Evolutionary Genetics

Bin S. He Ph.D.

Current
Bin
S.
He
Ph.D.
Assistant Professor
Biology
Address
336
Biology Building East
Research
Research Focus: 

Evolution of Stress Response

Our lab is broadly interested in the evolution of gene regulation. An astounding discovery from sequencing genomes is how organisms as different as human and fly, or even yeast, share a significant amount of their genes. This suggests, and has been experimentally shown that, changes in how genes are regulated are a major contributor to phenotypic evolution and adaptation. We study gene regulatory evolution in the context of stress response. Essential for survival, stress response must adapt as species evolve and encounter new challenges. So far this has been understudied and should deserve our attention both for basic understanding of the evolutionary principals, and also for disease and health purposes. One such example is the adaptation of commensal yeast species to the human host, an environment that poses very different stress profiles from what is experienced by their free-living relatives. To learn more about our research, click the button below.

Faculty affiliations: 

Maurine Neiman Ph.D.

Current
Maurine
Neiman
Ph.D.
Associate Professor
Biology
Address
324B
Biology Building
324
BB
Research
Research Focus: 
Evolution of sexual reproduction and ploidy level

WHY IS SEXUAL REPRODUCTION SO COMMON?

Sexual females produce both sons and daughters, while asexual females make only daughters. Because only females produce offspring, this "cost of males" predicts that sex should be rare because asexual females will leave many more descendants than will sexual females. In reality, however, sex predominates.

Why sex is so common despite its costs remains unclear, and is considered one of the most important unanswered questions in evolutionary biology. The central importance of sexual reproduction to biology means that solving the sex problem will require insights from all levels from biological organization. Accordingly, our approach to studying sex is very diverse, focused in evolutionary genetics and genomics but also including physiology, ecology, and behavior.

Because sex is distinguished from asexual reproduction by the production of genetically variable offspring, a deeper understanding of the benefits of sex will help illuminate the value of preserving genetic diversity within and among populations, species, and ecological communities. More broadly, our research program is relevant to scientists who use our snail study system as a model for ecotoxicology, host-parasite coevolution, and the causes and consequences of biological invasions. Our lab group is also very committed to training, mentoring, and community engagement, and we are involved in a variety of such efforts, from an award-winning partnership with the National Center for Science Education to pilot a grassroots effort to support science booster clubs to regular collaborations with 10th grade Biology students at a local high school and the development and testing of a genomics module for a national high school computer science curriculum to our central role in organizing the annual Iowa City Darwin Day celebration.

Faculty affiliations: 

Albert J Erives PhD

Current
Albert
J
Erives
PhD
Associate Professor
Biology
Research area(s): 
Bioinformatics, Developmental Genetics, Evolutionary Genetics, Gene Expression and Regulation
Address
424A
BB
424
BB
Research
Research Focus: 

The Genetics of Eukaryotic Transcriptional Enhancers

Transcriptional enhancers are DNA sequences that specify inducible, spatiotemporal patterns of gene expression at most gene loci. Several complementary results from genomic studies have shown that the majority of functional sites in a genome correspond to transcriptional enhancer sequences, thus underscoring their importance for understanding basic physiology. However, while transcriptional enhancers represent a major class of regulatory DNAs in eukaryotic genomes, the entire set of sequences that are necessary and sufficient for constructing a complex eukaryotic enhancer are not yet known.

Our laboratory is focused on using molecular biology, genomics, bioinformatics, and transgenic model systems to understand enhancer biology. A major area of focus in our laboratory is the study of how different morphogen-concentration specific responses are encoded at different loci. We are also interested in understanding the sequence-function relationship well enough to understand the complex patterns of molecular evolution occurring at enhancer sequences.

Ana Llopart Ph.D.

Current
Ana
Llopart
Ph.D.
Associate Professor
Biology
Research area(s): 
Speciation Genetics, Molecular and Population Genomics
Address
Research
Research Focus: 

In our laboratory we seek to understand the evolution of the genetic barriers responsible for species being reproductively isolated from one another; ultimately the genetic basis of speciation. Today we know that these barriers often involve genic incompatibilities among alleles that function normally in their usual genetic background and produce perfectly fit genotypes, but generate hybrid dysfunction (i.e. sterility and inviability) when encounter alleles from other species. 

To gain insight into the evolution of these genetic barriers we study hybrids where incompatibilities become apparent. Our approaches use methodologies that combine classic genetics, modern genomics and population genetics, and an ideal biological system of two very closely related species of fruit flies, Drosophila yakuba and D. santomea, which produce abundant hybrids in nature.

One of our current areas of research is centered on studying the genetic basis of sterility of female hybrids between D. yakuba and D. santomea. Hybrid female sterility is a trait that has been a bit more neglected than that of their counterparts hybrid males. In this system, sterility involves at least one factor of recent evolution in D. yakuba that is placed in the cytoplasm of the hybrid embryo and that is incompatible with D. santomea genes. We are also interested in evaluating natural introgression, that is, the effective exchange of genes between species through rare hybridization in nature. Experiments in the laboratory can be very useful to detect genomic regions associated with isolating barriers, but they seldom capture the full complexity of nature. By identifying genes that are able to transgress species boundaries in the natural habitat we can built introgression landscapes, which allow us to gain valuable insights into the chromosomal location of genes either responsible for local adaptation or involved in hybrid dysfunction. Our third on-going project focuses on a very special type of genic incompatibilities, those between cis-regulatory sequences of genes and transcription factors. Independent evolution of these two interacting components involved in transcription regulation in different species usually leads to breakdown of gene expression in hybrids.

Faculty affiliations: 

Bryant F McAllister Ph.D.

Current
Bryant
F
McAllister
Ph.D.
    Associate Professor
    Biology
    Research area(s): 
    Computational Genetics; Evolutionary Genetics
    Address
    Research
    Research Focus: 

    My research interests are in the field of evolutionary genetics, especially in processes occurring at or influenced by the genome. Active research projects in the lab are primarily concerned with using the fly species Drosophila americana to understand the factors influencing chromosomal change and the mechanisms involved in the differentiation of sex chromosomes. Changes in chromosomal arrangement are common, but their significance is unknown. We are currently examining a chromosomal rearrangement involving a centromeric fusion of the X chromosome and an autosome in D. americana. This derived arrangement exists as a polymorphism with the ancestral arrangement, showing a strong latitudinal cline in the central and eastern US. Population genetic analyses are used to examine the hypothesis that these alternative chromosomal arrangements coordinate adaptive genetic variation. Independently evolved pairs of sex chromosomes exhibit similar patterns of differentiation. The Y chromosome is genetically inert, and the X chromosome contains many active unique genes and often compensates for differences in dosage between genders. The X-4 centromeric fusion in D. americana provides a system for examining the earliest asymmetries between newly evolved sex chromosomes. We are testing models of sex chromosome evolution by examining patterns of sequence variation on this pair of neo-sex chromosomes.

    Faculty affiliations: 

    John Logsdon Ph.D.

    Current
    John
    Logsdon
    Ph.D.
    Associate Professor
    Biology
    Research area(s): 
    Computational Genetics; Molecular and Biochemical Genetics; Evolutionary Genetics
    Address
    310
    BB
    301
    BB
    Research
    Research Focus: 

    The Logsdon lab works on a variety of related topics in molecular evolutionary genetics:

    SEX & MEIOSIS:

    1. Exploring the origin and evolution of meiotic genes in diverse eukaryotes.
    2. Molecular evolution and phylogeny of meiotic genes.
    3. Isolation of meiosis-related genes from protists and other eukaryotes.
    4. Functional studies of meiotic genes isolated from diverse eukaryotes.
    5. Bioinformatic studies of meiosis and recombination/repair genes.

    TREES:

    1. Understanding the molecular phylogeny of eukaryotes.
    2. Using complex gene families to root the eukaryotic tree of life.
    3. Isolating new protein genes to address thorny issues in eukaryotic phylogeny.

    LATERAL GENE TRANSFER:

    1. Developing a better understanding of the frequency, roles, distribution and phylogenetic impacts of LGT in prokaryotes.
    2. Comparative bioinformatics of bacterial genomes.
    3. Mathematical modeling/ computer simulation.

    GENOMES:

    1. Discovery and analysis of genomic sequence from key protists.
    2. Comparative bioinformatics of protist genomes as grist for hypothesis-driven research in the lab.

    INTRONS:

    1. Understanding of the origin and evolution of spliceosomal introns
    2. What are their roles in eukaryotic genome evolution? What is their phylogenetic distribution?

    Josep M Comeron Ph.D.

    Current
    Josep
    M
    Comeron
    Ph.D.
    Associate Professor
    Biology
    Research area(s): 
    Computational Genetics; Evolutionary Genetics
    Address
    Research
    Research Focus: 

    We apply a multidisciplinary approach-combining empirical work to obtain sequence data, large-scale genomic analyses, and the development of theoretical, analytical and computational tools-to investigate: 1) variation in the efficacy of natural selection among species and across genomes, 2) the evolution of recombination across genomes and among species, 3) the evolution of introns (presence and size) and genome structure in eukaryotes, 4) the evolutionary consequences of changes in population size, and 5) the genetic basis of speciation. Likely, many mutations important to evolution have much smaller selection coefficients than it is practicable to demonstrate in the laboratory. Population genetics and molecular evolution analyses-the study of nucleotide variability within and between species, respectively-are powerful tools that allow us to detect the action of selection on naturally-occurring mutations, even if the fitness effects of these mutations are extremely weak. We study the causes and consequences of changes in recombination rates among species and across genomes, focusing on the influence of meiotic recombination on the efficacy of selection in eukaryotes. To measure possible changes in the effectiveness of selection, we study weakly selected mutations such as synonymous mutations (changes in the coding sequence that do not alter protein sequence) and small insertion/deletions (indels). The same population genetics techniques that are commonly applied to nucleotide changes can be also applied to genomic features, allowing us to investigate the forces involved in the evolution of gene number, the origin of introns, the evolution of exon-intron structures, and ultimately genome size. This genomics-meets-population genetics approach (i.e., population genomics) can be implemented with computer simulations mimicking the evolutionary process (in silico evolution), a computationally-intensive technique that provides new and valuable insights into the expected outcome of complex evolutionary processes. We also apply molecular evolution and population genetics techniques to study recent speciation events. In particular, we investigate Drosophila species to gain insight into the evolutionary patterns of genes involved in phenotypic differentiation and reproductive isolation.

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