species.
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Affiliation(s)
- Naiara Pereira Araújo
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Cayo Augusto Rocha Dias
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.,Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Rodolfo Stumpp
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marta Svartman
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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Dias FMS, Janzen D, Hallwachs W, Chacón I, Willmott K, Ortiz-Acevedo E, Mielke OHH, Casagrande MM. DNA barcodes uncover hidden taxonomic diversity behind the variable wing patterns in the Neotropical butterfly genusZaretis(Lepidoptera: Nymphalidae: Charaxinae). Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Fernando Maia Silva Dias
- Laboratório de Estudos de Lepidoptera Neotropical, Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Daniel Janzen
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Winnie Hallwachs
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Isidro Chacón
- Instituto Nacional de Biodiversidad (INBio), Santo Domingo de Heredia, Heredia, Costa Rica
| | - Keith Willmott
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Elena Ortiz-Acevedo
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Olaf Hermann Hendrik Mielke
- Laboratório de Estudos de Lepidoptera Neotropical, Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Mirna Martins Casagrande
- Laboratório de Estudos de Lepidoptera Neotropical, Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
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Topo-phylogeny: Visualizing evolutionary relationships on a topographic landscape. PLoS One 2017; 12:e0175895. [PMID: 28459802 PMCID: PMC5411050 DOI: 10.1371/journal.pone.0175895] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 04/02/2017] [Indexed: 11/25/2022] Open
Abstract
Phylogenetic trees are the de facto standard for visualizing evolutionary relationships, but large trees can be difficult to interpret because they require a high cognitive load to identify relationships between multiple operational taxonomic units (OTUs). We present a new tool for displaying phylogenetic relationships as a topographic map in which OTUs autonomously attract or repel one another based on their individual branch lengths and distance to a common ancestor. This data visualization paradigm makes it possible to preattentively identify the nature of the relationship between items without having to trace a complex network of branches back to the root. This tool was developed for exploring phylogenetic data, but the technique could be extended for visualizing other hierarchical structures as well.
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12
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A test of color-based taxonomy in nudibranchs: Molecular phylogeny and species delimitation of the Felimida clenchi (Mollusca: Chromodorididae) species complex. Mol Phylogenet Evol 2016; 103:215-229. [DOI: 10.1016/j.ympev.2016.07.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 07/01/2016] [Accepted: 07/18/2016] [Indexed: 12/19/2022]
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Karanovic T, Djurakic M, Eberhard SM. Cryptic Species or Inadequate Taxonomy? Implementation of 2D Geometric Morphometrics Based on Integumental Organs as Landmarks for Delimitation and Description of Copepod Taxa. Syst Biol 2015; 65:304-27. [PMID: 26608965 DOI: 10.1093/sysbio/syv088] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 11/13/2015] [Indexed: 12/16/2022] Open
Abstract
Discovery of cryptic species using molecular tools has become common in many animal groups but it is rarely accompanied by morphological revision, creating ongoing problems in taxonomy and conservation. In copepods, cryptic species have been discovered in most groups where fast-evolving molecular markers were employed. In this study at Yeelirrie in Western Australia we investigate a subterranean species complex belonging to the harpacticoid genus Schizopera Sars, 1905, using both the barcoding mitochondrial COI gene and landmark-based two-dimensional geometric morphometrics. Integumental organs (sensilla and pores) are used as landmarks for the first time in any crustacean group. Complete congruence between DNA-based species delimitation and relative position of integumental organs in two independent morphological structures suggests the existence of three distinct evolutionary units. We describe two of them as new species, employing a condensed taxonomic format appropriate for cryptic species. We argue that many supposedly cryptic species might not be cryptic if researchers focus on analyzing morphological structures with multivariate tools that explicitly take into account geometry of the phenotype. A perceived supremacy of molecular methods in detecting cryptic species is in our view a consequence of disparity of investment and unexploited recent advancements in morphometrics among taxonomists. Our study shows that morphometric data alone could be used to find diagnostic morphological traits and gives hope to anyone studying small animals with a hard integument or shell, especially opening the door to assessing fossil diversity and rich museum collections. We expect that simultaneous use of molecular tools with geometry-oriented morphometrics may yield faster formal description of species. Decrypted species in this study are a good example for urgency of formal descriptions, as they display short-range endemism in small groundwater calcrete aquifers in a paleochannel, where their conservation may be threatened by proposed mining.
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Affiliation(s)
- Tomislav Karanovic
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746, Korea; Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia;
| | - Marko Djurakic
- Department of Biology and Ecology, Faculty of Science, University of Novi Sad, Trg Dositeja Obradovića 2, Novi Sad 21000, Serbia
| | - Stefan M Eberhard
- Subterranean Ecology Pty Ltd, Coningham, Tasmania 7054, Australia; and Connected Waters Initiative Research Centre, University of New South Wales, Sydney 2052, Australia
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Carter RW, Sanford JC. A new look at an old virus: patterns of mutation accumulation in the human H1N1 influenza virus since 1918. Theor Biol Med Model 2012; 9:42. [PMID: 23062055 PMCID: PMC3507676 DOI: 10.1186/1742-4682-9-42] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/04/2012] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The H1N1 influenza A virus has been circulating in the human population for over 95 years, first manifesting itself in the pandemic of 1917-1918. Initial mortality was extremely high, but dropped exponentially over time. Influenza viruses have high mutation rates, and H1N1 has undergone significant genetic changes since 1918. The exact nature of H1N1 mutation accumulation over time has not been fully explored. METHODS We have made a comprehensive historical analysis of mutational changes within H1N1 by examining over 4100 fully-sequenced H1N1 genomes. This has allowed us to examine the genetic changes arising within H1N1 from 1918 to the present. RESULTS We document multiple extinction events, including the previously known extinction of the human H1N1 lineage in the 1950s, and an apparent second extinction of the human H1N1 lineage in 2009. These extinctions appear to be due to a continuous accumulation of mutations. At the time of its disappearance in 2009, the human H1N1 lineage had accumulated over 1400 point mutations (more than 10% of the genome), including approximately 330 non-synonymous changes (7.4% of all codons). The accumulation of both point mutations and non-synonymous amino acid changes occurred at constant rates (μ = 14.4 and 2.4 new mutations/year, respectively), and mutations accumulated uniformly across the entire influenza genome. We observed a continuous erosion over time of codon-specificity in H1N1, including a shift away from host (human, swine, and bird [duck]) codon preference patterns. CONCLUSIONS While there have been numerous adaptations within the H1N1 genome, most of the genetic changes we document here appear to be non-adaptive, and much of the change appears to be degenerative. We suggest H1N1 has been undergoing natural genetic attenuation, and that significant attenuation may even occur during a single pandemic. This process may play a role in natural pandemic cessation and has apparently contributed to the exponential decline in mortality rates over time, as seen in all major human influenza strains. These findings may be relevant to the development of strategies for managing influenza pandemics and strain evolution.
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