@article {9696, title = {Genetic variability of New Caledonian Boeckella de Guerne \& Richard, 1889 (Copepoda: Calanoida), with the description of a new species}, journal = {Journal of Crustacean Biology}, volume = {44}, year = {2024}, pages = {1{\textendash}17}, abstract = {Thirteen new freshwater populations of the copepod genus Boeckella De Guerne \& Richard, 1889 were found during three expeditions to New Caledonia ( La Planete Revisitee, 2016-2018). The 12 populations from the Plaine des Lacs, which show remarkable genetic diversity among themselves, were identified as B. spinogibba Defaye, 1998, the only species of its genus known from New Caledonia until now. The sole exception, the population from Mont-Dore 22 km further east, appeared genetically and morphologically distinct from the others and is described herein as a new species. The two species are distinguished from each other by the shapes of the male and female P5, female Th5, and body colour. A previously published key is amended to separate the species. Our concatenated COI+28S phylogeny places the two New Caledonia species as a new branch within Boeckella, distinct from the branches consisting of South American, Antarctic and Australasian species. All 13 Boeckella populations inhabit the extreme south of New Caledonia, an area known for endemism and high heavy metal concentrations in the soil. Extensive mining activity in this metal-rich area, begun in 1873, is now leading to conflict with conservation goals. By using aerial photographs to trace the fate of the pond that is the type locality of B. spinogibba, we confirmed that it disappeared between 2007 and 2014 as a result of the expansion of the Goro nickel mine.}, keywords = {Boeckella spinogibba, Conservation, Crustacea, freshwater zooplankton, micro-endemism, mining perturbation, morphology, Phylogeny, population genetics}, issn = {1937240X}, doi = {10.1093/jcbiol/ruae001}, author = {Royaux, Coline and Charpin, Nicolas and Nicolas Rabet} } @article {8728, title = {Exploration of chemosensory ionotropic receptors in cephalopods: the IR25 gene is expressed in the olfactory organs, suckers, and fins of Sepia officinalis.}, journal = {Chem Senses}, volume = {46}, year = {2021}, month = {2021 01 01}, abstract = {

While they are mostly renowned for their visual capacities, cephalopods are also good at olfaction for prey, predator, and conspecific detection. The olfactory organs and olfactory cells are well described but olfactory receptors-genes and proteins-are still undescribed in cephalopods. We conducted a broad phylogenetic analysis of the ionotropic glutamate receptor family in mollusks (iGluR), especially to identify IR members (Ionotropic Receptors), a variant subfamily whose involvement in chemosensory functions has been shown in most studied protostomes. A total of 312 iGluRs sequences (including 111 IRs) from gastropods, bivalves, and cephalopods were identified and annotated. One orthologue of the gene coding for the chemosensory IR25 co-receptor has been found in Sepia officinalis (Soff-IR25). We searched for Soff-IR25 expression at the cellular level by in situ hybridization in whole embryos at late stages before hatching. Expression was observed in the olfactory organs, which strongly validates the chemosensory function of this receptor in cephalopods. Soff-IR25 was also detected in the developing suckers, which suggests that the unique {\guillemotleft} taste by touch {\guillemotright} behavior that cephalopods execute with their arms and suckers share features with olfaction. Finally, Soff-IR25 positive cells were unexpectedly found in fins, the two posterior appendages of cephalopods, mostly involved in locomotory functions. This result opens new avenues of investigation to confirm fins as additional chemosensory organs in cephalopods.

}, keywords = {Animals, Cephalopoda, Phylogeny, Receptors, Ionotropic Glutamate, Receptors, Odorant, Sepia, Smell}, issn = {1464-3553}, doi = {10.1093/chemse/bjab047}, author = {Aude Andouche and Valera, St{\'e}phane and S{\'e}bastien Baratte} } @article {8133, title = {Gonadal transcriptomes associated with sex phenotypes provide potential male and female candidate genes of sex determination or early differentiation in Crassostrea gigas, a sequential hermaphrodite mollusc.}, journal = {BMC Genomics}, volume = {22}, year = {2021}, month = {2021 Aug 09}, pages = {609}, abstract = {

BACKGROUND: In the animal kingdom, mollusca is an important phylum of the Lophotrochozoa. However, few studies have investigated the molecular cascade of sex determination/early gonadal differentiation within this phylum. The oyster Crassostrea gigas is a sequential irregular hermaphrodite mollusc of economic, physiological and phylogenetic importance. Although some studies identified genes of its sex-determining/-differentiating pathway, this particular topic remains to be further deepened, in particular with regard to the expression patterns. Indeed, these patterns need to cover the entire period of sex lability and have to be associated to future sex phenotypes, usually impossible to establish in this sequential hermaphrodite. This is why we performed a gonadal RNA-Seq analysis of diploid male and female oysters that have not changed sex for 4 years, sampled during the entire time-window of sex determination/early sex differentiation (stages 0 and 3 of the gametogenetic cycle). This individual long-term monitoring gave us the opportunity to explain the molecular expression patterns in the light of the most statistically likely future sex of each oyster.

RESULTS: The differential gene expression analysis of gonadal transcriptomes revealed that 9723 genes were differentially expressed between gametogenetic stages, and 141 between sexes (98 and 43 genes highly expressed in females and males, respectively). Eighty-four genes were both stage- and sex-specific, 57 of them being highly expressed at the time of sex determination/early sex differentiation. These 4 novel genes including Trophoblast glycoprotein-like, Protein PML-like, Protein singed-like and PREDICTED: paramyosin, while being supported by RT-qPCR, displayed sexually dimorphic gene expression patterns.

CONCLUSIONS: This gonadal transcriptome analysis, the first one associated with sex phenotypes in C. gigas, revealed 57 genes highly expressed in stage 0 or 3 of gametogenesis and which could be linked to the future sex of the individuals. While further study will be needed to suggest a role for these factors, some could certainly be original potential actors involved in sex determination/early sex differentiation, like paramyosin and could be used to predict the future sex of oysters.

}, keywords = {Animals, Crassostrea, Female, Gene Expression Profiling, Gonads, Humans, Male, Phenotype, Phylogeny, Sex Differentiation, Transcriptome}, issn = {1471-2164}, doi = {10.1186/s12864-021-07838-1}, author = {Broquard, Coralie and Saowaros, Suwansa-Ard and Lepoittevin, M{\'e}lanie and Degremont, Lionel and Lamy, Jean-Baptiste and Morga, Benjamin and Elizur, Abigail and Anne-Sophie Martinez} } @article {7724, title = {New taxonomic and phylogeographic data on three nominal species of the genus Septaria F{\'e}russac, 1807 (Gastropoda: Cycloneritida: Neritidae)}, journal = {Zootaxa}, volume = {4915}, year = {2021}, month = {Jan-20-2021}, pages = {28 - 40}, abstract = {Due to superficial morphological similarities, there is often confusion in the identification of some species of the genus Septaria. A combined analysis of the genital anatomy, morphometric and DNA, based on a portion of the COI gene, applied to three nominal species of this genus, confirmed the validity of Septaria tahitiana Eichhorst, 2016, and suggested that Septaria borbonica (Bory de Saint Vincent, 1804) is a subspecies of Septaria porcellana (Linnaeus, 1758), both taxa with disjunct distribution areas: Septaria borbonica in the western Indian Ocean and Septaria porcellana the western Pacific and eastern Indian Oceans. The possible presence of Septaria tesselata (Lamarck, 1816) in Mayotte (Comoros Archipelago) needs to be confirmed.}, keywords = {Indo-Pacific, mitochondrial DNA, mollusc, Phylogeny, shell morphometrics, taxonomy}, issn = {1175-5326}, doi = {10.11646/zootaxa.4915.110.11646/zootaxa.4915.1.2}, url = {https://www.biotaxa.org/Zootaxa/issue/view/zootaxa.4915.1}, author = {Ahmed Abdou} } @article {9730, title = {Not Frozen in the Ice: Large and Dynamic Rearrangements in the Mitochondrial Genomes of the Antarctic Fish}, journal = {Genome Biology and Evolution}, volume = {13}, year = {2021}, month = {2021 Mar 01}, abstract = {

The vertebrate mitochondrial genomes generally present a typical gene order. Exceptions are uncommon and important to study the genetic mechanisms of gene order rearrangements and their consequences on phylogenetic output and mitochondrial function. Antarctic notothenioid fish carry some peculiar rearrangements of the mitochondrial gene order. In this first systematic study of 28 species, we analyzed known and undescribed mitochondrial genome rearrangements for a total of eight different gene orders within the notothenioid fish. Our reconstructions suggest that transpositions, duplications, and inversion of multiple genes are the most likely mechanisms of rearrangement in notothenioid mitochondrial genomes. In Trematominae, we documented an extremely rare inversion of a large genomic segment of 5,300 bp that partially affected the gene compositional bias but not the phylogenetic output. The genomic region delimited by nad5 and trnF, close to the area of the Control Region, was identified as the hot spot of variation in Antarctic fish mitochondrial genomes. Analyzing the sequence of several intergenic spacers and mapping the arrangements on a newly generated phylogeny showed that the entire history of the Antarctic notothenioids is characterized by multiple, relatively rapid, events of disruption of the gene order. We hypothesized that a pre-existing genomic flexibility of the ancestor of the Antarctic notothenioids may have generated a precondition for gene order rearrangement, and the pressure of purifying selection could have worked for a rapid restoration of the mitochondrial functionality and compactness after each event of rearrangement.

}, keywords = {Animals, Antarctic Regions, Evolution, Molecular, Fishes, Freezing, Gene Order, Gene Rearrangement, Genes, Mitochondrial, Genome, Mitochondrial, Genomics, Ice, Models, Genetic, Phylogeny, Vertebrates}, issn = {1759-6653}, doi = {10.1093/gbe/evab017}, url = {https://doi.org/10.1093/gbe/evab017}, author = {Papetti, Chiara and Babbucci, Massimiliano and Dettai, Agn{\`e}s and Basso, Andrea and Lucassen, Magnus and Harms, Lars and C{\'e}line Bonillo and Heindler, Franz Maximilian and Patarnello, Tomaso and Negrisolo, Enrico} } @article {9732, title = {Raising names from the dead: A time-calibrated phylogeny of frog shells (Bursidae, Tonnoidea, Gastropoda) using mitogenomic data.}, journal = {Mol Phylogenet Evol}, volume = {156}, year = {2021}, month = {2021 Mar}, pages = {107040}, abstract = {

With 59 Recent species, Bursidae, known as {\guillemotleft}frog shells{\guillemotright}, are a small but widely distributed group of tropical and subtropical gastropods that are most diverse in the Indo-West Pacific. The present study is aimed at reconstructing phylogenetic relationships of bursid gastropods based on extensive and representative taxon sampling. Five genetic markers (cytochrome c oxidase subunit I (cox1), 16\ s and 12\ s rRNA mitochondrial genes, 28\ s rRNA and Histone H3 nuclear gene) were sequenced for over 30 species in every known genus but Crossata. Furthermore, we sequenced the complete mt-genome of 9 species (10 specimens) (Aspa marginata, Marsupina bufo, Korrigania quirihorai, Korrigania fijiensis, Tutufa rubeta, Bursa lamarckii, Lampasopsis rhodostoma (twice), Bufonaria perelegans and Bursa aff. tuberosissima). Our analysis recovered Bursidae as a monophyletic group, whereas the genus Bursa was found to be polyphyletic. The genera Talisman and Dulcerana are resurrected and the genera Alanbeuella gen. nov. and Korrigania gen. nov. are described. Dating analysis using 21 extinct taxa for node and simplified tip calibrations was performed, showing a diversification of the group in two phases. Diversification may be linked to tectonic events leading to biodiversity relocation from the western Tethys toward the Indo-Pacific.

}, keywords = {Animals, Bayes Theorem, Calibration, Fossils, Gastropoda, Genes, Mitochondrial, Genome, Mitochondrial, Phylogeny, Sequence Analysis, DNA, Time Factors}, issn = {1095-9513}, doi = {10.1016/j.ympev.2020.107040}, author = {Sanders, Malcolm T and Merle, Didier and Laurin, Michel and C{\'e}line Bonillo and Puillandre, Nicolas} } @article {8449, title = {Passive rewilding may (also) restore phylogenetically rich and functionally resilient forest plant communities.}, journal = {Ecol Appl}, volume = {30}, year = {2020}, month = {2020 01}, pages = {e02007}, abstract = {

Passive rewilding is increasingly seen as a promising tool to counterbalance biodiversity losses and recover native forest ecosystems. One key question, crucial to understanding assembly processes and conservation issues underlying land-use change, is the extent to which functional and phylogenetic diversity may recover in spontaneous recent woodlands. Here, we compared understorey plant communities of recent woodlands (which result from afforestation on agricultural lands during the 20th century) with those of ancient forests (uninterrupted for several centuries) in a hotspot of farmland abandonment in western Europe. We combined taxonomic, functional, and phylogenetic diversity metrics to detect potential differences in community composition, structure (richness, divergence), conservation importance (functional originality and specialization, evolutionary distinctiveness) and resilience (functional redundancy, response diversity). The recent and ancient forests harbored clearly distinct compositions, especially regarding the taxonomic and phylogenetic facets. Recent woodlands had higher taxonomic, functional and phylogenetic richness and a higher evolutionary distinctiveness, whereas functional divergence and phylogenetic divergence were higher in ancient forests. On another hand, we did not find any significant differences in functional specialization, originality, redundancy, or response diversity between recent and ancient forests. Our study constitutes one of the first empirical pieces of evidence that recent woodlands may spontaneously regain plant communities phylogenetically rich and functionally resilient, at least as much as those of ancient relict forests. As passive rewilding is the cheapest restoration method, we suggest that it should be a very useful tool to restore and conserve native forest biodiversity and functions, especially when forest areas are restricted and fragmented.

}, keywords = {Biodiversity, Ecosystem, Europe, Forests, Phylogeny}, issn = {1051-0761}, doi = {10.1002/eap.2007}, author = {Morel, Lo{\"\i}s and Barbe, Lou and Jung, Vincent and Cl{\'e}ment, Bernard and Schnitzler, Annik and Fr{\'e}d{\'e}ric Ysnel} } @article {6044, title = {Does your lip stick? Evolutionary aspects of the mouth morphology of the Indo-Pacific clinging goby of the Sicyopterus genus (Teleostei: Gobioidei: Sicydiinae) based on mitogenome phylogeny.}, journal = {Journal of Zoological Systematics and Evolutionary Research}, year = {2019}, abstract = {

Sicydiinae gobies have an amphidromous life cycle. Adults grow, feed, and reproduce in rivers, while larvae have a marine dispersal phase. Larvae recruit back to rivers and settle in upstream habitats. Within the Sicydiinae subfamily, the\ Sicyopterus genus, one of the most diverse (24 species), is distributed in the tropical islands of the Indo-Pacific. One of the characters used to determine Sicyopterus species is the upper lip morphology, which can be either smooth, crenulated, or with papillae, and with (2 or 3) or without clefts. The mouth is used as a secondary locomotor organ along with the pelvic sucker. It is thus strongly related to the climbing ability of species and is of major importance for the upstream migration and the colonization of insular freshwater systems. The mouth also has an important role in the feeding mechanism of these herbivorous species. In this paper, we have established a molecular phylogeny of the genus based on the 13 mitochondrial protein-coding genes to discuss the relationship between 18 Sicyopterus species. There is a well-supported dichotomy in the molecular phylogeny of the Sicyopterus genus and this separation into two clades is also morphologically visible, with the distinction of species with three clefts and species with 0 or 2 clefts on the upper lip. The mouth morphology can thus be separated with regard to the molecular phylogeny obtained. The evolution of the mouth morphology is discussed in terms of the adaptation of the Sicyopterus genus to settlement and life in tropical insular river systems.

}, keywords = {mitogenome, mouth morphology, Phylogeny, Sicydiinae, Sicyopterus}, doi = {DOI: 10.1111/jzs.12291}, author = {Clara Lord and Laure Bellec and Dettai, Agn{\`e}s and C{\'e}line Bonillo and Philippe Keith} } @article {3631, title = {Looking for the bird Kiss: evolutionary scenario in sauropsids.}, journal = {BMC Evol Biol}, volume = {14}, year = {2014}, month = {2014}, pages = {30}, abstract = {

BACKGROUND: The neuropeptide Kiss and its receptor KissR are key-actors in the brain control of reproduction in mammals, where they are responsible for the stimulation of the activity of GnRH neurones. Investigation in other vertebrates revealed up to 3 Kiss and 4 KissR paralogs, originating from the two rounds of whole genome duplication in early vertebrates. In contrast, the absence of Kiss and KissR has been suggested in birds, as no homologs of these genes could be found in current genomic databases. This study aims at addressing the question of the existence, from an evolutionary perspective, of the Kisspeptin system in birds. It provides the first large-scale investigation of the Kisspeptin system in the sauropsid lineage, including ophidian, chelonian, crocodilian, and avian lineages.

RESULTS: Sauropsid Kiss and KissR genes were predicted from multiple genome and transcriptome databases by TBLASTN. Phylogenetic and syntenic analyses were performed to classify predicted sauropsid Kiss and KissR genes and to re-construct the evolutionary scenarios of both gene families across the sauropsid radiation.Genome search, phylogenetic and synteny analyses, demonstrated the presence of two Kiss genes (Kiss1 and Kiss2 types) and of two KissR genes (KissR1 and KissR4 types) in the sauropsid lineage. These four genes, also present in the mammalian lineage, would have been inherited from their common amniote ancestor. In contrast, synteny analyses supported that the other Kiss and KissR paralogs are missing in sauropsids as in mammals, indicating their absence in the amniote lineage. Among sauropsids, in the avian lineage, we demonstrated the existence of a Kiss2-like gene in three bird genomes. The divergence of these avian Kiss2-like sequences from those of other vertebrates, as well as their absence in the genomes of some other birds, revealed the processes of Kiss2 gene degeneration and loss in the avian lineage.

CONCLUSION: These findings contribute to trace back the evolutionary history of the Kisspeptin system in amniotes and sauropsids, and provide the first molecular evidence of the existence and fate of a Kiss gene in birds.

}, keywords = {Amino Acid Sequence, Animals, Avian Proteins, Biological Evolution, Birds, Humans, Kisspeptins, Molecular Sequence Data, Phylogeny, Receptors, G-Protein-Coupled, Reptiles, Sequence Alignment, Synteny}, issn = {1471-2148}, doi = {10.1186/1471-2148-14-30}, author = {Pasquier, J{\'e}r{\'e}my and Anne-Gaelle Lafont and Karine Rousseau and Qu{\'e}rat, Bruno and Chemineau, Philippe and Sylvie Dufour} } @article {4161, title = {A multilocus molecular phylogeny of combtooth blennies (Percomorpha: Blennioidei: Blenniidae): multiple invasions of intertidal habitats.}, journal = {Mol Phylogenet Evol}, volume = {70}, year = {2014}, month = {2014 Jan}, pages = {47-56}, abstract = {

The combtooth blennies (f. Blenniidae) is a diverse family of primarily marine fishes with approximately 387 species that inhabit subtidal, intertidal, supralittoral habitats in tropical and warm temperate regions throughout the world. The Blenniidae has typically been divided into six groups based on morphological characters: Blenniini, Nemophini, Omobranchini, Phenablenniini, Parablenniini, and Salariini. There is, however, considerable debate over the validity of these groups and their relationships. Since little is known about the relationships in this group, other aspects of their evolutionary history, such as habitat evolution and remain unexplored. Herein, we use Bayesian and maximum likelihood analyses of four nuclear loci (ENC1, myh6, ptr, and tbr1) from 102 species, representing 41 genera, to resolve the phylogeny of the Blenniidae, determine the validity of the previously recognized groupings, and explore the evolution of habitat association using ancestral state reconstruction. Bayesian and maximum likelihood analyses of the resulting 3100bp of DNA sequence produced nearly identical topologies, and identified many well-supported clades. Of these clades, Nemophini was the only traditionally recognized group strongly supported as monophyletic. This highly resolved and thoroughly sampled blenniid phylogeny provides strong evidence that the traditional rank-based classification does not adequately delimit monophyletic groups with the Blenniidae. This phylogeny redefines the taxonomy of the group and supports the use of 13 unranked clades for the classification of blenniids. Ancestral state reconstructions identified four independent invasions of intertidal habitats within the Blenniidae, and subsequent invasions into supralittoral and freshwater habitats from these groups. The independent invasions of intertidal habitats are likely to have played an important role in the evolutionary history of blennies.

}, keywords = {Animals, Bayes Theorem, Ecosystem, Likelihood Functions, Perciformes, Phylogeny, Sequence Analysis, DNA}, issn = {1095-9513}, doi = {10.1016/j.ympev.2013.09.001}, author = {Hundt, Peter J and Samuel Iglesias and Hoey, Andrew S and Simons, Andrew M} } @article {3486, title = {New Sicydiinae phylogeny (Teleostei: Gobioidei) inferred from mitochondrial and nuclear genes: insights on systematics and ancestral areas.}, journal = {Mol Phylogenet Evol}, volume = {70}, year = {2014}, month = {2014 Jan}, pages = {260-71}, abstract = {

The Sicydiinae subfamily (Teleostei: Gobioidei) is the biggest contributor to the diversity of fish communities in river systems of tropical islands. These species are found in the Indo-Pacific area, the Caribbean region and West Africa. They spawn in freshwater, their planktotrophic larvae drift downstream to the sea where they develop, before returning to the rivers to grow and reproduce. Hence, they are called amphidromous. Their phylogeny has been explored using a total of 3545 sites from 5 molecular markers (mitochondrial DNA: 16S rDNA, cytochrome oxidase I, cytochrome b; nuclear DNA: rhodopsin gene and a nuclear marker specially developed for this study, the interferon regulatory factor 2 binding protein 1-IRF2PB1). Sequences were obtained for 59 Sicydiinae specimens of 9 known genera. The Bayesian and maximum likelihood analyses support the monophyly of the subfamily as well as the monophylyof all genera except Sicydium, which is paraphyletic. Five major clades were identified within this subfamily. One clade contained the genus Stiphodon. Another clade contained Sicyopterus, Sicydium and Parasicydium with Sicyopterus as sister genus of Sicydium. The non-monophyly of Sicydium subclade, because it includes the monotypic genus Parasicydium, challenged the validity of Parasicydium genus. Ancestral area reconstruction showed that the subfamily emerged in the Central West Pacific region implying that previous hypotheses proposing a dispersal route for Sicydiinae into the Atlantic Ocean are unsupported by the present analysis. Our results suggest that the hypotheses for the dispersal route of the genus Sicydium should be reconsidered.

}, keywords = {Animals, Bayes Theorem, Cell Nucleus, Cytochromes b, DNA, Mitochondrial, DNA, Ribosomal, Electron Transport Complex IV, Evolution, Molecular, Female, Mitochondria, Perciformes, Phylogeny, Sequence Analysis, DNA}, issn = {1095-9513}, doi = {10.1016/j.ympev.2013.09.026}, author = {Taillebois, Laura and Castelin, Magalie and Clara Lord and Chabarria, Ryan and Dettai, Agn{\`e}s and Philippe Keith} }