Understanding the factors that determine the emergence of anthroponotic cutaneous leishmaniasis due to Leishmania tropica: Comparison of the density and mitochondrial lineage of Phlebotomus sergenti between endemic and free areas in Morocco

Anthroponotic cutaneous leishmaniasis (ACL) due to Leishmania tropica is spreading to new areas. Exposure to the vector, Phlebotomus sergenti, is the only proven risk factor. Our objective was to compare the densities and genetic characteristics of P. sergenti populations in two nearby localities in Morocco, one within an ACL endemic area (El Borouj) and another undamaged (Sidi Hajjaj). Statistically significant differences were detected between P. sergenti densities with a higher density of P. sergenti in the endemic town (p≤ 0.032). A different main P. sergenti mitochondrial lineage was evidenced in each one of the 2 localities, and for the first time, the lineage of P. sergenti specimens that are acting as a vector of L. tropica has been identified. Bioclimatic differences were detected between both localities. In conclusion, between an ACL endemic locality and another ACL free there are differences in both the density of P. sergenti and the mitochondrial lineage that may explain the different epidemiological situation. Given that the density of P. sergenti in the locality without ACL cases seems sufficient to allow transmission, the main factor that would justify its ACL undamaged character could be the absence of P. sergenti Lineage IV, which seems to prefer warmer and drier climates.

Unexpected mitochondrial lineage diversity within the genus Alonella Sars, 1862 (Crustacea: Cladocera) across the Northern Hemisphere

Representatives of the genus Alonella Sars (Crustacea: Cladocera: Chydorinae) belong to the smallest known water fleas. Although species of Alonella are widely distributed and often abundant in acidic and mountain water bodies, their diversity is poorly studied. Morphological and genetic approaches have been complicated by the minute size of these microcrustaceans. As a result, taxonomists have avoided revising these species. Here, we present genetic data on Alonella species diversity across the Northern Hemisphere with particular attention to the A. excisa species complex. We analyzed 82 16S rRNA sequences (all newly obtained), and 78 COI sequences (39 were newly obtained). The results revealed at least twelve divergent phylogenetic lineages, possible cryptic species, of Alonella, with different distribution patterns. As expected, the potential species diversity of this genus is significantly higher than traditionally accepted. The A. excisa complex is represented by nine divergent clades in the Northern Hemisphere, some of them have relatively broad distribution ranges and others are more locally distributed. Our results provide a genetic background for subsequent morphological analyses, formal descriptions of Alonella species and detailed phylogeographical studies.

A multidisciplinary approach to identify priority areas for the monitoring of a vulnerable family of fishes in Spanish Marine National Parks

Background Syngnathid fishes (Actinopterygii, Syngnathidae) are flagship species strongly associated with seaweed and seagrass habitats. Seahorses and pipefishes are highly vulnerable to anthropogenic and environmental disturbances, but most species are currently Data Deficient according to the IUCN (2019), requiring more biological and ecological research. This study provides the first insights into syngnathid populations in the two marine Spanish National Parks (PNIA—Atlantic- and PNAC—Mediterranean). Fishes were collected periodically, marked, morphologically identified, analysed for size, weight, sex and sexual maturity, and sampled for stable isotope and genetic identification. Due the scarcity of previous information, habitat characteristics were also assessed in PNIA. Results Syngnathid diversity and abundance were low, with two species identified in PNIA (Hippocampus guttulatus and Syngnathus acus) and four in PNAC (S. abaster, S. acus, S. typhle and Nerophis maculatus). Syngnathids from both National Parks (NP) differed isotopically, with much lower δ15N in PNAC than in PNIA. The dominant species were S. abaster in PNAC and S. acus in PNIA. Syngnathids preferred less exposed sites in macroalgal assemblages in PNIA and Cymodocea meadows in PNAC. The occurrence of very large specimens, the absence of small-medium sizes and the isotopic comparison with a nearby population suggest that the population of Syngnathus acus (the dominant syngnathid in PNIA) mainly comprised breeders that migrate seasonally. Mitochondrial cytochrome b sequence variants were detected for H. guttulatus, S. acus, and S. abaster, and a novel 16S rDNA haplotype was obtained in N. maculatus. Our data suggest the presence of a cryptic divergent mitochondrial lineage of Syngnathus abaster species in PNAC. Conclusions This is the first multidisciplinary approach to the study of syngnathids in Spanish marine NPs. Habitat preferences and population characteristics in both NPs differed. Further studies are needed to assess the occurrence of a species complex for S. abaster, discarding potential misidentifications of genus Syngnathus in PNAC, and evaluate migratory events in PNIA. We propose several preferential sites in both NPs for future monitoring of syngnathid populations and some recommendations for their conservation.

Phylogenetic Network of Mitochondrial COI Gene Sequences Distinguishes 10 Taxa Within the Neotropical Albitarsis Group (Diptera: Culicidae), Confirming the Separate Species Status of Anopheles albitarsis H (Diptera: Culicidae) and Revealing a Novel Lineage, Anopheles albitarsis J

The Neotropical Albitarsis Group is a complex assemblage of essentially isomorphic species which currently comprises eight recognized species—five formally described (Anopheles albitarsis Lynch-Arribalzaga, An. deaneorum Rosa-Freitas, An. janconnae Wilkerson and Sallum, An. marajoara Galvao and Damasceno, An. oryzalimnetes Wilkerson and Motoki) and three molecularly assigned (An. albitarsis F, G & I)—and one mitochondrial lineage (An. albitarsis H). To further explore species recognition within this important group, 658 base pairs of the mitochondrial DNA cytochrome oxidase subunit I (COI) were analyzed from 988 specimens from South America. We conducted statistical parsimony network analysis, generated estimates of haplotype, nucleotide, genetic differentiation, divergence time, and tested the effect of isolation by distance (IBD). Ten clusters were identified, which confirmed the validity of the eight previously determined species, and confirmed the specific status of the previous mitochondrial lineage An. albitarsis H. High levels of diversity were highlighted in two samples from Pará (= An. albitarsis J), which needs further exploration through additional sampling, but which may indicate another cryptic species. The highest intra-specific nucleotide diversity was observed in An. deaneorum, and the lowest in An. marajoara. Significant correlation between genetic and geographical distance was observed only in An. oryzalimnetes and An. albitarsis F. Divergence time within the Albitarsis Group was estimated at 0.58–2.25 Mya, during the Pleistocene. The COI barcode region was considered an effective marker for species recognition within the Albitarsis Group and a network approach was an analytical method to discriminate among species of this group.

Genetic structure of the Coconut Rhinoceros Beetle (Oryctes rhinoceros) population and the incidence of its biocontrol agent (Oryctes rhinoceros nudivirus) in the South Pacific Islands

Incursions of the Coconut rhinoceros beetle (CRB), Oryctes rhinoceros, have been detected in several countries of the south-west Pacific in recent years, resulting in an expansion of the pest's geographic range. It has been suggested that this resurgence is related to an O. rhinoceros mitochondrial lineage (previously referred to as the CRB-G biotype) that is reported to show reduced susceptibility to the well-established classical biocontrol agent, Oryctes rhinoceros nudivirus (OrNV). We investigated O. rhinoceros population genetics and the OrNV status of adult specimens collected in the Philippines and seven different South Pacific island countries (Fiji, New Caledonia, Papua New Guinea (PNG), Samoa, Solomon Islands, Tonga, and Vanuatu). Based on the presence of single nucleotide polymorphisms (snps) in the mitochondrial Cytochrome C Oxidase subunit I (CoxI) gene, we found three major mitochondrial lineages (CRB-G, a PNG lineage (CRB-PNG) and the South Pacific lineage (CRB-S)) across the region. Haplotype diversity varied considerably between and within countries. The O. rhinoceros population in most countries was monotypic and all individuals tested belonged to a single mitochondrial lineage (Fiji, CRB-S; Tonga, CRB-S; Vanuatu, CRB-PNG; PNG (Kimbe), CRB-PNG; New Caledonia CRB-G; Philippines, CRB-G). However, in Samoa we detected CRB-S and CRB-PNG and in Solomon Islands we detected all three haplotype groups. Genotyping-by-Sequencing (GBS) methods were used to genotype 10,000 snps from 230 insects across the Pacific and showed genetic differentiation in the O. rhinoceros nuclear genome among different geographical populations. The GBS data also provided evidence for gene flow and admixture between different haplotypes in Solomon Islands. Therefore, contrary to earlier reports, CRB-G is not solely responsible for damage to the coconut palms reported since the pest was first recorded in Solomon Islands in 2015. We also PCR-screened a fragment of OrNV from 260 insects and detected an extremely high prevalence of viral infection in all three haplotypes in the region. We conclude that the haplotype groups CRB-G, CRB-S, and PNG, do not represent biotypes, subspecies, or cryptic species, but simply represent different invasions of O. rhinoceros across the Pacific. This has important implications for management, especially biological control, of Coconut rhinoceros beetle in the region.

Recent mitochondrial lineage extinction in the critically endangered Javan rhinoceros

The Javan rhinoceros (Rhinoceros sondaicus) is one of five extant rhinoceros species and among the rarest large mammals on Earth. Once widespread across Southeast Asia, it is now on the verge of extinction, with only one wild population remaining (estimated at ~60 individuals) on the island of Java, Indonesia. To assess the past genetic diversity of the female lineage of R. sondaicus, we generated mitochondrial genome data from eight museum specimens dating back to the 19th century, before the range of the Javan rhinoceros was dramatically reduced, for comparison against mitochondrial DNA (mtDNA) sequences of current R. sondaicus and other rhinoceros species. We succeeded in reconstructing five full and three partial ancient mitogenomes from the eight samples. We used BEAST to assess the phylogenetic relationship of the five extant rhinoceros species and the historical samples. The results show that the oldest and most diverse mtDNA lineages of R. sondaicus are found in historical samples, indicating a significant reduction of mtDNA diversity in modern Javan rhinos. We anticipate that the newly sequenced data will represent a useful resource for improving our understanding of evolutionary history of this species, should future studies be able to increase the available dataset. We hope this information may help in conservation efforts for this species.

Genetic relationships between local Brazilian goat breeds based on mtDNA D-loop region similarity

Aim of study: Our objective was to investigate the mitochondrial DNA of local Brazilian goats to gain insights into the genetic composition of this precious genetic resource.Area of study: The study was developed in BrazilMaterial and methods: We analyzed a hypervariable region of the mitochondrial DNA of 83 goats belonging to four local Brazilian breeds, including Canindé (CAN-RN), Moxotó (MOX-CE), Marota (MAR-PI) and Azul (AZU-PE) as well as of exotic breeds raised in different states of the Federation. Sequences related to local Brazilian goats showed a dispersed distribution throughout the median-joining network, and clustering with sequences of exotic breeds occurred in some haplotypes. The obtained sequences were analyzed and compared with different haplogroups (A, B1, B2, C, D, F, and G) available on GenBank.Main results: The local Brazilian goat breeds showed significant diversity, with 16 (0.8240) haplotypes. Population structure analysis revealed substantial differences among breeds (p < 0.05). Mitochondrial lineage A was observed in Brazilian goats. Phylogeny showed European goats as the dominant stock for Brazilian goats, but there weare some haplotypes within haplogroup A, clustering with African and Asian haplotypes.Research highlights: These results could be suitable for creating a strategic conservation program, potentially benefitting future breeding programs.