Search

The complete mitochondrial genome of the stone loach Barbatula barbatula (Linnaeus, 1758) (Actinopterygii: Cypriniformes: Nemacheilidae) has been sequenced using a genome-skimming approach on an Illumina Hiseq 2500 platform. The mitochondrial genome of B. barbatula was determined to be 16,630 bp long and presents an organization typical of vertebrate mitogenomes. The mean coverage was 82× with a minimum coverage of 33× for the control region and 52× for the remaining part of the genome. A phylogenetic analysis of the Nemacheilidae family shows the monophyly of the Barbatula genus with strong support.

We report the high-coverage complete mitochondrial genome sequence of the gray mouse lemur Microcebus murinus. The sequencing has been performed on an Illumina Hiseq 2500 platform, with a genome skimming strategy. The total length of this mitogenome is 16 963 bp, containing 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 non-coding region (D-loop region). The genome organization, nucleotide composition and codon usage are similar to those reported from other primate's mitochondrial genomes. The complete mitochondrial genome sequence reported here will be useful for comparative genomics studies in primates.

Premise of the Study: The complex geological and climatic history of the Neotropics has had major implications on the diversification of plant lineages. Chrysobalanaceae is a pantropical family of trees and shrubs with 75% of its 531 species found in the Neotropics, and a time-calibrated phylogeny of this family should shed light on the tempo of diversification in the Neotropical flora. Previously published phylogenetic hypotheses of this family were poorly supported, and its biogeography remains unclear., Methods: We assembled the complete plastid genome of 51 Chrysobalanaceae species, and increased taxon sampling by Sanger-sequencing of five plastid regions for an additional 88 species. We generated a time-calibrated tree including all 139 Chrsyobalanaceae species and 23 outgroups. We then conducted an ancestral area reconstruction analysis and estimated diversification rates in the family., Key Results: The tree generated with the plastid genome alignment was almost fully resolved. It supports the polyphyly of Licania and Hirtella. The family has diversified starting around the Eocene-Oligocene transition. An ancestral area reconstruction confirms a Paleotropical origin for Chrysobalanaceae with several transoceanic dispersal events. The main Neotropical clade likely resulted from a single migration event from Africa around 28 mya ago, which subsequently underwent rapid diversification., Conclusions: Given the diverse ecologies exhibited by extant species, we hypothesize that the rapid diversification of Chrysobalanaceae following the colonization of the Neotropics was triggered by habitat specialization during the complex geological and paleoclimatic history of the Neotropics., (© 2016 Botanical Society of America.)

The complete mitochondrial genome of the cracker butterfly Hamadryas epinome (C. Felder and R. Felder, 1867) (Lepidoptera: Nymphalidae: Biblidinae) has been sequenced using a genome-skimming approach on an Illumina Hiseq 2000 platform. The mitochondrial genome of H. epinome was determined to be 15,207 bp long and presents an organization similar to other Ditrysia mitogenomes. A non-coding poly-AT region of uncertain length is present at position 6180.

A database providing information on mosquito specimens (Arthropoda: Diptera: Culicidae) collected in French Guiana is presented. Field collections were initiated in 2013 under the auspices of the CEnter for the study of Biodiversity in Amazonia (CEBA: http://www.labexceba.fr/en/). This study is part of an ongoing process aiming to understand the distribution of mosquitoes, including vector species, across French Guiana. Occurrences are recorded after each collecting trip in a database managed by the laboratory Evolution et Diversité Biologique (EDB), Toulouse, France. The dataset is updated monthly and is available online. Voucher specimens and their associated DNA are stored at the laboratory Ecologie des Forêts de Guyane (Ecofog), Kourou, French Guiana. The latest version of the dataset is accessible through EDB's Integrated Publication Toolkit at http://130.120.204.55:8080/ipt/resource.do?r=mosquitoes_of_french_guiana or through the Global Biodiversity Information Facility data portal at http://www.gbif.org/dataset/5a8aa2ad-261c-4f61-a98e-26dd752fe1c5 It can also be viewed through the Guyanensis platform at http://guyanensis.ups-tlse.fr.

Lace bugs (Tingidae) are a family of phytophagous heteropterans, some of which are important agricultural and forestry pests. They currently comprise around 2500 species distributed worldwide, for which only one mitochondrial genome has been described so far. We sequenced the complete mitochondrial genome and the nuclear ribosomal gene segment of the avocado lace bug Pseudacysta perseae using a genome skimming approach on an Illumina Hiseq 2000 platform. Fifty-four additional heteropteran mitogenomes, including the one of the sycamore lace bug Corythucha ciliata, were retrieved to allow for comparisons and phylogenetic analyses. P. perseae mitochondrial genome was determined to be 15,850 bp long, and presented the typical organisation of insect mitogenomes. The phylogenetic analysis placed P. perseae as a sister to C. ciliata but did not confirm the monophyly of Miroidae including Tingidae. Our results contradicted widely accepted phylogenetic hypothesis, which highlights the limits of analyses based on mitochondrial data only. Shotgun sequencing approaches should provide substantial improvements in harmonizing mitochondrial and nuclear databases., (Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.)

This dataset provides information on specimens of harvestmen (Arthropoda, Arachnida, Opiliones) collected in French Guiana. Field collections have been initiated in 2012 within the framework of the CEnter for the Study of Biodiversity in Amazonia (CEBA: www.labex-ceba.fr/en/). This dataset is a work in progress.  Occurrences are recorded in an online database stored at the EDB laboratory after each collecting trip and the dataset is updated on a monthly basis. Voucher specimens and associated DNA are also stored at the EDB laboratory until deposition in natural history Museums. The latest version of the dataset is publicly and freely accessible through our Integrated Publication Toolkit at http://130.120.204.55:8080/ipt/resource.do?r=harvestmen_of_french_guiana or through the Global Biodiversity Information Facility data portal at http://www.gbif.org/dataset/3c9e2297-bf20-4827-928e-7c7eefd9432c.

The complete mitochondrial genome of the assassin bug Brontostoma colossus (Distant, 1902) (Heteroptera: Reduviidae) has been sequenced using a genome-skimming approach on an Illumina Hiseq 2000 platform. Fifty-four additional heteropteran mitogenomes, including five assassin bug species, were retrieved to allow for comparisons and phylogenetic analyses. The mitochondrial genome of B. colossus was determined to be 16,625 bp long, and consists of 13 protein-coding genes (PCGs), 23 transfer-RNA genes (tRNAs), two ribosomal-RNA genes (rRNAs), and one control region. The nucleotide composition is biased toward adenine and thymine (A+T=73.4%). Overall, architecture, nucleotide composition and genome asymmetry are similar among all available assassin bug mitogenomes. All PCGs have usual start-codons (Met and Ile). Three T and two TA incomplete termination codons were identified adjacent to tRNAs, which was consistent with the punctuation model for primary transcripts processing followed by 3' polyadenylation of mature mRNA. All tRNAs exhibit the classic clover-leaf secondary structure except for tRNASer(AGN) in which the DHU arm forms a simple loop. Two notable features are present in the B. colossus mitogenome: (i) a 131 bp duplicated unit including the complete tRNAArg gene, resulting in 23 potentially functional tRNAs in total, and (ii) a 857 bp duplicated region comprising 277 bp of the srRNA gene and 580 bp of the control region. A phylogenetic analysis based on 55 true bug mitogenomes confirmed that B. colossus belongs to Reduviidae, but contradicted a widely accepted hypothesis. This highlights the limits of phylogenetic analyses based on mitochondrial data only., (Copyright © 2014 Elsevier B.V. All rights reserved.)

To address the phylogenetic relationships of the centipede order Geophilomorpha (more than 1000 species), we have reinterpreted and expanded the knowledge on their morphological disparity, and have doubled the amount of molecular data available. We performed maximum parsimony and maximum likelihood analyses, using 195 phylogenetically informative morphological characters for 80 species, and DNA sequences of 28S, 18S, 16S rRNA and COI for up to 48 species. We found strong support for the monophyly of Geophilomorpha, the basal dichotomy between Adesmata and Placodesmata = Mecistocephalidae, and the basal dichotomy within Adesmata between two clades that are recognized here as superfamilies Himantarioidea and Geophiloidea. With respect to the families currently in use, Himantarioidea comprises three well supported clades corresponding to (i) Oryidae, (ii) Himantariidae, and (iii) Schendylidae s.l. including Ballophilidae; Geophiloidea comprises another three supported clades corresponding to (iv) a new family Zelanophilidae, (v) Gonibregmatidae s.l. including Eriphantidae and Neogeophilidae, and (vi) Geophilidae s.l. including Aphilodontidae, Dignathodontidae, Linotaeniidae, and Macronicophilidae., (© The Willi Hennig Society 2013.)

Understanding climate-induced range shifts is crucial for biodiversity conservation. However, no general consensus has so far emerged about the mechanisms involved and the role of phylogeny in shaping species responses has been poorly explored. Here, we investigate whether species traits and their underlying phylogenetic constraints explain altitudinal shifts at the trailing and leading edges of stream fish species ranges. We demonstrate that these shifts are related to dissimilar mechanisms: whereas range retractions show some support for phylogenetic clustering due to a high level of conservatism in thermal safety margins, range expansions are underpinned by both evolutionarily conserved and labile traits, notably trophic position and life-history strategy, hence decreasing the strength of phylogenetic signal. Therefore, while climate change brings many difficulties in establishing a general understanding of species vulnerability, these findings emphasize how combining trait-based approaches in light of the species evolutionary history may offer new opportunities in facing conservation challenges.

The need for an updated list of spiders found in French Guiana rose recently due to many upcoming studies planned. In this paper, we list spiders from French Guiana from existing literature (with corrected nomenclature when necessary) and from 2142 spiders sampled in 12 sites for this baseline study. Three hundred and sixty four validated species names of spider were found in the literature and previous authors' works. Additional sampling, conducted for this study added another 89 identified species and 62 other species with only a genus name for now. The total species of spiders sampled in French Guiana is currently 515. Many other Morphospecies were found but not described as species yet. An accumulation curve was drawn with seven of the sampling sites and shows no plateau yet. Therefore, the number of species inhabiting French Guiana cannot yet be determined. As the very large number of singletons found in the collected materials suggests, the accumulation curve indicates nevertheless that more sampling is necessary to discover the many unknown spider species living in French Guiana, with a focus on specific periods (dry season and wet season) and on specific and poorly studied habitats such as canopy, inselberg and cambrouze (local bamboo monospecific forest).

The refugial speciation model, or 'species pump', is widely accepted in the context of tropical biogeography and has been advocated as an explanation for present species distributions in tropical Western and Central Africa. In order to test this hypothesis, a phylogeny of the cryptic arachnid order Ricinulei, based on four nuclear and mitochondrial DNA markers, was inferred. This ancient clade of litter-dwelling arthropods, endemic to the primary forests of Western and Central Africa and the Neotropics, might provide insights into the mode and tempo of evolution in Africa. Twenty-six African ricinuleid specimens were sampled from eight countries spanning the distribution of Ricinulei on the continent, and analysed together with Neotropical samples plus other arachnid outgroups. The phylogenetic and molecular dating results suggest that Ricinulei diversified in association with the fragmentation of Gondwana. The early diversification of Ricinoides in Western and Central Africa around 88 (±33) Ma fits old palaeogeographical events better than recent climatic fluctuations. Unlike most recent molecular studies, these results agree with fossil evidence, suggesting that refugia may have acted as 'museums' conserving ancient diversity rather than as engines generating diversity during successive episodes of climatic fluctuation in Africa.

A well-corroborated morphological scheme of interrelationships for centipedes, once broadly accepted, has been in conflict with molecular data with respect to deep branching events. Expanded taxonomic coverage compared to previous analyses adds longer fragments for 28S rRNA and a structural alignment as part of a sample of four genes (two nuclear ribosomal and two mitochondrial) for 111 extant species; these sequence data are combined with morphology under parsimony and maximum likelihood, exploring both traditional multiple sequence alignment and direct optimization approaches. Novel automated procedures to incorporate secondary structure information are also explored. The molecular data in combination yield trees that are highly congruent with morphology as regards the monophyly of all centipede orders as well as the major groups within each of the large orders. Regardless of the optimality criterion or alignment strategy, the Tasmanian/New Zealand Craterostigmomorpha is resolved in a different position by the molecular data than by morphology. Addition of morphology overturns the placement of Craterostigmomorpha in favour of the traditional morphological resolution and eliminates the need to posit major character reversals with respect to developmental mode and maternal care. Calibration of the tree with Palaeozoic and Mesozoic fossils for a relaxed clock analysis corroborates the palaeontological signal that divergences between centipede orders date to the Silurian and earliest Devonian, and familial divergences are likewise almost wholly Palaeozoic., (Copyright 2010 Elsevier Inc. All rights reserved.)

New Caledonia has generally been considered a continental island, the biota of which largely dates back to Gondwanan times owing to its geological origin and the presence of phylogenetic relicts. This view is contradicted by geological evidence indicating long Palaeocene and Eocene submersions and by recent biogeographic and phylogenetic studies, with molecular or geophysical dating placing the biota no older than the Oligocene. Phylogenetic relicts do not provide conclusive information in this respect, as their presence cannot be explained by simple hypotheses but requires assumption of many ad hoc extinction events. The implication of this new scenario is that all the New Caledonian biota colonized the island since 37 Ma Local richness can be explained by local radiation and adaptation after colonization but also by many dispersal events, often repeated within the same groups of organisms. Local microendemism is another remarkable feature of the biota. It seems to be related to recent speciation mediated by climate, orography, soil type and perhaps unbalanced biotic interactions created by colonization disharmonies. New Caledonia must be considered as a very old Darwinian island, a concept that offers many more fascinating opportunities of study.

The phylogenetic relationships of the major lineages of the arachnid order Pseudoscorpiones are investigated for the first time using molecular sequence data from two nuclear ribosomal genes and one mitochondrial protein-encoding gene. The data were analyzed using a dynamic homology approach with the new program POY v.4 under parsimony as the optimality criterion. The data show monophyly of Pseudoscorpiones as well as many of its superfamilies (Feaelloidea, Chthonioidea, Cheiridioidea and Sternophoroidea), but not for Neobisiodea or Garypoidea. Cheliferoidea was not monophyletic either due to the position of Neochelanops, which grouped with some garypoids. In all the analyses, Feaelloidea constituted the sister group to all other pseudoscorpions; Chthonioidea is the sister group to the remaining families, which constitute the group Iocheirata sensu Harvey--a clade including pseudoscorpions with venom glands within the pedipalpal fingers. This phylogenetic pattern suggests that venom glands evolved just once within this order of arachnids.

The pycnogonids (or sea spiders) are an enigmatic group of arthropods, classified in recent phylogenies as a sister-group of either euchelicerates (horseshoe crabs and arachnids), or all other extant arthropods. Because of their bizarre morpho-anatomy, homologies with other arthropod taxa have been difficult to assess. We review the main morphology-based hypotheses of correspondence between anterior segments of pycnogonids, arachnids and mandibulates. In an attempt to provide new relevant data to these controversial issues, we performed a PCR survey of Hox genes in two pycnogonid species, Endeis spinosa and Nymphon gracile, from which we could recover nine and six Hox genes, respectively. Phylogenetic analyses allowed to identify their orthology relationships. The Deformed gene from E. spinosa and the abdominal-A gene from N. gracile exhibit unusual sequence divergence in their homeodomains, which, in the latter case, may be correlated with the extreme reduction of the posterior region in pycnogonids. Expression patterns of two Hox genes (labial and Deformed) in the E. spinosa protonymphon larva are discussed. The anterior boundaries of their expression domains favour homology between sea spider chelifores, euchelicerates chelicerae and mandibulate (first) antennae, in contradistinction with previously proposed alternative schemes such as the protocerebral identity of sea spider chelifores or the absence of a deutocerebrum in chelicerates. In addition, while anatomical and embryological evidences suggest the possibility that the ovigers of sea spiders could be a duplicated pair of pedipalps, the Hox data support them as modified anterior walking legs, consistent with the classical views.

Arthropod head segments offer a paradigm for understanding the diversification of form during evolution, as a variety of morphologically diverse appendages have arisen from them. There has been long-running controversy, however, concerning which head appendages are homologous among arthropods, and from which ancestral arrangement they have been derived. This controversy has recently been rekindled by the proposition that the probable ancestral arrangement, with appendages on the first head segment, has not been lost in all extant arthropods as previously thought, but has been retained in the pycnogonids, or sea spiders. This proposal was based on the neuroanatomical analysis of larvae from the sea spider Anoplodactylus sp., and suggested that the most anterior pair of appendages, the chelifores, are innervated from the first part of the brain, the protocerebrum. Our examination of Hox gene expression in another sea spider, Endeis spinosa, refutes this hypothesis. The anterior boundaries of Hox gene expression domains place the chelifore appendages as clearly belonging to the second head segment, innervated from the second part of the brain, the deutocerebrum. The deutocerebrum must have been secondarily displaced towards the protocerebrum in pycnogonid ancestors. As anterior-most appendages are also deutocerebral in the other two arthropod groups, the Euchelicerata and the Mandibulata, we conclude that the protocerebral appendages have been lost in all extant arthropods.

In comparative biology, character observations initially separate similar and dissimilar characters. Only similar characters are considered for phylogeny reconstruction; their homology is attested in a two-step process, firstly a priori of phylogeny reconstruction by accurate similarity statements, and secondly a posteriori of phylogeny analysis by congruence with other characters. Any pattern of non-homology is then a homoplasy, commonly, but vaguely, associated with "convergence". In this logical scheme, there is no way to analyze characters which look similar, but cannot meet usual criteria for homology statements, i.e., false similarity detected a priori of phylogenetic analysis, even though such characters may represent evolutionarily significant patterns of character transformations. Because phylogenies are not only patterns of taxa relationships but also references for evolutionary studies, we propose to redefine the traditional concepts of parallelism and convergence to associate patterns of non-homology with explicit theoretical contexts: homoplasy is restricted to non-similarity detected a posteriori of phylogeny analysis and related to parallelism; non-similarity detected a priori of phylogenetic analysis and necessarily described by different characters would then correspond to a convergence event s. str. We propose to characterize these characters as heterologous (heterology). Heterology and homoplasy correspond to different non-similarity patterns and processes; they are also associated with different patterns of taxa relationships: homoplasy can occur only in non-sister group taxa; no such limit exists for heterology. The usefulness of these terms and concepts is illustrated with patterns of acoustic evolution in ensiferan insects., (© The Willi Hennig Society 2005.)

New Caledonia is well known as a hot spot of biodiversity whose origin as a land mass can be traced back to the Gondwanan supercontinent. The local flora and fauna, in addition to being remarkably rich and endemic, comprise many supposedly relictual groups. Does the New Caledonian biota date back to Gondwanan times, building up its richness and endemism over 100 Myr or does it result from recent diversifications after Tertiary geological catastrophic events? Here we use a molecular phylogenetic approach to answer this question with the study of the Neocaledonian cockroach genus Angustonicus belonging to the subfamily Tryonicinae from Australia and New Caledonia. Both geological and molecular dating show that the diversification of this group is less than two million years old, whatever the date of its origin itself. This dating is not consistent with hypotheses of Gondwanan richness and endemism in New Caledonian biota. In other terms, local richness and endemism at the specific level are not necessarily related to an old Gondwanan origin of the Neocaledonian groups., (© The Willi Hennig Society 2005.)

A character of special interest in evolutionary studies is usually optimized on a phylogenetic tree, with or without the outgroups employed in that analysis. Both practices are never justified and look like arbitrary choices. Focusing on one example, we draw the conclusion that authors retain or remove outgroups depending on the way these outgroups sample the diversity of states of the character(s) of special interest. The topology without outgroups is often used by authors when different outgroup taxa non-exhaustively sample the different states of the character of interest outside of the ingroup. This can make the analysis incoherent, because its different steps are not based on the same data matrix (outgroups are removed in the last step). It can provide several incoherent and possibly different patterns for a same character of interest, one issuing from the first step of phylogeny construction and the other resulting from the a posteriori optimization on the truncated topology. Phylogenetic analyses should be designed to minimize this problem, selecting outgroup and ingroup taxa whose diversity of character states is needed for reconstructing the evolutionary history of the character of interest., (© The Willi Hennig Society 2004.)

The geometric mean length (GML) is proposed as a new statistic aimed at describing the evenness of character changes on a tree for a given set of character optimizations. It is the geometric mean of the number of steps on each branch of the tree, varying between a maximum value when all branch lengths are equal, and a minimum value when all branches but one have only one character step. It can be scaled according to its theoretical maximum value, thus indicating a relative GML that allows a comparison of the evenness of character steps between different tree topologies.