Sympatric lineage divergence in cryptic Neotropical sweat bees (Hymenoptera: Halictidae: Lasioglossum)

Diversity of Parasitoid Wasps and Comparison of Sampling Strategies in Rice Fields Using Metabarcoding

A comprehensive and precise evaluation of Arthropoda diversity in agricultural landscapes can enhance biological pest control strategies. We used Malaise traps and sweep nets to collect insects from three double-cropping paddy fields. DNA was extracted from the ethanol preservative of the Malaise traps and from tissue samples of selected parasitoid wasps. This was followed by amplification using DNA barcoding primers to prepare high-throughput sequencing libraries. We annotated a total of 4956 operational taxonomic units (OTUs), encompassing 174 genera and 32 families of parasitoid wasps. The ethanol filter method efficiently captured a wide range of information. However, the method has low resolution and may result in a reduced estimate of species abundance. Additional insect species were also identified in the parasitoid samples. This suggests that high throughput sequencing from adult parasitoid wasps can also detect host species, enabling a better understanding of host species and providing insights into food webs.

The effect of landscape and human settlement on the genetic differentiation and presence of Paragonimus species in Mesoamerica

Foodborne diseases are a neglected research area, and despite the existence of many tools for diagnosis and genetic studies, very little is known about the effect of the landscape on the genetic diversity and presence of parasites. One of these foodborne disease is paragonimiasis, caused by trematodes of the genus Paragonimus, which is responsible for a high number of infections in humans and wild animals. The main Paragonimus sp reported in Mesoamerica is Paragonimus mexicanus, yet there are doubts about its correct identification as a unique species throughout the region. This, together with a lack of detailed knowledge about their ecology, evolution and differentiation, may complicate the implementation of control strategies across the Mesoamerican region. We had the goal of delimiting the species of P. mexicanus found throughout Mesoamerica and determining the effect of landscape and geology on the diversity and presence of the parasite. We found support for the delimitation of five genetic groups. The genetic differentiation among these groups was positively affected by elevation and the isolation of river basins, while the parasite's presence was affected negatively only by the presence of human settlements. These results suggest that areas with lower elevation, connected rivers basins, and an absence of human settlements have low genetic differentiation and high P. mexicanus presence, which may increase the risk of Paragonimus infection. These demonstrate the importance of accurate species delimitation and consideration of the effect of landscape on Paragonimus in the proposal of adequate control strategies. However, other landscape variables cannot be discarded, including temperature, rainfall regime, and spatial scale (local, landscape and regional). These additional variables were not explored here, and should be considered in future studies.

Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis)

In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle Frogs-a group that is widespread, phenotypically conserved, and exhibits high levels of geographically-based genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specific ways in which gene flow can cause overestimations of species diversity: (1) admixed populations can be inferred as distinct lineages characterized by long branches in phylograms; and (2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. We demonstrate that the relationship between mitochondrial and genome-wide nuclear p-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-by-distance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely-adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow.