Mark A. Batzer
Boyd Professor Louisiana State University
- Baton Rouge LA
Dr. Batzer's laboratory is interested in the study of mobile element related genetic variation.
Areas of Expertise
Biography
Research Focus
Mobile DNA & Human–Primate Comparative Genomics
Dr. Batzer’s research focuses on mobile DNA and comparative genomics of humans and primates, showing how LINE-1, Alu, and SVA retrotransposons shape genome structure, disease risk, and population history. A Boyd Professor and Dr. Mary Lou Applewhite Distinguished Professor, he applies high-throughput sequencing, bioinformatics, and population-genetic analysis to map transposable-element insertions, resolve primate relationships, and advance forensic genomics.
Education
Michigan State University
B.S.
Zoology and Microbiology
1983
Michigan State University
M.S.
Zoology
1985
Louisiana State University
Ph.D.
Zoology/Genetics
1988
Accomplishments
Fellow, National Academy of Inventors
2023
Media Appearances
LSU scientists develop new theory about human genome evolution by tracking ’stealth’ DNA elements
Innovations Report online
2005-07-01
A group of LSU researchers, led by biological sciences Professor Mark Batzer, have unraveled the details of a 25-million-year-old evolutionary process in the human genome. Their study focused on the origin and spread of transposable elements in the genome, many of which are known to be related to certain genetic disorders, such as hemophilia.
“Effectively, we’ve devised a theory that allows us to explain the origin of about half of all of the human genome,” said Batzer.
Research Shows the Spread of Mobile and Transposable Genetic Elements
Technology Networks online
2023-06-02
Today, an LSU research team led by Mark Batzer, a geneticist, along with 30 collaborators around the world present new research in the journal Science on surprising genetic diversity as well as commonality among six very different-looking species of African baboons.
Articles
Owl Monkey Alu Insertion Polymorphisms and Aotus Phylogenetics
Genes2022
Owl monkeys (genus Aotus), or “night monkeys” are platyrrhine primates in the Aotidae family. Early taxonomy only recognized one species, Aotus trivirgatus, until 1983, when Hershkovitz proposed nine unique species designations, classified into red-necked and gray-necked species groups based predominately on pelage coloration. Recent studies questioned this conventional separation of the genus and proposed designations based on the geographical location of wild populations. Alu retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phylogenetics. A scaffold-level genome assembly for one Aotus species, Aotus nancymaae [Anan_2.0], facilitated large-scale ascertainment of nearly 2000 young lineage-specific Alu insertions. This study provides candidate oligonucleotides for locus-specific PCR assays for over 1350 of these elements. For 314 Alu elements across four taxa with multiple specimens, PCR analyses identified 159 insertion polymorphisms, including 21 grouping A. nancymaae and Aotus azarae (red-necked species) as sister taxa, with Aotus vociferans and A. trivirgatus (gray-necked) being more basal.
Framework of the Alu Subfamily Evolution in the Platyrrhine Three-Family Clade of Cebidae, Callithrichidae, and Aotidae
Genes2023
The history of Alu retroposons has been choreographed by the systematic accumulation of inherited diagnostic nucleotide substitutions to form discrete subfamilies, each having a distinct nucleotide consensus sequence. The oldest subfamily, AluJ, gave rise to AluS after the split between Strepsirrhini and what would become Catarrhini and Platyrrhini. The AluS lineage gave rise to AluY in catarrhines and to AluTa in platyrrhines. Platyrrhine Alu subfamilies Ta7, Ta10, and Ta15 were assigned names based on a standardized nomenclature. However, with the subsequent intensification of whole genome sequencing (WGS), large scale analyses to characterize Alu subfamilies using the program COSEG identified entire lineages of subfamilies simultaneously. The first platyrrhine genome with WGS, the common marmoset (Callithrix jacchus; [caljac3]), resulted in Alu subfamily names sf0 to sf94 in an arbitrary order. Although easily resolved by alignment of the consensus sequences, this naming convention can become increasingly confusing as more genomes are independently analyzed.
Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons
Science2023
Baboons (genus Papio) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically distinct phylogenetic species. We used high-coverage whole-genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics and interspecies gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages. The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes.
Extensive Independent Amplification of Platy-1 Retroposons in Tamarins, Genus Saguinus
Genes2023
Platy-1 retroposons are short interspersed elements (SINEs) unique to platyrrhine primates. Discovered in the common marmoset (Callithrix jacchus) genome in 2016, these 100 bp mobile element insertions (MEIs) appeared to be novel drivers of platyrrhine evolution, with over 2200 full-length members across 62 different subfamilies, and strong evidence of ongoing proliferation in C. jacchus. Subsequent characterization of Platy-1 elements in Aotus, Saimiri and Cebus genera, suggested that the widespread mobilization detected in marmoset (family Callithrichidae) was perhaps an anomaly. Two additional Callithrichidae genomes are now available, a scaffold level genome assembly for Saguinus imperator (tamarin; SagImp_v1) and a chromosome-level assembly for Saguinus midas (Midas tamarin; ASM2_v1). Here, we report that each tamarin genome contains over 11,000 full-length Platy-1 insertions, about 1150 are shared by both Saguinus tamarins, 7511 are unique to S. imperator, and another 8187 are unique to S. midas. Roughly 325 are shared among the three callithrichids.
Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution
Nature Genetics2023
The role of structurally dynamic genomic regions in speciation is poorly understood due to challenges inherent in diploid genome assembly. Here we reconstructed the evolutionary dynamics of structural variation in five cat species by phasing the genomes of three interspecies F1 hybrids to generate near-gapless single-haplotype assemblies. We discerned that cat genomes have a paucity of segmental duplications relative to great apes, explaining their remarkable karyotypic stability. X chromosomes were hotspots of structural variation, including enrichment with inversions in a large recombination desert with characteristics of a supergene. The X-linked macrosatellite DXZ4 evolves more rapidly than 99.5% of the genome clarifying its role in felid hybrid incompatibility. Resolved sensory gene repertoires revealed functional copy number changes associated with ecomorphological adaptations, sociality and domestication. This study highlights the value of gapless genomes to reveal structural mechanisms underpinning karyotypic evolution, reproductive isolation and ecological niche adaptation.
Media
