Telomere-to-Telomere Genome Sequences across a Single Genus Reveal Highly Variable Chromosome Rearrangement Rates but Absolute Stasis of Chromosome Number.

Genome rearrangements in filamentous fungi are prevalent but little is known about the modalities of their evolution, in part because few complete genomes are available within a single genus. To address this, we have generated and compared 15 complete telomere-to-telomere genomes across the phylogeny of a single genus of filamentous fungi, Epichloë. We find that the striking distinction between gene-rich and repeat-rich regions previously reported for isolated species is ubiquitous across the Epichloë genus. We built a species phylogeny from single-copy gene orthologs to provide a comparative framing to study chromosome composition and structural change through evolutionary time. All Epichloë genomes have exactly seven nuclear chromosomes, but despite this conserved ploidy, analyses reveal low synteny and substantial rearrangement of gene content across the genus. These rearrangements are highly lineage-dependent, with most occurring over short evolutionary distances, with long periods of structural stasis. Quantification of chromosomal rearrangements shows they are uncorrelated with numbers of substitutions and evolutionary distances, suggesting that different modes of evolution are acting to create nucleotide and chromosome-scale changes.

The ectoparasites of hybrid ducks in New Zealand (Mallard x Grey Duck).

We studied the population genetics of one population sample of hybrid Mallard x Grey Ducks and their lice in New Zealand. We aimed to document the relationship between ectoparasite load and host phenotype, and test for an association between the mtDNA diversity of the lice and their hosts, which is predicted based on maternal care. We found three feather lice species previously described for these hosts: Anaticola crassicornis (wing louse), Anatoecus dentatus (head louse), and Trinoton querquedulae (body louse). No new or rare lice species were uncovered. Most ducks in our sample were more Mallard-like than Grey Duck-like hybrids for the five colour and plumage traits examined. We confirm that based solely on phenotypic characters it is difficult to distinguish between Mallards, hybrids and Grey Ducks. We detected no association between the number of lice and host phenotype for two of the three louse species (while controlling for bird size). However, the Grey Duck-like hybrids had fewer head lice (A. dentatus) than their Mallard-like counterparts. Only three of the 40 hosts had mtDNA haplotypes that characterise Grey Ducks. We present the first genetic data of Anaticola crassicornis, Anatoecus dentatus and Trinoton querquedulae from New Zealand waterfowl. We found that the lice mtDNA had greater sequence diversity than the homologous gene for the ducks. A mitochondrial phylogeny for A. crassicornis collected from hosts worldwide has been previously published, and we added our novel data to infer evolutionary relationships among worldwide populations of this louse. None of the three lice species showed a close association of parasite and host mtDNA lineage despite lack of paternal care in these duck species.