Beth Shapiro
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View article: Author Correction: Striking convergent selection history of wheat and barley and its potential for breeding
Author Correction: Striking convergent selection history of wheat and barley and its potential for breeding Open
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View article: Paleogenomics Reveals a Loss of Bovine Lineages in Mid-latitude Asia Over the Last 200,000 Years
Paleogenomics Reveals a Loss of Bovine Lineages in Mid-latitude Asia Over the Last 200,000 Years Open
Bovines have a complex yet poorly understood evolutionary history that is characterized by admixture and diversity loss during the Late Pleistocene. Unraveling this history is challenging in part because deep-time and geographically widesp…
View article: Rapid Derivation of Cloning-Competent Cells from Peripheral Blood Advances Conservation Biobanking
Rapid Derivation of Cloning-Competent Cells from Peripheral Blood Advances Conservation Biobanking Open
I. Abstract Establishing viable cell lines from endangered species is essential for conservation, yet traditional fibroblast derivation from skin biopsies faces challenges including variable success rates, contamination risk, and extended …
View article: Chromosome-scale Genomes Show Rapid Diversification and Ancient Gene Flow Among Bear Species
Chromosome-scale Genomes Show Rapid Diversification and Ancient Gene Flow Among Bear Species Open
Reconstructions of evolutionary history can be restricted by a lack of high-quality reference genomes. To date, only four of the eight species of bears (family Ursidae) have chromosome-level genome assemblies. Here, we present assemblies f…
View article: Ancient sedimentary <scp>DNA</scp> shows more than 5000 years of continuous beaver occupancy in Grand Teton National Park
Ancient sedimentary <span>DNA</span> shows more than 5000 years of continuous beaver occupancy in Grand Teton National Park Open
Beaver‐based restoration is emerging as a cost‐effective conservation and climate adaptation strategy, but efforts are constrained by limited knowledge of pre‐colonial beaver distribution and their long‐term ecosystem impacts. Here, we app…
View article: De-extinction technology and its application to conservation
De-extinction technology and its application to conservation Open
De-extinction, once the realm of science fiction, has evolved into a tangible scientific endeavor thanks to breakthroughs in genome sequencing, engineering, advanced assisted reproductive technologies, and stem cell biology. Alongside this…
View article: Both redox potential and climate control molecular proxies in Icelandic Holocene lake sediments
Both redox potential and climate control molecular proxies in Icelandic Holocene lake sediments Open
Ancient DNA and branched glycerol dialkyl glycerol tetraethers are powerful tools to reconstruct past ecosystems and climate in high-latitude lakes, but often require contrasting redox conditions for reliable interpretations. Here, we pres…
View article: Ancient host-associated microbes obtained from mammoth remains
Ancient host-associated microbes obtained from mammoth remains Open
Ancient genomic studies have extensively explored human-microbial interactions, yet research on non-human animals remains limited. In this study, we analyzed ancient microbial DNA from 483 mammoth remains spanning over 1 million years, inc…
View article: Recent Adaptation in a Threatened Salmonid Revealed by Museum Genomics
Recent Adaptation in a Threatened Salmonid Revealed by Museum Genomics Open
Steelhead/rainbow trout ( Oncorhynchus mykiss ) is an imperilled salmonid with two main life history strategies: migrate to the ocean or remain in freshwater. Domesticated hatchery forms of this species have been stocked into almost all Ca…
View article: Persistent Genomic Erosion in Whooping Cranes Despite Demographic Recovery
Persistent Genomic Erosion in Whooping Cranes Despite Demographic Recovery Open
Integrating in‐situ (wild) and ex‐situ (captive) conservation efforts can mitigate genetic diversity loss and help prevent extinction of endangered wild populations. The whooping crane ( Grus americana ) experienced severe population decli…
View article: The genomic history of Iberian horses since the last Ice Age
The genomic history of Iberian horses since the last Ice Age Open
Horses have inhabited Iberia (present-day Spain and Portugal) since the Middle Pleistocene, shaping a complex history in the region. Iberia has been proposed as a potential domestication centre and is renowned for producing world-class blo…
View article: Hi-reComb: constructing recombination maps from bulk gamete Hi-C sequencing
Hi-reComb: constructing recombination maps from bulk gamete Hi-C sequencing Open
Recombination is central to genetics and to evolution of sexually reproducing organisms. However, obtaining accurate estimates of recombination rates, and of how they vary along chromosomes, continues to be challenging. To advance our abil…
View article: Sustainability insights from Late Pleistocene climate change and horse migration patterns
Sustainability insights from Late Pleistocene climate change and horse migration patterns Open
Climate affects habitat, food availability, and the movement and sustainability of all life. In this work, we apply Indigenous and Western scientific methods, including genomics and isotope profiling, on fossils from across Beringia to exp…
View article: A chromosome-level genome of the Nicobar pigeon, <i>Caloenas nicobarica</i>
A chromosome-level genome of the Nicobar pigeon, <i>Caloenas nicobarica</i> Open
The Nicobar pigeon (Caloenas nicobarica), the closest living relative of the extinct Dodo (Raphus cucullatus), is endemic to Southeast Asia with a fragmented distribution across numerous small islands. It suffers from habitat loss, hunting…
View article: Genomic data from the extinct California brown bear suggests a source population for reintroduction to California
Genomic data from the extinct California brown bear suggests a source population for reintroduction to California Open
California brown bears, also known as California grizzlies or golden bears, are an extinct group that once thrived in North America’s western coastal habitats. Despite being common in the region as recently as the early 19th century, inten…
View article: Hi-reComb: constructing recombination maps from bulk gamete Hi-C sequencing
Hi-reComb: constructing recombination maps from bulk gamete Hi-C sequencing Open
Summary Recombination is central to genetics and to evolution of sexually reproducing organisms. However, obtaining accurate estimates of recombination rates, and of how they vary along chromosomes, continues to be challenging. To advance …
View article: Multiplex-edited mice recapitulate woolly mammoth hair phenotypes
Multiplex-edited mice recapitulate woolly mammoth hair phenotypes Open
SUMMARY The woolly mammoth ( Mammuthus primigenius ) possessed a thick woolly coat and other cold-adaptive traits that enabled survival in harsh arctic environments. Current de-extinction efforts focus on genetically modifying the closely …
View article: Direct Measurement of the Mutation Rate and Its Evolutionary Consequences in a Critically Endangered Mollusk
Direct Measurement of the Mutation Rate and Its Evolutionary Consequences in a Critically Endangered Mollusk Open
The rate at which mutations arise is a fundamental parameter of biology. Despite progress in measuring germline mutation rates across diverse taxa, such estimates are missing for much of Earth's biodiversity. Here, we present the first est…
View article: Persistent genomic erosion in whooping cranes despite demographic recovery
Persistent genomic erosion in whooping cranes despite demographic recovery Open
Integrating in-situ (wild) and ex-situ (captive) conservation efforts can mitigate genetic diversity loss and help prevent extinction of endangered wild populations. The whooping crane ( Grus americana ) experienced severe population decli…
View article: Ancient sedimentary DNA shows more than 5000 years of continuous beaver occupancy in Grand Teton National Park
Ancient sedimentary DNA shows more than 5000 years of continuous beaver occupancy in Grand Teton National Park Open
Beaver-based restoration is emerging as a cost-effective conservation and climate adaptation strategy, but efforts are constrained by limited knowledge of pre-colonial beaver distribution and their long-term ecosystem impacts. Here, we app…
View article: Most Beefalo cattle have no detectable bison genetic ancestry
Most Beefalo cattle have no detectable bison genetic ancestry Open
Hybridization is common among lineages in the genus Bos, often mediated through human management for the selection of adaptive or desirable traits. A recent example is the American Beefalo cattle breed, which was developed in the 1970s and…
View article: Most Beefalo cattle have no detectable bison genetic ancestry
Most Beefalo cattle have no detectable bison genetic ancestry Open
Hybridization is common among lineages in the genus Bos, often mediated through human management for the selection of adaptive or desirable traits. A recent example is the American Beefalo cattle breed, which was developed in the 1970s and…
View article: A chromosome-level genome assembly of the mountain lion, <i>Puma concolor</i>
A chromosome-level genome assembly of the mountain lion, <i>Puma concolor</i> Open
Mountain lions, Puma concolor, are widespread and adaptable carnivores. However, due to their large home ranges and long distance dispersals, they are strongly impacted by habitat fragmentation, which results in small and isolated populati…
View article: Enrichment of spermatogonial stem cells and staging of the testis cycle in a dasyurid marsupial, the fat-tailed dunnart
Enrichment of spermatogonial stem cells and staging of the testis cycle in a dasyurid marsupial, the fat-tailed dunnart Open
There is increasing interest in use of marsupial models in research, for use in next-generation conservation by improving fitness through genetic modification, and in de-extinction efforts. Specifically this includes dasyurid marsupials su…
View article: Direct measurement of the mutation rate and its evolutionary consequences in a critically endangered mollusk
Direct measurement of the mutation rate and its evolutionary consequences in a critically endangered mollusk Open
The rate at which mutations arise is a fundamental parameter of biology. Despite recent progress in measuring germline mutation rates across diverse taxa, such estimates are missing for much of Earth's biodiversity. We present the first es…
View article: Most Beefalo cattle have no detectable bison genetic ancestry
Most Beefalo cattle have no detectable bison genetic ancestry Open
Hybridization is common among lineages in the genus Bos , often mediated through human management for the selection of adaptive or desirable traits. A recent example is the American Beefalo cattle breed, which was developed in the 1970s an…
View article: Genome‐wide population affinities and signatures of adaptation in hydruntines, sussemiones and Asian wild asses
Genome‐wide population affinities and signatures of adaptation in hydruntines, sussemiones and Asian wild asses Open
The extremely rich palaeontological record of the horse family, also known as equids, has provided many examples of macroevolutionary change over the last ~55 Mya. This family is also one of the most documented at the palaeogenomic level, …