A complete time-calibrated multi-gene phylogeny of the European butterflies

AbstractWith the aim of supporting ecological analyses in butterflies, the third most species-rich superfamily of Lepidoptera, this paper presents the first time-calibrated phylogeny of all 496 extant butterfly species in Europe, including 18 very localized endemics for which no public DNA sequences had been available previously. It is based on a concatenated alignment of the mitochondrial gene COI and up to 11 nuclear gene fragments, using Bayesian inference of phylogeny. To avoid analytical biases that could result from our region-focus sampling, our European tree was grafted upon a global genuslevel backbone butterfly phylogeny for analyses. In addition to a consensus tree, we provide the posterior distribution of trees and the fully-concatenated alignment for future analyses.

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Molecular phylogeny of Fordini (Hemiptera: Aphididae: Pemphiginae) inferred from nuclear gene EF-1 α and mitochondrial gene COI

Bulletin of Entomological Research ◽

10.1017/s0007485307005020 ◽

2007 ◽

Vol 97 (4) ◽

pp. 379-386 ◽

Cited By ~ 17

Author(s):

H.C. Zhang ◽

G.X. Qiao

Keyword(s):

Phylogenetic Trees ◽

Host Plants ◽

Mitochondrial Gene ◽

Nuclear Gene ◽

Morphological Characters ◽

Primary Host ◽

Gene Coi ◽

The Common ◽

Different Parts ◽

Selection Of

AbstractThe tribe Fordini is a fascinating group because of its complicated life history, primary host specificity and gall-forming characteristic. Different species produce galls with different morphology on different parts of the host plants. The EF-1α-based, COI-based and combined sequences-based phylogenetic trees with three algorithms MP, ML and Bayes all strongly suggest that Fordini is a monophyletic group with two clades corresponding to two subtribes, Fordina and Melaphidina, each also monophyletic. Some important morphological characters and primary host plants of aphids were mapped onto the phylogenetic tree to analyse the division of subtribes and to uncover at which level the aphids correspond to their primary hosts, Pistacia and Rhus. Results suggest that the division of subtribes in Fordini is closely related to host selection of aphids. The evolution of gall morphology and the probable driving force behind it in this tribe were also discussed. The Fordini aphids seem to have evolved towards a better ability to manipulate their host plant, induce strong sinks and gain high reproductive success. Galls in this tribe evolved mainly along two directions to attain this goal: (i) by enlarging the gall from small bag to spherical, even big cauliflower-like, and changing the galls' location or forming two galls in their life cycle (Fordina); (ii) by moving the gall position from midrib, petiole of the leaflet, and eventually to the common petiole of the compound leaf (Melaphidina).

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European bumblebees (Hymenoptera: Bombini)- phylogenetic relationships inferred from DNA sequences

Insect Systematics & Evolution ◽

10.1163/187631202x00208 ◽

2002 ◽

Vol 33 (4) ◽

pp. 361-386 ◽

Cited By ~ 33

Author(s):

Vest Pedersen

Keyword(s):

Maximum Likelihood ◽

Dna Sequences ◽

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Mitochondrial Gene ◽

Elongation Factor ◽

Nuclear Gene ◽

The Other ◽

Elongation Factor 1Α ◽

Nucleotide Bias

AbstractThe phylogenetics of 40 taxa of European bumblebees were analysed based on PCR amplified and direct sequenced DNA from one region of the mitochondrial gene Cytochrome Oxidase I (1046 bp) and for 26 taxa from two regions in the nuclear gene Elongation Factor 1α (1056 bp). The sequences were aligned to the corresponding sequences in the honey bee. Phylogenetic analyses based on parsimony, as well as maximum likelihood, indicate that the bumblebees can be separated into several well-supported clades. Most of the terminal clades correspond very well with the clades known from former phylogenetic analyses based on morphology and recognized as the subgenera: Mendacibombus, Confusibombus, Psithyrus, Thoracobombus, Megabombus, Rhodobombus, Kallobombus, Alpinobombus, Subterraneobombus, Alpigenobombus, Pyrobombus, Bombus and Melanobombus. All the cuckoo bumblebees form a well-supported clade, the subgenus Psithyrus, within the true bumblebees. All the analyses place Kallobombus as the most basal taxon in contradiction to former analyses. The other deeper nodes of the phylogenetic trees, which are weakly supported, deviate significantly from former published trees - especially the trees based on mtCO-I. Presumably, the reasons are that multiple hits and the strong bias of the bases A and T blur the relationships in the deepest part of the trees. Analyses of the region in mtCO-I show a very strong A+T bias (A+T= 75%), which also indicate preferences in the use of codons with A or T in third positions. In closely related entities, there is only a weak transversion bias (A+T). In the studied regions in EF 1-α, no nucleotide bias is observed. The observed differences in bases between the investigated taxa are relatively small and the gene is too conserved to solve all the questions that the analyses of the deeper nodes using mtCO-I raise.

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Hundreds of nuclear and plastid loci yield insights into orchid relationships

10.1101/2020.11.17.386508 ◽

2020 ◽

Author(s):

Oscar Alejandro Pérez-Escobar ◽

Steven Dodsworth ◽

Diego Bogarín ◽

Sidonie Bellot ◽

Juan A. Balbuena ◽

...

Keyword(s):

Dna Sequences ◽

Phylogenetic Trees ◽

Nuclear Genome ◽

Nuclear Gene ◽

Gene Trees ◽

Deep Time ◽

Plastid Genomes ◽

Phylogenetic Informativeness ◽

History Of ◽

Phylogenetic Framework

ABSTRACTPremise of the studyEvolutionary relationships in the species-rich Orchidaceae have historically relied on organellar DNA sequences and limited taxon sampling. Previous studies provided a robust plastid-maternal phylogenetic framework, from which multiple hypotheses on the drivers of orchid diversification have been derived. However, the extent to which the maternal evolutionary history of orchids is congruent with that of the nuclear genome has remained uninvestigated.MethodsWe inferred phylogenetic relationships from 294 low-copy nuclear genes sequenced/obtained using the Angiosperms353 universal probe set from 75 species representing 69 genera, 16 tribes and 24 subtribes. To test for topological incongruence between nuclear and plastid genomes, we constructed a tree from 78 plastid genes, representing 117 genera, 18 tribes and 28 subtribes and compared them using a co-phylogenetic approach. The phylogenetic informativeness and support of the Angiosperms353 loci were compared with those of the 78 plastid genes.Key ResultsPhylogenetic inferences of nuclear datasets produced highly congruent and robustly supported orchid relationships. Comparisons of nuclear gene trees and plastid gene trees using the latest co-phylogenetic tools revealed strongly supported phylogenetic incongruence in both shallow and deep time. Phylogenetic informativeness analyses showed that the Angiosperms353 genes were in general more informative than most plastid genes.ConclusionsOur study provides the first robust nuclear phylogenomic framework for Orchidaceae plus an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely documented: nuclear and plastid phylogenetic trees are not fully congruent and therefore should not be considered interchangeable.

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Phylogeography of the New Zealand whelks Cominella maculosa and C. virgata

10.26686/wgtn.17064731.v1 ◽

2021 ◽

Author(s):

◽

Kerry Walton

Keyword(s):

New Zealand ◽

Dna Sequences ◽

High Frequency ◽

Phylogenetic Analyses ◽

Mitochondrial Gene ◽

Nuclear Gene ◽

Disjunct Distribution ◽

Phylogeographic Structure ◽

Interglacial Period ◽

Cook Strait

<p>Cominella maculosa and C. virgata are common rocky shore whelk species from New Zealand. This study used DNA sequences from the mitochondrial gene cytochrome c oxidase subunit 1 (CO1) to expand an earlier unpublished dataset and examine the phylogeographic structure of both species in the Cook Strait region, of C. maculosa in the Chatham Islands, and of C. virgata in the northern North Island. Both species are found to have a considerable degree of phylogeographic structure, concordant with that reported by an earlier study and for other species with direct development. South Island sites sampled for C. maculosa had several private haplotypes and a high frequency haplotype that is shared with populations from the southern North Island. Together, these formed a ‘southern haplogroup’. Low diversity in ‘southern’ populations may reflect founder effects that would have occurred as part of a southward range expansion during the onset of the present interglacial period. The Chatham Islands samples had two haplotypes that formed a separate sub-group to the ‘southern haplogroup’, suggesting Chatham Islands populations are moderately isolated from those on mainland New Zealand but may have been founded from ‘southern’ populations relatively recently. The high frequency haplotype present in South Island samples of C. virgata is absent in Wellington samples but widespread in those from the north-eastern North Island. South Island populations may have been founded from the Hauraki Gulf through human-mediated translocation events. Phylogenetic analyses with a focus on C. virgata were conducted using the mitochondrial genes CO1 and 16SrRNA, and the nuclear gene 18S rRNA, to expand an earlier published dataset. The purported northern subspecies C. virgata brookesi does not form a monophyletic lineage and voucher specimens fluidly intergrade with the nominal subspecies, with which it is synonymised. A lectotype is designated for Buccinum lineolatum Quoy & Gaimard, 1833, for which Cominella virgata is a replacement name. Potential causes of the disjunct distribution patterns of C. virgata and other mollusc taxa are discussed with particular reference to the formation and timing of marine straits through the Auckland Isthmus and Cook Strait.</p>

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Phylogeography of the New Zealand whelks Cominella maculosa and C. virgata

10.26686/wgtn.17064731 ◽

2021 ◽

Author(s):

◽

Kerry Walton

Keyword(s):

New Zealand ◽

Dna Sequences ◽

High Frequency ◽

Phylogenetic Analyses ◽

Mitochondrial Gene ◽

Nuclear Gene ◽

Disjunct Distribution ◽

Phylogeographic Structure ◽

Interglacial Period ◽

Cook Strait

<p>Cominella maculosa and C. virgata are common rocky shore whelk species from New Zealand. This study used DNA sequences from the mitochondrial gene cytochrome c oxidase subunit 1 (CO1) to expand an earlier unpublished dataset and examine the phylogeographic structure of both species in the Cook Strait region, of C. maculosa in the Chatham Islands, and of C. virgata in the northern North Island. Both species are found to have a considerable degree of phylogeographic structure, concordant with that reported by an earlier study and for other species with direct development. South Island sites sampled for C. maculosa had several private haplotypes and a high frequency haplotype that is shared with populations from the southern North Island. Together, these formed a ‘southern haplogroup’. Low diversity in ‘southern’ populations may reflect founder effects that would have occurred as part of a southward range expansion during the onset of the present interglacial period. The Chatham Islands samples had two haplotypes that formed a separate sub-group to the ‘southern haplogroup’, suggesting Chatham Islands populations are moderately isolated from those on mainland New Zealand but may have been founded from ‘southern’ populations relatively recently. The high frequency haplotype present in South Island samples of C. virgata is absent in Wellington samples but widespread in those from the north-eastern North Island. South Island populations may have been founded from the Hauraki Gulf through human-mediated translocation events. Phylogenetic analyses with a focus on C. virgata were conducted using the mitochondrial genes CO1 and 16SrRNA, and the nuclear gene 18S rRNA, to expand an earlier published dataset. The purported northern subspecies C. virgata brookesi does not form a monophyletic lineage and voucher specimens fluidly intergrade with the nominal subspecies, with which it is synonymised. A lectotype is designated for Buccinum lineolatum Quoy & Gaimard, 1833, for which Cominella virgata is a replacement name. Potential causes of the disjunct distribution patterns of C. virgata and other mollusc taxa are discussed with particular reference to the formation and timing of marine straits through the Auckland Isthmus and Cook Strait.</p>

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A molecular phylogeny of the Australian monitor lizards (Squamata:Varanidae) inferred from mitochondrial DNA sequences

Australian Journal of Zoology ◽

10.1071/zo05038 ◽

2006 ◽

Vol 54 (4) ◽

pp. 253 ◽

Cited By ~ 20

Author(s):

A. J. Fitch ◽

A. E. Goodman ◽

S. C. Donnellan

Keyword(s):

Dna Sequences ◽

Mitochondrial Gene ◽

Phylogenetic Study ◽

Trna Genes ◽

Preferred Habitat ◽

Mitochondrial Data ◽

Molecular Phylogenetic ◽

Tree Topologies ◽

Phylogenetic Framework ◽

Monitor Lizards

To date no complete phylogeny of all of the currently recognised Indo-Australian varanid species and subspecies has been published. This paper presents a comprehensive mitochondrial gene phylogeny of these lizards. A portion of the mitochondrial genome comprising part of the ND4 gene and three adjacent tRNA genes (hereafter referred to as ND4) was analysed alone and, for a subset of the taxa, combined with previously published mitochondrial data. Similar tree topologies were produced by both datasets although combining the data helped resolve some of the unresolved or weakly supported nodes in the ND4 analyses. The monophyly of the Indo-Australian group was strongly supported in all analyses. This group comprised three major lineages: the gouldii group, the Odatria group and the varius group. Mitochondrial ND4 nucleotide sequences were successfully amplified from all of the Indo-Australian monitor species and subspecies currently recognised and, as such, is the first comprehensive phylogenetic study of the Australian monitor lizards published. Analysis of the tempo of diversification and evolution of preferred habitat use identified six episodes of increased net speciation rate, with two closely adjacent episodes showing the highest rates of diversification and correlating with the appearance of all preferred habitat types. The comprehensive molecular phylogenetic framework will also be useful for the identification of varanid species and traded products derived from monitors and, as such, has important applications for wildlife management and conservation.

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Four new species and further records of Dorvilleidae (Annelida, Polychaeta) from deep-sea organic substrata, NE Atlantic

European Journal of Taxonomy ◽

10.5852/ejt.2021.736.1251 ◽

2021 ◽

Vol 736 ◽

pp. 44-81

Author(s):

Ascensão Ravara ◽

Helena Wiklund ◽

Marina R. Cunha

Keyword(s):

New Species ◽

Dna Sequences ◽

Phylogenetic Analyses ◽

Mitochondrial Gene ◽

Nuclear Gene ◽

Original Description ◽

Ne Atlantic ◽

Morphological Examination ◽

Bathymetric Distribution ◽

Molecular Phylogenetic

Eight species of Ophryotrocha and one of Parougia were identified from organic substrata (wood and alfalfa) sampled at the Gulf of Cadiz and Western Iberian Margin (NE Atlantic). Morphological examination and molecular phylogenetic analyses, based on the nuclear gene H3 and the mitochondrial gene 16S, indicate the presence of four species new to science: Ophryotrocha chemecoli sp. nov., O. nunezi sp. nov., O. geoffreadi sp. nov. and Parougia ougi sp. nov. The geographic and/or bathymetric distribution is extended for four previously known species: O. cantabrica, O. hartmanni, O. mammillata and O. scutellus. Another species may also have its distribution extended, pending the molecular confirmation of its identity: O. lipscombae. Full descriptions and figures are given for all the new species and, when justified, also for the previously known ones. The original description of O. scutellus is amended. New DNA sequences are given for eight of the nine species studied here. The ecology and geographic distribution of the reported species is discussed.

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Taxonomy and DNA Sequencing ofCrematogaster coriariaMayr, 1872 (Hymenoptera: Formicidae), with Redescriptions of the Worker, Queen, and Male Castes

Psyche A Journal of Entomology ◽

10.1155/2015/541351 ◽

2015 ◽

Vol 2015 ◽

pp. 1-8

Author(s):

Shingo Hosoishi ◽

Kazuo Ogata

Keyword(s):

Dna Sequencing ◽

Dna Sequences ◽

Mitochondrial Gene ◽

Gene Coi

Crematogaster coriariaMayr, 1872, is revised based on the nest series samples. The following new synonymies are proposed:C. coriariaMayr, 1872 = C. coriaria fraudatrixForel, 1911syn. nov. = C. spengeliForel, 1912syn. nov. = C. spengeli taipingensisForel, 1913syn. nov.Worker, queen, and male castes ofC. coriariaMayr, 1872, are redescribed. The polymorphism ofC. coriariaMayr, 1872, was also discussed. DNA sequences were generated forC. coriariaMayr, 1872, using an amplification of second half region of the mitochondrial gene COI with a total of 711 bp. The interspecific COI divergence is 17.4% forC. coriariaMayr, 1872, andC. modiglianiiEmery, 1900.

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Phylogeny of the water strider genus Aquarius Schellenberg (Heteroptera: Gerridae) based on nuclear and mitochondrial DNA sequences and morphology

Insect Systematics & Evolution ◽

10.1163/187631200x00327 ◽

2000 ◽

Vol 31 (1) ◽

pp. 71-90 ◽

Cited By ~ 26

Author(s):

Nils Møller Andersen ◽

Jakob Damgaard ◽

Felix A.H. Sperling

Keyword(s):

Dna Sequences ◽

Sequence Data ◽

Mitochondrial Gene ◽

Nuclear Gene ◽

Molecular Data ◽

Morphological Data ◽

Published Data ◽

Data Sets ◽

Gene Encoding ◽

Data Set

AbstractWe examined phylogenetic relationships among gerrid water striders of the genus Aquarius Schellenberg using molecular and morphological characters. The molecular data sets included 780 bp sequence data from the mitochondrial gene encoding cytochrome oxidase subunit I (COI), and 515 bp sequence data from the nuclear gene encoding elongation factor I alpha (EF-1α). The morphological data set was a slightly modified version of a previously published data set. We included all 17 known species and one subspecies of Aquarius as well as five species from three related genera, Gigantometra gigas, Limnoporus esakii, L. rufoscutellatus, Gerris pingreensis, and G. lacustris. Unweighted parsimony analyses of the COI data set gave a single most parsimonious tree (MPT) with a topology quite similar to the morphological tree. Parsimony analyses of the EF-1α data set gave 3 MPT's and a strict consensus of these trees gave a tree with a slightly different topology. A combined analysis of the three data sets gave a single MPT with the same topology as for the morphological data set alone. The phylogeny of Aquarius presented here supports the monophyly of the A. najas, remigis, conformis and paludum species groups as well as previous hypotheses about their relationships. On the other hand, the inclusion of molecular data weakens the support for the monophyly of the genus Aquarius, and questions the specific status of the eastern North American A. nebularis (as separate from A. conformis) and members of the Nearctic A. remigis group. Finally, we discuss the implications of the reconstructed phylogeny in the biogeography and ecological phylogenetics of Aquarius.

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