Publications by authors named "Harris A Lewin"

Article Synopsis
  • The study investigates the genetic and brain features linked to vocal learning in mammals by comparing data from the Egyptian fruit bat and 215 other placental mammals.* -
  • Researchers found that certain proteins evolve more slowly in vocal learners and identified a specific brain region responsible for vocal motor control in the Egyptian fruit bat.* -
  • Using machine learning, they uncovered 50 regulatory elements that are associated with vocal learning, suggesting that losses in these elements played a role in the evolution of vocal learning in mammals.*
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A comprehensive characterization of regulatory elements in the chicken genome across tissues will have substantial impacts on both fundamental and applied research. Here, we systematically identified and characterized regulatory elements in the chicken genome by integrating 377 genome-wide sequencing datasets from 23 adult tissues. In total, we annotated 1.

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  • Zoonomia is the largest resource for studying mammalian genomes, analyzing 240 species to find genetic mutations that could impact fitness and disease risk.
  • Around 332 million bases in the human genome are highly conserved across species, indicating evolutionary significance, with 4552 of these being ultraconserved.
  • The research highlights that most constrained bases are outside protein-coding regions and not annotated, revealing potential insights for understanding unique traits in mammals and informing medical research.
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The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signals using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes, and analyzed extensive catalogs of structural variants.

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  • * The study utilized genome assemblies from 23 mammalian orders and identified the ancestral karyotype, revealing the early mammal likely had 19 pairs of autosomes with many chromosomal features conserved over 320 million years.
  • * The researchers detailed various chromosome rearrangements, such as inversions and fusions, and found that purifying selection has maintained critical gene relationships throughout vertebrate evolution.
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Chromosome segregation in mammals relies on the maturation of a thick bundle of kinetochore-attached microtubules known as k-fiber. How k-fibers mature from initial kinetochore microtubule attachments remains a fundamental question. By combining molecular perturbations and phenotypic analyses in Indian muntjac fibroblasts containing the lowest known diploid chromosome number in mammals (2N = 6) and distinctively large kinetochores, with fixed/live-cell super-resolution coherent-hybrid stimulated emission depletion (CH-STED) nanoscopy and laser microsurgery, we demonstrate a key role for augmin in kinetochore microtubule self-organization and maturation, regardless of pioneer centrosomal microtubules.

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High throughput chromatin conformation capture (Hi-C) of leukocyte DNA was used to investigate the evolutionary stability of chromatin conformation at the chromosomal level in 11 species from three carnivore families: Felidae, Canidae, and Ursidae. Chromosome-scale scaffolds (C-scaffolds) of each species were initially used for whole-genome alignment to a reference genome within each family. This approach established putative orthologous relationships between C-scaffolds among the different species.

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  • * Key concerns include legal matters like sample collection, international treaties (e.g., Convention on Biological Diversity), and intellectual property, as well as ethical issues involving Indigenous peoples, endangered species, and cross-border collections.
  • * The EBP's Ethical, Legal, and Social Issues Committee emphasizes the need for an ethical framework to address these challenges and suggests that their findings could aid in developing guidelines for future genomic projects.
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A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals.

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Article Synopsis
  • Life on Earth has evolved from simple beginnings to complex systems, with bacteria, archaea, and eukaryotes contributing through metabolic and morphological innovations.
  • The Earth BioGenome Project aims to sequence the genomes of all 2 million named eukaryotic species to create a comprehensive digital library of life, enabling deeper understanding of evolution and biodiversity.
  • Sequencing all eukaryotic species will provide essential data to address key questions in phylogenetics, ecology, and conservation, while also enhancing knowledge in agriculture, bioindustry, and medicine.
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The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a high-quality genome assembly for kākāpō, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP).

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  • Scientists need good reference genomes to study biology, diseases, and protect wildlife, but there are only a few for non-microbial species.
  • The Genome 10K (G10K) group worked for five years to improve the way they create these high-quality genomes and gathered information from 16 different animal species.
  • Their work showed that special long-read technology improves genome quality, fixed errors in old genome sequences, and discovered new things about genes and chromosomes, leading to a new project to create complete genomes for about 70,000 vertebrate species.
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Egg-laying mammals (monotremes) are the only extant mammalian outgroup to therians (marsupial and eutherian animals) and provide key insights into mammalian evolution. Here we generate and analyse reference genomes of the platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus), which represent the only two extant monotreme lineages. The nearly complete platypus genome assembly has anchored almost the entire genome onto chromosomes, markedly improving the genome continuity and gene annotation.

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The study of chromosome evolution is undergoing a resurgence of interest owing to advances in DNA sequencing technology that facilitate the production of chromosome-scale whole-genome assemblies de novo. This review focuses on the history, methods, discoveries, and current challenges facing the field, with an emphasis on vertebrate genomes. A detailed examination of the literature on the biology of chromosome rearrangements is presented, specifically the relationship between chromosome rearrangements and phenotypic evolution, adaptation, and speciation.

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The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of COVID-19. The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of ACE2 sequences from 410 vertebrate species, including 252 mammals, to study the conservation of ACE2 and its potential to be used as a receptor by SARS-CoV-2.

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The novel coronavirus SARS-CoV-2 is the cause of Coronavirus Disease-2019 (COVID-19). The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of 410 vertebrates, including 252 mammals, to study cross-species conservation of ACE2 and its likelihood to function as a SARS-CoV-2 receptor.

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The confluence of two scientific disciplines may lead to nomenclature conflicts that require new terms while respecting historical definitions. This is the situation with the current state of cytology and genomics, which offer examples of distinct nomenclature and vocabularies that require reconciliation. In this article, we propose the new terms C-scaffold (for chromosome-scale assemblies of sequenced DNA fragments, commonly named scaffolds) and scaffotype (the resulting collection of C-scaffolds that represent an organism's genome).

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Background: The Masai giraffe (Giraffa camelopardalis tippelskirchi) is the largest-bodied giraffe and the world's tallest terrestrial animal. With its extreme size and height, the giraffe's unique anatomical and physiological adaptations have long been of interest to diverse research fields. Giraffes are also critical to ecosystems of sub-Saharan Africa, with their long neck serving as a conduit to food sources not shared by other herbivores.

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The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting.

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Interactions between embryo and endometrium at implantation are critical for the progression of pregnancy. These reciprocal actions involve exchange of paracrine signals that govern implantation and placentation. However, it remains unknown how these interactions between the conceptus and the endometrium are coordinated at the level of an individual pregnancy.

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The role of chromosome rearrangements in driving evolution has been a long-standing question of evolutionary biology. Here we focused on ruminants as a model to assess how rearrangements may have contributed to the evolution of gene regulation. Using reconstructed ancestral karyotypes of Cetartiodactyls, Ruminants, Pecorans, and Bovids, we traced patterns of gross chromosome changes.

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