Beth Shapiro

The DNA Legacy of Thomas Jefferson

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.

Paleogenomic insight into the collapse, recovery, and management of American bison

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

On the ancestry and evolution of the extinct dire wolf

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

Rapid Derivation of Cloning-Competent Cells from Peripheral Blood Advances Conservation Biobanking

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.

First Plant sedaDNA assemblage from California reveals ecological stability throughout 10,000 years of human presence at Lake Elsinore

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.

Genetic Diversity and Population Structure of the Black-Footed Cat: Insights into Felis's Deadliest Predator

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.

Ancient DNA from shells reveals delayed genomic erosion and rapid immune adaptation in the critically endangered black abalone

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.

Evolutionary history and genomic vulnerability of the extinct giant deer Megaloceros giganteus

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

Ancient metagenomics reveals subglacial microbiomes driven by oxygen availability

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

Ancient sedimentary DNA shows more than 5000 years of continuous beaver occupancy in Grand Teton National Park

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.

Persistent genomic erosion in whooping cranes despite demographic recovery

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

Hi-reComb: constructing recombination maps from bulk gamete Hi-C sequencing

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

Multiplex-edited mice recapitulate woolly mammoth hair phenotypes

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

Enrichment of spermatogonial stem cells and staging of the testis cycle in a dasyurid marsupial, the fat-tailed dunnart

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.

Direct measurement of the mutation rate and its evolutionary consequences in a critically endangered mollusk

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.

Most Beefalo cattle have no detectable bison genetic ancestry

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

Recent adaptation in an imperiled salmonid revealed by museum genomics

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

Mitochondrial genomes of Pleistocene megafauna retrieved from recent sediment layers of two Siberian lakes

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.

Integrating gene annotation with orthology inference at scale

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

Relating enhancer genetic variation across mammals to complex phenotypes using machine learning

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

Evolutionary constraint and innovation across hundreds of placental mammals

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.

Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia

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.

A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control

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.

Highly accurate long-read HiFi sequencing data for five complex genomes

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

Depletion of hemoglobin transcripts and long read sequencing improves the transcriptome annotation of the polar bear (Ursus maritimus)

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

Mitogenomes illuminate the origin and migration patterns of the indigenous people of the Canary Islands

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.

Mountain lion genomes provide insights into genetic rescue of inbred populations

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.

Early Pleistocene enamel proteome sequences from Dmanisi resolve Stephanorhinus phylogeny.

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

Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe

This paper analyzes ancient genomes from North Africa to show prehistoric migrations brought genetic influences from both the Levant and Europe to the Maghreb.

Natural selection shaped the rise and fall of passenger pigeon genomic diversity

The paper analyzes genomic data from passenger pigeons and their relatives to show that natural selection reduced neutral genetic diversity despite large population size, challenging previous extinction theories.