Biology subjects

Signore, A. V.

Publications and source records attributed to Signore, A. V..

8 recordsLinked to original sources

bioRxiv2026

Influenza A virus H5Nx genotypes assigned by genetic similarity are incongruent with global phylogenies

Influenza A virus H5N1 and other H5 subtypes (H5Nx) have broad host ranges and pose a pandemic risk. Since early 2022, H5 clade 2.3.4.4b has predominated globally, causing unprecedented mortality in wild birds, poultry, and mammals, with spillovers to humans. Accurate viral classification is essential for tracking H5Nx variant emergence and spread, but reassortment among genome segments with distinct evolutionary histories complicates genotyping. H5Nx genotype assignment tools, GenoFlu in North America and Genin2 in Europe, assign segments to clusters by genetic similarity to reference sequences and define genotypes as constellations of segment clusters. However, genetic similarity does not necessarily imply recent shared ancestry because mutations may occur multiple times across the tree and branches may exhibit variable evolutionary rates. Furthermore, similarity is defined relative to references that may inadequately represent diversity. We evaluated the congruence of genetic similarity-based H5Nx clusters and genotypes with phylogenies of global sequences across eight segments. Publicly available H5Nx nucleotide sequences from 41,366 samples were assigned genotypes using GenoFlu and Genin2, and maximum likelihood phylogenies were inferred for each segment. Phylogenetic clusters were identified using TreeCluster for a range of patristic distance thresholds and CD-HIT clusters were identified for a range of genetic similarity thresholds. Clustering methods were evaluated based on phylogenetic purity, monophyly, and diversity. Reassortment within predominant GenoFlu and Genin2 genotypes was evaluated based on their phylogenetic cluster spans. Expectedly, GenoFlu was largely unable to assign genomes from outside of North America, South America, and Antarctica from 2022 to 2025, whereas Genin2 assignments struggled outside of Europe, Africa, and Western Asia. Only 14.2% of GenoFlu clusters were monophyletic, while Genin2 clusters were more variable across segments (overall 49.3% monophyletic). Despite CD-HIT yielding genetic distance clusters of similar size to TreeCluster, they were less monophyletic (44%) and encompassed greater phylogenetic diversity. We identified several genotypes, such as GenoFlu B3.13, D1.1, and D1.3, with internal segments that had diversified into contiguous clusters. Similarly, the wide phylogenetic span of GenoFlu genotypes B3.5 and A3, and Genin2 genotypes EA-2020-C, EA-2021-AB, and EA-2022-CH suggest they may erroneously combine multiple reassortants. Genetic similarity-based H5Nx genotyping tools are rapid, stable, and sufficient for broad categorization, but may group viruses with distinct evolutionary histories and fail to assign divergent viruses, risking biased surveillance, modeling, and risk assessment.

bioinformatics↗

bioRxiv2023

Avian influenza viruses in wild birds in Canada following incursion of the highly pathogenic H5N1 virus from Eurasia in 2021/2022

Following detection of novel highly pathogenic avian influenza virus (HPAIV) H5N1 clade 2.3.4.4b in Newfoundland, Canada in late 2021, avian influenza surveillance in wild birds was scaled-up across Canada. Herein, we present results of Canadas Interagency Surveillance Program for Avian Influenza in wild birds during the first year (November 2021 - November 2022) following the incursions of HPAIV from Eurasia. Key objectives of the surveillance program were to (i) detect the presence, distribution and spread of HPAIV and other avian influenza viruses (AIVs), (ii) detect wild bird morbidity and mortality associated with HPAIV, (iii) identify the range of wild bird species infected by HPAIV, and (iv) characterize detected AIV. A total of 6,246 sick and dead wild birds were tested, of which 27.4% were HPAIV positive across 12 taxonomic orders and 80 species. Geographically, HPAIV detections occurred in all Canadian provinces and territories, with the highest numbers in the Atlantic and Central flyways. Temporally, peak detections differed across flyways, though the national peak occurred in April 2022. In an additional 11,295 asymptomatic harvested or live captured wild birds, 5.2% were HPAIV positive across 3 taxonomic orders and 19 species. Whole genome sequencing identified HPAIV of Eurasian origin as most prevalent in the Atlantic flyway, along with multiple reassortants of mixed Eurasian and North American origins distributed across Canada, with moderate structuring at the flyway scale. Wild birds were victims and reservoirs of HPAIV H5N1 2.3.4.4b, underscoring the importance of surveillance encompassing samples from sick and dead, as well as live and harvested birds to provide insights into the dynamics and potential impacts of the HPAIV H5N1 outbreak. This dramatic shift in presence and distribution of HPAIV in wild birds in Canada highlights a need for sustained investment in wild bird surveillance and collaboration across One Health partners.

zoology↗

bioRxiv2022

Evolution of an extreme hemoglobin phenotype contributed to the sub-Arctic specialization of extinct Steller's sea cows

The extinct Stellers sea cow (Hydrodamalis gigas; {dagger}1768) was a whale-sized marine mammal that manifested profound morphological specializations to exploit the harsh coastal climate of the North Pacific. Yet despite first-hand accounts of their biology, little is known regarding the physiological adjustments underlying their evolution to this environment. Here, the adult-expressed hemoglobin (Hb; 2{beta}/{delta}2) of this sirenian is shown to harbor a fixed amino acid replacement at an otherwise invariant position ({beta}/{delta}82Lys[->]Asn) that alters multiple aspects of Hb function. First, our functional characterization of recombinant sirenian Hb proteins demonstrate that the Hb-O2 affinity of this sub-Arctic species was less affected by temperature than those of living (sub)tropical sea cows. This phenotype presumably safeguarded O2 delivery to cool peripheral tissues and largely arises from a reduced intrinsic temperature sensitivity of the H. gigas protein. Additional experiments on H. gigas {beta}/{delta}82Asn[->]Lys mutant Hb further reveal this exchange renders Stellers sea cow Hb unresponsive to the potent intraerythrocytic allosteric effector 2,3-diphosphoglycerate, a radical modification that is the first documented example of this phenotype among mammals. Notably, {beta}/{delta}82Lys[->]Asn moreover underlies the secondary evolution of a reduced blood-O2 affinity phenotype that would have promoted heightened tissue and maternal/fetal O2 delivery. This conclusion is bolstered by analyses of two Stellers sea cow prenatal Hb proteins (Hb Gower I; {zeta}2{varepsilon}2 and HbF; 2{gamma}2) that suggest an exclusive embryonic stage expression pattern, and reveal uncommon replacements in H. gigas HbF ({gamma}38Thr[->]Ile and {gamma}101Glu[->]Asp) that increased Hb-O2 affinity relative to dugong HbF. Finally, the {beta}/{delta}82Lys[->]Asn replacement of the adult/fetal protein is shown to increase protein solubility, which may have elevated red blood cell Hb content within both the adult and fetal circulations and contributed to meeting the elevated metabolic (thermoregulatory) requirements and fetal growth rates associated with this species cold adaptation.

evolutionary biology↗

bioRxiv2022

Evolution and molecular basis of a novel allosteric property of crocodilian hemoglobin

Understanding the evolution of novel protein functions requires data on the mechanistic effects of causative mutations and the extent of coupling between the gain of new function and loss of ancestral function. Here, we use ancestral protein resurrection and directed mutagenesis to dissect the molecular basis of a novel mode of allosteric regulation in crocodilian hemoglobin. We discovered that regulation of Hb-O2 affinity via allosteric binding of bicarbonate ions (a biochemical adaptation unique to crocodilians) and the concomitant loss of allosteric regulation by ATP-binding are attributable to non-overlapping sets of substitutions. Gain of bicarbonate-sensitivity involved direct effects of few replacements at key sites in combination with indirect effects of numerous replacements at structurally disparate sites. Due to the context-dependence of causative substitutions, the unique allosteric properties of crocodilian hemoglobin cannot be easily transplanted into divergent homologs of other species. Significance StatementThe extraordinary breath-hold diving capacity of crocodilians is partly attributable to a unique mode of allosterically regulating hemoglobin-oxygenation in circulating red blood cells. We investigated the origin and mechanistic basis of this novel biochemical adaptation by performing directed mutagenesis experiments on resurrected ancestral crocodilian hemoglobins. Our results revealed that evolved changes in allosteric regulation involved the direct effect of few amino acid substitutions at key sites in combination with indirect effects of numerous other substitutions at structurally disparate sites. Such indirect interaction effects suggest that the evolution of novel protein functions may often depend on neutral mutations that produce no adaptive benefit when they first arise, but which contribute to a permissive background for subsequent function-altering mutations at other sites.

evolutionary biology↗

bioRxiv2021

High-altitude adaptation and incipient speciation in geladas

Survival at high altitude requires adapting to extreme conditions such as environmental hypoxia. To understand high-altitude adaptations in a primate, we assembled the genome of the gelada (Theropithecus gelada), an endemic Ethiopian monkey, and complemented it with population resequencing, hematological, and morphometric data. Unexpectedly, we identified a novel karyotype that may contribute to reproductive isolation between gelada populations. We also identified genomic elements including protein-coding sequences and gene families that exhibit accelerated changes in geladas and may contribute to high-altitude adaptation. Our findings lend insight into mechanisms of speciation and adaptation while providing promising avenues for functional hypoxia research.

genomics↗

bioRxiv2020

Evolved increases in hemoglobin-oxygen affinity and Bohr effect coincided with the aquatic specialization of penguins.

Dive capacities of air-breathing vertebrates are dictated by onboard O2 stores, suggesting that physiological specializations of diving birds like penguins may have involved adaptive changes in convective O2 transport. It has been hypothesized that increased hemoglobin (Hb)-O2 affinity improves pulmonary O2 extraction and enhance capacities for breath-hold diving. To investigate evolved changes in Hb function associated with the aquatic specialization of penguins, we integrated comparative measurements of whole-blood and purified native Hbs with protein engineering experiments based on site-directed mutagenesis. We reconstructed and resurrected ancestral Hbs representing the common ancestor of penguins and the more ancient ancestor shared by penguins and their closest nondiving relatives (order Procellariiformes, which includes albatrosses, shearwaters, petrels, and storm petrels). These two ancestors bracket the phylogenetic interval in which penguin-specific changes in Hb function would have evolved. The experiments revealed that penguins evolved a derived increase in Hb-O2 affinity and a greatly augmented Bohr effect (reduced Hb-O2 affinity at low pH). Although an increased Hb-O2 affinity reduces the gradient for O2 diffusion from systemic capillaries to metabolizing cells, this can be compensated by a concomitant enhancement of the Bohr effect, thereby promoting O2 unloading in acidified tissues. We suggest that the evolved increase in Hb-O2 affinity in combination with the augmented Bohr effect maximizes both O2 extraction from the lungs and O2 unloading from the blood, allowing penguins to fully utilize their onboard O2 stores and maximize underwater foraging time.

evolutionary biology↗

bioRxiv2020

Biochemical paedomorphosis and genetic assimilation in the hypoxia adaptation of Tibetan antelope

Developmental shifts in stage-specific gene expression can provide a ready mechanism of phenotypic change by altering the rate or timing of ontogenetic events. We discovered that the high-altitude Tibetan antelope (Panthelops hodgsonii) has evolved an adaptive increase in blood-O2 affinity by truncating the ancestral ontogeny of globin gene expression such that a high-affinity juvenile hemoglobin isoform (isoHb) completely supplants the lower-affinity isoHb that is expressed in the adult red blood cells of other bovids. This juvenilization of blood properties represents a canalization of an acclimatization response to hypoxia that has been well-documented in adult goats and sheep. We also discovered the genomic mechanism underlying this regulatory isoHb switch, revealing how a reversible acclimatization response became genetically assimilated as an irreversible adaptation to chronic hypoxia.

evolutionary biology↗

bioRxiv2019

The role of mutation bias in adaptive molecular evolution: insights from convergent changes in protein function

An underexplored question in evolutionary genetics concerns the extent to which mutational bias in the production of genetic variation influences outcomes and pathways of adaptive molecular evolution. In the genomes of at least some vertebrate taxa, an important form of mutation bias involves changes at CpG dinucleotides: If the DNA nucleotide cytosine (C) is immediately 5 to guanine (G) on the same coding strand, then - depending on methylation status - point mutations at both sites occur at an elevated rate relative to mutations at non-CpG sites. Here we examine experimental data from case studies in which it has been possible to identify the causative substitutions that are responsible for adaptive changes in the functional properties of vertebrate hemoglobin (Hb). Specifically, we examine the molecular basis of convergent increases in Hb-O2 affinity in high-altitude birds. Using a data set of experimentally verified, affinity-enhancing mutations in the Hbs of highland avian taxa, we tested whether causative changes are enriched for mutations at CpG dinucleotides relative to the frequency of CpG mutations among all possible missense mutations. The tests revealed that a disproportionate number of causative amino acid replacements were attributable to CpG mutations, suggesting that mutation bias can influence outcomes of molecular adaptation.

evolutionary biology↗