Assessment of snake DNA barcodes based on mitochondrial COI and Cytb genes revealed multiple putative cryptic species in Thailand

The efficacy of single mitochondrial genes at reconciling the complete mitogenome phylogeny-a case study on dwarf chameleons

Although genome-scale data generation is becoming more tractable for phylogenetics, there are large quantities of single gene fragment data in public repositories and such data are still being generated. We therefore investigated whether single mitochondrial genes are suitable proxies for phylogenetic reconstruction as compared to the application of full mitogenomes. With near complete taxon sampling for the southern African dwarf chameleons (Bradypodion), we estimated and compared phylogenies for the complete mitogenome with topologies generated from individual mitochondrial genes and various combinations of these genes. Our results show that the topologies produced by single genes (ND2, ND4, ND5, COI, and COIII) were analogous to the complete mitogenome, suggesting that these genes may be reliable markers for generating mitochondrial phylogenies in lieu of generating entire mitogenomes. In contrast, the short fragment of 16S commonly used in herpetological systematics, produced a topology quite dissimilar to the complete mitogenome and its concatenation with ND2 weakened the resolution of ND2. We therefore recommend the avoidance of this 16S fragment in future phylogenetic work.

DNA barcoding in herbal medicine: Retrospective and prospective

DNA barcoding has been widely used for herb identification in recent decades, enabling safety and innovation in the field of herbal medicine. In this article, we summarize recent progress in DNA barcoding for herbal medicine to provide ideas for the further development and application of this technology. Most importantly, the standard DNA barcode has been extended in two ways. First, while conventional DNA barcodes have been widely promoted for their versatility in the identification of fresh or well-preserved samples, super-barcodes based on plastid genomes have rapidly developed and have shown advantages in species identification at low taxonomic levels. Second, mini-barcodes are attractive because they perform better in cases of degraded DNA from herbal materials. In addition, some molecular techniques, such as high-throughput sequencing and isothermal amplification, are combined with DNA barcodes for species identification, which has expanded the applications of herb identification based on DNA barcoding and brought about the post-DNA-barcoding era. Furthermore, standard and high-species coverage DNA barcode reference libraries have been constructed to provide reference sequences for species identification, which increases the accuracy and credibility of species discrimination based on DNA barcodes. In summary, DNA barcoding should play a key role in the quality control of traditional herbal medicine and in the international herb trade.

DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs

DNA barcoding has greatly facilitated studies of taxonomy, biodiversity, biological conservation, and ecology. Here, we establish a reliable DNA barcoding library for Chinese snakes, unveiling hidden diversity with implications for taxonomy, and provide a standardized tool for conservation management. Our comprehensive study includes 1638 cytochrome c oxidase subunit I (COI) sequences from Chinese snakes that correspond to 17 families, 65 genera, 228 named species (80.6% of named species) and 36 candidate species. A barcode gap analysis reveals gaps, where all nearest neighbour distances exceed maximum intraspecific distances, in 217 named species and all candidate species. Three species-delimitation methods (ABGD, sGMYC, and sPTP) recover 320 operational taxonomic units (OTUs), of which 192 OTUs correspond to named and candidate species. Twenty-eight other named species share OTUs, such as Azemiops feae and A. kharini, Gloydius halys, G. shedaoensis, and G. intermedius, and Bungarus multicinctus and B. candidus, representing inconsistencies most probably caused by imperfect taxonomy, recent and rapid speciation, weak taxonomic signal, introgressive hybridization, and/or inadequate phylogenetic signal. In contrast, 43 species and candidate species assign to two or more OTUs due to having large intraspecific distances. If most OTUs detected in this study reflect valid species, including the 36 candidate species, then 30% more species would exist than are currently recognized. Several OTU divergences associate with known biogeographic barriers, such as the Taiwan Strait. In addition to facilitating future studies, this reliable and relatively comprehensive reference database will play an important role in the future monitoring, conservation, and management of Chinese snakes.

Molecular phylogeny reveals distinct evolutionary lineages of the banded krait, Bungarus fasciatus (Squamata, Elapidae) in Asia

The banded krait, Bungarus fasciatus is a widespread elapid snake, likely to comprise several distinct species in different geographic regions of Asia. Therefore, based on molecular phylogenetics and comparative morphology data, we present an overview of the systematic composition of the species to delimit potential biogeographic boundaries. Our phylogenetic analyses, based on four mitochondrial genes, reveal the existence of at least three evolutionary lineages within B. fasciatus, corresponding to Indo-Myanmar, Sundaic and eastern Asian lineages. We are convinced that there are at least three taxonomic entities within the nomen B. fasciatus and restrict the distribution of B. fasciatus sensu stricto to the Indo-Myanmar region. We also provide additional natural history data of the taxon from eastern India. Finally, we advocate further studies to establish the degree of reproductive isolation among these diverging evolutionary lineages and to reassess the systematic status of this species complex especially the Sundaic and eastern Asian lineages.

Quality control of fighting fish nucleotide sequences in public repositories reveals a dark matter of systematic taxonomic implication

BACKGROUND

The number of nucleotide sequences in public repositories has exploded recently. However, the data contain errors, leading to incorrect species identification. Several fighting fish (Betta spp.) are poorly described, with unresolved cryptic species complexes masking undescribed species. Here, DNA barcoding was used to detect erroneous sequences in public repositories.

OBJECTIVE

This study reflects the current quantitative and qualitative status of DNA barcoding in fighting fish and provides a rapid and reliable identification tool.

METHODS

A total of 1034 barcode sequences were analyzed from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes from 71 fighting fish species.

RESULTS

The nearest neighbor test showed the highest percentage of intraspecific nearest neighbors at 93.41% for COI and 91.67% for Cytb, which can be used as reference barcodes for certain taxa. Intraspecific variation was usually less than 13%, while most species differed by more than 54%. The barcoding gap, calculated from the difference between inter- and intraspecific sequence divergences, was negative in the COI data set indicating overlapping intra- and interspecific sequence divergence. Sequence saturation was observed in the Cytb data set but not in the COI data set.

CONCLUSION

The COI gene should thus be used as the main barcoding marker for fighting fish.

House-warming: Wild king cobra nests have thermal regimes that positively affect hatching success and hatchling size

Incubation temperature in nests of oviparous reptiles affects reproductive success indicators, including hatching time and success, offspring size, fitness, and behaviour. The female king cobra builds an above ground nest to incubate and protect its eggs. However, it is not clear how thermal regimes inside king cobra nests respond to external environmental temperature regimes, especially in subtropical regions that witness high diel and seasonal temperature fluctuations. To better understand the relationship between inside nest temperatures and hatching outcomes for this snake, we monitored the thermal regimes of 25 natural king cobra nests in the subtropical forests of the Western Himalayas in Uttarakhand state, northern India. We hypothesized that inside nest temperatures would be higher than outside (ambient) temperatures and that thermal regimes inside nests would affect hatching success and hatchling size. Internal and external temperatures at nest sites were measured every hour until hatching, via automatic data loggers. We then calculated hatching success of eggs and measured hatchling length and weight. Mean inside nest temperatures were consistently higher by about 3.0 °C than outside environmental temperatures. External temperature reduced with increasing elevation of nest sites and was the best determinant of inside nest temperature, which had a smaller range of variability. Physical characteristics of nests (size and leaf materials used) did not influence nest temperature significantly, but nest size was positively related to clutch size. Mean inside nest temperature was the best predictor of hatching success. Average daily minimum nest temperature, which indicates a possible lower threshold for thermal tolerance by eggs, was also correlated positively with hatching success. Mean daily maximum temperature was a significant predictor of mean length of hatchlings, but not of mean hatchling weight. Our study provides unequivocal evidence for the critical thermal benefits of king cobra nests for increased reproductive success, in subtropical environments with lower and sharply fluctuating temperature regimes.

Phylogenetic Analysis and Genetic Structure of Schlegel's Japanese Gecko (Gekko japonicus) from China Based on Mitochondrial DNA Sequences

Gekko japonicus, i.e., Schlegel's Japanese Gecko, is an important species which is widely distributed in East Asia. However, the information about population genetics of this species from China remains unclear. To address this issue, we used sequences from a fragment of the mitochondrial protein-coding gene cytochrome c oxidase I to estimate genetic diversity, genetic structure, and historical demography of G. japonicus populations from China. Phylogenetic analysis indicated that G. japonicus had a close relationship with Gekko wenxianensis. A total of 14 haplotypes were obtained, of which haplotype 1 was the most common and widely distributed. The genetic diversity of G. japonicus was comparatively low across different geographic populations. The populations of G. japonicus were divided into four groups which exhibited low levels of genetic differentiation, and expressed an unclear pattern of population structuring. In addition, potential population expansion of G. japonicus has occurred as well. Overall, these results demonstrate that the populations of G. japonicus reveal low genetic diversity in China, which is attributed to the founder and bottleneck events among populations. Our results will provide meaningful information on the population genetics of G. japonicus and will provide some insights into the study of origin of populations.

DNA barcoding of the National Museum of Natural History reptile tissue holdings raises concerns about the use of natural history collections and the responsibilities of scientists in the molecular age

Natural history collections are essential to a wide variety of studies in biology because they maintain large collections of specimens and associated data, including genetic material (e.g., tissues) for DNA sequence data, yet they are currently under-funded and collection staff have high workloads. With the advent of aggregate databases and advances in sequencing technologies, there is an increased demand on collection staff for access to tissue samples and associated data. Scientists are rapidly developing large DNA barcode libraries, DNA sequences of specific genes for species across the tree of life, in order to document and conserve biodiversity. In doing so, mistakes are made. For instance, inconsistent taxonomic information is commonly taken from different lending institutions and deposited in data repositories, such as the Barcode of Life Database (BOLD) and GenBank, despite explicit disclaimers regarding the need for taxonomic verification by the lending institutions. Such errors can have profound effects on subsequent research based on these mis-labelled sequences in data repositories. Here, we present the production of a large DNA barcode library of reptiles from the National Museum of Natural History tissue holdings. The library contains 2,758 sequences (2,205 COI and 553 16S) from 2260 specimens (four crocodilians, 37 turtles, and 2,219 lizards, including snakes), representing 583 named species, from 52 countries. In generating this library, we noticed several common mistakes made by scientists depositing DNA barcode data in public repositories (e.g., BOLD and GenBank). Our goal is to raise awareness of these concerns and offer advice to avoid such mistakes in the future to maintain accurate DNA barcode libraries to properly document Earth’s biodiversity.

Concerted and Independent Evolution of Control Regions 1 and 2 of Water Monitor Lizards (Varanus salvator macromaculatus) and Different Phylogenetic Informative Markers

Simple Summary

The evolutionary patterns and phylogenetic utility of duplicate control regions (CRs) in 72 individuals of Varanus salvator macromaculatus and other varanids have been observed. Divergence of the two CRs from each individual revealed a pattern of independent evolution in CRs of varanid lineage. This study is a first step towards developing new phylogenetic evolutionary models of the varanid lineage, with accurate evolutionary inferences to provide basic insights into the biology of mitogenomes.

Abstract

Duplicate control regions (CRs) have been observed in the mitochondrial genomes (mitogenomes) of most varanids. Duplicate CRs have evolved in either concerted or independent evolution in vertebrates, but whether an evolutionary pattern exists in varanids remains unknown. Therefore, we conducted this study to analyze the evolutionary patterns and phylogenetic utilities of duplicate CRs in 72 individuals of Varanus salvator macromaculatus and other varanids. Sequence analyses and phylogenetic relationships revealed that divergence between orthologous copies from different individuals was lower than in paralogous copies from the same individual, suggesting an independent evolution of the two CRs. Distinct trees and recombination testing derived from CR1 and CR2 suggested that recombination events occurred between CRs during the evolutionary process. A comparison of substitution saturation showed the potential of CR2 as a phylogenetic marker. By contrast, duplicate CRs of the four examined varanids had similar sequences within species, suggesting typical characteristics of concerted evolution. The results provide a better understanding of the molecular evolutionary processes related to the mitogenomes of the varanid lineage.

Phylogenetic analyses of distantly related clades of bent-toed geckos (genus Cyrtodactylus) reveal an unprecedented amount of cryptic diversity in northern and western Thailand

Cyrtodactylus species are the most diverse of the geckos and are widely distributed in Southeast Asia, including Thailand. However, their patterns of distribution, especially in northern and western parts of Thailand, remain unknown because few Cyrtodactylus species in these regions have been described. Thus, a data set of mitochondrial NADH dehydrogenase 2 (ND2) gene and flanking tRNAs from Cyrtodactylus found in northern and western Thailand, including contiguous areas, was assembled to elucidate phylogenetic relationships and identify the distribution patterns of these geckos. The results showed four well-supported clades, a northwestern clade (A), a northern clade (B), a western clade (C), and a special clade characterized by specific morphological features (D). Clades A-C were grouped with strong support by the geography of their localities from northern Thailand (Mae Hong Son and Chiang Mai Provinces) along the Tenasserim mountain ranges to Phang-Nga Province, Thailand. Clade D is a distinct clade of Cyrtodactylus species characterized by a tuberculate and prehensile tail and distributed widely in mainland Southeast Asia. Overall, the results suggest a pattern of geographic separation and distribution of Cyrtodactylus in northern and western Thailand. Additionally, this study provides evidence of a hidden biodiversity of Cyrtodactylus in these regions.

Existence of Bov-B LINE Retrotransposons in Snake Lineages Reveals Recent Multiple Horizontal Gene Transfers with Copy Number Variation

Transposable elements (TEs) are dynamic elements present in all eukaryotic genomes. They can “jump” and amplify within the genome and promote segmental genome rearrangements on both autosomes and sex chromosomes by disruption of gene structures. The Bovine-B long interspersed nuclear element (Bov-B LINE) is among the most abundant TE-retrotransposon families in vertebrates due to horizontal transfer (HT) among vertebrate lineages. Recent studies have shown multiple HTs or the presence of diverse Bov-B LINE groups in the snake lineage. It is hypothesized that Bov-B LINEs are highly dynamic and that the diversity reflects multiple HTs in snake lineages. Partial sequences of Bov-B LINE from 23 snake species were characterized. Phylogenetic analysis resolved at least two Bov-B LINE groups that might correspond to henophidian and caenophidian snakes; however, the tree topology differed from that based on functional nuclear and mitochondrial gene sequences. Several Bov-B LINEs of snakes showed greater than 80% similarity to sequences obtained from insects, whereas the two Bov-B LINE groups as well as sequences from the same snake species classified in different Bov-B LINE groups showed sequence similarities of less than 80%. Calculation of estimated divergence time and pairwise divergence between all individual Bov-B LINE copies suggest invasion times ranging from 79.19 to 98.8 million years ago in snakes. Accumulation of elements in a lineage-specific fashion ranged from 9 × 10⁻⁶% to 5.63 × 10⁻²% per genome. The genomic proportion of Bov-B LINEs varied among snake species but was not directly associated with genome size or invasion time. No differentiation in Bov-B LINE copy number between males and females was observed in any of the snake species examined. Incongruence in tree topology between Bov-B LINEs and other snake phylogenies may reflect past HT events. Sequence divergence of Bov-B LINEs between copies suggests that recent multiple HTs occurred within the same evolutionary timeframe in the snake lineage. The proportion of Bov-B LINEs varies among species, reflecting species specificity in TE invasion. The rapid speciation of snakes, coinciding with Bov-B LINE invasion in snake genomes, leads us to better understand the effect of Bov-B LINEs on snake genome evolution.

DNA barcoding reveals distinct population of Dopasia gracilis (Squamata: Anguidae) in Mizoram, Northeast India

The DNA barcode data of Asian Glass Lizard, Dopasia gracilis, is limited in the global database, especially from India. The present study aimed to generate a barcode sequence of morphologically identified D. gracilis from the Mizoram state in northeast India and compared with other Anguidae species. The studied species showed monophyletic clustering in the Bayesian analysis (BA) phylogeny with strong posterior probability support and also discriminated sufficient Kimura 2 parameter genetic distances. The barcode data of D. gracilis revealed high intra-species genetic variability and formed two clusters in BA phylogeny. The Templeton, Crandall, and Sing network also depicted four different haplotypes within the barcode sequences of D. gracilis. The DNA sequences generated from northeast India showed 6.5-6.6% and 7.3% genetic distances with the sequences generated from Yunnan Province and Tibetan Plateau, respectively. Considering the high genetic distances, multiple clustering, and distinct haplotypes, the present study assumed the presence of possible cryptic diversity of D. gracilis in the Indochina sub-region and a distinct population in northeast India. We recommended the generation of more DNA information from different localities to elucidate the actual diversity of D. gracilis within the known range distribution.

A new species of the genus Xenophrys Anura Megophryidae from northern Thailand

Species of Xenophrys are conserved morphologically and live primarily in forests. In Thailand, the genus harbors many cryptic species. Herein we report the collection of specimens from Doi Inthanon, Chiang Mai Province, northern Thailand, which were identified previously as X. minor. Molecular and morphological analyses find that these specimens differ significantly from other known congeners, and therefore we describe a new species. Further, our phylogenetic analyses indicate that X. latidactyla is a junior synonym of X. palpebralespinosa.

Diversity of PBI-DdeI satellite DNA in snakes correlates with rapid independent evolution and different functional roles

To better understand PBI-DdeI satellite DNA located in the centromeric region of python, molecular evolution analysis was conducted on 40 snake species. A ladder-like pattern of DNA bands with repetition of the 194–210 bp monomer was observed in 15 species using PCR. Molecular cloning was performed to obtain 97 AT-rich monomer sequences. Phylogenetic and network analyses showed three PBI-DdeI subfamilies with sequences grouped in species-specific clusters, suggesting rapid evolution. Slow evolution was found in eight species with shared PBI-DdeI sequences, suggesting recent species diversification, allowing PBI-DdeI no time to diverge, with limited homogenization and fixation processes. Quantitative real-time PCR showed large differences in copy number between Python bivittatus and other snakes, consistent with repeat scanning of whole genome sequences. Copy numbers were significantly higher in female Naja kaouthia than in males, concurring with chromosomal distribution of PBI-DdeI specifically localized to female W chromosomes. PBI-DdeI might act as an evolutionary driver with several repeats to promote W chromosome differentiation and heterochromatinization in N. kaouthia. Analysis revealed PBI-DdeI with a reduced copy number, compared to P. bivittatus, in most snakes studied, and it is possible that it subsequently dispersed and amplified on W chromosomes with different functional roles in N. kaouthia.

Genetic diversity analysis of Peking gecko (Gekko swinhonis) in mid-Eastern China based on mitochondrial COI and Cyt b gene sequences

To understand the genetic diversity of Peking gecko (Gekko swinhonis) populations in its endemic region, 60 individuals were sampled from Lushan, Qi, and Linying counties in Henan Province, China. Through PCR amplification and Sanger sequencing, 120 sequences with lengths of 652 bp (COI) and 739 bp (Cyt b) were obtained, and nine haplotypes were detected for each gene. Overall, results indicated that Peking gecko populations in China have high genetic diversity and significant genetic differentiation. This study provides necessary scientific basis for the protection of Peking gecko germplasm resources.

Influence of pairwise genetic distance computation and reference sample size on the reliability of species identification using Cyt b and COI gene fragments in a group of native passerines

Species identification is fundamental to wildlife forensic practice. The desirability of molecular genetic methods is increasing rapidly. The sequence of a marker, rather than its particular diagnostic nucleotides, provides greater safety through comparisons between intra- and inter-specific pairwise genetic distances. However, it has not been well described how reliability of species assignment is influenced by distance computing methods and reference sample sizes. In this study, the influences were tested using 12 species from 4 genera of passerine birds and the sequences of partial Cytochrome b (Cyt b) and Cytochrome Oxidase subunit I (COI) genes. Results showed that different substitution types have different outcomes of pairwise genetic distance estimation and this influences the risk of false inclusion and exclusion. Transition (Ts) is the most effective substitution type to reveal optimal species resolution for both Cyt b and COI gene fragments no matter whether K2P and p-distance are used. Sample size required to accurately estimate pairwise distance is essentially determined by the genetic diversity of a species in reference to a given strictness of predefined acceptable accuracy. These findings suggest that for future forensic work on birds by use of Cyt b and COI gene fragments, transition should be used exclusively for marker validation and identification practice when targeting closely related species. Meanwhile, the reference database should sufficiently represent overall genetic diversity of the species. The minimum sample size should be estimated based on existing knowledge of genetic diversity. Special caution should be used for species assignment when only several reference data are available for animals that are considered likely to have high genetic diversity.

Characterization of five complete Cyrtodactylus mitogenome structures reveals low structural diversity and conservation of repeated sequences in the lineage

Mitochondrial genomes (mitogenomes) of five Cyrtodactylus were determined. Their compositions and structures were similar to most of the available gecko lizard mitogenomes as 13 protein-coding, two rRNA and 22 tRNA genes. The non-coding control region (CR) of almost all Cyrtodactylus mitogenome structures contained a repeated sequence named the 75-bp box family, except for C. auribalteatus which contained the 225-bp box. Sequence similarities indicated that the 225-bp box resulted from the duplication event of 75-bp boxes, followed by homogenization and fixation in C. auribalteatus. The 75-bp box family was found in most gecko lizards with high conservation (55-75% similarities) and could form secondary structures, suggesting that this repeated sequence family played an important role under selective pressure and might involve mitogenome replication and the likelihood of rearrangements in CR. The 75-bp box family was acquired in the common ancestral genome of the gecko lizard, evolving gradually through each lineage by independent nucleotide mutation. Comparison of gecko lizard mitogenomes revealed low structural diversity with at least six types of mitochondrial gene rearrangements. Cyrtodactylus mitogenome structure showed the same gene rearrangement as found in most gecko lizards. Advanced mitogenome information will enable a better understanding of structure evolution mechanisms.

A novel method of caenophidian snake sex identification using molecular markers based on two gametologous genes

Sex identification provides important information for ecological and evolutionary studies, as well as benefiting snake conservation management. Traditional methods such as cloacal probing or cloacal popping are counterproductive for sex identification concerning very small species, resulting in difficulties in the management of their breeding programs. In this study, the nucleotide sequences of gametologous genes (CTNNB1 and WAC genes) were used for the development of molecular sexing markers in caenophidian snakes. Two candidate markers were developed with the two primer sets, and successfully amplified by a single band on the agarose gel in male (ZZ) and two bands, differing in fragment sizes, in female (ZW) of 16 caenophidian snakes for CTNNB1 and 12 caenophidian snakes for WAC. Another candidate marker was developed with the primer set to amplify the specific sequence for CTNNB1W homolog, and the PCR products were successfully obtained in a female‐specific 250‐bp DNA bands. The three candidate PCR sexing markers provide a simple sex identification method based on the amplification of gametologous genes, and they can be used to facilitate effective caenophidian snake conservation and management programs.