CO1 Sequence Data Research Articles

Rediscovery and phylogenetic analysis of Agnostrup, a least known genus of Mecistocephalidae (Chilopoda, Geophilomorpha) in China

The genus Agnostrup Foddai, Bonato, Pereira & Minelli, 2003 is one of the least known genera within the family Mecistocephalidae Bollman, 1893. In this study, we rediscovered the genus Agnostrup in China and provided a comprehensive redescription of A. striatus (Takakuwa, 1949). Additionally, we conducted a molecular phylogenetic analysis using CO1, 16S, and 28S sequence data, revealing a low genetic distance between Agnostrup and Nannarrup Foddai, Bonato, Pereira & Minelli, 2003. After comparing the morphological characteristics of these two genera, we synonymized the genus Nannarrupsyn. nov. with Agnostrup. As a result, three species previously belonging to the genus Nannarrup were transferred to Agnostrup: A. hoffmani (Foddai et al., 2003), comb. nov., A. innuptus (Tsukamoto, 2022), comb. nov., and A. oyamensis (Tsukamoto, 2022), comb. nov.

Integrative taxonomy provides evidence for a cryptic lineage in the velvet worm Peripatopsis birgeri species complex (Onychophora: Peripatopsidae) in KwaZulu-Natal, South Africa

During the present study, species boundaries in the velvet worm Peripatopsis birgeri species complex in KwaZulu-Natal, South Africa, were examined with the use of DNA sequence data, gross morphology, scanning electron microscopy (SEM) and ecological niche modelling. Mitochondrial CO1 and nuclear 18S rRNA sequence data were used to generate a phylogeny using both a Bayesian inference and maximum likelihood approaches. Both the CO1 sequence data and the combined DNA sequence topology (CO1 + 18S rRNA) revealed the presence of two geographically distinct clades within the P. birgeri species complex. Results from three species delimitation methods (GMYC, PTP and ASAP), were incongruent in determining the number of species within the species complex and generally overestimated the number of operational taxonomic units. The latter result can be attributed to the marked genetic structure within the species complex, a result corroborated by the CO1 haplotype network and statistically significant F ST values. Divergence time estimation suggests that the two clades diverged during the Plio/Pleistocene. Niche modelling revealed that the two clades were differentially impacted by bioclimatic variables and occupied different habitats. Gross morphological characteristics, such as leg pair numbers and colour revealed no fixed differences between the two clades, however, a creamy white headband/collar occurred exclusively in specimens of clade 1 (P. birgeri). In contrast, SEM revealed fixed dorsal and ventral scale rank differences between the two clades. The results corroborate the presence of a novel species within the P. birgeri s.s. species complex. Peripatopsis birgeri s.s. is revised and restricted to the southern Drakensberg and a new species, P. polychroma sp. nov. (clade 2), from the northern Drakensberg and adjacent Afrotemperate forests in the interior of KwaZulu-Natal is described. https://zoobank.org/urn:lsid:zoobank:org:pub:569557AB-8BC8-49B6-B8AA-96507371297B

New data on Garra makiensis (Cyprinidae, Labeoinae) from the Awash River (Ethiopia) with remarks on its relationships to congeners on the Arabian Peninsula

On the African continent, the genus Garra consists of several species often insufficiently separated from each other by diagnostic characters. Herein, a detailed morphological redescription of Garra makiensis from the Awash River drainage is presented, together with additional data on the type specimens of G. makiensis and G. rothschildi. Mitochondrial CO1 sequence data are also provided, including the historic paralectotype of G. makiensis, with a comparison to Garra species from Africa and the Middle East. Based on these sequences, G. makiensis clusters outside the group of African congeners and is a sister lineage to species from the south-east of the Arabian Peninsula. Although morphologically variable, G. makiensis is characterised by having a single unbranched pectoral-fin ray, a short distance between vent and anal-fin origin (7.3–19.7 % of pelvic – anal distance), chest and belly covered with scales, and a prominent axillary scale at base of pelvic fin (18.8–35.5 % of pelvic-fin length).

A new species of the genus Achalinus (Squamata: Xenodermatidae) from southeastern Yunnan Province, China

A new species of the xenodermatid snake genus Achalinus Peters, 1869 is described from Yunnan Province, Southwest China, based on a single male specimen. The new species is assigned to the genus Achalinus on the basis of absence of preocular and postocular, subcaudals arranged in single row, and results of phylogenetic analyses of mitochondrial DNA CO1 sequence data. Achalinus pingbianensis sp. nov. differs from its congeners by the combination of following morphological characters: absence of a loreal, internasals subequal to that between prefrontals and dorsal scales strongly keeled, 23 rows throughout. Currently, 13 species are in the genus Achalinus, further taxonomical and phylogenetic studies based on more extensive samples and more markers will help understand the cryptic diversity and clarify their interspecific relationships.

High genetic variation within mitochondrial CO1 in Middle EuropeanThanasimus formicarius (Linné, 1758) (Coleoptera: Cleridae).

The aim of this study is to assess the species status of the Middle-European Thanasimus Latreille, 1806 species using mitochondrial CO1 sequence data. Molecular biological results clearly support the synonymy of T. pectoralis (Fuss, 1863) and T. rufipes (Brahm, 1797) with T. femoralis (Zetterstedt, 1828) as already proposed by Kolibáč (1992). Results of the present study indicate high genetic variation within T. formicarius (Linné, 1758) and emphasize the study of population dynamics of T. formicarius within Europe. Furthermore, preliminary screening of all available T. formicarius sequences on BOLD and Genbank (shorter than 500bp) indicates the presence of a "Continental" and a more "Atlantic" clade in T. formicarius. To support our hypothesis of a probably cryptic species among T. formicarius, more studies, with more specimens from different populations, especially from southern England, northern France and the northern part of the Iberian Peninsula, will be necessary.

A new genus Gnathospinosa (Lepidoptera: Tineidae: Euplocaminae) from China, with description of a new species and its taxonomic position.

The genus Gnathospinosa Liao Huang, gen. nov., belonging to the subfamily Euplocaminae, is described with a new species G. qinlingensis Liao Huang, sp. nov. from China as its type species. The new species was illustrated with photographs of the adults and male genitalia. A preliminary phylogenetic study based on mitochondrial cytochrome c oxidase subunit I gene (co1) sequence data of the new species and Psecadioides cuneus are presented.

Repurposing of archived CO1 sequence data reveals unusually high genetic structure between North American and European zebra mussels (Dreissena polymorpha)

The invasion of the zebra mussel, Dreissena polymorpha in the Great Lakes of North America is regarded as one of the most catastrophic ecological events in recent history. Previous studies showed a close kinship between European zebra mussels and their invasive cohorts in the Great Lakes. In this study, we repurposed and reanalyzed archived CO1 sequence data from Lake Superior and multiple sites in Europe that were collected between 1991 and 2011 to illustrate an interesting pattern of genetic isolation that was overlooked in previous studies. The results showed extreme genetic isolation of Lake Superior zebra mussels as evident by high ϕST values and strong geographic patterning of Lake Superior haplotypes.

Southern high latitude squat lobsters II: description of Uroptychus macquariae sp. nov. from Macquarie Ridge.

Squat lobsters have only recently been recorded from the Macquarie Ridge, which extends south between New Zealand and Antarctica. Among these, Uroptychus insignis (Henderson, 1885) was recorded for the first time outside the western Indian Ocean, exhibiting only subtle morphological differences. Reexamination of the Macquarie Ridge and Indian Ocean specimens attributed to U. insignis using morphological and molecular data revealed the Macquarie Ridge form to represent a separate species. Subtle but consistent morphological differences are evident and partial CO1 sequence data indicates that the specimens collected on Macquarie Ridge differ from those collected in the Indian Ocean by more than 7%. The Macquarie Ridge species is described herein as Uroptychus macquariae n.sp. Subtle morphological differences between the new species and U. insignis are discussed.

Spermatogenic and Phylo-molecular Characterizations of Isolated Fasciola Spp. From Cattle, North West Iran.

Fascioliasis is economically important to the livestock industry that caused with Fasciola hepatica and Fasciola gigantica. The objective of this study was to identify these two species F. hepatica and F. gigantica by using nuclear and mitochondrial markers (ITS1, ND1 and CO1) and have been employed to analyze intraspecific phylogenetic relations of Fasciola spp. Approximately 150 Fasciola specimens were collected, then stained with haematoxylin-carmine dye and observed under an optical microscope to examine for the existence of sperm. The ITS1 marker was used to identify different Fasciola and phylogenetic analysis based on ND1 and CO1 sequence data were conducted by maximum likelihood algorithm. Fasciola samples were separated into 2 groups. Almost all specimens had many sperms in the seminal vesicle (spermic fluke) and one fluke did not contain any sperm in the seminal vesicle. The aspermic sample had F. gigantica RFLP pattern with ITS1 gene. Phylogenetic analysis based on NDI and COI sequence data were conducted by maximum likelihood showed a similar topology of the trees obtained particularly for F. hepatica and F. gigantica. This study demonstrated that aspermic Fasciola found in this region of Iran has same genetic structures through the spermic F. gigantica populations in accordance to phylogenetic tree.

A new interstitial ostracod species of the genus Paracobanocythere from Vietnam, with mitochondrial CO1 sequence data of three Asian species.

This study is a first report of an interstitial ostracod from Southeast Asia. The ostracod species, Paracobanocythere vietnamensis sp. n., was found in the marine interstitial environment of Phu Quoc Island, Vietnam. Thus far, three species of this genus have been described. The morphology of the carapace as well as the appendages of this new species are quite similar to Paracobanocythere hawaiiensis and Paracobanocythere watanabei. However, we found that they could be easily distinguished according to the morphology of the male copulatory organ. Additionally, we estimated the evolutionary distances among these three species based on nucleotide and amino acid sequences of the mitochondrial CO1 gene. Similar morphologies of carapaces and appendages, and relatively small evolutionary distances according to CO1 between Paracobanocythere vietnamensis sp. n. and Paracobanocythere watanabei suggest that these two species are very closely related.

Comparative Phylogenetic Study of Four Genes of Mitochondrial Genome in Tenpounder Fishes (Order: Elopiformes)

The Elopiformes represent a group of seven known species of fishes found in marine and estuarine ecosystem and many of them are endemic to East Asia. To date published morphological and molecular phylogenetic hypothesis of Tenpounder fishes are part congruent and there are some areas of significant disagreement with respect to species relationships. The present study analyzed the sequence data from four genes (Cytb, CO1, 16S and 12S rRNA) of mitochondrial genome for the attempt to estimate the relationships among five species such as Elops saurus, E. affinis, E. smithi, E. machnata and E. hawaiensis and to assess the phylogenetic utility of these markers. The Kimura 2- parameter (K2P) genetic distance, average nucleotide frequencies, nucleotide substitution patterns and phylogenetic trees were reconstructed using neighbour joining (NJ) method. The interspecies K2P genetic distance was 0.0158 and intraspecies distance was 0.0042 based on the barcoding gene, CO1 sequence data. Whereas the interspecies K2P genetic distance was 0.6140 and intraspecies genetic distance was 0.0020 based on the Cytb data. The four mitochondrial marker genes used in this study showed different type of cluster and we could not confirm the relationship between the five Elops species. This is due to the independent mutation rate of each mtDNA genes. However, this problem can be overcome by analysing in parallel other gene markers.

Characterization of the orchid bee Euglossa viridissima (Apidae: Euglossini) and a novel cryptic sibling species, by morphological, chemical, and genetic characters

In orchid bees, males signal their availability as mates by fanning ‘perfumes’, i.e. blends of volatiles that are collected from environmental sources and stored in hind leg pouches. The chemical composition of such perfumes in males with either two or three mandibular teeth has previously led to the discovery of two sympatric, cryptic lineages within Euglossa viridissima Friese on the Yucatan peninsula, Mexico. Here, we combine chemical, morphological, and genetic data for an integrated characterization of the two lineages. The lectotype of E. viridissima Friese in the Museum of Natural History in Vienna has two mandibular teeth, and the species name viridissima must thus be assigned to the predominantly bidentate lineage, whereas the completely tridentate lineage is described as a novel species, Euglossa dilemma sp. nov. Bembe & Eltz. Chemical profiling and microsatellite genotyping revealed that E. viridissima males can occasionally (∼10% of individuals) express a third mandibular tooth, but this tooth is not positioned centrally on the mandible as in E. dilemma, but is displaced towards the tip. Thus, males of the two lineages can be unambiguously diagnosed by mandibular characters alone. Based on 889 bp of CO1 sequence data, we confirm that E. viridissima and E. dilemma constitute a monophyletic group within the genus Euglossa. However, CO1 alone failed to separate these two lineages due to the lack of parsimony-informative sites. Both species occur in broad sympatry across Central America, but the orchid bees recently introduced to Florida have three mandibular teeth in males, i.e. belong to E. dilemma. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163, 1064–1076.

Genetic differentiation in the circum—Antarctic sea spider Nymphon australe (Pycnogonida; Nymphonidae)

Nymphon australe Hodgson 1902 is the most abundant species of sea spiders in the Southern Ocean. The species is recognised as highly morphologically variable, circumpolar and eurybathic—which is surprising given that sea spiders lack a planktonic stage; the fertilised eggs and larvae remain attached to the ovigers of the father, and consequently have limited dispersal capacity. In this study, we investigate the genetic structure of N. australe populations around Antarctica, confronting the apparent limited dispersal ability with its recognised circumpolarity. Here we analyse mitochondrial DNA of specimens from Antarctic Peninsula, Weddell Sea and East Antarctica to determine if they represent populations of the widespread N. australe — or instead we can recognise cryptic species – and how genetically different they are. Both CO1 and 16S sequence data produced single haplotype networks for N. australe from all three Antarctic locations without indication of cryptic speciation. However, we found strong phylogeographic structure among the three Antarctic locations based on CO1 data. There was only a single shared haplotype between the Antarctic Peninsula and the East Antarctica locations, and all three regions were significantly subdivided from each other ( F ST =0.28, p<0.01). Furthermore, within the Antarctic Peninsula and East Antarctic locations, we found evidence of genetic subdivision between populations of N. australe separated by 10–100 s of km ( F ST =0.07–0.22, p<0.05), consistent with sea spiders life history traits indicating a limited dispersal capability. We conclude N. australe represents a single circum-Antarctic species that, despite its limited dispersal abilities, has successfully colonised large parts of the Antarctic marine ecosystem through geological history. However, clear genetic differences among and within locations indicate contemporary gene flow is limited, and that populations of N. australe around Antarctica are effectively isolated.

A new, disjunct species of Speleonectes (Remipedia, Crustacea) from the Canary Islands

We describe Speleonectes atlantida n. sp. as the third species of Remipedia that was found outside the main distribution area of this group in the Caribbean region. S. atlantida was collected by cave divers equipped with closed circuit rebreathers from the far interior of the Tunel de la Atlantida, an anchialine volcanic lava tube, on the Canarian island of Lanzarote. The new species occurs in sympatry with S. ondinae, to which it is morphologically closely related. S. atlantida can be distinguished from S. ondinae by a more slender habitus and smaller pleurotergites in the posterior trunk. The valid status of S. atlantida as a new species of Remipedia could be corroborated by intra- and interspecific comparisons of 16S rDNA and CO1 sequence data.

Evidence for a discrete evolutionary lineage within Equatorial Guinea suggests that the tsetse flyGlossina palpalis palpalisexists as a species complex

Tsetse flies of the palpalis group are major vectors of Human African Trypanosomiasis in Africa. Accurate knowledge of species identity is essential for vector control. Here, we combine ribosomal internal transcribed spacer 1 (ITS1), mitochondrial Cytochrome Oxidase 1 (COI) and microsatellites to determine the population structure and phylogenetic relations of Glossina p. palpalis in Equatorial Guinea. CO1 sequence data suggest that G. p. palpalis in Equatorial Guinea is a distinct subspecies from previously described G. p. palpalis in West Africa and Democratic Republic of Congo. Glossina p. palpalis in Equatorial Guinea and DRC share a common ancestor which diverged from West African G. p. palpalis around 1.9 Ma. Previous ITS1 length polymorphism data suggested the possible presence of hybrids in Equatorial Guinea. However, ITS1 showed incomplete lineage sorting compared with clearly defined COI groups, and data from 12 unlinked microsatellites provided no evidence of hybridization. Microsatellite data indicated moderate but significant differentiation between the populations analysed (Rio Campo, Mbini and Kogo). Moreover, unlike previous studies of G. p. palpalis, there was no evidence for heterozygote deficiency, presence of migrants or cryptic population structure. Variance effective population size at Rio Campo was estimated at 501-731 assuming eight generations per year. This study of the population genetics of G. p. palpalis in central Africa provides the first estimate of genetic differentiation between geographically separated G. p. palpalis populations.

Anischia, Perothops and the phylogeny of Elateroidea (Coleoptera: Elateriformia)

AbstractThe larvae of Anischia Fleutiaux and Perothops Laporte are described. Cladistic analyses based on adult and larval morphology, as well as CO1 sequence data, place both genera in the Eucnemidae clade within the Elateroidea (sensu stricto). The subfamily Anischiinae Fleutiaux, 1936 is placed in the family Eucnemidae in a clade containing the more derived eucnemid subfamilies (Melasinae, Eucneminae and Macraulacinae), while Perothops and Phyllocerus Lepeletier &amp; Serville represent subfamilies basal to the remaining eucnemid taxa. The genus Afranischia Basilewsky, 1955 is synonymized with Anischia Fleutiaux, 1896, and Anischia boliviana Fleutiaux is selected as the type species of the latter. Three new species are described: Anischia bicolor (New Caledonia), Anischia kuscheli (New Caledonia) and Anischia monteithi (NE Australia), and Anischia stupenda Fleutiaux, 1897 is recorded from Australia. Anischia crassicornis Champion, 1897 is synonymized with Anischia mexicana Fleutiaux, 1896. One new combination is made, Anischia ruandana (Basilewsky, 1955).

Evolutionary relationships of Drosophila mojavensis geographic host races and their sister species Drosophila arizonae

The cactophilic Drosophila mojavensis species group living in the deserts and dry tropical forests of the southwestern United States and Mexico provides a valuable system for studies in diversification and speciation. Rigorous studies of the relationships between host races of D. mojavensis and the relationships among the members of the species group (D. mojavensis, Drosophila arizona, and Drosophila navojoa) are lacking. We used mitochondrial CO1 sequence data to address the phylogenetics and population genetics of this species group. In this study we have found that the sister species D. mojavensis and D. arizonae share no mitochondrial haplotypes and thus show no evidence for recent introgression. We estimate the divergence time between D. mojavensis and D. arizonae to be between 1.91 and 2.97 million years ago. D. arizonae shows little structure in our population genetic analyses but there is phylogenetic differentiation between southeastern and northern populations of D. arizonae. Drosophila mojavensis shows significant population and phylogenetic structure across the four geographic regions of its distribution. The mitochondrial data support an origin of D. mojavensis on the mainland with early differentiation into the populations now found in the Mojave Desert and the Mainland Sonoran Desert and later colonization of the Baja Peninsula, in contrast to previous models. Also, the sister clade to D. mojavensis/D. arizonae includes D. navojoa and Drosophila huaylasi. By defining the genetic relationships among these populations, we provide a foundation for more sophisticated hypothesis testing regarding the timing of early speciation events and host switches in this species group.