Work in the MacManes lab centers around the basic theme of adaptation. The systems we use to better understand the eco-evolutionary forces driving pattern are varied, but 2 main systems form the core of the lab.

1. Adaptation to Deserts: Understanding the evolution of adaptive traits is one of the primary goals in evolutionary biology, with the study of the relationships between fitness and phenotype often providing deep insight into the processes that underlie adaptive phenotypes. Systems in which the mechanisms (e.g., the genotype) linking fitness to phenotype are tractable are uncommon, and deserve continued study. The proposed research of one such system leverages a deep understanding of desert ecology against modern whole genome sequencing and population genomics. Specifically, we will study the evolution of adaptation to deserts using wild animals in a natural setting, then perform a classic common garden experiment using wild animals from highly divergent populations taken into captivity to perform carefully controlled experiments of gene expression and to determine fitness. This work integrates multiple disciplines including evolutionary genomics, computational biology, and ecological physiology. Gaining a deeper understanding of the genome architecture of desert adaptation (e.g., osmoregulation and water metabolism) has important and broad impacts, with implications for studies of conservation, climate change, and human health (for instance, kidney disease).
2. Neurogenomics of parental care in the rock dove: With Becca Calisi Becoming a parent causes big changes in behavior. For animals that exhibit parental care, the successful rearing of offspring involves a shift from aggressive and sexual behaviors to caring and nurturing ones, but what in the brain mediates this transition? How flexible are these changes in response to unpredictable environmental perturbations, and how is behavior altered because of them? In a rapidly changing world, understanding how the environment affects the brain and how, in turn, the brain affects the behavioral transition into parental care will shed light on how changes in environment can ultimately affect fitness. In an interdisciplinary collaboration, Dr. Calisi-Rodríguez (Barnard College) and Dr. MacManes (University of New Hampshire) will characterize changes the entire transcriptome and specific proteomic levels in the brains of male and female rock doves (Columba livia) during the transition into parental care and, via environmental manipulations, discover the cause of these changes
3. Color Polymorphism in Dendrobatid frogs: With collaborators (Rasmus Nielsen, Kyle Summers). The evolution of color pattern diversity in the context of mimicry has been a key focus of theoretical and empirical attention in evolutionary biology, yet knowledge of the genetic basis of this diversity remains limited. Most work on this topic has focused on a small number of systems (e.g. Heliconius butterflies), limiting the generality of inferences. Recent progress makes it feasible to elucidate the genetic basis of color pattern diversity and evolution in non-model organisms. We propose an integrative approach to investigate the genetic basis and population genomic processes underlying color pattern divergence in the context of mimicry in the Peruvian mimic poison frog, Ranitomeya imitator. We will combine the efforts of three research groups with complementary skills and realms of knowledge to elucidate the genetic and molecular evolutionary underpinnings of color pattern divergence in a this vertebrate mimetic radiation. Dr. Summers’ group has been studying this color pattern radiation in the field in Peru for over a decade. Dr. MacManes has developed substantial genomic resources for this system, and is an expert in de novo transcriptome assembly and functional genomic analyses using next-generation sequencing data. Dr. Nielsen and his research group are pioneers in the development of new methods in population genomics, particularly in the area of detecting selection and mapping adaptive trait loci.
4. Superb starling (Lamprotornis superbus) genome sequencing project: With Dustin Rubenstein and the NY Genome Center
5. Soft-shell clam (Mya arenaria) genome sequencing project: With Charles Walker and Michael Lesser.
6. Other projects: I am happy to collaborate with researchers or advise students interested in using high throughput sequencing to understand the pattern or process of evolutionary change. Please contact me!