Genomic differentiation tracks earth-historic isolation in an Indo-Australasian archipelagic pitta (Pittidae; Aves) complex.

Item request has been placed! ×
Item request cannot be made. ×
loading   Processing Request
Read Online Read More Add to Saved list
  • Additional Information
    • Source:
      Publisher: BioMed Central Country of Publication: England NLM ID: 100966975 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2148 (Electronic) Linking ISSN: 14712148 NLM ISO Abbreviation: BMC Evol Biol Subsets: MEDLINE
    • Publication Information:
      Original Publication: London : BioMed Central, [2001-
    • Subject Terms:
      Earth, Planet* ; Genome* ; Islands*; Passeriformes/*genetics; Animals ; Australia ; Gene Flow ; Genetic Variation ; India ; Phylogeny ; Phylogeography ; Population Dynamics ; Principal Component Analysis ; Time Factors
    • Abstract:
      Background: Allopatric speciation has played a particularly important role in archipelagic settings where populations evolve in isolation after colonizing different islands. The Indo-Australasian island realm is an unparalleled natural laboratory of biotic diversification. Here we explore how the level of earth-historic isolation has influenced genetic differentiation across the region by investigating phylogeographic patterns in the Pitta sordida species complex.
      Results: We generated a de novo genome and compared population genomics of 29 individuals of Pitta sordida from the entire distributional range and we reconstructed phylogenetic relationship using mitogenomes, a multi-nuclear gene dataset and single nucleotide polymorphisms (SNPs). We found deep divergence between an eastern and a western group of taxa across Indo-Australasia. Within both groups we have identified major lineages that are geographically separated into Philippines, Borneo, western Sundaland, and New Guinea, respectively. Although these lineages are genetically well-differentiated, suggesting a long-term isolation, there are signatures of extensive gene flow within each lineage throughout the Pleistocene, despite the wide geographic range occupied by some of them. We found little evidence of hybridization or introgression among the studied taxa, but forsteni from Sulawesi makes an exception. This individual, belonging to the eastern clade, is genetically admixed between the western and eastern clades. Geographically this makes sense as Sulawesi is not far from Borneo that houses a population of hooded pittas that belongs to the western clade.
      Conclusions: We found that geological vicariance events cannot explain the current genetic differentiation in the Pitta sordida species complex. Instead, the glacial-interglacial cycles may have played a major role therein. During glacials the sea level could be up to 120 m lower than today and land bridges formed within both the Sunda Shelf and the Sahul Shelf permitting dispersal of floral and faunal elements. The geographic distribution of hooded pittas shows the importance of overwater, "stepping-stone" dispersals not only to deep-sea islands, but also from one shelf to the other. The most parsimonious hypothesis is an Asian ancestral home of the Pitta sordida species complex and a colonization from west to east, probably via Wallacea.
    • References:
      Mol Biol Evol. 2011 Aug;28(8):2239-52. (PMID: 21325092)
      Mol Biol Evol. 2017 Dec 1;34(12):3299-3302. (PMID: 29029172)
      Nat Genet. 2011 Sep 18;43(10):1031-4. (PMID: 21926973)
      Mol Biol Evol. 2017 Feb 1;34(2):483-499. (PMID: 28069777)
      Bioinformatics. 2014 May 1;30(9):1312-3. (PMID: 24451623)
      Genome Res. 2009 Feb;19(2):327-35. (PMID: 19029536)
      Syst Biol. 2017 Nov 01;66(6):1028-1044. (PMID: 28637293)
      Nature. 2009 Feb 12;457(7231):830-6. (PMID: 19212401)
      Mol Biol Evol. 2002 Dec;19(12):2092-100. (PMID: 12446801)
      PLoS One. 2013;8(1):e54848. (PMID: 23382987)
      PLoS Genet. 2016 Mar 04;12(3):e1005877. (PMID: 26943927)
      Nat Genet. 2006 Aug;38(8):904-9. (PMID: 16862161)
      Genome Res. 2009 Sep;19(9):1655-64. (PMID: 19648217)
      Mol Ecol. 2016 Jun;25(11):2661-79. (PMID: 26937625)
      Syst Biol. 2018 Sep 1;67(5):901-904. (PMID: 29718447)
      Nature. 2009 Sep 24;461(7263):489-94. (PMID: 19779445)
      G3 (Bethesda). 2018 Feb 2;8(2):551-566. (PMID: 29196497)
      Science. 2007 Mar 16;315(5818):1574-6. (PMID: 17363673)
      BMC Evol Biol. 2017 Aug 22;17(1):201. (PMID: 28830337)
      Am J Hum Genet. 2007 Sep;81(3):559-75. (PMID: 17701901)
      Genome Res. 2016 Sep;26(9):1211-8. (PMID: 27412854)
      Am Nat. 2007 Mar;169(3):285-97. (PMID: 17230401)
      Genet Epidemiol. 2005 May;28(4):289-301. (PMID: 15712363)
    • Contributed Indexing:
      Keywords: Allopatric divergence; Phylogenomics; Pitta sordida; Pleistocene glaciations; Population genomics; Sea level fluctuations; de novo genome
    • Publication Date:
      Date Created: 20190726 Date Completed: 20190927 Latest Revision: 20200309
    • Publication Date:
      20240105
    • Accession Number:
      PMC6657069
    • Accession Number:
      10.1186/s12862-019-1481-5
    • Accession Number:
      31340765