COI Sequence Divergence Research Articles

A new jewel-like species of the pill-millipede genus Sphaerobelum Verhoeff, 1924 (Diplopoda, Sphaerotheriida, Zephroniidae) from Thailand.

A new species of the giant pill millipede genus Sphaerobelum is described: Sphaerobelumturcosasp. nov. from the northeastern part of Thailand. Species delimitation is based on morphological characters and COI sequence data. The new species can be clearly discriminated from congeners by its greenish-blue body color, the face mask-like appearance of the thoracic and anal shields jointly when rolled up, and the combination of the following four characters: (1) the coxa of the second leg laterally with a sharp and long process, (2) the tarsi of legs 4-21 with 6-7 ventral spines, (3) the anterior telopods consisting of four conspicuous telopoditomeres, and (4) the immovable, slender (not strongly humped) and distally curved finger of the posterior telopods without a membranous spot. The interspecific COI sequence divergence between the new species and other Sphaerobelum species ranges from 17% to 23% (mean 20%). The intergeneric COI sequence divergence between the new species and Zephronia species ranges from 18% to 21% (mean 20%). The relationships among Sphaerobelum and Zephronia species based on the COI sequence data were not resolved in this study. Sphaerobelumturcosasp. nov. is restricted to limestone habitat in Loei province and is probably endemic for the Thai fauna.

A new genus of Pseudospirobolellidae (Diplopoda, Spirobolida) from limestone karst areas in Thailand, with descriptions of three new species

A new genus of the millipede family Pseudospirobolellidae, Siliquobolellusgen. nov., is described from limestone mountains in Thailand, based on three new species, viz. Siliquobolellus amicusdraconisgen. et sp. nov. from Uthaithani Province, Siliquobolellus constrictusgen. et sp. nov. from Prachuap Khiri Khan Province and Siliquobolellus prasankokaegen. et sp. nov. (type species) from Lampang Province. The descriptions are based on gonopod morphology and mitochondrial DNA data (COI barcodes). The COI barcodes grouped the three new species in a well-supported Siliquobolellusgen. nov. clade. The mean interspecific COI sequence divergence among the three new species was 12% (range: 8–15%). The mean intergeneric COI sequence divergence between Siliquobolellusgen. nov., Coxobolellus Pimvichai, Enghoff, Panha & Backeljau, 2020, and Pseudospirobolellus Carl, 1912 was 19% (range: 14–23%). Three conspicuous gonopodal synapomorphies differentiate Siliquobolellusgen. nov. from other pseudospirobollellid genera: (1) the telopodital part of the posterior gonopod forms a deep concavity, (2) the telopodite of the anterior gonopod is directed distad and does not reach the tip of the coxal part of the anterior gonopod, and (3) the tip of the anterior gonopod coxa is narrowed, curving mesad. As such, the monophyly of the new genus is well supported by both morphological and mitochondrial DNA data. A distribution map and an identification key to the species are provided.

A closer look reveals hidden diversity in the intertidal Caribbean Fortuyniidae (Acari, Oribatida).

A molecular genetic and morphometric investigation revealed the supposedly widespread Caribbean and Western Atlantic intertidal oribatid mite species Fortuynia atlantica to comprise at least two different species. Although there are no distinct morphological differences separating these taxa, COI and 18S sequence divergence data, as well as different species delimitation analyses, clearly identify the two species. Fortuynia atlantica is distributed in the northern Caribbean and the Western Atlantic and the new Fortuynia antillea sp. nov. is presently endemic to Barbados. Vicariance is supposed to be responsible for their genetic diversification and stabilizing selection caused by the extreme intertidal environment is suggested to be the reason for the found morphological stasis. The genetic structure of Fortuynia atlantica indicates that Bermudian populations are derived from the northern Caribbean and thus support the theory of dispersal by drifting on the Gulf Stream. Haplotype network data suggest that Bermudian and Bahamian populations were largely shaped by colonization, expansion and extinction events caused by dramatic sea level changes during the Pleistocene. A preliminary phylogenetic analysis based on 18S gene sequences indicates that the globally distributed genus Fortuynia may be a monophyletic group, whereas Caribbean and Western Atlantic members are distinctly separated from the Indo-Pacific and Western Pacific species.

Morphological characteristics and mitochondrial COI gene of the green water dragon in Phu Quoc island, Vietnam

The green water dragons of Phu Quoc island, Vietnam have been given a VU rating (vulnerable) by the Vietnam red data book and the International Union for conservation of nature and natural resources. A description of the morphological characteristics and sequenced mitochondrial cytochrome oxidase subunit 1 COI gene was completed following a survey of thirty individuals from September 2018 to May 2019. Their body weights ranged from 115 to 850 g and their snout-vent length ranged from 120 to 280 mm. They were identified to have the highest similarity to the species Physignathus cocincinus by the barcode of life data system. Their COI gene sequence was compared to GenBank (KM272197.1) and the following alternations were found: C5483T, A5486C, C5537A, A5564G, A5591G, T5633C, G5684A, A5771G, A5849C, C5927T, T5942C, C5993T, G6002A, and A6020G. The neighbourjoining tree of their COI sequence divergence indicated a distance (compared to the same published species) from 2.3 to 2.8%. Thus, it might be possible that the green water dragons of Phu Quoc island are evolving into a specific subspecies. However, more green water dragon specimens from Phu Quoc should be sequenced to ensure a conclusion and further research into farming should be initiated to protect this vulnerable species.

Blue mussels of the Mytilus edulis species complex from South America: The application of species delimitation models to DNA sequence variation.

Smooth-shelled blue mussels, Mytilus spp., have a worldwide antitropical distribution and are ecologically and economically important. Mussels of the Mytilus edulis species complex have been the focus of numerous taxonomic and biogeographical studies, in particular in the Northern hemisphere, but the taxonomic classification of mussels from South America remains unclear. The present study analysed 348 mussels from 20 sites in Argentina, Chile, Uruguay and the Falkland Islands on the Atlantic and Pacific coasts of South America. We sequenced two mitochondrial locus, Cytochrome c Oxidase subunit I (625 bp) and 16S rDNA (443 bp), and one nuclear gene, ribosomal 18S rDNA (1770 bp). Mitochondrial and nuclear loci were analysed separately and in combination using maximum likelihood and Bayesian inference methods to identify the combination of the most informative dataset and model. Species delimitation using five different models (GMYC single, bGMYC, PTP, bPTP and BPP) revealed that the Mytilus edulis complex in South America is represented by three species: native M. chilensis, M. edulis, and introduced Northern Hemisphere M. galloprovincialis. However, all models failed to delimit the putative species Mytilus platensis. In contrast, however, broad spatial scale genetic structure in South America using Geneland software to analyse COI sequence variation revealed a group of native mussels (putatively M. platensis) in central Argentina and the Falkland Islands. We discuss the scope of species delimitation methods and the use of nuclear and mitochondrial genetic data to the recognition of species within the Mytilus edulis complex at regional and global scales.

A new hydrobiid species (Caenogastropoda, Truncatelloidea) from insular Greece

Daphniola dionesp. nov., a valvatiform hydrobiid gastropod from Western Greece, is described based on conchological, anatomical and molecular data. D. dione is distinguished from the other species of the Greek endemic genus Daphniola by a unique combination of shell and soft body character states and by a 7–13% COI sequence divergence when compared to congeneric species. The only population of D. dione inhabits a cave spring on Lefkada Island, Ionian Sea.

Integrative taxonomy reveals an even greater diversity within the speciose genus

Phyllodistomum is one of the most species-rich genera of parasitic platyhelminths, with 120 species described worldwide; they infect the urinary bladder of marine and freshwater fishes. As the number of new species within the genus has increased, morphological conservatism, and the lack of reliable diagnostic traits make the separation of species a challenging task. The increase of genetic data for Phyllodistomum species has permitted the use of an integrative taxonomy approach as a framework for species discovery and delimitation. DNA sequences (28S rRNA and COI mtDNA) were obtained from individuals of Phyllodistomum sampled in 29 locations across Middle America, and used in combination with morphology, host association and geographic distribution to uncover five new congeneric species. Morphologically, the new species are relatively similar; there are no unique morphological traits to readily distinguish them. We first investigated species boundaries through phylogenetic analyses of the independent and concatenated datasets; analyses recognised five candidate species showing reciprocal monophyly and strong clade support, particularly for COI data. The interspecific 28S rRNA and COI sequence divergence among the new species from 0.4 to 18.4% and from 5.1 to 27% respectively. These results were further validated by a Bayesian species delimitation approach. The five new species are well supported by molecular data used in combination with other sources of information such as host association and geographical distribution and are described herein as Phyllodistomum romualdae sp. nov., P. virmantasi sp. nov., P. isabelae sp. nov., P. scotti sp. nov., and P. simonae sp. nov.

Redescription of Stenothyra glabra A. Adam, 1861 (Truncatelloidea, Stenothyridae), with the first complete mitochondrial genome in the family Stenothyridae.

In this study, Stenothyra glabra belonging to the truncatelloid family Stenothyridae is redescribed using morphological characters from the shell, operculum, and radula. The species is distinguished from other species in the group by its shell without spotted spiral lines and by its dome-shaped, mostly smooth, protoconch with some pits. Together with the morphological description, the complete mitogenome for the species is provided, which fill a knowledge gap in Stenothyridae. The mitogenome of S. glabra is 15,830 bp in length and has a circular structure. It contains 37 genes: 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and 13 protein-encoding genes (PCGs). The overall A+T content of the mitogenome is 68.9%. Molecular phylogenetic analysis and COI sequence divergence separate S. glabra from its congeners and show that S. glabra and S. cf. divalis form a sister clade.

Three new species of Synergini wasps from same galls on Lithocarpus glaber (Thunb.) in Hunan, China (Hymenoptera, Cynipidae)

Three new species of the tribe Synergini (Hymenoptera, Cynipidae), i.e., Lithosaphonecrus arcoverticus Liu, Zhu et Pang, sp. n. Lithosaphonecrus decarinatus Liu, Zhu et Pang, sp. n. and Saphonecrus emarginatus Liu, Zhu et Pang, sp. n. are described from Hunan, China. The three species have emerged from the same galls collected on Lithocarpus glaber (Thunb.) in December, June, and April, respectively. Phylogenetic reconstruction of Synergini based on mtDNA COI and rRNA 28S D2 genes resolved two independent monophyletic clades exclusively associated with Lithocarpus plant hosts, i.e., the genus Lithosaphonecus and the lithocarpii species complex of Saphonecrus. The three species each have a sister relationship with a congener in Taiwan, an island off the southeastern coast of continental China. This recurrent disjunct distribution and relatively low COI sequence variation between the sister species in each species pair are considered attributable to the formation of the Taiwan Strait in Holocene ca 10,000 years ago. We also discussed the possible speciation mechanism for Lithosaphonecrus due to seasonality and topography in subtropical China. Finally, we addressed the need for conservation consideration in urbanization planning.

Epinephelus tankahkeei, a new species of grouper (Teleostei, Perciformes, Epinephelidae) from the South China Sea.

A new species of grouper, Epinephelus tankahkeeisp. nov. is described from the South China Sea based on examination of morphological and molecular characteristics. This new species has been treated as, and is similar to, its congener E. chlorostigma. Epinephelus tankahkeeisp. nov. can be distinguished from E. chlorostigma by the following combination of characters: a convex anal fin; closer dark spots on the body; a lack of dark spots on the abdomen, cheek, and pectoral fin; the absence of a clear posterior white margin on the caudal fin. Molecular analyses of the mitochondrial COI sequence variation, genetic distances, and a phylogeny, all highly support E. tankahkeeisp. nov. as a distinct species. A key to E. tankahkeeisp. nov. and its most closely related species is provided.

Identification of some Egyptian leafhopper species (Hemiptera: Cicadellidae) using DNA barcoding

Leafhoppers (Cicadellidae) occur in all biogeographical regions and feed on a wide range of host plants. Classic identification of leafhoppers is based only on the morphology of male genitalia, while DNA barcoding is an effective tool to identify different leafhopper species in any stage of their life cycle. Phylogenetic relationships among leafhoppers remain unexplored, but recent phylogenies have begun to interpret the evolutionary relationships of previously recognized tribes and subfamilies. Here we used mitochondrial Cytochrome Oxidase I sequences to barcode and determine the phylogenetic relationship among eight leafhopper genera collected from Egypt. Eight leafhopper samples from eight different genera were collected from various plants using a sweeping net and aspirator. Males of seven species were available while females only were available from the one genus (Austroagallia sp.). Novel leafhopper-specific mtDNA COI degenerate primers were designed. Our results showed that the mean of intraspecific COI sequence divergence in leafhoppers was 0.45%, with a range from 0.15% to 1.23%, and the divergences of most species were over 2%. For the first time, we were exploring the evolutionary relationships among surveyed genera (Austroagallia, Empoasca, Eupteryx, Exitianus, Macrosteles, Nephotettix, and Orosius) using a robust phylogenetic supertree. Our results demonstrate that DNA barcoding is likely to be a powerful tool for identifying and understanding leafhoppers’ evolution.

Integrative taxonomy of the new millipede genus Coxobolellus, gen. nov. (Diplopoda : Spirobolida : Pseudospirobolellidae), with descriptions of ten new species

Pseudospirobolellidae is a poorly known family of spirobolidan millipedes with only two genera and five described species. Yet, the descriptive taxonomy and molecular systematics of this group have been largely neglected. Therefore, the present work presents an integrative taxonomic study of new pseudospirobolellid taxa in Thailand. To this end, two mitochondrial gene fragments (COI and 16S rRNA) combined with morphological characters were used to define the genus Coxobolellus, gen. nov. with 10 new species, viz. C. albiceps, sp. nov., C. compactogonus, sp. nov., C. fuscus, sp. nov., C. nodosus, sp. nov., C. serratus, sp. nov., C. simplex, sp. nov., C. tenebris, sp. nov., C. tigris, sp. nov., C. transversalis, sp. nov. and C. valvatus, sp. nov. The interspecific COI sequence divergences among the new species ranged from 6 to 15%. The intergeneric COI sequence divergence between species of Coxobolellus, gen. nov., Benoitolus birgitae and Pseudospirobolellus sp. ranged from 20 to 23%. Three major morphological differences separate Coxobolellus, gen. nov. from Benoitolus and Pseudospirobolellus, namely (1) the protruding process on the 3rd (and 4th) coxae on male legs, (2) the posterior gonopod telopodite divided into two parts, and (3) a conspicuous opening pore at the mesal margin at the end of the coxal part of the posterior gonopod. Thus, the new genus is well supported by both mtDNA and morphological evidence, while the delimitation of the 10 new species is supported by the congruence between mtDNA and morphological data. Yet, with respect to the relationships of Benoitolus birgitae, morphological data suggest a similarity with Coxobolellus, gen. nov. and Pseudospirobolellus, whereas mtDNA data place this species in the Pachybolidae. Further phylogenetic analyses are needed to explore this apparent incongruence and test the monophyly of Pseudospirobolellidae.

DNA barcoding uncovers extensive cryptic diversity in the African long-fin tetra Bryconalestes longipinnis (Alestidae: Characiformes).

To investigate the presence of cryptic diversity in the African longfin-tetra Bryconalestes longipinnis, we employed DNA barcoding in a phylogeographic context, as well as geometric morphometrics, documenting for the first time genetic and body shape variation in the species. Analysis of cytochrome oxidase I gene (coI) sequence variation exposed extremely high levels of genetic differentiation among samples from across the geographic range of the species (up to 18%), certainly much greater than the traditionally employed c. 3% sequence divergence heuristic threshold for conspecifics. Phylogeographic analyses of coI data revealed eight clusters/clades that diverge by >4% and up to 18% (p-distance), potentially representing cryptic members of a species complex. A clear biogeographic pattern was also uncovered, in which the two main coI lineages corresponded geographically with the upper Guinea (UG) and lower Guinea (LG) ichthyofaunal provinces of continental Africa, respectively. Within each of these main lineages, however, no apparent phylogeographic structuring was found. Despite strong genetic differentiation, there is considerable overlap in body shape variation between UG and LG populations. For the most part, morphological variation does not match the strength of the molecular phylogeographic signal. Therefore, the ability to reliably utilise external body shape for regional delimitation remains elusive. Further anatomical investigation appears necessary to establish whether compelling diagnostic morphological features do exist between the divergent lineages of the B. longipinnis complex uncovered in this study.

New taxonomic status of <i>Tripteroides bambusa</i> (Yamada), 1917 from Japan, based on experimental crossing and COI sequence divergence

New taxonomic status of <i>Tripteroides bambusa</i> (Yamada), 1917 from Japan, based on experimental crossing and COI sequence divergence

Genetic structure among Charadrius plovers on the African mainland and islands of Madagascar and St Helena

Colonization of islands by long‐distance dispersers has great impact on genetic diversification among populations and may spearhead speciation events. We investigated intra‐ and interspecific divergence in Charadrius plovers with populations on mainland Africa, Madagascar and St Helena. We analysed microsatellite loci and sequence data from four nuclear and two mitochondrial gene regions. Charadrius plovers are shorebirds with high dispersal and mobility. Our results confirmed genetic differentiation between Madagascar and mainland populations of three plover species (White‐fronted Plover Charadrius marginatus, Kittlitz's Plover Charadrius pecuarius and, based on sequence data only, Three‐banded Plover Charadrius tricollaris) but highlight substantial variation in levels of intraspecific divergence among the three species. Namely, the Kittlitz's Plover, a dispersive habitat generalist with a polygamous mating system, exhibited lower island–mainland differentiation (0.05% COI sequence divergence) compared with the two monogamous species, the White‐fronted Plover (0.6% COI divergence) and Three‐banded Plover (1.6% COI divergence). In addition, past colonization of the islands of St Helena and Madagascar by ancestors of today's Kittlitz's Plover has led to the evolution of two endemic island species, the Madagascar Plover Charadrius thoracicus and the more closely‐related St Helena Plover Charadrius sanctaehelenae. We discuss the factors driving species differences in island–mainland divergence and highlight the importance of conserving genetically unique island populations and island habitats to safeguard future evolutionary potential.

On Plesionika persica (Kemp, 1925) and P. reflexa Chace, 1985 (Crustacea: Decapoda: Pandalidae) from India.

The availability of Indian specimens of Plesionika persica(Kemp, 1925)and P. reflexa Chace, 1985 provided more information on the taxonomy around these two species. Moreover, it is the first record of P. persica to India. Although P. taiwanica Chan and Yu, 2000 is superficially rather similar to P. persica, there are many differences between them and probably it is inappropriate to establish a species group for these two species. It is likely that all previous records of P. ensis (A. Milne-Edwards, 1881) from India actually represent P. reflexa Chace, 1985. Nevertheless, the present Indian specimens of P. reflexa have more than 10% COI sequence divergence from the topotypic materials of both P. ensis and P. reflexa, and the epipods at the pereiopods III and IV reduced or absent. This data further highlights the confusing taxonomy in the "P. ensis" group.

Integrative taxonomy of Merodon caerulescens complex (Diptera: Syrphidae) - evidence of cryptic speciation

In this research, we applied integrative taxonomy approach in order to delimit species of Merodon caerulescens species complex. Molecular analyses confirmed COI sequence divergence between the Rhodes and Crete populations. Additionally, ITS2 sequences show certain differences which should be additionally tested. 28S rRNA gene sequences once again proved to be too conserved for closely related species delimitation. Geometric morphometry results indicate differences in wings shape between males and females of the two islands populations. Additionally, subtle differences between the two populations in the body coverage and colouration of hairs are also observed. Thus, based on the all presented evidence we concluded that taxon Merodon caerulescens is a complex of two species, M. caerulescens (Rhodes) and M. atricapillatus sp. n. (Crete).

Desoria trispinata (MacGillivray, 1896), a promising model Collembola species to study biological invasions in soil communities

The species Desoria trispinata (MacGillivray, 1896) is globally distributed but probably not native to Europe. Reports on its occurrence have increased substantially over the last years, proving that it is extremely successful, often dominating in number not only Collembola but the entire macroscopic soil fauna under favourable conditions. Still, D. trispinata has seldom been studied, and its systematic position is poorly understood. We compiled available literature on the ecology of this species, rendering information with respect to its success. In addition, during the past years we established a controlled laboratory culture and recorded life history data. Finally, we ran a molecular genetic analysis. COI sequence divergence between specimens of D. trispinata was low among specimens from Germany, UK and Russia (up to 0.1%) clearly separating these specimens from other species of the genus Desoria. However, distance to specimens of D. trispinata from Japan was high (up to 15.3%).

A PCR-RFLP method for stock assignment in the endemic Macaronesian gastropod, Patella candei d’Orbigny, and its potential for future conservation strategies

Patella candei d’Orbigny is an exploited limpet endemic to the archipelagos of the Azores, Madeira, Selvagens and Canaries (Macaronesia). Marked declines reported for the species likely reflect overexploitation and inadequacy of current management measures with biodiversity further threatened by illegal harvesting and anthropogenic movement of limpets among archipelagos. Previous phylogeographic analyses of mtDNA COI sequence variation revealed that the (i) Azores, (ii) Madeira and (iii) Canaries and Selvagens represent three reciprocally monophyletic genetic stocks. The objective of this research was to identify diagnostic DNA sequence polymorphisms among the stocks that could be assayed by PCR-RFLP, thus permitting cost effective high throughput stock assignment. PCR-RFLP analysis of a COI fragment with two restriction enzymes (TaqI and AvaI) was sufficient to define diagnostic stock genotypes for the three stocks and permitted unambiguous stock assignment of a large sample of individuals (n=952). This PCR-RFLP approach can be readily extended to discriminate other Patella stocks, through judicious selection of restriction enzymes and similar protocols and offers great potential for eco-certification associated practises.

Synalpheus pinkfloydi sp. nov., a new pistol shrimp from the tropical eastern Pacific (Decapoda: Alpheidae).

A new, conspicuously coloured species of the alpheid genus Synalpheus Spence Bate, 1888, is described based on material collected on the Pacific coast of Panama. Synalpheus pinkfloydi sp. nov. is closely related to the western Atlantic S. antillensis Coutière, 1909, the two taxa being transisthmian, cryptic sister species. Both species are characterised by the distal areas of their major and minor chelae coloured in an intense, almost glowing pink-red. The morphological differences between S. pinkfloydi sp. nov. and S. antillensis Coutière, 1909 are subtle, being limited to the slightly different proportions of the merus of both chelipeds, distodorsal armature of the major cheliped merus, relative length of the antennal scaphocerite, and body size. However, they are genetically different with a 10.2% sequence divergence in COI. Based on molecular clock estimates, these transisthmian taxa diverged around 6.8-7.8 mya, i.e. well before the final closure of the Isthmus of Panama 2.5-3 mya.