Biology subjects

Miyaki, C. Y.

Publications and source records attributed to Miyaki, C. Y..

4 recordsLinked to original sources

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↗

bioRxiv2021

Population dynamics of Amazonian floodplain forest species support spatial variation on genetic diversity but not range expansions through time

AimWe tested if historical demographic changes of populations occurring on the floodplains of a major Amazon Basin tributary could be associated with range expansions from upper and middle sections of the river, following the establishment of widespread river-created environments during the Late Pleistocene and Holocene. LocationSolimoes River, Western Amazon, South America TaxonMyrmoborus lugubris, Thamnophilus cryptoleucus and Myrmotherula assimilis Methods: We analyzed thousands of UltraConserved Elements to explore spatial patterns of genetic diversity and connectivity between individuals. Range expansions were tested with alternative methods. We quantified habitat preference for the analyzed species in order to test if the occupation of dynamic habitats could predict spatial patterns of genetic diversity. ResultsOur study did not support shared population range expansions related to historical regionalized changes in habitat availability. We found considerable variation in the spatial distribution of the genetic diversity between studied taxa, and that species with higher levels of specialization to dynamic environments have a more heterogeneous distribution of genetic diversity and reduced levels of gene flow across space. Main conclusionsOur results suggest that demographic expansions along the Solimoes River might be linked to geographic homogeneous oscillation in the distribution of floodplain environments, promoting effective population size changes but not range expansion. We found that habitat specificity might be a good predictor of population connectivity along the Amazonian floodplains.

evolutionary biology↗

bioRxiv2018

Climate explains recent population divergence, introgression and persistence in tropical mountains: phylogenomic evidence from Atlantic Forest warbling finches

Taxa with disjunct distributions are common in montane biotas and offer excellent opportunities to investigate historical processes underlying genetic and phenotypic divergence. In this context, subgenomic datasets offer novel opportunities to explore historical demography in detail, which is key to better understand the origins and maintenance of diversity in montane regions. Here we used a large ultraconserved elements dataset to get insights into the main biogeographic processes driving the evolution of the Montane Atlantic Forest biota. Specifically, we studied two species of warbling finches disjunctly distributed across a region of complex geological and environmental history. We found that a scenario of three genetically differentiated populations is best supported by genomic clustering methods. Also, demographic simulations support simultaneous isolation of these populations at ~10 kya, relatively stable population sizes over recent time, and recent gene flow. Our results suggest a dual role of climate: population divergence, mediated by isolation in mountain tops during warm periods, as well as population maintenance - allowing persistence mediated by shifts in elevation distribution during periods of climate change, with episodic bouts contact and gene flow. Additional support for the role of climate comes from evidence of their contact in a recent past. We propose that two major gaps, which we call Sao Paulo and Caparao subtropical gaps, have been historically important in the divergence of cold adapted organisms in the Atlantic Forest, and could be associated to cryptic diversity. Finally, our results suggest that shallow divergence and past gene flow may be common in montane organisms, but complex demographic histories may be detectable only when using subgenomic or genomic datasets.

evolutionary biology↗