Research

Selections in molecular and phenotypic evolution, Zhang Lab, Department of Ecology and Evolutionary Biology, University of Michigan, 09/05/2019 - present

During my PhD studies, I explored selections in molecular and phenotypic evolution based on large datasets of genotypes and phenotypes. (1) I challenged the neutral theory of molecular evolution and proposed a quasi-neutral model that reconciles the abundance of beneficial mutations with seemingly neutral, long-term molecular evolution. (2) I delved into the genetics of human same-sex sexual behavior (SSB), revealing a shift in its genetic maintenance due to widespread contraception. I established a genetic distinction between bisexual behavior (BSB) and exclusive SSB (eSSB) and discovered that alleles associated with male BSB are reproductively advantageous, whereas those associated with eSSB are reproductively disadvantageous. (3) I explored the heritability of human sex ratio at birth, using biobanks to identify genetic variants influencing sex ratio and evaluating Fisher’s principlein explaining sex ratio evolution. Collectively, these studies challenge existing paradigms of molecular and phenotypic evolution and provide fresh perspectives on the role of selection.

Lepidoptera LW opsin evolution diurnal and nocturnal species, Pierce Lab, Department of Organismic and Evolutionary Biology, Harvard University, 10/06/2017-04/01/2018

In this project, I studied the evolution of opsin genes with the goal of comparing spectral sensitivities between diurnal and nocturnal species of Lepidoptera. Under the supervision of a postdoc, we screened long wavelength opsins from 10 different species of moths and butterflies, and made expression constructs to transfect them into cell lines for future functional tests. For the bioinformatic work, we mined databases of insect genomes to look for opsin motifs. This training enabled me to develop a script to automate the process of finding potential opsin orthologs from public genome and proteome datasets even without existing annotation.

Phylogeny of Ambystomatidae project, Shaffer Lab, Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 07/09/2017-09/15/2017

This project is about using targeted gene enrichment method to reveal the phylogeny of Ambystomatidae (a salamander family). We used the RNA probes for 5237 exon genes, totaling about 3.5 million bp. I selected and picked representative samples, and performed DNA extraction and library preparation for 190 samples (4-6 per species). During this time, I learned how to process NGS data and perform SNP calling. I didn’treceivet the sequenig results before I left, so the postdoc in the lab took over the project. This work would eventually present the most comprehensive phylogeny of Ambystomatidae.

Hymenoptera Taxonomy & Phylogeny Practice, Xuexin Chen Lab, the Institute of Insect sciences, Zhejiang University, 11/01/2015-07/2017

1) I studied the morphology, taxonomy and basic biology about Hymenoptera on the family level, and further studied the taxonomy of the family Braconidae. I observed specimens under the stereo microscope, and classified them by checking the keys.

2) I learned how to conduct phylogenetic analysis, and became familiar with common phylogenetic software such as MrBayes, RAxML, PAML, BEAST. With the help of a doctoral student, I began my first project investigating the influence of parasitic behavior and sociality on mitochondrial DNA evolution of Hymenoptera. We collected published mtDNA coding sequences of 42 species from 23 families, then applied PAML branch model to infer the shift of dN/dS ratio between social and non-social, as well as parasitic and non-parasitic groups.