DNA based method for determining source country of the short beaked echidna (Tachyglossus aculeatus) in the illegal wildlife trade

Color vision evolution in egg-laying mammals: insights from visual photoreceptors and daily activities of Australian echidnas

Egg-laying mammals (monotremes) are considered "primitive" due to traits such as oviparity, cloaca, and incomplete homeothermy, all of which they share with reptiles. Two groups of monotremes, the terrestrial echidna (Tachyglossidae) and semiaquatic platypus (Ornithorhynchidae), have evolved highly divergent characters since their emergence in the Cenozoic era. These evolutionary differences, notably including distinct electrosensory and chemosensory systems, result from adaptations to species-specific habitat conditions. To date, very few studies have examined the visual adaptation of echidna and platypus. In the present study, we show that echidna and platypus have different light absorption spectra in their dichromatic visual sensory systems at the molecular level. We analyzed absorption spectra of monotreme color opsins, long-wavelength sensitive opsin (LWS) and short-wavelength sensitive opsin 2 (SWS2). The wavelength of maximum absorbance (λmax) in LWS was 570.2 in short-beaked echidna (Tachyglossus aculeatus) and 560.6 nm in platypus (Ornithorhynchus anatinus); in SWS2, λmax was 451.7 and 442.6 nm, respectively. Thus, the spectral range in echidna color vision is ~ 10 nm longer overall than in platypus. Natural selection analysis showed that the molecular evolution of monotreme color opsins is generally functionally conserved, suggesting that these taxa rely on species-specific color vision. In order to understand the usage of color vision in monotremes, we made 24-h behavioral observations of captive echidnas at warm temperatures and analyzed the resultant ethograms. Echidnas showed cathemeral activity and various behavioral repertoires such as feeding, traveling, digging, and self-grooming without light/dark environment selectivity. Halting (careful) behavior is more frequent in dark conditions, which suggests that echidnas may be more dependent on vision during the day and olfaction at night. Color vision functions have contributed to dynamic adaptations and dramatic ecological changes during the ~ 60 million years of divergent monotreme evolution. The ethogram of various day and night behaviors in captive echidnas also contributes information relevant to habitat conservation and animal welfare in this iconic species, which is locally endangered.

An evaluation of DNA sample source and molecular markers to determine gender in the short-beaked echidna (Tachyglossus aculeatus)

The short-beaked echidna is sexually monomorphic such that gender identification without veterinary intervention is challenging. The aim of this study was to evaluate and compare the most optimal noninvasive genetic source by extracting echidna genomic DNA (gDNA) from fecal scats, plucked hair, and quills to perform genetic sex testing using a range of molecular markers. Sex determination of 14 captive short-beaked echidnas was determined by amplifying isolated DNA from noninvasive samples, targeting two Y chromosome (male-specific) genes (mediator complex subunit 26 Y-gametologue [CRSPY] and anti-Müllerian hormone Y-gametologue [AMHY]), in addition to four confirmed sex-specific RADseq markers. Results of noninvasive samples were compared with blood samples and clinical records. Receiver operating characteristic curves were used to assess accuracy of sex determination of markers for each sample type. The gender of the echidnas was successfully identified on 75% of occasions using fecal samples, 90.6% occasions using hair, and 84.6% occasions with quills. Overall, the male-specific RADseq markers accurately identified the sex of echidnas with all sample types for 90% of animals; compared with 81.5% using CRSPY, and 82.0% using AMHY to identify sex. Collection of hair, quills, and feces provides a useful alternative to invasively collected samples, however, the accuracy of results depends on sample type and genetic marker selected. We found gender determination in the short-beaked echidna was most accurate using four male-specific RADseq markers on gDNA isolated from blood and hair. The noninvasive genetic sexing techniques documented here will inform and facilitate husbandry and genetic management of captive echidna populations.

A forensically validated genetic toolkit for the species and lineage identification of the highly trafficked shingleback lizard (Tiliqua rugosa)

Shingleback lizards (Tiliqua rugosa) are among the most trafficked native fauna from Australia in the illegal pet trade. There are four morphologically recognised subspecies of shinglebacks, all with differing overseas market values. Shinglebacks from different geographic locales are often trafficked and housed together, which may complicate identifying the State jurisdiction where the poaching event occurred. Additionally, shinglebacks can be housed and trafficked with other species within the same genus, which may complicate DNA analysis, especially in scenarios where indirect evidence (e.g. swabs, faeces) is taken for analysis. In this study, a forensic genetic toolkit was designed and validated to target shingleback DNA for species identification and geographic origin. To do this, field sampling across Australia was conducted to expand the phylogeographic sampling of shinglebacks across their species range and include populations suspected to be poaching hotspots. A commonly used universal reptile primer set (ND4/LEU) was then validated for use in forensic casework related to the genus Tiliqua. Two additional ND4 primer sets were designed and validated. The first primer set was designed and demonstrated to preferentially amplify an ∼510 bp region of the genus Tiliqua over other reptiles and builds on existing data to expand the available phylogeographic database. The second primer set was designed and demonstrated to solely amplify an ∼220 bp region of T. rugosa ND4 over any other reptile species. Through the validation process, all primers were demonstrated to amplify T. rugosa DNA from a variety of sample types (e.g. degraded, low quality and mixed). Two of the primer sets were able to distinguish the genetic lineage of T. rugosa from the phylogeographic database. This work provides the first forensically validated toolkit and phylogeographic genetic database for Squatmate lizards.

EchidnaCSI: Engaging the public in research and conservation of the short-beaked echidna

The short-beaked echidna is an iconic Australian animal and the most-widespread native mammal, inhabiting diverse environments. The cryptic nature of echidnas has limited research into their ecology in most areas; however, from the well-researched and endangered Kangaroo Island echidna population, we understand that the threats include habitat loss, roads, and invasive species. To obtain more information about echidnas Australia-wide, we established the Echidna Conservation Science Initiative (EchidnaCSI) citizen science project. EchidnaCSI calls on members of the public to submit photographs of wild echidnas and learn to identify and collect echidna scats for molecular analysis. To facilitate participation, we developed a smartphone application as well as ongoing social and traditional media activities and community events. In 3 y, more than 9,000 members of the public have downloaded the EchidnaCSI app, collecting 400 scats and submitting over 8,000 sightings of echidnas from across Australia. A subset of submitted scat samples were subjected to DNA extraction and PCR, which validated the approach of using citizen science for scat collection and viability for molecular analysis. To assess the impact of the project through public participation, we surveyed our participants (n = 944) to understand their demographics and motivations for engagement. Survey results also revealed that EchidnaCSI served as a gateway into citizen science more generally for many participants. EchidnaCSI demonstrates the potential for using citizen science approaches to collect high-quality data and material from a cryptic species over a very large geographic area and the considerable engagement value of citizen science research.

Diet, feeding behaviour and echidna beaks: a review of functional relationships within the tachyglossids

Echidnas are commonly known as ‘spiny ant-eaters’, but long-beaked echidnas (Zaglossus spp.) do not eat ants, whereas short-beaked echidnas (Tachyglossus aculeatus) eat other invertebrates as well as ants. The differences in skull morphology between short- and long-beaked echidnas are related to the differences in their diets, and I tested the hypothesis that there would be differences in beak length of short-beaked echidnas from populations with different diets. Published data on diet from echidnas from different parts of Australia show that echidnas from arid and semi-arid areas (subspecies acanthion) and Kangaroo Island (subspecies multiaculeatus) principally eat ants and termites, whereas the main dietary items of echidnas from south-eastern Australia (subspecies aculeatus) and Tasmania (subspecies setosus) are ants and scarab larvae. Using museum specimens and photographs I measured skull dimensions on echidnas from different parts of Australia: acanthion and multiaculeatus have narrower skulls and shorter beaks than aculeatus and setosus, with setosus being the only Australian subspecies where beak length exceeds cranium length. Australian short-beaked echidnas fall into two groups: aculeatus and setosus from the wetter east and south-east, which eat ant and scarab larvae, and the arid and semi-arid zone acanthion and multiaculeatus, with shorter, narrower skulls, and which eat ants and termites.

Development and validation of simultaneous identification of 26 mammalian and poultry species by a multiplex assay

A multiplex PCR assay was developed to simultaneously identify 22 mammalian species (alpaca, Asiatic black bear, Bactrian camel, brown rat, cat, cattle, common raccoon, dog, European rabbit, goat, horse, house mouse, human, Japanese badger, Japanese wild boar, masked palm civet, pig, raccoon dog, red fox, sheep, Siberian weasel, and sika deer) and four poultry species (chicken, domestic turkey, Japanese quail, and mallard), even from a biological sample containing a DNA mixture of multiple species. The assay was designed to identify species through multiplex PCR and capillary electrophoresis, with a combination of amplification of a partial region of the mitochondrial D-loop by universal primer sets and a partial region of the cytochrome b (cyt b) gene by species-specific primer sets. The assay was highly sensitive, with a detection limit of 100 copies of mitochondrial DNA. The assay's ability to identify species from complex DNA mixtures was demonstrated using an experimental sample consisting of 10 species. Efficacy, accuracy, and reliability of the assay were validated for use in forensic analysis with the guidelines of Scientific Working Group on DNA Analysis Methods (SWGDAM). The multiplex PCR assay developed in this study enables cost-effective, highly sensitive, and simultaneous species identification without massively parallel sequencing (MPS) platforms. Thus, the technique described is straightforward and suitable for routine forensic investigations.

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.

Wildlife crime in Australia

Wildlife crime is on a massive scale by whatever metric is used. The illegal trade in wildlife and related products is leading to the decline and extinction of many iconic species from rhino to tigers. Almost all countries are signatures to CITES and therefore should enforce national legislation if alleged infringements of trade of wildlife occur. No country is immune from this illegal trade although countries like Australia have their own specific wildlife crimes. Australia is home to many reptilian, amphibian and avian species that are highly prized, predominantly as pets. Collection of protected species from the wild is illegal in all jurisdictions yet policing remote areas of the outback, where so much of the native endemic fauna and flora lives, is nearly impossible. The illegal international trade in these species is highlighted by two case studies provided in this review. A further case highlights the issues of each of the six states of Australia having separate legislation, which is compounded when wildlife crime can be inter-state crime. Australia is one of the few countries having an institute, based at the Australian Museum, with an accredited wildlife forensic science laboratory and therefore the capability to undertake forensic testing of seized samples. One way to reduce wildlife crime may be by educating those who buy illegally seized products that there is a direct connection between the dead animal from which it came and the devasting effect this purchase has on the environment.

Threats from wildlife trade: The importance of genetic data in safeguarding the endangered Four-eyed Turtle (Sacalia quadriocellata)

Wildlife trade has been considered one of the largest threats to biodiversity in Southeast Asia. Many vertebrates, such as pangolins, elephants and turtles have been heavily hunted as a result of high demand from emerging markets in China and other countries in the region. In Vietnam, over-exploitation of turtles over several decades to supply the international trade has extirpated numerous populations and driven several species to the brink of extinction. To reverse this trend, conservation measures, such as re-introduction of confiscated or captive-bred animals to their native habitats, should be implemented to recover severely declined local populations. For species with a complex phylogeographic structure, however, it is crucial to understand geographic patterns of genetically-distinct populations to avoid releasing animals of unknown origin to wrong localities. In this study, we investigate the phylogeographic pattern of the Four-eyed Turtle (Sacalia quadriocellata), a widely traded species, which occurs in southern China, northern and central Laos and much of Vietnam, using samples with known localities and those collected from the local trade. Our range-wide phylogenetic and network study, based on the complete mitochondrial cytochrome b gene, recovered at least three major clades and seven subclades within the species range. Amongst these, two subclades, one from northern Annamites, Vietnam and the other from north-eastern Laos, are newly discovered. The fine scale phylogeographic analysis helped us to assign misidentified sequences from GenBank and those from confiscated animals with unknown origin to well-defined geographic populations. The results highlight the importance of incorporating samples collected from the local trade and the wild in genetic analyses to support both ex-situ and in-situ conservation programmes of highly-threatened species in accordance with the IUCN’s One Plan Approach.

Past, present and future contributions of evolutionary biology to wildlife forensics, management and conservation

Successfully implementing fundamental concepts into concrete applications is challenging in any given field. It requires communication, collaboration and shared will between researchers and practitioners. We argue that evolutionary biology, through research work linked to conservation, management and forensics, had a significant impact on wildlife agencies and department practices, where new frameworks and applications have been implemented over the last decades. The Quebec government's Wildlife Department (MFFP: Ministère des Forêts, de la Faune et des Parcs) has been proactive in reducing the “research–implementation” gap, thanks to prolific collaborations with many academic researchers. Among these associations, our department's outstanding partnership with Dr. Louis Bernatchez yielded significant contributions to harvest management, stocking programmes, definition of conservation units, recovery of threatened species, management of invasive species and forensic applications. We discuss key evolutionary biology concepts and resulting concrete examples of their successful implementation that derives directly or indirectly from this successful partnership. While old and new threats to wildlife are bringing new challenges, we expect recent developments in eDNA and genomics to provide innovative solutions as long as the research–implementation bridge remains open.