Low cost sequencing of mitogenomes from museum samples using baits capture and Ion Torrent

Paid Open Acces

Isolation and characterization of twelve microsatellite loci for the Japanese Devilray (Mobula japanica)

Twelve polymorphic microsatellites loci were characterized for Mobula japanica (Japanese Devilray) using an enrichment protocol. All but two loci were in Hardy-Weinberg equilibrium with no evidence of linkage disequilibrium or null-alleles for a sample of 40 individuals from two populations. The number of alleles varied from 5 to 28. Expected heterozygosity ranged from 0.2332 to 0.9589, making these microsatellite loci good candidates for population genetic studies

Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification

Submitted version (preprint).This is the pre-peer reviewed version of the following article: Smolina, I., Kollias, S., Poortvliet, M., Nielsen, T.G., Lindeque, P., Castellani, C., ... Hoarau, G.G. (2014). Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification. Molecular Ecology Resources, 14(5), 1072-1079, which has been published in final form at http://dx.doi.org/10.1111/1755-0998.12241. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving (http://olabout.wiley.com/WileyCDA/Section/id-820227.html)

Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification

Submitted version (preprint).This is the pre-peer reviewed version of the following article: Smolina, I., Kollias, S., Poortvliet, M., Nielsen, T.G., Lindeque, P., Castellani, C., ... Hoarau, G.G. (2014). Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification. Molecular Ecology Resources, 14(5), 1072-1079, which has been published in final form at http://dx.doi.org/10.1111/1755-0998.12241. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving (http://olabout.wiley.com/WileyCDA/Section/id-820227.html)

Vulnerabilities and fisheries impacts:The uncertain future of manta and devil rays

Manta and devil rays of the subfamily Mobulinae (mobulids) are rarely studied, large, pelagic elasmobranchs, with all eight of well-evaluated species listed on the IUCN Red List as threatened or near threatened. Mobulids have life history characteristics (matrotrophic reproduction, extremely low fecundity, and delayed age of first reproduction) that make them exceptionally susceptible to overexploitation. Targeted and bycatch mortality from fisheries is a globally important and increasing threat, and targeted fisheries are incentivized by the high value of the global trade in mobulid gill plates. Fisheries bycatch of mobulids is substantial in tuna purse seine fisheries. Thirteen fisheries in 12 countries specifically targeting mobulids, and 30 fisheries in 23 countries with mobulid bycatch were identified. Aside from a few recently enacted national restrictions on capture, there is no comprehensive monitoring, assessment or control of mobulid fisheries or bycatch. Recent listing through the Convention on the International Trade in Endangered Species (CITES) may benefit mobulids of the genus Manta (manta rays), but none of the mobulids in the genus Mobula (devil rays) are protected. The relative economic costs of catch mitigation are minimal, particularly compared with a broad range of other, more complicated, marine conservation issues

Phylogenomics and species delimitation for effective conservation of manta and devil rays

Practical biodiversity conservation relies on delineation of biologically meaningful units. Manta and devil rays (Mobulidae) are threatened worldwide, yet morphological similarities and a succession of recent taxonomic changes impede the development of an effective conservation strategy. Here, we generate genome‐wide single nucleotide polymorphism (SNP) data from a geographically and taxonomically representative set of manta and devil ray samples to reconstruct phylogenetic relationships and evaluate species boundaries under the general lineage concept. We show that nominal species units supported by alternative data sources constitute independently evolving lineages, and find robust evidence for a putative new species of manta ray in the Gulf of Mexico. Additionally, we uncover substantial incomplete lineage sorting indicating that rapid speciation together with standing variation in ancestral populations has driven phylogenetic uncertainty within Mobulidae. Finally, we detect cryptic diversity in geographically distinct populations, demonstrating that management below the species level may be warranted in certain species. Overall, our study provides a framework for molecular genetic species delimitation that is relevant to wide‐ranging taxa of conservation concern, and highlights the potential for genomic data to support effective management, conservation and law enforcement strategies

Genetics of manta and devil rays: Evolution, population genetics and conservation of a group of vulnerable pelagic filter-feeders

Duivelsroggen (de collectieve naam voor Manta en Mobula roggen van de Familie Mobulidae) zijn grote pelagische planktoneters (filteraars) en behoren, door hun langzame voortplanting en extreem lage vruchtbaarheid, tot de meest kwetsbare haaiachtigen. Helaas bestaat er een intensieve en zich uitbreidende visserij in talloze Aziatische landen, die gedreven wordt door het gebruik van filterplaten in de Chinese Geneeskunde. Duivelsroggen worden ook frequent en over hun hele verspreidingsgebied gevangen als bijvangst in de tonijnvisserij. Door de lage intrinsieke groei van duivelsrogpopulaties kunnen zelfs lage vangsten tot significante negatieve populatietrends lijden. De evolutionaire geschiedenis van duivelsroggen is lang onduidelijk gebleven, ondanks een recente interesse in de ecologie en bescherming van deze groep roggen. Deze thesis is ontworpen om een basis aan kennis te verwerven over duivelsrog evolutie en populatie genetica, zodat management- en beschermingsmaatregelen beter geïnformeerd en doeltreffender kunnen worden uitgevoerd. Ik heb Next Generation Sequencing (NGS) van hele mitochondriële genomen, conventionele Sanger sequenties en aanvullende GenBank sequenties gebruikt om: 1) de timing, patronen, en drijvende krachten achter de evolutie van alle mobulid soorten; en 2) de invloed van historische klimaatsverandering op de historische populatie structuur en demografie van een van de grotere mobulid soorten, de gestekelde duivelsrog, te onderzoeken. Bovendien geef ik aanbevelingen die potentieel het behoud van deze kwetsbare soorten ten goede komen

The complete mitochondrial genome of the Spinetail Devilray, Mobula japanica

The complete mitochondrial genome of a widely distributed pelagic ray, the Spinetail Devilray (Mobula japanica), consists of 18,880 bp with high A+T and low G content. Gene configuration and length is similar to other vertebrates and comprises 13 protein-coding genes, 2 rRNAs genes (12S and 16S rRNA), 22 tRNAs genes, and 1 major non-coding sequence, the control region. A remarkable feature in the mitochondrial genome of M. japanica is three tandemly repeated areas in the control region, together comprising a length of almost 1500 bp, making this to our knowledge the longest elasmobranch mitochondrial genome published so far