Evolution of Ecosystems


Watch your step! Exploring the evolution of robust joint-level control

Craig McGowan Ph.D.

Many animals demonstrate remarkable feats of locomotive agility, reaction, and maneuvering; the ability to jump, turn, and accelerate has direct implications for survival. Further, they exhibit these behaviors cross a wide range of substrates (loose sand, soil, rocks) to which their neuromuscular systems must respond almost instantaneously during locomotion. At the lowest level, intrinsic properties of muscles, tendons and bones contribute stabilizing forces, producing a joint-level control mechanism that is extremely robust even to large perturbations. In the proposed multidisciplinary project, we integrate computational evolution, detailed neuromuscular models, and experiments with 3D-printed robotic joints in order to explore the evolution of robust joint-level control. Our basic approach is to evolve joint behaviors and morphological characteristics in 3D animats using an abstract neuromuscular model called digital muscles, then map the results into detailed models of both biological and robotic systems. In doing so, this project will help to answer fundamental questions in biology and improve the design of engineered systems, including all-terrain autonomous robots and robotic prostheses.


Spread of antibiotic resistance genes through spreading dairy cow manure and wastewater biosolids?

Eva Top Ph.D.

The high abundance of multi-drug resistant bacteria observed today is the result of years of exposure of bacteria to antibiotics and other antimicrobial products in humans, animals, and the environment. This has created a selective pressure that favors resistant bacteria over their susceptible counterparts. Recent studies indicate that the alarming rise in bacteria that are resistant to multiple antibiotics is largely caused by horizontal transfer of antibiotic resistance genes (ARG) by means of plasmids. Plasmids bearing multiple ARGs are not uncommon. Over the past decade it has become quite clear that the spreading of manure and sewage sludge (biosolids) as fertilizer on agricultural land contributes to ARG dissemination in soil. Less understood is the potential role of resistance plasmids and heavy metals in this resistance spread. Copper and other metals have been shown to co-select for antibiotic resistance since the corresponding resistance genes are often found on the same self-transferable plasmids. Two specific questions are being addressed with regard to the effects of spreading manure from Southern Idaho dairy farms and sewage sludge on the abundance and spread of ARGs in manure-treated soils: (i) Does manure or sludge treatment result in an increase in the relative abundance of antibiotic resistance genes soil and soil leachate? (ii) Can plasmids that encode Cu resistance be detected, and how often do they also code for antibiotic resistance?  (In collaboration with Drs. Matthew Morra, Inna Popova, Amber Moore, John Hammel, and James Nagler).


Microbial Diversity and Ecology

James A. Foster Ph.D.

We develop algorithmic and statistical techniques and tools with which to infer the makeup of a microbial community from the total DNA in a sample. We are particularly interested in microbial communities in the human microbiome, but our results generalize to any microbial ecosystem. Our goal is to understand why different ecosystems host the communities they do, and how those communities change as they and their ecosystems evolve.


Conservation genomic applications: hybridization and introgression in trout

Paul Hohenlohe Ph.D.

Genomic technology promises to revolutionize many areas of biology, including conservation and management of threatened taxa.  Westslope cutthroat trout are threatened by hybridization with introduced rainbow trout across their range.  With collaborators at the University of Montana, we are studying why certain regions of the genome show elevated introgression – higher frequencies of rainbow trout alleles compared to the rest of the genome – even though hybrids in general are selected against.  We are also using genomic techniques to rapidly develop large numbers of genetic markers in multiple trout populations to allow managers to efficiently genotype large numbers of individuals.


Emergence, transmission, and evolution of Tasmanian devil facial tumor disease

Paul Hohenlohe Ph.D., Sarah Hendricks

The iconic Tasmanian devil is threatened with extinction from a unique transmissible cancer, which has caused over 90% declines in many populations and will have spread across the species range within a few years.  With collaborators at Washington State University and multiple institutions in Australia, we are using a range of tools to study the coevolution and infection dynamics of this disease.  We are using next-generation DNA sequencing of both devil and tumor samples to test for signatures of selection at the genetic level.  One goal is to identify a panel of genetic markers that can be used to predict susceptibility and disease transmission dynamics in yet-uninfected populations.


Predicting Cryptic Diversity using Ecosystem Phyloeography

Jack Sullivan Ph.D., Dave Tank Ph.D., Bryan Carstens Ph.D.

The discovery of cryptic biodiversity is a major focus of systematics, but has historically been overlooked in comparison to the estimation of phylogenetic relationships. Recently introduced methods for species delimitation approach the discovery of cryptic diversity on a species-by-species basis, and thus assume detailed phylogeographic analysis of each species as a starting point. Here, we are developing an ecosystem framework for predicting cryptic diversity in unstudied taxa from features shared by taxa that have been shown to harbor cryptic diversity. The temperate rainforests of the Pacific Northwest of North America serve as the model system for this comparative phylogeographic work. These forests are rich in endemics and harbor the potential for substantial cryptic diversity, and the disjunction of conspecific populations or putative sister-species pairs between Pacific coastal and interior Rocky Mountain habitats presents clear hypotheses regarding this potential: either pre-Pleistocene vicariance, which predicts high cryptic diversity, or post-Pleistocene dispersal where we predict a lack of cryptic diversity. 


A tractable animal model for experimental viral evolution

Holly Wichman Ph.D., Tanya Miura Ph.D. and Jim Bull Ph.D.

In an age of synthetic biology, experimental models of viral evolution are increasingly important for testing the impact of interventions on virulence evolution, the potential for evolution to overcome transgenic modifications of genomes, the evolutionary consequences of live vaccine designs, and the population dynamics of released synthetic organisms. Current experimental models are limited largely to bacteriophages, plant viruses and animal viruses in cell culture.  We are developing viruses of Drosophila as a system that provides a eukaryotic, multicellular host that is a model for studies of the innate immune system; well-studied host genetics; and the capacity for large host populations with short generation time. The aim is both to develop the system for our own future research and to make the resources available for others.


Evolving Robots in "The Cloud"

Robert Heckendorn Ph.D., and Terence Soule Ph.D.

Swarms of small robots offer many advantages over single larger robots. Like bees and ants they offer a robust solution to sensory input, control, and manipulation of the environment. One approach to programming large swarms of robots is to use evolutionary techniques that evolve control software across all robots in the swarm. Specifically, we are exploring geographically and environmentally dispersed subpopulations of robots that share the genetics of the their behavior in the cloud. This is similar to a species scattered over an environment that varies in a slow continuous manner with geography. Visit project website here.


Community phylogenetics across scales and systems: investigating the generation, maintenance, and loss of biodiversity across spatial, taxonomic, and temporal scales

Hannah Marx and David Tank Ph.D.

Evolutionary processes that drive the patterns of diversity that we observe in nature are complex and depend largely on the scale of the community. We are interested in understanding how species diversity is generated, maintained, and lost at different spatial, taxonomic, and temporal scales using bioinformatic, phylogenetic, and genomic techniques to identify evolutionary patterns, along side modeling and simulations to infer ecological processes. Collaborations across IBEST allow us to work on communities ranging from invasive plants on oceanic islands, to alpine floras and vaginal microbiomes. By exploring similar patterns across spatial and temporal scales, we hope to improve our understanding of the relative importance of the abiotic and biotic drivers of community assembly, as well as the generation and maintenance of biodiversity.


Why hop? Understanding morphology, mechanics, and natural selection in the evolution of bipedal hopping

Craig McGowan Ph.D. and Anne Gutmann Ph.D.

The goal of this project is to understand why animals as diverse as kangaroos, wallabies, kangaroo rats, and jerboas all hop. These animals span a surprisingly wide range of body sizes and habitats, but all have the same basic leg design and use a two-legged hopping gait. An interdisciplinary approach that integrates biomechanics, computation, and physics-based simulation is used to understand how selective pressures shape the evolution of leg design and gait. This project provides funding for a female postdoctoral fellow, research and training opportunities for undergraduate students from underrepresented populations, and education and outreach programs for the community. 


Phenotypic plasticity and evolution of life history in Chinook salmon

Brian Kennedy Ph.D. and Jens Hegg

The process of migration for salmon reflects an adaptive balance between fecundity and mortality. Fast juvenile growth conditions and high late summer temperatures in their rearing habitat appears to have historically placed selective pressure on outmigration at young ages for fall Chinook salmon in the Snake River. Human impacts have changed the temperature and flow regime of the river in many ways and consequently the prevailing outmigration strategies. Our work explores these changes of evolutionary significance in migration timing and the selective pressures that may be affecting behaviors in a complex habitat. Using a life-long record of radiogenic isotopes in calcified tissues, we reconstruct detailed spatially explicit movements of juvenile salmon and using state-dependent modeling we are relating the conditions experienced at each life stage to the fitness of downstream movement decisions. Linking optimal migratory behavior at any location and time, given the current and past growth conditions a fish has experienced, allows us to investigate the relative fitness of each migration strategy across a changing landscape.


Distinguishing environmental and genetic drivers of central life-history decisions in Oncorhynchus mykiss

Brian Kennedy Ph.D. and Marius Myrvold Ph.D.

Individual behavior results from the interplay between an organism’s genotype and the environment it inhabits. Whereas the genotype outlines the range and probability of possible behavior, ambient environmental conditions can influence which decisions are actually made. Organisms that display a range of distinct life-history characteristics hence provide a unique opportunity to investigate the causal connections between genotype-environment interactions.  Oncorhynchus mykiss individuals exhibit both a resident form (rainbow trout) and an anadromous form (steelhead). An ongoing long term study in Idaho (2008 - 2015), which has quantified the fates of individually tagged O. mykiss finds that survival and life-history decisions are influenced by a combination of environmental factors, individual phenotypes and biotic interactions. Proposed research would combine genomic and isotopic approaches to distinguish genetic and environmental drivers of the migration behaviors of individuals. The work would seek an improved understanding the extent to which changes in climate are likely to influence the distribution, dynamics and life-history diversity in wild populations.