Data from: Closing the gap: avian lineage splits at a young, narrow seaway imply a protracted history of mixed population response

The evolutionary significance of spatial habitat gaps has been well recognized since Alfred Russel Wallace compared the faunas of Bali and Lombok. Gaps between islands influence population structuring of some species, and flightless birds are expected to show strong partitioning even where habitat gaps are narrow. We examined the population structure of the most numerous living flightless land bird in New Zealand, Weka (Gallirallus australis). We surveyed Weka and their feather lice in native and introduced populations using genetic data gathered from DNA sequences of mitochondrial genes and nuclear β-fibrinogen and five microsatellite loci. We found low genetic diversity among extant Weka population samples. Two genetic clusters were evident in the mtDNA from Weka and their lice, but partitioning at nuclear loci was less abrupt. Many formerly recognized subspecies/species were not supported; instead, we infer one subspecies for each of the two main New Zealand islands. Although currently range restricted, North Island Weka have higher mtDNA diversity than the more wide-ranging southern Weka. Mismatch and neutrality statistics indicate North Island Weka experienced rapid and recent population reduction, while South Island Weka display the signature of recent expansion. Similar haplotype data from a widespread flying relative of Weka and other New Zealand birds revealed instances of North Island—South Island partitioning associated with a narrow habitat gap (Cook Strait). However, contrasting patterns indicate priority effects and other ecological factors have a strong influence on spatial exchange at this scale.Weka_micro_matrixMatrix of alleles at five microsatellite loci for individual weka (Gallirallus australis) in New ZealandWeka Control Region haplotypes A–TPartial, homologous, mitochondrial Control Region DNA sequences representing each of 20 haplotypes encountered in a sample of weka (Gallirallus australis)Weka fibrinogen 7 three allelesDNA sequences representing three alleles found in weka (Gallirallus australis) at the nuclear locus β-fibrinogen intron 7 (FGB-7), using PCR with the primers Fib-BI7U (5´ GGA GAA AAC ACA ATG ACA ATT CAC 3´) and Fib-BI7L (5´ TCC CCA GTA GTA TCT GCC ATT AGG GTT T 3´) (Prychitko & Moore 1997)Pseudomenopon lice weka, BR, pukekoRepresentative partial DNA sequences from the mitochondrial Cytochrome oxidase subunit 1 gene in Pseudomenopon feather lice (Phthiraptera) found on Gallirallus australis, Gallirallus philippensis and Porphyrio melanotus bird hosts.Rallicola lice weka, banded rail pukekoRepresentative partial DNA sequences from the mitochondrial Cytochrome oxidase subunit 1 gene in Rallicola feather lice (Phthiraptera) found on Gallirallus australis, Gallirallus philippensis and Porphyrio melanotus bird hosts