Biology subjects

Valqui, T.

Publications and source records attributed to Valqui, T..

6 recordsLinked to original sources

bioRxiv2025

The genomic landscape of asymmetric introgression tracks chromosomal characteristics in tinamous (Aves: Tinamidae)

We use single genomes from seven tinamou species (Palaeognathae: Tinamidae) and apply a genome-architecture-aware phylogenomic approach to (1) quantify the landscape of introgression, (2) discriminate among conflicting genealogical signals in the genome, and (3) reconstruct evolutionary history. Using summary statistics and full likelihood, we detect pervasive asymmetric introgression between two sympatric Amazonian species clouding phylogenetic relationships in this group. However, these introgression results are sensitive to the assumed species tree. When assuming the Z-chromosome phylogeny as the species tree, the landscape of introgression is non-random; introgression is negatively associated with chromosome length, elevated at macrochromosome ends, and near zero for the Z-chromosome (the avian sex chromosome). A pseudo-autosomal region on the Z-chromosome, which recombines homologously with that of the W-chromosome, shows elevated introgression comparable to that of autosomes. Our results resolve the species tree of tinamous and imply a history of linked selection purging migrant alleles that are deleterious in the hybrid genome. This selection is countered in regions of the genome expected to experience elevated recombination, allowing introgressed alleles to accumulate across >20% of the genome. This work demonstrates a genome-architecture-aware approach to resolving the species tree in the face of introgression. As chromosome-level reference genomes spanning the tree of life become increasingly available, phylogenomic studies would benefit from the adoption of genome-architecture-aware approaches like ours. This is because the genomic landscapes of introgression and genealogy are largely predicted by chromosomal characteristics.

genomics↗

bioRxiv2025

Songs distinguish the cryptic giant hummingbird species and clarify range limits

Vocal traits are often essential for distinguishing phenotypically cryptic taxa. The hummingbird genus Patagona comprises two species, near identical in plumage and morphology, that differ in almost every aspect of their ecology and evolution: The Northern Giant Hummingbird (Patagona peruviana) and Southern Giant Hummingbird (Patagona gigas). Here, we characterized the songs of both giant hummingbird species and assessed whether song can be used to distinguish the two in the field. We recorded both species in Peru, Bolivia, and Chile in 2023 and 2025 and used public data to analyze song variation of 217 individuals recorded across the Andes. Sampling spanned 49 years, >36{degrees} of latitude, and >4,300 meters in elevation. We first quantified species-level song differences in allopatric breeding populations and trained a linear discriminant model to identify individuals to species. The trained model had 100% classification accuracy. We then used our trained model to identify individuals recorded during co-occurring, non- breeding periods of overlap, and subsequently analyzed range-wide song variation; this model had 98.72% classification accuracy (1.28% error rate; one individual misidentified). We found striking song divergence between the two species, uncovering that Northern and Southern Giant Hummingbirds can be reliably and easily identified by song across their ranges and during any month of the year. We provide new data on the range limits of both species in northern Bolivia, highlighting a previously unknown zone of overlap around Lake Titicaca. Unlike other phenotypic traits, song provides a robust method for identifying the giant hummingbird species, opening doors to future research on ecology, trait evolution, hybrid zone dynamics, and conservation of the worlds largest hummingbirds.

evolutionary biology↗

bioRxiv2024

Taxonomy and nomenclature of the giant hummingbirds (Patagona spp.) (Aves: Trochilidae)

Giant hummingbirds (Patagona spp.) are extraordinarily large hummingbirds whose taxonomy has been muddled for two centuries. Patagona systematics were recently redefined in a study of migration, physiology, and genomics, revealing two species: the Southern Giant Hummingbird and Northern Giant Hummingbird. Here, we re-evaluate taxonomy and nomenclature of the genus in light of its newly-clarified biology and species limits, analyzing data from 608 specimens and wild-caught individuals spanning 1864-2023. The forms gigas and peruviana were both described based on multiple syntypes. No adequate syntypes for P. gigas are extant, so we designate a neotype for this taxon. We then critically consider the identity and usage of gigas and peruviana, respectively, and examine identification challenges that have fostered taxonomic uncertainty. We endorse the names Patagona gigas for the Southern Giant Hummingbird and P. peruviana for the Northern Giant Hummingbird. The genetic identity of the peruviana lectotype remains untested, but its plumage appears to match the northern species. We found that [~]33% of Patagona gigas specimens in major museum collections are misidentified as peruviana; we provide this list to correct the historical record. To facilitate identification and future study of these two cryptic species, we provide comprehensive information on plumage, measurements, and seasonal ranges.

zoology↗

bioRxiv2024

Whole-genome phylogenomics of the tinamous (Aves: Tinamidae): comparing gene tree estimation error between BUSCOs and UCEs illuminates rapid divergence with introgression

As an old group that has diversified in South America over millions of years, the tinamous (Palaeognathae: Tinamidae) are of high interest for understanding the evolution of birds and the assembly of the Neotropical biota. However, there are currently no complete species-level phylogenies of this group. Most prior work has been based on either morphological data or a small number of molecular markers, each of which has limited capability for reconstructing the tinamou phylogeny. Therefore, the interrelationships of most tinamou species are uncertain. We analyzed 80 whole-genomes from a mix of historical study skins and frozen tissues, including all 46 recognized species of tinamous to (1) reconstruct their interrelationships, (2) estimate the timeframe of tinamou evolution, and (3) examine for the effects of incomplete lineage sorting (ILS) and ancestral introgression on genome evolution. We compared results for coding (BUSCO) and ultraconserved element (UCE) loci, as well as sex-linked and autosomal markers, and used fossil-calibrated tip-dating to estimate divergence times. Tinamous diverged from their sister-group, the extinct Moas, 50-60 mya, and their crown divergence occurred roughly 30-40 mya, followed by constant diversification rates until the present. Phylogenetic reconstructions were largely robust across methods and datasets. Only one clade in the genus Crypturellus displayed substantial species-tree discordance across the different data sets. To investigate the impacts of introgression on this discordance, we quantified introgression for 100kb non-overlapping windows across the genome, and identified pervasive genome-wide introgression. The distribution of this introgression across the genome was dependent on the assumed phylogeny applied to the f-branch model. When assuming one of these topologies in the f-branch model, patterns of introgression matched theoretical predictions about genome architecture. Overall, we present the most complete phylogeny for tinamous to date, identify an unrecognized species, and provide a case study for species-level phylogenomic analysis using whole-genomes.

genomics↗

bioRxiv2021

Blood variation implicates respiratory limits on elevational ranges of Andean birds

The extent to which species ranges reflect intrinsic physiological tolerances is a major, unsolved question in evolutionary ecology. To date, consensus has been hindered by the limited tractability of experimental approaches across most of the tree of life. Here, we apply a macrophysiological approach to understand how hematological traits related to oxygen transport shape elevational ranges in a tropical biodiversity hotspot. Along Andean elevational gradients, we measured traits that affect blood oxygen-carrying capacity--total and cellular hemoglobin concentration and hematocrit--for 2,355 individuals of 136 bird species. We used these data to evaluate the influence of hematological traits on elevational ranges. First, we asked whether hematological plasticity is predictive of elevational range breadth. Second, we asked whether variance in hematological traits changed as a function of distance from the midpoint of the elevational range. We found that the correlation between hematological plasticity and elevational range breadth was slightly positive, consistent with a facilitative role for plasticity in elevational range expansion. We further found reduced local variation in hematological traits near elevational range limits and at high elevations, patterns consistent with intensified natural selection, reduced effective population size, or compensatory changes in other cardiohematological traits with increasing distance from species-specific optima for oxygen availability. Our findings suggest that constraints on hematological plasticity and local genetic adaptation to oxygen availability promote the evolution of the narrow elevational ranges that underpin tropical montane biodiversity.

ecology↗

bioRxiv2018

Deeply conserved susceptibility in a multi-host, multi-parasite system

Variation in susceptibility is ubiquitous in multi-host, multi-parasite assemblages, and can have profound implications for ecology and evolution. The extent to which susceptibility is phylogenetically conserved among hosts is poorly understood and has rarely been appropriately tested. We screened for haemosporidian parasites in 3983 birds representing 40 families and 523 species, spanning ~4500 meters elevation in the tropical Andes. To quantify the influence of host phylogeny on infection status, we applied Bayesian phylogenetic multilevel models that included a suite of environmental, spatial, temporal, life history, and ecological predictors. We found evidence of deeply-conserved susceptibility across the avian tree; host phylogeny explained substantial variation in infection rate, and results were robust to phylogenetic uncertainty. Our study suggests that susceptibility is governed, in part, by conserved, latent aspects of anti-parasite defense. This demonstrates the importance of deep phylogeny for understanding the outcomes of present-day ecological interactions.\n\nStatement of authorshipLNB, SMM, NM, and CCW designed the study; SMM, SCG, HLL, HS, TV, JDW, and CCW collected the data; LNB and NM analyzed the data; LNB, NM, and CCW wrote the paper with input from all authors.\n\nData accessibility statementSpecimen information is available from the Arctos database (arctosdb.org) and in supplementary tables (Appendix S1). Files used for analysis will be archived in Dryad. DOI: XXX.

evolutionary biology↗