Biology subjects

Bautista, E.

Publications and source records attributed to Bautista, E..

6 recordsLinked to original sources

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↗

bioRxiv2022

CRISPR-Analytics (CRISPR-A): a platform for precise analytics and simulations for gene editing

Gene editing characterization with currently available tools does not always give precise relative proportions among the different types of gene edits present in an edited bulk of cells. We have developed CRISPR-Analytics, CRISPR-A, which is a comprehensive and versatile genome editing web application tool and a nextflow pipeline to give support to gene editing experimental design and analysis. CRISPR-A provides a robust gene editing analysis pipeline composed of data analysis tools and simulation. It achieves higher accuracy than current tools and expands the functionality. The analysis includes mock-based noise correction, spike-in calibrated amplification bias reduction, and advanced interactive graphics. This expanded robustness makes this tool ideal for analyzing highly sensitive cases such as clinical samples or experiments with low editing efficiencies. It also provides an assessment of experimental design through the simulation of gene editing results. Therefore, CRISPR-A is ideal to support multiple kinds of experiments such as double-stranded DNA break-based engineering, base editing (BE), primer editing (PE), and homology-directed repair (HDR), without the need of specifying the used experimental approach.

bioinformatics↗

bioRxiv2022

New algorithms for accurate and efficient de-novo genome assembly from long DNA sequencing reads

Producing de-novo genome assemblies for complex genomes is possible thanks to long-read DNA sequencing technologies. However, maximizing the quality of assemblies based on long reads is a challenging task that requires the development of specialized data analysis techniques. In this paper, we present new algorithms for assembling long-DNA sequencing reads from haploid and diploid organisms. The assembly algorithm builds an undirected graph with two vertices for each read based on minimizers selected by a hash function derived from the k-mers distribution. Statistics collected during the graph construction are used as features to build layout paths by selecting edges, ranked by a likelihood function that is calculated from the inferred distributions of features on a subset of safe edges. For diploid samples, we integrated a reimplementation of the ReFHap algorithm to perform molecular phasing. The phasing procedure is used to remove edges connecting reads assigned to different haplotypes and to obtain a phased assembly by running the layout algorithm on the filtered graph. We ran the implemented algorithms on PacBio HiFi and Nanopore sequencing data taken from bacteria, yeast, Drosophila, rice, maize, and human samples. Our algorithms showed competitive efficiency and contiguity of assemblies, as well as superior accuracy in some cases, as compared to other currently used software. We expect that this new development will be useful for researchers building genome assemblies for different species.

bioinformatics↗

bioRxiv2022

Oxygen availability drives blood traits and the cell number-size tradeoff across Andean hummingbirds

Predictable trait variation across environmental gradients suggests that adaptive evolution repeatedly finds the same solution to a challenge. Trait-environment associations can reflect long-term, genetic evolution across phylogenies, or short-term, plastic responses of individuals. When phylogenetic and population-level patterns match, it implies consistency between the long timescale of adaptation and the short timescale of acclimatization. Alternatively, genetic adaptation can find solutions that break the rules of trait-environment covariation. For example, blood-hemoglobin concentration ([Hb]) increases at high elevations in animals, but genetic adaptations in some populations have been shown to augment tissue oxygenation while curtailing hemoglobin production, altering this predictable [Hb]-elevation association. Here, we tested whether species adaptation to elevation generally alters trait-environment relationships for blood. To do this, we measured blood traits of 1,217 individuals representing 77 species of Andean hummingbirds, across a 4,600 m elevational gradient. We used hierarchical Bayesian modeling to estimate blood trait responses to elevation, environmental temperature, precipitation, individual and species characteristics, and phylogeny. Strikingly, the effects of elevation on [Hb] and hematocrit (Hct) were nearly identical for individuals and species, implying that rules of elevational blood variation are set by physics of gas exchange in the hummingbird respiratory system and are unchanged by species adaptation. However, when we looked at mechanisms of [Hb] adjustment--by changes in red blood cell size or number--we did find a signal of species adaptation: To adjust [Hb], species at low and high elevations, respectively, tended to adjust cell size, whereas species at mid-elevations tended to adjust cell number. Despite scale-independent elevational variation in [Hb] and Hct, the species-specific balance of red blood cell size versus number appears to have been affected by adaptations that distinguish hummingbird species living at moderate versus high elevations.

evolutionary biology↗

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↗

bioRxiv2017

Why are tropical mountain passes ‘low’ for some species? Genetic and stable-isotope tests for differentiation, migration, and expansion in elevational generalist songbirds

Most tropical bird species have narrow elevational ranges, likely reflecting climatic specialization. This is consistent with Janzens Rule, the tendency for mountain passes to be effectively higher in the tropics. Hence, those few tropical species that occur across broad elevational gradients raise questions. Are they being sundered by diversifying selection along the gradient? Does elevational movement cause them to resist diversification or specialization? Have they recently expanded, suggesting that elevational generalism is short-lived in geological time? Here we tested for differentiation, movement, and expansion in four elevational generalist songbird species on the Andean west slope. We used morphology and mtDNA to test for genetic differentiation between high- and low-elevation populations. Morphology differed for House Wren (Troglodytes aedon) and Hooded Siskin (Spinus magellanicus), but not for Cinereous Conebill (Conirostrum cinereum) and Rufous-collared Sparrow (Zonotrichia capensis), respectively. mtDNA was structured by elevation only in Z. capensis. To test for elevational movements, we measured hydrogen isotope ({delta}2H) values of metabolically inert feathers and metabolically active liver. {delta}2H data indicated elevational movements by two tree- and shrub-foraging species with moderate-to-high vagility (C. cinereum and S. magellanicus), and sedentary behavior by two terrestrial-foraging species with low-to-moderate vagility (T. aedon and Z. capensis). In S. magellanicus, elevational movements and lack of mtDNA structure contrast with striking morphological divergence, suggesting strong diversifying selection on body proportions across the [~]50 km gradient. All species except C. cinereum exhibited mtDNA-haplotype variation consistent with recent population expansion across the elevational gradient.In sum,three out of four elevational generalist species underwent genetic divergence despite gene flow, two of four make seasonal elevational movements, and three of four have recently expanded. In different ways, each species defies the tendency for tropical birds to have long-term stable distributions and sedentary habits. We conclude that tropical elevational generalism is rare due to evolutionary instability.

evolutionary biology↗