The white-bellied pangolin () is the world's most trafficked mammal and is at risk of extinction. Reducing the illegal wildlife trade requires an understanding of its origins. Using a genomic approach for tracing confisc...The white-bellied pangolin () is the world's most trafficked mammal and is at risk of extinction. Reducing the illegal wildlife trade requires an understanding of its origins. Using a genomic approach for tracing confiscations and analyzing 111 samples collected from known geographic localities in Africa and 643 seized scales from Asia between 2012 and 2018, we found that poaching pressures shifted over time from West to Central Africa. Recently, Cameroon's southern border has emerged as a site of intense poaching. Using data from seizures representing nearly 1 million African pangolins, we identified Nigeria as one important hub for trafficking, where scales are amassed and transshipped to markets in Asia. This origin-to-destination approach offers new opportunities to disrupt the illegal wildlife trade and to guide anti-trafficking measures.
Ancestral Coast Salish societies in the Pacific Northwest kept long-haired "woolly dogs" that were bred and cared for over millennia. However, the dog wool-weaving tradition declined during the 19th century, and the popu...Ancestral Coast Salish societies in the Pacific Northwest kept long-haired "woolly dogs" that were bred and cared for over millennia. However, the dog wool-weaving tradition declined during the 19th century, and the population was lost. In this study, we analyzed genomic and isotopic data from a preserved woolly dog pelt from "Mutton," collected in 1859. Mutton is the only known example of an Indigenous North American dog with dominant precolonial ancestry postdating the onset of settler colonialism. We identified candidate genetic variants potentially linked with their distinct woolly phenotype. We integrated these data with interviews from Coast Salish Elders, Knowledge Keepers, and weavers about shared traditional knowledge and memories surrounding woolly dogs, their importance within Coast Salish societies, and how colonial policies led directly to their disappearance.
Liu Y, Liu S, Tomar A
… +21 more, Yen FS, Unlu G, Ropek N, Weber RA, Wang Y, Khan A, Gad M, Peng J, Terzi E, Alwaseem H, Pagano AE, Heissel S, Molina H, Allwein B, Kenny TC, Possemato RL, Zhao L, Hite RK, Vinogradova EV, Mansy SS, Birsoy K
Mitochondria must maintain adequate amounts of metabolites for protective and biosynthetic functions. However, how mitochondria sense the abundance of metabolites and regulate metabolic homeostasis is not well understood...Mitochondria must maintain adequate amounts of metabolites for protective and biosynthetic functions. However, how mitochondria sense the abundance of metabolites and regulate metabolic homeostasis is not well understood. In this work, we focused on glutathione (GSH), a critical redox metabolite in mitochondria, and identified a feedback mechanism that controls its abundance through the mitochondrial GSH transporter, SLC25A39. Under physiological conditions, SLC25A39 is rapidly degraded by mitochondrial protease AFG3L2. Depletion of GSH dissociates AFG3L2 from SLC25A39, causing a compensatory increase in mitochondrial GSH uptake. Genetic and proteomic analyses identified a putative iron-sulfur cluster in the matrix-facing loop of SLC25A39 as essential for this regulation, coupling mitochondrial iron homeostasis to GSH import. Altogether, our work revealed a paradigm for the autoregulatory control of metabolic homeostasis in organelles.
Although most ancient DNA studies have focused on the last 50,000 years, paleogenomic approaches can now reach into the early Pleistocene, an epoch of repeated environmental changes that shaped present-day biodiversity....Although most ancient DNA studies have focused on the last 50,000 years, paleogenomic approaches can now reach into the early Pleistocene, an epoch of repeated environmental changes that shaped present-day biodiversity. Emerging deep-time genomic transects, including from DNA preserved in sediments, will enable inference of adaptive evolution, discovery of unrecognized species, and exploration of how glaciations, volcanism, and paleomagnetic reversals shaped demography and community composition. In this Review, we explore the state-of-the-art in paleogenomics and discuss key challenges, including technical limitations, evolutionary divergence and associated biases, and the need for more precise dating of remains and sediments. We conclude that with improvements in laboratory and computational methods, the emerging field of deep-time paleogenomics will expand the range of questions addressable using ancient DNA.
Herbaria are undergoing a renaissance as valuable sources of genomic data for exploring plant evolution, ecology, and diversity. Ancient DNA retrieved from herbarium specimens can provide unprecedented glimpses into past...Herbaria are undergoing a renaissance as valuable sources of genomic data for exploring plant evolution, ecology, and diversity. Ancient DNA retrieved from herbarium specimens can provide unprecedented glimpses into past plant communities, their interactions with biotic and abiotic factors, and the genetic changes that have occurred over time. Here, we highlight recent advances in the field of herbarium genomics and discuss the challenges and opportunities of combining data from modern and time-stamped historical specimens. We also describe how integrating herbarium genomics data with other data types can yield substantial insights into the evolutionary and ecological processes that shape plant communities. Herbarium genomic analysis is a tool for understanding plant life and informing conservation efforts in the face of dire environmental challenges.
DNA methylation can identify evolutionary relationships among close plant lineages.DNA methylation can identify evolutionary relationships among close plant lineages.
A fundamental goal in evolutionary biology is to understand the genetic architecture of adaptive traits. Using whole-genome data of 3955 of Darwin's finches on the Galápagos Island of Daphne Major, we identified six loci...A fundamental goal in evolutionary biology is to understand the genetic architecture of adaptive traits. Using whole-genome data of 3955 of Darwin's finches on the Galápagos Island of Daphne Major, we identified six loci of large effect that explain 45% of the variation in the highly heritable beak size of a key ecological trait. The major locus is a supergene comprising four genes. Abrupt changes in allele frequencies at the loci accompanied a strong change in beak size caused by natural selection during a drought. A gradual change in occurred across 30 years as a result of introgressive hybridization with . This study shows how a few loci with large effect on a fitness-related trait contribute to the genetic potential for rapid adaptive radiation.
Machines don't have eyes, but you wouldn't know that if you followed the progression of deep learning models for accurate interpretation of medical images, such as x-rays, computed tomography (CT) and magnetic resonance...Machines don't have eyes, but you wouldn't know that if you followed the progression of deep learning models for accurate interpretation of medical images, such as x-rays, computed tomography (CT) and magnetic resonance imaging (MRI) scans, pathology slides, and retinal photos. Over the past several years, there has been a torrent of studies that have consistently demonstrated how powerful "machine eyes" can be, not only compared with medical experts but also for detecting features in medical images that are not readily discernable by humans. For example, a retinal scan is rich with information that people can't see, but machines can, providing a gateway to multiple aspects of human physiology, including blood pressure; glucose control; risk of Parkinson's, Alzheimer's, kidney, and hepatobiliary diseases; and the likelihood of heart attacks and strokes. As a cardiologist, I would not have envisioned that machine interpretation of an electrocardiogram would provide information about the individual's age, sex, anemia, risk of developing diabetes or arrhythmias, heart function and valve disease, kidney, or thyroid conditions. Likewise, applying deep learning to a pathology slide of tumor tissue can also provide insight about the site of origin, driver mutations, structural genomic variants, and prognosis. Although these machine vision capabilities for medical image interpretation may seem impressive, they foreshadow what is potentially far more expansive terrain for artificial intelligence (AI) to transform medicine. The big shift ahead is the ability to transcend narrow, unimodal tasks, confined to images, and broaden machine capabilities to include text and speech, encompassing all input modes, setting the foundation for multimodal AI.
There are no cures for the most common neurodegenerative diseases. None of the currently approved treatments cure or halt these conditions; rather, they address symptoms or slow disease progression. A focus on protein de...There are no cures for the most common neurodegenerative diseases. None of the currently approved treatments cure or halt these conditions; rather, they address symptoms or slow disease progression. A focus on protein deposits in the brain-a hallmark of Alzheimer's disease (AD) and Parkinson's disease (PD)-has led to the development of immunotherapy drugs. Other promising avenues of investigation include the roles of neuroinflammation in neurodegeneration. However, the clinical impact of these approaches is still uncertain. What about exploiting our knowledge of the human genome and the ability to modify it with surgically precise tools? Can functional genomics approaches in neurodegenerative disease research provide the breakthroughs we need?
Population size history is essential for studying human evolution. However, ancient population size history during the Pleistocene is notoriously difficult to unravel. In this study, we developed a fast infinitesimal tim...Population size history is essential for studying human evolution. However, ancient population size history during the Pleistocene is notoriously difficult to unravel. In this study, we developed a fast infinitesimal time coalescent process (FitCoal) to circumvent this difficulty and calculated the composite likelihood for present-day human genomic sequences of 3154 individuals. Results showed that human ancestors went through a severe population bottleneck with about 1280 breeding individuals between around 930,000 and 813,000 years ago. The bottleneck lasted for about 117,000 years and brought human ancestors close to extinction. This bottleneck is congruent with a substantial chronological gap in the available African and Eurasian fossil record. Our results provide new insights into our ancestry and suggest a coincident speciation event.
Spatial omics has been widely heralded as the new frontier in life sciences. This term encompasses a wide range of techniques that promise to transform many areas of biology and eventually revolutionize pathology by meas...Spatial omics has been widely heralded as the new frontier in life sciences. This term encompasses a wide range of techniques that promise to transform many areas of biology and eventually revolutionize pathology by measuring physical tissue structure and molecular characteristics at the same time. Although the field came of age in the past 5 years, it still suffers from some growing pains: barriers to entry, robustness, unclear best practices for experimental design and analysis, and lack of standardization. In this Review, we present a systematic catalog of the different families of spatial omics technologies; highlight their principles, power, and limitations; and give some perspective and suggestions on the biggest challenges that lay ahead in this incredibly powerful-but still hard to navigate-landscape.
Ancient DNA is used to connect enslaved African Americans to modern descendants.Ancient DNA is used to connect enslaved African Americans to modern descendants.
Tsui JL, McCrone JT, Lambert B
… +38 more, Bajaj S, Inward RPD, Bosetti P, Pena RE, Tegally H, Hill V, Zarebski AE, Peacock TP, Liu L, Wu N, Davis M, Bogoch II, Khan K, Kall M, Abdul Aziz NIB, Colquhoun R, O'Toole Á, Jackson B, Dasgupta A, Wilkinson E, de Oliveira T, COVID-19 Genomics UK (COG-UK) consortium¶, Connor TR, Loman NJ, Colizza V, Fraser C, Volz E, Ji X, Gutierrez B, Chand M, Dellicour S, Cauchemez S, Raghwani J, Suchard MA, Lemey P, Rambaut A, Pybus OG, Kraemer MUG
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) now arise in the context of heterogeneous human connectivity and population immunity. Through a large-scale phylodynamic analysis of...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) now arise in the context of heterogeneous human connectivity and population immunity. Through a large-scale phylodynamic analysis of 115,622 Omicron BA.1 genomes, we identified >6,000 introductions of the antigenically distinct VOC into England and analyzed their local transmission and dispersal history. We find that six of the eight largest English Omicron lineages were already transmitting when Omicron was first reported in southern Africa (22 November 2021). Multiple datasets show that importation of Omicron continued despite subsequent restrictions on travel from southern Africa as a result of export from well-connected secondary locations. Initiation and dispersal of Omicron transmission lineages in England was a two-stage process that can be explained by models of the country's human geography and hierarchical travel network. Our results enable a comparison of the processes that drive the invasion of Omicron and other VOCs across multiple spatial scales.
Understanding the mechanisms that maintain microbial biodiversity is a critical aspiration in ecology. Past work on microbial coexistence has largely focused on species pairs, but it is unclear whether pairwise coexisten...Understanding the mechanisms that maintain microbial biodiversity is a critical aspiration in ecology. Past work on microbial coexistence has largely focused on species pairs, but it is unclear whether pairwise coexistence in isolation is required for coexistence in a multispecies community. To address this question, we conducted hundreds of pairwise competition experiments among the stably coexisting members of 12 different enrichment communities in vitro. To determine the outcomes of these experiments, we developed an automated image analysis pipeline to quantify species abundances. We found that competitive exclusion was the most common outcome, and it was strongly hierarchical and transitive. Because many species that coexist within a stable multispecies community fail to coexist in pairwise co-culture under identical conditions, we concluded that multispecies coexistence is an emergent phenomenon. This work highlights the importance of community context for understanding the origins of coexistence in complex ecosystems.
Budd . challenge the identity of neural traces reported for the Cambrian lobopodian Their argumentation is unsupported, as are objections with reference to living Onychophora that misinterpret established genomic, genet...Budd . challenge the identity of neural traces reported for the Cambrian lobopodian Their argumentation is unsupported, as are objections with reference to living Onychophora that misinterpret established genomic, genetic, developmental, and neuroanatomical evidence. Instead, phylogenetic data corroborate the finding that the ancestral panarthropod head and brain is unsegmented, as in .
Shao Y, Zhou L, Li F
… +40 more, Zhao L, Zhang BL, Shao F, Chen JW, Chen CY, Bi X, Zhuang XL, Zhu HL, Hu J, Sun Z, Li X, Wang D, Rivas-González I, Wang S, Wang YM, Chen W, Li G, Lu HM, Liu Y, Kuderna LFK, Farh KK, Fan PF, Yu L, Li M, Liu ZJ, Tiley GP, Yoder AD, Roos C, Hayakawa T, Marques-Bonet T, Rogers J, Stenson PD, Cooper DN, Schierup MH, Yao YG, Zhang YP, Wang W, Qi XG, Zhang G, Wu DD
Comparative analysis of primate genomes within a phylogenetic context is essential for understanding the evolution of human genetic architecture and primate diversity. We present such a study of 50 primate species spanni...Comparative analysis of primate genomes within a phylogenetic context is essential for understanding the evolution of human genetic architecture and primate diversity. We present such a study of 50 primate species spanning 38 genera and 14 families, including 27 genomes first reported here, with many from previously less well represented groups, the New World monkeys and the Strepsirrhini. Our analyses reveal heterogeneous rates of genomic rearrangement and gene evolution across primate lineages. Thousands of genes under positive selection in different lineages play roles in the nervous, skeletal, and digestive systems and may have contributed to primate innovations and adaptations. Our study reveals that many key genomic innovations occurred in the Simiiformes ancestral node and may have had an impact on the adaptive radiation of the Simiiformes and human evolution.