Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

ND2 haplotype alignemt of the pine siskin and black-capped siskin complex

Spinus pinus, Spinus atriceps and Spinus notatus haplotype alignment; NADH dehydrogenase subunit 2 (ND2) gene, partial cds; mitochondria

Speciation in mountain refugia: Phylogeography and demographic history of the pine siskin and black-capped siskin complex

Following Pleistocene glacial maxima, species that adapted to temperate climates in low-latitude refugia had to modify their ranges as climate changed, expanding either latitudinally towards the poles, or altitudinally to higher elevations in mountainous regions. Within just a few thousand years, populations taking alternative routes during interglacials became isolated from each other and subjected to different selection pressures, often leading to lineage divergence and speciation. The pine siskin Spinus pinus is a common and widespread songbird showing relative phenotypic uniformity across the North American continent. One exception is the subspecies found in the highlands of northern Central America (S. p. perplexus), which shows marked differentiation in plumage color and shares some traits with the endemic and partly sympatric black-capped siskin S. atriceps, suggesting potential introgression or even a hybrid origin of perplexus. Relationships and species limits among pinus, perplexus and atriceps have been controversial for decades. We provide new molecular evidence to help resolve the evolutionary history of the group. Phylogenetic analysis of mitochondrial DNA and nuclear intron sequences revealed three distinct lineages within the complex, corresponding to: 1) S. pinus individuals from Canada through central Mexico (S. p. pinus and S. p. macropterus), 2) individuals from the highlands of Guatemala and Chiapas (S. p. perplexus), and 3) S. atriceps. Pine siskins across North America show evidence of a recent postglacial population expansion and extremely low levels of diversity and structure. In contrast, S. p. perplexus shows evidence of demographic stasis, reflecting long-term isolation and restricted dispersal. Marked and diagnostic genetic differences among the three lineages in mtDNA and at least one intron, suggest that a hybrid origin of S. p. perplexus is unlikely, yet some degree of introgression between S. p. perplexus and S. atriceps cannot be ruled out in localities where they occur in sympatry.Peer Reviewe

Data from: Speciation in mountain refugia: phylogeography and demographic history of the pine siskin and black-capped siskin complex

Following Pleistocene glacial maxima, species that adapted to temperate climates in low-latitude refugia had to modify their ranges as climate changed, expanding either latitudinally towards the poles, or altitudinally to higher elevations in mountainous regions. Within just a few thousand years, populations taking alternative routes during interglacials became isolated from each other and subjected to different selection pressures, often leading to lineage divergence and speciation. The pine siskin Spinus pinus is a common and widespread songbird showing relative phenotypic uniformity across the North American continent. One exception is the subspecies found in the highlands of northern Central America (S. p. perplexus), which shows marked differentiation in plumage color and shares some traits with the endemic and partly sympatric black-capped siskin S. atriceps, suggesting potential introgression or even a hybrid origin of perplexus. Relationships and species limits among pinus, perplexus and atriceps have been controversial for decades. We provide new molecular evidence to help resolve the evolutionary history of the group. Phylogenetic analysis of mitochondrial DNA and nuclear intron sequences revealed three distinct lineages within the complex, corresponding to: 1) S. pinus individuals from Canada through central Mexico (S. p. pinus and S. p. macropterus), 2) individuals from the highlands of Guatemala and Chiapas (S. p. perplexus), and 3) S. atriceps. Pine siskins across North America show evidence of a recent postglacial population expansion and extremely low levels of diversity and structure. In contrast, S. p. perplexus shows evidence of demographic stasis, reflecting long-term isolation and restricted dispersal. Marked and diagnostic genetic differences among the three lineages in mtDNA and at least one intron, suggest that a hybrid origin of S. p. perplexus is unlikely, yet some degree of introgression between S. p. perplexus and S. atriceps cannot be ruled out in localities where they occur in sympatry

BRM15 haplotype alignemt of the pine siskin and black-capped siskin complex

Spinus pinus, Spinus atriceps and Spinus notatus haplotype alignment; brahma protein (BRM) gene, intron 1

ATP haplotype alignemt of the pine siskin and black-capped siskin complex

Spinus pinus, Spinus atriceps and Spinus notatus haplotype alignment; cytochrome c oxidase subunit II gene, partial cds; tRNA-Lys gene, complete sequence; ATP synthase 8 gene, complete cds; and ATP synthase 6 gene, partial cds; mitochondria

A Highly Contiguous Reference Genome for Northern Bobwhite (Colinus virginianus)

Northern bobwhites (Colinus virginianus) are small quails in the New World Quail family (Odontophoridae) and are one of the most phenotypically diverse avian species. Despite extensive research on bobwhite ecology, genomic studies investigating the evolution of phenotypic diversity in this species are lacking. Here, we present a new, highly contiguous assembly for bobwhites using tissue samples from a vouchered, wild, female bird collected in Louisiana. By performing a de novo assembly and scaffolding the assembly with Dovetail Chicago and HiC libraries and the HiRise pipeline, we produced an 866.8 Mb assembly including 1,512 scaffolds with a scaffold N50 of 66.8 Mb, a scaffold L90 of 17, and a BUSCO completeness score of 90.8%. This new assembly represents approximately 96% of the non-repetitive and 84% of the entire bobwhite genome size, greatly improves scaffold lengths and contiguity compared to an existing draft bobwhite genome, and provides an important tool for future studies of evolutionary and functional genomics in bobwhites

Extensive paraphyly in the typical owl family (Strigidae)

© 2019 American Ornithological Society 2019. Published by Oxford University Press for the American Ornithological Society. The typical owl family (Strigidae) comprises 194 species in 28 genera, 14 of which are monotypic. Relationships within and among genera in the typical owls have been challenging to discern because mitochondrial data have produced equivocal results and because many monotypic genera have been omitted from previous molecular analyses. Here, we collected and analyzed DNA sequences of ultraconserved elements (UCEs) from 43 species of typical owls to produce concatenated and multispecies coalescent-based phylogenetic hypotheses for all but one genus in the typical owl family. Our results reveal extensive paraphyly of taxonomic groups across phylogenies inferred using different analytical approaches and suggest the genera Athene, Otus, Asio, Megascops, Bubo, and Strix are paraphyletic, whereas Ninox and Glaucidium are polyphyletic. Secondary analyses of protein-coding mitochondrial genes harvested from off-target sequencing reads and mitochondrial genomes downloaded from GenBank generally support the extent of paraphyly we observe, although some disagreements exist at higher taxonomic levels between our nuclear and mitochondrial phylogenetic hypotheses. Overall, our results demonstrate the importance of taxon sampling for understanding and describing evolutionary relationships in this group, as well as the need for additional sampling, study, and taxonomic revision of typical owl species. Additionally, our findings highlight how both divergence and convergence in morphological characters have obscured our understanding of the evolutionary history of typical owls, particularly those with insular distributions