DOI: 10.5061/dryad.ngf1vhht5
title: Pitta sordida cucullatus genome assembly

description: 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.
description: DNA extracted from a fresh sample of <i>Pitta sordida
 cucullata</i> 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 <i>de novo</i> 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