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1.
Mol Phylogenet Evol ; 139: 106570, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31349101

RESUMO

The subfamily Leptaxinae is included within the highly diverse land snail family Hygromiidae. In the absence of clear diagnostic morphological differences, the subfamily status is currently based solely on molecular information and includes three disjunctly distributed tribes, Leptaxini, Cryptosaccini and Metafruticicolini. However, the phylogenetic relationships among these tribes are not fully resolved and the clustering of some of the genera to the tribes is not statistically supported. To resolve the relationships within Leptaxinae and their position within Hygromiidae, we reconstructed their phylogeny using a multi-locus approach with two mitochondrial genes and eight nuclear markers. The phylogeny was further calibrated and an analysis of ancestral area estimation was carried out to infer the biogeographic history of the group. We elevated Metafruticicolini to subfamily level (Metafruticicolinae) and we restricted Leptaxinae to Cryptosaccini and Leptaxini. The Lusitanian genus Portugala was moved to Leptaxini, previously containing only the Macaronesian genus Leptaxis. Within Cryptosaccini, a new genus strictly confined to the Sierra de la Cabrera (Spain) is described, Fractanella gen. nov. According to our results, Leptaxinae originated in the Early Miocene in the Iberian Peninsula, from which the Macaronesian Islands were colonized. Due to the old split recovered for the divergence between Macaronesian and Iberian lineages, we hypothesize that this colonization may have occurred via the once emerged seamounts located between the archipelagos and the European and African continents, although this could also have occurred through the oldest now emerged islands of Macaronesia. In the Iberian Peninsula, the climatic shift that began during the Middle Miocene, changing progressively from subtropical climate towards the present-day Mediterranean climate, was identified as an important factor shaping the subfamily's diversification, along with Pleistocene climatic fluctuations.


Assuntos
Caramujos/classificação , Animais , Complexo IV da Cadeia de Transporte de Elétrons/química , Complexo IV da Cadeia de Transporte de Elétrons/classificação , Complexo IV da Cadeia de Transporte de Elétrons/genética , Mitocôndrias/genética , Filogenia , Filogeografia , RNA Ribossômico/química , RNA Ribossômico/classificação , RNA Ribossômico/genética , Caramujos/genética , Espanha
2.
Mol Phylogenet Evol ; 139: 106565, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31326515

RESUMO

So far, the phylogenetic studies on ciliated protists have mainly based on single locus, the nuclear ribosomal DNA (rDNA). In order to avoid the limitations of single gene/genome trees and to add more data to systematic analyses, information from mitochondrial DNA sequence has been increasingly used in different lineages of ciliates. The systematic relationships in the subclass Scuticociliatia are extremely confused and largely unresolved based on nuclear genes. In the present study, we have characterized 72 new sequences, including 40 mitochondrial cytochrome oxidase c subunit I (COI) sequences, 29 mitochondrial small subunit ribosomal DNA (mtSSU-rDNA) sequences and three nuclear small subunit ribosomal DNA (nSSU-rDNA) sequences from 47 isolates of 44 morphospecies. Phylogenetic analyses based on single gene as well as concatenated data were performed and revealed: (1) compared to mtSSU-rDNA, COI gene reveals more consistent relationships with those of nSSU-rDNA; (2) the secondary structures of mtSSU-rRNA V4 region are predicted and compared in scuticociliates, which can contribute to discrimination of closely related species; (3) neither nuclear nor mitochondrial data support the monophyly of the order Loxocephalida, which may represent some divergent and intermediate lineages between the subclass Scuticociliatia and Hymenostomatia; (4) the assignments of thigmotrichids to the order Pleuronematida and the confused taxon Sulcigera comosa to the genus Histiobalantium are confirmed by mitochondrial genes; (5) both nuclear and mitochondrial data reveal that the species in the family Peniculistomatidae always group in the genus Pleuronema, suggesting that peniculistomatids are more likely evolved from Pleuronema-like ancestors; (6) mitochondrial genes support the monophyly of the order Philasterida, but the relationships among families of the order Philasterida remain controversial due to the discrepancies between their morphological and molecular data.


Assuntos
Núcleo Celular/genética , Mitocôndrias/genética , Oligoimenóforos/classificação , DNA Ribossômico/química , DNA Ribossômico/classificação , DNA Ribossômico/genética , Complexo IV da Cadeia de Transporte de Elétrons/química , Complexo IV da Cadeia de Transporte de Elétrons/classificação , Complexo IV da Cadeia de Transporte de Elétrons/genética , Conformação de Ácido Nucleico , Oligoimenóforos/genética , Filogenia , RNA Ribossômico/química , RNA Ribossômico/classificação , RNA Ribossômico/genética , Análise de Sequência de DNA
3.
PLoS One ; 13(12): e0208615, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30586406

RESUMO

Argasid ticks (Acari: Argasidae) carry and transmit a variety of pathogens of animals and humans, including viruses, bacteria and parasites. There are several studies reporting ixodid ticks (Acari: Ixodidae) and associated tick-borne pathogens in Xinjiang, China. However, little is known about the argasid ticks and argasid tick-associated pathogens in this area. In this study, a total of 3829 adult argasid ticks infesting livestock were collected at 12 sampling sites of 10 counties in the Peripheral Oases, which carry 90% of the livestock and humans population, around the Tarim Basin (southern Xinjiang) from 2013 to 2016. Tick specimens were identified to two species from different genera by morphology and sequences of mitochondrial 16S rRNA and 12S rRNA were derived to confirm the species designation. The results showed that the dominant argasid ticks infesting livestock in southern Xinjiang were Ornithodoros lahorensis (87.86%, 3364/3829). Ornithodoros lahorensis was distributed widely and were collected from 10 counties of southern Xinjiang. Argas japonicus was collected from Xinjiang for the first time. In addition, we screened these ticks for tick-associated pathogens and showed the presence of DNA sequences of Rickettsia spp. of Spotted fever group and Anaplasma spp. in the argasid ticks. This finding suggests the potential role for Argas japonicus as a vector of pathogens to livestock and humans.


Assuntos
Anaplasma/isolamento & purificação , Argas/microbiologia , Ornithodoros/microbiologia , Rickettsia/isolamento & purificação , Anaplasma/classificação , Anaplasma/genética , Anaplasma/patogenicidade , Animais , Argas/classificação , Argas/genética , Bovinos , China , Vetores de Doenças , Mitocôndrias/genética , Ornithodoros/classificação , Ornithodoros/genética , Filogenia , RNA Ribossômico/classificação , RNA Ribossômico/genética , RNA Ribossômico/metabolismo , RNA Ribossômico 16S/classificação , RNA Ribossômico 16S/genética , RNA Ribossômico 16S/metabolismo , Rickettsia/classificação , Rickettsia/genética , Rickettsia/patogenicidade , Análise de Sequência de DNA , Ovinos , Infestações por Carrapato/parasitologia , Infestações por Carrapato/patologia , Infestações por Carrapato/veterinária
4.
BMC Genomics ; 19(1): 520, 2018 Jul 04.
Artigo em Inglês | MEDLINE | ID: mdl-29973152

RESUMO

BACKGROUND: Monogenean flatworms are the main ectoparasites of fishes. Representatives of the species-rich families Gyrodactylidae and Dactylogyridae, especially those infecting cichlid fishes and clariid catfishes, are important parasites in African aquaculture, even more so due to the massive anthropogenic translocation of their hosts worldwide. Several questions on their evolution, such as the phylogenetic position of Macrogyrodactylus and the highly speciose Gyrodactylus, remain unresolved with available molecular markers. Also, diagnostics and population-level research would benefit from the development of higher-resolution genetic markers. We aim to offer genetic resources for work on African monogeneans by providing mitogenomic data of four species (two belonging to Gyrodactylidae, two to Dactylogyridae), and analysing their gene sequences and gene order from a phylogenetic perspective. RESULTS: Using Illumina technology, the first four mitochondrial genomes of African monogeneans were assembled and annotated for the cichlid parasites Gyrodactylus nyanzae, Cichlidogyrus halli, Cichlidogyrus mbirizei (near-complete mitogenome) and the catfish parasite Macrogyrodactylus karibae (near-complete mitogenome). Complete nuclear ribosomal operons were also retrieved, as molecular vouchers. The start codon TTG is new for Gyrodactylus and for Dactylogyridae, as is the incomplete stop codon TA for Dactylogyridae. Especially the nad2 gene is promising for primer development. Gene order was identical for protein-coding genes and differed between the African representatives of these families only in a tRNA gene transposition. A mitochondrial phylogeny based on an alignment of nearly 12,500 bp including 12 protein-coding and two ribosomal RNA genes confirms that the Neotropical oviparous Aglaiogyrodactylus forficulatus takes a sister group position with respect to the other gyrodactylids, instead of the supposedly 'primitive' African Macrogyrodactylus. Inclusion of the African Gyrodactylus nyanzae confirms the paraphyly of Gyrodactylus. The position of the African dactylogyrid Cichlidogyrus is unresolved, although gene order suggests it is closely related to marine ancyrocephalines. CONCLUSIONS: The amount of mitogenomic data available for gyrodactylids and dactylogyrids is increased by roughly one-third. Our study underscores the potential of mitochondrial genes and gene order in flatworm phylogenetics, and of next-generation sequencing for marker development for these non-model helminths for which few primers are available.


Assuntos
Ciclídeos/parasitologia , Mitocôndrias/genética , Platelmintos/genética , Animais , DNA de Protozoário/química , DNA de Protozoário/isolamento & purificação , DNA de Protozoário/metabolismo , Ordem dos Genes , Genoma Mitocondrial , Sequenciamento de Nucleotídeos em Larga Escala , Mitocôndrias/classificação , Filogenia , Proteínas de Protozoários/classificação , Proteínas de Protozoários/genética , RNA Ribossômico/classificação , RNA Ribossômico/genética , Análise de Sequência de DNA
5.
PLoS One ; 13(3): e0194672, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29584761

RESUMO

In the present study, we report five complete and one nearly complete mitochondrial genomes of the Pyraloidea including the first representatives from the Pyralinae (Pyralidae) and Glaphyriinae (Crambidae). We also conduct a comparative analysis of mitogenomic features of this group. Our results show that Pyraloidea mitogenomes evolved under a common trend found in lepidopteran mitogenomes and share several typical genomic characters. The extra conserved blocks are identified in the Pyraloidea control region, and diverse missing codons formed another unique trait within Pyraloidea mitogenome. Furthermore, we reconstruct the mitogenomic phylogeny of Pyraloidea and confirm the phylogenetic position of Pyralinae and Glaphyriinae within the Pyraloidea using BI and ML method based on multiple mitochondrial datasets.


Assuntos
Genoma Mitocondrial , Mariposas/genética , Animais , Códon , DNA/química , DNA/isolamento & purificação , DNA/metabolismo , Bases de Dados Genéticas , Mariposas/classificação , Filogenia , RNA Ribossômico/classificação , RNA Ribossômico/genética , RNA de Transferência/classificação , RNA de Transferência/genética , Análise de Sequência de DNA
6.
Mol Phylogenet Evol ; 120: 118-128, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-29196204

RESUMO

Biogeographic and evolutionary patterns in the North African portion of the Western Palaearctic are poorly known. A high fraction of undescribed diversity is expected in this region, especially in groups such as reptiles. Here we used mitochondrial (12S, 16S, cytb) and nuclear (pomc, rag2, cmos) markers and morphological data to investigate phyletic diversification and phylogeographical structure in the amphisbaenian Trogonophis wiegmanni endemic to the Maghreb. Phylogenetic and molecular dating analyses based on gene trees and species trees support three deeply divergent lineages of Pliocene origin, two in Morocco and one in central Algeria and Tunisia. Parapatry, reciprocal monophyly, high genetic divergence and limited morphological differentiation between them suggest that these lineages represent independent cryptic taxonomic units. Emerging lines of evidence from this study and from available literature on Maghreb taxa support (i) a major biogeographic break between western and eastern Maghreb and (ii) a role of the Atlas as a biogeographic divide within the western Maghreb (Morocco). The origin of these biogeographic units is probably associated with the evolutionary events prompted by the Late Miocene palaeogeographic setting and later by Plio-Pleistocene climatic changes and their interplay with prominent orographic barriers within North Africa.


Assuntos
Lagartos/classificação , África do Norte , Proteínas de Anfíbios/classificação , Proteínas de Anfíbios/genética , Proteínas de Anfíbios/metabolismo , Animais , Biodiversidade , Evolução Biológica , DNA Mitocondrial/química , DNA Mitocondrial/classificação , DNA Mitocondrial/genética , Proteínas de Ligação a DNA/classificação , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Lagartos/genética , Marrocos , Filogenia , Filogeografia , Pró-Opiomelanocortina/classificação , Pró-Opiomelanocortina/genética , Pró-Opiomelanocortina/metabolismo , RNA Ribossômico/química , RNA Ribossômico/classificação , RNA Ribossômico/genética
7.
Mol Phylogenet Evol ; 120: 158-169, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-29196205

RESUMO

We present different approaches to a multi-locus phylogeny for the Liolaemus elongatus-kriegi group, including almost all species and recognized lineages. We sequenced two mitochondrial and five nuclear gene regions for 123 individuals from 35 taxa, and compared relationships resolved from concatenated and species tree methods. The L. elongatus-kriegi group was inferred as monophyletic in three of the five analyses (concatenated mitochondrial, concatenated mitochondrial + nuclear gene trees, and SVD quartet species tree). The mitochondrial gene tree resolved four haploclades, three corresponding to the previously recognized complexes: L. elongatus, L. kriegi and L. petrophilus complexes, and the L. punmahuida group. The BEAST species tree approach included the L. punmahuida group within the L. kriegi complex, but the SVD quartet method placed it as sister to the L. elongatus-kriegi group. BEAST inferred species of the L. elongatus and L. petrophilus complexes as one clade, while SVDquartet inferred these two complexes as monophyletic (although with no statistical support for the L. petrophilus complex). The species tree approach also included the L. punmahuida group as part of the L. elongatus-kriegi group. Our study provides detailed multilocus phylogenetic hypotheses for the L. elongatus-kriegi group, and we discuss possible reasons for differences in the concatenation and species tree methods.


Assuntos
Núcleo Celular/genética , Lagartos/classificação , Mitocôndrias/genética , Animais , Teorema de Bayes , Citocromos b/classificação , Citocromos b/genética , Citocromos b/metabolismo , DNA/química , DNA/isolamento & purificação , DNA/metabolismo , Bases de Dados Genéticas , Lagartos/genética , Filogenia , RNA Ribossômico/química , RNA Ribossômico/classificação , RNA Ribossômico/genética , Análise de Sequência de DNA
8.
Gigascience ; 7(2)2018 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-29267854

RESUMO

Background: Milu, also known as Père David's deer (Elaphurus davidianus), was widely distributed in East Asia but recently experienced a severe bottleneck. Only 18 survived by the end of the 19th century, and the current population of 4500 individuals was propagated from just 11 kept by the 11th British Duke of Bedford. This species is known for its distinguishable appearance, the driving force behind which is still a mystery. To aid efforts to explore these phenomena, we constructed a draft genome of the species. Findings: In total, we generated 321.86 gigabases (Gb) of raw DNA sequence from whole-genome sequencing of a male milu deer using an Illumina HiSeq 2000 platform. Assembly yielded a final genome with a scaffold N50 size of 3.03 megabases (Mb) and a total length of 2.52 Gb. Moreover, we identified 20 125 protein-coding genes and 988.1 Mb of repetitive sequences. In addition, homology-based searches detected 280 rRNA, 1335 miRNA, 1441 snRNA, and 893 tRNA sequences in the milu genome. The divergence time between E. davidianus and Bos taurus was estimated to be about 28.20 million years ago (Mya). We identified 167 species-specific genes and 293 expanded gene families in the milu lineage. Conclusions: We report the first reference genome of milu, which will provide a valuable resource for studying the species' demographic history of severe bottleneck and the genetic mechanism(s) of special phenotypic evolution.


Assuntos
Evolução Biológica , Mapeamento Cromossômico/métodos , Cervos/genética , Genoma , Sequenciamento de Nucleotídeos em Larga Escala , Animais , Bovinos , Cervos/classificação , Masculino , MicroRNAs/classificação , MicroRNAs/genética , Fases de Leitura Aberta , Filogenia , Proteínas/classificação , Proteínas/genética , RNA Ribossômico/classificação , RNA Ribossômico/genética , RNA Nuclear Pequeno/classificação , RNA Nuclear Pequeno/genética , RNA de Transferência/classificação , RNA de Transferência/genética , Sequenciamento Completo do Genoma
9.
RNA Biol ; 15(1): 95-103, 2018 01 02.
Artigo em Inglês | MEDLINE | ID: mdl-29099311

RESUMO

Small RNAs (sRNAs) in bacteria have emerged as key players in transcriptional and post-transcriptional regulation of gene expression. Here, we present a statistical analysis of different sequence- and structure-related features of bacterial sRNAs to identify the descriptors that could discriminate sRNAs from other bacterial RNAs. We investigated a comprehensive and heterogeneous collection of 816 sRNAs, identified by northern blotting across 33 bacterial species and compared their various features with other classes of bacterial RNAs, such as tRNAs, rRNAs and mRNAs. We observed that sRNAs differed significantly from the rest with respect to G+C composition, normalized minimum free energy of folding, motif frequency and several RNA-folding parameters like base-pairing propensity, Shannon entropy and base-pair distance. Based on the selected features, we developed a predictive model using Random Forests (RF) method to classify the above four classes of RNAs. Our model displayed an overall predictive accuracy of 89.5%. These findings would help to differentiate bacterial sRNAs from other RNAs and further promote prediction of novel sRNAs in different bacterial species.


Assuntos
RNA Mensageiro/genética , RNA Ribossômico/genética , Pequeno RNA não Traduzido/genética , RNA de Transferência/genética , Bactérias/genética , Composição de Bases/genética , Pareamento de Bases , Regulação Bacteriana da Expressão Gênica , RNA Bacteriano/classificação , RNA Bacteriano/genética , RNA Mensageiro/classificação , RNA Ribossômico/classificação , Pequeno RNA não Traduzido/classificação , RNA de Transferência/classificação
10.
Nature ; 551(7681): 472-477, 2017 11 23.
Artigo em Inglês | MEDLINE | ID: mdl-29143818

RESUMO

Chemical modifications of human ribosomal RNA (rRNA) are introduced during biogenesis and have been implicated in the dysregulation of protein synthesis, as is found in cancer and other diseases. However, their role in this phenomenon is unknown. Here we visualize more than 130 individual rRNA modifications in the three-dimensional structure of the human ribosome, explaining their structural and functional roles. In addition to a small number of universally conserved sites, we identify many eukaryote- or human-specific modifications and unique sites that form an extended shell in comparison to bacterial ribosomes, and which stabilize the RNA. Several of the modifications are associated with the binding sites of three ribosome-targeting antibiotics, or are associated with degenerate states in cancer, such as keto alkylations on nucleotide bases reminiscent of specialized ribosomes. This high-resolution structure of the human 80S ribosome paves the way towards understanding the role of epigenetic rRNA modifications in human diseases and suggests new possibilities for designing selective inhibitors and therapeutic drugs.


Assuntos
Microscopia Crioeletrônica , RNA Ribossômico/química , RNA Ribossômico/ultraestrutura , Ribossomos/química , Ribossomos/ultraestrutura , Sítios de Ligação , Epistasia Genética , Células HeLa , Humanos , Ligantes , Modelos Moleculares , Estabilidade de RNA , RNA Ribossômico/biossíntese , RNA Ribossômico/classificação , Subunidades Ribossômicas Maiores de Eucariotos/genética , Subunidades Ribossômicas Menores de Eucariotos/genética , Ribossomos/efeitos dos fármacos , Ribossomos/genética
11.
Mol Phylogenet Evol ; 115: 181-189, 2017 10.
Artigo em Inglês | MEDLINE | ID: mdl-28782594

RESUMO

Molecular analyses of the ecologically important gorgonian octocoral genus Leptogorgia are scant and mostly deal with few species from restricted geographical regions. Here we explore the phylogenetic relationships and the evolutionary history of Leptogorgia using the complete mitochondrial genomes of six Leptogorgia species from different localities in the Atlantic, Mediterranean and eastern Pacific as well as four other genera of Gorgoniidae and Plexauridae. Our mitogenomic analyses showed high inter-specific diversity, variable nucleotide substitution rates and, for some species, novel genomic features such as ORFs of unknown function. The phylogenetic analyses using complete mitogenomes and an extended mtMutS dataset recovered Leptogorgia as polyphyletic, and the species considered in the analyses were split into two defined groups corresponding to different geographic regions, namely the eastern Pacific and the Atlantic-Mediterranean. Our phylogenetic analysis based on mtMutS also showed a clear separation between the eastern Atlantic and South African Leptogorgia, suggesting the need of a taxonomic revision for these forms. A time-calibrated phylogeny showed that the separation of eastern Pacific and western Atlantic species started ca. 20Mya and suggested a recent divergence for eastern Pacific species and for L. sarmentosa-L. capverdensis. Our results also revealed high inter-specific diversity among eastern Atlantic and South African species, highlighting a potential role of the geographical diversification processes and geological events occurring during the last 30Ma in the Atlantic on the evolutionary history of these organisms.


Assuntos
Antozoários/classificação , Mitocôndrias/genética , Animais , Antozoários/genética , Evolução Biológica , DNA/química , DNA/isolamento & purificação , DNA/metabolismo , Variação Genética , ATPases Mitocondriais Próton-Translocadoras/classificação , ATPases Mitocondriais Próton-Translocadoras/genética , Filogenia , RNA Ribossômico/classificação , RNA Ribossômico/genética , Análise de Sequência de DNA
12.
Mol Phylogenet Evol ; 114: 234-248, 2017 09.
Artigo em Inglês | MEDLINE | ID: mdl-28666786

RESUMO

Placobdella is a genus of blood-feeding leeches in the family Glossiphoniidae. Historically, species of Placobdella have posed difficulty for systematists owing to a lack of informative morphological characters and the preponderance of inadequate or incomplete species descriptions. Here, we conduct a phylogenetic analysis of 55 individuals representing 20 of the 24 currently recognized nominal taxa using COI, ND1, 12S rDNA and ITS sequences under parsimony, maximum likelihood and Bayesian inference. We also examine the isolated COI phylogeny for the genus using an expanded dataset encompassing three additional species not included in the concatenated dataset. Finally, we assess genetic variation at the COI locus to validate initial specimen identifications and estimate how COI variation may reflect species boundaries. We conclude that Placobdella is a monophyletic group that places as the sister group to a clade formed by the genera Haementeria and Helobdella. We discuss the evolutionary implications of several internal relationships that are robustly resolved by all three optimality criteria, paying particular attention to the apparent fluidity of morphological characters exhibited by members of Placobdella. We also find preliminary evidence for the presence of cryptic and undescribed diversity within the genus.


Assuntos
Sanguessugas/classificação , Animais , Teorema de Bayes , DNA/química , DNA/isolamento & purificação , DNA/metabolismo , Complexo IV da Cadeia de Transporte de Elétrons/classificação , Complexo IV da Cadeia de Transporte de Elétrons/genética , Variação Genética , Sanguessugas/genética , Filogenia , RNA Ribossômico/classificação , RNA Ribossômico/genética , Análise de Sequência de DNA
13.
Mol Phylogenet Evol ; 115: 171-180, 2017 10.
Artigo em Inglês | MEDLINE | ID: mdl-28756134

RESUMO

Caridean shrimps constitute one of the most diverse groups of decapod crustaceans, notwithstanding their poorly resolved infraordinal relationships. One of the systematically controversial families in Caridea is the predominantly pelagic Pasiphaeidae, comprises 101 species in seven genera. Pasiphaeidae species exhibit high morphological disparity, as well as ecological niche width, inhabiting shallow to very deep waters (>4000m). The present work presents the first molecular phylogeny of the family, based on a combined dataset of six mitochondrial and nuclear gene markers (12S rDNA, 16S rDNA, histone 3, sodium-potassium ATPase α-subunit, enolase and ATP synthase ß-subunit) from 33 species belonged to six genera of Pasiphaeidae with 19 species from 12 other caridean families as outgroup taxa. Maximum likelihood and Bayesian inference analyses conducted on the concatenated dataset of 2265bp suggest the family Pasiphaeidae is not monophyletic, with Psathyrocaris more closely related to other carideans than to the other five pasiphaeid genera included in this analysis. Leptochela occupies a sister position to the remaining genera and is genetically quite distant from them. At the generic level, the analysis supports the monophyly of Pasiphaea, Leptochela and Psathyrocaris, while Eupasiphae is shown to be paraphyletic, closely related to Parapasiphae and Glyphus. The present molecular result strongly implies that certain morphological characters used in the present systematic delineation within Pasiphaeidae may not be synapomorphies and the classification within the family needs to be urgently revised.


Assuntos
Decápodes/classificação , Animais , Teorema de Bayes , DNA/química , DNA/isolamento & purificação , DNA/metabolismo , Decápodes/genética , Histonas/classificação , Histonas/genética , ATPases Mitocondriais Próton-Translocadoras/classificação , ATPases Mitocondriais Próton-Translocadoras/genética , Filogenia , RNA Ribossômico/classificação , RNA Ribossômico/genética , RNA Ribossômico 16S/classificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
14.
Mol Phylogenet Evol ; 114: 382-385, 2017 09.
Artigo em Inglês | MEDLINE | ID: mdl-28647619

RESUMO

This study presents a multi-gene phylogenetic analysis of the Achatinoidea and provides an initial basis for a taxonomic re-evaluation of family level groups within the superfamily. A total of 5028 nucleotides from the nuclear rRNA, actin and histone 3 genes and the 1st and 2nd codon positions of the mitochondrial cytochrome c oxidase subunit I gene were sequenced from 24 species, representing six currently recognised families. Results from maximum likelihood, neighbour joining, maximum parsimony and Bayesian inference trees revealed that, of currently recognised families, only the Achatinidae are monophyletic. For the Ferussaciidae, Ferussacia folliculus fell separately to Cecilioides gokweanus and formed a sister taxon to the rest of the Achatinoidea. For the Coeliaxidae, Coeliaxis blandii and Pyrgina umbilicata did not group together. The Subulinidae was not resolved, with some subulinids clustering with the Coeliaxidae and Thyrophorellidae. Three subfamilies currently included within the Subulinidae based on current taxonomy likewise did not form monophyletic groups.


Assuntos
Gastrópodes/classificação , Actinas/classificação , Actinas/genética , Animais , Teorema de Bayes , Códon , DNA/química , DNA/isolamento & purificação , DNA/metabolismo , Complexo IV da Cadeia de Transporte de Elétrons/classificação , Complexo IV da Cadeia de Transporte de Elétrons/genética , Gastrópodes/genética , Histonas/classificação , Histonas/genética , Filogenia , RNA Ribossômico/classificação , RNA Ribossômico/genética , Análise de Sequência de DNA
15.
Sci Rep ; 6: 39153, 2016 12 15.
Artigo em Inglês | MEDLINE | ID: mdl-27974854

RESUMO

The complete mitochondrial genome (mitogenome) of Leucoma salicis (Lepidoptera: Lymantriidae) was sequenced and annotated. It is a circular molecule of 15,334 bp, containing the 37 genes usually present in insect mitogenomes. All protein-coding genes (PCGs) are initiated by ATN codons, other than cox1, which is initiated by CGA. Three of the 13 PCGs had an incomplete termination codon, T or TA, while the others terminated with TAA. The relative synonymous codon usage of the 13 protein-coding genes (PCGs) was consistent with those of published lepidopteran sequences. All tRNA genes had typical clover-leaf secondary structures, except for the tRNASer (AGN), in which the dihydrouridine (DHU) arm could not form a stable stem-loop structure. The A + T-rich region of 325 bp had several distinctive features, including the motif 'ATAGA' followed by an 18 bp poly-T stretch, a microsatellite-like (AT)7 element, and an 11-bp poly-A present immediately upstream of tRNAMet. Relationships among 32 insect species were determined using Maximum Likelihood (ML), Neighbor Joining (NJ) and Bayesian Inference (BI) phylogenetic methods. These analyses confirm that L. salicis belongs to the Lymantriidae; and that Lymantriidae is a member of Noctuoidea, and is a sister taxon to Erebidae, Nolidae and Noctuidae, most closely related to Erebidae.


Assuntos
Genoma Mitocondrial , Lepidópteros/genética , Mariposas/genética , Animais , Sequência de Bases , Teorema de Bayes , Códon de Terminação , DNA Mitocondrial/química , DNA Mitocondrial/isolamento & purificação , DNA Mitocondrial/metabolismo , Lepidópteros/classificação , Funções Verossimilhança , Mariposas/classificação , Conformação de Ácido Nucleico , Fases de Leitura Aberta/genética , Filogenia , RNA Ribossômico/classificação , RNA Ribossômico/genética , RNA de Transferência/química , RNA de Transferência/classificação , RNA de Transferência/genética , Análise de Sequência de DNA
16.
Sci Rep ; 6: 35878, 2016 10 21.
Artigo em Inglês | MEDLINE | ID: mdl-27767191

RESUMO

The mitochondrial genome (mitogenome) provides important information for understanding molecular evolution and phylogeny. To determine the systematic status of the family Limacodidae within Lepidoptera, we infer a phylogenetic hypothesis based on the complete mitogenome of Monema flavescens (Lepidoptera: Limacodidae). The mitogenome of M. flavescens is 15,396 base pairs (bp), and includes 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (CR). The AT skew of this mitogenome is slightly negative and the nucleotide composition is also biased towards A + T nucleotides (80.5%). All PCGs are initiated by ATN codons, except for the cytochrome c oxidase subunit 1 (cox1) gene, which is initiated by CGA. All tRNAs display the typical clover-leaf structure characteristic of mitochondrial tRNAs, with the exception of trnS1 (AGN). The mitogenome CR is 401 bp and consists of several features common to Lepidoptera. Phylogenetic analysis using Bayesian Inference (BI) and Maximum Likelihood (ML) based on nucleotide and amino acid sequences of 13 mitochondrial PCGs indicates that M. flavescens belongs to Zygaenoidea. We obtain a well-supported phylogenetic tree consisting of Yponomeutoidea + (Tortricoidea + Zygaenoidea + (Papilionoidea + (Pyraloidea + (Noctuoidea + (Geometroidea + Bombycoidea))))).


Assuntos
Genoma Mitocondrial , Lepidópteros/genética , Mariposas/genética , Animais , Sequência de Bases , Teorema de Bayes , Códon de Iniciação , DNA/isolamento & purificação , DNA/metabolismo , Complexo IV da Cadeia de Transporte de Elétrons/química , Complexo IV da Cadeia de Transporte de Elétrons/classificação , Complexo IV da Cadeia de Transporte de Elétrons/genética , Lepidópteros/classificação , Mariposas/classificação , Conformação de Ácido Nucleico , Filogenia , RNA Ribossômico/química , RNA Ribossômico/classificação , RNA Ribossômico/genética , RNA de Transferência/química , RNA de Transferência/genética , Análise de Sequência de DNA
17.
Mol Phylogenet Evol ; 104: 99-111, 2016 11.
Artigo em Inglês | MEDLINE | ID: mdl-27497607

RESUMO

The Coleoptera (beetles) exhibits tremendous morphological, ecological, and behavioral diversity. To better understand the phylogenetics and evolution of beetles, we sequenced three complete mitogenomes from two families (Cleridae and Meloidae), which share conserved mitogenomic features with other completely sequenced beetles. We assessed the influence of six datasets and three inference methods on topology and nodal support within the Coleoptera. We found that both Bayesian inference and maximum likelihood with homogeneous-site models were greatly affected by nucleotide compositional heterogeneity, while the heterogeneous-site mixture model in PhyloBayes could provide better phylogenetic signals for the Coleoptera. The amino acid dataset generated more reliable tree topology at the higher taxonomic levels (i.e. suborders and series), where the inclusion of rRNA genes and the third positions of protein-coding genes improved phylogenetic inference at the superfamily level, especially under a heterogeneous-site model. We recovered the suborder relationships as (Archostemata+Adephaga)+(Myxophaga+Polyphaga). The series relationships within Polyphaga were recovered as (Scirtiformia+(Elateriformia+((Bostrichiformia+Scarabaeiformia+Staphyliniformia)+Cucujiformia))). All superfamilies within Cucujiformia were recovered as monophyletic. We obtained a cucujiform phylogeny of (Cleroidea+(Coccinelloidea+((Lymexyloidea+Tenebrionoidea)+(Cucujoidea+(Chrysomeloidea+Curculionoidea))))). This study showed that although tree topologies were sensitive to data types and inference methods, mitogenomic data could provide useful information for resolving the Coleoptera phylogeny at various taxonomic levels by using suitable datasets and heterogeneous-site models.


Assuntos
Genoma Mitocondrial , Animais , Teorema de Bayes , Besouros/classificação , Besouros/genética , DNA/química , DNA/isolamento & purificação , DNA/metabolismo , DNA Mitocondrial/classificação , DNA Mitocondrial/genética , DNA Mitocondrial/metabolismo , Filogenia , RNA Ribossômico/classificação , RNA Ribossômico/genética , RNA Ribossômico/metabolismo , RNA de Transferência/classificação , RNA de Transferência/genética , RNA de Transferência/metabolismo , Alinhamento de Sequência , Análise de Sequência de DNA
18.
Mol Phylogenet Evol ; 104: 73-82, 2016 11.
Artigo em Inglês | MEDLINE | ID: mdl-27475496

RESUMO

Here we consider the role of depth as a driver of evolution in a genus of deep-sea fishes. We provide a phylogeny for the genus Coryphaenoides (Gadiformes: Macrouridae) that represents the breadth of habitat use and distributions for these species. In our consensus phylogeny species found at abyssal depths (>4000m) form a well-supported lineage, which interestingly also includes two non-abyssal species, C. striaturus and C. murrayi, diverging from the basal node of that lineage. Biogeographic analyses suggest the genus may have originated in the Southern and Pacific Oceans where contemporary species diversity is highest. The abyssal lineage seems to have arisen secondarily and likely originated in the Southern/Pacific Oceans but diversification of this lineage occurred in the Northern Atlantic Ocean. All abyssal species are found in the North Atlantic with the exception of C. yaquinae in the North Pacific and C. filicauda in the Southern Ocean. Abyssal species tend to have broad depth ranges and wide distributions, indicating that the stability of the deep oceans and the ability to live across wide depths may promote population connectivity and facilitate large ranges. We also confirm that morphologically defined subgenera do not agree with our phylogeny and that the Giant grenadier (formerly Albatrossia pectoralis) belongs to Coryphaenoides, indicating that a taxonomic revision of the genus is needed. We discuss the implications of our findings for understanding the radiation and diversification of this genus, and the likely role of adaptation to the abyss.


Assuntos
Gadiformes/classificação , Adaptação Fisiológica , Animais , Oceano Atlântico , Citocromos c/classificação , Citocromos c/genética , Citocromos c/metabolismo , DNA/química , DNA/isolamento & purificação , DNA/metabolismo , Ecossistema , Gadiformes/genética , Proteínas de Homeodomínio/classificação , Proteínas de Homeodomínio/genética , Proteínas de Homeodomínio/metabolismo , Oceanos e Mares , Oceano Pacífico , Filogenia , Filogeografia , RNA Ribossômico/classificação , RNA Ribossômico/genética , RNA Ribossômico/metabolismo , Alinhamento de Sequência , Análise de Sequência de DNA
19.
Mol Phylogenet Evol ; 104: 14-20, 2016 11.
Artigo em Inglês | MEDLINE | ID: mdl-27444707

RESUMO

The phylogeny of tits has been studied using various molecular markers, but their phylogenetic relationships remain controversial. To further investigate their taxonomic status and phylogenetic relationships, the entire mitochondrial genomes (mitogenomes) and five nuclear segments were sequenced from 10 species of tits and two outgroups (Sylviparus modestus and Remiz consobrinus), followed by the comparison of mitogenomic characteristics and reconstruction of phylogenetic relationship based on the different datasets. The results revealed the following: the mitogenomes of 10 ingroup tits, each 16,758-16,799bp in length, displayed typical mitogenome organization and the gene order found in most previously determined Passeriformes mitogenomes; close relationships existed between Parus major and P. monticolus, between P. montanus and P. palustris, and between P. ater and P. venustulus; and Pseudopodoces humilis was a sister group to P. spilonotus, P. cyanus, or the clade containing P. major and P. monticolus.


Assuntos
Passeriformes/classificação , Animais , DNA/química , DNA/isolamento & purificação , DNA/metabolismo , Genoma Mitocondrial , Passeriformes/genética , Filogenia , RNA Ribossômico/classificação , RNA Ribossômico/genética , RNA Ribossômico/metabolismo , RNA de Transferência/classificação , RNA de Transferência/metabolismo , Alinhamento de Sequência , Análise de Sequência de DNA
20.
Mol Phylogenet Evol ; 103: 6-18, 2016 10.
Artigo em Inglês | MEDLINE | ID: mdl-27395778

RESUMO

Acanthodactylus lizards are among the most diverse and widespread diurnal reptiles in the arid regions spanning from North Africa across to western India. Acanthodactylus constitutes the most species-rich genus in the family Lacertidae, with over 40 recognized species inhabiting a wide variety of dry habitats. The genus has seldom undergone taxonomic revisions, and although there are a number of described species and species-groups, their boundaries, as well as their interspecific relationships, remain largely unresolved. We constructed a multilocus phylogeny, combining data from two mitochondrial (12S, cytb) and three nuclear (MC1R, ACM4, c-mos) markers for 302 individuals belonging to 36 known species, providing the first large-scale time-calibrated molecular phylogeny of the genus. We evaluated phylogenetic relationships between and within species-groups, and assessed Acanthodactylus biogeography across its known range. Acanthodactylus cladogenesis is estimated to have originated in Africa due to vicariance and dispersal events from the Oligocene onwards. Radiation started with the separation into three clades: the Western and scutellatus clades largely distributed in North Africa, and the Eastern clade occurring mostly in south-west Asia. Most Acanthodactylus species diverged during the Miocene, possibly as a result of regional geological instability and climatic changes. We support most of the current taxonomic classifications and phylogenetic relationships, and provide genetic validity for most species. We reveal a new distinct blanfordii species-group, suggest new phylogenetic positions (A. hardyi, A. masirae), and synonymize several species and subspecies (A. lineomaculatus, A. boskianus khattensis and A. b. nigeriensis) with their phylogenetically closely-related species. We recommend a thorough systematic revision of taxa, such as A. guineensis, A. grandis, A. dumerilii, A. senegalensis and the pardalis and erythrurus species-groups, which exhibit high levels of intraspecific variability, and clear evidence of phylogenetic complexity.


Assuntos
Lagartos/classificação , Animais , Evolução Biológica , Citocromos b/classificação , Citocromos b/genética , DNA/química , DNA/isolamento & purificação , DNA/metabolismo , DNA Mitocondrial/genética , Clima Desértico , Especiação Genética , Lagartos/genética , Filogenia , Filogeografia , RNA Ribossômico/classificação , RNA Ribossômico/genética , Análise de Sequência de DNA
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