Author
Andrew Dixon
Other affiliations: Environment Agency Abu Dhabi, University of Leicester
Bio: Andrew Dixon is an academic researcher from Cardiff University. The author has contributed to research in topics: Saker falcon & Population. The author has an hindex of 15, co-authored 41 publications receiving 3319 citations. Previous affiliations of Andrew Dixon include Environment Agency Abu Dhabi & University of Leicester.
Topics: Saker falcon, Population, Nest, Electrocution, Emberiza schoeniclus
Papers
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Duke University1, University of Texas at Austin2, Heidelberg Institute for Theoretical Studies3, Xi'an Jiaotong University4, Beijing Genomics Institute5, American Museum of Natural History6, New Mexico State University7, University of Sydney8, University of California9, Uppsala University10, University of Copenhagen11, Okinawa Institute of Science and Technology12, University of Georgia13, Griffith University14, Catalan Institution for Research and Advanced Studies15, Joint Institute for Nuclear Research16, Oak Ridge National Laboratory17, Aarhus University18, Washington University in St. Louis19, University of California, Santa Cruz20, Cardiff University21, Kunming Institute of Zoology22, China Agricultural University23, Louisiana State University24, Tulane University25, Copenhagen Zoo26, Oregon Health & Science University27, Federal University of Pará28, Technical University of Denmark29, Canterbury Museum30, Curtin University31, Novosibirsk State University32, Smithsonian Institution33, National University of Singapore34, National Museum of Natural History35, Nova Southeastern University36, Occidental College37, University of Edinburgh38, Harvard University39, University of California, San Francisco40, University of Florida41, University of Illinois at Urbana–Champaign42
TL;DR: A genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves recovered a highly resolved tree that confirms previously controversial sister or close relationships and identifies the first divergence in Neoaves, two groups the authors named Passerea and Columbea.
Abstract: To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
1,624 citations
University of Copenhagen1, Beijing Genomics Institute2, Royal Veterinary College3, Seoul National University4, University of Nebraska–Lincoln5, University of Porto6, University of South Carolina7, Montclair State University8, Uppsala University9, National University of Singapore10, University of California, Berkeley11, South China University of Technology12, Chinese Academy of Sciences13, Kunming Institute of Zoology14, Howard Hughes Medical Institute15, Aberystwyth University16, University of Kent17, University of California, Riverside18, Mississippi State University19, Austral University of Chile20, Swedish University of Agricultural Sciences21, China Agricultural University22, Cardiff University23, Copenhagen Zoo24, Louisiana State University25, Washington University in St. Louis26, Xi'an Jiaotong University27, University of California, Santa Cruz28, Nova Southeastern University Oceanographic Center29, Smithsonian Conservation Biology Institute30, National Museum of Natural History31, Natural History Museum32, University of California, San Francisco33, Harvard University34, University of Florida35, University of Edinburgh36, New Mexico State University37, Macau University of Science and Technology38, Curtin University39
TL;DR: This work explored bird macroevolution using full genomes from 48 avian species representing all major extant clades to reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
Abstract: Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
872 citations
TL;DR: An exceptionally high proportion of extra-pair paternity is found in a wild population of reed buntings using single-locus DNA fingerprinting and it is proposed that males can assess their likelihood of paternity and adjust their nestling provisioning rates accordingly.
Abstract: EXTRA-PAIR copulations, in which a female copulates with a male other than her mate, are known to occur in many bird species1. Here we study a wild population of reed buntings, Emberiza schoeniclus, using single-locus DNA fingerprinting2,3 and find an exceptionally high proportion of extra-pair paternity that accounts for 55% (118/216) of young and 86% (50/58) of nests. Twelve pairs each raised two broods in a single season in which the proportion of extra-pair young differed between the two broods. A highly significant relationship between a male's parental investment and his degree of paternity was revealed by a comparison between the first and second brood of each pair, with more paternal care usually being provided at the nest that contained a lower proportion of extra-pair young. We propose that males can assess their likelihood of paternity and adjust their nestling provisioning rates accordingly.
345 citations
TL;DR: The isolation and characterization of six microsatellite loci in the reed bunting, Ernberim schoeniclus (Fringillidae) is reported and cross-species amplification of the loci was also investigated in 13 other passerine species.
Abstract: Microsatellite loci consist of tandem repeats of short DNA sequences (5 5 bp), usually of less than 100 bp total length. These loci can be polymorphic due to variation between alleles in the number of repeat units. The application of such markers in molecular ecology is a recent development but it seems very likely that that they will be intensively used in the future (see Bruford & Wayne 1993 for a review). Polymorphic microsatellites have been reported in a variety of organisms including birds ( e g Ellegren 1992). Here, we report the isolation and characterization of six microsatellite loci in the reed bunting, Ernberim schoeniclus (Fringillidae). Cross-species amplification of the loci was also investigated in 13 other passerine species. Microsatellite loci were isolated after screening a reed bunting plasmid library with the dinucleotide probes (AC/GT),, and (AG/CT),, (Pharmacia) following standard procedures (Rassmann et al. 1991; Sambrook et al. 1989). Twenty-three positive clones were sequenced. Primers were designed for six loci (Escpl, Esc& Escp3, Esq.14, EscS , Escp6) (Table 1). PCR reactions were performed under the following conditions: 1 min at 94 \"C, 1 min at 55 \"C (Escpl, Escp2, Escp4, Escp5) or 52 \"C (Escp3, Escp6), and 1 min at 72 \"C (25 cycles) using a DNA thermal cycler (Techne PHC-3). Each PCR reaction (following Jeffreys et al. 1988) included 10-20 ng of total genomic DNA, 67m Tris-HC1 (pH 8.8), 16.6-m ammonium sulphate, 6.7mM MgCl,, 1 0 w 2-mercaptoethanol, 6 . 7 p ~ EDTA, 1.5 m of each nucleotide (Pharmacia), 170 mg/mL BSA (DNAase free, Pharmacia) and 10 pmoles of each primer in a total of 10 pL of distilled water. The PCR was initiated with a 'hot start' by first heating the samples for 5 min at 94 \"C and by adding the Tnq DNA polymerase (1 unit/ sample, Advanced Biotechnologies) just before the first annealing step at 55 or 52 \"C. Following this PCR, a single band of the predicted size was seen for all the loci except
171 citations
TL;DR: In this paper, the genomes of both the peregrine and saker falcons were sequenced using Illumina deep sequencing with greater than 100-fold coverage, with transcriptome-assisted prediction of approximately 16,200 genes for both species.
Abstract: As top predators, falcons possess unique morphological, physiological and behavioral adaptations that allow them to be successful hunters: for example, the peregrine is renowned as the world's fastest animal. To examine the evolutionary basis of predatory adaptations, we sequenced the genomes of both the peregrine (Falco peregrinus) and saker falcon (Falco cherrug), and we present parallel, genome-wide evidence for evolutionary innovation and selection for a predatory lifestyle. The genomes, assembled using Illumina deep sequencing with greater than 100-fold coverage, are both approximately 1.2 Gb in length, with transcriptome-assisted prediction of approximately 16,200 genes for both species. Analysis of 8,424 orthologs in both falcons, chicken, zebra finch and turkey identified consistent evidence for genome-wide rapid evolution in these raptors. SNP-based inference showed contrasting recent demographic trajectories for the two falcons, and gene-based analysis highlighted falcon-specific evolutionary novelties for beak development and olfaction and specifically for homeostasis-related genes in the arid environment–adapted saker.
156 citations
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Journal Article•
TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
11,521 citations
TL;DR: The approach to utilizing available RNA-Seq and other data types in the authors' manual curation process for vertebrate, plant, and other species is summarized, and a new direction for prokaryotic genomes and protein name management is described.
Abstract: The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.
4,104 citations
TL;DR: PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses that includes the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, and new output formats to facilitate interoperability with downstream software.
Abstract: PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder. The source code is available at https://github.com/brettc/partitionfinder.
3,445 citations
Journal Article•
TL;DR: In this paper, a test based on two conserved CHD (chromo-helicase-DNA-binding) genes that are located on the avian sex chromosomes of all birds, with the possible exception of the ratites (ostriches, etc.).
2,554 citations
01 Jan 1998
TL;DR: This chapter discusses Sperm Competition in Birds, Sexual Selection in Spiders and Other Arachnids, and Reproduction, Mating Strategies and Sperm competition in Marsupials and Monotremes.
Abstract: General Themes: G.A. Parker, Sperm Competition and the Evolution of Ejaculates: Towards a Theory Base. A.P. Moller, Sperm Competition and Sexual Selection. W.G. Eberhard, Female Roles in Sperm Competition. J. Wright, Paternity and Paternal Care. Taxonomic Treatments: L.F. Delph and K. Havens, Pollen Competition in Flowering Plants. D.R. Levitan, Sperm Limitation, Gamete Competition and Sexual Selection in External Fertilizers. N.K. Michiels, Mating Conflicts and Sperm Competition in Simultaneous Hermaphrodites. B. Baur, Sperm Competition in Molluscs. M.A. Elgar, Sperm Competition and Sexual Selection in Spiders and Other Arachnids. L.W. Simmons and M.T. Siva-Jothy, Sperm Competition in Insects: Mechanisms and the Potential for Selection. C.W. Petersen and R.R. Warner, Sperm Competition in Fishes. T.R. Halliday, Sperm Competition in Amphibians. M. Olsson and T. Madsen, Sexual Selection and Sperm Competition in Reptiles. T.R. Birkhead, Sperm Competition in Birds: Mechanisms and Function. D.A. Taggart, W.G. Breed, P.D. Temple-Smith, A. Purvis, and G. Shimmin, Reproduction, Mating Strategies and Sperm Competition in Marsupials and Monotremes. M. Gomendio, A.H. Harcourt, and E.R.S. Roldan, Sperm Competition in Mammals. T.R. Birkhead and A.P. Moller, Sperm Competition, Sexual Selection and Different Routes to Fitness. Index.
2,051 citations