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      Du’an Karst of Guangxi: a kingdom of the cavernicolous genus Dongodytes Deuve (Coleoptera, Carabidae, Trechinae)

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      ZooKeys
      Pensoft Publishers
      Ground beetles, anophthalmic, troglobitic, new species, specific diversity, China

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          Abstract

          Abstract

          Recent cave biodiversity surveys carried out in Du’an County and its adjacent areas of northwestern Guangxi, China, have revealed some exciting scientific findings. In a very limited area seven new species of the cavernicolous trechine genus Dongodytes Deuve, 1993 were found and are described: Dongodytes (s. str.) elongatus sp. n., Dongodytes (s. str.) troglodytes sp. n., Dongodytes (s. str.) lani sp. n., Dongodytes ( Dongodytodes) brevipenis sp. n., Dongodytes ( Dongodytodes) jinzhuensis sp. n., Dongodytes ( Dongodytodes) inexpectatus sp. n. and Dongodytes ( Dongodytodes) yaophilus sp. n. Diagnoses and notes on the genus, subgenera, and two known species in Du’an Karst, Dongodytes (s. str.) baxian Tian, 2011 and Dongodytes ( Dongodytodes) deharvengi Tian, 2011, are also given. A key to subgenera and all species of Dongodytes is provided. To date, Dongodytes becomes one of the richest in species genera of subterranean carabid trechines in China with 12 species which are arranged into two subgenera. Dongodytes (s. str.) Deuve is composed of seven species, four of which from Du’an County, each of other three from Bama, Fengshan and Tian’e Counties, respectively. All species of the subgenus Dongodytodes Tian, 2011 are recorded from Du’an Karst. By having 10 species (nine Dongodytes and one Libotrechus Uéno, 1998), Du’an Karst holds the richest specific diversity of cavernicolous Trechinae in China. Dongodytes species are distributed in a very limited area of the river Hongshui He drainages in northwestern Guangxi, and the river acts as a natural barrier of Dongodytes dispersal at only a specific level. However, all members of Dongodytodes are recorded from the eastern or northern bank of Hongshui He.

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          New approaches for unravelling reassortment pathways

          Background Every year the human population encounters epidemic outbreaks of influenza, and history reveals recurring pandemics that have had devastating consequences. The current work focuses on the development of a robust algorithm for detecting influenza strains that have a composite genomic architecture. These influenza subtypes can be generated through a reassortment process, whereby a virus can inherit gene segments from two different types of influenza particles during replication. Reassortant strains are often not immediately recognised by the adaptive immune system of the hosts and hence may be the source of pandemic outbreaks. Owing to their importance in public health and their infectious ability, it is essential to identify reassortant influenza strains in order to understand the evolution of this virus and describe reassortment pathways that may be biased towards particular viral segments. Phylogenetic methods have been used traditionally to identify reassortant viruses. In many studies up to now, the assumption has been that if two phylogenetic trees differ, it is because reassortment has caused them to be different. While phylogenetic incongruence may be caused by real differences in evolutionary history, it can also be the result of phylogenetic error. Therefore, we wish to develop a method for distinguishing between topological inconsistency that is due to confounding effects and topological inconsistency that is due to reassortment. Results The current work describes the implementation of two approaches for robustly identifying reassortment events. The algorithms rest on the idea of significance of difference between phylogenetic trees or phylogenetic tree sets, and subtree pruning and regrafting operations, which mimic the effect of reassortment on tree topologies. The first method is based on a maximum likelihood (ML) framework (MLreassort) and the second implements a Bayesian approach (Breassort) for reassortment detection. We focus on reassortment events that are found by both methods. We test both methods on a simulated dataset and on a small collection of real viral data isolated in Hong Kong in 1999. Conclusions The nature of segmented viral genomes present many challenges with respect to disease. The algorithms developed here can effectively identify reassortment events in small viral datasets and can be applied not only to influenza but also to other segmented viruses. Owing to computational demands of comparing tree topologies, further development in this area is necessary to allow their application to larger datasets.
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            A molecular phylogeny shows the single origin of the Pyrenean subterranean Trechini ground beetles (Coleoptera: Carabidae).

            Trechini ground beetles include some of the most spectacular radiations of cave and endogean Coleoptera, but the origin of the subterranean taxa and their typical morphological adaptations (loss of eyes and wings, depigmentation, elongation of body and appendages) have never been studied in a formal phylogenetic framework. We provide here a molecular phylogeny of the Pyrenean subterranean Trechini based on a combination of mitochondrial (cox1, cyb, rrnL, tRNA-Leu, nad1) and nuclear (SSU, LSU) markers of 102 specimens of 90 species. We found all Pyrenean highly modified subterranean taxa to be monophyletic, to the exclusion of all epigean and all subterranean species from other geographical areas (Cantabrian and Iberian mountains, Alps). Within the Pyrenean subterranean clade the three genera (Geotrechus, Aphaenops and Hydraphaenops) were polyphyletic, indicating multiple origins of their special adaptations to different ways of life (endogean, troglobitic or living in deep fissures). Diversification followed a geographical pattern, with two main clades in the western and central-eastern Pyrenees respectively, and several smaller lineages of more restricted range. Based on a Bayesian relaxed-clock approach, and using as an approximation a standard mitochondrial mutation rate of 2.3% MY, we estimate the origin of the subterranean clade at ca. 10 MY. Cladogenetic events in the Pliocene and Pleistocene were almost exclusively within the same geographical area and involving species of the same morphological type.
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              A molecular phylogeny of Alpine subterranean Trechini (Coleoptera: Carabidae)

              Background The Alpine region harbours one of the most diverse subterranean faunas in the world, with many species showing extreme morphological modifications. The ground beetles of tribe Trechini (Coleoptera, Carabidae) are among the best studied and widespread groups with abundance of troglobionts, but their origin and evolution is largely unknown. Results We sequenced 3.4 Kb of mitochondrial (cox1, rrnL, trnL, nad1) and nuclear (SSU, LSU) genes of 207 specimens of 173 mostly Alpine species, including examples of all subterranean genera but two plus a representation of epigean taxa. We applied Bayesian methods and maximum likelihood to reconstruct the topology and to estimate divergence times using a priori rates obtained for a related ground beetle genus. We found three main clades of late Eocene-early Oligocene origin: (1) the genus Doderotrechus and relatives; (2) the genus Trechus sensu lato, with most anisotopic subterranean genera, including the Pyrenean lineage and taxa from the Dinaric Alps; and (3) the genus Duvalius sensu lato, diversifying during the late Miocene and including all subterranean isotopic taxa. Most of the subterranean genera had an independent origin and were related to epigean taxa of the same geographical area, but there were three large monophyletic clades of exclusively subterranean species: the Pyrenean lineage, a lineage including subterranean taxa from the eastern Alps and the Dinarides, and the genus Anophthalmus from the northeastern Alps. Many lineages have developed similar phenotypes independently, showing extensive morphological convergence or parallelism. Conclusions The Alpine Trechini do not form a homogeneous fauna, in contrast with the Pyrenees, and show a complex scenario of multiple colonisations of the subterranean environment at different geological periods and through different processes. Examples go from populations of an epigean widespread species going underground with little morphological modifications to ancient, geographically widespread lineages of exclusively subterranean species likely to have diversified once fully adapted to the subterranean environment.
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                Author and article information

                Journal
                Zookeys
                Zookeys
                ZooKeys
                ZooKeys
                Pensoft Publishers
                1313-2989
                1313-2970
                2014
                14 November 2014
                : 454
                : 69-107
                Affiliations
                [1 ]Department of Entomology, College of Natural Resources and Environment, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
                Author notes
                Corresponding author: Mingyi Tian ( mytian168@ 123456aliyun.com )

                Academic editor: T. Assmann

                Article
                10.3897/zookeys.454.7269
                4258740
                25493067
                4e70a079-104c-4b6c-bdf7-bc28b7e77e7d
                Mingyi Tian, Haomin Yin, Sunbin Huang

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 16 February 2014
                : 17 October 2014
                Categories
                Research Article

                Animal science & Zoology
                ground beetles,anophthalmic,troglobitic,new species,specific diversity,china,animalia,coleoptera,carabidae

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