Phylogenetic Analyses of Two Mitochondrial Genes and One Nuclear Intron Region Illuminate European Subterranean Termite (Isoptera: Rhinotermitidae) Gene Flow, Taxonomy, and Introduction Dynamics

Abstract Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.

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Tracing the origins of hybrids through history: monstrous cultivars and Napoléon Bonaparte’s exiled paper daisies (Asteraceae; Gnaphalieae)

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boab020 ◽

2021 ◽

Author(s):

Timothy L Collins ◽

Jeremy J Bruhl ◽

Alexander N Schmidt-Lebuhn ◽

Ian R H Telford ◽

Rose L Andrew

Keyword(s):

Gene Flow ◽

Phylogenetic Analyses ◽

Strong Support ◽

Napoleon Bonaparte ◽

Snp Data ◽

Cast Doubt ◽

Molecular Phylogenetic ◽

St Helena ◽

New Evidence

Abstract Golden everlasting paper daisies (Xerochrysum, Gnaphalieae, Asteraceae) were some of the earliest Australian native plants to be cultivated in Europe. Reputedly a favourite of Napoléon Bonaparte and Empress Joséphine, X. bracteatum is thought to have been introduced to the island of St Helena in the South Atlantic during Napoléon’s exile there. Colourful cultivars were developed in the 1850s, and there is a widely held view that these were produced by crossing Xerochrysum with African or Asian Helichrysum spp. Recent molecular phylogenetic analyses and subtribal classification of Gnaphalieae cast doubt on this idea. Using single-nucleotide polymorphism (SNP) data, we looked for evidence of gene flow between modern cultivars, naturalized paper daisies from St Helena and four Xerochrysum spp. recorded in Europe in the 1800s. There was strong support for gene flow between cultivars and X. macranthum. Paper daisies from St Helena were genotypically congruent with X. bracteatum and showed no indications of ancestry from other species or from the cultivars, consistent with the continuous occurrence of naturalized paper daisies introduced by Joséphine and Napoléon. We also present new evidence for the origin of colourful Xerochrysum cultivars and hybridization of congeners in Europe from Australian collections.

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The taxonomic status of the Castelo dos Sonhos Hantavirus reservoir, Oligoryzomys utiaritensis Allen 1916 (Rodentia: Cricetidae: Sigmodontinae)

Zootaxa ◽

10.11646/zootaxa.3220.1.1 ◽

2012 ◽

Vol 3220 (1) ◽

pp. 1 ◽

Cited By ~ 14

Author(s):

RODRIGO AGRELLOS ◽

CIBELE R. BONVICINO ◽

ELIZABETH SALBÉ T. ROSA ◽

APARECIDO A.R. MARQUES ◽

PAULO S. D’ANDREA ◽

...

Keyword(s):

Cytochrome B ◽

Diploid Number ◽

Phylogenetic Analyses ◽

Taxonomic Status ◽

Sympatric Species ◽

Junior Synonym ◽

Natural Reservoir ◽

Nuclear Intron ◽

Phylogenetic Reconstructions ◽

Mitochondrial Cytochrome B

Species of the genus Oligoryzomys are commonly found accross Latin America, and several of them play important rolesas natural reservoirs of Hantaviruses. Here we demonstrate that O. utiaritensis, the natural reservoir of hantavirus Castelodos Sonhos in northwestwern Brazil and previously considered a junior synonym of O. nigripes or O. eliurus, is a validspecies. Morphology, morphometry, karyotyping, and phylogenetic reconstructions based on nuclear (intron 7 of the beta-fibrinogen gene) and mitochondrial (cytochrome b) DNA show that O. utiaritensis differs from O. nigripes and from otherforms of the genus, including the recently described taxon O. moojeni. Oligoryzomys utiaritensis differs in external (whit-ish ventral pelage and tail weakly bicolored) and cranial (incisive foramina never extending posteriorly the alveolus lineof M1) characters from sympatric species. It has the highest diploid number (2n=72) within Oligoryzomys, and is charac-terized by three putative synapomorphies in cytochrome b, and one in intron 7 of beta fibrinogen. We also point to theassignment of Oligoryzomys eliurus as a junior synonym of O. nigripes. Finally, we present phylogenetic analyses of in-trageneric relationships showing that O. utiaritensis is a member of a clade containing Amazonian and Cerrado taxa, including O. moojeni, O. rupestris, and O. delicatus.

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Pinnule-less polyps: a new genus and new species of Indo-Pacific Clavulariidae and validation of the soft coral genus Acrossota and the family Acrossotidae (Coelenterata: Octocorallia)

Zootaxa ◽

10.11646/zootaxa.1400.2 ◽

2007 ◽

Vol 1400 (1) ◽

pp. 27 ◽

Cited By ~ 4

Author(s):

PHILP ALDERSLADE ◽

CATHERINE S. McFADDEN

Keyword(s):

New Genus ◽

Soft Coral ◽

Phylogenetic Analyses ◽

Mitochondrial Genes ◽

New Combination ◽

New Genus And Species ◽

Coral Genus ◽

The Family ◽

Lateral Margins ◽

Number Of Authors

Clavularia amboinensis Burchardt, a species described as possessing simple, pinnule-less tentacles (a fact refuted by later authors) is confirmed to be as described and is transferred as a new combination to Acrossota Bourne — a genus dismissed until now by a number of authors. The species is compared to recently collected material with live photographs. A second new genus and species, Knopia octocontacanalis, is also described. This taxon resembles Acrossota in general form, but has tentacles where the pinnules appear as though they are fused side to side along the tentacles’ lateral margins. Preliminary phylogenetic analyses of two mitochondrial genes support placement of Knopia in Clavulariidae and retention of genus Acrossota in Bourne’s unrecognised family Acrossotidae.

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Population Transcriptomics Reveals Gene Flow and Introgression Between Two Non-sister Alpine Gentians

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2021.638230 ◽

2021 ◽

Vol 9 ◽

Author(s):

Chunlin Chen ◽

Wenjie Yang ◽

Jianquan Liu ◽

Zhenxiang Xi ◽

Lei Zhang ◽

...

Keyword(s):

Gene Flow ◽

Phylogenetic Analyses ◽

Population Data ◽

Tibet Plateau ◽

Interspecific Gene Flow ◽

Climatic Oscillations ◽

Distributional Shifts ◽

Qinghai Tibet Plateau ◽

Two Populations ◽

Hybridization And Introgression

Distributional shifts driven by Quaternary climatic oscillations have been suggested to cause interspecific hybridization and introgression. In this study, we aimed to test this hypothesis by using population transcriptomes and coalescent modeling of two alpine none-sister gentians. Previous studies suggested that historical hybridizations occurred between Gentiana siphonantha and G. straminea in the high-altitude Qinghai-Tibet Plateau although both species are not sister to each other with the most recent divergence. In the present study, we sequenced transcriptomes of 33 individuals from multiple populations of G. siphonantha and G. straminea. The two species are well delimited by nuclear genomic SNPs while phylogenetic analyses of plastomes clustered one G. straminea individual into the G. siphonantha group. Further population structure analyses of the nuclear SNPs suggested that two populations of G. siphonantha were admixed with around 15% ancestry from G. straminea. These analyses suggested genetic introgressions from G. straminea to G. siphonantha. In addition, our coalescent-based modeling results revealed that gene flow occurred between the two species since Last Glacier Maximum after their initial divergence, which might have leaded to the observed introgressions. Our results underscore the significance of transcriptome population data in determining timescale of interspecific gene flow and direction of the resulting introgression.

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Whole genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

10.1101/143859 ◽

2017 ◽

Cited By ~ 18

Author(s):

Milan Malinsky ◽

Hannes Svardal ◽

Alexandra M. Tyers ◽

Eric A. Miska ◽

Martin J. Genner ◽

...

Keyword(s):

Gene Flow ◽

Fish Species ◽

Phylogenetic Analyses ◽

Cichlid Fish ◽

Sequence Divergence ◽

Single Species ◽

Lake Malawi ◽

Genomic Diversity ◽

Average Sequence Divergence ◽

Deep Water Species

AbstractThe hundreds of cichlid fish species in Lake Malawi constitute the most extensive recent vertebrate adaptive radiation. Here we characterize its genomic diversity by sequencing 134 individuals covering 73 species across all major lineages. Average sequence divergence between species pairs is only 0.1-0.25%. These divergence values overlap diversity within species, with 82% of heterozygosity shared between species. Phylogenetic analyses suggest that diversification initially proceeded by serial branching from a generalistAstatotilapia-likeancestor. However, no single species tree adequately represents all species relationships, with evidence for substantial gene flow at multiple times. Common signatures of selection on visual and oxygen transport genes shared by distantly related deep water species point to both adaptive introgression and independent selection. These findings enhance our understanding of genomic processes underlying rapid species diversification, and provide a platform for future genetic analysis of the Malawi radiation.One Sentence Summary: The genomes of 73 cichlid fish species from Lake Malawi uncover evolutionary processes underlying a large adaptive evolutionary radiation.

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Orientobilharzia turkestanicum is grouped within African schistosomes based on phylogenetic analyses using sequences of mitochondrial genes

Parasitology Research ◽

10.1007/s00436-007-0857-4 ◽

2008 ◽

Vol 102 (5) ◽

pp. 939-943 ◽

Cited By ~ 12

Author(s):

L. Li ◽

L. Y. Yu ◽

X. Q. Zhu ◽

C. R. Wang ◽

Y. Q. Zhai ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Mitochondrial Genes

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Biogeographical and evolutionary patterns in the Macaronesian shield-backed katydid genusCalliphonaKrauss, 1892 (Orthoptera: Tettigoniidae) and allies as inferred from phylogenetic analyses of multiple mitochondrial genes

Systematic Entomology ◽

10.1111/j.1365-3113.2007.00393.x ◽

2007 ◽

Vol 33 (1) ◽

pp. 145-158 ◽

Cited By ~ 9

Author(s):

MIQUEL A. ARNEDO ◽

PEDRO OROMÍ ◽

SONIA MARTÍN DE ABREU ◽

CARLES RIBERA

Keyword(s):

Phylogenetic Analyses ◽

Mitochondrial Genes ◽

Evolutionary Patterns

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Biology and evolution of the Epichloë-associated Botanophila species found in Europe (Diptera: Anthomyiidae)

Insect Systematics & Evolution ◽

10.1163/1876312x-46052130 ◽

2016 ◽

Vol 47 (1) ◽

pp. 1-14 ◽

Cited By ~ 2

Author(s):

Adrian Leuchtmann ◽

Verner Michelsen

Keyword(s):

Representative Sample ◽

Food Source ◽

Phylogenetic Analyses ◽

Species Group ◽

Mitochondrial Genes ◽

Additional Food ◽

Mutualistic Relationship ◽

Associated Species ◽

Fungal Tissue ◽

Relationship Of

The anthomyiid genus Botanophila consists of over 200, mostly phytophagous, species. One species group maintains a mutualistic relationship with Epichloë fungi, thereby acting as vector of fungal spermatia required for fertilization, similar to pollinating parasites. The phylogenetic relationship of these flies with other Botanophila and the related Chiastocheta species (obligatory associated with globeflowers) remains largely unresolved. In this study, we obtained new sequences of the mitochondrial genes COI and COII from a representative sample of 17 European Botanophila and Chiastocheta species including all six Epichloë-associated species, as well as from four outgroup taxa. Phylogenetic analyses indicated that Epichloë-associated Botanophila form a distinct clade suggesting that ancestral Botanophila may have expanded its niche to European fungal hosts once and then successfully radiated while exploiting fungal tissue as additional food source. Furthermore, the three included Chiastocheta species formed a distinct clade nested within Botanophila, leaving the genus paraphyletic as currently circumscribed.

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