tcsBU: a tool to extend TCS network layout and visualization

Santos, António M.; Cabezas, M. Pilar; Tavares, Ana I.; Xavier, Raquel; Branco, Madalena

doi:10.1093/bioinformatics/btv636

Cited by 283 publications

(140 citation statements)

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“…The same COI region was sequenced at these various regions and the maximum likelihood phylogenetic tree was constructed using MEGA 7.0 35 . Genealogical relationships between haplotype in this current study was assessed using TCS version 1.21 36 and tcsBU ( http://cibio.up.pt/software/tcsBU/) 37 software.…”

Section: Methodsmentioning

confidence: 99%

Geographical distribution of Aedes aegypti and Aedes albopictus (Diptera: Culicidae) and genetic diversity of invading population of Ae. albopictus in the Republic of the Congo

Kamgang¹,

Wilson-Bahun²,

Irving³

et al. 2018

Wellcome Open Res

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Background: The arbovirus vector, Aedes albopictus, originating from Asia, has recently invaded African countries, including the Republic of the Congo, where it was associated with a chikungunya outbreak. Up until now, little was known about its distribution in relation to the native Aedes aegypti and how the invasion will modify the epidemiology of arboviral diseases. Here, we assessed the current distribution of Ae. albopictus and Ae. aegypti in the Republic of the Congo and explored the genetic diversity of the invading species, Ae. albopictus. Methods: Immature stages of Aedes were collected in nine locations in the Republic of the Congo in 2017 following a north-south transect and reared to adult stage. Adults were morphologically identified, counted and grouped according to species and location. Genetic diversity of Ae. albopictus was assessed by analyzing the cytochrome oxidase I ( COI) gene. Results: Ae. albopictus and Ae. aegypti were found together across the country in all the locations investigated. The invasive species is predominant over the native species in all locations except Brazzaville, suggesting that Ae. albopictus is displacing Ae. aegypti across Congo. When comparing the species distributions across the two largest cities, Brazzaville and Pointe Noire, Ae. albopictus was more prevalent than Ae. aegypti in the suburbs whereas the opposite situation was reported in the city centre. Mitochondrial DNA analysis revealed very low genetic diversity of Ae. albopictus with only three haplotypes recorded across the country supporting the recent introduction of this species in the Republic of the Congo. Phylogenetic tree analysis revealed that Ae. albopictus from Congo originated from other tropical Asian countries such as China, likely as a result of increasing trade links. Conclusion: These findings are important for the implementation of vector control strategies and can serve as a foundation for further research on these vectors in the country.

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Section: Methodsmentioning

confidence: 99%

Geographical distribution of Aedes aegypti and Aedes albopictus (Diptera: Culicidae) and genetic diversity of invading population of Ae. albopictus in the Republic of the Congo

Kamgang¹,

Wilson-Bahun²,

Irving³

et al. 2018

Wellcome Open Res

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“…The genealogical relationships were established using a minimum spanning network implemented in TCS v. 1.21 with the statistical parsimony analysis (Clement, Posada, & Crandall, ; Templeton, Crandall, & Sing, ). The network was constructed with a connection limit of 95%, and graphically plotted using tcsBU (Múrias dos Santos, Cabezas, Tavares, Xavier, & Branco, ).…”

Section: Methodsmentioning

confidence: 99%

Evolutionary history of the scorpionfly Dicerapanorpa magna (Mecoptera, Panorpidae)

Hua

2018

Zoologica Scripta

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Climate changes can have fundamental impacts on the distributional patterns of montane species, and range shifts frequently lead to allopatric divergence followed by the establishment of secondary contact zones. Many European and North American organisms have retreated to southern refugia during glacial periods and colonized northward during postglacial periods, but little is known about the evolutionary response of cold‐adapted insects to Pleistocene climate changes in eastern Asia. The scorpionfly Dicerapanorpa magna (Chou), with cold temperate habitat preference and weak dispersal ability, provides a good model system to explore how climate changes have influenced the distribution and divergence of cold‐adapted insects in eastern Asia. This study reconstructed the demographic dynamics and evolutionary history of D. magna with phylogeographic approaches, and predicted the species’ suitable areas under the Last Glacial Maximum (LGM) and current scenarios with the ecological niche modelling analysis. The mitochondrial cytochrome c oxidase subunit I resolved three phylogenetic lineages in D. magna dating back to Pleistocene, corresponding well with the geographically isolated Qinling, Bashan and Minshan Mountains. The ecological niche modelling recovered the suitable habitats for D. magna were the Qinling and Bashan Mountains under LGM and current conditions. The three lineages of D. magna might be in a process of incipient speciation, and likely derived their current distribution from separate glacial origins, followed by vicariance and divergence.

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“…This method is particularly appropriate when few characters for phylogenetic analysis are available due to shallow levels of divergence [78] as we observed in the acm4 and mc1r datasets. Networks were constructed under the 95% probability criterion for a parsimonious connection and represented graphically using the tool tcsBU [79]. Additionally, since mc1r sequences are available in GenBank for other Podarcis species, we combined them with sequence data from the present study to examine the phylogenetic relationships of mc1r haplotypes from different populations and species.…”

Section: Methodsmentioning

confidence: 99%

Digging up the roots of an insular hotspot of genetic diversity: decoupled mito-nuclear histories in the evolution of the Corsican-Sardinian endemic lizard Podarcis tiliguerta

Salvi

Pinho²,

Harris³

2017

BMC Evol Biol

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BackgroundMediterranean islands host a disproportionately high level of biodiversity and endemisms. Growing phylogeographic evidence on island endemics has unveiled unexpectedly complex patterns of intra-island diversification, which originated at diverse spatial and temporal scales. We investigated multilocus genetic variation of the Corsican-Sardinian endemic lizard Podarcis tiliguerta with the aim of shedding more light on the evolutionary processes underlying the origin of Mediterranean island biodiversity.ResultsWe analysed DNA sequences of mitochondrial (12S and nd4) and nuclear (acm4 and mc1r) gene fragments in 174 individuals of P. tiliguerta from 81 localities across the full range of the species in a geographic and genealogical framework. We found surprisingly high genetic diversity both at mitochondrial and nuclear loci. Seventeen reciprocally monophyletic allopatric mitochondrial haplogroups were sharply divided into four main mitochondrial lineages (two in Corsica and two in Sardinia) of Miocene origin. In contrast, shallow divergence and shared diversity within and between islands was observed at the nuclear loci. We evaluated alternative biogeographic and evolutionary scenarios to explain such profound discordance in spatial and phylogenetic patterning between mitochondrial and nuclear genomes. While neutral models provided unparsimonious explanations for the observed pattern, the hypothesis of environmental selection driving mitochondrial divergence in the presence of nuclear gene flow is favoured.ConclusionsOur study on the genetic variation of P. tiliguerta reveals surprising levels of diversity underlining a complex phylogeographic pattern with a striking example of mito-nuclear discordance. These findings have profound implications, not only for the taxonomy and conservation of P. tiliguerta. Growing evidence on deep mitochondrial breaks in absence of geographic barriers and of climatic factors associated to genetic variation of Corsican-Sardinian endemics warrants additional investigation on the potential role of environmental selection driving the evolution of diversity hotspots within Mediterranean islands.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-0899-x) contains supplementary material, which is available to authorized users.

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tcsBU: a tool to extend TCS network layout and visualization

Abstract: tcsBU is available on-line at http://cibio.up.pt/software/tcsBU/. The source code is freely available from https://github.com/sairum/tcsbu/ under a standard MIT license.

Cited by 283 publications

References 6 publications

Geographical distribution of Aedes aegypti and Aedes albopictus (Diptera: Culicidae) and genetic diversity of invading population of Ae. albopictus in the Republic of the Congo

Geographical distribution of Aedes aegypti and Aedes albopictus (Diptera: Culicidae) and genetic diversity of invading population of Ae. albopictus in the Republic of the Congo

Evolutionary history of the scorpionfly Dicerapanorpa magna (Mecoptera, Panorpidae)

Digging up the roots of an insular hotspot of genetic diversity: decoupled mito-nuclear histories in the evolution of the Corsican-Sardinian endemic lizard Podarcis tiliguerta

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