Lise Dupont

Fine- and regional-scale genetic structure of the exotic ascidian Styela clava (Tunicata) in southwest England, 50 years after its introduction

Styela clava, an ascidian native to the northwest Pacific, was first recorded in the Atlantic at Plymouth, southwest England, in 1953. It now ranges in the northeast Atlantic from Portugal to northern Denmark, and has colonized the east coast of North America. Within the region of first introduction, we aimed to characterize current genetic diversity in the species, elucidate the respective roles of human‐aided vs. natural dispersal, and assess the extent of larval dispersal by looking for genetic differentiation at very small scales. Eight sites, mostly marinas, were studied along c. 200 km of coast in southwest England encompassing Plymouth. Five microsatellite loci were genotyped in 303 individuals to analyse gene flow at regional (among sites) and fine (within sites) scales. F‐statistics and assignment tests were used to investigate regional genetic structure. At the fine scale, deviation from mutation–drift equilibrium was tested, and isolation by distance and genetic clustering analyses were undertaken. Significant genetic differentiation existed between sites, unrelated to geographical separation; migration between geographically distant marinas was inferred, highlighting the likely importance of human‐mediated dispersal in range expansion and occupancy by S. clava. Fine‐scale population structure was present within at least four sites, which may be explained by the limited dispersal ability of this ascidian and recruitment from differentiated pools of larvae. Populations in enclosed marinas had higher self‐recruitment rates than those in open sites. Some marinas might therefore function as reservoirs of propagules for subsequent spread, whereas others might be sinks for migrants.

Global Phylogeography of the Widely Introduced North West Pacific Ascidian Styela clava

The solitary ascidian Styela clava Herdman, 1882 is considered to be native to Japan, Korea, northern China and the Russian Federation in the NW Pacific, but it has spread globally over the last 80 years and is now established as an introduced species on the east and west coasts of North America, Europe, Australia and New Zealand. In eastern Canada it reaches sufficient density to be a serious pest to aquaculture concerns. We sequenced a fragment of the cytochrome oxidase subunit I mitochondrial gene (COI) from a total of 554 individuals to examine the genetic relationships of 20 S. clava populations sampled throughout the introduced and native ranges, in order to investigate invasive population characteristics. The data presented here show a moderate level of genetic diversity throughout the northern hemisphere. The southern hemisphere (particularly New Zealand) displays a greater amount of haplotype and nucleotide diversity in comparison. This species, like many other invasive species, shows a range of genetic diversities among introduced populations independent of the age of incursion. The successful establishment of this species appears to be associated with multiple incursions in many locations, while other locations appear to have experienced rapid expansion from a potentially small population with reduced genetic diversity. These contrasting patterns create difficulties when attempting to manage and mitigate a species that continues to spread among ports and marinas around the world.

Hybridization relics complicate barcode-based identification of species in earthworms

Introgressive hybridization results in mito‐nuclear discordance which could obscure the delimitation of closely related taxa. Although such events are increasingly reported, they have been poorly studied in earthworms. Here, we propose a method for investigating the degree of introgressive hybridization between three taxa of the Allolobophora chlorotica aggregate within two field populations (N = 67 and N = 105) using a reference data set including published DNA barcoding and microsatellite data of all known A. chlorotica lineages (N = 85). For this, we used both molecular phylogenetic and population genetic approaches. The test of correspondence between mitochondrial cytochrome c oxidase I (COI) lineages and clusters of nuclear microsatellite genotypes allowed individuals to be sorted in three categories (matching, admixed and nonmatching) and additional markers (mitochondrial NADH dehydrogenase subunit 1, nuclear Histone 3 and Internal transcribed Spacer Region 2) were used for phylogenetic reconstructions in order to check assignments. Although 15 admixed individuals were observed, no early‐generation hybrids were detected within the two populations. Interestingly, 14 nonmatching individuals (i.e. with a mtDNA haplotype that did not correspond to their nuclear cluster) were detected, a pattern that would result after multiple generations of unidirectional hybridization of female from one taxon to male of the other taxon. Because earthworms are simultaneous hermaphrodites, these events of unidirectional hybridization suggest sterility of the male function in several crosses and highlight that some individuals can be misidentified if reliance is placed on COI barcodes alone. These findings could improve the use of these barcodes in earthworms for species delineation.

Genetic variability of the soil-feeding termite Labiotermes labralis (Termitidae, Nasutitermitinae) in the Amazonian primary forest and remnant patches.

Abstract.  1 Tropical rainforest fragmentation may increase the risk of extinction of limited dispersers such as soil‐feeding termites which play a fundamental role in soil structure and fertility. 2 We tested the hypothesis that population genetic structure of Labiotermes labralis, one of the most abundant soil‐feeders in the Amazonian primary forest, may vary in response to local ecological conditions. 3 As a pre‐requisite, two factors that may have important consequences on population genetic structure were examined: colony social organisation and infection by Wolbachia bacterium. This cytoplasmic endosymbiont is able to manipulate arthropod reproduction and thus, to alter patterns of mtDNA variation. 4 Three sites in French Guiana showing variable level of forest disturbance were studied. Three hundred and thirty‐eight neuters and 14 primary reproductives from 17 colonies were genotyped using six microsatellites to analyse colony and population genetic structure. Moreover, one sequence of the COII mitochondrial gene was obtained for each nest. 5 We showed that all nests were monogamous. In a single site, all nests were infected by the same Wolbachia strain. This pattern of infection was not associated to a particular mitochondrial haplotype. 6 In the most disturbed site, a significant inbreeding coefficient associated with high relatedness between primary reproductives suggested that anthropogenic habitat fragmentation has induced genetic isolation of the population; a result reinforced by the mitochondrial data. Thus, habitat fragmentation might have serious consequences for the persistence of L. labralis populations in French Guiana.

New perspectives for population genetics of Chagas'disease vectors in the Northeastern Brazil: isolation of polymorphic microsatellite markers in Triatoma brasiliensis.

Triatoma brasiliensis is the most important Chagas disease vector in semiarid areas of Northeastern Brazil. Although generally found in natural environment, it regularly colonizes or reinvades domiciliary ecotopes. In order to analyse gene flow between habitats, we identified and characterized six microsatellite loci using a microsatellite-enriched genomic library. To assess the usefulness of these microsatellites for genetic studies, we investigated their variability in two natural populations of the T. brasiliensis complex sampled in two Brazilian districts (Corone Jose Dia, South of Piaui state; Curaça, North of Bahia state). The taxonomic status of the samples was checked using cytb sequences. Phylogenetic analyses confirmed that the individuals from Bahia belonged to the T. juazeirensis species. Moreover, primers cross-amplification was tested in 5 Triatoma species and 4 loci successfully amplified in T. infestans and T. guasayana.

Landscape features impact connectivity between soil populations: a comparative study of gene flow in earthworms

Landscape features are known to alter the spatial genetic variation of aboveground organisms. Here, we tested the hypothesis that the genetic structure of belowground organisms also responds to landscape structure. Microsatellite markers were used to carry out a landscape genetic study of two endogeic earthworm species, Allolobophora chlorotica (N = 440, eight microsatellites) and Aporrectodea icterica (N = 519, seven microsatellites), in an agricultural landscape in the North of France, where landscape features were characterized with high accuracy. We found that habitat fragmentation impacted genetic variation of earthworm populations at the local scale. A significant relationship was observed between genetic diversity (He, Ar) and several landscape features in A. icterica populations and A. chlorotica. Moreover, a strong genetic differentiation between sites was observed in both species, with a low degree of genetic admixture and high Fst values. The landscape connectivity analysis at the regional scale, including isolation by distance, least‐cost path and cost‐weighted distance approaches, showed that genetic distances were linked to landscape connectivity in A. chlorotica. This indicates that the fragmentation of natural habitats has shaped their dispersal patterns and local effective population sizes. Landscape connectivity analysis confirmed that a priori favourable habitats such as grasslands may constitute dispersal corridors for these species.

The complete mitochondrial DNA sequence of the pantropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Clitellata): Mitogenome characterization and phylogenetic positioning

Abstract Pontoscolex corethrurus (Müller, 1857) plays an important role in tropical soil ecosystems and has been widely used as an animal model for a large variety of ecological studies in particular due to its common presence and generally high abundance in human-disturbed tropical soils. In this study we describe the complete mitochondrial genome of the peregrine earthworm P. corethrurus. This is the first record of a mitochondrial genome within the Rhinodrilidae family. Its mitochondrial genome is 14 835 bp in length containing 37 genes (13 protein-coding genes (PCG) 2 rRNA genes and 22 tRNA genes). It has the same gene content and structure as in other sequenced earthworms but unusual among invertebrates it hasseveral overlapping open reading frames. All genes are encoded on the same strand. Most of the PCGs use ATG as the start codon except for ND3 which uses GTG as the start codon. The A+T content of the mitochondrial genome is 59.9% (31.8% A 28.1% T 14.6% G and 25.6% for C). The annotated genome sequence has been deposited in GenBank under the accession number KT988053.

Application of Molecular Genetics to Earthworm Ecology: Current Research and Promising Future Directions

In earthworm ecology, the use of molecular tools has been restricted to certain fields such as ecotoxicology. In this chapter, we highlight two key issues of earthworm ecology that would greatly benefit from molecular information: dispersal behaviour and reproductive strategies. Elucidating patterns of dispersal is fundamental in guiding our understanding of earthworms’ distribution in both time and space. Field methods traditionally employed for measuring dispersal are difficult to use in species hidden in the soil, such as earthworms. Alternatively, genetic tools allow assessing dispersal from the detailed analysis of the genetic structure within and among populations. Besides, a good understanding of the mating strategy is essential to interpret population genetic patterns, particularly in species that present a great diversity of reproductive modes such as earthworms. After a short presentation of available genetic markers for earthworm genetics and a summary of the recent advances in molecular taxonomy of earthworms, current research in earthworm dispersal and mating behaviour are presented and the interest of using molecular markers for genetic inference is discussed.

Parentage analysis in Gabonese colonies of soil-feeding termites belonging to the Cubitermes sp. affinis subarquatus complex of species (Termitidae: Termitinae)

Abstract  Cubitermes spp. are widely distributed soil‐feeding termite species in sub‐Saharan Africa which play a fundamental role in soil structure and fertility. A complex of at least four cryptic species (i.e., Cubitermes sp. affinis subarquatus complex of species) has been recently described using molecular markers. In order to investigate the breeding system of these species, five microsatellite markers were used to carry out parentage and relatedness analyses in 15 Gabonese colonies. Monogamy was confirmed as the predominant reproductive organization in Cubitermes spp. (76% of the colonies). Within 30% of these monogamous colonies, a high relatedness between reproductives was shown, suggesting that mating between related individuals occurs. However, Cubitermes colonies can deviate from monogamy. Indeed, parental contributions by at least two related reproductives of the same sex were revealed in four colonies and polyandry was demonstrated in two of them. Infiltration of reproductives in the colony is the most plausible explanation for such cases of polygamy in Cubitermes spp.

Complex taxonomy of the 'brush tail' peregrine earthworm #Pontoscolex corethrurus#

Pontoscolex corethrurus is the most widespread earthworm species in tropical and sub-tropical zones and one of the most studied in soil science. Although, ecological interactions of P. corethrurus with its environment are well documented, the taxonomic status of the species remains unclear. In this study, we investigated phylogenetic relationships within the genus Pontoscolex, in particular focusing on morphologically indistinguishable (i.e., cryptic) lineages. A total of 792 specimens collected from 25 different countries and islands all over the world were analyzed using two mitochondrial (COI and 16S rDNA) and two nuclear (internal transcribed spacers 2 and 28S rDNA) markers, and a total of 11 morphological characters both internal and external were investigated in all genetically characterized lineages. A large-scale multilocus sequence data matrix was also obtained for Pontoscolex spp. specimens using the Anchored Hybrid Enrichment (AHE) method. Multilocus phylogenetic and phylogenomic analyses, combined with species delimitation methods; including single locus (mPTP, ABGD) and multilocus (BPP) approaches, revealed congruent results. Four cryptic species were supported within the P. corethrurus species complex, and four potentially new species within the genus Pontoscolex. One widespread lineage (L1), within P. corethrurus complex was observed in the current population of Fritz Müllers garden where P. corethrurus was first described in 1856. Cryptic lineages were observed in sympatry at several localities. This, in combination with observed heteroplasmy in COI gene in one population raises an important question of reproductive isolation between these species.