Evolutionary constraint and acceleration are powerful, cell-type agnostic measures of functional importance. Previous studies in mammals were limited by species number and reliance on human-referenced alignments. We explore the evolution of placental mammals, including humans, through reference-free whole-genome alignment of 240 species and protein-coding alignments for 428 species. We estimate 10.7% of the human genome is evolutionarily constrained. We resolve constraint to single nucleotides, pinpointing functional positions, and refine and expand by over seven-fold the catalog of ultraconserved elements. Overall, 48.5% of constrained bases are as yet unannotated, suggesting yet-to-be-discovered functional importance. Using species-level phenotypes and an updated phylogeny, we associate coding and regulatory variation with olfaction and hibernation. Focusing on biodiversity conservation, we identify genomic metrics that predict species at risk of extinction.

Evolutionary constraint and innovation across hundreds of placental mammals

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 signal using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic timetrees reveal an accumulation of cladogenic events before and immediately following the KPg boundary implying important roles for Cretaceous continental vicariance and the KPg extinction in the placental radiation. One-Sentence Summary A comprehensive whole genome phylogeny of extant placental mammals reveals timing and patterns of ordinal diversification.

A genomic timescale for placental mammal evolution

Abstract Chromosomes are a central unit of genome organization. One-tenth of all described species on Earth are butterflies and moths, the Lepidoptera, which generally possess 31 chromosomes. However, some species display dramatic variation in chromosome number. Here we analyse 210 chromosomally complete lepidopteran genomes and show that the chromosomes of extant lepidopterans are derived from 32 ancestral linkage groups, which we term Merian elements. Merian elements have remained largely intact through 250 million years of evolution and diversification. Against this stable background, eight lineages have undergone extensive reorganization either through numerous fissions or a combination of fusion and fission events. Outside these lineages, fusions are rare and fissions are rarer still. Fusions often involve small, repeat-rich Merian elements and the sex-linked element. Our results reveal the constraints on genome architecture in Lepidoptera and provide a deeper understanding of chromosomal rearrangements in eukaryotic genome evolution. 

Comparative genomics reveals the dynamics of chromosome evolution in Lepidoptera.

Abstract Chromosomes are a central unit of genome organisation. One tenth of all described species on Earth are Lepidoptera, butterflies and moths, and these generally possess 31 holocentric chromosomes. However, a subset of lepidopteran species display dramatic variation in chromosome counts. By analysing 210 chromosomally-complete lepidopteran genomes, the largest analysis of eukaryotic chromosomal-level reference genomes to date, we show that the diverse karyotypes of extant species are derived from 32 ancestral linkage groups, which we term Merian elements. Merian elements have remained largely intact across 250 million years of evolution and diversification. Against this stable background, we identify eight independent lineages that have evaded constraint and undergone extensive reorganisation - either by numerous fissions or a combination of fusion and fission events. Outside these lineages, fusions are rare and fissions are rarer still. Fusions tend to involve small, repeat-rich Merian elements and/or the Z chromosome. Together, our results reveal the constraints on genome architecture in Lepidoptera and enable a deeper understanding of the importance of chromosomal rearrangements in shaping the evolution of eukaryotic genomes. 

/pdf/chromosome-evolution-in-lepidoptera-27y1rmod.pdf

Chromosome evolution in Lepidoptera

Kay Lucek1, Mabel D. Giménez2,3, Mathieu Joron4, Marina Rafajlović5,6, Jeremy B. Searle7, Nora Walden8, Anja Marie Westram9,10 and Rui Faria11,12 1Biodiversity Genomics Laboratory, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland 2Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Genética Humana de Misiones (IGeHM), Parque de la Salud de la Provincia de Misiones “Dr. Ramón Madariaga,” N3300KAZ Posadas, Misiones, Argentina 3Facultad de Ciencias Exactas Químicas y Naturales, Universidad Nacional de Misiones, N3300LQH Posadas, Misiones, Argentina 4Centre d'Ecologie Fonctionnelle et Evolutive, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier, France 5Department of Marine Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden 6Centre for Marine Evolutionary Biology, University of Gothenburg, 405 30 Gothenburg, Sweden 7Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA 8Centre for Organismal Studies, University of Heidelberg, 69117 Heidelberg, Germany 9Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria 10Faculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway 11CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, CIBIO, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal 12BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal Correspondence: kay.lucek{at}unine.ch; ruifaria{at}cibio.up.pt 

The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.

Significance Computational reconstruction of ancestral mammalian karyotypes revealed a comprehensive picture of the chromosome rearrangements that occurred over the evolutionary history of mammals. Ancient gene order, in some cases extending to full chromosomes, was found conserved for more than 300 My, demonstrating strong evolutionary constraint against rearrangements in some regions. Conserved segments of chromosomes are enriched for genes that control developmental processes. Therefore, Darwinian selection likely maintains ancient gene combinations while allowing for genomic innovations within or near chromosomal sites that break and rearrange over evolutionary time. The revealed relationship between the three-dimensional structure of chromosomes and the evolutionary stability of chromosome segments provides additional insights into the mechanisms of chromosome evolution and diseases associated with genome rearrangements.

Evolution of the ancestral mammalian karyotype and syntenic regions

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Evolution of the ancestral mammalian karyotype and syntenic regions