Genetic diversity and population structure of Rhipicephalus sanguineus sensu lato across different regions of Colombia

Background There has been a long-standing debate over the taxonomic status of Rhipicephalus sanguineus sensu lato. Different studies worldwide have reported the occurrence of different well-defined lineages, in addition to Rhipicephalus sanguineus sensu stricto. To date, there are very few studies examining the diverse aspects of this tick in Colombia. We assessed the population structure and genetic diversity of R. sanguineus s.l. in eight departmental regions across Colombia. Methods A total of 170 ticks were collected from dogs in different departments of Colombia. All specimens were morphologically compatible with R. sanguineus s.l. and subjected to genetic analysis. DNA sequences were obtained for the 12S rDNA, cytochrome oxidase I (COI) and internal transcribed spacer 2 (ITS2) markers. A concatenated set of all mitochondrial markers was also constructed. Next, maximum likelihood phylogenetic trees were constructed using the sequences generated herein and sequences available in GenBank. Finally, we assessed different summary statistics and analysed population structure and divergence with Fst and Dxy and demographic changes with Tajima's D and Fu and Li’s statistical tests. Results Analysis of the 12S rDNA and COI revealed that all R. sanguineus s.l. specimens collected across different regions of Colombia clustered within the tropical lineage. Micro-geographical analyses showed that the tick population from Amazonas formed a distinct cluster separated from the other sequences, with moderate Fst and Dxy values. However, no signs of a robust population structure were found within the country. The results of Fu’s FS tests, together with the haplotype networks and diversity values, signal a possible population expansion of this tick species in Colombia. Conclusions Evidence provided herein supports the tropical lineage as the main circulating lineage in Colombia, exhibiting a general lack of genetic structure except for the Amazonas region. Graphical Abstract

Molecular analysis of the mitochondrial markers COI, 12S rDNA and 16S rDNA for six species of Iranian scorpions

Objectives Annually, 1.2 million humans are stung by scorpions and severely affected by their venom. Some of the scorpion species of medical importance have a similar morphology to species with low toxicity. To establish diagnostic tools for surveying scorpions, the current study was conducted to generate three mitochondrial markers, Cytochrome Oxidase I (COI gene), 12S rDNA and 16S rDNA for six species of medically important Iranian scorpions: Androctonus crassicauda, Hottentotta saulcyi, Mesobuthus caucasicus, M. eupeus, Odontobuthus doriae, and Scorpio maurus. Results Phylogenetic analyses of the obtained sequences corroborated the morphological identification. For the first time, 12S rDNA sequences are reported from Androctonus crassicauda, Hottentotta saulcyi, Mesobuthus caucasicus and M. eupeus and also the 16S rDNA sequence from Hottentotta saulcyi. We conclude that the mitochondrial markers are useful for species determination among these medically important species of scorpions.

Ultrastructural and molecular characteristics of Setaria species based on sequence analysis of genomic and mitochondrial gene markers in cattle (Bos taurus) and buffaloes (Bubalus bubalis) from Iran

The aim of the present study was to investigate the ultrastructural characteristics and genetic diversity of Setaria parasites from cattle (n=696) and buffalo (n= 522) from Khuzestan province of Iran and to compare them with available data from other countries/regions by sequences analysis of the 12S Rdna and the mitochondrial cytochrome C oxidase subunit I (cox1) genes. Based on SEM (Scanning Electron Micrographs) and light microscopy, all the isolated worms were identified as Setaria labiatopapillosa. Our results showed that 12.3% of cattle were infected with Setaria spp., while no infection was found in buffaloes. The maximal prevalence was observed in cattle younger than one year old. The prevalence rate was not influenced by the season of the year or gender. Comparison of the obtained sequences from Setaria with sequences of Setaria spp. from GenBank confirmed that all samples belong to the species S. labiatopapillosa. The phylogenetic tree constructed using cox1 and 12S rDNA genes of several other filarial nematodes showed that the Khuzestan isolates share a common branch with S. labiatopapillosa from other regions. Intra-specific variation was observed in 12S rDNA but not in cox1. In conclusion, our results indicating that S. labiatopapillosa is the main species involved in the spread of setarial infection in south-west of Iran and the identified worms corresponded mostly to worms that reported previously throughout other continents.

A new species of the coral associated barnacle (Thoracica: Pyrgomatidae: Pyrgoma) from a deep-sea oculinid coral in New Caledonian waters

The present study describes a new species of Pyrgoma Leach, 1817, a coral associated barnacle attached to Tubastrea, from the south of New Caledonia. Pyrgoma spurtruncata sp. nov. is morphologically close to P. cancellatum Leach, 1818, P. japonica Weltner, 1897 and P. kuri Hoek, 1913 in the absence of extended tergal muscle crests. Pyrgoma cancellatum and P. kuri have a shallow, fully open, medial furrow of the tergal spur, whereas in P. spurtruncata sp. nov. the medial furrow is deeper and closed. Pyrgoma spurtruncata sp. nov. differs from P. japonica Weltner, 1897 in the width of the tergal spur and the length of the rostral tooth of the scutum. Phylogenetic analyses based on two mitochondrial markers, 12S rDNA and COI, confirm a unique, distinct clade of P. spurtruncata sp. nov. among the current available molecular information regarding Pyrgoma species.

Comparison of some Molecular Markers for Tick Species Identification

Background: Ticks are obligate blood-sucking ectoparasites of vertebrates. Since many tick identification studies are based on the analysis of 16S rDNA, 12S rDNA and ITS-1, 2 rDNA genes, we aimed to compare the performance of these molecular markers of common use for the identification of ticks, under a diagnostic laboratory environment. Methods: Overall, 192 tick specimens were collected through the state of Texas from January 2014 to August 2015 and the species was determined by both morphology and molecular amplification using the 16S rDNA, 12S rDNA, ITS1 and ITS2. Results: The species collected were identified by molecular techniques as Dermacentor albipictus, D. variabilis, Am­blyomma americanum, Ixodes scapularis, A. cajennense, Rhipicephalus sanguineus and Carios capensis. ITS1 and ITS2 were not able to prove consistent amplification and therefore have been considered as potential markers for tick iden­tification. Conclusion: The use of mitochondrial genes in tick identification showed to provide more consistent results in the diagnostic environment.

Phylogenetic analysis of colubrid snakes based on 12S rDNA reveals distinct lineages of Dendrelaphis pictus (Gmelin, 1789) populations in Sumatra and Java

Nugraha FAD, Fatchiyah F, Smith EN, Nia Kurniawan N. 2018. Phylogenetic analysis of colubrid snakes based on 12S rDNA reveals distinct lineages of Dendrelaphis pictus (Gmelin, 1789) populations in Sumatra and Java. Biodiversitas 19: 303-310. The phylogenetic relationship among the major colubrid snakes, particularly those of the subfamily Colubrinae, has been the subject of much debate. Also, there was limited data on the molecular relationships of Sundaland colubrid snakes. This study aimed to examine the relationships among colubrid snakes from Sumatra and Java based on fragments of 12S rDNA gene. We sequenced 17 specimens of colubrid snakes representing 5 genera and 2 subfamilies: Colubrinae and Ahaetullinae. We used maximum likelihood, maximum parsimony and Bayesian inference methods for inferring phylogenetic relationships. The result of our phylogenetic analyses is in line with the previous findings for the separation between Colubrinae and Ahaetullinae. Interestingly, we found two distinct clades of Dendrelaphis pictus species with the high genetic divergence between them where D. pictus from Sumatra and West Java separated from Central and East Java clade. Our divergence time estimation showed that the differentiation between these clades of D. pictus occurred in the late Miocene epoch (8.9 Ma) when Sumatra and Java separated after being inundated in the early Miocene epoch.

CONTRIBUTION TO THE PHYLOGENY OF THE PANGASIIDAE BASED ON MITOCHONDRIAL 12S RDNA

Catfishes are generally one of the economically important groups of fresh and brackish water fishes in the world. In many countries, they form a significant part of inland fisheries, and several species have been introduced in fish culture. Judging from literature, the main constraint to cultivate wild species and to optimise the production of pangasiid catfishes is due to the poorly documented systematics of this family. In the present contribution, the phylogenetic relationships within Pangasiidae are studied to contribute to a better insight in their taxonomy and evolution. The genetic relatedness is inferred using mitochondrial 12S rDNA gene sequences. To resolve the phylogenetic position of Laides in this group of catfish, five genera of Asian and African Schilbeidae are also considered. The results showed that a species group (complex) could be clearly seen in the genetic tree. Pangasius is more derive than the other genera. By using approximate molecular clock/evolutionary calibration from mitochondrial gene, a new episode of speciation for the family marked explosive radiation about 5- 8 million years ago (mya). This adaptive radiation extended until the Late Pleistocene. Regarding the relationships between the Pangasiidae and Schilbeidae, two families show an allopatric distribution with slight overlap. The Pangasiidae occur mainly in Southeast Asia, while the Schilbeidae are seen mainly on the Indian subcontinent (including Myanmar) and Africa. It confirms the separation between Schilbeidae and Pangasiidae occurred in the Early Miocene.