Detection Of Cryptic Species Research Articles

Cryptic Taxa Revealed through Combined Analysis of Chromosomes and DNA Barcodes: The Polyommatus ripartii Species Complex in Armenia and NW Iran.

The detection of cryptic species in complexes that have undergone recent speciation is often difficult, since many standard nuclear markers have not yet accumulated differences between closely related taxa, and differences in mitochondrial markers can be leveled out due to mitochondrial introgressions. In these cases, the use of derived chromosomal characters such as non-ancestral chromosomal numbers and/or unusual karyotype features may be a solution to the species delimitation problem. However, non-ancestral but similar karyotypes may arise secondarily as a result of homoplastic evolution, and their interpretation as homologies may lead to incorrect taxonomic conclusions. In our study, we show that the combined use of mitochondrial DNA barcodes and karyotypes helps to solve this problem and identifies cryptic species in situations where each of these markers does not work individually. Using this approach, we show that the fauna of Armenia and adjacent Iran includes the following cryptic taxa of the Polyommatus ripartii species complex (haploid chromosome number, n in parentheses): P. ripartii paralcestis (n = 90), P. ripartii kalashiani, subsp. nov (n close to 90), P. emmeli, sp. nov. (n = 77-79), P. keleybaricus, sp. nov. (n = 86), P. demavendi belovi (n = 73-75), P. demavendi antonius, subsp. nov. (n = 71-73), P. admetus anatoliensis (n = 79) and P. eriwanensis (n = 29-34). Polyommatus admetus yeranyani is synonymized with P. admetus anatoliensis.

Curating BOLD records via Bayesian phylogenetic assignments enables harmonization of regional subgeneric classifications and cryptic species detection within the genus Tachina (Diptera: Tachinidae)

Abstract DNA barcoding is a popular tool for species identification of insect samples, with important applications for plant protection. However, Barcode of Life Database queries related to tachinid samples can produce ambiguous results due to contradictory species assignments. Therefore, we applied Bayesian phylogenetic inference to 811 Tachina Meigen, 1803 COI-5P sequences containing all contradictory species assignments of Tachina Barcode Index Numbers. Based on phylogenetic assignment, the assemble species by automatic partitioning (ASAP) analysis, the MonoPhy test and analyses of genetic divergence, we identified 805 sequences representing species of the Tachina genus, whereas six sequences were incorrectly assigned to Tachina. The dataset contained 21 described species and at least seven unidentified species. Additionally, we found that the described species Tachina marklini Zetterstedt, 1838, includes two cryptic species based on ASAP partitioning of sequences, phylogenetic inference and geographical metadata. Furthermore, we harmonized conflicting subgeneric classifications of the Palearctic and Nearctic by employing different subgenera assignments from both partitions. We aimed at monophyletic subgenera partitions. We largely confirmed the validity of the Palearctic Tachina subgenera and Nowickia as a subgenus of Tachina. However, Palearctic Nowickia species formerly allocated to the outdated genus Fabriciella appeared to constitute one monophyletic group with the subgenus Rhachogaster. We conclude that this set of bioinformatics tools is suitable for curating COI-5P-based DNA barcode libraries. Although, curation is limited due to possible species introgression, horizontal gene transfer, incomplete lineage sorting and human errors the resulting dataset enabled the revision of subgenera concepts and the unambiguous cryptic species detection.

A DNA barcode reference library of Croatian mosquitoes (Diptera: Culicidae): implications for identification and delimitation of species, with notes on the distribution of potential vector species

BackgroundMosquitoes pose a risk to human health worldwide, and correct species identification and detection of cryptic species are the most important keys for surveillance and control of mosquito vectors. In addition to traditional identification based on morphology, DNA barcoding has recently been widely used as a complementary tool for reliable identification of mosquito species. The main objective of this study was to create a reference DNA barcode library for the Croatian mosquito fauna, which should contribute to more accurate and faster identification of species, including cryptic species, and recognition of relevant vector species.MethodsSampling was carried out in three biogeographical regions of Croatia over six years (2017–2022). The mosquitoes were morphologically identified; molecular identification was based on the standard barcoding region of the mitochondrial COI gene and the nuclear ITS2 region, the latter to identify species within the Anopheles maculipennis complex. The BIN-RESL algorithm assigned the COI sequences to the corresponding BINs (Barcode Index Number clusters) in BOLD, i.e. to putative MOTUs (Molecular Operational Taxonomic Units). The bPTP and ASAP species delimitation methods were applied to the genus datasets in order to verify/confirm the assignment of specimens to specific MOTUs.ResultsA total of 405 mosquito specimens belonging to six genera and 30 morphospecies were collected and processed. Species delimitation methods assigned the samples to 31 (BIN-RESL), 30 (bPTP) and 28 (ASAP) MOTUs, with most delimited MOTUs matching the morphological identification. Some species of the genera Culex, Aedes and Anopheles were assigned to the same MOTUs, especially species that are difficult to distinguish morphologically and/or represent species complexes. In total, COI barcode sequences for 34 mosquito species and ITS2 sequences for three species of the genus Anopheles were added to the mosquito sequence database for Croatia, including one individual from the Intrudens Group, which represents a new record for the Croatian mosquito fauna.ConclusionWe present the results of the first comprehensive study combining morphological and molecular identification of most mosquito species present in Croatia, including several invasive and vector species. With the exception of some closely related species, this study confirmed that DNA barcoding based on COI provides a reliable basis for the identification of mosquito species in Croatia.Graphical

DNA barcoding aids in generating a preliminary checklist of the lichens and allied fungi of Calvert Island, British Columbia: Results from the 2018 Hakai Terrestrial BioBlitz.

Bioblitzes are a tool for the rapid appraisal of biodiversity and are particularly useful in remote and understudied regions and for understudied taxa. Lichens are an example of an often overlooked group, despite being widespread in virtually all terrestrial ecosystems and having many important ecological functions. We report the lichens and allied fungi collected during the 2018 terrestrial bioblitz conducted on Calvert Island on the Central Coast of British Columbia, Canada. We identified 449 specimens belonging to 189 species in 85 genera, increasing the total number of species known from Calvert Island to 194, and generated Internal Transcribed Spacer (ITS) sequences for 215 specimens from 121 species. Bryoriafurcellata, Chaenothecopsislecanactidis and C.nigripunctata were collected for the first time in British Columbia. We also found Pseudocyphellariarainierensis, which is listed as Special Concern on the federal Species at Risk Act, and other rarely reported species in British Columbia including Opegraphasphaerophoricola, Protomicarealimosa, Raesaeneniahuuskonenii and Sareadifformis. We demonstrate that DNA barcoding improves the scope and accuracy of expert-led bioblitzes by facilitating the detection of cryptic species and allowing for consistent identification of chemically and morphologically overlapping taxa. Despite the spatial and temporal limitations of our study, the results highlight the value of intact forest ecosystems on the Central Coast of British Columbia for lichen biodiversity, education and conservation.

Faster and Better: Comparison between Traditional and Drone Monitoring in a Cryptic Species, the Purple Heron Ardea purpurea

Monitoring waterbirds is fundamental to understand the health status of wetland habitats. However, this monitoring has to be conducted by means of reliable data collection that can provide accurate information on population trends. Usually, waterbird monitoring is difficult, as nesting grounds are usually located in inaccessible reedbed, and by eye detection of cryptic species is hard. Drones have the capacity to overcome most of these problems, as they can provide with an aerial view of places otherwise unreachable, while reducing the disturbance and time spent in the field. The present study aims to compare the accuracy, disturbance levels, and managerial efficiency between ground (traditional) and drone counts of a cryptic species, the Purple Heron Ardea purpurea. Traditional monitoring methods were only capable of detecting 35% of the nesting pairs detected by the drone surveys (8.0 ± 11.8 versus 22.9 ± 38.2 nesting pairs in ground and drone surveys, respectively). Consequently, colony size estimates between methods showed poor agreement, to the point that traditional methods missed colonies otherwise detected by the drone. No apparent negative effects on nesting pairs where found when flying the drone. In addition, mean time spent to survey breeding sites with a drone was far less than with the traditional approach, down to a six-fold time reduction. This reduction, together with a lack of disturbance observed when conducting the drone monitoring, and an increasing monitoring precision and accuracy, supports the use of drones as the least invasive option for studies on population monitoring on hardly accessible sites.

DNA-barcoding reveals cryptic diversity and re-evaluation of Ocypode (family: Ocypodidae) from the Sundarbans - UNESCO World Heritage Centre

Crabs are one of the most diversified crustaceans among metazoans, from both morphological and ecological point of view. Among them, ghost crabs (Genus Ocypode; Family Ocypodidae) play an important role in the tropical and sub-tropical intertidal ecosystems. Due to a lack of comprehensive data, their cryptic behaviour, mimicry or camouflage, and a lack of formal taxonomic documentation, identification of this group is often difficult. Molecular taxonomy can help to overcome these barriers by assisting in species identification. The present study is the first large scale attempt to identify ghost crabs using DNA barcodes, which are now available globally, for 16 morphospecies in the genus Ocypode. A total of 164 barcodes were analysed for species delimitation that are available globally including specimens collected from the Indian Sundarbans. Various species delimitation methods (K2P, NJ, Bayesian supported PTP and Bayesian tree) revealed a total of 19 MOTUs for 16 distinct species where multiple MOTUs were observed in 3 species with inconsistencies in genetic distances and tree topologies. We recognised cryptic diversity in Ocypode macrocera, O. platytarsis and O. quadrata with intraspecies distances greater than the species delimitation threshold of 0.053 ± 0.01. The current study also concluded that O. platytarsis and O. brevicornis are two distinct species, putting an end to the debate over their species synonymy. Furthermore, our Bayesian analysis confirmed the retraction of the genus Hoplocypode specified only for O. occidentalis. As a result, the current research added a new dimension to ghost crab taxonomy by contributing to the detection of cryptic species, thus speculating the possibility of new species and reaffirming the effectiveness of the DNA barcoding while demanding enrichment of the global database for comprehensive species identification and extensive approach of molecular taxonomy as well as morphological interventions in solving taxonomic puzzles.

A prospective and iterative approach to finding safe weed biological control agents – testing ecological and evolutionary hypotheses with molecular evidence

Biological control is often the most cost effective and environmentally sound method of managing widespread environmental weeds. Earlier detection of cryptic species and improved understanding of host-herbivore associations during the initial screening for effective natural enemies should further boost success rates. We formalise a framework for improved prioritisation of biological control agents through the successive feedback between ecological surveys and molecular screening. Incorporating enhanced molecular methods to strengthen hypothesis testing in the initial phases of exploratory research will help prioritise herbivores and regions for subsequent native range surveys, and should more readily uncover unrecognised cryptic species that may otherwise remain hidden. We postulate that this iterative methodology should enhance the environmental safety and cost-benefit ratios of future biological control programs, and this approach should help to elucidate problematic aspects of existing programs.

A new country record of Raorchestes cangyuanensis Wu, Suwannapoom, Xu, Murphy amp; Che 2019 and additional record of Kurixalus yangi Yu, Hui, Rao amp; Yang 2018 (Anura: Rhacophoridae: Rhacophorinae) from India.

Most studies on the diversity of amphibians in northeast India were based on classical morpho-taxonomy, which have a high probability of errors in species identification. DNA barcoding of amphibians using the mitochondrial 16S rRNA gene has been used successfully for the identification of species and detection of cryptic species. In the present study, we carry out DNA barcoding of two rhacophorid species of the genus Raorchestes and Kurixalus that are not readily identifiable to the species level based on their morphology. Our analysis on the 16S rRNA gene revealed that these species were Raorchestes cangyuanensis and Kurixalus yangi, species which were recorded for the first time and second time from India respectively. We discuss on the records of R. longchuanensis from Bangladesh and India, which were based on the misidentification of R. cangyuanensis. We therefore propose to delist this species from the faunal list of Bangladesh and India. We further raise a question as to why the population of Kurixalus from Motuo, Xizang province of China was assigned as K. naso and not the population described as K. yangi, which is morphologically similar to K. naso and is also recorded from a locality close to the type locality of K. naso.

Integrative Description of Cryptic Tigriopus Species From Korea Using MALDI-TOF MS and DNA Barcoding

MALDI Time-of-Flight Mass Spectrometry (MALDI-TOF MS) provides a fast and reliable alternative method for species-level identification of pathogens and various metazoans. Compared to the commonly used mitochondrial cytochrome c oxidase subunit I (mtCOI) barcoding, advantages of MALDI-TOF MS are rapid species identifications and low costs. In this study, we used MALDI-TOF MS to determine whether spectra patterns of different species can be used for species identification. We obtained a total of 138 spectra from individual specimens of Tigriopus, which were subsequently used for various cluster analyses. Our findings revealed these spectra form three clear clusters with high AU value support. This study validates the viability of MALDI-TOF MS as a methodology for higher-resolution species identification, allowing detection of cryptic species of harpacticoida. In addition, we propose a new species, Tigriopus koreanus sp. nov. by utilizing integrative methods such as morphological comparison, mtCOI barcoding, and MALDI-TOF MS.

Resolving cryptic species complexes in marine protists: phylogenetic haplotype networks meet global DNA metabarcoding datasets

Marine protists have traditionally been assumed to be lowly diverse and cosmopolitan. Yet, several recent studies have shown that many protist species actually consist of cryptic complexes of species whose members are often restricted to particular biogeographic regions. Nonetheless, detection of cryptic species is usually hampered by sampling coverage and application of methods (e.g. phylogenetic trees) that are not well suited to identify relatively recent divergence and ongoing gene flow. In this paper, we show how these issues can be overcome by inferring phylogenetic haplotype networks from global metabarcoding datasets. We use the Chaetoceros curvisetus (Bacillariophyta) species complex as study case. Using two complementary metabarcoding datasets (Ocean Sampling Day and Tara Oceans), we equally resolve the cryptic complex in terms of number of inferred species. We detect new hypothetical species in both datasets. Gene flow between most of species is absent, but no barcoding gap exists. Some species have restricted distribution patterns whereas others are widely distributed. Closely related taxa occupy contrasting biogeographic regions, suggesting that geographic and ecological differentiation drive speciation. In conclusion, we show the potential of the analysis of metabarcoding data with evolutionary approaches for systematic and phylogeographic studies of marine protists.

Phylogeny, taxonomic reassessment and ‘ecomorph’ relationship of theOrientallactaga sibiricacomplex (Rodentia: Dipodidae: Allactaginae)

AbstractThe ecological gradient–morphological variation (‘ecomorph’) relationship has long interested ecologists and evolutionary biologists, but it is applied far less frequently than genetic differentiation in cryptic species detection and species identification. With integrative methods, we revise taxonomic uncertainties in the Orientallactaga sibirica complex (OSC), with 298 sequence specimens and 469 voucher specimens from 138 localities covering nearly the entire distribution of the OSC. Phylogenetic relationships are assessed by Bayesian inference and maximum likelihood using two mitochondrial and nine nuclear genes. We use species-delimitation approaches to divide and validate the ‘candidate species’. We evaluate correlations between ecological divergence and phylogenetic splits, and visualize geographical patterns of morphological variation. The OSC is divided into four phylogenetic groups, the Ognevi, Altay, Bogda and Sibirica groups, and the OSC exhibits a significant ecomorph relationship and ecological divergence pattern. Morphological variations not only follow the general regularity under a large gradient of ecological factors, but are also closely related to the local environment/habitat. We suggest considering the comprehensive ecomorph relationship to identify species. Molecular analyses reveal that the OSC more easily forms deeply divergent lineages in the foothills and this differentiation depth may be related to mountain system size.

An annotated checklist and integrative biodiversity discovery of barnacles (Crustacea, Cirripedia) from the Moluccas, East Indonesia.

To contribute to the taxonomic knowledge of barnacles in this understudied area, the first checklist of barnacles from the Moluccas is presented, including additional information on morphology, distribution, and substrate as well as molecular data. The species of barnacles from the Moluccas have been determined using morphological analysis and DNA sequences. During 19 field trips conducted between January 2016 and September 2017, 1,513 specimens of 24 species of intertidal and one species of deep-sea barnacles were collected from 51 localities from the islands. Morphological and molecular analysis of the collected material detected members of three families of stalked barnacles and four families of acorn barnacles. In addition to sampling in the field, we also surveyed the literature on barnacles from the Moluccas. In total, our checklist comprises 97 species from the Moluccas including 23 new records, two of them yet to be described species. Results suggest that the Moluccas have a much higher diversity of barnacles than previously known, for example, from the reports of Challenger and Siboga expeditions. For further work, routine application of molecular systematics could aid the detection of cryptic species, while increased sampling of more islands and a taxonomic revision of several groups would likely lead to an even higher number of species than currently known.

Capture of Environmental DNA (eDNA) from Water Samples by Flocculation.

The analysis of environmental DNA (eDNA) has become a widely used approach to problem solving in species management. The detection of cryptic species including invasive and (or) species at risk is the goal, typically accomplished by testing water and sediment for the presence of characteristic DNA signatures. Reliable and efficient procedures for the capture of eDNA are required, especially those that can be performed easily in the field by personnel with limited training and citizen scientists. The capture of eDNA using membrane filtration is widely used currently. This approach has inherent issues that include the choice of filter material and porosity, filter fouling, and time required on site for the process to be performed. Flocculation offers an alternative that can be easily implemented and applied to sampling regimes that strive to cover broad territories in limited time.

Comparison of fish detections, community diversity, and relative abundance using environmental DNA metabarcoding and traditional gears

AbstractBackgroundDetecting species at low abundance, including aquatic invasive species (AIS), is critical for making informed management decisions. Environmental DNA (eDNA) methods have become a powerful tool for rare or cryptic species detection; however, many eDNA assays offer limited utility for community‐level analyses due to their use of species‐specific (presence/absence) ‘barcodes’. Metabarcoding methods provide information on entire communities based on sequencing of all taxon‐specific barcodes within an eDNA sample.AimsEvaluate measures of fish species detections, community diversity, and estimates of relative abundance based on eDNA metabarcoding and traditional fisheries sampling approaches in the context of fish community characterization and AIS survellience.Materials and MethodsIn 2016, eight limnologically diverse lakes (surface area range: 13 – 1,728 ha) in Michigan, USA were sampled using a variety of traditional fisheries gears to characterize fish community composition. Environmental DNAs from surface (33 ± 6, mean ± 1 SD) and benthic (14 ± 2) water samples from each lake were isolated and amplified for two metabarcoding markers (mitochondrial 12S and 16S rDNA loci) using fish‐specific primers. Fish species detected within each lake were determined by comparing the sequencing data to a database of sequences from native Michigan fish species and 19 AIS on the Michigan's Watch List.ResultsAnalysis of species accumulation curves indicated multi‐locus eDNA metabarcoding assays can enhance species detection capacities and characterize 95% of a fish community in fewer sampling efforts than traditional gear (range: 2 – 62, median: 14). In addition, all AIS detected in traditional gear samples were also detected by eDNA, while some AIS detected by eDNA assays were absent from traditional gear samples.DiscussionResults reported here are, in part, driven by the lack of species‐selectivity during eDNA sampling events. Given the efficacy of eDNA assays, we suggest multi‐locus eDNA metabarcoding assays be implemented in early detection efforts.

Global distribution and diversity of Chaetoceros (Bacillariophyta, Mediophyceae): integration of classical and novel strategies.

Information on taxa distribution is a prerequisite for many research fields, and biological records are a major source of data contributing to biogeographic studies. The Global Biodiversity Information Facility (GBIF) and the Ocean Biogeographic Information System (OBIS) are important infrastructures facilitating free and open access to classical biological data from several sources in both temporal and spatial scales. Over the last ten years, high throughput sequencing (HTS) metabarcoding data have become available, which constitute a great source of detailed occurrence data. Among the global sampling projects that have contributed to such data are Tara Oceans and the Ocean Sampling Day (OSD). Integration of classical and metabarcoding data may aid a more comprehensive assessment of the geographic range of species, especially of microscopic ones such as protists. Rare, small and cryptic species are often ignored in surveys or mis-assigned with the classical approaches. Here we show how integration of data from various sources can contribute to insight in the biogeography and diversity at the genus- and species-level using Chaetoceros as study system, one of the most diverse and abundant genera among marine planktonic diatoms. Chaetoceros records were extracted from GBIF and OBIS and literature data were collected by means of a Google Scholar search. Chaetoceros references barcodes where mapped against the metabarcode datasets of Tara Oceans (210 sites) and OSD (144 sites). We compared the resolution of different data sources in determining the global distribution of the genus and provided examples, at the species level, of detection of cryptic species, endemism and cosmopolitan or restricted distributions. Our results highlighted at genus level a comparable picture from the different sources but a more complete assessment when data were integrated. Both the importance of the integration but also the challenges related to it were illustrated. Chaetoceros data collected in this study are organised and available in the form of tables and maps, providing a powerful tool and a baseline for further research in e.g., ecology, conservation and evolutionary biology.

Cryptic biodiversity in the freshwater fishes of the Kimberley endemism hotspot, northwestern Australia

The prevalence of unrecognised cryptic species impairs biodiversity estimates, clouds biological research and hinders conservation planning. As the rate of cryptic species detection increases globally, research is needed to determine how frequent cryptic species are, whether they are more common in given management regions, and whether these patterns are consistent across taxonomic groups. The Kimberley region in remote northwestern Australia harbours some of the most speciose, and morphologically and functionally diverse, endemic animal and plant communities on the continent. The rugged and changeable landscape also appears to contain a large proportion of cryptic terrestrial species, raising the question of whether similar patterns are also found among aquatic taxa, which have yet to be studied using integrative systematic approaches. If true, then the actual levels of aquatic biodiversity are yet to be fully realised. Here we conducted a molecular assessment of where species boundaries may exist in the Kimberley regions’ most speciose freshwater fish family, the Terapontidae (grunters), with a combined morphological assessment of the regions’ most speciose terapontid genus, Syncomistes. Assessment of nuclear markers (54 allozyme loci), sequence data (mitochondrial cytochrome b (cytb); nuclear recombination activation gene one (RAG1)) and 31 meristic and 36 morphometric characters provides evidence for 13 new candidate species across three different genera. Many of these candidate species are narrow range endemics. Our findings raise several questions about the evolutionary origin of the Kimberley’s endemic fish fauna and highlight the likelihood that freshwater fish species diversity in the Kimberley is severely under-represented by current systematic frameworks, with significant implications for ecological research, conservation and management.

Investigating detection success: lessons from trials using decoy rare plants

Imperfect detection leads to underestimates of species presence and decreases the reliability of survey data. Imperfect detection has not been examined in detail for boreal forest understory plants, despite widespread use of surveys for rare plants prior to development. We addressed this issue using detectability trials conducted in Alberta, Canada with decoy vascular plants. Volunteer observers searched in survey plots for species while unaware of their true presence or abundance. Our findings indicate that the detection of cryptic species is very low when abundance is low (0–35%) and plot size is large (< 50% in ≥ 100 m2). Plant density (individuals per unit area) was the most important determinant of detection probability, where more abundant species were detected more often and with less survey effort. When abundance was held constant, diffusely arranged species were twice as likely to be detected compared to those in clumps. Detection of cryptic species can be low even when individuals are flowering, and even morphologically distinct species can go unnoticed in small plots. We suggest that future decoy trials investigate search strategies that could improve detection and that field surveys for vascular plants address imperfect detection through careful consideration of plot size, characteristics of the target species, and survey effort, both in terms of time expenditure within an area and the number of observers employed.

Cryptic diversity of the subfamily Calaphidinae (Hemiptera: Aphididae) revealed by comprehensive DNA barcoding.

Aphids are a species rich group comprising many important pests. However, species identification can be very difficult for aphids due to their morphological ambiguity. DNA barcoding has been widely adopted for rapid and reliable species identification as well as cryptic species detection. In this study, we investigated cryptic diversity in the subfamily Calaphidinae (Hemiptera: Aphididae) based on 899 sequences of cytochrome c oxidase I (COI) for 115 morphospecies (78 species collected in this study and sequences of 73 species downloaded from Genbank). Among these 115 morphospecies, DNA barcoding results of 90 (78.3%) species were identical to results of morphological identification. However, 25 (21.7%) morphospecies showed discrepancies between DNA barcoding and traditional taxonomy. Among these 25 discordances, a total of 15 cryptic species were identified from 12 morphospecies. We also found three morphologically distinct species pairs that sharing DNA barcoding. Based on molecular operational taxonomic unit (MOTU) estimation, we discussed on species delimitation threshold value for these taxa. Our findings confirm that Calaphidinae has high cryptic diversity even though aphids are relatively well-studied.

New putative cryptic species detection and genetic network analysis of Bemisia tabaci (Hempitera: Aleyrodidae) in China based on mitochondrial COI sequences

The whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex and widely distributed throughout tropical and subtropical regions. To understand the B. tabaci cryptic species diversity in China more comprehensively, in the year 2014 and 2016, a large-scale sampling was conducted from the famous biodiversity hotspot of China, Yunnan province. Mitochondrial cytochrome oxidase I gene sequences were used to identify new putative cryptic species. Phylogenetic analyses were performed using Bayesian methods to evaluate the position of new cryptic species in the context of the B. tabaci diversity in Asia. Two new cryptic species, China 5 and Asia V were identified. In total, 19 B. tabaci cryptic species are present in China, two invasive (MED and MEAM1) and 17 indigenous. A new sibling species of B. tabaci was first defined and reported. Based on the mtCOI sequences and haplotype network analyses, the genetic diversity of MED was far higher than MEAM1. We confirmed the exotic MED was originated from the western Mediterranean regions and first invaded into Yunnan, China. The genetic structures of other four indigenous species (Asia I, Asia II 1, Asia II 6, and China 1) with relatively wide distribution ranges in China were also discussed.

DNA barcoding uncovers cryptic diversity in 50% of deep-sea Antarctic polychaetes.

The Antarctic marine environment is a diverse ecosystem currently experiencing some of the fastest rates of climatic change. The documentation and management of these changes requires accurate estimates of species diversity. Recently, there has been an increased recognition of the abundance and importance of cryptic species, i.e. those that are morphologically identical but genetically distinct. This article presents the largest genetic investigation into the prevalence of cryptic polychaete species within the deep Antarctic benthos to date. We uncover cryptic diversity in 50% of the 15 morphospecies targeted through the comparison of mitochondrial DNA sequences, as well as 10 previously overlooked morphospecies, increasing the total species richness in the sample by 233%. Our ability to describe universal rules for the detection of cryptic species within polychaetes, or normalization to expected number of species based on genetic data is prevented by taxon-specific differences in phylogenetic outputs and genetic variation between and within potential cryptic species. These data provide the foundation for biogeographic and functional analysis that will provide insight into the drivers of species diversity and its role in ecosystem function.