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Pitta sordida cucullatus genome assembly

Citation

Ericson, Per (2021), Pitta sordida cucullatus genome assembly, Dryad, Dataset, https://doi.org/10.5061/dryad.ngf1vhht5

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.

Methods

DNA extracted from a fresh sample of Pitta sordida cucullata collected in Bukit Batok Nature Park in Singapore was used for de-novo sequencing. Four DNA libraries, one short-insert-sized, paired-end (180 bp) and three mate-pair (3 and 5-8 kb) DNA libraries, were sequenced on an Illumina HiSeq X platform at the National Genomics Institute. Low quality and duplicated reads were filtered out before assembly. Unfortunately the 5-8 kb mate-pair library did not work well despite having tried to sequence it twice. The final genome was assembled by Science for Life Laboratory (National Genomics Institute, Stockholm) using their best-practice analysis for de novo assembly and assembly evaluation. Three different assemblers were used and their performances were evaluated by aligning a subset of Illumina reads back to the assembled sequence. The lowest number of scaffolds (12,146) and the highest scaffold N50 values (405 kb) were obtained by the ALLPATHS_LG assembler and this assembly was used for the downstream analyses

Funding

Vetenskapsrådet, Award: 621–2013–5161

Vetenskapsrådet, Award: 621–2017–3693

Vetenskapsrådet, Award: 621–2014–5113