Evolution of the “world’s only alpine parrot”: Genomic adaptation or phenotypic plasticity, behaviour and ecology?

Abstract

Climate warming, in particular in island environments, where opportunities for species to disperse are limited, may become a serious threat to cold adapted alpine species. In order to understand how alpine species may respond to a warming world, we need to understand the drivers that have shaped their habitat specialisation and the evolutionary adaptations that allow them to utilize alpine habitats. The endemic, endangered New Zealand kea (Nestor notabilis) is considered the only alpine parrot in the world. As a species commonly found in the alpine zone it may be highly susceptible to climate warming. But is it a true alpine specialist? Is its evolution driven by adaptation to the alpine zone, or is the kea an open habitat generalist that simply uses the alpine zone to, for example, avoid lower lying anthropogenic landscapes?We use whole genome data of the kea and its close, forest adapted sister species, the kākā (Nestor meridionalis) to reconstruct the evolutionary history of both species and identify the functional genomic differences that underlie their habitat specialisations. Our analyses do not identify major functional genomic differences between kea and kākā in pathways associated with high-altitude. Rather, we found evidence that selective pressures on adaptations commonly found in alpine species are present in both Nestor species, suggesting that selection for alpine adaptations has not driven their divergence. Strongly divergent demographic responses to past climate warming between the species nevertheless highlight potential future threats to kea survival in a warming world.

Genomic insights into the evolutionary relationships and demographic history of kiwi

“…Although it is difficult to precisely pinpoint the driver of past population fluctuations, we form a number of hypotheses mostly based on correlations with volcanic activity. To date, few studies have used whole-genome data to investigate the longer-term demographic histories of New Zealand avian species, and those that have, have focussed on glaciation as a major influence [50][51][52]. As more genomes from a wider range of New Zealand species are made available, it will be possible to test whether volcanic eruptions may have also been a previously overlooked major evolutionary force shaping the biota of New Zealand.…”

Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater

“…The consensus sequence was transformed to fastq format with vcfutils.pl vcf2fq keeping loci with read depth between 66× and 400× (average depth was 200×). We ran PSMC v0.6.5-r67 with parameter –p 4+30*2+4+6+10 and 100 bootstraps based on previous studies done for birds [ 69 , 70 ]. Results were plotted assuming a generation time of 3.17 years [ 71 ] and mutation rate of 3.44 × 10 –9 per generation (estimated for another passerine, the medium ground finch, Geospiza fortis [ 69 , 72 ]).…”

Advancing Genetic Methods in the Study of Parrot Biology and Conservation

“…Landscape genetics was also used to study the historical and current distributions of the Crimson Rosella Platycercus elegans complex, showing that population expansion followed by secondary contact and hybridization might be responsible for their present genetic structure [207]. A recent study looked at functional genomic differences between the alpine Kea and the forest adapted Kākā in New Zealand, and showed that these adaptations are not driving the ecological differentiation between the two species [208].…”