Genetic divergence and reproductive isolation in the Ochthebius (Calobius) complex (Coleoptera: Hydraenidae)

Novel Microsatellite Loci, Cross-Species Validation of Multiplex Assays, and By-Catch Mitochondrial Genomes on Ochthebius Beetles from Supratidal Rockpools

Here we focus on designing, for the first time, microsatellite markers for evolutionary and ecological research on aquatic beetles from the genus Ochthebius (Coleoptera, Hydraenidae). Some of these non-model species, with high cryptic diversity, exclusively inhabit supratidal rockpools, extreme and highly dynamic habitats with important anthropogenic threats. We analysed 15 individuals of four species (O. lejolisii, O. subinteger, O. celatus, and O. quadricollis) across 10 localities from the Mediterranean coasts of Spain and Malta. Using next-generation sequencing technology, two libraries were constructed to interpret the species of the two subgenera present consistently (Ochthebius s. str., O. quadricollis; and Cobalius, the rest of the species). Finally, 20 markers (10 for each subgenus) were obtained and successfully tested by cross-validation in the four species under study. As a by-catch, we could retrieve the complete mitochondrial genomes of O. lejolisii, O. quadricollis, and O. subinteger. Interestingly, the mitochondrial genome of O. quadricollis exhibited high genetic variability compared to already published data. The novel SSR panels and mitochondrial genomes for Ochthebius will be valuable in future research on species identification, diversity, genetic structure, and population connectivity in highly dynamic and threatened habitats such as supratidal coastal rockpools.

The population genetics of speciation by cascade reinforcement

Species interactions drive diverse evolutionary outcomes. Speciation by cascade reinforcement represents one example of how species interactions can contribute to the proliferation of species. This process occurs when the divergence of mating traits in response to selection against interspecific hybridization incidentally leads to reproductive isolation among populations of the same species. Here, we investigated the population genetic outcomes of cascade reinforcement in North American chorus frogs (Hylidae: Pseudacris). Specifically, we estimated the frequency of hybridization among three taxa, assessed genetic structure within the focal species, P. feriarum, and ascertained the directionality of gene flow within P. feriarum across replicated contact zones via coalescent modeling. Through field observations and preliminary experimental crosses, we assessed whether hybridization is possible under natural and laboratory conditions. We found that hybridization occurs among P. feriarum and two conspecifics at a low rate in multiple contact zones, and that gene flow within the former species is unidirectional from allopatry into sympatry with these other species in three of four contact zones studied. We found evidence of substantial genetic structuring within P. feriarum including a divergent western allopatric cluster, a behaviorally-distinct sympatric South Carolina cluster, and several genetically-overlapping clusters from the remainder of the distribution. Furthermore, we found sub-structuring between reinforced and nonreinforced populations in the two most intensely-sampled contact zones. Our literature review indicated that P. feriarum hybridizes with at least five heterospecifics at the periphery of its range providing a mechanism for further intraspecific diversification. This work strengthens the evidence for cascade reinforcement in this clade, revealing the geographic and genetic landscape upon which this process can contribute to the proliferation of species.

Legacies of domestication, Neolithic diffusion and trade between Indian subcontinent and Island Southeast Asia shape maternal genetic diversity of Andaman cattle

Andaman cattle is a precious indigenous livestock species endemic to Andaman and Nicobar Islands, India. Till date, origin and genetic makeup of the breed which is warranted for breed conservation is not known. Moreover, the spread of zebu cattle from Indus valley to different parts of Island Southeast Asia (ISEA) is not properly understood. Here, we report the genetic diversity, population structure of Andaman cattle and their evolution in the context of epicentre of zebu domestication and ISEA. High genetic diversity in complete mitochondrial D-loop sequences indicated the ability of the breed to withstand impending climate change. Total 81 haplotypes were detected and all of them except three belonged to Bos indicus. The presence of taurine haplotypes in Andaman cattle indicate introgression by European-derived cattle. A poor phylogenetic signal of Andaman cattle with genetic affinities with cattle of Indian subcontinent and ISEA was observed. The poor phylogenetic structure may be due to multidirectional gene flow from Indian subcontinent and ISEA, with which Andaman shares a close cultural and trade relationship from Neolithic age. We hypothesize that Andaman cattle is the outcome of Neolithic diffusion from centre of zebu domestication along with multidirectional commercial exchange between Indian subcontinent and ISEA.

Origin, genetic diversity and evolution of Andaman local duck, a native duck germplasm of an insular region of India

Domestic ducks are of paramount importance as a cheap source of protein in rural India. Andaman local duck (ALD) is an indigenous avian genetic resource of Andaman and Nicobar islands (ANI) and is mainly distributed in Middle and Northern parts of these islands. Negligence has brought this breed on the edge of extinction necessitating immediate conservation efforts. Here, we report the genetic diversity, population structure and matrilineal genetic root of ALD. Partial mtDNA D-loop sequences were analyzed in 71 ALD samples and analysis revealed 19 polymorphic sites and 13 haplotypes. Estimated haplotype (Hd ± SD) and nucleotide diversity (π ± SD) were 0.881 ± 0.017 and 0.00897 ± 0.00078 respectively. The high genetic diversity of ALD indicates introgression of genetic material from other local duck breeds. In addition, it can be postulated that ALD bearing high genetic diversity has strong ability to adapt to environmental changes and can withstand impending climate change. Phylogenetic and network analysis indicate that ALD falls under Eurasian clade of mallard and ALD forms three clusters; one cluster is phylogenetically close to Southeast Asian countries, one close to Southern part of mainland India and the third one forms an independent cluster. Therefore, ALD might have migrated either from Southeast Asian countries which enjoy a close cultural bondage with ANI from time immemorial or from Southern part of India. The independent cluster may have evolved locally in these islands and natural selection pressure imposed by environmental conditions might be the driving force for evaluation of these duck haplotypes; which mimics Darwin's theory of natural selection. The results of the study will be beneficial for formulating future breeding programme and conservation strategy towards sustainable development of the duck breed.

Ancient hybridization and mtDNA introgression behind current paternal leakage and heteroplasmy in hybrid zones

Hybridization between heterospecific individuals has been documented as playing a direct role in promoting paternal leakage and mitochondrial heteroplasmy in both natural populations and laboratory conditions, by relaxing the egg-sperm recognition mechanisms. Here, we tested the hypothesis that hybridization can lead to mtDNA heteroplasmy also indirectly via mtDNA introgression. By using a phylogenetic approach, we showed in two reproductively isolated beetle species, Ochthebius quadricollis and O. urbanelliae, that past mtDNA introgression occurred between them in sympatric populations. Then, by developing a multiplex allele-specific PCR assay, we showed the presence of heteroplasmic individuals and argue that their origin was through paternal leakage following mating between mtDNA-introgressed and pure conspecific individuals. Our results highlight that mtDNA introgression can contribute to promote paternal leakage, generating genetic novelty in a way that has been overlooked to date. Furthermore, they highlight that the frequency and distribution of mtDNA heteroplasmy can be deeply underestimated in natural populations, as i) the commonly used PCR-Sanger sequencing approach can fail to detect mitochondrial heteroplasmy, and ii) specific studies aimed at searching for it in populations where mtDNA-introgressed and pure individuals co-occur remain scarce, despite the fact that mtDNA introgression has been widely documented in several taxa and populations.

Transcriptome of larvae representing the Rhipicephalus sanguineus complex

Rhipicephalus sanguineus sensu lato (Ixodida: Ixodidae) is possibly the most widespread tick species worldwide, responsible for transmitting several vector-borne pathogens of medical and veterinary importance. Here, we explore the transcriptome of R. sanguineus s.l. larvae (Putignano strain). We sequenced total RNA from R. sanguineus s.l. larvae. A total of 15,566,986 short paired-end reads were de novo-assembled into 33,396 transcripts and then annotated and analyzed. Particular attention was paid to transcripts putatively encoding ATP-binding proteins, due to their importance as mechanisms of detoxification and acaricide resistance. Additionally, microsatellite loci were investigated, as these are useful markers for population genetic studies. The present data and analyses provide a comprehensive transcriptomic resource for R. sanguineus. The results presented here will aid further genetic and genomic studies of this important tick species.

Evolution of premating reproductive isolation among conspecific populations of the sea rock-pool beetle Ochthebius urbanelliae driven by reinforcing natural selection

How natural selection might be involved in speciation remains a fundamental question in evolutionary biology. When two or more species co-occur in the same areas, natural selection may favor divergence in mating traits. By acting in sympatric but not allopatric populations, natural selection can also affect mate choice within species and ultimately initiate speciation among conspecific populations. Here, we address this potential effect in the sea rock-pool beetles Ochthebius quadricollis and O. urbanelliae. The two species, which inhabit the Mediterranean coasts, co-occurr syntopically in an area along the Italian Tyrrhenian coast and completed reproductive isolation by reinforcement. In this article, through mating trials under laboratory conditions between conspecific populations, we found in O. quadricollis no deviations from random mating. Conversely, in O. urbanelliae, we found a clear pattern of premating isolation between the reinforced populations sympatric with O. quadricollis and those nonreinforced allopatric. This pattern is consistent with the view that natural selection, which completed the reproductive isolation between the two species in sympatry, led incidentally also to partial premating reproductive isolation (I(PSI) estimator from 0.683 to 0.792) between conspecific populations of O. urbanelliae. This case study supports an until recently underappreciated role of natural selection resulting from species interactions in initiating speciation.

Evidence of reinforcement of premating isolation between two species of the genus Ochthebius (Coleoptera: Hydraenidae)

The increase in premating reproductive isolation between recently diverged and potentially interbreeding taxa resulting from selection against hybridization (reinforcement) is one of the most contentious issues in evolutionary biology. After many years of debate, its plausibility under various conditions has been shown by theoretical studies and some cases have been documented. At present, interest is arising about the frequency and importance of reinforcement in nature. Ochthebius quadricollis and Ochthebius sp. A are two hydraenid beetles inhabiting marine rock pools in the Mediterranean basin. By molecular analysis of a contact zone between the two species along the Italian Tyrrhenian coast, full reproductive isolation between the two species was evidenced. However, the finding of introgressed specimens at some diagnostic loci suggested that gene flow occurred in the past but then ceased. In this article, by analyzing species composition of mating couples collected in sympatric localities, we show the existence of strong assortative mating between the two species in nature. In laboratory multiple-choice mating trials, sympatric populations showed greater assortative mating than allopatric populations. Reinforcement is suggested as the most parsimonious hypothesis to explain the evolution of discriminative mate recognition systems occurring among O. quadricollis and Ochthebius sp. A under sympatric, but not allopatric, populations.

Multilocus test for introgression between the cactophilic species Drosophila mojavensis and Drosophila arizonae

Information obtained from laboratory studies regarding the efficacy of barriers to gene flow (reproductive isolation) between species is often incomplete or misleading, so detailed genetic analyses are needed to determine whether hybridization and introgression occur in nature. Previous laboratory studies of the cactophilic species Drosophila mojavensis and Drosophila arizonae suggest that reproductive isolation is incomplete and that gene flow may occur in sympatry. We sampled 18 nuclear and one mitochondrial loci from multiple populations of D. arizonae and D. mojavensis to test for the signature of recent or historic gene flow between these two species. We located chromosomal regions that were inverted between these species and analyzed those regions independently of others. Statistical tests for introgression using all loci or only collinear loci failed to reject expectations of an isolation model. Further tests using average nucleotide differences between species and phylogenetic analyses also failed to find support for introgression between D. mojavensis and D. arizonae. Additional ecological and behavioral studies of these species in their natural habitats are required to explain why the signature of gene flow was not detected at the DNA sequence level in populations when laboratory studies suggest such gene flow should be possible.