Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny

International audienceBACKGROUND: Tunicates represent a key metazoan group as the sister-group of vertebrates within chordates. The six complete mitochondrial genomes available so far for tunicates have revealed distinctive features. Extensive gene rearrangements and particularly high evolutionary rates have been evidenced with regard to other chordates. This peculiar evolutionary dynamics has hampered the reconstruction of tunicate phylogenetic relationships within chordates based on mitogenomic data. RESULTS: In order to further understand the atypical evolutionary dynamics of the mitochondrial genome of tunicates, we determined the complete sequence of the solitary ascidian Herdmania momus. This genome from a stolidobranch ascidian presents the typical tunicate gene content with 13 protein-coding genes, 2 rRNAs and 24 tRNAs which are all encoded on the same strand. However, it also presents a novel gene arrangement, highlighting the extreme plasticity of gene order observed in tunicate mitochondrial genomes. Probabilistic phylogenetic inferences were conducted on the concatenation of the 13 mitochondrial protein-coding genes from representatives of major metazoan phyla. We show that whereas standard homogeneous amino acid models support an artefactual sister position of tunicates relative to all other bilaterians, the CAT and CAT+BP site- and time-heterogeneous mixture models place tunicates as the sister-group of vertebrates within monophyletic chordates. Moreover, the reference phylogeny indicates that tunicate mitochondrial genomes have experienced a drastic acceleration in their evolutionary rate that equally affects protein-coding and ribosomal-RNA genes. CONCLUSION: This is the first mitogenomic study supporting the new chordate phylogeny revealed by recent phylogenomic analyses. It illustrates the beneficial effects of an increased taxon sampling coupled with the use of more realistic amino acid substitution models for the reconstruction of animal phylogeny

Rapid microevolution during recent range expansion to harsh environments

Background: Adaptive evolution is one of the crucial mechanisms for organisms to survive and thrive in new environments. Recent studies suggest that adaptive evolution could rapidly occur in species to respond to novel environments or environmental challenges during range expansion. However, for environmental adaptation, many studies successfully detected phenotypic features associated with local environments, but did not provide ample genetic evidence on microevolutionary dynamics. It is therefore crucial to thoroughly investigate the genetic basis of rapid microevolution in response to environmental changes, in particular on what genes and associated variation are responsible for environmental challenges. Here, we genotyped genome-wide gene-associated microsatellites to detect genetic signatures of rapid microevolution of a marine tunicate invader, Ciona robusta, during recent range expansion to the harsh environment in the Red Sea. Results: The Red Sea population was significantly differentiated from the other global populations. The genome-wide scan, as well as multiple analytical methods, successfully identified a set of adaptive genes. Interestingly, the allele frequency largely varied at several adaptive loci in the Red Sea population, and we found significant correlations between allele frequency and local environmental factors at these adaptive loci. Furthermore, a set of genes were annotated to get involved in local temperature and salinity adaptation, and the identified adaptive genes may largely contribute to the invasion success to harsh environments. Conclusions: All the evidence obtained in this study clearly showed that environment-driven selection had left detectable signatures in the genome of Ciona robusta within a few generations. Such a rapid microevolutionary process is largely responsible for the harsh environmental adaptation and therefore contributes to invasion success in different aquatic ecosystems with largely varied environmental factors

Deep Sequencing of Mixed Total DNA without Barcodes Allows Efficient Assembly of Highly Plastic Ascidian Mitochondrial Genomes

Ascidians or sea squirts form a diverse group within chordates, which includes a few thousand members of marine sessile filter-feeding animals. Their mitochondrial genomes are characterized by particularly high evolutionary rates and rampant gene rearrangements. This extreme variability complicates standard polymerase chain reaction (PCR) based techniques for molecular characterization studies, and consequently only a few complete Ascidian mitochondrial genome sequences are available. Using the standard PCR and Sanger sequencing approach, we produced the mitochondrial genome of Ascidiella aspersa only after a great effort. In contrast, we produced five additional mitogenomes (Botrylloides aff. leachii, Halocynthia spinosa, Polycarpa mytiligera, Pyura gangelion, and Rhodosoma turcicum) with a novel strategy, consisting in sequencing the pooled total DNA samples of these five species using one Illumina HiSeq 2000 flow cell lane. Each mitogenome was efficiently assembled in a single contig using de novo transcriptome assembly, as de novo genome assembly generally performed poorly for this task. Each of the new six mitogenomes presents a different and novel gene order, showing that no syntenic block has been conserved at the ordinal level (in Stolidobranchia and in Phlebobranchia). Phylogenetic analyses support the paraphyly of both Ascidiacea and Phlebobranchia, with Thaliacea nested inside Phlebobranchia, although the deepest nodes of the Phlebobranchia–Thaliacea clade are not well resolved. The strategy described here thus provides a cost-effective approach to obtain complete mitogenomes characterized by a highly plastic gene order and a fast nucleotide/amino acid substitution rate

An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

<p>Abstract</p> <p>Background</p> <p>Tunicates have been recently revealed to be the closest living relatives of vertebrates. Yet, with more than 2500 described species, details of their evolutionary history are still obscure. From a molecular point of view, tunicate phylogenetic relationships have been mostly studied based on analyses of 18S rRNA sequences, which indicate several major clades at odds with the traditional class-level arrangements. Nonetheless, substantial uncertainty remains about the phylogenetic relationships and taxonomic status of key groups such as the Aplousobranchia, Appendicularia, and Thaliacea.</p> <p>Results</p> <p>Thirty new complete 18S rRNA sequences were acquired from previously unsampled tunicate species, with special focus on groups presenting high evolutionary rate. The updated 18S rRNA dataset has been aligned with respect to the constraint on homology imposed by the rRNA secondary structure. A probabilistic framework of phylogenetic reconstruction was adopted to accommodate the particular evolutionary dynamics of this ribosomal marker. Detailed Bayesian analyses were conducted under the non-parametric CAT mixture model accounting for site-specific heterogeneity of the evolutionary process, and under RNA-specific doublet models accommodating the occurrence of compensatory substitutions in stem regions. Our results support the division of tunicates into three major clades: 1) Phlebobranchia + Thaliacea + Aplousobranchia, 2) Appendicularia, and 3) Stolidobranchia, but the position of Appendicularia could not be firmly resolved. Our study additionally reveals that most Aplousobranchia evolve at extremely high rates involving changes in secondary structure of their 18S rRNA, with the exception of the family Clavelinidae, which appears to be slowly evolving. This extreme rate heterogeneity precluded resolving with certainty the exact phylogenetic placement of Aplousobranchia. Finally, the best fitting secondary-structure and CAT-mixture models suggest a sister-group relationship between Salpida and Pyrosomatida within Thaliacea.</p> <p>Conclusion</p> <p>An updated phylogenetic framework for tunicates is provided based on phylogenetic analyses using the most realistic evolutionary models currently available for ribosomal molecules and an unprecedented taxonomic sampling. Detailed analyses of the 18S rRNA gene allowed a clear definition of the major tunicate groups and revealed contrasting evolutionary dynamics among major lineages. The resolving power of this gene nevertheless appears limited within the clades composed of Phlebobranchia + Thaliacea + Aplousobranchia and Pyuridae + Styelidae, which were delineated as spots of low resolution. These limitations underline the need to develop new nuclear markers in order to further resolve the phylogeny of this keystone group in chordate evolution.</p

Uspostavljanje popisa morskih invazivnih vrsta u ESENIAS području: sadašnja situacija i buduća očekivanja

In this study we present a list of invasive/potential invasive alien species in the East and South European Network for Invasive Alien Species (ESENIAS) countries with marine borders. The species were classified according to the existing literature and experts’ judgment, as established, casual, invasive and expected. Finally, factsheets were compiled for ten species of high importance based on their expanding/invading character. Of the 160 species comprising the list, 149 were already present in the ESENIAS countries, while eleven were invasive species either present in the Mediterranean or in other European Seas, likely to be recorded in the ESENIAS countries. The majority of the species were of Red Sea/IndoPacific origin (97 species; 60.6%). Italy, Turkey and Greece were the countries with the highest representation of species (159, 152 and 139 species respectively), due to their extended coastline and the number of scholars working on marine invasive species. The highest number of established species was recorded in Turkey (116 species), whereas in Italy and Greece the most numerous species were the “expected” ones (85 and 48 species, respectively). The eastern Adriatic Sea countries (i.e. Albania, Croatia, Montenegro and Slovenia) had generally low numbers of species in this list, many of which are still “expected” to arrive from the neighbouring countries of Greece and Italy. Finally, the most frequently potential pathway was transfer stowaways (ship ballast water: 41 cases; ship hull fouling: 55), whereas unaided spread of Lessepsian immigrants followed (95 cases). This list is intended to serve as an early warning system that through horizon scanning process would assist ESENIAS countries to prioritise invasive alien species, their pathways and the areas of higher likelihood to appear, in order to take management measures.U ovom radu predstavljamo popis invazivnih i potencijalno invazivnih vrsta na istoku i jugu Europske mreže za invazivne vrste (ESENIAS) u zemljama s morskim granicama. Vrste su klasificirane prema postojećoj literaturi i procjeni stručnjaka, pa su tako utvrđene grupe povremenih, invazivnih i očekivanih vrsta. Podaci su dati za deset vrsta čija se važnost temelji na njihovom širenju i invazivnom karakteru. Od 160 vrsta koje sadrži popis, 148 je već bilo prisutno u ESENIAS zemljama, dok je 9 invazivnih vrsta bilo prisutno u Sredozemnom ili u drugim europskim morima, a vjerojatno je da će se zabilježiti i u zemljama udruženim u ESENIAS. Većina vrsta je bile iz Crvenog mora / indopacifičkog podrijetla (97 vrsta, 60,6%). Italija, Turska i Grčka su zemlje s najvišom zastupljenošću vrsta (159, 152 i 139), zbog njihove proširene obale i broja znanstvenika koji rade na morskim invazivnim vrstama. Najveći broj utvrđenih vrsta zabilježen je u Turskoj (116 vrsta), dok su u Italiji i Grčkoj najbrojnije vrste bile “očekivane” (85 i 48 vrsta, respektivno). Istočne zemlje Jadranskog mora (npr. Albanija, Hrvatska, Crna Gora i Slovenija) imale su općenito nizak broj vrsta na ovom popisu, od kojih mnoge još “očekujemo” da pristignu iz susjednih zemalja: Grčke i Italije. Konačno, najčešće su potencijalni putovi bili „transferni putnici“ (balastna voda broda: 41 slučaj, obraštaj brodskog trupa: 55), dok je slijedilo i širenje lesepsijskih migranata (95 slučajeva). Ovaj popis je namijenjen da služi kao sustav ranog upozorenja koji bi kroz proces skeniranja pomogao državama ESENIAS da daju prioritet invazivnim stranim vrstama, njihovim putovima i područjima veće vjerojatnosti pojavljivanja, kako bi se poduzele potrebne mjere upravljanja

Global Diversity of Ascidiacea

The class Ascidiacea presents fundamental opportunities for research in the fields of development, evolution, ecology, natural products and more. This review provides a comprehensive overview of the current knowledge regarding the global biodiversity of the class Ascidiacea, focusing in their taxonomy, main regions of biodiversity, and distribution patterns. Based on analysis of the literature and the species registered in the online World Register of Marine Species, we assembled a list of 2815 described species. The highest number of species and families is found in the order Aplousobranchia. Didemnidae and Styelidae families have the highest number of species with more than 500 within each group. Sixty percent of described species are colonial. Species richness is highest in tropical regions, where colonial species predominate. In higher latitudes solitary species gradually contribute more to the total species richness. We emphasize the strong association between species richness and sampling efforts, and discuss the risks of invasive species. Our inventory is certainly incomplete as the ascidian fauna in many areas around the world is relatively poorly known, and many new species continue to be discovered and described each year

The Magnitude of Global Marine Species Diversity

Background: The question of how many marine species exist is important because it provides a metric for how much we do and do not know about life in the oceans. We have compiled the first register of the marine species of the world and used this baseline to estimate how many more species, partitioned among all major eukaryotic groups, may be discovered. Results: There are ∼226,000 eukaryotic marine species described. More species were described in the past decade (∼20,000) than in any previous one. The number of authors describing new species has been increasing at a faster rate than the number of new species described in the past six decades. We report that there are ∼170,000 synonyms, that 58,000–72,000 species are collected but not yet described, and that 482,000–741,000 more species have yet to be sampled. Molecular methods may add tens of thousands of cryptic species. Thus, there may be 0.7–1.0 million marine species. Past rates of description of new species indicate there may be 0.5 ± 0.2 million marine species. On average 37% (median 31%) of species in over 100 recent field studies around the world might be new to science. Conclusions: Currently, between one-third and two-thirds of marine species may be undescribed, and previous estimates of there being well over one million marine species appear highly unlikely. More species than ever before are being described annually by an increasing number of authors. If the current trend continues, most species will be discovered this century

Boltenia yossiloya Shenkar & Lambert 2010, n. sp.

Boltenia yossiloya n. sp. Figs. 2–6 Material examined: Israel, Eilat, Gulf of Aqaba (Fig.1 29°30' N, 34°56' E). Holotype: AS25420, paratype: AS 25231, The National Collections of Natural History at Tel Aviv University, Israel. External appearance. Individuals have a somewhat spherical body with long siphons, up to 3 cm in diameter. The test is thick and hard with embedded sand, shell fragments and rubble, grayish in living specimens (Fig. 2). The tunic is unusually thin on both left and right sides of the body of the holotype because it was in the middle of a clump of other stolidobranchs and tightly adherent to them, with only the siphons and upper part of the body extending above the clump. Internal appearance. Both siphons are long, with 4 lobes, and directed anteriorly. The body wall is tightly attached to the whitish tunic lining. The bright orange–red siphons retain their color in formalin. The body musculature is well developed, the predominant pattern consisting of strong circular muscles around the siphons and body wall, overlying numerous wide longitudinal muscles covering the entire body wall (Fig. 3A, 3B). About 37 longitudinal muscle bands originate from each siphon and extend ventrally and posteriorly, while numerous bands circle the base of each siphon. The longitudinal muscles cross each other and interweave over the body forming a meshwork; posteriorly there are also numerous narrower muscles also interweaving to form a third irregular layer of musculature (Fig. 3C). There are about 20 branchial tentacles sparsely branched in two orders (Fig. 3D); there are no atrial tentacles. A large velum is present at the base of both siphons and the siphonal lining is thick, white and irregularly ridged (Fig. 3E), without any siphonal spines. The stigmata, diagnostic of the genus, are transversely oriented in longitudinal rows and the longitudinal vessels cross them (Fig. 3F). The branchial sac has six high folds on each side with 12–21 longitudinal vessels on the folds and 4–10 between the folds. The branchial formula of the holotype specimen (approximately 3.2 cm in width) is: DL 5(20)8(21)8(16)9(16)6(16)6(12)5 E Left side E 5(18)8(20)9(17)9(20)10(18)5(16)4 DL Right side Paratype specimen (3 cm in width) is: DL 4(17)4(24)6(22)8(19)8(17)5(12)4 E The dorsal lamina is composed of numerous short languets; the dorsal tubercle is C-shaped opening to the left (Fig. 4A) inside a large V with brown pigments (in preserved material) in the peribranchial area. The stomach is short, with numerous longitudinal folds. The liver, about equal in size to the stomach, consists of a large mass of glandular yellowish tubules (Fig. 4B). On the secondary intestinal curve there are 2 very small endocarps, one on the outer side and one on the inner side opposite the liver. The short rectum is attached directly and firmly to the branchial sac (as in B. transversaria). The anus is somewhat flattened into two halves, the rim with about 12 very small lobes and 4 slightly larger lobes (Fig. 5). There is one gonad on each side comprised of 5 large overlapping blocks of tissue closely but narrowly connected (Fig. 6). The left gonad lies diagonally above the secondary gut loop with the last lobe close to the rectum (Figs. 3A, 6). The right gonad lies diagonal to the ventral line (Fig. 3B). A short oviduct and sperm duct, with small brown pigmented spots on them, terminate from the distal end of each gonad, opening close together near the base of the atrial siphon. Remarks. This new species has some characters in common with Boltenia transversaria (Sluiter, 1904), from Indonesian waters: the body tightly attached to the tunic (not actually a valid feature distinguishing species), the number of branchial folds, and the dorsal lamina description. However, the branchial formulas are quite different. According to Sluiter (1904), his B. transversaria type specimen of 3 cm (similar in size to our B. yossiloya type) had 5 broad branchial folds per side each with 10 longitudinal vessels and a smaller fold on each side of the endostyle with only 4 longitudinal vessels, and 4–7 vessels between the folds, a much different and smaller formula than for B. yossiloya. The formulas given by Tokioka (1960) and Nishikawa (1991) are not really comparable because the animals they examined were much smaller. Boltenia yossiloya has strongly developed musculature (Fig. 3A, B, C) similar to Tokioka’s description but in contrast to Sluiter’s remark on the weak musculature of B. transversaria except on the siphons. B. yossiloya has a C-shaped dorsal tubercle opening to the left in contrast to the longitudinally ovate slit described for B. transversaria by Sluiter (1904), Herdman (1906) and Tokioka (1960); Nishikawa (1991) did not include a description of this character. Boltenia echinata (Linnaeus, 1767) which is a cold water species has eight branchial folds and long bushy tunic spines (Van Name 1945, Nishikawa 1991). Boltenia hirta Monniot and Monniot, 1977 is an abyssal Indian Ocean species that has recently been assigned to the genus Hemistyela (Sanamyan and Sanamyan 2006). The most closely related species to B. yossiloya appears to be Boltenia africana (Millar, 1962) described from the southern coasts of South Africa, which has a similar tunic, dorsal tubercle, number of folds and longitudinal vessels, and musculature arrangement. We were not allowed to borrow the holotype of B. africana (SAM A25620) from the South African Museum but Dr. M. Rius from the University of Cape Town kindly examined and photographed it for us, and they are clearly separate species. The holotype measures 4.5 cm in the tunic. The gonads of the two species have a very dissimilar appearance (compare Fig. 7 with Fig. 6); indeed, the flattened undulating gonads of B. africana resemble those illustrated for B. transversaria by Tokioka (1960). B. africana has a much more closed and narrow gut loop with the left gonad lying very close to the secondary loop. In B. yossiloya the gut loop is broadly open until the rectal region which lies very close to the esophagus (Fig. 6), and the left gonad does not lie closely in the secondary gut loop as described for B. africana (and also clearly visible in Fig. 7) but is rather above it and diagonal (Fig. 3A). There are two small endocarps on the secondary intestinal loop in B. yossiloya (Fig. 6) which are apparently not present in B. africana. In B. yossiloya the anus has lobed margins versus the apparently plain margin of B. africana mentioned by Millar (1962) and Rius (pers. comm.). In B. africana the largest oral tentacles are tripinnate (Millar 1962) while in B. yossiloya there is only secondary branching (those of the holotype were not described by Rius). B. africana also has not been recorded from tropical coral reefs. These specimens were collected only from artificial substrates which makes it difficult to determine whether the species is endemic to the Gulf of Eilat. However, due to its external camouflaged appearance it may be very difficult to spot this animal in the natural environment.Published as part of Shenkar, Noa & Lambert, Gretchen, 2010, A new species of the genus Boltenia (Ascidiacea) from the Red Sea, pp. 61-68 in Zootaxa 2391 (1) on pages 62-67, DOI: 10.11646/zootaxa.2391.1.4, http://zenodo.org/record/530704

Ascidian introductions through the Suez Canal: the case study of an Indo-Pacific species

Although marine biological invasions via the Suez Canal have been extensively documented, little is known about the introduction of non-indigenous ascidians (Chordata, Ascidiacea), a group containing particularly aggressive invasive species. Here, we used a multidisciplinary approach to study the introduction of the ascidian Herdmania momus into the Mediterranean Sea. We reviewed its taxonomy and global distribution, and analyzed how genetic variation is partitioned between sides of the Suez Canal. The taxonomic revision showed that H. momus currently has a wide Indo-Pacific distribution. Genetic data indicated two well-differentiated colonization histories across the eastern Mediterranean. Our findings suggest that the range expansion of H. momus has been greatly facilitated by the combined effect of human-mediated transport and the species' ability to adapt to different environments. The integrative approach presented here is critical to attain a holistic understanding of marine biological invasions, especially when studying groups with a poorly resolved taxonomy