Evolution, systematics and historical biogeography of sand flies of the subgenus Paraphlebotomus (Diptera, Psychodidae, Phlebotomus) inferred using restriction-site associated DNA markers

Phlebotomine sand flies are the main natural vectors of Leishmania, which cause visceral and tegumentary tropical diseases worldwide. However, their taxonomy and evolutionary history remain poorly studied. Indeed, as for many human disease vectors, their small size is a challenge for morphological and molecular works. Here, we successfully amplified unbiased copies of whole genome to sequence thousands of restriction-site associated DNA (RAD) markers from single specimens of phlebotomines. RAD markers were used to infer a fully resolved phylogeny of the subgenus Paraphlebotomus (11 species + 5 outgroups, 32 specimens). The subgenus was not recovered as monophyletic and we describe a new subgenus Artemievus subg. nov. Depaquit for Phlebotomus alexandri. We also confirm the validity of Ph. riouxi which is reinstated as valid species. Our analyses suggest that Paraphlebotomus sensu nov. originated ca 12.9–8.5 Ma and was possibly largely distributed from peri-Mediterranean to Irano-Turranian regions. Its biogeographical history can be summarized into three phases: i) a first split between Ph. riouxi + Ph. chabaudi and other species that may have resulted from the rise of the Saharan belt ca 8.5 Ma; ii) a Messinian vicariant event (7.3–5.3 Ma) during which the prolonged drought could have resulted in the divergence of main lineages; iii) a recent radiation event (3–2 Ma) that correspond to cycles of wet and dry periods in the Middle East and the East African subregions during the Pleistocene. Interestingly these cycles are also hypothetical drivers of the diversification of rodents, in the burrows of which Paraphlebotomus larvae develop. By meeting the challenge of sequencing pangenomics markers from single, minute phlebotomines, this work opens new avenues for improving our understanding of the epidemiology of leishmaniases and possibly other human diseases transmitted by arthropod vectors.

Phylogeography and palaeomodelling of Duseniella patagonica (Barnadesioideae), an early-diverging member of Asteraceae endemic to the Argentinean Monte and Patagonia

We performed an integrated phylogeographical and palaeoclimatic study of an early-diverging member of Asteraceae, Duseniella patagonica, endemic to Argentina. Chloroplast and nuclear markers were sequenced from 106 individuals belonging to 20 populations throughout the species range. We analysed genetic spatial distribution, diversity and structure, tested for range expansion, estimated divergence times, reconstructed ancestral areas and modelled present and past species distributions based on climatic data. Duseniella diverged from its sister genera during the Late/Middle Miocene. Its ancestral area included southern Monte plus eastern and central Patagonia. A vicariant event separated Monte and Patagonian clades during the Plio-Pleistocene. This would have involved unfavourable climate, soil, elevation, volcanism and/or other geomorphological processes between 40 and 43.5°S, in the sourroundings of the Somuncura plateau. Each clade possesses its own haplotypes and nucleotypes. Two populations, one in southern Monte and the other in eastern Patagonia, contain the highest diversity and exclusive haplotypes, representing hypothetical ancestral refugia. Northern Monte and southern Patagonian populations show low to null genetic diversity, being the most recently colonized areas. Climatic models indicate that winter temperature influenced the distribution of Duseniella, with an increase in probability of occurrence during colder periods, thus enabling diversification during glacial episodes.

Historical biogeography of a Brazilian lineage of Tillandsioideae (subtribe Vrieseinae, Bromeliaceae): the Paranaean Sea hypothesized as the main vicariant event

Subtribe Vrieseinae comprise four genera, Alcantarea, Stigmatodon, Vriesea s.s. and Waltillia, encompassing c. 20% of species in Tillandsioideae (Bromeliaceae), almost all of which are exclusive to Brazil. Here, we explore the biogeographic history of Vrieseinae, sampling 21 of the 22 genera of Tillandsioideae (130 terminals) and three DNA sequence markers (two plastid: rps16-trnK and matK; one nuclear: PHYC). We inferred a dated phylogeny and the ancestral areas of this lineage through RASP (reconstruct ancestral state in phylogeny) analyses. Vrieseinae were recovered as monophyletic, but tribe Vrieseeae (subtribe Vrieseinae + subtribe Cipuropsidinae) were not. A vicariant event between the Andes and Brazilian Shield probably occurred c. 10 Mya, when two clades, Cipuropsidineae + Tillandsieae and Vrieseineae, diverged. The Atlantic Forest plus the Chacoan region is recognized as the ancestral area for Vrieseinae. The results confirmed the recent origin of genera of Vrieseinae, with estimated crown ages in the Pliocene (5.3–2.6 Mya). We propose that the Paranaean Sea influenced the divergence of the main clades; Pleistocene events were probably responsible for the diversification of the most recent clades. This study sheds light on the biogeographic history of a key group of Neotropical plants, providing a new hypothesis for the evolution of bromeliads.

A new Lamellibrachia species and confirmed range extension for Lamellibrachia barhami (Siboglinidae, Annelida) from Costa Rica methane seeps

Lamellibrachia Webb, 1969 has eight currently recognized species reported from chemosynthetic environments in the Pacific, Atlantic, and Mediterranean. Of these, Lamellibrachia barhami Webb, 1969 has been reported in the eastern Pacific from Canada to Costa Rica. In this study, phylogenetic analyses of Lamellibrachia tubeworms sampled from the Costa Rica margin confirm the large geographic range of L. barhami and reveal a new Lamellibrachia species from a single methane seep between 999 and 1,040 meters. Lamellibrachia donwalshi sp. nov. differs genetically and morphologically from all congeneric species. Despite its geographic proximity to the eastern Pacific L. barhami, L. donwalshi sp. nov. formed a clade with Atlantic and Mediterranean Lamellibrachia species. This suggests a vicariant event may have occurred after an Atlantic radiation of Lamellibrachia.

Concordant patterns of mtDNA and nuclear phylogeographic structure reveal Pleistocene vicariant event in the green crab Carcinus aestuarii across the Siculo-Tunisian Strait

This study focuses on the population genetic structure of the green crab Carcinus aestuarii along part of the African Mediterranean coast, with the main target to confirm genetic subdivision across the well documented genetic boundary of the Siculo-Tunisian Strait. For this purpose, the mitochondrial COI (cytochrome oxidase I) gene and five polymorphic microsatellite loci were analysed in 144 and 120 specimens, respectively. Our results show the existence of two distinct haplogroups, separated by 16 mutational steps and revealed a non random distribution of the genetic variation along the African Mediterranean coast. Dating analyses, based on the use of different molecular clock models and rates, placed the divergence among both haplogroups at 1.91 Myr (95% HPD: 1.11–2.68 Myr) to 0.69 Myr (95% HPD: 0.44–0.98 Myr). This range of divergence time estimation corresponds to the Early Pleistocene. The particular pattern of genetic divergence among Eastern and Western African Mediterranean populations of C. aestuarii, detected by 2-level AMOVA at the mitochondrial level, was consistent with that inferred from microsatellite analysis and suggests a vicariant event in C. aestuarii. Demographic reconstruction, inferred from mismatch distribution and BSP analyses, yielded different patterns of demographic history between both African Mediterranean groups. The distribution pattern of the two haplogroups across the African Mediterranean coast, along with results of Bayesian analysis of genetic structure revealing an intermediate geographic group between the two divergent groups of the African coast, support the hypothesis of a secondary contact between two historically isolated groups. Although this hypothetical contact zone, thought to be located near the Siculo-Tunisian Strait, still needs to be verified, the asymmetric gene flow from Western to Eastern African Mediterranean, as inferred by the results of a MIGRATE analysis, reinforces the previously mentioned results.

Distributions and phylogeographic data of rheophilic freshwater fishes provide evidences on the geographic extension of a central-brazilian amazonian palaeoplateau in the area of the present day Pantanal Wetland

The analysis of the distribution patterns presented by examples of freshwater fishes restricted to headwater habitat: the anostomid Leporinus octomaculatus, the characins Jubiaba acanthogaster, Oligosarcus perdido, Moenkhausia cosmops, Knodus chapadae, Planaltina sp., the loricariid Hypostomus cochliodon, and the auchenipterid Centromochlus sp. provided evidences of a relatively recent shared history between the highlands of the upper rio Paraguay and adjoining upland drainage basins. Restricted to headwater of the uplands in the upper rio Paraguay and adjoining basins, these species provide biological evidence of the former extension of the central Brazilian plateau before the origin of the Pantanal Wetland. Disjunction took place due to an ecological barrier to these rheophilic taxa represented tectonic subsidence related to the origin of the Pantanal Wetland. Molecular analysis of Jubiaba acanthogaster revealed that the sample from the upper rio Xingu basin are the sister-group of a clade that includes samples from the upper rio Arinos (upper rio Tapajós) plus the upper rio Paraguay basin, supporting the assumption that the origin of the upper rio Paraguay basin causing vicariance between this basin and the upper rio Tapajós is the least vicariant event in the evolutionary history of the group.