Special Issue "Genomic Analyses of Avian Evolution"

A special issue of Diversity (ISSN 1424-2818).

Deadline for manuscript submissions: 31 May 2019

Special Issue Editors

Guest Editor
Prof. Peter Houde

New Mexico State University Las Cruces, Department of Biology, Las Cruces, United States
Website | E-Mail
Interests: higher level avian phylogeny; phylogenomics; paleontology
Guest Editor
Prof. Dr. Michael Wink

Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
Website | E-Mail
Phone: 06221 544881
Fax: +49 6221 544884
Interests: phytochemistry, molecular pharmacology of medicinal and toxic plants, alkaloids, evolution, chemical ecology

Special Issue Information

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

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diversity is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 850 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • avian genomes
  • genetics of adaptive traits
  • phylogenomics

Published Papers (3 papers)

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Research

Open AccessArticle No Signs of Genetic Erosion in a 19th Century Genome of the Extinct Paradise Parrot (Psephotellus pulcherrimus)
Diversity 2019, 11(4), 58; https://doi.org/10.3390/d11040058
Received: 7 March 2019 / Revised: 5 April 2019 / Accepted: 8 April 2019 / Published: 15 April 2019
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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. [...] Read more.
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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Graphical abstract

Open AccessArticle Mitochondrial Genomes from New Zealand’s Extinct Adzebills (Aves: Aptornithidae: Aptornis) Support a Sister-Taxon Relationship with the Afro-Madagascan Sarothruridae
Diversity 2019, 11(2), 24; https://doi.org/10.3390/d11020024
Received: 4 December 2018 / Revised: 25 January 2019 / Accepted: 28 January 2019 / Published: 15 February 2019
PDF Full-text (2222 KB) | HTML Full-text | XML Full-text | Supplementary Files
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 [...] Read more.
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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Open AccessArticle Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation
Diversity 2018, 10(4), 113; https://doi.org/10.3390/d10040113
Received: 29 August 2018 / Revised: 25 September 2018 / Accepted: 29 September 2018 / Published: 18 October 2018
Cited by 1 | PDF Full-text (3346 KB) | HTML Full-text | XML Full-text | Supplementary Files
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 [...] Read more.
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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