Genetic variation in intraspecific populations of Rabdophaga rosaria (Diptera: Cecidomyiidae) indicating possible diversification scenarios into sibling species along with host range expansion on willows (Salicaceae: Salix)

2020 ◽  
Vol 189 (4) ◽  
pp. 1426-1437
Author(s):  
Shinsuke Sato ◽  
Keith M Harris ◽  
Dominique M Collet ◽  
Wanggyu Kim ◽  
Junichi Yukawa
Keyword(s):  
Sibling Species ◽  
Genetic Data ◽  
Coi Gene ◽  
Salix Alba ◽  
Host Range Expansion ◽  
Maximum Likelihood Tree ◽  
Holarctic Region ◽  
Species Groups ◽  
Clade 1 ◽  
The Uk

Abstract We analysed the COI gene of mitochondrial DNA extracted from larvae of Rabdophaga (Diptera: Cecidomyiidae) that induce rosette galls on Salix in the Holarctic Region. Genetic data show that they belong to species groups of Rabdophaga rosaria and Rabdophaga strobiloides. A maximum likelihood tree indicates that R. rosaria and R. strobiloides populations are divided into clades 1 and 2, respectively. Clade 1 is divided into subclades 1 and 2, and the latter is further divided into subclades 2A and 2B. Subclade 1 consists of populations on several Salix species of section Cinerella in subgenus Vetrix in Georgia and the UK. Subclade 2A contains populations on Salix alba (section Salix, subgenus Salix) in The Netherlands and the UK. Subclade 2B consists of populations on section Helix in Poland, Phylicifoliae in Alaska and Salix species in the Eastern Palaearctic Region. The genetic differences between populations of subclades 1, 2A and 2B range from 1.06 to 3.46%. We propose a possible diversification scenario of R. rosaria into sibling species through the expansion of host plant ranges. Clade 2 consists of R. strobiloides populations on two Alaskan Salix species of the sections Hastatae and Sitchenses in subgenus Vetrix.

scholarly journals A BARCODE-BASED PHYLOGENETIC SCAFFOLD FOR XYSTICUS AND ITS RELATIVES (ARANEAE: THOMISIDAE: CORIARACHNINI)

2019 ◽  
Vol 20 ◽  
pp. 198-206 ◽  
Author(s):  
Rainer Breitling
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Barcoding ◽  
Phylogenetic Relationships ◽  
Genetic Data ◽  
Target Area ◽  
Starting Point ◽  
Main Target ◽  
Holarctic Region ◽  
Species Groups ◽  
Crab Spider

The phylogenetic relationships and taxonomy of the crab spider genus Xysticus and its closest relatives (i.e., the tribe Coriarachnini, also including, e.g., Ozyptila, Coriarachne and Bassaniana) have long been controversial, with several alternative classifications being proposed, none of which has gained universal acceptance. As Coriarachnini is largely confined to the Holarctic region, the main target area of recent DNA barcoding projects for spiders, a large amount of genetic data for the group is now publicly available. The results of a phylogenetic analysis of this sequence dataset are largely congruent with earlier morphology-based results regarding the evolutionary structure of the group. In particular, they highlight the fact that Xysticus s. lat. is a paraphyletic assembly and that several species groups need to be placed in separate genera to achieve monophyly of Xysticus s. str. Similarly, Coriarachne and Bassaniana appear as independent clades rather than a joined monophyletic Coriarachne s. lat. In contrast, further subdivision of Ozyptila is not supported by the genetic data. Importantly, the analysis also shows that anapophysate members of Xysticus s. lat. form two widely separated groups: a primarily anapophysate division, also including Coriarachne and Bassaniana, at the base of Xysticus s. lat., and a secondarily anapophysate clade deeply nested within Xysticus s. str. This might explain some of the earlier difficulties when trying to define generally accepted subgroups within Xysticus s. lat. The phylogenetic scaffold based on barcode sequences is sufficiently dense and well resolved to attempt the tentative and provisional placement of the majority of species in Xysticus s. lat. in the independent genera Xysticus s. str., Bassaniodes, Psammitis and Spiracme as a starting point for a future more formal revision of the group.

Morphology and molecular analysis ofOncicola venezuelensis(Acanthocephala: Oligacanthorhynchidae) from the ocelotLeopardus pardalisin Brazil

2016 ◽  
Vol 91 (5) ◽  
pp. 605-612 ◽  
Author(s):  
E.G.N. Santos ◽  
M. Chame ◽  
V.A. Chagas-Moutinho ◽  
C.P. Santos
Keyword(s):  
Maximum Likelihood ◽  
Genetic Analysis ◽  
National Park ◽  
Genetic Data ◽  
Genetic Profile ◽  
28S Rrna ◽  
Leopardus Pardalis ◽  
Ultrastructural Studies ◽  
Maximum Likelihood Tree ◽  
Geographical Locality

AbstractOncicola venezuelensisMarteau, 1977 was found parasitizing adults ofLeopardus pardalis(Linnaeus) found dead in Serra da Capivara National Park, Piauí state, Brazil, a new geographical locality reported for the species. The diversity ofOncicolaTravassos, 1916 species is large, but genetic data are scarce. This article presents the results of genetic, morphological and ultrastructural studies carried out for taxonomic purposes. The first ultrastructural view showed a globular, short proboscis with 36 hooks, divided into six longitudinal rows of six hooks each. Hooks differ in size and shape: hooks I, II and III have a ‘chisel-shaped’ tip. The genetic profile included new sequences of ribosomal DNA ITS1, 5.8S and ITS2, and partial 28S rRNA regions. The results of maximum-likelihood tree analyses for each region showed Oligacanthorhynchidae Southwell et Macfie, 1925 close to Gigantorhynchidae Hamann, 1892 (supported >91%). Both use mammals and birds as definitive hosts. Morphological and ultrastructural studies combined with genetic analysis shed more light on the diversity ofOncicolaspecies.

Placing the Fijian Honeyeaters within the meliphagid radiation: implications for origins and conservation

2016 ◽  
Vol 22 (3) ◽  
pp. 262 ◽  
Author(s):  
Mere Yabaki ◽  
Richard C. Winkworth ◽  
Patricia A. McLenachan ◽  
William Aalbersberg ◽  
Linton Winder ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Decision Making Process ◽  
Network Analyses ◽  
Ubiquinone Oxidoreductase ◽  
Phylogenetic Studies ◽  
Maximum Likelihood Tree ◽  
Nadh Ubiquinone Oxidoreductase ◽  
Species Groups ◽  
Tree Building

Understanding the evolutionary relationships of threatened species provides an important framework for making decisions about their conservation. However, unrecognised problems with the underlying phylogenetic analyses may bias the decision-making process. Recent phylogenetic studies have improved our understanding of Meliphagidae, but also indicate discordance between molecular datasets. Here, we examine the causes of this discordance using maximum likelihood tree-building and network analyses of identically sampled datasets for four genetic loci. Our results suggest that while we can be reasonably confident of relationships within species groups, discordance within and between molecular datasets tends to obscure relationships towards the base of the meliphagid tree. This ongoing uncertainty likely reflects differences in the sampling of markers and taxa between previously published analyses. To avoid the problems of conflicting data we used divergence time analyses of only the most densely sampled marker, NADH-ubiquinone oxidoreductase chain 2, to investigate the age and origins of the Fijian Meliphagidae. Our analyses suggest two temporally distinct colonisations of the Fijian archipelago. The large-bodied honeyeaters arrived ~15.6 million years ago, subsequently diversifying and spreading to Tonga and Samoa. In contrast, Myzomela appears to have arrived within the last 5.0 million years. The phylogenetic results therefore imply that conserving the evolutionary diversity of Meliphagidae in Polynesia requires that effort be spread across both the currently recognised taxa and geographical range.

Integrating DNA barcodes and morphology for species delimitation in theCorynoneuragroup (Diptera: Chironomidae: Orthocladiinae)

2013 ◽  
Vol 104 (1) ◽  
pp. 65-78 ◽  
Author(s):  
F.L. Silva ◽  
S. Wiedenbrug
Keyword(s):  
Dna Markers ◽  
Species Delimitation ◽  
Pupal Stage ◽  
Coi Gene ◽  
Morphological Divergence ◽  
Dna Barcodes ◽  
Morphological Criteria ◽  
Species Groups ◽  
Excellent Tool ◽  
Eleven Species

AbstractIn this study, we use DNA barcodes for species delimitation to solve taxonomic conflicts in 86 specimens of 14 species belonging to theCorynoneuragroup (Diptera: Chironomidae: Orthocladiinae), from the Atlantic Forest, Brazil. Molecular analysis of cytochrome c-oxidase subunit I (COI) gene sequences supported 14 cohesive species groups, of which two similar groups were subsequently associated with morphological variation at the pupal stage. Eleven species previously described based on morphological criteria were linked to DNA markers. Furthermore, there is the possibility that there may be cryptic species within theCorynoneuragroup, since one group of species presented internal grouping, although no morphological divergence was observed. Our results support DNA-barcoding as an excellent tool for species delimitation in groups where taxonomy by means of morphology is difficult or even impossible.

Molecular characterization of Urocleidoides cuiabai and U. malabaricusi (Monogenea: Dactylogyridae) from the trahira fish Hoplias aff. malabaricus in the Paraná River, Brazil

2015 ◽  
Vol 90 (6) ◽  
pp. 693-697 ◽  
Author(s):  
L.S. Gasques ◽  
R.J. Graça ◽  
S.M.A.P. Prioli ◽  
R.M. Takemoto ◽  
A.J. Prioli
Keyword(s):  
Cryptic Species ◽  
Molecular Characterization ◽  
Dna Sequences ◽  
Mitochondrial Gene ◽  
Genetic Data ◽  
Flood Plain ◽  
Fish Parasites ◽  
Coi Gene ◽  
Coi Sequences

AbstractUrocleidoides ectoparasites are mainly found on fish of the neotropical regions. Although molecular research on monogeneans is available, no genetic data exist characterizing species in the Urocleidoides genus. Some DNA sequences have been efficacious in systematic studies and in the reconstruction of phylogenies of fish parasites. Relevant roles have been given to the sequence of the mitochondrial gene of cytochrome c oxidase I (COI). This study characterized COI sequences of the parasites Urocleidoides malabaricusi and U. cuiabai in trahira fish Hoplias aff. malabaricus of the flood plain of the Upper River Paraná, Brazil. The two species under analysis were distinguished by sequencing and analysing a 420-bp fragment of the COI gene, which suggested the existence of the cryptic species U. malabaricusi.

scholarly journals Associations between COVID-19 Risk Perceptions and Mental Health, Wellbeing, and Risk Behaviours

2021 ◽  
Author(s):  
Maddy Dyer ◽  
Hannah Sallis ◽  
Jasmine Natalie Khouja ◽  
Sarah Dryhurst ◽  
Marcus Robert Munafo
Keyword(s):  
Mental Health ◽  
Substance Use ◽  
Risk Perceptions ◽  
Genetic Data ◽  
Polygenic Risk Score ◽  
Risk Behaviours ◽  
Cross Sectional ◽  
Causal Pathways ◽  
Parents And Children ◽  
The Uk

Background: Mental health has worsened, and substance use has increased for some individuals during the coronavirus (COVID-19) pandemic. Cross-sectional studies suggest that COVID-19 risk perceptions are related to mental health and risk behaviours (potentially including substance use). However, longitudinal and genetic data are needed to support stronger inferences regarding whether these associations reflect causal pathways. Methods: Using cross-sectional, longitudinal, and polygenic risk score (PRS) data from the UK Avon Longitudinal Study of Parents and Children (ALSPAC), we examined cross-sectional and prospective associations between COVID-19 risk perceptions and mental health, wellbeing, and risk behaviours. Participants (85% female) were aged between 27-72 years. We used pandemic (April-July 2020) and pre-pandemic (2003-2017) data (ns = 233-5,115). Results: COVID-19 risk perceptions were positively associated with anxiety (OR 2.78, 95% confidence interval [CI] 2.20 to 3.52), depression (OR 1.65, 95% CI 1.24 to 2.18), low wellbeing (OR 1.76, 95% CI 1.45 to 2.13), increased alcohol use (OR 1.46, 95% CI 1.24 to 1.72), and COVID-19 prevention behaviours (ps < .05). Pre-pandemic anxiety (OR 1.64, 95% CI 1.29 to 2.09) and low wellbeing (OR 1.41, 95% CI 1.15 to 1.74) were positively associated with COVID-19 risk perceptions. The depression (b 0.21, 95% CI 0.02 to 0.40) and wellbeing (b -0.29, 95% CI -0.48 to -0.09) PRS were associated with higher and lower COVID-19 risk perceptions, respectively. Conclusions: Poorer mental health and wellbeing are associated with higher COVID-19 risk perceptions, and longitudinal and genetic data suggest that they may play a casual role in COVID-19 risk perceptions.

scholarly journals Abyssal fauna of polymetallic nodule exploration areas, eastern Clarion-Clipperton Zone, central Pacific Ocean: Annelida: Capitellidae, Opheliidae, Scalibregmatidae, and Travisiidae

ZooKeys ◽  
2019 ◽  
Vol 883 ◽  
pp. 1-82 ◽  
Author(s):  
Helena Wiklund ◽  
Lenka Neal ◽  
Adrian G. Glover ◽  
Regan Drennan ◽  
Muriel Rabone ◽  
...  
Keyword(s):  
New Species ◽  
Pacific Ocean ◽  
Phylogenetic Analyses ◽  
Genetic Data ◽  
Ocean Basin ◽  
Central Pacific ◽  
Dna Taxonomy ◽  
Central Pacific Ocean ◽  
Polymetallic Nodule ◽  
The Uk

We present DNA taxonomy of abyssal polychaete worms from the eastern Clarion-Clipperton Zone (CCZ), central Pacific Ocean, using material collected as part of the Abyssal Baseline (ABYSSLINE) environmental survey cruises ‘AB01’ and ‘AB02’ to the UK Seabed Resources Ltd (UKSRL) polymetallic nodule exploration contract area ‘UK-1’, the Ocean Mineral Singapore exploration contract area ‘OMS-1’ and an Area of Particular Environmental Interest, ‘APEI-6’. This is the fourth paper in a series to provide regional taxonomic data with previous papers reporting on Cnidaria, Echinodermata and Mollusca. Taxonomic data are presented for 23 species from 85 records within four polychaete families: Capitellidae, Opheliidae, Scalibregmatidae and Travisiidae, identified by a combination of morphological and genetic data, including molecular phylogenetic analyses. Two taxa (genetically separated from one another) morphologically matched the same known cosmopolitan species,Ophelina abranchiatathat has a type locality in a different ocean basin and depth from where no genetic data was available. These two species were assigned the open nomenclature ‘cf.’ as a precautionary approach in taxon assignments to avoid over-estimating species ranges. Twelve (12) taxa are here described as new species,Ammotrypanella keenanisp. nov.,Ammotrypanella kerstenisp. nov.,Ophelina curlisp. nov.,Ophelina ganaesp. nov.,Ophelina juhazisp. nov.,Ophelina martinezarbizuisp. nov.,Ophelina meyeraesp. nov.,Ophelina nunnallyisp. nov.,Oligobregma brasieraesp. nov.,Oligobregma tanisp. nov.,Oligobregma whaleyisp. nov.andTravisia ziegleraesp. nov.For the remaining nine taxa, we have determined them to be potentially new species, for which we make the raw data, imagery and vouchers available for future taxonomic study. The CCZ is a region undergoing intense exploration for potential deep-sea mineral extraction from polymetallic nodules. We present these data to facilitate future taxonomic and environmental impact study by making both data and voucher materials available through curated and accessible biological collections.

scholarly journals Molecular Taxonomy and Phylogenetic Analysis of Dove and Pigeon Species (Aves: Columbidae) of Pakistan, Based on COI Region of Mitochondrial DNA

2020 ◽  
Vol 7 (3) ◽  
pp. 35-44
Author(s):  
Fakhar -i-Abbas ◽  
Fakhar -i-Abbas ◽  
Fakhra Nazir ◽  
Fida Muhammad Khan
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Trees ◽  
Molecular Taxonomy ◽  
Columba Livia ◽  
Taxonomic Diversity ◽  
Coi Gene ◽  
Maximum Parsimony Tree ◽  
Maximum Likelihood Tree ◽  
Wide Range ◽  
Parsimony Tree

Doves and Pigeons are the members of living family Columbidae (Order: Columbiformes) having a wide range of taxonomic diversity and geographic distribution. Seven species with one sample each of family Columbidae were collected via random sampling from different districts of Pakistan to carry out this study. The targeted gene region was sequenced and identified by using BLAST tool at National Center for Biotechnology Information (NCBI). CLUSTALW was used for sequence alignment and MEGA6 for reconstruction of phylogenetic trees to predict the effective ancestry of different Columbidae species. The following phylogenetic trees were obtained i.e. Maximum Likelihood tree, Neighborhood joining tree, Maximum parsimony tree and UPGMA tree. In the current study, COI gene barcoding and phylogenetic analysis of family Columbidae gave results of multiple alignment which showed that Columba livia livia and Columba eversmanni, closely resembled as well as Spilopelia senegalensis and Streptopelia decaocta. While Streptopelia tranquebarica and Spilopelia chinensis have great affinity due to small clade difference and Treron phoenicoptera was distinctly related to other species due to large clade difference.

scholarly journals Ancestry inference and grouping from principal component analysis of genetic data

2020 ◽  
Author(s):  
Florian Privé
Keyword(s):  
Principal Component Analysis ◽  
Principal Component ◽  
Genetic Data ◽  
Component Analysis ◽  
Easy Access ◽  
1000 Genomes Project ◽  
1000 Genomes ◽  
Euclidean Distances ◽  
Ancestry Inference ◽  
The Uk

AbstractHere we propose a simple, robust and effective method for global ancestry inference and grouping from Principal Component Analysis (PCA) of genetic data. The proposed approach is particularly useful for methods that need to be applied in homogeneous samples. First, we show that Euclidean distances in the PCA space are proportional to FST between populations. Then, we show how to use this PCA-based distance to infer ancestry in the UK Biobank and the POPRES datasets. We propose two solutions, either relying on projection of PCs to reference populations such as from the 1000 Genomes Project, or by directly using the internal data. Finally, we conclude that our method and the community would benefit from having an easy access to a reference dataset with an even better coverage of the worldwide genetic diversity than the 1000 Genomes Project.

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