Beth Shapiro

This study uses DNA from museum hair samples to confirm Thomas Jefferson's ancestry in descendants of Sally Hemings and Martha Wayles Jefferson, supporting paternity over alternative explanations.

This study uses ancient and modern bison genomes to show past population connectivity and reveal human impacts on bison diversity, informing conservation efforts.

This study uses paleogenomes of dire wolves to resolve their evolutionary relationships and identify genes under diversifying selection.

This study shows that blood-derived endothelial progenitor cells and pericytes can be used to create viable cell lines faster and more reliably than fibroblasts for conservation biobanking in endangered species.

This paper reports the first derivation of elephant induced pluripotent stem cells (emiPSCs) using a modified reprogramming protocol that inhibits TP53 expansion genes.

Angiosperms353 capture of Lake Elsinore sedimentary DNA recovers 50 land-plant orders across 24,000 years, with a fire-linked community shift preceding a persistent Holocene chaparral assemblage.

This study sequenced whole genomes of black-footed cats to analyze their population structure and genetic diversity, finding low diversity but no long runs of homozygosity and evidence of recent population contraction.

The paper uses ancient DNA from shells to analyze genetic stability and immune adaptation in black abalone post-bottleneck, finding delayed genomic erosion and rapid immune-related selection.

This study reconstructs the genomic history of the extinct giant deer, revealing genetic vulnerabilities linked to its extinction.

The paper uses ancient metagenomics to characterize subglacial microbiomes, showing they split into two clusters based on oxygen availability and redox conditions.

This study uses sedimentary ancient DNA to show beavers occupied two lakes in Grand Teton National Park for over 5000 years, with continuous presence at one lake and intermittent at another, while influencing local plant communities.

The paper analyzes genomic diversity loss in whooping cranes despite population recovery, finding 70% genetic diversity loss and increased inbreeding.

Hi-reComb estimates recombination maps from bulk gamete Hi-C data, showing accurate results in fish sperm and enabling structural variant analysis.

This study creates a multiplex-edited mouse model with woolly mammoth hair traits, showing curly and textured coats through gene modifications.

This study enriches spermatogonial stem cells in fat-tailed dunnarts using fluorescent dye technology and defines the testis cycle in dasyurids for marsupial conservation research.

The paper estimates the germline mutation rate in the white abalone and uses it to infer population history and evolutionary patterns in the Haliotis genus.

The paper analyzes genomic data from Beefalo cattle and finds most lack detectable bison ancestry, challenging the breed association's 3/8 bison requirement.

The paper analyzes the genomes of black abalone to assess genetic impacts of a population collapse and finds no spatial genetic structure, high genetic diversity, and low WS prevalence, suggesting translocation could aid recovery.

The paper uses museum genomics to compare historical and contemporary steelhead populations, finding minimal introgression and a decline in migration-associated haplotypes over time.

The paper retrieves mitochondrial genomes of extinct Pleistocene megafauna from recent sediment layers in Siberian lakes, showing that permafrost thawing affects aeDNA preservation and stratigraphic signal.

TOGA integrates gene annotation and orthology inference across hundreds of genomes, improving ortholog detection and creating large comparative gene resources.

A machine learning approach identifies enhancer-phenotype associations across mammals, revealing links to brain size and behavior evolution.

A 240-species placental mammal alignment resolves constraint to single bases, estimating at least 10.7% of the human genome is constrained, with 48.5% of constrained bases unannotated.

The paper identifies bats as a hotspot for horizontal transfer of DNA transposons, finding over 200 putative elements and shared transposons across mammals and reptiles.

The paper reports a SARS-CoV-2 lineage with mutations from known variants of concern that is rejected by sequence repositories due to a deletion, suggesting underestimation of its frequency.

The paper provides highly accurate long-read HiFi sequencing datasets for five complex genomes to evaluate and develop bioinformatic tools.

The paper depletes hemoglobin transcripts using Long-DASH to improve transcriptome annotation in polar bears, discovering 6,000 high-confidence isoforms and novel genes.

The paper analyzes ancient mitogenomes from the Canary Islands to trace the origin and migration patterns of indigenous populations, identifying new lineages and supporting a model of two distinct migrations.

The paper analyzes mountain lion genomes to study genetic rescue effects in inbred populations, finding that translocated individuals quickly lose genetic diversity due to local inbreeding.

This study uses Early Pleistocene dental enamel proteome sequences to resolve the phylogeny of Stephanorhinus, showing it is paraphyletic and requiring systematic revision.