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Genomic Analyses of Avian Evolution

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A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Animal Diversity".

Deadline for manuscript submissions: closed (31 May 2019) | Viewed by 95878

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Prof. Dr. Peter Houde

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Guest Editor

Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA
Interests: higher level avian phylogeny; phylogenomics; paleontology

Prof. Dr. Michael Wink

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Guest Editor

Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 329, D-69120 Heidelberg, Germany
Interests: phytochemistry; molecular pharmacology of medicinal and toxic plants; alkaloids; evolution; chemical ecology; ornithology; phylogeny and evolution
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Dear Colleagues,

Birds have been the focus of pioneering studies of evolutionary biology for generations, largely because they are abundant, diverse, conspicuous, and charismatic. It is little surprise then that this tradition has positioned birds at the forefront of evolutionary biology in the generation of genomics. Ongoing extensively collaborative programs to sequence whole genomes or a variety of pan-genomic markers of all 10,000 species of living birds further promise to keep birds in the limelight in the near and indefinite future. Such comprehensive taxon sampling provides untold opportunities for comparative studies in well documented phenotypic, adaptive, ecological, behavioral, and demographic contexts, while elucidating differing characteristics of evolutionary processes across the genome and among lineages. This comparative approach is leveraged by coordination and standardization of data pipelines, as well as by encyclopedic knowledge of the natural history of closely-related birds that differ little except with respect to singular traits. Indeed, genomics is a natural extension of many studies of population genetics and speciation that have been ongoing for decades.

This Special Issue of Diversity, “Genomic Analyses of Avian Evolution”, will feature a broad spectrum of original research articles reflecting comprehensive taxonomic sampling projects, the genomic basis and evolution of specific adaptive traits, genome structural variation among lineages, and phylogenetic signal of pan-genomic markers in novel contexts to address potential incomplete lineage sorting. Genomic studies of avian phylogeography and of extinct birds are also anticipated. Committed authors include both icons and up-and-coming mavericks, representing the efforts of both extensive collaborations and independent laboratories. We openly invite further submissions for what will be a prominent thematic compendium of cutting-edge genomic approaches to the evolutionary biology of birds and of genome evolution within birds.

Prof. Peter Houde
Prof. Dr. Michael Wink
Guest Editors

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Keywords

avian genomes
genetics of adaptive traits
phylogenomics

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Published Papers (9 papers)

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Editorial

Jump to: Research, Review

3 pages, 146 KiB

Open AccessEditorial

Special Issue: Genomic Analyses of Avian Evolution

by Peter Houde

Diversity 2019, 11(10), 178; https://doi.org/10.3390/d11100178 - 29 Sep 2019

Cited by 1 | Viewed by 2527

Abstract

“Genomic Analyses of Avian Evolution” is a “state of the art” showcase of the varied and rapidly evolving fields of inquiry enabled and driven by powerful new methods of genome sequencing and assembly as they are applied to some of the world’s most familiar and charismatic organisms—birds. The contributions to this Special Issue are as eclectic as avian genomics itself, but loosely interrelated by common underpinnings of phylogenetic inference, de novo genome assembly of non-model species, and genome organization and content. Full article

(This article belongs to the Special Issue Genomic Analyses of Avian Evolution)

Research

Jump to: Editorial, Review

18 pages, 2024 KiB

Open AccessArticle

A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae)

by Laís A. Coelho, Lukas J. Musher and Joel Cracraft

Diversity 2019, 11(9), 144; https://doi.org/10.3390/d11090144 - 23 Aug 2019

Cited by 8 | Viewed by 5300

Abstract

Current generation high-throughput sequencing technology has facilitated the generation of more genomic-scale data than ever before, thus greatly improving our understanding of avian biology across a range of disciplines. Recent developments in linked-read sequencing (Chromium 10×) and reference-based whole-genome assembly offer an exciting prospect of more accessible chromosome-level genome sequencing in the near future. We sequenced and assembled a genome of the Hairy-crested Antbird (Rhegmatorhina melanosticta), which represents the first publicly available genome for any antbird (Thamnophilidae). Our objectives were to (1) assemble scaffolds to chromosome level based on multiple reference genomes, and report on differences relative to other genomes, (2) assess genome completeness and compare content to other related genomes, and (3) assess the suitability of linked-read sequencing technology for future studies in comparative phylogenomics and population genomics studies. Our R. melanosticta assembly was both highly contiguous (de novo scaffold N50 = 3.3 Mb, reference based N50 = 53.3 Mb) and relatively complete (contained close to 90% of evolutionarily conserved single-copy avian genes and known tetrapod ultraconserved elements). The high contiguity and completeness of this assembly enabled the genome to be successfully mapped to the chromosome level, which uncovered a consistent structural difference between R. melanosticta and other avian genomes. Our results are consistent with the observation that avian genomes are structurally conserved. Additionally, our results demonstrate the utility of linked-read sequencing for non-model genomics. Finally, we demonstrate the value of our R. melanosticta genome for future researchers by mapping reduced representation sequencing data, and by accurately reconstructing the phylogenetic relationships among a sample of thamnophilid species. Full article

(This article belongs to the Special Issue Genomic Analyses of Avian Evolution)

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25 pages, 2515 KiB

Open AccessArticle

The Vertebrate TLR Supergene Family Evolved Dynamically by Gene Gain/Loss and Positive Selection Revealing a Host–Pathogen Arms Race in Birds

by Imran Khan, Emanuel Maldonado, Liliana Silva, Daniela Almeida, Warren E. Johnson, Stephen J. O’Brien, Guojie Zhang, Erich D. Jarvis, M. Thomas P. Gilbert and Agostinho Antunes

Diversity 2019, 11(8), 131; https://doi.org/10.3390/d11080131 - 12 Aug 2019

Cited by 24 | Viewed by 6945

Abstract

The vertebrate toll-like receptor (TLRs) supergene family is a first-line immune defense against viral and non-viral pathogens. Here, comparative evolutionary-genomics of 79 vertebrate species (8 mammals, 48 birds, 11 reptiles, 1 amphibian, and 11 fishes) revealed differential gain/loss of 26 TLRs, including 6 (TLR3, TLR7, TLR8, TLR14, TLR21, and TLR22) that originated early in vertebrate evolution before the diversification of Agnatha and Gnathostomata. Subsequent dynamic gene gain/loss led to lineage-specific diversification with TLR repertoires ranging from 8 subfamilies in birds to 20 in fishes. Lineage-specific loss of TLR8-9 and TLR13 in birds and gains of TLR6 and TLR10-12 in mammals and TLR19-20 and TLR23-27 in fishes. Among avian species, 5–10% of the sites were under positive selection (PS) (omega 1.5–2.5) with radical amino-acid changes likely affecting TLR structure/functionality. In non-viral TLR4 the 20 PS sites (posterior probability PP > 0.99) likely increased ability to cope with diversified ligands (e.g., lipopolysaccharide and lipoteichoic). For viral TLR7, 23 PS sites (PP > 0.99) possibly improved recognition of highly variable viral ssRNAs. Rapid evolution of the TLR supergene family reflects the host–pathogen arms race and the coevolution of ligands/receptors, which follows the premise that birds have been important vectors of zoonotic pathogens and reservoirs for viruses. Full article

(This article belongs to the Special Issue Genomic Analyses of Avian Evolution)

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35 pages, 4018 KiB

Open AccessArticle

A Phylogenomic Supertree of Birds

by Rebecca T. Kimball, Carl H. Oliveros, Ning Wang, Noor D. White, F. Keith Barker, Daniel J. Field, Daniel T. Ksepka, R. Terry Chesser, Robert G. Moyle, Michael J. Braun, Robb T. Brumfield, Brant C. Faircloth, Brian Tilston Smith and Edward L. Braun

Diversity 2019, 11(7), 109; https://doi.org/10.3390/d11070109 - 10 Jul 2019

Cited by 91 | Viewed by 25863

Abstract

It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used these branch lengths to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well. Full article

(This article belongs to the Special Issue Genomic Analyses of Avian Evolution)

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23 pages, 4985 KiB

Open AccessArticle

Phylogenetic Signal of Indels and the Neoavian Radiation

by Peter Houde, Edward L. Braun, Nitish Narula, Uriel Minjares and Siavash Mirarab

Diversity 2019, 11(7), 108; https://doi.org/10.3390/d11070108 - 6 Jul 2019

Cited by 32 | Viewed by 9160

Abstract

The early radiation of Neoaves has been hypothesized to be an intractable “hard polytomy”. We explore the fundamental properties of insertion/deletion alleles (indels), an under-utilized form of genomic data with the potential to help solve this. We scored >5 million indels from >7000 pan-genomic intronic and ultraconserved element (UCE) loci in 48 representatives of all neoavian orders. We found that intronic and UCE indels exhibited less homoplasy than nucleotide (nt) data. Gene trees estimated using indel data were less resolved than those estimated using nt data. Nevertheless, Accurate Species TRee Algorithm (ASTRAL) species trees estimated using indels were generally similar to nt-based ASTRAL trees, albeit with lower support. However, the power of indel gene trees became clear when we combined them with nt gene trees, including a striking result for UCEs. The individual UCE indel and nt ASTRAL trees were incongruent with each other and with the intron ASTRAL trees; however, the combined indel+nt ASTRAL tree was much more congruent with the intronic trees. Finally, combining indel and nt data for both introns and UCEs provided sufficient power to reduce the scope of the polytomy that was previously proposed for several supraordinal lineages of Neoaves. Full article

(This article belongs to the Special Issue Genomic Analyses of Avian Evolution)

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10 pages, 808 KiB

Open AccessArticle

No Signs of Genetic Erosion in a 19th Century Genome of the Extinct Paradise Parrot (Psephotellus pulcherrimus)

by Martin Irestedt, Per G. P. Ericson, Ulf S. Johansson, Paul Oliver, Leo Joseph and Mozes P. K. Blom

Diversity 2019, 11(4), 58; https://doi.org/10.3390/d11040058 - 15 Apr 2019

Cited by 13 | Viewed by 10642

Abstract

The Paradise Parrot, Psephotellus pulcherrimus, was a charismatic Australian bird that became extinct around 1928. While many extrinsic factors have been proposed to explain its disappearance, it remains unclear as to what extent genetic erosion might have contributed to the species’ demise. In this study, we use whole-genome resequencing to reconstruct a 15x coverage genome based on a historical museum specimen and shed further light on the evolutionary history that preceded the extinction of the Paradise Parrot. By comparing the genetic diversity of this genome with genomes from extant endangered birds, we show that during the species’ dramatic decline in the second half of the 19th century, the Paradise Parrot was genetically more diverse than individuals from species that are currently classified as endangered. Furthermore, demographic analyses suggest that the population size of the Paradise Parrot changed with temperature fluctuations during the last glacial cycle. We also confirm that the Golden-shouldered Parrot, Psephotellus chrysopterygius, is the closest living relative of this extinct parrot. Overall, our study highlights the importance of museum collections as repositories of biodiversity across time and demonstrates how historical specimens can provide a broader context on the circumstances that lead to species extinctions. Full article

(This article belongs to the Special Issue Genomic Analyses of Avian Evolution)

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21 pages, 2222 KiB

Open AccessArticle

Mitochondrial Genomes from New Zealand’s Extinct Adzebills (Aves: Aptornithidae: Aptornis) Support a Sister-Taxon Relationship with the Afro-Madagascan Sarothruridae

by Alexander P. Boast, Brendan Chapman, Michael B. Herrera, Trevor H. Worthy, R. Paul Scofield, Alan J. D. Tennyson, Peter Houde, Michael Bunce, Alan Cooper and Kieren J. Mitchell

Diversity 2019, 11(2), 24; https://doi.org/10.3390/d11020024 - 15 Feb 2019

Cited by 21 | Viewed by 13932

Abstract

The recently extinct New Zealand adzebills (Aptornithidae, Aptornis spp.) were an enigmatic group of large flightless birds that have long eluded precise taxonomic assignment as they do not closely resemble any extant birds. Adzebills were nearly wingless, weighed approximately 16–19 kg, and possessed massive adze-like reinforced bills whose function remains unknown. Using hybridisation enrichment and high-throughput sequencing of DNA extracted from subfossil bone and eggshell, near-complete mitochondrial genomes were successfully assembled from the two Quaternary adzebill species: the North Island Adzebill (Aptornis otidiformis) and South Island Adzebill (A. defossor). Molecular phylogenetic analyses confirm that adzebills are members of the Ralloidea (rails and allies) and are sister-taxon to the Sarothruridae, which our results suggest comprises the Madagascan wood rails (Mentocrex, two likely sp.) in addition to the tiny (<50 gram) rail-like Afro-Madagascan flufftails (Sarothrura, 9 spp.). Node age estimates indicate that the split between adzebills and Sarothruridae occurred ~39.6 Ma, suggesting that the ancestors of the adzebills arrived in New Zealand by long-distance dispersal rather than continental vicariance. This newly identified biogeographic link between physically distant New Zealand and Afro-Madagascar, echoed by the relationship between the New Zealand kiwi (Apterygiformes) and Madagascan elephant-birds (Aepyornithiformes), suggests that the adzebill’s near relatives were formerly more widespread. In addition, our estimate for the divergence time between the two Quaternary adzebill species (0.2–2.3 Ma) coincides with the emergence of a land-bridge between the North and South islands of New Zealand (ca. 1.5–2 Ma). This relatively recent divergence suggests that North Island adzebills are the result of a relatively recent dispersal from the South Island, from which the earliest (Miocene) adzebill fossil has been described. Full article

(This article belongs to the Special Issue Genomic Analyses of Avian Evolution)

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12 pages, 3346 KiB

Open AccessArticle

Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation

by Sunitha Joseph, Rebecca E. O’Connor, Abdullah F. Al Mutery, Mick Watson, Denis M. Larkin and Darren K. Griffin

Diversity 2018, 10(4), 113; https://doi.org/10.3390/d10040113 - 18 Oct 2018

Cited by 26 | Viewed by 7606

Abstract

Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology, including morphology, ecology, and physiology, and are thus essential for their care and conservation. A key aspect of the genome of any species is its karyotype, which can then be linked to the whole genome sequence to generate a so-called chromosome-level assembly. Chromosome-level assemblies are essential for marker assisted selection and genotype-phenotype correlations in breeding regimes, as well as determining patterns of gross genomic evolution. To date, only two falcon species have been sequenced and neither initially were assembled to the chromosome level. Falcons have atypical avian karyotypes with fewer chromosomes than other birds, presumably brought about by wholesale fusion. To date, however, published chromosome preparations are of poor quality, few chromosomes have been distinguished and standard ideograms have not been made. The purposes of this study were to generate analyzable karyotypes and ideograms of peregrine, saker, and gyr falcons, report on our recent generation of chromosome level sequence assemblies of peregrine and saker falcons, and for the first time, sequence the gyr falcon genome. Finally, we aimed to generate comparative genomic data between all three species and the reference chicken genome. Results revealed a diploid number of 2n = 50 for peregrine falcon and 2n = 52 for saker and gyr through high quality banded chromosomes. Standard ideograms that are generated here helped to map predicted chromosomal fragments (PCFs) from the genome sequences directly to chromosomes and thus generate chromosome level sequence assemblies for peregrine and saker falcons. Whole genome sequencing was successful in gyr falcon, but read depth and coverage was not sufficient to generate a chromosome level assembly. Nonetheless, comparative genomics revealed no differences in genome organization between gyr and saker falcons. When compared to peregrine falcon, saker/gyr differed by one interchromosomal and seven intrachromosomal rearrangements (a fusion plus seven inversions), whereas peregrine and saker/gyr differ from the reference chicken genome by 14/13 fusions (11 microchromosomal) and six fissions. The chromosomal differences between the species could potentially provide the basis of a screening test for hybrid animals. Full article

(This article belongs to the Special Issue Genomic Analyses of Avian Evolution)

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Review

Jump to: Editorial, Research

19 pages, 2527 KiB

Open AccessReview

Comparative Phylogenomics, a Stepping Stone for Bird Biodiversity Studies

by Josefin Stiller and Guojie Zhang

Diversity 2019, 11(7), 115; https://doi.org/10.3390/d11070115 - 18 Jul 2019

Cited by 24 | Viewed by 12268

Abstract

Birds are a group with immense availability of genomic resources, and hundreds of forthcoming genomes at the doorstep. We review recent developments in whole genome sequencing, phylogenomics, and comparative genomics of birds. Short read based genome assemblies are common, largely due to efforts of the Bird 10K genome project (B10K). Chromosome-level assemblies are expected to increase due to improved long-read sequencing. The available genomic data has enabled the reconstruction of the bird tree of life with increasing confidence and resolution, but challenges remain in the early splits of Neoaves due to their explosive diversification after the Cretaceous-Paleogene (K-Pg) event. Continued genomic sampling of the bird tree of life will not just better reflect their evolutionary history but also shine new light onto the organization of phylogenetic signal and conflict across the genome. The comparatively simple architecture of avian genomes makes them a powerful system to study the molecular foundation of bird specific traits. Birds are on the verge of becoming an extremely resourceful system to study biodiversity from the nucleotide up. Full article

(This article belongs to the Special Issue Genomic Analyses of Avian Evolution)

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