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Genetic Diversity and Phyletic Evolution of Eleven Chinese Indigenous and Three Commercial Chicken Breeds by mtDNA Sequences Rev. Bras. Ciênc. Avic.
Yu,C; Qiu,M; Jiang,X; Zhang,Z; Du,H; Li,Q; Xia,B; Song,X; Hu,C; Xiong,X; Yang,L; Peng,H; Chen,J; Wang,Y; Yang,C.
ABSTRACT Chinese indigenous chicken breeds are geographically widespread, and a total of 116 indigenous chicken breeds are listed as Chinese national genetic resources. However, these indigenous chicken breeds are facing serious challenges as declining population and germplasm degeneration because lots of commercial chicken breeds had been introduced. In this study, the genetic variations of eleven Chinese indigenous chicken breeds of Sichuan province and three commercial chicken breeds were investigated based on the partial mitochondrial DNA D-loop of 487bp in length. 147 individuals from 14 breeds were examined and 34 haplotypes were observed. Genetic diversity analysis showed that the highest haplotype diversity level was found in Dahen Chicken (DH)...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Chinese chicken; Mitochondrial DNA; Cluster analysis; Gene flow; Phylogeny.
Ano: 2019 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-635X2019000400308
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Genetic variability of the Amazon River prawn Macrobrachium amazonicum (Decapoda, Caridea, Palaemonidae) Naturalis
Vergamini, F.G.; Pileggi, L.G.; Mantelatto, F.L..
The freshwater prawn Macrobrachium amazonicum is widely distributed in South America, and occupies habitats with a wide range of salinities. Several investigations have revealed the existence of wide intraspecific variability among different populations, although the understanding of this variability is still fragmentary and incomplete. We compared and characterized inland and coastal populations of M. amazonicum from Brazil, using molecular data (16S and COI mtDNA) to describe the degree of variability, structure, and relationships among them. Genetic divergence rates among populations showed variability at the intraspecific level. All the analyses evidenced significant genetic divergence among populations, structuring them in three groups: I- inland...
Tipo: Article / Letter to the editor Palavras-chave: Brazil; Genetic distance; Inland versus coastal populations; Phylogeny; Mitochondrial DNA; Population; 42.74.
Ano: 2011 URL: http://www.repository.naturalis.nl/record/369711
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Genetics and morphology of the genus Tritetrabdella (Hirudinea, Haemadipsidae) from the mountainous rain forests of Sabah, Borneo, reveal a new species with two new subspecies Naturalis
Kappes, H..
Blood-feeding terrestrial leeches of the family Haemadipsidae are a notorious part of the invertebrate diversity in Asian and Australian rain forests. All hitherto published records of terrestrial leeches of Borneo belong to the genus Haemadipsa. Here, a second, poorly known haemadipsid genus is reported from Mount Kinabalu and Crocker Range National Park. The individuals were barcoded and compared to sequences available in GenBank. The results show that the genus Tritetrabdella has representatives in the Indochinese and the Sundaic bioregions. All six specimens from Borneo are from a single new Tritetrabdella lineage, T. kinabaluensis spec. nov. Within the Bornean lineage, two groups differing 4-5% in the COI barcoding sequence were identified. Because 1)...
Tipo: Article / Letter to the editor Palavras-chave: Annelida; Clitellata; Ecological specialization; Genetic distance; Parasite; Phylogeny; Speciation; Tropical mountains; 42.76; 42.64.
Ano: 2013 URL: http://www.repository.naturalis.nl/record/462900
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Genome-wide analysis of the Glycerol-3-Phosphate Acyltransferase (GPAT) gene family reveals the evolution and diversification of plant GPATs Genet. Mol. Biol.
Waschburger,Edgar; Kulcheski,Franceli Rodrigues; Veto,Nicole Moreira; Margis,Rogerio; Margis-Pinheiro,Marcia; Turchetto-Zolet,Andreia Carina.
Abstract sn-Glycerol-3-phosphate 1-O-acyltransferase (GPAT) is an important enzyme that catalyzes the transfer of an acyl group from acyl-CoA or acyl-ACP to the sn-1 or sn-2 position of sn-glycerol-3-phosphate (G3P) to generate lysophosphatidic acids (LPAs). The functional studies of GPAT in plants demonstrated its importance in controlling storage and membrane lipid. Identifying genes encoding GPAT in a variety of plant species is crucial to understand their involvement in different metabolic pathways and physiological functions. Here, we performed genome-wide and evolutionary analyses of GPATs in plants. GPAT genes were identified in all algae and plants studied. The phylogenetic analysis showed that these genes group into three main clades. While clades...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Plant lipids; GPAT enzymes; Phylogeny; Evolution; Gene expression.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572018000200355
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Genome-Wide Assessment of Putative Superoxide Dismutases in Unicellular and Filamentous Cyanobacteria BABT
Prajapati,Rajesh; Yadav,Shivam; Mitra,Sonali; Rai,Priya; Mishra,Rajeev; Atri,Neelam.
Abstract Cyanobacteria are photoautotrophic prokaryotes capable to grow in diverse ecological habitats, originated 2.5-3.5 billion years ago and were first to produce oxygen. Since then superoxide dismutases (SOD) acquired great significance due to their ability to catalyze detoxification of byproducts of oxygenic photosynthesis i.e. superoxide radicals. In the present study, we extracted information regarding SODs from species of sequenced cyanobacteria and investigated their diversity, conservation, domain structure, and evolution. 144 putative SOD homologs were identified. Unlike other protein families (ex. serine-threonine kinases) SODs are present in all cyanobacterial species reflecting their significant role in survival. However, their distribution...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Superoxide dismutases; Cyanobacteria; Comparative genomics; Phylogeny.
Ano: 2019 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132019000100422
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Genomics and mollusc pathogens: trends and perspective ArchiMer
Renault, Tristan.
Global mollusc production is continuously increasing and reached 12.8 million tonnes in 2004 representing 28.2 percent of the total world production valued at US$ 9.4 billions. However, cultivated molluscs may suffer from severe mortality outbreaks. Among the possible causes is the occurrence of infectious diseases due to a variety of pathogens including protozoan parasites, bacteria and viruses. Preventing and controlling diseases has become a priority for aquaculture sustainability. However, molluscs are unique in terms of health management. Molluscs like other invertebrates, lack a true adaptative immune system. Vaccination can not be used to protect them against pathogens. Moreover, molluscs are usually reared in the open sea which strongly limits the...
Tipo: Text Palavras-chave: Diagnosis; Phylogeny; Genomics; Mollluscs; Pathogens.
Ano: 2008 URL: http://archimer.ifremer.fr/doc/2008/publication-4574.pdf
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Geometric morphometric analysis of skull morphology reveals loss of phylogenetic signal at the generic level in extant lagomorphs (Mammalia: Lagomorpha) Naturalis
Deyan Ge, D.; Yao, L.; Xia, L.; Zhang, Z.; Yang, Q..
The intergeneric phylogeny of Lagomorpha had been controversial for a long time before a robust phylogeny was reconstructed based on seven nuclear and mitochondrial DNA sequences. However, skull morphology of several endemic genera remained poorly understood. The morphology of supraorbital processes in Lagomorpha is normally used as a diagnostic characteristic in taxonomy, but whether shape change of this structure parallels its genetic divergence has not been investigated. In this study, we conducted a comparative analysis of the skull morphology of all 12 extant genera using geometric morphometrics. These results indicated that no significant phylogenetic signal is observed in the shape change of the dorsal and ventral views of the cranium as well as in...
Tipo: Article / Letter to the editor Palavras-chave: Centroid size Leporidae; Morphometry; Ochotonidae; Phylogeny; Skeletal features morphometry Ochotonidae phylogeny skeletal features 42.84 42.62.
Ano: 2015 URL: http://www.repository.naturalis.nl/record/578953
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Green and brown bridges between weeds and crops reveal novel Diaporthe species in Australia Naturalis
Thompson, S.M.; Tan, Y.P.; Shivas, R.G.; Neate, S.M.; Morin, L.; Bissett, A.; Aitken, E.A.B..
Diaporthe (syn. Phomopsis) species are well-known saprobes, endophytes or pathogens on a range of plants. Several species have wide host ranges and multiple species may sometimes colonise the same host species. This study describes eight novel Diaporthe species isolated from live and/or dead tissue from the broad acre crops lupin, maize, mungbean, soybean and sunflower, and associated weed species in Queensland and New South Wales, as well as the environmental weed bitou bush (Chrysanthemoides monilifera subsp. rotundata) in eastern Australia. The new taxa are differentiated on the basis of morphology and DNA sequence analyses based on the nuclear ribosomal internal transcribed spacer region, and part of the translation elongation factor-1α and ß-tubulin...
Tipo: Article / Letter to the editor Palavras-chave: Alternate weed hosts; Multi-locus; Phomopsis; Phylogeny; Taxonomy.
Ano: 2015 URL: http://www.repository.naturalis.nl/record/588699
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Gross anatomy and histology of the alimentary system of Characidae (Teleostei: Ostariophysi: Characiformes) and potential phylogenetic information Neotropical Ichthyology
Alonso,Felipe; Mirande,Juan Marcos; Pandolfi,Matías.
A compared study of the morphology of the alimentary tract and liver of seven selected species corresponding to the main clades of the Characidae family is presented herein. Three new set of characters corresponding to 1) alimentary tract gross anatomy, 2) alimentary tract histology and 3) liver gross anatomy are evaluated as potential sources of data for future phylogenetic studies of the Characidae. Not considerable interspecific variation was observed at the histological level and therefore this source is not considered to be phylogenetically informative at the taxonomic level analyzed. In contrast, liver and alimentary tract gross anatomy presented important interspecific variation while a relatively homogenous intraspecific morphology was observed....
Tipo: Info:eu-repo/semantics/article Palavras-chave: Alimentary tract; Comparative anatomy; Gastrointestinal tract; Morphological characters; Phylogeny.
Ano: 2015 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1679-62252015000200273
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Hepatitis C virus: molecular and epidemiological evidence of male-to-female transmission BJID
Cavalheiro,Norma de Paula; de La Rosa,Abel; Elagin,Slava; Tengan,Fatima Mitiko; Barone,Antonio Alci.
INTRODUCTION: There is general consensus that hepatitis C virus is efficiently transmitted by the parenteral route, whereas data on viral transmission by sexual or non-sexual intrafamilial contact are conflicting. OBJECTIVE AND METHOD: The aim of this study was to investigate the transmission of hepatitis C virus in nine heterosexual couples. RESULT: The mean age of the couples was 43.7 years. When interviewed, all of the women denied the presence of risk factors for acquisition of the infection, whereas the cause of infection in the nine husbands could be attributed to blood transfusions in two of them (22.2%), use of intravenous and inhaled drugs in six (66.7%), acupuncture in one (11.1%), and tattooing in one (11.1%). All men and none of the women...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Sexually transmitted diseases; Phylogeny; Hepatitis C.
Ano: 2010 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1413-86702010000500001
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Heterochrony, generic distinction and phylogeny in the family Hydractiniidae (Hydrozoa: Cnidaria) Naturalis
Boero, F.; Bouillon, J.; Piraino, S..
The taxonomy of Hydractinia, Stylactaria and Podocoryna is discussed and the three genera are merged into Hydractinia since their diagnostic characters are liable to lead to polyphyly and paraphyly, due to repeated episodes of medusa reduction via heterochrony (paedomorphosis). The phylogeny of the Hydractiniidae is reconstructed by using two outgroups, Clava and Cytaeis, both having some characters in common with the Hydractiniidae. The resulting phylogenetic trees agree in identifying affinities among Hydractinia, Kinetocodium and Hydrocorella, all with polymorphic colonies with gastrozooids having oral tentacles. The position of Clavactinia (characterized by gastrozooids with widely scattered tentacles) is at the root of the tree if Clava is the...
Tipo: Article / Letter to the editor Palavras-chave: Cnidaria; Hydrozoa; Anthomedusae; Phylogeny; Life cycle; Classification; Heterochrony; Paedomorphosis.; 42.72.
Ano: 1998 URL: http://www.repository.naturalis.nl/record/317695
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Highly diverse recombining populations of Vibrio cholerae and Vibrio parahaemolyticus in French Mediterranean coastal lagoons ArchiMer
Esteves, Kevin; Mosser, Thomas; Aujoulat, Fabien; Hervio-heath, Dominique; Monfort, Patrick; Jumas-bilak, Estelle.
Vibrio parahaemolyticus and Vibrio cholerae are ubiquitous to estuarine and marine environments. Thes two species found in Mediterranean coastal systems can induce infection in humans. Environmental isolates of V. cholerae (n = 109) and V. parahaemotycius (n = 89) sampled at different dates, stations and water salinities were investigated for virulence genes and by a mutilocus sequence-based analysis (MLSA). V. cholerae isolate were all ctxA negative and only one isolate of V. parahaemolyticus displayed trh2 gene. Most Sequence Types (ST) corresponded to uique ST isolated at one date or one station. Frequent recombination events were detected among different pathogenic species, V. parahaemotyticus, V. cholerae, Vibrio mimicus, and Vibrio metoecus....
Tipo: Text Palavras-chave: Vibrio; Human pathogens; French coastal lagoons; Phylogeny; Recombination; Multi-locus sequence analysis; Virulence factor.
Ano: 2015 URL: http://archimer.ifremer.fr/doc/00274/38528/37039.pdf
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Histopathological, immunohistochemical and ultraestructural evaluation of inflammatory response in Arius genus fish under experimental inoculation of BCG BABT
Sado,Ricardo Yuji; Matushima,Eliana Reiko.
The aim of this study was to evaluate the inflammatory response kinetics after experimental inoculation with BCG in the primitive Arius sp. fish. The BCG was applied through the intramuscular injection in the caudal peduncular region, and the samples were collected for the analyses at days 1, 3, 7, 14, 21, and 33 post-injection. Acute phase inflammatory infiltrate was characterized by the predominant mononuclear cells, intersticial edema, and muscular tissue necrosis. As the inflammatory response evolved, a large number of multinuclear giant cells were formed containing the BCG. These giant cells were positive for the S100 protein at the histochemical analysis, which demonstrate the macrofage activity, confirmed by the ultra-structural analysis showing the...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Fish; Arius; Phylogeny; BCG; Inflammation; Giant cells.
Ano: 2008 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132008000500009
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Historical biogeography of Fungia (Pleuractis) spp. (Scleractinia: Fungiidae), including a new species from the Seychelles Naturalis
Hoeksema, B.W..
An update of the phylogeny and biogeography of mushroom coral species belonging to Fungia (Pleuractis) is presented. Among the five species of this monophyletic group, one is described as new to science. This species, Fungia seychellensis spec, nov., was discovered during the Netherlands Seychelles Expedition (1992-1993) in the framework of the Netherlands Indian Ocean Programme 1990/1995.
Tipo: Article / Letter to the editor Palavras-chave: Scleractinia; Fungiidae; Fungia; Pleuractis; Mushroom corals; New species; Phylogeny; Biogeography; Seychelles; 42.72.
Ano: 1993 URL: http://www.repository.naturalis.nl/record/319240
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Historical biogeography of Western Palaearctic pelobatid and pelodytid frogs: a molecular phylogenetic perspective Naturalis
Veith, M.; Fromhage, L.; Kosuch, J.; Vences, M..
Spadefoot toads (Pelobates) and Parsley frogs (Pelodytes) are an enigmatic group of Western Palaearctic anurans. In the genus Pelobates, a fossorial lifestyle has enforced a conserved bauplan that masks their intraspecific evolutionary history. We used partial sequences of the mitochondrial 16S and 12S rRNA genes to infer a paleobiogeographic scenario of speciation events in these two anuran genera. Based on two alternative, mutually exclusive calibrations of the Iberian-African split within Pelobates (Pb. cultripes and Pb. varaldii), the disjunction of the Betic Cordillera ca. 14-16 million years ago (mya), and the end of the Messinian Salinity crisis 5.33 mya, we inferred alternative scenarios for species evolution within both genera applying...
Tipo: Article / Letter to the editor Palavras-chave: Phylogeny; Paleobiogeography; Speciation; Regression-based molecular clock; Bayesian molecular dating; Messinian salinity crisis; 16S; 12S; 42.82.
Ano: 2006 URL: http://www.repository.naturalis.nl/record/214531
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Homoplasies, Consistency Index and the Complexity of Morphological Evolution: Catfishes as a Case Study for General Discussions on Phylogeny and Macroevolution International Journal of Morphology
Diogo,Rui.
Catfishes constitute a highly diversified, cosmopolitan group that represents about one third of all freshwater fishes and is one of the most diverse Vertebrate taxa. The detailed study of the Siluriformes can, thus, provide useful data, and illustrative examples, for broader discussions on general phylogeny and macroevolution. In this short note I briefly expose how the study of this remarkably diverse group of fishes reveals an example of highly homoplasic, complex 'mosaic' morphological evolution
Tipo: Journal article Palavras-chave: Catfishes; Homoplasies; Morphological macroevolution; Phylogeny; Siluriformes; Teleostei.
Ano: 2007 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-95022007000400024
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How complex is the Bufo bufo species group? Naturalis
Arntzen, J.W.; Recuero, E.; Canestrelli, D.; Martínez-Solano, I..
Species delineation remains one of the most challenging tasks in the study of biodiversity, mostly owing to the application of different species concepts, which results in contrasting taxonomic arrangements. This has important practical consequences, since species are basic units in fields like ecology and conservation biology. We here review molecular genetic evidence relevant to the systematics of toads in the Bufo bufo species group (Anura, Bufonidae). Two studies recently published in this journal (Recuero et al., MPE 62: 71–86 and Garci´a-Porta et al., MPE 63: 113–130) addressed this issue but reached opposing conclusions on the taxonomy of the group (four versus two species). In particular, allozyme data in the latter paper were interpreted as...
Tipo: Article / Letter to the editor Palavras-chave: Bufo bufo; Bufo spinosus; Molecular systematics; Bufo verrucosissimus; Phylogeny; Allozymes; 42.82.
Ano: 2013 URL: http://www.repository.naturalis.nl/record/470065
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How to tackle revisions of large genera: lessons from Macaranga and Mallotus (Euphorbiaceae) Naturalis
Welzen, P.C. van; Kulju, K.K.M.; Sierra, S.E.C..
Two approaches to revise large genera are discussed. The first approach can be done by a single person, who revises the genus area after area. The other approach is by a team that revises per infrageneric taxon (preferably a single person per infrageneric group). The two approaches have their positive and negative sides, but both give good results. One problem with both approaches is to keep an overview of a possible infrageneric classification. The latter problem can be tackled by performing phylogenetic analyses based on molecular markers (providing core phylogeny) in combination with morphological, palynological, and anatomical data (providing apomorphies for infrageneric taxa).
Tipo: Article / Letter to the editor Palavras-chave: Euphoriaceae; Macaranga; Mallotus; Phylogeny; Revision; Species rich genera.
Ano: 2009 URL: http://www.repository.naturalis.nl/record/524736
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Identification and characterization of pathogenic Pestalotiopsis species to pecan tree in Brazil PAB
Lazarotto,Marília; Bovolini,Marciéli Pitorini; Muniz,Marlove Fátima Brião; Harakawa,Ricardo; Reiniger,Lia Rejane Silveira; Santos,Álvaro Figueredo dos.
The objective of this work was to characterize and cluster isolates of Pestalotiopsis species and to identify those that are pathogenic to pecan, based on morphological and molecular characters. Pestalotiopsis spp. isolates were identified by sequencing the internal transcribed spacer (ITS) and β?tubulin regions. Identification methods were compared to indicate the key morphological characters for species characterization. Thirteen isolates were used for the pathogenicity tests. Morphological characterization was performed using the following variables: mycelial growth rate, sporulation, colony pigmentation, and conidial length and width. Ten pathogenic isolates were identified, three as -tubulin regions. Identification methods were compared to indicate...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Carya illinoinensis; ?-tubulin; ITS rDNA; Morphological characters; Phylogeny; UPGMA.
Ano: 2014 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2014000600440
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Identification and in silico characterization of soybean trihelix-GT and bHLH transcription factors involved in stress responses Genet. Mol. Biol.
Osorio,Marina Borges; Bücker-Neto,Lauro; Castilhos,Graciela; Turchetto-Zolet,Andreia Carina; Wiebke-Strohm,Beatriz; Bodanese-Zanettini,Maria Helena; Margis-Pinheiro,Márcia.
Environmental stresses caused by either abiotic or biotic factors greatly affect agriculture. As for soybean [Glycine max (L.) Merril], one of the most important crop species in the world, the situation is not different. In order to deal with these stresses, plants have evolved a variety of sophisticated molecular mechanisms, to which the transcriptional regulation of target-genes by transcription factors is crucial. Even though the involvement of several transcription factor families has been widely reported in stress response, there still is a lot to be uncovered, especially in soybean. Therefore, the objective of this study was to investigate the role of bHLH and trihelix-GT transcription factors in soybean responses to environmental stresses. Gene...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Drought; Gene expression; Glycine max; Phylogeny; Plant-microbe interactions.
Ano: 2012 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572012000200005
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