About

Beth Alison Shapiro is a Professor in the Ecology & Evolutionary Biology Department within the Division of Physical & Biological Sciences at UC Santa Cruz. She is also an Investigator at the Howard Hughes Medical Institute. Her research focuses on understanding how populations and species change through time, particularly in response to environmental and habitat changes. Her group employs the latest experimental and computational approaches to analyze genetic information isolated from fossil and archived remains, with a special interest in the processes of speciation and extinction. Dr. Shapiro's educational background includes a BS and MS in Ecology from the University of Georgia, obtained in 1999, and a DPhil in Zoology from Oxford University, completed in 2003. Her expertise encompasses ancient DNA, genomics, ecology, molecular evolution, and evolution. She has received numerous awards and honors, including being named a MacArthur Fellow in 2009, a National Geographic Emerging Explorer in 2010, and a Packard Fellow in 2010. Her work aims to shed light on the mechanisms driving evolutionary change by analyzing genetic data from historical and fossilized remains.

Research topics

• Biology
• Genetics
• Evolutionary biology
• Ecology
• Computational biology
• Computer Science
• Demography
• Geography
• Zoology
• Artificial Intelligence
• Machine Learning
• Mathematics
• Archaeology
• Physics
• Algorithm
• Ethnology
• Astrophysics
• Epistemology
• Statistics
• History
• Environmental resource management
• Philosophy
• Cell biology
• Paleontology

Selected publications

• Evolutionary history and genomic vulnerability of the extinct giant deer <i>Megaloceros giganteus</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-05-14

  articleOpen access

  Abstract The extinct giant deer ( Megaloceros giganteus ) was one of the most striking megafaunal species of the Late Quaternary, distinguished by its enormous palmated antlers reaching up to 3.5 m across, the largest known among both living and extinct cervids. Despite its iconic status, little is known about its genomic history prior to extinction ∼8 thousand years ago (kya). We generated the first nuclear palaeogenomes for Megaloceros , represented by nine individuals from Germany (∼40 kya) and Ireland (∼11 kya), mapped to a new chromosome-level reference genome of the fallow deer ( Dama dama ). Phylogenomic analyses placed Megaloceros as sister to Dama (divergence ∼3.5 Ma) and revealed evidence of gene flow with ancestral Cervus lineages. Population analyses identified clear differentiation between German and Irish lineages, with higher genetic diversity in the German individuals. Two genes under strong positive selection, BNIPL and SLC10A7, are associated with apoptosis regulation and skeletal development/bone mineralisation, respectively, and may relate to the species’ large body and antler size. Demographic reconstructions indicate a long-term decline in effective population size, extremely low heterozygosity, little evidence of extensive runs of homozygosity, and an elevated burden of predicted deleterious alleles. Together, these results suggest that Megaloceros entered the terminal Pleistocene in a genomically fragile state, offering new insight into the biology and evolutionary legacy of one of the largest and most distinctive cervids that ever lived.

  PublisherDOI

• Ancient sedimentary <scp>DNA</scp> shows more than 5000 years of continuous beaver occupancy in Grand Teton National Park

  Ecosphere · 2025-10-01

  articleOpen access

  Abstract 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 apply sedimentary ancient DNA (sedaDNA) techniques to investigate the history of beaver occupancy at three lakes in Grand Teton National Park, Wyoming, over the last ~10,000 years, as well as interactions with the local plant community. We document a dynamic history of beaver presence in two subalpine lakes (Taggart and Jenny Lakes) and demonstrate no history of beaver occupancy at the higher elevation alpine lake (Lake Solitude). Beavers were first detected at Jenny Lake around 7200 years BP and intermittently thereafter. At nearby Taggart Lake, beavers were first detected at ~5900 years BP and continuously from 5200 years BP onward. Vegetation metabarcoding revealed a shift in plant community coinciding with beaver establishment in these two subalpine lakes, as well as an increase in taxonomic diversity. These changes coincide with regional trends toward wetter conditions. Notably, beavers persist at Taggart Lake during inferred droughts, indicating a potential role in maintaining wetlands through extended periods of climatic stress. Our results demonstrate sedaDNA as a powerful, novel technique for reconstructing robust time series data of historical beaver occupancy dynamics.

  PublisherOA PDFDOI

• Author Correction: Striking convergent selection history of wheat and barley and its potential for breeding

  Nature Plants · 2025-11-24

  erratumOpen access

  Correction to: Nature Plantshttps://doi.org/10.1038/s41477-025-02128-0, published online 14 November 2025. In the version of the article initially published, the surname of Manon Delahaye appeared incorrectly (as Delayhe) and has now been corrected. Additionally, in Fig. 7, the labels “AGW” and “BW” were shifted to the left and have been amended. These corrections have been made to the HTML and PDF versions of the article.

  PublisherOA PDFDOI

• Ancient metagenomics reveals subglacial microbiomes driven by oxygen availability

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-12-05

  articleOpen access

  Abstract Beneath Earth’s glaciers and ice sheets lies an aquatic realm where ice, water, rock, and microbial life interact, driving chemical reactions that can collectively influence the global carbon cycle, polar oceans, and climate. Efforts to describe subglacial microbiomes have been limited by the challenge of cleanly drilling through hundreds of meters of ice, such that only a few sites have ever been directly sampled. Here we use ancient metagenomics to present the first spatiotemporal characterization of subglacial bacteria and archaea. We extracted DNA from 25 subglacial precipitate samples, sedimentary accumulations of minerals that form in subglacial waters prior to exposure on the surface. The precipitates studied here formed between 16,000 and 570,000 years ago beneath the Antarctic and Laurentide Ice Sheets. We show that postmortem DNA damage patterns can reliably distinguish between ancient subglacial and modern surface taxa, and that this approach can enable reconstruction of subglacial microbiomes across poles and ice ages. Our analysis suggests that subglacial microbiomes are dominated by chemolithoautotrophs, ultra-small microbes, and taxa closely related to those found in deep subsurface or extreme cold and hypersaline environments. These microbiomes split into two distinct clusters distinguished by oxygen availability and redox conditions, irrespective of geography or age. Geochemical measurements of subglacial redox state, measured either indirectly via precipitate calcite Fe and Mn concentrations or directly via water reduction potential, reproduce these same two clusters exactly. Our findings describe how subglacial water redox states are held in balance by microbes, hydrology, and oxygen input from fresh subglacial meltwater, that we interpret to be controlled by the ice sheet response to past climate variations.

  PublisherDOI

• Striking convergent selection history of wheat and barley and its potential for breeding

  Nature Plants · 2025-11-17 · 4 citations

  articleOpen access

  Over the past 10,000 years, the development of civilization has been enabled by the domestication of plants and animals tailored to human needs. The Triticeae tribe, including barley and wheat, has emerged as one of the most important sources of staple foods worldwide. Here, comparing genomes of wheat and barley genotypes from around the world, we unveiled genomic footprints of convergent selection affecting genes involved in crop adaptation and productivity, as well as a lack of parallel selection for diverse genes delivering genetic diversity specific to particular geographic and associated environmental conditions. We demonstrate that studying convergent selection between crops can help to identify genes crucial for adaptation and sources of diversity for improving cultivated species—forming the basis of the proposed concept of inter-crop translational research for breeding. Convergent selection between crops can help to identify genetic variants with important roles in adaptation as a source of diversity for the improvement of cultivated species through the concept of inter-crop translational research for breeding.

  PublisherOA PDFDOI

• Sustainability insights from Late Pleistocene climate change and horse migration patterns

  Science · 2025-05-15 · 8 citations

  article

  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 explore the effect of climate change on horses. We find that Late Pleistocene horses from Alaska and northern Yukon are related to populations from Eurasia and crossed the Bering land bridge multiple times during the last glacial interval. We also find deeply divergent lineages north and south of the American ice sheets that genetically influenced populations across Beringia and into Eurasia. As climate warmed and horses entered the ice-free corridor connecting Beringia and midcontinental America, restricted mobility and food availability impeded population growth. Our combined Western and Indigenous framework offers critical guidance for wildlife conservation amid ongoing climate change.

  PublisherDOI

• Genome engineering in biodiversity conservation and restoration

  Nature Reviews Biodiversity · 2025-07-17 · 11 citations

  article
  PublisherDOI

• Genomic data from the extinct California brown bear suggests a source population for reintroduction to California

  Journal of Heredity · 2025-04-24 · 1 citations

  articleOpen accessSenior author

  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, intense poisoning, trapping, and hunting led to their extinction by 1924. Today, California is emerging as a candidate for brown bear reintroduction as a component of larger ecosystem restoration efforts. Questions remain, however, about whether living brown bears are suitable proxies for the bears that once inhabited California. While recent work suggests that brown bears from California were similar in size and overall diet to brown bears living today in continental North America, the 1) extent to which California bears were genetically differentiated from other populations, and 2) what this means for proposed reintroductions, remain outstanding questions. We generated genomes from two of the last living California brown bears and compared them to genomes from living brown bears. Genomic estimates of divergence time combined with radiocarbon dating points towards brown bears arriving recently in California, having diverged within the last 10,000 years from a common ancestor with brown bears found today in Yellowstone National Park, Wyoming. This timeline, the overall genetic similarity between the California and Yellowstone populations, and the strong pattern of isolation-by-distance we observe all suggest that no closer living relatives are likely to be found. If genetic background is to be a consideration for reintroduction efforts in California, brown bears from Yellowstone might serve as a source population.

  PublisherOA PDFDOI

• Recent Adaptation in a Threatened Salmonid Revealed by Museum Genomics

  Molecular Ecology · 2025-09-01

  articleOpen access

  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 California waterways, possibly resulting in introgression into natural populations and altered population structure. We compared whole-genome sequence data from contemporary populations against a set of museum population samples of steelhead from the same locations that were collected prior to most hatchery stocking. We observed minimal introgression and few steelhead-hatchery trout hybrids despite a century of extensive stocking. Our historical data show signals of introgression with a sister species and indications of an early hatchery facility. Finally, we found that migration-associated haplotypes have become less frequent over time, a likely adaptation to decreased opportunities for migration. Since contemporary migration-associated haplotype frequencies have been used to guide species management, we consider this to be a rare example of shifting baseline syndrome that has been validated with historical data. We suggest cautious optimism that a century of hatchery stocking has had minimal impact on California steelhead population genetic structure, but we note that continued shifts in life history may lead to further declines in the ocean-going form of the species.

  PublisherOA PDFDOI

• Persistent Genomic Erosion in Whooping Cranes Despite Demographic Recovery

  Molecular Ecology · 2025-08-26 · 7 citations

  articleOpen access

  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 declines in the 18th century, culminating in a collapse to ~20 individuals by 1944. Legal protections and conservation actions have since increased the census population from a stock of 16 individuals to approximately 840 individuals, yet the impact on genomic diversity remains unclear. We analysed the temporal dynamics of genomic erosion by sequencing a high-quality reference genome, and re-sequencing 16 historical (years 1867-1893) and 37 modern (2007-2020) genomes, including wild individuals and four generations of captive-bred individuals. Genomic demographic reconstructions reveal a steady decline, accelerating over the past 300 years with the European settlement of North America. Temporal genomic analyses show that despite demographic recovery, the species has lost 70% of its historical genetic diversity and has increased its inbreeding. Although the modern population bottleneck reduced the ancestral genetic load, modern populations possess more realised load than masked load, possibly resulting in a chronic loss of fitness. Integrating pedigree and genomic data, we underscore the role of breeding management in reducing recent inbreeding. Yet ongoing heterozygosity loss, load accumulation, and persistent effects of historical inbreeding (i.e., background inbreeding) argue against the species' downlisting from its current Endangered status on the IUCN Red List and the Endangered Species Act. The presence of private genetic variation in wild and captive populations suggests that wild-captive crosses could enhance genetic diversity and reduce the realised load. Our findings emphasise the role of genomics in informing conservation management and policy.

  PublisherOA PDFDOI

Recent grants

• Collaborative Research: Inferring admixture history in non-model organisms using local ancestry detection

  NSF · $600k · 2018–2023

• Collaborative Research: Land Bridges, Ice-Free Corridors, and Biome Shifts: Impacts on the Evolution and Extinction of Horses in Ice-Age Beringia

  NSF · $423k · 2015–2019

• Collaborative research: Understanding the role of environmental change on the long-term population dynamics of one surviving and two extinct arctic mammals

  NSF · $268k · 2009–2012

• Belmont Forum Collaborative Research: Future ArcTic Ecosystems (FATE): drivers of diversity and future scenarios from ethno-ecology, contemporary ecology and ancient DNA

  NSF · $186k · 2019–2022

• Collaborative Research: The Lost Pastures of Alaska's Last Megafauna

  NSF · $294k · 2022–2026

Frequent coauthors

• Alexei J. Drummond

  University of Auckland

  779 shared

• H. Bradley Shaffer

  California Department of Conservation

  763 shared

• Brant C. Faircloth

  Louisiana State University

  758 shared

• Michael Charleston

  University of Tasmania

  757 shared

• Bastien Boussau

  Laboratoire de Biométrie et Biologie Evolutive

  757 shared

• F. Keith Barker

  Science Museum of Minnesota

  756 shared

• John E. McCormack

  755 shared

• John Trueman

  Australian National University

  754 shared

Labs

• Beth Alison Shapiro LabPI

Education

• DPhil, Zoology

  University of Oxford

  2003

Awards & honors

• Packard Fellow, 2010
• PopTech Science and Public Leadership Fellow, 2010
• National Geographic Emerging Explorer, 2010
• MacArthur Fellow, 2009
• Searle Scholar, 2009