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Abstract

1. The sand tiger shark (Carcharias taurus) is a coastal species distributed in temperate and sub-tropical waters, classified as “Vulnerable” at global level and “Critically endangered” in Eastern Australia, Southwestern Atlantic Ocean and Mediterranean Sea. Six populations (Northwestern Atlantic, Brazil, South Africa, Japan, Eastern Australia and Western Australia) with low genetic diversity and limited gene flow were identified worldwide, but genetic information for many other geographic areas are still missing. Specifically, this species is listed in several reports as part of the Mediterranean fauna, even if there is a lack of catches and sightings in recent years in this basin. In order to clarify the origin of C. taurus individuals caught in the past in the Mediterranean Sea, historical samples were genetically analysed. 2. Nine samples with a certain Mediterranean origin were collected from different European museums. Genomic DNA was extracted and ~ 600 bp of the mitochondrial DNA control region was amplified using eight overlapping species-specific primer pairs. Sequences obtained were aligned with all the haplotypes globally known so far. 3. Genetic analysis revealed the misidentification of one museum specimen. Among the remaining Mediterranean historical samples, three different haplotypes were recovered. Two of them previously observed only in South Africa and one described in both South African and Brazilian populations. 4. Results suggest a genetic relationship between Mediterranean sand tiger sharks and those from the Western Indian Ocean. According to previous studies, we hypothesized that during the Pleistocene the cold Benguela upwelling barrier was temporarily reduced allowing the passage of C. taurus individuals from the Indian to Atlantic Ocean. After the restoration of this phylogeographic barrier some individuals were trapped in the Atlantic Ocean and probably migrated northward colonizing the Western African coasts and the Mediterranean Sea.

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The penguin species Tasidyptes hunteri van Tets & O’Connor, 1983, the sole representative of an extinct penguin genus, was described on the basis of four bones excavated from a prehistoric midden on Tasmania’s Hunter Island. Several authors have since questioned the validity of T. hunteri, citing the fragmentary nature of the remains and the similarity of some elements (coracoid and tarsometatarsus) to those of extant crested penguin (Eudyptes) species. We designed four overlapping primer pairs to amplify a 499 bp region of mitochondrial cytochrome c oxidase 1 (COI) in penguins and used these to amplify and sequence COI from all known bones attributed to T. hunteri. The T. hunteri COI sequences were assessed within a phylogenetic framework against COI sequences for all extant penguin species. Our results reveal that the T. hunteri bones are an assemblage of remains from three extant penguin species (Eudyptes pachyrhynchus, E. robustus, Eudyptula novaehollandiae), and we find no molecular support for any of these bones representing an extinct penguin lineage.
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Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here we assess and optimize the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called “bio-swarf”, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20,000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high yield sources of DNA for genomic scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield. This article is protected by copyright. All rights reserved.
Article
For purposes of the Endangered Species Act (ESA), a "species' is defined to include "any distinct population segment of any species of vertebrates fish or wildlife which interbreeds when mature'. Federal agencies charged with carrying out the provisions of the ESA have struggled to develop a consistent approach for interpreting the term "distinct population segment'. This paper outlines such an approach and explains how it can be applied to ESA evaluations of anadromous Pacific salmonids. The following definition is proposed: a population (or group of populations) will be considered "distinct" (and hence a "species') for purposes of the ESA if it represents an evolutionarily significant unit (ESU) of the biological species. A population must satisfy two criteria to be considered an ESU: 1) it must be substantially reproductively isolated from other conspecific population units, and 2) it must represent an important component in the evolutionary legacy of the species. -from Author
Article
To date, movement patterns of juvenile sand tigers (Carcharias taurus) along the east coast of the USA have been loosely defined. Given the magnitude of the purported decline in the sand tiger population in the western North Atlantic (WNA), characterization of the species' movement patterns throughout this broad area is essential for the effective management and recovery of this population. Using passive acoustic telemetry, pop-up satellite archival transmitting tags, and conventional fishery-dependent tag/recapture data, seasonal movements of juvenile sand tigers (ages 0-2 years; < 125 cm fork length) were monitored between Maine and Florida along the US east coast from 2007 to 2013. Collectively, tag data indicated that juvenile sand tigers undergo extensive seasonal coastal migrations moving between summer (June-October) habitat (Maine to Delaware Bay) and winter (December-April) habitat (Cape Hatteras to central Florida) during the spring (April-June) and fall/early winter (October-December). Juvenile sand tigers occurred in a wide range of temperatures (9.8-26.9 A degrees C) throughout the year, but spent the majority of their time in water from 12 to 20 A degrees C. Given the extensive movements and continuous utilization of relatively shallow (< 80 m) nearshore waters exhibited by these relatively small individuals throughout their first years of life, it is imperative that precautions be taken to limit negative effects of anthropogenic interactions on this species (i.e., fisheries bycatch, coastal degradation) in an effort to rebuild and sustain the WNA population.
Article
Knowledge of migratory movements and depth/temperature-related use of coastal waters by sharks can lead to more sustainable fisheries and assist in managing the long-term conservation of those species now considered threatened. Pop-up archival satellite tags (PATs) provide an alternative to conventional tagging for documenting migratory movements. This study focussed on the migratory movements of Carcharias taurus, a critically endangered shark found along the east coast of Australia. From October 2003 to July 2008, 15 C. taurus individuals were tagged with PATs with varying deployments (60-150 days) and acoustic tags linked to an acoustic monitoring system providing accurate geo-location. Distances moved by C. taurus individuals ranged from 5 to 1550 km and varied according to sex and season. Migrations north and south were punctuated en route by occupation of sites for varying periods of time. The deepest depth recorded was 232 m off South West Rocks on the New South Wales mid-north coast. On average, C. taurus males and females spent at least 71% of their time in waters <40 m and 95% of their time in waters 17-248 degrees C. By mainly occupying inshore waters, C. taurus is exposed to potentially adverse fishing-related interactions that may be difficult to mitigate.
Article
Photo-identification techniques were used to investigate temporal and spatial distributions of Carcharias taurus (Rafinesque, 1810) in relation to maturity, sex and pregnancy status at 19 sites along Australia's eastern coastline. Of 931 individual sharks identified between 2004 and 2008, 479 were female (271 mature, 208 immature) and 452 male (288 mature, 164 immature). Mature, non-gravid females and mature males were mostly observed in the southern to central parts of this species range, along the eastern coast of Australia, in early summer to early winter. These sharks subsequently moved northward, and mating occurred in late spring to early summer in waters off the coast of northern New South Wales and southern Queensland. Pregnant C. taurus aggregated at Wolf Rock in southern Queensland, at the most northerly part of their known range, from late summer to early winter. These sharks subsequently migrated south to pup in central and southern waters of their range in late winter to late spring. Immature sharks of both sexes moved less than mature sharks, showed no synchronised migration patterns, and were mostly restricted to central and southern waters. The improved understanding of sex-and maturity-based migration of C. taurus provided here should facilitate a conservation strategy appropriate for this species in Australian waters.
Article
Catches from competitive shore-anglers, inshore boat-based anglers and sightings by spearfishers and divers were used to infer the spatial and seasonal movement patterns of young-of-the-year (2.4m TL) ragged-tooth sharks Carcharias taurus along the coast of South Africa. Adult sharks inhabited the entire coast between Maputaland in the east and St Helena Bay on the West Coast. The geographical range of sharks at earlier life-history stages decreased with size. The vast majority (93.8%) of young-of-the-year sharks recorded from competitive shore-angling club records were between East London and St Francis Bay on the East Coast, suggesting this region to be the primary nursery area for C. taurus. Estuarine systems, although utilised by young-of-the-year and juvenile C. taurus, do not form an important component of their nursery area in South Africa. Catches of pregnant and post partum females taken during the same time of year and in different areas indicated a biennial reproductive cycle. C. taurus appears to display a high degree of affinity for particular reefs. The reason some reefs are chosen over others, despite having similar physical characteristics, remains unclear. A significant increase in the number of C. taurus caught in competitions held by the Border Rock and Surf Angling Association between 1984 and 2004 suggests an increase in the abundance of C. taurus.
Article
Releasing aquarium-held sharks when no longer needed by the holding institution may help mitigate the impacts that aquaria have on declining wild populations. To investigate the viability of releasing display specimens, four raggedtooth sharks (Carcharias taurus) that had been held at Two Oceans Aquarium, Cape Town were released back to the wild between 2004 and 2008. To test the hypothesis that they survived and that their movement patterns were similar to wild conspecifics, wild-caught sharks were also tagged and released at the same time and locality. Aquarium- and wild-caught sharks were equipped with pop-up archival (PAT) tags, VEMCO ultrasonic tags, and numbered spaghetti dart tags. With the exception of one individual, all the aquarium-released sharks survived. Both aquarium-released and wild-captured sharks displayed eastward movements and travelled hundreds of kilometres after release. Data from the PAT tags indicated that individuals from both groups swam mainly in shallow waters, but dived as deep as 80 m to mid-shelf waters. A wide temperature tolerance was exhibited as they travelled though temperatures ranging from 10 to 22oC. Movement tracks of the sharks revealed ‘station keeping’ and an autumn migration between April and May. Rates of movement between individuals were variable. The depth range recorded in this study supports published information on habitat and prey choice. This study illustrates that this species can survive aquarium release after years of captivity and that they appear to behave similarly to wild-caught conspecifics.
Article
Genetic diversity is one of three levels of biological diversity requiring conservation. Genetic theory predicts that levels of genetic variation should increase with effective population size. Soule (1976) compiled the first convincing evidence that levels of genetic variation in wildlife were related to population size, but this issue remains controversial. The hypothesis that genetic variation is related to population size leads to the following predictions: (1) genetic variation within species should be related to population size; (2) genetic variation within species should be related to island size; (3) genetic variation should be related to population size within taxonomic groups; (4) widespread species should have more genetic variation than restricted species; (5) genetic variation in animals should be negatively correlated with body size; (6) genetic variation should be negatively correlated with rate of chromosome evolution; (7) genetic variation across species should be related to population size; (8) vertebrates should have less genetic variation than invertebrates or plants; (9) island populations should have less genetic variation than mainland populations; and (10) endangered species should have less genetic variation than nonendangered species. Empirical observations support all these hypotheses. There can be no doubt that genetic variation is related to population size, as Soule proposed. Small population size reduces the evolutionary potential of wildlife species.
Article
The capture of recently inseminated or pregnant specimens ofCarcharias taurus, Isurus paucus, I. oxyrinchus, Alopias superciliosus andA. vulpinus has allowed new information to be obtained on the reproductive biology of these species. Oophagy and embryonic cannibalism (adelphophagy) have been documented inC. taurus, but only oophagy in other lamnoid species. The occurrence of up to nine embryos of similar size per uterus inIsurus and no indication of functional erect teeth in embryos leaves considerable doubt that embryophagy occurs in this genus. Considerable data has been collected onCarcharias taurus which allows a lamnoid reproductive model to be developed and tested, in spite of the obvious differences between the reproductive biology of this species and other lamnoids. Gonad structure, ovarian development, fertilization, early embryonic differentiation, embryonic nutrition and parturition, inC. taurus and other lamnoids differs significantly from other elasmobranchs.
Article
Since the first investigation 25 years ago, the application of genetic tools to address ecological and evolutionary questions in elasmobranch studies has greatly expanded. Major developments in genetic theory as well as in the availability, cost effectiveness and resolution of genetic markers were instrumental for particularly rapid progress over the last 10 years. Genetic studies of elasmobranchs are of direct importance and have application to fisheries management and conservation issues such as the definition of management units and identification of species from fins. In the future, increased application of the most recent and emerging technologies will enable accelerated genetic data production and the development of new markers at reduced costs, paving the way for a paradigm shift from gene to genome-scale research, and more focus on adaptive rather than just neutral variation. Current literature is reviewed in six fields of elasmobranch molecular genetics relevant to fisheries and conservation management (species identification, phylogeography, philopatry, genetic effective population size, molecular evolutionary rate and emerging methods). Where possible, examples from the Indo-Pacific region, which has been underrepresented in previous reviews, are emphasized within a global perspective.
Article
This paper reports on the development and application of methods for using DNA analysis for species identification of archaeological salmon bone. Short fragments (less than 300 bp) of mitochondrial DNA from the control region (D-loop) and cytochrome B (CytB) gene were targeted for amplification using the polymerase chain reaction (PCR) technique. The method was used on more than 20 salmon bone samples (dated 7000 to 2000 BP) from the site of Namu on the central coast of British Columbia. Four species: coho, sockeye, pink and chum salmon were identified from the samples. The results are considered valid since systematic contaminations were not detected, multiple species and multiple DNA haplotypes of the same species were identified from the same set of bone samples, and the identified species are consistent with those inferred from other lines of evidence. The results demonstrate the applicability of the ancient DNA technique to species identification of even single salmon vertebrae from archaeological sites in the Pacific Northwest of North America.
Article
The role of genetic factors in extinction has been a controversial issue, especially since Lande’s paper [Genetics and demography in biological conservation, Science 241 (1988) 1455–1460] paper in Science. Here I review the evidence on the contribution of genetic factors to extinction risk. Inbreeding depression, loss of genetic diversity and mutation accumulation have been hypothesised to increase extinction risk. There is now compelling evidence that inbreeding depression and loss of genetic diversity increase extinction risk in laboratory populations of naturally outbreeding species. There is now clear evidence for inbreeding depression in wild species of naturally outbreeding species and strong grounds from individual case studies and from computer projections for believing that this contributes to extinction risk. Further, most species are not driven to extinction before genetic factors have time to impact. The contributions of mutation accumulation to extinction risk in threatened taxa appear to be small and to require very many generations. Thus, there is now sufficient evidence to regard the controversies regarding the contribution of genetic factors to extinction risk as resolved. If genetic factors are ignored, extinction risk will be underestimated and inappropriate recovery strategies may be used.
Article
Grey nurse sharks off the east coast of Australia are listed nationally as “critically endangered” under Schedule 1 of the Environmental Protection and Biodiversity Conservation Act (1999) and may number no more than 300 in New South Wales and southern Queensland waters. They are an inshore, coastal dwelling species and were severely depleted by spearfishing in the 1960s. The population has continued to decline despite protection since 1984. Their life history (long-lived to 25+ years), late maturation (6–8 years), low fecundity (maximum 2 live young biennially), specific habitat requirements, limited inshore distribution, and small population size render them particularly vulnerable to extinction. We estimated the time to quasi-extinction (years elapsed for the population to consist of ⩽50 females) for the grey nurse shark population off the east coast of Australia based on current estimates of abundance and known anthropogenic rates of mortality. Estimated minimum population size was 300 as of 2002, and minimum anthropogenic mortality assessed from recovered carcasses was 12/year of which 75% were females. We modelled time to quasi-extinction using deterministic age- and stage-classified models for worst-, likely and best-case scenarios. Population size was estimated at 300 (worst), 1000 (likely) and 3000 (best). Anthropogenic mortality was added to the model assuming either all carcasses are being recovered (best), or conservatively, that only 50% are reported (realistic). Depending on model structure, if all carcasses are being reported, quasi-extinction times for worst-, likely and best-case scenarios range from 13 to 16 years, 84–98 years and 289–324 years, respectively. If under-reporting is occurring, time to quasi-extinction ranges from 6 to 8 years, 45–53 years and 173–200 years, respectively. In all scenarios modelled the grey nurse shark population will decline if no further steps are taken to remove anthropogenic sources of mortality. Because estimates of quasi-extinction rate depend on initial population size, and sensitivity analysis revealed that population rate of change was most sensitive to changes in the survival probability of the smallest length classes, obtaining precise estimates of abundance and annual survival of young females is critical.
Article
Reconstructing phylogenies from intraspecific data (such as human mitochondrial DNA variation) is often a challenging task because of large sample sizes and small genetic distances between individuals. The resulting multitude of plausible trees is best expressed by a network which displays alternative potential evolutionary paths in the form of cycles. We present a method ("median joining" [MJ]) for constructing networks from recombination-free population data that combines features of Kruskal's algorithm for finding minimum spanning trees by favoring short connections, and Farris's maximum-parsimony (MP) heuristic algorithm, which sequentially adds new vertices called "median vectors", except that our MJ method does not resolve ties. The MJ method is hence closely related to the earlier approach of Foulds, Hendy, and Penny for estimating MP trees but can be adjusted to the level of homoplasy by setting a parameter epsilon. Unlike our earlier reduced median (RM) network method, MJ is applicable to multistate characters (e.g., amino acid sequences). An additional feature is the speed of the implemented algorithm: a sample of 800 worldwide mtDNA hypervariable segment I sequences requires less than 3 h on a Pentium 120 PC. The MJ method is demonstrated on a Tibetan mitochondrial DNA RFLP data set.
Article
Examining genomic data for traces of selection provides a powerful tool for identifying genomic regions of functional importance. Many methods for identifying such regions have focused on conserved sites. However, positive selection may also be an indication of functional importance. This article provides a brief review of some of the statistical methods used to detect selection using DNA sequence data or other molecular data. Statistical tests based on allelic distributions or levels of variability often depend on strong assumptions regarding population demographics. In contrast, tests based on comparisons of the level of variability in nonsynonymous and synonymous sites can be constructed without demographic assumptions. Such tests appear to be useful for identifying specific regions or specific sites targeted by selection.