Gavin J.P. Naylor

Conservation genomics of natural and managed populations: building a conceptual and practical framework

The boom of massive parallel sequencing (MPS) technology and its applications in conservation of natural and managed populations brings new opportunities and challenges to meet the scientific questions that can be addressed. Genomic conservation offers a wide range of approaches and analytical techniques, with their respective strengths and weaknesses that rely on several implicit assumptions. However, finding the most suitable approaches and analysis regarding our scientific question are often difficult and time‐consuming. To address this gap, a recent workshop entitled ‘ConGen 2015’ was held at Montana University in order to bring together the knowledge accumulated in this field and to provide training in conceptual and practical aspects of data analysis applied to the field of conservation and evolutionary genomics. Here, we summarize the expertise yield by each instructor that has led us to consider the importance of keeping in mind the scientific question from sampling to management practices along with the selection of appropriate genomics tools and bioinformatics challenges.

A new species of guitarfish, Rhinobatos borneensis sp. nov. with a redefinition of the family-level classification in the order Rhinopristiformes (Chondrichthyes: Batoidea)

A new guitarfish, Rhinobatos borneensis sp. nov., is described from material collected at fish markets in Malaysian Borneo (South China Sea). This ray, which is almost plain coloured with faint orange blotches in adults, has a more colourful embryo marked with small pale ocelli with dark centres. Confused with R. schlegelii (Japan to Taiwan) and its junior synonym R. formosensis, new molecular data suggests it is more closely related to a subgroup of Rhinobatos from the Indo-Malay Archipelago that includes R. jimbaranensis, R. sainsburyi and R. whitei. Based on evidence from recent phylogenetic studies, the genus Rhinobatos is non-monophyletic, nor is the Rhinobatidae a monophyletic family-level group. Former subgenera of Rhinobatos, Acroteriobatus and Glaucostegus, are valid genus-level taxa supported by both morphological and molecular evidence. Moreover, amphi-American members of Rhinobatos, assigned herein to a new genus Pseudobatos, are not monophyletic with Rhinobatos, Acroteriobatus and Glaucostegus and its position within the newly erected order Rhinopristiformes needs to be reassessed. Several molecular studies have suggested that the family Rhinobatidae is polyphyletic and needs to be redefined. We propose a revised classification of the order Rhinopristiformes based on molecular analyses and supported by morphological data, making strong use of oronasal morphology. The group now contains 5 family-level taxa: three valid nominal taxa, Pristidae (2 genera, 5 species), Rhinidae (incorporating Rhynchobatidae, 2 genera, 9 species), Rhinobatidae (3 genera, 31 species); and two new taxa, Glaucostegidae (single genus, 6 species) and Trygonorrhinidae (3 genera, 8 species).

Resurrection of the family Aetobatidae (Myliobatiformes) for the pelagic eagle rays, genus Aetobatus

Molecular and morphological data show that the pelagic eagle rays of the genus Aetobatus form a distinct family-level grouping separate from the true eagle rays, Aetomylaeus and Myliobatis (family Myliobatidae). The family Aetobatidae is herein resurrected to include the pelagic eagle rays and definitions are provided for this family and for the Myliobatidae. The key characters separating Aetobatidae from Myliobatidae are: pectoral fins joining head at level of eyes (vs. below level of eyes), internasal flap deeply notched (vs. nearly straight), free rear tip of pectoral fins broadly rounded (vs. angular), spiracles dorsolateral on head and visible in dorsal view (spiracles lateral on head and not visible in dorsal view), dorsal fin with obvious free rear tip (vs. no free rear tip evident, posterior margin joining dorsal surface of tail).

Population genomics of C. melanopterus using target gene capture data: demographic inferences and conservation perspectives

Population genetics studies on non-model organisms typically involve sampling few markers from multiple individuals. Next-generation sequencing approaches open up the possibility of sampling many more markers from fewer individuals to address the same questions. Here, we applied a target gene capture method to deep sequence ~1000 independent autosomal regions of a non-model organism, the blacktip reef shark (Carcharhinus melanopterus). We devised a sampling scheme based on the predictions of theoretical studies of metapopulations to show that sampling few individuals, but many loci, can be extremely informative to reconstruct the evolutionary history of species. We collected data from a single deme (SID) from Northern Australia and from a scattered sampling representing various locations throughout the Indian Ocean (SCD). We explored the genealogical signature of population dynamics detected from both sampling schemes using an ABC algorithm. We then contrasted these results with those obtained by fitting the data to a non-equilibrium finite island model. Both approaches supported an Nm value ~40, consistent with philopatry in this species. Finally, we demonstrate through simulation that metapopulations exhibit greater resilience to recent changes in effective size compared to unstructured populations. We propose an empirical approach to detect recent bottlenecks based on our sampling scheme.

Three new stingrays (Myliobatiformes: Dasyatidae) from the Indo–West Pacific

Three undescribed stingrays were discovered as part of a broader revision of the family Dasyatidae that formed part of the Chondrichthyan Tree of Life project. This research forms part of a sequence of papers on rays aimed at describing unnamed species for inclusion in a multi-authored guide to rays of the world. The first part of this series focused on a redefinition of genera of the family Dasyatidae. The new Indo-West Pacific taxa are represented by separate genera from three dasyatid subfamilies: Himantura australis sp. nov. (northern Australia and Papua New Guinea), Taeniura lessoni sp. nov. (Melanesia) and Telatrygon biasa sp. nov. (Indo-Malay Archipelago). Himantura australis sp. nov., which belongs to a complex of four closely related reticulate whiprays, differs subtly from its congeners in coloration, morphometrics and distribution. Taeniura lessoni sp. nov. is the second species in a genus containing the widely-distributed T. lymma, which is possibly the most abundant stingray in shallow coral-reef habitats of the Indo-Pacific, with the new species apparently restricted to Melanesia. Taeniura lessoni sp. nov. is distinguishable by the absence of a distinctive pair of vivid blue longitudinal stripes on the dorsolateral edges of the tail which is one of the most distinctive features of T. lymma. Telatrygon biasa sp. nov. belongs to a small, recently designated genus of stingrays represented by four species in the tropical Indo-West Pacific. Telatrygon biasa sp. nov. differs from these species in morphometrics. The new species differs markedly from T. zugei in its NADH2 sequence. Telatrygon crozieri is resurrected as a valid northern Indian Ocean representative of the T. zugei complex.

Long-PCR based next generation sequencing of the whole mitochondrial genome of the peacock skate Pavoraja nitida (Elasmobranchii: Arhynchobatidae)

Abstract We determined the complete mitochondrial genome sequence (16,760 bp) of the peacock skate Pavoraja nitida using a long-PCR based next generation sequencing method. It has 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region in the typical vertebrate arrangement. Primers, protocols, and procedures used to obtain this mitogenome are provided. We anticipate that this approach will facilitate rapid collection of mitogenome sequences for studies on phylogenetic relationships, population genetics, and conservation of cartilaginous fishes.

Historical introgression drives pervasive mitochondrial admixture between two species of pelagic sharks

We use a genomic sampling of both nuclear and mitochondrial DNA markers to examine a pattern of genetic admixture between Carcharhinus galapagensis (Galapagos sharks) and Carcharhinus obscurus (dusky sharks), two well-known and closely related sharks that have been recognized as valid species for more than 100years. We describe widespread mitochondrial-nuclear discordance in which these species are readily distinguishable based on 2152 nuclear single nucleotide polymorphisms from 910 independent autosomal regions, but show pervasive mitochondrial admixture. The species are superficially morphologically cryptic as adults but show marked differences in internal anatomy, as well as niche separation. There was no indication of ongoing hybridization between the species. We conclude that the observed mitochondrial-nuclear discordance is likely due to historical mitochondrial introgression following a range expansion.

Redescription of Chimaera ogilbyi (Chimaeriformes; Chimaeridae) from the Indo-Australian region

An integrated taxonomic approach, combining both morphological and molecular data, was adopted to investigate the Hydrolagus lemures-ogilbyi group in the Indo-Australian region. Single mitochondrial markers (CO1 and NADH2) provided evidence supporting the separation of four distinct species in this group. However, detailed morphological data collected from specimens from across their range failed to find any consistent differences, and many features previously considered to be diagnostic were found to be variable. Nuclear DNA data also failed to support the differences found with the single mitochondrial markers and, together with the morphological data, supported the hypothesis that only a single species in this group is present in the Indo-Australian region. In addition, the results failed to support the current generic placement of this group in Hydrolagus, suggesting they belong to the genus Chimaera with doubt over the validity of Hydrolagus as a valid genus. The oldest available name for this group is Chimaera ogilbyi and a redescription is provided. This species occurs throughout Australia, eastern Indonesia (Java, Bali, and Lombok) and northern Papua New Guinea.

Determination of complete mitochondrial genome sequence from the holotype of the southern Mandarin dogfish Cirrhigaleus australis (Elasmobranchii: Squalidae).

Abstract We determined the complete mitochondrial genome sequence from the holotype of the southern Mandarin dogfish Cirrhigaleus australis. It has a length of 16,543 bp and consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. The gene composition and genome organization is similar to most other vertebrates. Data obtained in this study will be important for resolving possible taxonomic issues related to C. australis and will contribute to the reconstruction of phylogenetic relationships among chondrichthyan species.

Segmentations of the cartilaginous skeletons of chondrichthyan fishes by the use of state-of-the-art computed tomography

AIM To apply dual-source multidetector computed tomography (DSCT) scanning technology in conjunction with computationally assisted segmentation in order to explore and document skeletal variation that has occurred over the course of evolution. METHODS We examined 4 divergent species of elasmobranchs with high-resolution 3rd generation DSCT. The formalin prepared species examined were: Aptychotrema vincentiana, Mitsukurina owstoni, Negaprion brevirostris and Dactylobatus armatus. RESULTS All three structures of the hyoid arch (hyomandibular, ceratohyal, and basihyal) were clearly visible whereas in the two batoids, the hyomandibular was the prominent feature, the ceratohyal was not visible and the basihyal was more reduced and closer to the gill arches. The general shape of the puboischiadic bar, or pelvic girdle, illustrated a closer relationship between the two sharks and the two batoids than between the two groups. CONCLUSION In exquisite detail, DSCT imaging revealed important morphological variations in various common structures in the four elasmobranch specimens studied, providing insights into their evolutionary diversification.