DNA barcoding reveals CITES-listed species among Taiwanese government-seized chelonian specimens

Sex identification of birds in Taipei Zoo

As a conservation and breeding institution for birds, Taipei Zoo plays an important role in restoring endangered species. As approximately half of all bird species are monomorphic, precisely confirming the sex of individuals is critical for the management of ex-situ conservation breeding populations, as well as for understanding the sex ratio of those in the wild. Generally, PCR is used more reliably for sex determination versus traditional methods such as plumage, behavior or hormone levels. Nevertheless, the various primer sets and annealing temperatures vary between species, and so inaccurate sexing can occasionally happen due to inadequate PCR conditions. To reduce the probability of misidentification, and to establish a PCR condition database for sex determination across the diverse range of avian taxa, we tested multiple primer sets and annealing temperatures for amplification of the bird sex-specific gene fragments (CHD1) for each captive or rescued avian species held at Taipei Zoo since 2014. A total of 162 species across 22 orders were tested using one or two primer sets. One hundred and fifty-five species were successfully sexed by the primer set 2550F/2718R and the success rate of sex typing reached over 90% of species tested in each order. Most species have suitable PCR annealing temperatures between 45°C and 55°C, and the species in the same avian taxa showed similar results in temperature. This indicates that it is possible to select the annealing temperature of other species in the same family when the species had not been tested before. We expect this study will improve the success rate of identifying sex by using applicable PCR conditions and reduce the time for searching references every time before attempts to PCR sex birds.

Matrilineal phylogeny and habitat suitability of the endangered spotted pond turtle (Geoclemys hamiltonii; Testudines: Geoemydidae): a two-dimensional approach to forecasting future conservation consequences

The spotted pond turtle (Geoclemys hamiltonii) is a threatened and less explored species endemic to Bangladesh, India, Nepal, and Pakistan. To infer structural variation and matrilineal phylogenetic interpretation, the present research decoded the mitogenome of G. hamiltonii (16,509 bp) using next-generation sequencing technology. The mitogenome comprises 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one AT-rich control region (CR) with similar strand symmetry in vertebrates. The ATG was identified as a start codon in most of the PCGs except Cytochrome oxidase subunit 1 (cox1), which started with the GTG codon. The non-coding CR of G. hamiltonii was determined to have a unique structure and variation in different domains and stem-loop secondary structure as compared with other Batagurinae species. The PCGs-based Bayesian phylogeny inferred strong monophyletic support for all Batagurinae species and confirmed the sister relationship of G. hamiltonii with Pangshura and Batagur taxa. We recommend generating more mitogenomic data for other Batagurinae species to confirm their population structure and evolutionary relationships. In addition, the present study aims to infer the habitat suitability and habitat quality of G. hamiltonii in its global distribution, both in the present and future climatic scenarios. We identify that only 58,542 km2 (7.16%) of the total range extent (817,341 km2) is suitable for this species, along with the fragmented habitats in both the eastern and western ranges. Comparative habitat quality assessment suggests the level of patch shape in the western range is higher (71.3%) compared to the eastern range. Our results suggest a massive decline of approximately 65.73% to 70.31% and 70.53% to 75.30% under ssp245 and ssp585 future scenarios, respectively, for the years between 2021-2040 and 2061-2080 compared with the current distribution. The present study indicates that proper conservation management requires greater attention to the causes and solutions to the fragmented distribution and safeguarding of this endangered species in the Indus, Ganges, and Brahmaputra (IGB) river basins.

Mitochondrial DNA and Distribution Modelling Evidenced the Lost Genetic Diversity and Wild-Residence of Star Tortoise, Geochelone elegans (Testudines: Testudinidae) in India

The Indian star tortoise (Geochelone elegans) is a massively traded animal in South Asia. To mitigate this risk, the conservation agencies recommended guidelines to safeguard this charismatic species in nature. We adopted mitochondrial DNA-based investigation and performed species distribution modeling of G. elegans throughout its distribution range in the Indian subcontinent. The genetic analyses revealed weak genetic landscape shape interpolations, low intraspecific distances (0% to 1.5%) with mixed haplotype diversity, and a single molecular operational taxonomic unit (MOTU) in the cytochrome b gene dataset. The star tortoise, G. elegans, and its sister species Geochelone platynota showed a monophyletic clustering in the Bayesian (BA) phylogeny. We also attempt to understand the habitat suitability and quality of G. elegans in its distribution range. Our results suggest that, out of the extant area, only 56,495 km² (9.90%) is suitable for this species, with regions of highest suitability in Sri Lanka. Comparative habitat quality estimation suggests the patch shape complexity and habitat fragmentation are greater in the western and southern ranges of India, which have been greatly influenced by an increased level of urbanization and agriculture practices. We have also provided a retrospect on the potential threat to G. elegans related to the wildlife trade on the regional and international spectrum. Our results detected multiple trading hubs and junctions overlying within the suitable ranges which need special attention in the vicinity. The present study calls for a proper conservation strategy to combat the fragmented distribution and explicitly recommends intensive genetic screening of founder individuals or isolated adult colonies, implementing scientific breeding, and subsequent wild release to restore the lost genetic diversity of star tortoises.

Assessing the reliability of medicinal Dendrobium sequences in GenBank for botanical species identification

DNA-based method is a promising tool in species identification and is widely used in various fields. DNA barcoding method has already been included in different pharmacopoeias for identification of medicinal materials or botanicals. Accuracy and validity of DNA-based methods rely on the accuracy and taxonomic reliability of the DNA sequences in the database to be compared against. Here we evaluated the annotation quality and taxonomic reliability of selected barcode loci (rbcL, matK, psbA-trnH, trnL-trnF and ITS) of 41 medicinal Dendrobium species downloaded from GenBank. Annotations of most accessions are incomplete. Only 53.06% of the 2041 accessions downloaded contain a reference to a voucher specimen. Only 31.60% and 4.8% of the entries are annotated with country of origin and collector or assessor, respectively. Taxonomic reliability of the sequences was evaluated by a Megablast search based on similarity to sequences submitted by other research groups. A small number of sequences (211, 7.14%) was regarded as highly doubted. Moreover, 10 out of 60 complete chloroplast genomes contain highly doubted sequences. Our findings suggest that sequences of GenBank should be used with caution for species-level identification. The scientific community should provide more important information regarding identity and traceability of the sample when they deposit sequences to public databases.

The Barcoding Table of Animal Species (BaTAnS): a new tool to select appropriate methods for animal species identification using DNA barcoding

Food and feed products derived from animal materials have a long history of being adulterated. Methods for the identification of animal samples based on DNA barcoding are very potent tools to reveal species substitution. Since numerous DNA barcoding methods are available for different taxa, it is challenging to choose an appropriate and verified method for each sample in question. To overcome this obstacle the working group "Molecular biological methods for plant and animal species differentiation" developed the "Barcoding Table of Animal Species". This working group is established through the German food and feed law and is mandated to validate standard methods, especially for the official food and feed control laboratories in Germany. In this paper, a collection of currently available and verified DNA barcoding methods for the identification of animal species is presented as a Microsoft Excel^® file-"The Barcoding Table of Animal Species (BaTAnS)". It consists of several components: The method collection, the results collection and a section for reporting new entries and problems. It is focusing on the validity and applicability of DNA barcoding methods to test food and feed products for correct species declaration. Each method is listed with its reference and is verified by at least two laboratories for their applicability. Since additional information will be available in future, this table will be updated regularly. The BaTAnS is an easy tool that helps to choose the right verified method to identify a certain specimen to taxon, genus or species level in food samples.

BOLD and GenBank revisited - Do identification errors arise in the lab or in the sequence libraries?

Applications of biological knowledge, such as forensics, often require the determination of biological materials to a species level. As such, DNA-based approaches to identification, particularly DNA barcoding, are attracting increased interest. The capacity of DNA barcodes to assign newly encountered specimens to a species relies upon access to informatics platforms, such as BOLD and GenBank, which host libraries of reference sequences and support the comparison of new sequences to them. As parameterization of these libraries expands, DNA barcoding has the potential to make valuable contributions in diverse applied contexts. However, a recent publication called for caution after finding that both platforms performed poorly in identifying specimens of 17 common insect species. This study follows up on this concern by asking if the misidentifications reflected problems in the reference libraries or in the query sequences used to test them. Because this reanalysis revealed that missteps in acquiring and analyzing the query sequences were responsible for most misidentifications, a workflow is described to minimize such errors in future investigations. The present study also revealed the limitations imposed by the lack of a polished species-level taxonomy for many groups. In such cases, applications can be strengthened by mapping the geographic distributions of sequence-based species proxies rather than waiting for the maturation of formal taxonomic systems based on morphology.