Fig 1.
Phylogenetic relationships and distribution ranges of the five extant kiwi species.
Modern and historic distributions are based on [51]. Lightly shaded areas show estimated distributions prior to human arrival and dark shading shows current distribution. Current distribution for the little spotted kiwi is not shown, as it is presently only found on small offshore islands and wildlife sanctuaries. Population size estimates are shown in parentheses under each species name [51].
Fig 2.
(A) Species tree; (B) and (C) Species tree in expanded form, with internal branches as dotted lines. The values in the matrix refer to excess allele sharing between the expanded tree branch (relative to its sister branch) and the species on the x-axis. Grey squares are comparisons that could not be made due to the topological input requirements of the test and its inability to infer gene flow between sister lineages. Lines connecting branches show: (B) gene flow events inferred directly from the f-branch results. Dark purple coloured lines show results supported by QuIBL; (C) gene flow events that we hypothesise from the f-branch results, while accounting for (i) the inability to detect gene flow between sister lineages, and (ii) a lack of a positive means less gene flow relative to the sister lineage, rather than no gene flow.
Fig 3.
Genetic diversity and inbreeding estimates.
(A) Autosome-wide heterozygosity calculated using ROHan for the four kiwi species with conspecific reference genomes, and four other palaeognath species. Error bars show maximum and minimum values. (B) Autosomal runs of homozygosity calculated using various window sizes (0.5 Mb, 1 Mb, and 2 Mb) for the four kiwi species with conspecific reference genomes. Differential shading shows the window size used.
Fig 4.
Effective population sizes over the past one million years calculated using PSMC.
Faded lines show the 100 bootstrap replicates produced for each species.