A comparative genomics multitool for scientific discovery and conservation

A whole-genome alignment of 240 phylogenetically diverse species of eutherian mammal-including 131 previously uncharacterized species-from the Zoonomia Project provides data that support biological discovery, medical research and conservation. The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.Peer reviewe

Isumaqatigingniq: Building a Transformational Science Education Model to Engage the Next Generation of Inuit and Western Scientific Investigators

Inuit Qaujimajatuqangit (IQ), “the Inuit way of knowing,” and science each approach observation of the natural and physical world from shared yet different epistemologies. Studies that integrate IQ and science demonstrate the inherent value of using observations and findings from both to understand Arctic systems. Yet holders of IQ and scientists often do not fully comprehend the practice of the other because they think and approach observation and knowledge differently. Using the concept of Isumaqatigingniq, or “thinking together,” we will form an educational program, Isumaqatigingniq-Science, Technology, Engineering and Mathematics, (I-STEM), that will highlight and integrate studies of the narwhal and the Arctic environment undertaken with contributions from IQ and science. Program outreach will target high school students from both Inuit and non-Inuit backgrounds. Understanding existing efforts that combine these knowledge frames will hopefully inspire future collaborations by these groups. Learning through I-STEM will better equip students to address scientific themes that design, optimize, and implement collaborative observation systems. Inuit and scientific research efforts are essential for a deeper understanding of the Arctic environment. Implementing an active educational program that engages high school youth to understand the value of incorporating these two ways of knowing will help foster a future educational environment of collaboration. The educational I-STEM model will bring a new Inuit perspective to formal scientific education programs and share perspectives of science and Inuit knowledge within Inuit educational programs. Isumaqatigingniq can continue growing, incorporating new perspectives on Arctic observations and knowledge.L’Inuit Qaujimajatuqangit (IQ), soit « la façon de savoir des Inuits », et la science abordent toutes deux le monde physique et le monde naturel à partir d’épistémologies partagées, quoique différentes. Les études qui font appel à l’IQ et à la science démontrent la valeur inhérente de recourir aux observations et aux constatations de ces deux branches pour comprendre les systèmes arctiques. Pourtant, il arrive souvent que les détenteurs de l’IQ et les scientifiques ne comprennent pas entièrement la pratique de l’autre parce qu’ils considèrent et approchent l’observation et les connaissances différemment. En nous appuyant sur le concept de l’Isumaqatigingniq, ou de la « réflexion collective », nous formerons un programme éducatif appelé Isumaqatigingniq-science, technologie, ingénierie et mathématiques (I-STEM), qui mettra en évidence et intégrera les études sur le narval et l’environnement arctique réalisées à l’aide de l’IQ et de la science. Ce programme visera les élèves du secondaire deuxième cycle, inuits et non inuits. Le fait de comprendre les efforts actuels faisant appel à ces deux cadres de connaissances inspireront, espérons-le, des collaborations futures de la part de ces groupes. Grâce aux apprentissages faits par le biais du programme I-STEM, les élèves seront mieux outillés pour aborder les thèmes scientifiques donnant lieu à la conception, à l’optimisation et à la mise en oeuvre des systèmes d’observation collaboratifs. Les efforts de recherche menés à bien par les Inuits et les scientifiques sont essentiels à une compréhension approfondie de l’environnement arctique. La mise en oeuvre d’un programme éducatif actif incitant les jeunes de l’école secondaire deuxième cycle à comprendre la valeur de l’incorporation de ces deux méthodes de connaissances aidera à favoriser un milieu éducatif axé sur la collaboration. Le modèle éducatif I-STEM permettra d’intégrer une nouvelle perspective inuite aux programmes d’éducation scientifique officiels et de partager les perspectives des connaissances de la science et des Inuits à l’échelle des programmes éducatifs inuits. L’Isumaqatigingniq peut permettre de continuer à cultiver et à incorporer de nouvelles perspectives sur les observations et les connaissances propres à l’Arctique

(Table 1) Morphometrics of narwhal (Monodon monoceros) fluke planforms

In this study, we compared the fluke geometries of male and female narwhals, which may be associated with hydrodynamic effects. Computerized tomography (CT) scanning was used to obtain data for analyses of the three-dimensional geometry of the flukes. The flukes from four narwhals (two males and two females) were obtained from aboriginal hunters in the vicinity of Broughton Island, Canada. The body lengths of the animals ranged from 2.98 to 3.60 m. Both males had erupted, upper left tusks. Standard body measurements were made including the span of the fluke (i.e., linear distance between fluke tips)

Quest Volume 4 Number 3

Contents: Discovering the deep African past at Wonderwerk Cave - Archaeological dating points to the birth of human technology and culture right here in southern Africa: Storing and restoring plant-life from seeds - How to store genetic material once considered unstorable: Nutrition - you are what you eat: Diet and lifestyle for good health - From molecules to society: Micronutrients for healthy living -Eating and exercise: How blood clots form and disintegrate: Treating children with HIV/AIDS: Careers: Why maths counts Opening the door to a future in science, technology, and engineering - Getting back to basics: Girls doing science (maths is the key) Conditioning - Notes from TIMSS-R Girls and boys on a par: Reading, maths, and gender equality: Maths and environmental science - Out of the classroom, into the field - The why (and how) of biomaths: Viewpoint - How bad is 'child labour'? - What's really best for the children?: Watching whale-tusks grow - Measuring the amazing tusk of the Arctic narwhal - Diamond and mammography screening: Improved measurement of X-ray doses: The drinking habits of sunbirds - A taste for sugary nectars: Drug-resistant TB in South Africa The struggle continues: Fact files - More on the Arctic narwhal Bird nectars in flowers - TB facts and stats - Science news - Spider webs for hungry times; Brain food -Energy options: How smoke affects cloud cover and climate; Fact and fiction - The case for early antiretroviral therapy for HIV/AIDS: Your questions answered Life on planet Earth? - Reducing greenhouse gases: Boiling water: The S&T tourist Not just elephants at Addo: QUEST the first four years; Wind power; People on the move; On teaching evolution:The Department of Science and Innovation: Academy of Science of South Afric

Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates.

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. We designed a five-category ranking score based on the conservation properties of 25 amino acids important for the binding between receptor and virus, classifying all species from very high to very low. Only mammals fell into the medium to very high categories, and only catarrhine primates in the very high category, suggesting that they are at high risk for SARS-CoV-2 infection. We employed a protein structural analysis to qualitatively assess whether amino acid changes at variable residues would be likely to disrupt ACE2/SARS-CoV-2 binding, and found the number of predicted unfavorable changes significantly correlated with the binding score. Extending this analysis to human population data, we found only rare (<0.1%) variants in 10/25 binding sites. In addition, we observed evidence of positive selection in ACE2 in multiple species, including bats. Utilized appropriately, our results may lead to the identification of intermediate host species for SARS-CoV-2, justify the selection of animal models of COVID-19, and assist the conservation of animals both in native habitats and in human care

Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates.

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. We designed a five-category binding score based on the conservation properties of 25 amino acids important for the binding between ACE2 and the SARS-CoV-2 spike protein. Only mammals fell into the medium to very high categories and only catarrhine primates into the very high category, suggesting that they are at high risk for SARS-CoV-2 infection. We employed a protein structural analysis to qualitatively assess whether amino acid changes at variable residues would be likely to disrupt ACE2/SARS-CoV-2 spike protein binding and found the number of predicted unfavorable changes significantly correlated with the binding score. Extending this analysis to human population data, we found only rare (frequency <0.001) variants in 10/25 binding sites. In addition, we found significant signals of selection and accelerated evolution in the ACE2 coding sequence across all mammals, and specific to the bat lineage. Our results, if confirmed by additional experimental data, may lead to the identification of intermediate host species for SARS-CoV-2, guide the selection of animal models of COVID-19, and assist the conservation of animals both in native habitats and in human care

Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates

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. We designed a five-category binding score based on the conservation properties of 25 amino acids important for the binding between ACE2 and the SARS-CoV-2 spike protein. Only mammals fell into the medium to very high categories and only catarrhine primates into the very high category, suggesting that they are at high risk for SARS-CoV-2 infection. We employed a protein structural analysis to qualitatively assess whether amino acid changes at variable residues would be likely to disrupt ACE2/SARS-CoV-2 spike protein binding and found the number of predicted unfavorable changes significantly correlated with the binding score. Extending this analysis to human population data, we found only rare (frequency <0.001) variants in 10/25 binding sites. In addition, we found significant signals of selection and accelerated evolution in the ACE2 coding sequence across all mammals, and specific to the bat lineage. Our results, if confirmed by additional experimental data, may lead to the identification of intermediate host species for SARS-CoV-2, guide the selection of animal models of COVID-19, and assist the conservation of animals both in native habitats and in human care

Evolution of the ancestral mammalian karyotype and syntenic regions

Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes and syntenic relationships at 16 nodes along the mammalian phylogeny. Three different reference genomes (human, sloth, and cattle) representing phylogenetically distinct mammalian superorders were used to assess reference bias in the reconstructed ancestral karyotypes and to expand the number of clades with reconstructed genomes. The mammalian ancestor likely had 19 pairs of autosomes, with nine of the smallest chromosomes shared with the common ancestor of all amniotes (three still conserved in extant mammals), demonstrating a striking conservation of synteny for similar to 320My of vertebrate evolution. The numbers and types of chromosome rearrangements were classified for transitions between the ancestral mammalian karyotype, descendent ancestors, and extant species. For example, 94 inversions, 16 fissions, and 14 fusions that occurred over 53 My differentiated the therian from the descendent eutherian ancestor. The highest breakpoint rate was observed between the mammalian and therian ancestors (3.9 breakpoints/My). Reconstructed mammalian ancestor chromosomes were found to have distinct evolutionary histories reflected in their rates and types of rearrangements. The distributions of genes, repetitive elements, topologically associating domains, and actively transcribed regions in multispecies homologous synteny blocks and evolutionary breakpoint regions indicate that purifying selection acted over millions of years of vertebrate evolution to maintain syntenic relationships of developmentally important genes and regulatory landscapes of gene-dense chromosomes

Evolution of the ancestral mammalian karyotype and syntenic regions

Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes and syntenic relationships at 16 nodes along the mammalian phylogeny. Three different reference genomes (human, sloth, and cattle) representing phylogenetically distinct mammalian superorders were used to assess reference bias in the reconstructed ancestral karyotypes and to expand the number of clades with reconstructed genomes. The mammalian ancestor likely had 19 pairs of autosomes, with nine of the smallest chromosomes shared with the common ancestor of all amniotes (three still conserved in extant mammals), demonstrating a striking conservation of synteny for ∼320 My of vertebrate evolution. The numbers and types of chromosome rearrangements were classified for transitions between the ancestral mammalian karyotype, descendent ancestors, and extant species. For example, 94 inversions, 16 fissions, and 14 fusions that occurred over 53 My differentiated the therian from the descendent eutherian ancestor. The highest breakpoint rate was observed between the mammalian and therian ancestors (3.9 breakpoints/My). Reconstructed mammalian ancestor chromosomes were found to have distinct evolutionary histories reflected in their rates and types of rearrangements. The distributions of genes, repetitive elements, topologically associating domains, and actively transcribed regions in multispecies homologous synteny blocks and evolutionary breakpoint regions indicate that purifying selection acted over millions of years of vertebrate evolution to maintain syntenic relationships of developmentally important genes and regulatory landscapes of gene-dense chromosomes