# positions[].organizations[].parent[].label
College of Agriculture and Life Sciences

# overview
Our group is interested in studying genome evolution and adaptation in plants, beetles and other organisms using both experimental and computational approaches.

Research topics in our group include gene evolution via de novo formation, gene duplication and horizontal transfer; genetic basis of drought tolerance and adaptation to aridity in conifers; evolution of the tree-killing habit in bark beetles.

We work in collaboration with scientists at TAMU, the University of Kentucky, Pisa University (Italy), the Texas A&M Forest Service, the ESSM Department Forest Science Laboratory and the USDA Forest Service Southern Research Station.

# keywords[]
3102 Bioinformatics And Computational Biology

# educationAndTraining[].organization.label
University of Pisa - (Pisa, Toscana, Italy)

# educationAndTraining[].organization.label
The University of Texas at Arlington - (Arlington, Texas, United States)

# educationAndTraining[].organization.label
University of Pisa - (Pisa, Toscana, Italy)

# publications[].label
TP53 Gene and Cancer Resistance in Elephants.

# publications[].label
The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.

# publications[].label
Adaptive evolution of young gene duplicates in mammals.

# publications[].label
Quality of regulatory elements in Drosophila retrogenes.

# publications[].label
Nonallelic gene conversion in the genus Drosophila.

# publications[].label
Gene conversion among paralogs results in moderate false detection of positive selection using likelihood methods.

# publications[].label
The Genomic Impact of Gene Retrocopies: What Have We Learned from Comparative Genomics, Population Genomics, and Transcriptomic Analyses?

# publications[].label
Comparative and demographic analysis of orang-utan genomes.

# publications[].label
Evolution of the Schlafen genes, a gene family associated with embryonic lethality, meiotic drive, immune processes and orthopoxvirus virulence.

# publications[].label
Gametogenesis of intergroup hybrids of hemiclonal frogs.

# publications[].label
Extensive Variation in Drought-Induced Gene Expression Changes Between Loblolly Pine Genotypes.

# publications[].label
Pinaceae show elevated rates of gene turnover that are robust to incomplete gene annotation.

# publications[].label
Daz- and pumilio-like genes are asymmetrically localized in Pelophylax (Rana) oocytes and are expressed during early spermatogenesis.

# publications[].label
Beyond RuBisCO: convergent molecular evolution of multiple chloroplast genes in C4 plants.

# publications[].label
Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila.

# publications[].label
Molecular investigations in western Palearctic water frogs

# publications[].label
The nonrandom evolution of gene families.

# publications[].label
LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes.

# publications[].label
Gibbon genome and the fast karyotype evolution of small apes.

# publications[].label
PIF-like transposons are common in drosophila and have been repeatedly domesticated to generate new host genes.

# publications[].label
Convergent evolution of endometrial prolactin expression in primates, mice, and elephants through the independent recruitment of transposable elements.

# publications[].label
The common marmoset genome provides insight into primate biology and evolution.

# publications[].label
From De Novo to "De Nono": The Majority of Novel Protein-Coding Genes Identified with Phylostratigraphy Are Old Genes or Recent Duplicates.

# publications[].label
Interactions of long-term grazing and woody encroachment can shift soil biogeochemistry and microbiomes in savanna ecosystems

# publications[].label
SECNVs: A Simulator of Copy Number Variants and Whole-Exome Sequences From Reference Genomes.

# publications[].label
Accurate identification of de novo genes in plant genomes using machine learning algorithms

# publications[].label
A hAT-related family of interspersed repetitive elements in genomes of western Palaearctic water frogs

# publications[].label
Chromosome number evolves at equal rates in holocentric and monocentric clades.

# publications[].label
Minimal effect of ectopic gene conversion among recent duplicates in four mammalian genomes.

# publications[].label
Evolutionary origin of regulatory regions of retrogenes in Drosophila.

# publications[].label
Differential expression of two vasa/PL10-related genes during gametogenesis in the special model system Rana.

# publications[].label
Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.

# publications[].publisher
American Association for the Advancement of Science (AAAS)

# publications[].label
An Ancient Transkingdom Horizontal Transfer of Penelope-Like Retroelements from Arthropods to Conifers.

# publications[].label
Convergent domestication of pogo-like transposases into centromere-binding proteins in fission yeast and mammals.

# publications[].label
Recurrent co-domestication of PIF/Harbinger transposable element proteins in insects.

# publications[].label
Resequencing of massive pine genomes helps to unlock the genetic underpinning of quantitative traits in conifer trees.

# publications[].label
Transposase-derived transcription factors regulate light signaling in Arabidopsis.

# publications[].publisher
American Association for the Advancement of Science (AAAS)

# publications[].label
Interlocus gene conversion events introduce deleterious mutations into at least 1% of human genes associated with inherited disease.

# publications[].label
Beyond RuBisCO: Convergent molecular evolution of multiple chloroplast genes in C4 plants

# publications[].label
Isolation and expression of RlYB2, a germ cell-specific Y-box gene in Rana

# publications[].label
The ecoresponsive genome of Daphnia pulex.

# publications[].publisher
American Association for the Advancement of Science (AAAS)

# publications[].label
Very low rate of gene conversion in the yeast genome.

# publications[].label
Report on the Thirty-Fifth Southern Forest Tree Improvement Conference (SFTIC 2019)

# researcherOn[].label
Molecular Cytogenetics to Support Forest Genetics and Tree Breeding

# researcherOn[].awardedBy.label
United States Department of Agriculture - (Washington D.C., District of Columbia, United States)

# researcherOn[].label
Cooperative Forest Genomics - Enhancing and Conserving Tree Populations for a Changing Climate

# researcherOn[].awardedBy.label
United States Department of Agriculture - (Washington D.C., District of Columbia, United States)

# researcherOn[].label
Genomics applications to the study of gene evolution and adaptation in pine trees

# researcherOn[].awardedBy.label
National Institute of Food and Agriculture - (Washington D.C., District of Columbia, United States)

# researcherOn[].label
Integrating Genomic Data and Physiological Measurements To Identify Fast Growing, Drought-Tolerant Loblolly Pine Varieties

# researcherOn[].awardedBy.label
United States Department of Agriculture - (Washington D.C., District of Columbia, United States)

# researcherOn[].awardedBy.preferredLabel
USDA-National Institute of Food And Agriculture

# researcherOn[].label
Identifying the genetic basis of adaptation to environmental stressors in loblolly pine and other conifers to improve forest health and productivity

# researcherOn[].awardedBy.label
National Institute of Food and Agriculture - (Washington D.C., District of Columbia, United States)

# streetAddress
TEXAS A&M AGRILIFE RESEARCH; Ecosystem Science & Management; 2138 TAMU

# schools[]
College of Agriculture and Life Sciences

# etdChairOf[].label
Li, Jingjia (2020-12). Functional and Evolutionary Dynamics of Genes Involved in Drought Tolerance in Loblolly Pine (Pinus Taeda L.). Doctoral Dissertation.

# etdChairOf[].label
Zhu, Weixi (2020-07). Improving CNV Detection Efficacy in a Nonmodel Organism Through Simulations and Optimization of Parameters in the ExomeDepth Program. Master's Thesis.