Fragile Y Hypothesis

Chromosomal sex determination is phylogenetically widespread, having arisen independently in many lineages. Decades of theoretical work provide predictions about sex chromosome differentiation that are well supported by observations in both XY and ZW systems. However, the phylogenetic scope of previous work gives us a limited understanding of the pace of sex chromosome gain and loss and why Y or W chromosomes are more often lost in some lineages than others, creating XO or ZO systems. Contrary to our initial expectations, we find that highly degenerated Y chromosomes of many members of the Coleoptera suborder Polyphaga are rarely lost and that cases of Y chromosome loss are strongly associated with chiasmatic segregation during male meiosis. We propose the "Fragile Y Hypothesis" that recurrent selection to reduce recombination between the X and Y chromosome leads to the evolution of a small pseudoautosomal region, which, in taxa that require XY chiasmata for proper segregation during meiosis, increases the probability of aneuploid gamete production, with Y chromosome loss. This hypothesis predicts that taxa that evolve achiasmatic segregation during male meiosis will rarely lose the Y chromosome.

Genetic Architecture

The pace and direction of evolution are governed by the genetic architecture of trait variation. Evolutionary biologists have disagreed about whether genes can be considered to act in isolation, or in the context of their genetic background (Fisher Wright debate). Line cross analysis (LCA) estimates genetic architecture parameters conditional on the best model chosen from a vast model space using relatively few line means and ignores uncertainty in model choice. To address these issues, we introduced an information theoretic approach to LCA, which comprehensively assesses the potential model space, quantifies model selection uncertainty, and uses model weighted averaging to estimate composite genetic effects accurately. Using simulated data and previously published LCA studies we have shown the utility of our approach to define the components of complex genetic architectures. Our analysis of 20+ previously published datasets also shows that traditional approaches have underestimated the importance of epistasis.

Insect Karyotypes

Insects exhibit variation in both chromosome number and sex chromosome systems. Insect karyotypes have been an important source of data for both taxonomic and basic evolutionary biology research. Unfortunately, this data has always been scattered among journals and dissertations that are not accessible without subscriptions. We created the Tree of Sex Database to make this data open and available to all researchers. We curate the insect portion of this database that currently has over 15,000 records and has proven to be a valuable resource to explore and test ideas about the evolution of high-level genome evolution. Recently we published a synthesis of this vast dataset and uncovered many interesting patterns and avenues for future investigations.

Chromosome Number

It has long been thought that in Eusocial insect selection to increase genetic diversity within a colony should indirectly select for increases in the number of chromosomes. To test this long-standing hypothesis, we investigated the relationship between eusociality and chromosome number across Hymenoptera. We found that solitary and social Hymenoptera do not have significantly different numbers of chromosomes. However, we did find that chromosome number evolves more quickly in social than solitary Hymenoptera. It remains unclear whether variable selection pressure or drift are responsible for this difference.

Lab Meetings

Teaching

Experimental Design Course: This course is intended to provide a foundation in the proper design of scientific research projects in the field of biology. A wide range of biological experiments are covered, and each type of experiment is explored with an eye toward choosing the appropriate statistical technique for analysis. By the end of the course, successful students will be able to design biological studies that are statistically tractable and perform basic statistical analyses using the programming language R.

R for biologists seminar: R is currently an essential tool for most evolutionary biologists. This seminar includes tutorials and example datasets for many basic analyses in R that are commonly encountered in ecology and evolution. The seminar starts off with the most basic steps (installation) so no prior experience is needed to use these exercises.

Foundations of evolutionary biology: An understanding of the foundational ideas that the modern synthesis of evolutionary biology is built on is essential for asking intelligent questions and understanding how your research fits into a larger understanding of life. I offered a foundations of evolutionary biology seminar course for graduate students that provided a structured environment to discuss some of the most important papers in evolutionary biology. This website contains a schedule and PDF files for all of the readings in this course.

GitHub software repository: I do most all of my development and analyses in public repositories.

GitHub Pages Tutorial

R packages

chromePlus is a collection of R functions generate markov models appropriate for the evolution of chromosome number and binary traits. These models once constructed can be fit via maximum likelihood or Bayesian MCMC methods avaialable in the package diversitree.

micRocounter is an R package to identify all 2-6mer repeates in a genome assembly. It has been optimized for speed and can calculate statitics for larger genomes in a manner of minutes.

evobiR is a collection of R functions that I have developed for different projects. The functions in this package can be loosely organized into either analysis of empirical data, simulation functions, or those created primarily for didactic purposes. A vignette demonstrating its use is available. Instructions for installing the latest version from github are available here.

The package SAGA2 is a collection functions to ease and hopefully improve the quality of line cross analysis of genetic architecture. The overall goal is to allow for an easy and straightforward implementation of model averaged analysis using AICc. A vignette demonstrating its use is available. Instructions for installing the latest version from github are available here.

Databases

Karyotype Databases: Karyotypes are a highly variable and complex trait that offers an opportunity to detect changes in genome organization, uncover phylogenetic history, and distinguish cryptic species. The current databases contains more than 8,000 records for amphibians, coleoptera, and polyneoptera. The databases allows users to select the records that they wish to retrieve based on either taxonomy or trait values and builds customized tables of the results in a new window.

The Tree of Sex Database: this is a product of a working group sponsored by the National Evolutionary Synthesis Center which sought to compile all information on sex determination systems across the tree of life. To date, we have collected over 30K records including more than 10K invertebrates. Much like the Coleoptera Karyotype Database, our goal is to make this data widely available allowing researchers across the globe to use data that was previously difficult to collect.

Other

I recently built a cluster consisting of 26 Raspberry Pi 4Bs. I have assembled some notes to guide anyone else through this process

I have assembled some links to graduate student funding opportunities for graduate students.

We believe strongly in the importance of creating an inclusive supportive environment for all lab members. To achieve this we ask all lab members to sign a document that makes explicit our expectations for all lab members. This document includes the following statements:

• I will participate in weekly lab meetings and journal clubs.
• I will attend departmental and IDP seminars.
• I will prepare for our regular progress/pitfalls meetings
• I will proof-read manuscripts from other lab members.
• I will maintain a set of lab notes, including directories of data, annotated codes and versions, detailed methods. Lab notes will be sufficient to reproduce results without additional instructions.
• I will participate in general lab responsibilities (beetle maintenance, maintain common areas, community outreach events).
• As a graduate student I will be available in the lab/office most days from 9:00 – 17:00.
• As an undergraduate researcher I devote a minimum of 10 hours a week to research and I will make a two semester commitment to work in the lab.
• I value diversity in intellectual background, race, sex, and identity.
• I will treat all others with respect and dignity.