Biology subjects

Penalba, J. V.

Publications and source records attributed to Penalba, J. V..

4 recordsLinked to original sources

bioRxiv2022

Sustained plumage divergence despite weak genomic differentiation and broad sympatry in sister species of Australian woodswallows (Artamus spp.)

Plumage divergence can function as a strong premating barrier when species come into secondary contact. When it fails to do so, the results are often genome homogenization and phenotypic hybrids at the zone of contact. This is not the case in the largely sympatric masked woodswallow and white-browed woodswallow species (Passeriformes: Artamidae: Artamus spp) complex in Australia where phenotypic integrity is sustained despite no discernible mitochondrial structure in earlier work. This lack of structure may suggest recent divergence, ongoing gene flow or both, and phenotypic hybrids are reported albeit rarely. Here, we further assessed the population structure and differentiation across the species nuclear genomes using ddRAD-seq. As found in the mitochondrial genome, no structure or divergence within or between the two species was detected in the nuclear genome. This coarse sampling of the genome nonetheless revealed peaks of differentiation around the genes SOX5 and Axin1. Both are involved in the Wnt//-catenin signaling pathway, which regulates feather development. Reconstruction of demographic history and estimation of parameters supports a scenario of secondary contact. Our study informs how divergent plumage morphs may arise and be sustained despite whole-genome homogenization and reveals new candidate genes potentially involved in plumage divergence.

evolutionary biology↗

bioRxiv2019

Inferring punctuated evolution in the learned songs of African sunbirds

Signals used in animal communication, especially those that are learned, are thought to be prone to rapid and/or regular evolution. It has been hypothesized that the evolution of song learning in birds has resulted in elevated diversification rates, as learned song may be subject to especially rapid evolution, and song is involved in mate choice. However, we know little about the evolutionary modes of learned song divergence over timescales relevant to speciation. Here we provide evidence that aspects of the territorial songs of Eastern Afromontane sky island sunbirds Cinnyris evolve in a punctuated fashion, with periods of stasis, on the order of hundreds of thousands of years or more, broken up by strong evolutionary pulses. Stasis in learned songs is inconsistent with learned traits being subject to constant or frequent change, as would be expected if selection does not constrain song phenotypes, or if novel phenotypes are frequently advantageous. Learned song may instead follow a process resembling peak shifts on adaptive landscapes. While much research has focused on the potential for rapid evolution in bird song, our results suggest that selection can tightly constrain the evolution of learned songs over fairly long timescales. More broadly, these results demonstrate that some aspects of highly variable, plastic traits can exhibit punctuated evolution, with stasis over fairly long time periods.

evolutionary biology↗

bioRxiv2019

Genome of an iconic Australian bird: Chromosome-scale assembly and linkage map of the superb fairy-wren (Malurus cyaneus)

The superb fairy-wren, Malurus cyaneus, is one of the most iconic Australian passerine species. This species belongs to an endemic Australasian clade, Meliphagides, which diversified early in the evolution of the oscine passerines. Today, the oscine passerines comprise almost half of all avian species diversity. Despite the rapid increase of available bird genome assemblies, this part of the avian tree has not yet been represented by a high-quality reference. To rectify that, we present the first chromosome-scale genome assembly of a Meliphagides representative: the superb fairy-wren. We combined Illumina shotgun and mate-pair sequences, PacBio long-reads, and a genetic linkage map from an intensively sampled pedigree of a wild population to generate this genome assembly. Of the final assembled 1.07Gb genome, 894Mb (84.8%) was anchored onto 25 chromosomes resulting in a final scaffold N50 of 68.11 Mb. This high-quality bird genome assembly is also one of only a handful which is also accompanied by a genetic map and recombination landscape. In comparison to other pedigree-based bird genetic maps, we find that the zebrafinch (Taeniopygia) genetic map more closely resembles the fairy-wren map rather than the map from the more closely-related Ficedula flycatcher. Lastly, we also provide a predictive gene and repeat annotation of the genome assembly. This new high quality, annotated genome assembly will be an invaluable resource not only to the superb fairy-wren species and relatives but also broadly across the avian tree by providing a new reference point for comparative genomic analyses.

genomics↗

bioRxiv2017

Current geography masks dynamic history of gene flow during speciation in northern Australian birds

During early stages of speciation, genome divergence is greatly influenced by gene flow. As populations diverge, geography can allow or restrict gene flow in the form of barriers. Current geography, e.g. whether sister species are allopatric or parapatric, is often used to predict the potential for gene flow during the divergence process. We test the validity of this assumption in eight meliphagoid bird species codistributed across four regions. These regions are separated by known biogeographic barriers within and between northern Australia and Papua New Guinea. We find that bird populations across the same barrier have a range of divergence levels and probability of gene flow regardless of range connectivity. Geographic distance and maximum range connectivity over time can better predict divergence and probability of gene flow than whether populations are currently allopatric or parapatric. We also find support for a nonlinear decrease of the probability of gene flow during the divergence process. This implies that although gene flow influences divergence early in speciation, other factors associated with higher divergence restrict gene flow later in speciation. Current geography may then mislead inferences regarding potential for gene flow during speciation under a complex and dynamic history of geographic and reproductive isolation.

evolutionary biology↗