Testing of microsatellite multiplexes for individual identification of Cape Parrots (Poicephalus robustus): paternity testing and monitoring trade

Genetic assessment of eight zoo populations of golden snub-nosed monkey (Rhinopithecus roxellana) implication to the conservation management of captive populations

Captive breeding programs play an important role in preserving the genetic diversity of endangered species. It is of utmost importance to conduct genetic assessment for captive populations in order to develop scientific breeding plans and conservation management strategies. Here, we genotyped 10 microsatellite loci and sequenced 368 bp of mitochondrial DNA control region for the golden snub-nosed monkey (Rhinopithecus roxellana) from eight captive populations in China, and compared the genetic indices of captive populations with a wild population. Meanwhile, we performed paternity tests to verify the genealogical records and established genetic lineages. A total of 157 individuals were identified from 161 fecal samples, including 135 captive individuals (approximately 25% of captive individuals in China). Microsatellite analysis showed that the nine populations had moderate levels of genetic diversity, with polymorphism information content (PIC) ranging from 0.43 to 0.542; the genetic diversity of captive populations (average PIC: 0.503) was slightly higher than that of the wild population (PIC: 0.438). The Structure analysis indicated that individuals of the eight captive populations contained two different genetic components. We conducted either single-blind or double-blind paternity testing on 40 offspring of captive individuals and found that five offspring from two zoos (Nanjing Hongshan Forest Zoo and Shanghai Wild Animal Park) showed discrepant kinships from their pedigree records, probably due to the inaccuracies in pedigree records. By constructing genetic pedigrees, inbred offspring were found in Beijing Zoo, Shanghai Zoo, Hangzhou Zoo, and Chengdu Zoo. Analysis based on mitochondrial DNA showed a high level of genetic diversity in the eight captive populations (mean nucleotide diversity: 0.047). However, no nucleotide diversity was found in the wild population. This study conducted a genetic survey for captive golden snub-nosed monkeys and will significantly benefit the genetic conservation management for captive populations in the future.

Determining the sustainability of legal wildlife trade

Exploitation of wildlife represents one of the greatest threats to species survival according to the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. Whilst detrimental impacts of illegal trade are well recognised, legal trade is often equated to being sustainable despite the lack of evidence or data in the majority of cases. We review the sustainability of wildlife trade, the adequacy of tools, safeguards, and frameworks to understand and regulate trade, and identify gaps in data that undermine our ability to truly understand the sustainability of trade. We provide 183 examples showing unsustainable trade in a broad range of taxonomic groups. In most cases, neither illegal nor legal trade are supported by rigorous evidence of sustainability, with the lack of data on export levels and population monitoring data precluding true assessments of species or population-level impacts. We propose a more precautionary approach to wildlife trade and monitoring that requires those who profit from trade to provide proof of sustainability. We then identify four core areas that must be strengthened to achieve this goal: (1) rigorous data collection and analyses of populations; (2) linking trade quotas to IUCN and international accords; (3) improved databases and compliance of trade; and (4) enhanced understanding of trade bans, market forces, and species substitutions. Enacting these core areas in regulatory frameworks, including CITES, is essential to the continued survival of many threatened species. There are no winners from unsustainable collection and trade: without sustainable management not only will species or populations become extinct, but communities dependent upon these species will lose livelihoods.

Understanding Singapore's dynamic parrot trade ecosystem

Singapore is prominent in the global trade of pet birds, primarily parrots. This includes its role as a key international transit hub, and also its growing domestic market, including for threatened species. There is a need to understand the trade beyond volumes and flows, including consumer knowledge, preferences and behaviours, and interactions with vendors, hobbyist groups and supporting industries. We used three methods to examine this: (1) a questionnaire with stakeholders (including parrot owners, hobbyist group members, breeders and supporting industry professionals), about the motivations for parrot ownership and interest in sustainable trade, (2) semi-structured interviews with key informants about trade dynamics, and (3) a review of online hobbyist groups. Based on our findings, we provide an initial mapping of the country's parrot trade ecosystem. Fifty-one per cent of respondents claimed to be a member of a parrot hobbyist group and 64% agreed their participation in such groups had encouraged them to purchase more parrots. The majority (71%) of parrot owners reported a preference for captive-bred rather than wild-caught parrots, and 72% were concerned about the illegal hunting of parrots for commercial trade. Most were willing to pay more (70%) and wait longer (73%) to procure a sustainably sourced parrot. Our approach presents the wildlife trade as a complex social phenomenon, with multiple physical and online channels, regulatory challenges, social networks, and evolving consumer preferences. We also document the pivotal role of hobbyist groups and their untapped potential to leverage these networks to improve sustainable trade.

Polly Wants a Genome: The Lack of Genetic Testing for Pet Parrot Species

Parrots are considered the third most popular pet species, after dogs and cats, in the United States of America. Popular birds include budgerigars, lovebirds and cockatiels and are known for their plumage and vocal learning abilities. Plumage colour variation remains the main driving force behind breeder selection. Despite the birds' popularity, only two molecular genetic tests-bird sexing and pathogen screening-are commercially available to breeders. For a limited number of species, parentage verification tests are available, but are mainly used in conservation and not for breeding purposes. No plumage colour genotyping test is available for any of the species. Due to the fact that there isn't any commercial plumage genotype screening or parentage verification tests available, breeders mate close relatives to ensure recessive colour alleles are passed to the next generation. This, in turn, leads to inbreeding depression and decreased fertility, lower hatchability and smaller clutch sizes, all important traits in commercial breeding systems. This review highlights the research carried out in the field of pet parrot genomics and points out the areas where future research can make a vital contribution to understanding how parrot breeding can be improved to breed healthy, genetically diverse birds.

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.

A Literature Synthesis of Actions to Tackle Illegal Parrot Trade

The order Psittaciformes is one of the most prevalent groups in the illegal wildlife trade. Efforts to understand this threat have focused on describing the elements of the trade itself: actors, extraction rates, and routes. However, the development of policy-oriented interventions also requires an understanding of how research aims and actions are distributed across the trade chain, regions, and species. We used an action-based approach to review documents published on illegal Psittaciformes trade at a global scale to analyze patterns in research aims and actions. Research increased exponentially in recent decades, recording 165 species from 46 genera, with an over representation of American and Australasian genera. Most of the research provided basic knowledge for the intermediary side of the trade chain. Aims such as the identification of network actors, zoonosis control, and aiding physical detection had numerous but scarcely cited documents (low growth rate), while behavior change had the highest growth rate. The Americas had the highest diversity of research aims, contributing with basic knowledge, implementation, and monitoring across the whole trade chain. Better understanding of the supply side dynamics in local markets, actor typology, and actor interactions are needed. Protecting areas, livelihood incentives, and legal substitutes are actions under-explored in parrots, while behavior change is emerging.

Opportunistic or Non-Random Wildlife Crime? Attractiveness Rather Than Abundance in the Wild Leads to Selective Parrot Poaching

Illegal wildlife trade, which mostly focuses on high-demand species, constitutes a major threat to biodiversity. However, whether poaching is an opportunistic crime within high-demand taxa such as parrots (i.e., harvesting proportional to species availability in the wild), or is selectively focused on particular, more desirable species, is still under debate. Answering this question has important conservation implications because selective poaching can lead to the extinction of some species through overharvesting. However, the challenges of estimating species abundances in the wild have hampered studies on this subject. We conducted a large-scale survey in Colombia to simultaneously estimate the relative abundance of wild parrots through roadside surveys (recording 10,811 individuals from 25 species across 2221 km surveyed) and as household, illegally trapped pets in 282 sampled villages (1179 individuals from 21 species). We used for the first time a selectivity index to test selection on poaching. Results demonstrated that poaching is not opportunistic, but positively selects species based on their attractiveness, defined as a function of species size, coloration, and ability to talk, which is also reflected in their local prices. Our methodological approach, which shows how selection increases the conservation impacts of poaching for parrots, can be applied to other taxa also impacted by harvesting for trade or other purposes.

Genome-wide screening of microsatellites in golden snub-nosed monkey (Rhinopithecus roxellana), for the development of a standardized genetic marker system

Golden snub-nosed monkey (Rhinopithecus roxellana) is an endangered primate endemic to China. The lack of standardized genetic markers limits its conservation works. In the present study, a total of 1,400,552 perfect STRs was identified in the reference genome of R. roxellana. By comparing it with the 12 resequencing genomes of four geographical populations, a total of 1,927 loci were identified as perfect tetranucleotides and shared among populations. We randomly selected 74 loci to design primer pairs. By using a total of 64 samples from the Chengdu Zoo captive population and the Pingwu wild population, a set of 14 novel STR loci were identified with good polymorphism, strong stability, high repeatability, low genotyping error rate that were suitable for non-invasive samples. These were used to establish a standardized marker system for golden snub-nosed monkeys. The genetic diversity analysis showed the average H_O, H_E, and PIC was 0.477, 0.549, and 0.485, respectively, in the Chengdu Zoo population; and 0.516, 0.473, and 0.406, respectively, in Pingwu wild population. Moreover, an individual identification method was established, which could effectively distinguish individuals with seven markers. The paternity tests were conducted on seven offspring with known mothers from two populations, and their fathers were determined with high confidence. A genotyping database for the captive population in the Chengdu Zoo (n = 25) and wild population in Pingwu country (n = 8) was acquired by using this marker system.

Promiscuity and sex ratio in the terrestrial isopod Armadillidium vulgare and consequences on genetic diversity

In promiscuous mating systems, both males and females mate with several partners. While the benefits of multiple mating are well recognized for males, there are several non-mutually exclusive hypotheses to explain multiple mating for females. Promiscuity is widespread in terrestrial isopods. Here, we placed experimental populations of the terrestrial isopod Armadillidium vulgare under varying sex ratios to manipulate the number of available partners, and better characterise the mating system in this species by performing paternity tests using microsatellite markers. We observed that females usually mate multiply with up to 5 males in a single event of reproduction. A higher number of fathers in broods did not increase brood size nor heterozygosity, but increased allelic richness. Promiscuity seems to be asymmetric in this species, with females being less affected by changes in sex ratio than were males and would be an adaptive mating system maximising the offspring genetic diversity.

Development and characterization of 19 polymorphic microsatellite loci from the Red-cowled Cardinal (Paroaria dominicana, Passeriformes, Aves) using next-generation sequencing

The Red-cowled Cardinal (Paroaria dominicana) is an endemic passerine of the Caatinga biome in Brazil, and is one of the most traded passerines in the country. Illegal trade can have serious impacts on wild populations, such as reduced population sizes, the introduction of the species to areas outside their historical range or mixing individuals from different populations. Microsatellites constitute an important tool for population genetics and forensics studies, and hold great potential to help authorities manage illegal trafficking and inspect commercial breeders. We developed new microsatellite loci using massive parallel sequencing and characterized them in 23 seized Red-cowled Cardinals with unknown geographic origin. The DNA sequencing generated 2,068,684 paired-reads of which we identified 10,322 tri- to hexanucleotide loci. We selected 30 loci for amplification and polymorphism tests, of which 21 successfully amplified and 19 were polymorphic. The number of alleles ranged from 7 to 18 and the mean expected heterozygosity was 0.863. Six loci deviated from Hardy-Weinberg equilibrium probably due to null alleles and/or the Wahlund effect. Polymorphic loci in Hardy-Weinberg equilibrium showed low identity probability and high paternity exclusion probability. Our results indicate that this new set of microsatellite loci constitutes an important tool for both population genetic and forensic studies, with ultimate potential for assisting authorities in managing animal victims of illegal trafficking and the inspection of commercial breeders of the Red-cowled Cardinal.

Evaluation of 17 microsatellite markers for parentage testing and individual identification of domestic yak (Bos grunniens)

BACKGROUND

Yak (Bos grunniens) is the most important domestic animal for people living at high altitudes. Yak ordinarily feed by grazing, and this behavior impacts the accuracy of the pedigree record because it is difficult to control mating in grazing yak. This study aimed to evaluate the pedigree system and individual identification in polled yak.

METHODS

A total of 71 microsatellite loci were selected from the literature, mostly from the studies on cattle. A total of 35 microsatellite loci generated excellent PCR results and were evaluated for the parentage testing and individual identification of 236 unrelated polled yaks. A total of 17 of these 35 microsatellite loci had polymorphic information content (PIC) values greater than 0.5, and these loci were in Hardy-Weinberg equilibrium without linkage disequilibrium.

RESULTS

Using multiplex PCR, capillary electrophoresis, and genotyping, very high exclusion probabilities were obtained for the combined core set of 17 loci. The exclusion probability (PE) for one candidate parent when the genotype of the other parent is not known was 0.99718116. PE for one candidate parent when the genotype of the other parent is known was 0.99997381. PE for a known candidate parent pair was 0.99999998. The combined PEI (PE for identity of two unrelated individuals) and PESI (PE for identity of two siblings) were >0.99999999 and 0.99999899, respectively. These findings indicated that the combination of 17 microsatellite markers could be useful for efficient and reliable parentage testing and individual identification in polled yak.

DISCUSSION

Many microsatellite loci have been investigated for cattle paternity testing. Nevertheless, these loci cannot be directly applied to yak identification because the two bovid species have different genomic sequences and organization. A total of 17 loci were selected from 71 microsatellite loci based on efficient amplification, unambiguous genotyping, and high PIC values for polled yaks, and were suitable for parentage analysis in polled yak populations.

Microsatellite instability testing in colorectal cancer using the QiaXcel advanced platform

Background

Microsatellite instability (MSI) is a major predictive and diagnostic marker in several cancers including colorectal carcinomas. Diagnostic testing for microsatellites is generally performed using capillary sequencers, which requires expensive high-end equipment including expensive chemistry using fluorescent dyes labelling the PCR products of interest. In this study we have modified such a diagnostic protocol and established the microsatellite testing on the QiaXcel Advanced platform.

Methods

MSI testing was based on a previously established protocol describing a multiplex PCR followed by fluorescent detection of PCR products in a capillary sequencing device. Ten microsatellites were included in the new protocol: BAT25, BAT26, BAT40, D2s123, D10s197, D13s153, D17s250, D18s58, D5s346, and MycI. In this protocol the PCR was demultiplexed and established on the QiaXcel Advanced system (Qiagen, Hilden, Germany).

Results

Making use of a series of FFPE control samples with known MSI status including those with and without MSI a protocol for MSI testing was successfully established on the QiaXcel Advanced platform.

Conclusions

MSI testing for human colorectal cancers using the QiaXcel Advanced system could serve as an economic acceptable tool for rapid diagnostics in laboratories that do not have access to a capillary sequencing unit.