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 Genetic analysis reveals Finnish Formica fennica populations do not form a separate genetic entity from F. exsecta

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6013 ◽  
Author(s):  
Sanja Maria Hakala ◽  
Perttu Seppä ◽  
Maria Heikkilä ◽  
Pekka Punttila ◽  
Jouni Sorvari ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Morphological Characters ◽  
Coi Gene ◽  
Species Status ◽  
Separate Species ◽  
Mitochondrial Coi ◽  
Recent Addition ◽  
Morphological Differences ◽  
Dna Microsatellite ◽  
Dna Microsatellite Markers

Coptoformica Müller, 1923 is a subgenus of Formica Linnaeus, 1758 that consists of c. a dozen species of ants that typically inhabit open grassy habitats and build small nest mounds. The most recent addition to the group is Formica fennica Seifert, 2000. The description was based on morphological characters, but the species status has not been confirmed by molecular methods. In this study, we use thirteen DNA microsatellite markers and a partial mitochondrial COI gene sequence to assess the species status of F. fennica, by comparing the genetic variation among samples identified as F. fennica and six other boreal Formica (Coptoformica) species. Most of the species studied form separate, discontinuous clusters in phylogenetic and spatial analyses with only little intraspecific genetic variation. However, both nuclear and mitochondrial markers fail to separate the species pair F. exsecta Nylander, 1846 and F. fennica despite established morphological differences. The genetic variation within the F. exsecta/fennica group is extensive, but reflects spatial rather than morphological differences. Finnish F. fennica populations studied so far should not be considered a separate species, but merely a morph of F. exsecta.

Pycnoclavella stolonialis n. sp. (Tunicata: Ascidiacea), with phylogenetic and distributional remarks on the genus in Europe

Zootaxa ◽  
2010 ◽  
Vol 2407 (1) ◽  
pp. 51 ◽  
Author(s):  
R. PÉREZ-PORTELA ◽  
C. E. GOODWIN ◽  
B. E. PICTON ◽  
X. TURON
Keyword(s):  
New Species ◽  
Phylogenetic Trees ◽  
Sequence Divergence ◽  
Molecular Data ◽  
Coi Gene ◽  
Irish Sea ◽  
Colony Structure ◽  
Colonial Ascidian ◽  
Sea Squirt ◽  
The Irish Sea

Morphological and molecular data based on the COI gene were used to describe a new species of the colonial ascidian genus Pycnoclavella. The new species, P. stolonialis, is widespread sublittorally in the Irish Sea and also occurs on the western Irish coast, Wales and eastern England and may be locally common. It has been commonly known as the ‘pin head’ sea squirt since first recorded from Northern Ireland in 1984 but has not yet been formally described. P. stolonialis is the only described species of Pycnoclavella combining the presence of stolons, peribranchial incubation mode and a larva lacking an otolith. In addition, it features ca. 10% sequence divergence with the closest species of the genus in our phylogenetic trees. P. stolonialis showed intermediate characters between two groups of Pycnoclavella; the stanleyi and the aurilucens groups. Larval morphology and molecular data supported the inclusion of P. stolonialis within the aurilucens group, but the stolonial colony structure is characteristic of the stanleyi group. This implies that colony structure may not be a good character for separating these two groups. New information on distribution is given for P. atlantica, P. aurilucens and P. communis.

Haplotype diversity in the Antarctic springtail Gressittacantha terranova at fine spatial scales - a Holocene twist to a Pliocene tale

2010 ◽  
Vol 22 (6) ◽  
pp. 766-773 ◽  
Author(s):  
T.C. Hawes ◽  
G. Torricelli ◽  
M.I. Stevens
Keyword(s):  
Spatial Scales ◽  
Haplotype Diversity ◽  
Sequence Divergence ◽  
Reference Population ◽  
Landscape Scale ◽  
Coi Gene ◽  
Phylogeographic Structure ◽  
Mitochondrial Coi ◽  
Terra Nova Bay ◽  
The Antarctic

AbstractThe mitochondrial COI gene of the Antarctic springtail, Gressittacantha terranova, was sequenced across a polar coastal landscape at Terra Nova Bay, northern Victoria Land. Samples from two altitudinal transects in the foothills directly south of Campbell Glacier were compared with samples from Springtail Valley (northern foothills) as an external reference population. We found that mtDNA haplotypes clustered into two lineages (clades) with a mean sequence divergence of 10% (uncorrected distance). However, there was no phylogeographic structure found at this spatial (landscape) scale with haplotypes from both divergent clades found sympatric across most populations. At the landscape scale, the considerable genetic divergence revealed within G. terranova is around five times greater than any other continental Antarctic springtail examined to date. These data indicate a Pliocene divergence event in G. terranova around 4–5 million years ago. The unusual distributional profile of haplotypes - occurrence of multiple haplotypes at single sites and genetic contiguity between sites that are not physically contiguous - suggests a subsequent ‘reshuffling’ of haplotypes in the Holocene that has an ecological basis.

Phylogeography of "glacial relict" Gammaracanthus (Crustacea, Amphipoda) from boreal lakes and the Caspian and White seas

2001 ◽  
Vol 58 (11) ◽  
pp. 2247-2257 ◽  
Author(s):  
Risto Väinölä ◽  
Jouni K Vainio ◽  
Jukka U Palo
Keyword(s):  
Caspian Sea ◽  
Sequence Divergence ◽  
Boreal Lakes ◽  
Coi Gene ◽  
Phylogeographic Structure ◽  
Morphological Evidence ◽  
The Caspian Sea ◽  
Mitochondrial Coi ◽  
Glacial Relict ◽  
Allozyme Loci

As with a number of "glacial relict" crustacean genera, species of Gammaracanthus are vicariously distributed in circumarctic coastal waters, in boreal freshwater lakes, and in the Caspian Sea. Various hypotheses have been invoked to explain the origins and diversity of the non-marine taxa. Data on 28 allozyme loci and 558 bp of the mitochondrial COI gene demonstrate a close affinity between G. caspius of the Caspian Sea and G. aestuariorum of the White Sea area (Nei's allozyme distance D = 0.09, COI sequence divergence d = 5%), and a threefold divergence of the two from the Fennoscandian freshwater G. lacustris (D = 0.33, d = 12%). The relative molecular affinities agree with morphological evidence but contradict the idea of a common ancestry of the non-marine taxa, rather they suggest two independent invasions of continental waters. The generally low molecular divergence refutes the recently suggested generic splitting of Gammaracanthus. Previous speculations of an affinity of Gammaracanthus to the Baikalian acanthogammarids or to the Eusiroidea are not substantiated. The interspecific phylogeographic structure of Gammaracanthus is not concordant with that of other "glacial relict" crustacean genera. Phylogeographically, Gammaracanthus seems to match with the genus Monoporeia alone, rather than with Pontoporeia sensu lato.

scholarly journals Genetic and morphological analyses indicate that the Australian endemic scorpion Urodacus yaschenkoi (Scorpiones: Urodacidae) is a species complex

2016 ◽  
Author(s):  
Karen Luna-Ramirez ◽  
Adam D Miller ◽  
Gordana Rašić
Keyword(s):  
Species Complex ◽  
Evolutionary History ◽  
Morphological Data ◽  
Arid Zones ◽  
Evolutionary Potential ◽  
Linear Discriminant ◽  
Putative Species ◽  
History Of ◽  
Nuclear Locus ◽  
Mitochondrial Loci

Background. Australian scorpions have received far less attention from researchers than their overseas counterparts. Here we provide the first insight into the molecular variation and evolutionary history of the endemic Australian scorpion Urodacus yaschenkoi. Also known as the inland robust scorpion, it is widely distributed throughout arid zones of the continent and is emerging as a model organism in biomedical research due to the chemical nature of its venom. Methods. We employed Bayesian Inference (BI) methods for the phylogenetic reconstructions and divergence dating among lineages, using unique haplotype sequences from two mitochondrial loci (COXI, 16S) and one nuclear locus (28S). We also implemented two DNA taxonomy approaches (GMYC and PTP/dPTP) to evaluate the presence of cryptic species. Linear Discriminant Analysis was used to test whether the linear combination of 21 variables (ratios of morphological measurements) can predict individual’s membership to a putative species. Results. Genetic and morphological data suggest that U. yaschenkoi is a species complex. High statistical support for the monophyly of several divergent lineages was found both at the mitochondrial loci and at a nuclear locus. The extent of mitochondrial divergence between these lineages exceeds estimates of interspecific divergence reported for other scorpion groups. The GMYC model and the PTP/bPTP approach identified major lineages and several sub-lineages as putative species. Ratios of several traits that approximate body shape had a strong predictive power (83–100%) in discriminating two major molecular lineages. A time-calibrated phylogeny dates the early divergence at the onset of continental-wide aridification in late Miocene and Pliocene, with finer-scale phylogeographic patterns emerging during the Pleistocene. This structuring dynamics is congruent with the diversification history of other fauna of the Australian arid zones. Discussion. Our results indicate that the taxonomic status of U. yaschenkoi requires revision, and we provide recommendations for such future efforts. A complex evolutionary history and extensive diversity highlights the importance of conserving U. yaschenkoi populations from different Australian arid zones in order to preserve patterns of endemism and evolutionary potential.

Genetic variation and population structure of the carpet shell clam Ruditapes decussatus along the Tunisian coast inferred from mtDNA and ITS1 sequence analysis

Biologia ◽  
2010 ◽  
Vol 65 (4) ◽  
Author(s):  
Aicha Gharbi ◽  
Noureddine Chatti ◽  
Khaled Said ◽  
Alain Wormhoudt
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Haplotype Frequency ◽  
Western Mediterranean ◽  
Coi Gene ◽  
Ruditapes Decussatus ◽  
Internal Transcribed Spacer Region ◽  
Its1 Sequence ◽  
Mitochondrial Coi

AbstractSurveys of allozyme polymorphisms in the carpet shell clam Ruditapes decussatus have revealed sharp genetic differentiation of populations. Analysis of population structure in this species has now been extended to include nuclear and mitochondrial genes. A partial sequence of a mitochondrial COI gene and of the internal transcribed spacer region (ITS-1) were used to study haplotype distribution, the pattern of gene flow, and population genetic structure of R. decussatus. The samples were collected from twelve populations from the eastern and western Mediterranean coasts of Tunisia, one from Concarneau and one from Thau. A total of twenty and twenty-one haplotypes were detected in the examined COI and ITS1 regions respectively. The study revealed higher levels of genetic diversity for ITS1 compared to COI. The analysis of haplotype frequency distribution and molecular variation indicated that the majority of the genetic variation was distributed within populations (93% and 86% for COI and ITS1 respectively). No significant differentiation was found among eastern and western groups on either side of the Siculo-Tunisian strait. However, distinct and significant clinal changes in haplotypes frequencies between eastern and western samples were found at the most frequent COI haplotype and at three out of five major ITS1 haplotypes. These results suggest the relative importance of historical processes and contemporary hydrodynamic features on the observed patterns of genetic structure.

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).

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