Publications by authors named "Beth Shapiro"

152 Publications

The origins and spread of domestic horses from the Western Eurasian steppes.

Nature 2021 Oct 20. Epub 2021 Oct 20.

UMR 5199 De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), CNRS, Université de Bordeaux, Pessac Cedex, France.

Domestication of horses fundamentally transformed long-range mobility and warfare. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling at Botai, Central Asia around 3500 BC. Other longstanding candidate regions for horse domestication, such as Iberia and Anatolia, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 BC, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 BC driving the spread of Indo-European languages. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BC Sintashta culture.
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http://dx.doi.org/10.1038/s41586-021-04018-9DOI Listing
October 2021

Museum Genomics.

Annu Rev Genet 2021 Sep 23. Epub 2021 Sep 23.

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; email:

Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences. Expected final online publication date for the , Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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http://dx.doi.org/10.1146/annurev-genet-071719-020506DOI Listing
September 2021

Ancient and modern genomes unravel the evolutionary history of the rhinoceros family.

Cell 2021 Sep 24;184(19):4874-4885.e16. Epub 2021 Aug 24.

Department of Earth Sciences, Natural History Museum, London, UK.

Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.
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http://dx.doi.org/10.1016/j.cell.2021.07.032DOI Listing
September 2021

Lifetime mobility of an Arctic woolly mammoth.

Science 2021 08;373(6556):806-808

Department of Biostatistics, University of Washington, Seattle, WA, USA.

Little is known about woolly mammoth () mobility and range. Here we use high temporal resolution sequential analyses of strontium isotope ratios along an entire 1.7-meter-long tusk to reconstruct the movements of an Arctic woolly mammoth that lived 17,100 years ago, during the last ice age. We use an isotope-guided random walk approach to compare the tusk's strontium and oxygen isotope profiles to isotopic maps. Our modeling reveals patterns of movement across a geographically extensive range during the animal's ~28-year life span that varied with life stages. Maintenance of this level of mobility by megafaunal species such as mammoth would have been increasingly difficult as the ice age ended and the environment changed at high latitudes.
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http://dx.doi.org/10.1126/science.abg1134DOI Listing
August 2021

An ancestral recombination graph of human, Neanderthal, and Denisovan genomes.

Sci Adv 2021 Jul 16;7(29). Epub 2021 Jul 16.

Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.

Many humans carry genes from Neanderthals, a legacy of past admixture. Existing methods detect this archaic hominin ancestry within human genomes using patterns of linkage disequilibrium or direct comparison to Neanderthal genomes. Each of these methods is limited in sensitivity and scalability. We describe a new ancestral recombination graph inference algorithm that scales to large genome-wide datasets and demonstrate its accuracy on real and simulated data. We then generate a genome-wide ancestral recombination graph including human and archaic hominin genomes. From this, we generate a map within human genomes of archaic ancestry and of genomic regions not shared with archaic hominins either by admixture or incomplete lineage sorting. We find that only 1.5 to 7% of the modern human genome is uniquely human. We also find evidence of multiple bursts of adaptive changes specific to modern humans within the past 600,000 years involving genes related to brain development and function.
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http://dx.doi.org/10.1126/sciadv.abc0776DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8284891PMC
July 2021

Large-scale genomic analysis reveals the genetic cost of chicken domestication.

BMC Biol 2021 06 16;19(1):118. Epub 2021 Jun 16.

Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh.

Background: Species domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks, but also post-divergence gene flow and introgression. Although domestication potentially affects the occurrence of both desired and undesired mutations, the way wild relatives of domesticated species evolve and how expensive the genetic cost underlying domestication is remain poorly understood. Here, we investigated the demographic history and genetic load of chicken domestication.

Results: We analyzed a dataset comprising over 800 whole genomes from both indigenous chickens and wild jungle fowls. We show that despite having a higher genetic diversity than their wild counterparts (average π, 0.00326 vs. 0.00316), the red jungle fowls, the present-day domestic chickens experienced a dramatic population size decline during their early domestication. Our analyses suggest that the concomitant bottleneck induced 2.95% more deleterious mutations across chicken genomes compared with red jungle fowls, supporting the "cost of domestication" hypothesis. Particularly, we find that 62.4% of deleterious SNPs in domestic chickens are maintained in heterozygous states and masked as recessive alleles, challenging the power of modern breeding programs to effectively eliminate these genetic loads. Finally, we suggest that positive selection decreases the incidence but increases the frequency of deleterious SNPs in domestic chicken genomes.

Conclusion: This study reveals a new landscape of demographic history and genomic changes associated with chicken domestication and provides insight into the evolutionary genomic profiles of domesticated animals managed under modern human selection.
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http://dx.doi.org/10.1186/s12915-021-01052-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8207802PMC
June 2021

Landscape analyses using eDNA metabarcoding and Earth observation predict community biodiversity in California.

Ecol Appl 2021 09 8;31(6):e02379. Epub 2021 Jul 8.

Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA.

Ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system-level patterns and that can be applied rapidly across space and time. Using modern ecological models and community science, we integrate environmental DNA and Earth observations to produce a time snapshot of regional biodiversity patterns and provide multi-scalar community-level characterization. We collected 278 samples in spring 2017 from coastal, shrub, and lowland forest sites in California, a complex ecosystem and biodiversity hotspot. We recovered 16,118 taxonomic entries from eDNA analyses and compiled associated traditional observations and environmental data to assess how well they predicted alpha, beta, and zeta diversity. We found that local habitat classification was diagnostic of community composition and distinct communities and organisms in different kingdoms are predicted by different environmental variables. Nonetheless, gradient forest models of 915 families recovered by eDNA analysis and using BIOCLIM variables, Sentinel-2 satellite data, human impact, and topographical features as predictors, explained 35% of the variance in community turnover. Elevation, sand percentage, and photosynthetic activities (NDVI32) were the top predictors. In addition to this signal of environmental filtering, we found a positive relationship between environmentally predicted families and their numbers of biotic interactions, suggesting environmental change could have a disproportionate effect on community networks. Together, these analyses show that coupling eDNA with environmental predictors including remote sensing data has capacity to test proposed Essential Biodiversity Variables and create new landscape biodiversity baselines that span the tree of life.
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http://dx.doi.org/10.1002/eap.2379DOI Listing
September 2021

Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge.

Mol Ecol 2021 May 10. Epub 2021 May 10.

Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.

The Bering Land Bridge (BLB) last connected Eurasia and North America during the Late Pleistocene. Although the BLB would have enabled transfers of terrestrial biota in both directions, it also acted as an ecological filter whose permeability varied considerably over time. Here we explore the possible impacts of this ecological corridor on genetic diversity within, and connectivity among, populations of a once wide-ranging group, the caballine horses (Equus spp.). Using a panel of 187 mitochondrial and eight nuclear genomes recovered from present-day and extinct caballine horses sampled across the Holarctic, we found that Eurasian horse populations initially diverged from those in North America, their ancestral continent, around 1.0-0.8 million years ago. Subsequent to this split our mitochondrial DNA analysis identified two bidirectional long-range dispersals across the BLB ~875-625 and ~200-50 thousand years ago, during the Middle and Late Pleistocene. Whole genome analysis indicated low levels of gene flow between North American and Eurasian horse populations, which probably occurred as a result of these inferred dispersals. Nonetheless, mitochondrial and nuclear diversity of caballine horse populations retained strong phylogeographical structuring. Our results suggest that barriers to gene flow, currently unidentified but possibly related to habitat distribution across Beringia or ongoing evolutionary divergence, played an important role in shaping the early genetic history of caballine horses, including the ancestors of living horses within Equus ferus.
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http://dx.doi.org/10.1111/mec.15977DOI Listing
May 2021

Towards complete and error-free genome assemblies of all vertebrate species.

Nature 2021 Apr 28;592(7856):737-746. Epub 2021 Apr 28.

UQ Genomics, University of Queensland, Brisbane, Queensland, Australia.

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species. To address this issue, the international Genome 10K (G10K) consortium has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.
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http://dx.doi.org/10.1038/s41586-021-03451-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8081667PMC
April 2021

An Annotated Draft Genome for the Andean Bear, Tremarctos ornatus.

J Hered 2021 07;112(4):377-384

Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA.

The Andean bear is the only extant member of the Tremarctine subfamily and the only extant ursid species to inhabit South America. Here, we present an annotated de novo assembly of a nuclear genome from a captive-born female Andean bear, Mischief, generated using a combination of short and long DNA and RNA reads. Our final assembly has a length of 2.23 Gb, and a scaffold N50 of 21.12 Mb, contig N50 of 23.5 kb, and BUSCO score of 88%. The Andean bear genome will be a useful resource for exploring the complex phylogenetic history of extinct and extant bear species and for future population genetics studies of Andean bears.
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http://dx.doi.org/10.1093/jhered/esab021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8280923PMC
July 2021

Environmental genomics of Late Pleistocene black bears and giant short-faced bears.

Curr Biol 2021 Jun 19;31(12):2728-2736.e8. Epub 2021 Apr 19.

Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Wellcome Sanger Institute, Cambridge CB10 1SA, UK; MARUM, University of Bremen, Bremen, Germany. Electronic address:

Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time, by allowing for parallel sequencing of DNA from all trophic levels. However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species, the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies. This is in contrast to data from fossils where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable. Here, we report the retrieval of three low-coverage (0.03×) environmental genomes from American black bear (Ursus americanus) and a 0.04× environmental genome of the extinct giant short-faced bear (Arctodus simus) from cave sediment samples from northern Mexico dated to 16-14 thousand calibrated years before present (cal kyr BP), which we contextualize with a new high-coverage (26×) and two lower-coverage giant short-faced bear genomes obtained from fossils recovered from Yukon Territory, Canada, which date to ∼22-50 cal kyr BP. We show that the Late Pleistocene black bear population in Mexico is ancestrally related to the present-day Eastern American black bear population, and that the extinct giant short-faced bears present in Mexico were deeply divergent from the earlier Beringian population. Our findings demonstrate the ability to separately analyze genomic-scale DNA sequences of closely related species co-preserved in environmental samples, which brings the use of ancient eDNA into the era of population genomics and phylogenetics.
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http://dx.doi.org/10.1016/j.cub.2021.04.027DOI Listing
June 2021

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

bioRxiv 2021 Apr 6. Epub 2021 Apr 6.

We report a SARS-CoV-2 lineage that shares N501Y, P681H, and other mutations with known variants of concern, such as B.1.1.7. This lineage, which we refer to as B.1.x (COG-UK sometimes references similar samples as B.1.324.1), is present in at least 20 states across the USA and in at least six countries. However, a large deletion causes the sequence to be automatically rejected from repositories, suggesting that the frequency of this new lineage is underestimated using public data. Recent dynamics based on 339 samples obtained in Santa Cruz County, CA, USA suggest that B.1.x may be increasing in frequency at a rate similar to that of B.1.1.7 in Southern California. At present the functional differences between this variant B.1.x and other circulating SARS-CoV-2 variants are unknown, and further studies on secondary attack rates, viral loads, immune evasion and/or disease severity are needed to determine if it poses a public health concern. Nonetheless, given what is known from well-studied circulating variants of concern, it seems unlikely that the lineage could pose larger concerns for human health than many already globally distributed lineages. Our work highlights a need for rapid turnaround time from sequence generation to submission and improved sequence quality control that removes submission bias. We identify promising paths toward this goal.
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http://dx.doi.org/10.1101/2021.04.05.438352DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8043452PMC
April 2021

A Fast and Efficient Single-stranded Genomic Library Preparation Method Optimized for Ancient DNA.

J Hered 2021 05;112(3):241-249

Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA.

We present a protocol to prepare extracted DNA for sequencing on the Illumina sequencing platform that has been optimized for ancient and degraded DNA. Our approach, the Santa Cruz Reaction or SCR, uses directional splinted ligation of Illumina's P5 and P7 adapters to convert natively single-stranded DNA and heat denatured double-stranded DNA into sequencing libraries in a single enzymatic reaction. To demonstrate its efficacy in converting degraded DNA molecules, we prepare 5 ancient DNA extracts into sequencing libraries using the SCR and 2 of the most commonly used approaches for preparing degraded DNA for sequencing: BEST, which targets and converts double-stranded DNA, and ssDNA2.0, which targets and converts single-stranded DNA. We then compare the efficiency with which each approach recovers unique molecules, or library complexity, given a standard amount of DNA input. We find that the SCR consistently outperforms the BEST protocol in recovering unique molecules and, despite its relative simplicity to perform and low cost per library, has similar performance to ssDNA2.0 across a wide range of DNA inputs. The SCR is a cost- and time-efficient approach that minimizes the loss of unique molecules and makes accessible a taxonomically, geographically, and a temporally broader sample of preserved remains for genomic analysis.
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http://dx.doi.org/10.1093/jhered/esab012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8141684PMC
May 2021

Ancient plant DNA reveals High Arctic greening during the Last Interglacial.

Proc Natl Acad Sci U S A 2021 03;118(13)

Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado, Boulder, CO 80303.

Summer warming is driving a greening trend across the Arctic, with the potential for large-scale amplification of climate change due to vegetation-related feedbacks [Pearson et al., (3), 673-677 (2013)]. Because observational records are sparse and temporally limited, past episodes of Arctic warming can help elucidate the magnitude of vegetation response to temperature change. The Last Interglacial ([LIG], 129,000 to 116,000 y ago) was the most recent episode of Arctic warming on par with predicted 21st century temperature change [Otto-Bliesner et al., (371), 20130097 (2013) and Post et al., (5), eaaw9883 (2019)]. However, high-latitude terrestrial records from this period are rare, so LIG vegetation distributions are incompletely known. Pollen-based vegetation reconstructions can be biased by long-distance pollen transport, further obscuring the paleoenvironmental record. Here, we present a LIG vegetation record based on ancient DNA in lake sediment and compare it with fossil pollen. Comprehensive plant community reconstructions through the last and current interglacial (the Holocene) on Baffin Island, Arctic Canada, reveal coherent climate-driven community shifts across both interglacials. Peak LIG warmth featured a ∼400-km northward range shift of dwarf birch, a key woody shrub that is again expanding northward. Greening of the High Arctic-documented here by multiple proxies-likely represented a strong positive feedback on high-latitude LIG warming. Authenticated ancient DNA from this lake sediment also extends the useful preservation window for the technique and highlights the utility of combining traditional and molecular approaches for gleaning paleoenvironmental insights to better anticipate a warmer future.
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http://dx.doi.org/10.1073/pnas.2019069118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8020792PMC
March 2021

Conserving intraspecific variation for nature's contributions to people.

Nat Ecol Evol 2021 05 1;5(5):574-582. Epub 2021 Mar 1.

Department of Ecology & Evolutionary Biology, University of California, Santa Cruz, CA, USA.

The rapid loss of intraspecific variation is a hidden biodiversity crisis. Intraspecific variation, which includes the genomic and phenotypic diversity found within and among populations, is threatened by local extinctions, abundance declines, and anthropogenic selection. However, biodiversity assessments often fail to highlight this loss of diversity within species. We review the literature on how intraspecific variation supports critical ecological functions and nature's contributions to people (NCP). Results show that the main categories of NCP (material, non-material, and regulating) are supported by intraspecific variation. We highlight new strategies that are needed to further explore these connections and to make explicit the value of intraspecific variation for NCP. These strategies will require collaboration with local and Indigenous groups who possess critical knowledge on the relationships between intraspecific variation and ecosystem function. New genomic methods provide a promising set of tools to uncover hidden variation. Urgent action is needed to document, conserve, and restore the intraspecific variation that supports nature and people. Thus, we propose that the maintenance and restoration of intraspecific variation should be raised to a major global conservation objective.
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http://dx.doi.org/10.1038/s41559-021-01403-5DOI Listing
May 2021

Million-year-old DNA sheds light on the genomic history of mammoths.

Nature 2021 03 17;591(7849):265-269. Epub 2021 Feb 17.

Centre for Palaeogenetics, Stockholm, Sweden.

Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale, the oldest genomic data recovered so far are from a horse specimen dated to 780-560 thousand years ago. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.
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http://dx.doi.org/10.1038/s41586-021-03224-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7116897PMC
March 2021

A Reference Genome Assembly of American Bison, Bison bison bison.

J Hered 2021 03;112(2):174-183

USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA.

Bison are an icon of the American West and an ecologically, commercially, and culturally important species. Despite numbering in the hundreds of thousands today, conservation concerns remain for the species, including the impact on genetic diversity of a severe bottleneck around the turn of the 20th century and genetic introgression from domestic cattle. Genetic diversity and admixture are best evaluated at genome-wide scale, for which a high-quality reference is necessary. Here, we use trio binning of long reads from a bison-Simmental cattle (Bos taurus taurus) male F1 hybrid to sequence and assemble the genome of the American plains bison (Bison bison bison). The male haplotype genome is chromosome-scale, with a total length of 2.65 Gb across 775 scaffolds (839 contigs) and a scaffold N50 of 87.8 Mb. Our bison genome is ~13× more contiguous overall and ~3400× more contiguous at the contig level than the current bison reference genome. The bison genome sequence presented here (ARS-UCSC_bison1.0) will enable new research into the evolutionary history of this iconic megafauna species and provide a new tool for the management of bison populations in federal and commercial herds.
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http://dx.doi.org/10.1093/jhered/esab003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8006816PMC
March 2021

Reintroduction of the archaic variant of in cortical organoids alters neurodevelopment.

Science 2021 02;371(6530)

Department of Pediatrics and Department of Cellular & Molecular Medicine, School of Medicine, Center for Academic Research and Training in Anthropogeny (CARTA), Kavli Institute for Brain and Mind, University of California, San Diego, La Jolla, CA 92037, USA.

The evolutionarily conserved splicing regulator neuro-oncological ventral antigen 1 () plays a key role in neural development and function. also includes a protein-coding difference between the modern human genome and Neanderthal and Denisovan genomes. To investigate the functional importance of an amino acid change in humans, we reintroduced the archaic allele into human induced pluripotent cells using genome editing and then followed their neural development through cortical organoids. This modification promoted slower development and higher surface complexity in cortical organoids with the archaic version of Moreover, levels of synaptic markers and synaptic protein coassociations correlated with altered electrophysiological properties in organoids expressing the archaic variant. Our results suggest that the human-specific substitution in , which is exclusive to modern humans since divergence from Neanderthals, may have had functional consequences for our species' evolution.
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http://dx.doi.org/10.1126/science.aax2537DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8006534PMC
February 2021

Dire wolves were the last of an ancient New World canid lineage.

Nature 2021 03 13;591(7848):87-91. Epub 2021 Jan 13.

Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently.
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http://dx.doi.org/10.1038/s41586-020-03082-xDOI Listing
March 2021

A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus.

J Hered 2021 03;112(2):184-191

USDA, ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD.

Genomics research has relied principally on the establishment and curation of a reference genome for the species. However, it is increasingly recognized that a single reference genome cannot fully describe the extent of genetic variation within many widely distributed species. Pangenome representations are based on high-quality genome assemblies of multiple individuals and intended to represent the broadest possible diversity within a species. A Bovine Pangenome Consortium (BPC) has recently been established to begin assembling genomes from more than 600 recognized breeds of cattle, together with other related species to provide information on ancestral alleles and haplotypes. Previously reported de novo genome assemblies for Angus, Brahman, Hereford, and Highland breeds of cattle are part of the initial BPC effort. The present report describes a complete single haplotype assembly at chromosome-scale for a fullblood Simmental cow from an F1 bison-cattle hybrid fetus by trio binning. Simmental cattle, also known as Fleckvieh due to their red and white spots, originated in central Europe in the 1830s as a triple-purpose breed selected for draught, meat, and dairy production. There are over 50 million Simmental cattle in the world, known today for their fast growth and beef yields. This assembly (ARS_Simm1.0) is similar in length to the other bovine assemblies at 2.86 Gb, with a scaffold N50 of 102 Mb (max scaffold 156.8 Mb) and meets or exceeds the continuity of the best Bos taurus reference assemblies to date.
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http://dx.doi.org/10.1093/jhered/esab002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8006815PMC
March 2021

Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France.

Curr Biol 2021 03;31(5):1072-1083.e10

Centre d'Anthropobiologie et de Génomique de Toulouse CAGT, CNRS UMR 5288, Université Toulouse III Paul Sabatier, Faculté de Médecine Purpan, Bâtiment A, 37 allées Jules Guesde, 31000 Toulouse, France. Electronic address:

The transition from the Late Neolithic to the Bronze Age has witnessed important population and societal changes in western Europe. These include massive genomic contributions of pastoralist herders originating from the Pontic-Caspian steppes into local populations, resulting from complex interactions between collapsing hunter-gatherers and expanding farmers of Anatolian ancestry. This transition is documented through extensive ancient genomic data from present-day Britain, Ireland, Iberia, Mediterranean islands, and Germany. It remains, however, largely overlooked in France, where most focus has been on the Middle Neolithic (n = 63), with the exception of one Late Neolithic genome sequenced at 0.05× coverage. This leaves the key transitional period covering ∼3,400-2,700 cal. years (calibrated years) BCE genetically unsampled and thus the exact time frame of hunter-gatherer persistence and arrival of steppe migrations unknown. To remediate this, we sequenced 24 ancient human genomes from France spanning ∼3,400-1,600 cal. years BCE. This reveals Late Neolithic populations that are genetically diverse and include individuals with dark skin, hair, and eyes. We detect heterogeneous hunter-gatherer ancestries within Late Neolithic communities, reaching up to ∼63.3% in some individuals, and variable genetic contributions of steppe herders in Bell Beaker populations. We provide an estimate as late as ∼3,800 years BCE for the admixture between Neolithic and Mesolithic populations and as early as ∼2,650 years BCE for the arrival of steppe-related ancestry. The genomic heterogeneity characterized underlines the complex history of human interactions even at the local scale.
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http://dx.doi.org/10.1016/j.cub.2020.12.015DOI Listing
March 2021

A mummified Pleistocene gray wolf pup.

Curr Biol 2020 12;30(24):R1467-R1468

Government of Yukon, Department of Tourism and Culture, Yukon Palaeontology Program, PO Box 2703, Whitehorse, YT, Y1A 2C6, Canada; Collections and Research, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, ON, K1P 6P4, Canada.

In July 2016, a mummified carcass of an ancient wolf (Canis lupus) pup (specimen YG 648.1) was discovered in thawing permafrost in the Klondike goldfields, near Dawson City, Yukon, Canada (Figure 1A). The wolf pup mummy was recovered along a small tributary of Last Chance Creek during hydraulic thawing that exposed the permafrost sediment in which it was preserved. This mummified wolf pup is important to the local Tr'ondëk Hwëch'in people, who named it Zhùr, meaning 'wolf' in the Hän language of their community. Here, we report detailed morphometric, isotopic, and genetic analyses of Zhùr that reveal details of her appearance, evolutionary relationships to other wolves and short life-history and ecology. Zhùr is the most complete wolf mummy known. She lived approximately 57,000 years ago and died in her den during a collapse of the sediments. During her short life, she ate aquatic resources, and is related to ancient Beringian and Russian gray wolves and her clade is basal to all living gray wolves. VIDEO ABSTRACT.
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http://dx.doi.org/10.1016/j.cub.2020.11.011DOI Listing
December 2020

Ten strategies for a successful transition to remote learning: Lessons learned with a flipped course.

Ecol Evol 2020 Nov 16;10(22):12620-12634. Epub 2020 Oct 16.

Department of Ecology and Evolutionary Biology University of California Los Angeles Los Angeles CA USA.

Transitioning from in-person to remote learning can present challenges for both the instructional team and the students. Here, we use our course "Biodiversity in the Age of Humans" to describe how we adapted tools and strategies designed for a flipped classroom to a remote learning format. Using anonymous survey data collected from students who attended the course either in-person (2019) or remotely (2020), we quantify student expectations and experiences and compare these between years. We summarize our experience and provide ten "tips" or recommendations for a transition to remote learning, which we divide into three categories: (a) precourse instructor preparation; (b) outside of class use of online materials; and (c) during class student engagement. The survey results indicated no negative impact on student learning during the remote course compared to in-person instruction. We found that communicating with students and assessing specific needs, such as access to technology, and being flexible with the structure of the course, simplified the transition to remote instruction. We also found that short, pre-recorded videos that introduce subject materials were among the most valuable elements for student learning. We hope that instructors of undergraduate ecology and evolution courses can use these recommendations to help establish inclusive online learning communities that empower students to acquire conceptual knowledge and develop scientific inquiry and literacy skills.
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http://dx.doi.org/10.1002/ece3.6760DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7679550PMC
November 2020

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

Sci Data 2020 11 17;7(1):399. Epub 2020 Nov 17.

Pacific Biosciences of California Inc., 1305 O'Brien Dr., Menlo Park, CA, 94025, USA.

The PacBio HiFi sequencing method yields highly accurate long-read sequencing datasets with read lengths averaging 10-25 kb and accuracies greater than 99.5%. These accurate long reads can be used to improve results for complex applications such as single nucleotide and structural variant detection, genome assembly, assembly of difficult polyploid or highly repetitive genomes, and assembly of metagenomes. Currently, there is a need for sample data sets to both evaluate the benefits of these long accurate reads as well as for development of bioinformatic tools including genome assemblers, variant callers, and haplotyping algorithms. We present deep coverage HiFi datasets for five complex samples including the two inbred model genomes Mus musculus and Zea mays, as well as two complex genomes, octoploid Fragaria × ananassa and the diploid anuran Rana muscosa. Additionally, we release sequence data from a mock metagenome community. The datasets reported here can be used without restriction to develop new algorithms and explore complex genome structure and evolution. Data were generated on the PacBio Sequel II System.
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http://dx.doi.org/10.1038/s41597-020-00743-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7673114PMC
November 2020

Dense sampling of bird diversity increases power of comparative genomics.

Nature 2020 11 11;587(7833):252-257. Epub 2020 Nov 11.

Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark.

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity. Sparse taxon sampling has previously been proposed to confound phylogenetic inference, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.
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http://dx.doi.org/10.1038/s41586-020-2873-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7759463PMC
November 2020

Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros.

Curr Biol 2020 10 13;30(19):3871-3879.e7. Epub 2020 Aug 13.

Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm 10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm 10405, Sweden; Department of Zoology, Stockholm University, Stockholm 10691, Sweden. Electronic address:

Ancient DNA has significantly improved our understanding of the evolution and population history of extinct megafauna. However, few studies have used complete ancient genomes to examine species responses to climate change prior to extinction. The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted megaherbivore widely distributed across northern Eurasia during the Late Pleistocene and became extinct approximately 14 thousand years before present (ka BP). While humans and climate change have been proposed as potential causes of extinction [1-3], knowledge is limited on how the woolly rhinoceros was impacted by human arrival and climatic fluctuations [2]. Here, we use one complete nuclear genome and 14 mitogenomes to investigate the demographic history of woolly rhinoceros leading up to its extinction. Unlike other northern megafauna, the effective population size of woolly rhinoceros likely increased at 29.7 ka BP and subsequently remained stable until close to the species' extinction. Analysis of the nuclear genome from a ∼18.5-ka-old specimen did not indicate any increased inbreeding or reduced genetic diversity, suggesting that the population size remained steady for more than 13 ka following the arrival of humans [4]. The population contraction leading to extinction of the woolly rhinoceros may have thus been sudden and mostly driven by rapid warming in the Bølling-Allerød interstadial. Furthermore, we identify woolly rhinoceros-specific adaptations to arctic climate, similar to those of the woolly mammoth. This study highlights how species respond differently to climatic fluctuations and further illustrates the potential of palaeogenomics to study the evolutionary history of extinct species.
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http://dx.doi.org/10.1016/j.cub.2020.07.046DOI Listing
October 2020

863 genomes reveal the origin and domestication of chicken.

Cell Res 2020 08 25;30(8):693-701. Epub 2020 Jun 25.

Department of Animal Science, Iowa State University, Ames, IA, USA.

Despite the substantial role that chickens have played in human societies across the world, both the geographic and temporal origins of their domestication remain controversial. To address this issue, we analyzed 863 genomes from a worldwide sampling of chickens and representatives of all four species of wild jungle fowl and each of the five subspecies of red jungle fowl (RJF). Our study suggests that domestic chickens were initially derived from the RJF subspecies Gallus gallus spadiceus whose present-day distribution is predominantly in southwestern China, northern Thailand and Myanmar. Following their domestication, chickens were translocated across Southeast and South Asia where they interbred locally with both RJF subspecies and other jungle fowl species. In addition, our results show that the White Leghorn chicken breed possesses a mosaic of divergent ancestries inherited from other subspecies of RJF. Despite the strong episodic gene flow from geographically divergent lineages of jungle fowls, our analyses show that domestic chickens undergo genetic adaptations that underlie their unique behavioral, morphological and reproductive traits. Our study provides novel insights into the evolutionary history of domestic chickens and a valuable resource to facilitate ongoing genetic and functional investigations of the world's most numerous domestic animal.
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http://dx.doi.org/10.1038/s41422-020-0349-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7395088PMC
August 2020
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