Chromosome assembly and preliminary gene and repeat annotations for Myzomela tristrami reference genome

Secondary contact between closely related taxa represents a “moment of
truth” for speciation — an opportunity to test the efficacy of
reproductive isolation that evolved in allopatry and to identify the
genetic, behavioral, and/or ecological barriers that separate species in
sympatry. Sex chromosomes are known to rapidly accumulate differences
between species, an effect that may be exacerbated for neo-sex chromosomes
that are transitioning from autosomal to sex-specific inheritance. Here we
report that, in the Solomon Islands, two closely related bird species in
the honeyeater family — Myzomela cardinalis and Myzomela tristrami — carry
neo-sex chromosomes and have come into recent secondary contact after ~1.1
my of geographic isolation. Hybrids of the two species were first observed
in sympatry ~100 years ago. To determine the genetic consequences of
hybridization, we use population genomic analyses of individuals sampled
in allopatry and in sympatry to characterize gene flow in the contact
zone. Using genome-wide estimates of diversity, differentiation, and
divergence, we find that the degree and direction of introgression varies
dramatically across the genome. For sympatric birds, autosomal
introgression is bidirectional, with phenotypic hybrids and phenotypic
parentals of both species showing admixed ancestry. In other regions of
the genome, however, the story is different. While introgression on the
Z/neo-Z-linked sequence is limited, introgression of W/neo-W regions and
mitochondrial sequence (mtDNA) is highly asymmetric, moving only from the
invading M. cardinalis to the resident M. tristrami. The recent
hybridization between these species has thus enabled gene flow in some
genomic regions but the interaction of admixture, asymmetric mate choice,
and/or natural selection has led to the variation in the amount and
direction of gene flow at sex-linked regions of the genome.