Genetic evidence of illegal trade in protected whales links Japan with the US and South Korea

Global patterns of illegal marine turtle exploitation

Human exploitation of wildlife for food, medicine, curios, aphrodisiacs, and spiritual artifacts represents a mounting 21st-century conservation challenge. Here, we provide the first global assessment of illegal marine turtle exploitation across multiple spatial scales (i.e., Regional Management Units [RMUs] and countries) by collating data from peer-reviewed studies, grey literature, archived media reports, and online questionnaires of in-country experts spanning the past three decades. Based on available information, we estimate that over 1.1 million marine turtles were exploited between 1990 and 2020 against existing laws prohibiting their use in 65 countries or territories and in 44 of the world's 58 marine turtle RMUs, with over 44,000 turtles exploited annually over the past decade. Exploitation across the 30-year period primarily consisted of green (56%) and hawksbill (39%) turtles when identified by species, with hawksbills (67%) and greens (81%) comprising the majority of turtles exploited in the 1990s and 2000s, respectively, and both species accounting for similar levels of exploitation in the 2010s. Although there were no clear overarching trends in the magnitude or spatial patterns of exploitation across the three decades, there was a 28% decrease in reported exploitation from the 2000s to the 2010s. The 10 RMUs with the highest exploitation in the 2010s included seven green and three hawksbill turtle RMUs, with most reported exploitation occurring in RMUs that typically exhibit a low risk of population decline or loss of genetic diversity. Over the past decade, the number of RMUs with "moderate" or "high" exploitation impact scores decreased. Our assessment suggests that illegal exploitation appears to have declined over the past decade and, with some exceptions, is primarily occurring in large, stable, and genetically diverse marine turtle populations.

Whole genome survey of big cats (Genus: Panthera) identifies novel microsatellites of utility in conservation genetic study

Big cats (Genus: Panthera) are among the most threatened mammal groups of the world, owing to hunting, habitat loss, and illegal transnational trade. Conservation genetic studies and effective curbs on poaching are important for the conservation of these charismatic apex predators. A limited number of microsatellite markers exists for Panthera species and researchers often cross-amplify domestic cat microsatellites to study these species. We conducted data mining of seven Panthera genome sequences to discover microsatellites for conservation genetic studies of four threatened big cat species. A total of 32 polymorphic microsatellite loci were identified in silico and tested with 152 big cats, and were found polymorphic in most of the tested species. We propose a set of 12 novel microsatellite markers for use in conservation genetics and wildlife forensic investigations of big cat species. Cumulatively, these markers have a high discriminatory power of one in a million for unrelated individuals and one in a thousand for siblings. Similar PCR conditions of these markers increase the prospects of achieving efficient multiplex PCR assays. This study is a pioneering attempt to synthesise genome wide microsatellite markers for big cats.

DNA barcoding augments conventional methods for identification of medicinal plant species traded at Tanzanian markets

ETHNOPHARMALOGICAL RELEVANCE

In Africa, traditional medicine is important for local healthcare and plants used for these purposes are commonly traded. Identifying medicinal plants sold on markets is challenging, as leaves, barks and roots are often fragmented or powdered. Vernacular names are often homonymic, and identification of material lacking sufficient morphological characters is time-consuming, season-dependent and might lead to incorrect assessments of commercialised species diversity.

AIM OF THE STUDY

In this study, we identified cases of vernacular heterogeneity of medicinal plants using a tiered approach of literature research, morphology and DNA barcoding.

MATERIAL AND METHODS

A total of 870 single ingredient medicinal plant samples corresponding to 452 local names were purchased from herbal markets in Dar-es-Salaam and Tanga, Tanzania, and identified using conventional methods as well as DNA barcoding using rbcL, matK and nrITS.

RESULTS

Using conventional methods, we could identify 70% of samples to at least family level, while 62% yielded a DNA barcode for at least one of the three markers. Combining conventional methods and DNA barcoding, 76% of the samples could be identified to species level, revealing a diversity of at least 175 species in 65 plant families. Analysis of the market samples revealed 80 cases of multilingualism and over- and under-differentiation. Afzelia quanzensis Welw., Zanthoxylum spp., Allophylus spp. and Albizia anthelmintica Brongn. were the most evident cases of multilingualism and over-differentiation, as they were traded under 8-12 vernacular names in up to five local languages. The most obvious case of under-differentiation was mwingajini (Swahili), which matched to eight scientific species in five different plant families.

CONCLUSIONS

Use of a tiered approach increases the identification success of medicinal plants sold in local market and corroborates findings that DNA barcoding can elucidate the identity of material that is unidentifiable based on morphology and literature as well as verify or disqualify these identifications. Results of this study can be used as a basis for quantitative market surveys of fragmented herbal medicine and to investigate conservation issues associated with this trade.

Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery

Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next-generation sequencing, in conjunction with novel bioinformatic tools, allows large numbers of microsatellite loci to be simultaneously genotyped, presenting new opportunities for individual assignment and genetic mixture analysis. Here, we scanned the published Atlantic salmon genome to identify 706 microsatellite loci, from which we developed a final panel of 101 microsatellites distributed across the genome (average 3.4 loci per chromosome). Using samples from 35 Atlantic salmon populations (n = 1,485 individuals) from coastal Labrador, Canada, a region characterized by low levels of differentiation in this species, this panel identified 844 alleles (average of 8.4 alleles per locus). Simulation-based evaluations of assignment and mixture identification accuracy revealed unprecedented resolution, clearly identifying 26 rivers or groups of rivers spanning 500 km of coastline. This baseline was used to examine the stock composition of 696 individuals harvested in the Labrador Atlantic salmon fishery and revealed that coastal fisheries largely targeted regional groups (<300 km). This work suggests that the development and application of large sequenced microsatellite panels presents great potential for stock resolution in Atlantic salmon and more broadly in other exploited anadromous and marine species.

Unidentifiable by morphology: DNA barcoding of plant material in local markets in Iran

Local markets provide a rapid insight into the medicinal plants growing in a region as well as local traditional health concerns. Identification of market plant material can be challenging as plants are often sold in dried or processed forms. In this study, three approaches of DNA barcoding-based molecular identification of market samples are evaluated, two objective sequence matching approaches and an integrative approach that coalesces sequence matching with a priori and a posteriori data from other markers, morphology, ethnoclassification and species distribution. Plant samples from markets and herbal shops were identified using morphology, descriptions of local use, and vernacular names with relevant floras and pharmacopoeias. DNA barcoding was used for identification of samples that could not be identified to species level using morphology. Two methods based on BLAST similarity-based identification, were compared with an integrative identification approach. Integrative identification combining the optimized similarity-based approach with a priori and a posteriori information resulted in a 1.67, 1.95 and 2.00 fold increase for ITS, trnL-F spacer, and both combined, respectively. DNA barcoding of traded plant material requires objective strategies to include data from multiple markers, morphology, and traditional knowledge to optimize species level identification success.

Testing the reliability of standard and complementary DNA barcodes for the monocot subfamily Alooideae from South Africa

Although a standard DNA barcode has been identified for plants, it does not always provide species-level specimen identifications for investigating important ecological questions. In this study, we assessed the species-level discriminatory power of standard (rbcLa + matK) and complementary barcodes (ITS1 and trnH-psbA) within the subfamily Alooideae (Asphodelaceae), a large and recent plant radiation, whose species are important in horticulture yet are threatened. Alooideae has its centre of endemism in southern Africa, with some outlier species occurring elsewhere in Africa and Madagascar. We sampled 360 specimens representing 235 species within all 11 genera of the subfamily. With three distance-based methods, all markers performed poorly for our combined data set, with the highest proportion of correct species-level specimen identifications (30%) found for ITS1. However, when performance was assessed across genera, the discriminatory power varied from 0% for all single markers and combinations in Gasteria to 63% in Haworthiopsis, again for ITS1, suggesting that DNA barcoding success may be related to the evolutionary history of the lineage considered. Although ITS1 could be a good barcode for Haworthiopsis, the generally poor performance of all markers suggests that Alooideae remains a challenge. As species boundaries within Alooideae remain controversial, we call for continued search for suitable markers or the use of genomics approaches to further explore species discrimination in the group.

Development of Molecular Markers for Determining Continental Origin of Wood from White Oaks (Quercus L. sect. Quercus)

To detect and avoid illegal logging of valuable tree species, identification methods for the origin of timber are necessary. We used next-generation sequencing to identify chloroplast genome regions that differentiate the origin of white oaks from the three continents; Asia, Europe, and North America. By using the chloroplast genome of Asian Q. mongolica as a reference, we identified 861 variant sites (672 single nucleotide polymorphisms (SNPs); 189 insertion/deletion (indel) polymorphism) from representative species of three continents (Q. mongolica from Asia; Q. petraea and Q. robur from Europe; Q. alba from North America), and we identified additional chloroplast polymorphisms in pools of 20 individuals each from Q. mongolica (789 variant sites) and Q. robur (346 variant sites). Genome sequences were screened for indels to develop markers that identify continental origin of oak species, and that can be easily evaluated using a variety of detection methods. We identified five indels and one SNP that reliably identify continent-of-origin, based on evaluations of up to 1078 individuals representing 13 white oak species and three continents. Due to the size of length polymorphisms revealed, this marker set can be visualized using capillary electrophoresis or high resolution gel (acrylamide or agarose) electrophoresis. With these markers, we provide the wood trading market with an instrument to comply with the U.S. and European laws that require timber companies to avoid the trade of illegally harvested timber.

"Pig in a poke (gato por liebre)": the "mota" (Calophysus macropterus) fishery, molecular evidence of commercialization in Colombia and toxicological analyses

Overfishing has affected the population abundance trends of many commercial fish species. In the Amazon, the fishery of a catfish commonly known as "mota" or "piracatinga" (Calophysus macropterus) has become an important economic activity in the region as this species has replaced a number of other overexploited great catfish species in the markets. Due to this high exploitation, ways in which to increase captures have been identified. One strategy is to use decomposing animal carcasses as bait. Such strategy has increased the hunting pressure on endangered species such as caimans and river dolphins. We investigated which catfish species are currently commercialized in Colombian fish markets using DNA barcoding, and measured mercury concentration in the tissues of fish molecularly identified as C. macropterus. We collected 86 fish samples in markets of four Colombian cities. Sixty-eight of these were identified molecularly as C.macropterus. The mercury concentration of 29 such samples was analyzed. Samples presented total Hg concentrations higher than the limit for human consumption established by the WHO (0.5 μg/g). These results are worrisome and suggest that (1) C. macropterus is a widely used fish species for human consumption in Colombia and (2) C. macropterus has high concentrations of total Hg, making its consumption a public health risk. Results presented here suggest that C. macropterus has replaced capaz in most Colombian markets. This fishery threatens wild species of river dolphins and caimans, and is also a public health risk given the high mercury levels we found in a subsample of these fishes.

Genotyping errors in a calibrated DNA register: implications for identification of individuals

BACKGROUND

The use of DNA methods for the identification and management of natural resources is gaining importance. In the future, it is likely that DNA registers will play an increasing role in this development. Microsatellite markers have been the primary tool in ecological, medical and forensic genetics for the past two decades. However, these markers are characterized by genotyping errors, and display challenges with calibration between laboratories and genotyping platforms. The Norwegian minke whale DNA register (NMDR) contains individual genetic profiles at ten microsatellite loci for 6737 individuals captured in the period 1997-2008. These analyses have been conducted in four separate laboratories for nearly a decade, and offer a unique opportunity to examine genotyping errors and their consequences in an individual based DNA register. We re-genotyped 240 samples, and, for the first time, applied a mixed regression model to look at potentially confounding effects on genotyping errors.

RESULTS

The average genotyping error rate for the whole dataset was 0.013 per locus and 0.008 per allele. Errors were, however, not evenly distributed. A decreasing trend across time was apparent, along with a strong within-sample correlation, suggesting that error rates heavily depend on sample quality. In addition, some loci were more error prone than others. False allele size constituted 18 of 31 observed errors, and the remaining errors were ten false homozygotes (i.e., the true genotype was a heterozygote) and three false heterozygotes (i.e., the true genotype was a homozygote).

CONCLUSIONS

To our knowledge, this study represents the first investigation of genotyping error rates in a wildlife DNA register, and the first application of mixed models to examine multiple effects of different factors influencing the genotyping quality. It was demonstrated that DNA registers accumulating data over time have the ability to maintain calibration and genotyping consistency, despite analyses being conducted on different genotyping platforms and in different laboratories. Although errors were detected, it is demonstrated that if the re-genotyping of individual samples is possible, these will have a minimal effect on the database's primary purpose, i.e., to perform individual identification.

Thar she blows! A novel method for DNA collection from cetacean blow

Background

Molecular tools are now widely used to address crucial management and conservation questions. To date, dart biopsying has been the most commonly used method for collecting genetic data from cetaceans; however, this method has some drawbacks. Dart biopsying is considered inappropriate for young animals and has recently come under scrutiny from ethical boards, conservationists, and the general public. Thus, identifying alternative genetic collection techniques for cetaceans remains a priority, especially for internationally protected species.

Methodology/Principal Findings

In this study, we investigated whether blow-sampling, which involves collecting exhalations from the blowholes of cetaceans, could be developed as a new less invasive method for DNA collection. Our current methodology was developed using six bottlenose dolphins, Tursiops truncatus, housed at the National Aquarium, Baltimore (USA), from which we were able to collect both blow and blood samples. For all six individuals, we found that their mitochondrial and microsatellite DNA profile taken from blow, matched their corresponding mitochondrial and microsatellite DNA profile collected from blood. This indicates that blow-sampling is a viable alternative method for DNA collection.

Conclusion/Significance

In this study, we show that blow-sampling provides a viable and less invasive method for collection of genetic data, even for small cetaceans. In contrast to dart biopsying, the advantage of this method is that it capitalizes on the natural breathing behaviour of dolphins and can be applied to even very young dolphins. Both biopsy and blow-sampling require close proximity of the boat, but blow-sampling can be achieved when dolphins voluntarily bow-ride and involves no harmful contact.