Volume 11 Issue 1
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George P. Tiley, Akanksha Pandey, Rebecca T. Kimball, Edward L. Braun, J. Gordon Burleigh. 2020: Whole genome phylogeny of Gallus: introgression and data-type effects. Avian Research, 11(1): 7. DOI: 10.1186/s40657-020-00194-w
Citation: George P. Tiley, Akanksha Pandey, Rebecca T. Kimball, Edward L. Braun, J. Gordon Burleigh. 2020: Whole genome phylogeny of Gallus: introgression and data-type effects. Avian Research, 11(1): 7. DOI: 10.1186/s40657-020-00194-w
shu

Whole genome phylogeny of Gallus: introgression and data-type effects

  • 1.

    Department of Biology, University of Florida, Gainesville, FL 32611, USA

  • 2.

    Department of Biology, Duke University, Durham, NC 27708, USA

More Information
  • Corresponding author:

    J. Gordon Burleigh, gburleigh@ufl.edu

  • Received Date: 05 Nov 2019
  • Accepted Date: 06 Mar 2020
  • Available Online: 24 Apr 2022
  • Publish Date: 16 Mar 2020
    Graphical Abstract
    • Abstract
  • Background 

    Previous phylogenetic studies that include the four recognized species of Gallus have resulted in a number of distinct topologies, with little agreement. Several factors could lead to the failure to converge on a consistent topology, including introgression, incomplete lineage sorting, different data types, or insufficient data.

    Methods 

    We generated three novel whole genome assemblies for Gallus species, which we combined with data from the published genomes of Gallus gallus and Bambusicola thoracicus (a member of the sister genus to Gallus). To determine why previous studies have failed to converge on a single topology, we extracted large numbers of orthologous exons, introns, ultra-conserved elements, and conserved non-exonic elements from the genome assemblies. This provided more than 32 million base pairs of data that we used for concatenated maximum likelihood and multispecies coalescent analyses of Gallus.

    Results 

    All of our analyses, regardless of data type, yielded a single, well-supported topology. We found some evidence for ancient introgression involving specific Gallus lineages as well as modest data type effects that had an impact on support and branch length estimates in specific analyses. However, the estimated gene tree spectra for all data types had a relatively good fit to their expectation given the multispecies coalescent.

    Conclusions 

    Overall, our data suggest that conflicts among previous studies probably reflect the use of smaller datasets (both in terms of number of sites and of loci) in those analyses. Our results demonstrate the importance of sampling large numbers of loci, each of which has a sufficient number of sites to provide robust estimates of gene trees. Low-coverage whole genome sequencing, as we did here, represents a cost-effective means to generate the very large data sets that include multiple data types that enabled us to obtain a robust estimate of Gallus phylogeny.

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  • On 21 May, 2012, a female Brown-fronted Woodpecker (Dendrocopos auriceps) was observed and photographed (Fig. 1) at 11:20 am in the Jilong Valley of the Mount Qomolangma Region, China. This is the first record in China of this bird (MacKinnon et al., 2000; Zheng, 2011). The coordinates of the site are 28°19′25.03″N, 85°20′29.70″E and its elevation is 2150 m. As well, at a distance of about 3 km, we sighted one male woodpecker at 11:08 on 8 August. The record site is 28°20′02.49″N, 85°20′46.30″E at an elevation of 2197 m.

    Figure  1.  A female Brown-fronted Woodpecker (Dendrocopos auriceps) (Photo by Jingjing LI)
    DownLoad: Full-Size Img PowerPoint

    From top to bottom, the biotope types of the Jilong Valley are subtropical evergreen broadleaved forests, temperate coniferous and broadleaved mixed mountain forests, cold-temperate coniferous mountain forests, subalpine shrubs and meadows, alpine cold meadow cushion vegetation and alpine cryic moraine lichen belts. The range in elevation of the temperate coniferous and dry broadleaved mixed forests in the mountains is between 1900 and 2200 m.

    When we sighted the Brown-fronted female Woodpecker, she was foraging on a tree, a Celtis tetrandra, belonging to the Rhamnaceae family. The male was taking a break at a dead pine tree. The cover type is a mountain temperate coniferous and dry broadleaved mixed forest (mainly coniferous forest).

    The morphological traits of the female are as follows: brownish forehead and crown, white-barred upperparts, prominent black moustachial stripe, a black stripe from the back of neck extending through to the dorsum, well-defined streaking on the underparts, pink undertail-coverts and unbarred central tail feathers (Fig. 1). The male has a distinct yellow central crown on his head, which is prominently different from the female.

    It has been recorded as a resident in Afghanistan, India, Nepal and Pakistan. In Nepal, it is fairly common and widespread in coniferous and dry broadleaved mixed forests, ranging in elevation from 1065 to 2440 m. In Pakistan it is also resident but rare and uncommon (Raja et al., 1999; Grimmett et al., 2000; Girish and Asad, 2006; Darulaman, 2008). Because of a lack of more information, we may deduce that the Brown-fronted Woodpecker is found mainly in the valleys of southern exposed Himalayan slopes.

    The elevations at which this species is found at Jilong are essentially the same as those in other countries. We assume it is also a resident species in Jilong because of its appearance at this season. We believe more individuals and nests will be found after further surveys and searches.

    We are grateful to Prof. Zhang Zhengwang who works in Beijing Normal University for verifying the new record. We thank Prof. Xie Qiang who works in Guangxi Normal University for identifying the broadleaved trees.

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