Biology subjects

Hackett, S. J.

Publications and source records attributed to Hackett, S. J..

5 recordsLinked to original sources

bioRxiv2026

Drift drives phenotypic evolution in a rapid island radiation

Understanding the processes that generate phenotypic diversity is central to explaining how new species form1,2. Evolutionary theory predicts that rapid evolution of signaling traits, such as feather coloration, can promote speciation3,4 but empirical support is inconsistent5,6. Phenotypic divergence of such traits is expected during speciation4, but these microevolutionary dynamics are rarely examined at macroevolutionary scales or linked to underlying population demography. Here, we leverage complete taxon sampling across an iconic insular bird radiation that helped shape early theories of allopatric speciation. We integrate whole-genome data with a comprehensive, fine-scale dataset of whole-body plumage coloration to directly test whether signaling trait evolution covaries with lineage diversification and to disentangle the roles of selection and drift. We find that lineages with faster rates of color evolution diversify more rapidly. Strikingly, rates of color evolution accelerate as genomic diversity declines, providing direct evidence that genetic drift--rather than strong sexual or ecological selection--can drive rapid phenotypic change in small, isolated insular populations. Together, these results provide compelling evidence that neutral demographic processes can accelerate the evolution of sexual signals and play a central role in generating phenotypic diversity during island radiations.

zoology↗

bioRxiv2026

Range-wide phylogeography, population genomics, and demography of three widespread Ara macaws (Psittacidae)

Macaws of the genus Ara comprise eight extant species distributed throughout the Neotropics. Among them, four have broad geographic ranges, yet little is known about the evolutionary history and demographic processes that shaped their genomic variation and present-day distributions. This is particularly relevant because, although these wide-ranging macaws are classified as Least Concern by the IUCN, many of their populations are declining due to habitat fragmentation, illegal trade, and climate change. Here, we used nuclear and mitochondrial genomic data to characterize the evolutionary relationships, population structure, genetic diversity, and demographic histories of three widely distributed species (A. ararauna, A. chloropterus, and A. severus) across their geographic distributions. We identified two main populations within Ara severus, and this species showed the highest heterozygosity levels among the three species. In A. ararauna and A. chloropterus, we observed four main genetic clusters corresponding to two populations in the Amazon rainforest biome and and two populations in the Cerrado savanna biome. Cerrado populations in both species exhibited markedly reduced heterozygosity and elevated inbreeding relative to Amazonian populations, consistent with smaller effective population sizes and increased isolation. Genome-wide scans suggested that genetic drift and divergent demographic histories played a predominant role in driving the strong differentiation between Amazon and Cerrado in these two species. Nevertheless, we detected two candidate genes, NALCN and RBBP6, with convergent selection signals across A. ararauna and A. chloropterus, suggesting possible local adaptation to the Cerrado biome.

evolutionary biology↗

bioRxiv2026

Phylogenomics and biogeography of the parrot genus Pyrrhura with implications for systematics and conservation

The genus Pyrrhura (Psittacidae: Arini) is one of the most diverse groups of Neotropical parrots. Its species are charismatic, widely kept as pets, and frequently bred outside their native ranges. Yet, nearly half are currently listed as threatened by the IUCN within their natural distributions. Conservation assessments and population estimates often depend on the validity of accepted taxonomic boundaries. However, despite previous systematic efforts, the evolutionary relationships among and within many Pyrrhura species remain poorly resolved, largely due to a recent and rapid radiation. Here, we generated whole-genome sequences for all currently recognized Pyrrhura species, including multiple intraspecific taxa, to reconstruct a robust nuclear phylogeny under the multi-species coalescent model, alongside the most comprehensive mitogenome-based phylogeny of the genus to date. Although both phylogenies supported the monophyly of most currently accepted species, we identified several instances of mito-nuclear discordance, particularly involving the placement of early-diverging lineages, which are best explained by incomplete lineage sorting and historical gene flow. Additionally, we detected three distinct captive lineages that do not cluster with any known wild populations, suggesting substantial overlooked genetic diversity in the worlds captive populations. Ancestral range reconstructions indicate multiple and relatively recent colonization events into the northern and central Andes, likely associated with the uplift of the Andes and the emergence of new ecological niches. Together, our results reveal a complex evolutionary history in Pyrrhura, shaped by rapid radiations, incomplete lineage sorting, and gene flow. We show that integrating nuclear and mitochondrial data with broad geographic and taxonomic sampling, including captive individuals, can uncover overlooked genetic diversity and help to resolve long-standing systematic uncertainties. Finally, we show that several topological discrepancies among previous studies can be attributed to differences in sampling strategies, particularly within the most polytypic Pyrrhura species.

evolutionary biology↗

bioRxiv2024

Phylogenomics of a genus of "Great Speciators" reveals rampant incomplete lineage sorting, gene flow, and mitochondrial capture in island systems

The flora and fauna of island systems, especially those in the Indo-Pacific, are renowned for their high diversification rates and outsized contribution to the development of evolutionary theories. The total diversity of geographic radiations of many Indo-Pacific fauna is often incompletely sampled in phylogenetic studies due to the difficulty in obtaining single island endemic forms across the Pacific and the relatively poor performance of degraded DNA when using museum specimens for inference of evolutionary relationships. New methods for production and analysis of genome-wide datasets sourced from degraded DNA are facilitating insights into the complex evolutionary histories of these influential island faunas. Here, we leverage whole genome resequencing (20X average coverage) and extensive sampling of all taxonomic diversity within Todiramphus kingfishers, a rapid radiation of largely island endemic Great Speciators. We find that whole genome datasets do not outright resolve the evolutionary relationships of this clade: four types of molecular markers (UCEs, BUSCOs, SNPs, and mtDNA) and tree building methods did not find a single well-supported and concordant species-level topology. We then uncover evidence of widespread incomplete lineage sorting and both ancient and contemporary gene flow and demonstrate how these factors contribute to conflicting evolutionary histories. Our complete taxonomic sampling allowed us to further identify a novel case of mitochondrial capture between two allopatric species, suggesting a potential historical (but since lost) hybrid zone as islands were successively colonized. Taken together, these results highlight how increased genomic and taxon sampling can reveal complex evolutionary patterns in rapid island radiations.

zoology↗

bioRxiv2022

Complex plumages spur rapid color diversification in island kingfishers (Aves: Alcedinidae)

Oceanic islands are cradles for diversity. Differences in predation pressures and lack of competition on islands are thought to drive both phenotypic and species diversification. While most work exploring these patterns has focused on life history, behavioral and morphological traits, many island species are uniquely colorful. Yet, a recent study of island bird coloration found that insular species are duller than continental species. Whether such shifts in color are associated with increased rates of color evolution on islands remains unknown. Here, we incorporate geometric morphometric techniques to study plumage color diversity in a speciose clade of colorful birds that inhabit nearly all areas of the globe--kingfishers (Aves: Alcedinidae). In particular, we test two hypotheses: (i) that plumage complexity enhances interspecific rates of color evolution and (ii) that plumage color diversity is elevated on islands. Our results show that more complex plumages result in more diverse colors among species and plumage color evolves faster on islands. Importantly, we found that insular species did not have more complex plumages than their continental relatives. Thus, complexity may be a key innovation that facilitates response to divergent (or relaxed) selection pressures on islands. Lack of support for competition driving rates of evolution along different color axes hints at an allopatric model of color evolution in which species adapt to local conditions on different islands. This work demonstrates how a truly multivariate treatment of color data can reveal evolutionary patterns that might otherwise go unnoticed.

evolutionary biology↗