scholarly journals Molecular divergence between Gryllus rubens and Gryllus texensis, sister species of field crickets (Orthoptera: Gryllidae)

2006 ◽  
Vol 138 (3) ◽  
pp. 305-313 ◽  
Author(s):  
D.A. Gray ◽  
P. Barnfield ◽  
M. Seifried ◽  
M.H. Richards
Keyword(s):  
Genetic Variation ◽  
Phylogenetic Trees ◽  
Gene Tree ◽  
Sequence Divergence ◽  
Sister Species ◽  
Interspecific Gene Flow ◽  
Gryllus Texensis ◽  
Field Crickets ◽  
Ancestral Lineage ◽  
Gryllus Rubens

AbstractWe assess the degree of sequence divergence in the maternally inherited mitochondrial cytochrome c oxidase I (COI) and cytochrome b (CytB) genes between two sister species of field crickets, Gryllus rubens Scudder, 1902 and Gryllus texensis Cade and Otte, 2000. We analyzed 1460 base pairs from 10 individuals of each species; individuals were sampled from areas of both allopatry and sympatry. Overall average pairwise mitochondrial sequence divergence between species was 1.4% ± 0.1% (mean ± SD); however, there was almost an order of magnitude more divergence in COI (2.59% ± 2.25%) than in CytB (0.35% ± 0.24%). Gryllus texensis appears to harbor a much greater level of genetic variation than does G. rubens. Phylogenetic trees constructed from these sequences show reasonable separation of species; however, sequences are not reciprocally monophyletic. Gene tree polyphyly may reflect recent species-level divergence and (or) interspecific gene flow. The pattern of sequence divergence and genetic variation in these taxa is consistent with allopatric or peripatric speciation in Pleistocene glacial refugia in the southeastern (G. rubens ancestral lineage) and southcentral United States (G. texensis ancestral lineage).

Combining Nuclear and Mitochondrial Loci Provides Phylogenetic Information in the Philopterus Complex of Lice (Psocodea: Ischnocera: Philopteridae)

2020 ◽  
Author(s):  
Tomas Najer ◽  
Ivo Papousek ◽  
Oldrich Sychra ◽  
Andrew D Sweet ◽  
Kevin P Johnson
Keyword(s):  
Genetic Variation ◽  
Phylogenetic Trees ◽  
Sequence Divergence ◽  
Nuclear Genes ◽  
Morphological Data ◽  
Coi Gene ◽  
Phylogenetic Information ◽  
Mitochondrial Coi ◽  
Putative Species ◽  
Mitochondrial Loci

Abstract The Philopterus Complex includes several lineages of lice that occur on birds. The complex includes the genera Philopterus (Nitzsch, 1818; Psocodea: Philopteridae), Philopteroides (Mey, 2004; Psocodea: Philopteridae), and many other lineages that have sometimes been regarded as separate genera. Only a few studies have investigated the phylogeny of this complex, all of which are based on morphological data. Here we evaluate the utility of nuclear and mitochondrial loci for recovering the phylogeny within this group. We obtained phylogenetic trees from 39 samples of the Philopterus Complex (Psocodea: Philopteridae), using sequences of two nuclear (hyp and TMEDE6) and one mitochondrial (COI) marker. We evaluated trees derived from these genes individually as well as from concatenated sequences. All trees show 20 clearly demarcated taxa (i.e., putative species) divided into five well-supported clades. Percent sequence divergence between putative species (~5–30%) for the COI gene tended to be much higher than those for the nuclear genes (~1–15%), as expected. In cases where species are described, the lineages identified based on molecular divergence correspond to morphologically defined species. In some cases, species that are host generalists exhibit additional underlying genetic variation and such cases need to be explored by further future taxonomic revisions of the Philopterus Complex.

scholarly journals Extensive Phylogenetic Analysis of Piscine Orthoreovirus Genomic Sequences Shows the Robustness of Subgenotype Classification

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 41
Author(s):  
Marcos Godoy ◽  
Daniel A. Medina ◽  
Rudy Suarez ◽  
Sandro Valenzuela ◽  
Jaime Romero ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Sequence Analysis ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Genomic Segment ◽  
Double Stranded Rna ◽  
The Family ◽  
Original Classification

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which differentiates PRV into two major genotypes, I and II, and each of these into two subgenotypes, designated as Ia and Ib, and IIa and IIb, respectively. Moreover, some clusters of country- and host-specific PRV subgenotypes were observed in the subset of sequences used. This work strengthens the subgenotype classification of PRV based on the S1 segment and can be used to enhance research on the virulence of PRV.

scholarly journals Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4499 ◽  
Author(s):  
Aisha Tahir ◽  
Fatma Hussain ◽  
Nisar Ahmed ◽  
Abdolbaset Ghorbani ◽  
Amer Jamil
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Sequence Divergence ◽  
Species Level ◽  
Practical Implementation ◽  
Medicinal Species ◽  
Level Identification ◽  
Geographically Isolated

In pursuit of developing fast and accurate species-level molecular identification methods, we tested six DNA barcodes, namely ITS2, matK, rbcLa, ITS2+matK, ITS2+rbcLa, matK+rbcLa and ITS2+matK+rbcLa, for their capacity to identify frequently consumed but geographically isolated medicinal species of Fabaceae and Poaceae indigenous to the desert of Cholistan. Data were analysed by BLASTn sequence similarity, pairwise sequence divergence in TAXONDNA, and phylogenetic (neighbour-joining and maximum-likelihood trees) methods. Comparison of six barcode regions showed that ITS2 has the highest number of variable sites (209/360) for tested Fabaceae and (106/365) Poaceae species, the highest species-level identification (40%) in BLASTn procedure, distinct DNA barcoding gap, 100% correct species identification in BM and BCM functions of TAXONDNA, and clear cladding pattern with high nodal support in phylogenetic trees in both families. ITS2+matK+rbcLa followed ITS2 in its species-level identification capacity. The study was concluded with advocating the DNA barcoding as an effective tool for species identification and ITS2 as the best barcode region in identifying medicinal species of Fabaceae and Poaceae. Current research has practical implementation potential in the fields of pharmaco-vigilance, trade of medicinal plants and biodiversity conservation.

scholarly journals SHOOT: phylogenetic gene search and ortholog inference

2021 ◽  
Author(s):  
David Emms ◽  
Steven Kelly
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Phylogenetic Trees ◽  
Query Sequence ◽  
Gene Tree ◽  
Biological Research ◽  
Gene Sequences ◽  
Multiple Sequence ◽  
Gene Search

Determining the evolutionary relationships between gene sequences is fundamental to comparative biological research. However, conducting such analyses requires a high degree of technical proficiency in several computational tools including gene family construction, multiple sequence alignment, and phylogenetic inference. Here we present SHOOT, an easy to use phylogenetic search engine for fast and accurate phylogenetic analysis of biological sequences. SHOOT searches a user-provided query sequence against a database of phylogenetic trees of gene sequences (gene trees) and returns a gene tree with the given query sequence correctly grafted within it. We show that SHOOT can perform this search and placement with comparable speed to a conventional BLAST search. We demonstrate that SHOOT phylogenetic placements are as accurate as conventional multiple sequence alignment and maximum likelihood tree inference approaches. We further show that SHOOT can be used to identify orthologs with equivalent accuracy to conventional orthology inference methods. In summary, SHOOT is an accurate and fast tool for complete phylogenetic analysis of novel query sequences. An easy to use webserver is available online at www.shoot.bio.

scholarly journals A new cryptic arboreal species of the Cyrtodactylus brevipalmatus group (Squamata: Gekkonidae) from the uplands of western Thailand

2021 ◽  
Vol 71 ◽  
pp. 723-746
Author(s):  
L. Lee Grismer ◽  
Chatmongkon Suwannapoom ◽  
Parinya Pawangkhanant ◽  
Roman A. Nazarov ◽  
Platon V. Yushchenko ◽  
...  
Keyword(s):  
New Species ◽  
Mitochondrial Gene ◽  
Sequence Divergence ◽  
Field Work ◽  
Morphological Characters ◽  
Sister Species ◽  
Base Pairs ◽  
Meristic Characters ◽  
Nadh Dehydrogenase Subunit 2 ◽  
A New Species

The first integrative taxonomic analysis of the Cyrtodactylus brevipalmatus group of Southeast Asia recovered two newly discovered populations from the Tenasserim Mountains in Suan Phueng District, Ratchaburi Province, Thailand as a new species described here as C. rukhadeva sp. nov. Based on 1397 base pairs of the mitochondrial gene NADH dehydrogenase subunit 2 (ND2), C. rukhadeva sp. nov. is the well-supported sister species to a clade containing three undescribed species, C. ngati, and C. cf. interdigitalis with a large uncorrected pairwise sequence divergence from other species in the brevipalmatus group ranging from 15.4–22.1%. Cyrtodactylus elok and C. brevipalmatus are recovered as poorly supported sister species and the well-supported sister lineage to the remainder of the brevipalmatus group. Cyrtodactylus rukhadeva sp. nov. is putatively diagnosable on the basis of a number of meristic characters and easily separated from the remaining species of the brevipalmatus group by a number of discrete morphological characters as well as its statistically significant wide separation in multivariate morphospace. The discovery of C. rukhadeva sp. nov. continues to underscore the unrealized herpetological diversity in the upland forests of the Tenasserim Mountains and that additional field work will undoubtedly result in the discovery of additional new species.

scholarly journals Is there low maternal genetic variation in West Asian populations of leopard?

2020 ◽  
Vol 65 (4) ◽  
pp. 701-708
Author(s):  
Mohammad S. Farhadinia ◽  
Mohammad Reza Ashrafzadeh ◽  
Helen Senn ◽  
Sohrab Ashrafi ◽  
Hamid Farahmand ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Phylogenetic Trees ◽  
Nadh Dehydrogenase ◽  
Spatial Genetic Structure ◽  
Population Connectivity ◽  
The Caucasus ◽  
Cold Environments ◽  
Asian Populations ◽  
Low Diversity ◽  
Amova Analysis

Abstract Persian leopards Panthera pardus saxicolor have been extirpated from over 84% of their historic range and are now limited to rugged landscapes of West Asia and the Caucasus. Understanding and maintaining genetic diversity and population connectivity is important for preventing inbreeding and genetic drift, both of which can threaten population viability. All previous analyses of intraspecific genetic variation of West Asian leopards based on the NADH dehydrogenase subunit 5 gene have reported low mitogenomic diversity. In the current study, we sequenced 959 bp of the mtDNA cytochrome b gene to describe the spatial genetic structure of 22 wild Persian leopards across Iran, which hosts most of the subspecies extant range. The findings based on phylogenetic trees and median-joining network indicated that leopards from Iran formed a distinct subclade, i.e., P. p. saxicolor. The AMOVA analysis showed significant differentiation (88.55%) between the subclades of Persian leopards and other Asian leopards. The lowest levels of haplotype (0.247) and nucleotide (0.00078) diversity were estimated in Persian leopards from Iran. Mitochondrial genome sequencing revealed only two closely related haplotypes. There was no evidence for recent sudden demographic expansion scenario in Persian leopards. The low diversity in cytochrome b gene could potentially be brought about by selective pressure on mitochondria to adapt to oxidative stress and higher metabolic rates in cold environments.

scholarly journals Genetic Variability and Taxonomic Status of the Nihoa and Laysan Millerbirds

The Condor ◽  
2007 ◽  
Vol 109 (4) ◽  
pp. 954-962
Author(s):  
Robert C. Fleischer ◽  
Beth Slikas ◽  
Jon Beadell ◽  
Colm Atkins ◽  
Carl E. McINTOSH ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Microsatellite Loci ◽  
Sequence Divergence ◽  
Taxonomic Status ◽  
Small Population ◽  
Base Pairs ◽  
Stochastic Effects ◽  
Mtdna Sequence ◽  
Species Pairs ◽  
Two Populations

Abstract The Millerbird (Acrocephalus familiaris) is an endemic Northwestern Hawaiian Islands reed warbler that existed until about 1923 on Laysan Island (A. f. familiaris) and currently occurs in a small population on Nihoa Island (A. f. kingi). The two populations are described as separate subspecies or species on the basis of size and plumage differences. We assessed genetic variation in blood samples from 15 individuals in the modern Nihoa population using approximately 3000 base pairs (bp) of mitochondrial DNA (mtDNA) sequence and 14 microsatellite loci. We also obtained up to 1028 bp of mtDNA sequence from the fragmented DNA of museum specimens of three birds collected on Nihoa in 1923 and five birds collected on Laysan in 1902 and 1911 (ancient samples). Genetic variation in both marker types was extremely low in the modern Nihoa population (nucleotide diversity [π]  =  0.00005 for mtDNA sequences; observed heterozygosity was 7.2% for the microsatellite loci). In contrast, we found three mtDNA haplotypes among the five Laysan individuals (π  =  0.0023), indicating substantially greater genetic variation. The Nihoa and Laysan taxa differed by 1.7% uncorrected mtDNA sequence divergence, a magnitude that would support designation at the subspecies, and perhaps species, level relative to other closely related Acrocephalus species pairs. However, in light of strong ecological similarity between the two taxa, and a need to have additional populations to prevent extinction from stochastic effects and catastrophes, we believe these genetic differences should not deter a potential translocation of individuals from Nihoa to Laysan.

Protosticta joepani sp. nov. from Borneo with notes on P. kinabaluensis Laidlaw, 1915 (Odonata: Zygoptera: Platystictidae)

Zootaxa ◽  
2020 ◽  
Vol 4729 (3) ◽  
pp. 371-387
Author(s):  
RORY A. DOW ◽  
QUOC TOAN PHAN ◽  
CHEE YEN CHOONG
Keyword(s):  
Gene Tree ◽  
Sensu Stricto ◽  
Sister Species ◽  
Coi Gene ◽  
Holotype Male ◽  
Malaysian Borneo

Protosticta joepani sp. nov. is described from Malaysian Borneo (holotype male Bario, Kelabit Highlands, Miri Division, Sarawak, Malaysia, deposited in the Naturalis Biodiversity Center, Leiden). It is the sister species of P. kinabaluensis Laidlaw, 1915; some descriptive notes and a set of illustrations are provided of the latter species. A COI gene tree for both species is provided. The placement of both P. joepani and P. kinabaluensis is discussed, but although it is very unlikely that they belong in Protosticta sensu stricto, the issue is left open here. 

scholarly journals Streptacidiphilus oryzae sp. nov., an actinomycete isolated from rice-field soil in Thailand

2006 ◽  
Vol 56 (6) ◽  
pp. 1257-1261 ◽  
Author(s):  
Liming Wang ◽  
Ying Huang ◽  
Zhiheng Liu ◽  
Michael Goodfellow ◽  
Carlos Rodríguez
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Rice Field ◽  
Gene Tree ◽  
Morphological Properties ◽  
Rrna Gene ◽  
New Taxon ◽  
Field Soil ◽  
Rice Field Soil

The taxonomic position of ten acidophilic actinomycetes isolated from an acidic rice-field soil was established using a polyphasic approach. 16S rRNA gene sequences determined for the isolates were aligned with corresponding sequences of representatives of the genera Kitasatospora, Streptacidiphilus and Streptomyces and phylogenetic trees were inferred using four tree-making algorithms. The isolates had identical sequences and formed a distinct branch at the periphery of the Streptacidiphilus 16S rRNA gene tree. The chemotaxonomic and morphological properties of representative isolates were consistent with their assignment to the genus Streptacidiphilus. The isolates shared nearly identical phenotypic profiles that readily distinguished them from representatives of the established species of Streptacidiphilus. It is evident from the genotypic and phenotypic data that the isolates form a homogeneous group that corresponds to a novel species in the genus Streptacidiphilus. The name proposed for this new taxon is Streptacidiphilus oryzae sp. nov.; the type strain is strain TH49T (=CGMCC 4.2012T=JCM 13271T).

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