Investigating the population structure and genomic architectures underpinning locally adapted burying beetles (Nicrophorus nepalensis)
The burying beetle metapopulation in Northern Taiwan is locally adapted to different mountain elevations, such that high mountain individuals breed year-long whereas low mountain individuals only breed during winter. Using low depth of coverage genomic data of over 100 individuals sampled across elevational gradient, I illustrated that the entire metapopulation in northern Taiwan is panmictic. In contrast to the local-adaptation-due-to-physical-isolation scenario, this metapopulation showed minimum levels of genomic differentiation. I also discovered a large chromosomal inversion, the frequency of which varies by elevation, but its relation with the locally adapted phenotypes is still an enigma. Evidence suggests that not only environmental selection, buts also the genomic architecture as well as organismal behaviors (i.e. willingness to cooperate and breeding season) are intertwined to shape the development of this inversion. This is part of a larger project from Dr. Sheng-feng Shen's lab in Academia Sinica. More later!
This figure shows Fst between individuals identified as homozygous non-inverted and those identified as homozygous-inverted by split reads. Highlighted between red, dotted lines is the speculative inversion region, spanning over 12 Mbp.
Resolving the phylogeny of squat lobsters (Galatheoidea), with a focus on the two Pleuroncodes species
Recent applications of genomic data bring uncertainty into the once stable phylogeny of the Galatheoidea superfamily, known as the squat lobsters. Using CO1 and 16S sequences, I reconstructed the phylogeny of the superfamily. Moreover, I used haplotype data of over 40+ tuna crabs (P. monodon and P. planipes) to specifically investigate their classification as two separate species. Haplotype relationships, along with average pairwise genetic distances show that the two species should actually be one. Currently I am incorporating phenotypic and geographic data to finish the story and aiming for a publication.
This is a reconstruction of the superfamily phylogeny. For most pats, it is consistent with published phylogeny Ahyong et al. (2011). However, it is concluded, with a high support that the two Pleuroncodes species are from one cluster, which is a sister cluster with Munida quadrispina.
Investigating the relationships between the biological assemblage and environmental measurements in methane seep ecosystems
Methane seep ecosystems form around methane leaked from earth's crust and harbor an abundance of biodiversity (micro- and macrofauna), which in turn plays significant roles in modulating carbon cycling in the deep sea. However, these deep-sea ecosystems are vulnerable to human disturbances and the ongoing climate change. Relying on pushcores collected from sediment and contemporary environmental data, I investigated the relationships between biological measurements (including biomass, Shannon's biodiversity etc.) and environmental measurements (including seep activity, salinity, oxygen concentration, temperature etc.), using generalized additive models (GAMs). I determined methane seep activity as the most predominant factor dictating all aspects of biological measurements.
See manuscripts below for more information!