DNA barcoding and the identification of tree frogs (Amphibia: Anura: Rhacophoridae)

Integrative species delimitation and five new species of lynx spiders (Araneae, Oxyopidae) in Taiwan

An accurate assessment of species diversity is a cornerstone of biology and conservation. The lynx spiders (Araneae: Oxyopidae) represent one of the most diverse and widespread cursorial spider groups, however their species richness in Asia is highly underestimated. In this study, we revised species diversity with extensive taxon sampling in Taiwan and explored species boundaries based on morphological traits and genetic data using a two-step approach of molecular species delimitation. Firstly, we employed a single COI dataset and applied two genetic distance-based methods: ABGD and ASAP, and two topology-based methods: GMYC and bPTP. Secondly, we further analyzed the lineages that were not consistently delimited, and incorporated H3 to the dataset for a coalescent-based analysis using BPP. A total of eight morphological species were recognized, including five new species, Hamataliwa cordivulva sp. nov., Hamat. leporauris sp. nov., Tapponia auriola sp. nov., T. parva sp. nov. and T. rarobulbus sp. nov., and three newly recorded species, Hamadruas hieroglyphica (Thorell, 1887), Hamat. foveata Tang & Li, 2012 and Peucetia latikae Tikader, 1970. All eight morphological species exhibited reciprocally monophyletic lineages. The results of molecular-based delimitation analyses suggested a variety of species hypotheses that did not fully correspond to the eight morphological species. We found that Hamat. cordivulva sp. nov. and Hamat. foveata showed shallow genetic differentiation in the COI, but they were unequivocally distinguishable according to their genitalia. In contrast, T. parva sp. nov. represented a deep divergent lineage, while differences of genitalia were not detected. This study highlights the need to comprehensively employ multiple evidence and methods to delineate species boundaries and the values of diagnostic morphological characters for taxonomic studies in lynx spiders.

Characteristics Evaluation of a Barcode Sequence of Two Limnonectes (Anura) Sympatric Populations from Kendari, Southeast Sulawesi

<b>Background and Objective:</b> Cytochrome c oxidase gene subunit-I (COI) has conserved and variable regions and along with the 658 nucleotide base pairs at the '5 of these have been used as animal barcode, species identification and evolutionary studies of several vertebrates, especially Anura. This research was conducted to characterize the nucleotides of the COI sequence gene of (<i>Limnonectes cf. grunniens</i>) that live sympatrically with <i>L. modestus</i> on several headwater streams in Kendari, Southeast Sulawesi. <b>Materials and Methods:</b> This research is explorative, samples of frogs were obtained from the Lahundape and Moramo headwater streams. A total of 16 frogs were sampled and the genomic DNA of frog samples was extracted and, then amplified using the PCR method. The next steps are sequencing and analysis using MEGA 7. <b>Results:</b> The result showed nucleotides along 688 to 705 base pairs. There were two haplotypes of <i>L. cf. grunniens</i> and three <i>L. modestus</i>. <i>L. cf. grunniens </i>consist of 32.6% Thymine (Uracil), 32.3% Cytisine, 17.9% Adenine and 17.9% Guanine. While <i>L. modestus</i> is 37.6% Thymine, 26.0% Cytosine, 20.7% Adenine and 15.8% Guanine. Based on Kimura-2 parameter, the genetic distance between genera ranges from 0.25-0.26 while the genetic distance between species is 0.00-0.01. <b>Conclusion:</b> Phylogeny trees based on partial sequences of COI frog genes showed that <i>L. cf. grunniens</i> and <i>L. modestus</i> are monophyletic with bootstrapped values ranging from 86-100% and differentiated between species. There is a genetic variability of COI sequences of <i>Limnonectes cf. grunniens</i> and <i>L. modestus</i> from Kendari, Southeast Sulawesi.

Diversity, distribution and molecular species delimitation in frogs and toads from the Eastern Palaearctic

Biodiversity analyses can greatly benefit from coherent species delimitation schemes and up-to-date distribution data. In this article, we have made the daring attempt to delimit and map described and undescribed lineages of anuran amphibians in the Eastern Palaearctic (EP) region in its broad sense. Through a literature review, we have evaluated the species status considering reproductive isolation and genetic divergence, combined with an extensive occurrence dataset (nearly 85k localities). Altogether 274 native species from 46 genera and ten families were retrieved, plus eight additional species introduced from other realms. Independent hotspots of species richness were concentrated in southern Tibet (Medog County), the circum-Sichuan Basin region, Taiwan, the Korean Peninsula and the main Japanese islands. Phylogeographic breaks responsible for recent in situ speciation events were shared around the Sichuan Mountains, across Honshu and between the Ryukyu Island groups, but not across shallow water bodies like the Yellow Sea and the Taiwan Strait. Anuran compositions suggested to restrict the zoogeographical limits of the EP to East Asia. In a rapidly evolving field, our study provides a checkpoint to appreciate patterns of species diversity in the EP under a single, spatially explicit, species delimitation framework that integrates phylogeographic data in taxonomic research.

Cryptic Diversity, but to What Extent? Discordance Between Single-Locus Species Delimitation Methods Within Mainland Anoles (Squamata: Dactyloidae) of Northern Central America

Single-locus molecular barcoding is a useful method for identifying overlooked and undescribed biodiversity, providing the groundwork for further systematic study and taxonomic investigation. A variety of methods for delimiting species from barcoding libraries have been developed and applied, allowing for rapid estimates of species diversity in a broad range of taxa. However, tree-based and distance-based analyses can infer different group assignments, potentially over- or underestimating the number of putative species groups. Here, we explore diversity of mainland species of anole lizards from the Chortís Block biogeographical province of northern Central America using a DNA barcoding approach, generating and analyzing cytochrome oxidase subunit I (COI) sequences for over 400 samples assignable to 33 of 38 (86.8%) native and one introduced mainland species. We subsequently tested the effects different models of nucleotide substitution, different species-delimitation algorithms, and reducing our dataset had on species delimitation estimates. We performed of two distance-based (ABGD, RESL) and three tree-based (bPTP, mPTP, GMYC) analyses on both the full dataset and a dataset consisting only of unique halotypes. From 34 nominal taxa, analyses of the full dataset recovered between 34 and 64 operational taxonomic units (OTUs), while analyses of the reduced dataset inferred between 36 and 59. Reassigning individuals to either mPTP-inferred or ABGD clustered (7.2% threshold) groups improved the detection of a barcoding gap across three different models of nucleotide substitution, removing overlap between intra- and interspecific distances. Our results highlight the underestimated diversity of mainland Chortís Block anoles, but the lack of congruence between analyses demonstrates the importance of considering multiple analytical methods when dealing with single-locus datasets. We recommend future studies consider the effects of different models of nucleotide substitution on proposed barcoding gaps, as well as the effect reducing a dataset to unique haplotypes may have on proposed diversity estimates.