Biology subjects

Escalante, A. A.

Publications and source records attributed to Escalante, A. A..

6 recordsLinked to original sources

bioRxiv2026

The Monophyly of Nycteria and Polychromophilus Parasites A Missing Piece in the Evolution of Malaria and Other Haemosporida

Haemosporida is a diverse order of vector-borne apicomplexan parasites infecting terrestrial vertebrates worldwide, including humans, but the evolutionary relationships among its genera remain unresolved. The phylogenetic placement of two bat-restricted genera, Nycteria and Polychromophilus, both of which lack erythrocytic schizogony, has varied across studies depending on taxon sampling and marker choice. To address this problem, an expanded dataset of near-complete mitochondrial (mtDNA) genomes together with nine nuclear loci were analyzed. Phylogenetic analyses of mtDNA recovered Nycteria and Polychromophilus as a strongly supported monophyletic clade. In contrast, analyses based only on the three mitochondrial coding genes (CDS) or a reduced nuclear dataset failed to recover their monophyly and showed low support and extensive topological conflict at deeper nodes. These results indicate that near-complete mitochondrial genomes recover phylogenetic signal that is not captured by reduced mitochondrial coding sequences or partial nuclear datasets. Molecular dating analyses further showed that divergence estimates for a putative Nycteria-Polychromophilus clade are compatible with the proposed times for bats diversification, and consistent with the broader haemosporidian timescale. When the Nycteria-Polychromophilus clade was incorporated as a calibration prior, divergence-time estimates became more precise without altering the overall evolutionary timeframe. Substantial mitochondrial gene-order rearrangements in a distinct Nycteria lineage were confirmed, highlighting structural divergence within this bat-associated group. In addition, heterogeneity in rates across mtDNA haemosporidian lineages was observed. Together, these findings support the existence of a distinct bat-associated clade whose deeper placement and evolutionary significance should be tested with broader phylogenomic sampling. Author SummaryMalaria parasites belong to a diverse group of organisms that infect many kinds of vertebrates, including birds, reptiles, and mammals (such as humans). Understanding how these parasites are related to each other is important for explaining how key biological traits have evolved. However, the relationships among major groups of haemosporidian parasites, including malaria parasites, remain unclear, particularly for those infecting bats. In this study, we focused on two groups of bat parasites, Nycteria and Polychromophilus, which share unusual biological features. The inferred evolutionary relationships of these two genera to other haemosporidians have been inconsistent across previous studies. By analyzing near-complete mitochondrial genomes, we found strong evidence that these two groups descended from a common evolutionary ancestor. In contrast, smaller datasets including nuclear genes failed to recover this relationship and produced conflicting results, suggesting that they lack sufficient information to resolve deep evolutionary relationships. We also found that this bat-associated lineage likely originated around the same time as early bats. In addition, we identified structural changes in the mitochondrial genome of one lineage, highlighting its evolutionary distinctiveness. Together, our results suggest that bats host a unique group of malaria parasites and demonstrate that more complete genetic data are essential for resolving their evolutionary history.

evolutionary biology↗

bioRxiv2024

Pathogens spread by high-altitude windborne mosquitoes

Recent studies have revealed that many mosquito species regularly engage in high-altitude windborne migration, but its epidemiological significance was debated. The hypothesis that high-altitude mosquitoes spread pathogens over large distances has not been directly tested. Here, we report for the first time that high-altitude windborne mosquitoes are commonly infected with arboviruses, protozoans, and helminths affecting vertebrates and humans, and provide the first description of this pathogen-vector aerial network. A total of 1,017 female mosquitoes (81.4%, N=1,249) intercepted on nets suspended from helium balloons at altitudes of 120-290 m above ground over Mali and Ghana were screened for infection with arboviruses, plasmodia, and filariae, using pan-genus qPCR analyses followed by sequencing of positive samples. The mosquito fauna collected at altitude comprised 61 species, across 9 genera, dominated by Culex, Aedes, and Anopheles. Infection and infectiousness rates of high-altitude migrant mosquitoes were 7.2% and 4.4% with plasmodia, 1.6% and 0.6% with filariae, 3.5% and 1.1% with flaviviruses, respectively. Nineteen mosquito-borne pathogens were identified, including three arboviruses: dengue, West Nile and MPoko viruses, 13 putative plasmodia species including Plasmodium matutinum and P. relictum, three filariids, including Pelecitus spp., 27 insect-specific viruses and 5 non-mosquito-borne pathogens (e.g., Trypanosoma theileri). Confirmed head-thorax (disseminated) infections of multiple pathogens in multiple mosquito species, eg., Culex perexiguus, Coquilletidia metallica, Mansonia uniformis, and Anopheles squamosus provides evidence that pathogens carried by high-altitude windborne mosquitoes are infectious and likely capable of infecting naive hosts far from their starting location. This traffic of sylvatic pathogens may be key to their maintenance among foci as well as initiating outbreaks away from them.

microbiology↗

bioRxiv2022

Great-tailed Grackles (Quiscalus mexicanus) as a tolerant host of avian malaria parasites

Great-tailed Grackles (Quiscalus mexicanus) are a social, polygamous bird species whose populations have rapidly expanded their geographic range across North America over the past century. Before 1865, Great-tailed Grackles were only documented in Central America, Mexico, and southern Texas in the USA. Given the rapid northern expansion of this species, it is relevant to study its role in the dynamics of avian blood parasites. Here, 87 Great-tailed grackles in Arizona (a population in the new center of the range) were screened for haemosporidian parasites using microscopy and PCR targeting the parasite mitochondrial cytochrome b gene. Individuals were caught in the wild from January 2018 until February 2020. Haemosporidian parasite prevalence was 60.9% (53/87). A high Plasmodium prevalence was found (59.8%, 52/87), and one grackle was infected with Haemoproteus (Parahaemoproteus) sp. (lineage SIAMEX01). Twenty-one grackles were infected with P. cathemerium, sixteen with P. homopolare, four with P. relictum (strain GRW04), and eleven with three different genetic lineages of Plasmodium spp. that have not been characterized to species level (MOLATE01, PHPAT01, and ZEMAC01). Gametocytes were observed in birds infected with three different Plasmodium lineages, revealing that grackles are competent hosts for some parasite species. This study also suggests that grackles are highly susceptible and develop chronic infections consistent with parasite tolerance, making them competent to transmit some generalist haemosporidian lineages. It can be hypothesized that, as the Great-tailed Grackle expands its geographic range, it may affect local bird communities by increasing the transmission of local parasites but not introducing new species into the parasite species pool.

zoology↗

bioRxiv2020

Contrast-FEL: a test for differences in selective pressures at individual sites among clades and sets of branches.

A number of evolutionary hypotheses can be tested by comparing selective pressures among sets of branches in a phylogenetic tree. When the question of interest is to identify specific sites within genes that may be evolving differently, a common approach is to perform separate analyses on subsets of sequences, and compare parameter estimates in a post hoc fashion. This approach is statistically suboptimal, and not always applicable. Here, we develop a simple extension of a popular fixed effects likelihood method in the context of codon-based evolutionary phylogenetic maximum likelihood testing, Contrast-FEL. It is suitable for identifying individual alignment sites where any among the K [≥] 2 sets of branches in a phylogenetic tree have detectably different dN/dS ratios, indicative of different selective regimes. Using extensive simulations, we show that Contrast-FEL delivers good power, exceeding 90% for sufficiently large differences, while maintaining tight control over false positive rates. We conclude by applying Contrast-FEL to data from five previously published studies spanning a diverse range of organisms and focusing on different evolutionary questions.

bioinformatics↗

bioRxiv2020

Malaria in Southern Venezuela: The Hottest Hotspot in Latin America

Malaria cases in Latin America reached ~1 million in 2017 and 2018, with 53% and 51% reported from Venezuela, respectively. In this study, we characterized the spatiotemporal dynamics of malaria transmission between 2007-2017 in southern Venezuela, the main endemic area of the country. We found that disease transmission was focal and more prevalent in the southeast of southern Venezuela where two persistent hotspots of Plasmodium vivax (76%) and P. falciparum (18%) linked to deforestation for illegal gold mining accounted for ~60% of the country-wide number of cases. Incidence has increased nearly tenfold in the last decade, showing an explosive epidemic growth due to a significant lack of disease control. We suggest that a source-sink pattern of Plasmodium sp. dispersal account for the re-emergence and progression of malaria transmission in the last 4 years across the country due to the internal migration of infected people to and from the hotspots and other malaria-prone ecosystems. We observe a similar pattern explaining the spillover of cases across international borders affecting neighboring countries. This study provides baseline epidemiological data and guidance for malaria control to further assess the dynamics of cross-border malaria, the role of asymptomatic carriers, drug-resistant evolution, and innovative control efforts in the Latin America region.

ecology↗

bioRxiv2017

Human Migration And The Spread Of Malaria Parasites To The New World

BackgroundThe Americas were the last continent to be settled by modern humans, but how and when human malaria parasites arrived in the New World is uncertain. Here, we apply phylogenetic analysis and coalescent-based gene flow modeling to a global collection of Plasmodium falciparum and P. vivax mitogenomes to infer the demographic history and geographic origins of malaria parasites circulating in the Americas. Importantly, we examine P. vivax mitogenomes from previously unsampled forest-covered sites along the Atlantic Coast of Brazil, including the vivax-like species P. simium that locally infects platyrrhini monkeys.\n\nResultsThe best-supported gene flow models are consistent with migration of both malaria parasites from Africa and South Asia to the New World, with no genetic signature of a population bottleneck upon parasite's arrival in the Americas. We found evidence of additional gene flow from Melanesia in P. vivax (but not P. falciparum) mitogenomes from the Americas and speculate that some P. vivax lineages might have arrived with the Australasian peoples who contributed genes to Native Americans in pre-Columbian times. Mitochondrial haplotypes characterized in P. simium from monkeys from the Atlantic Forest are shared by local humans. These vivax-like lineages have not spread to the Amazon Basin, are much less diverse than P. vivax circulating elsewhere in Brazil, and show no close genetic relatedness with P. vivax populations from other continents.\n\nConclusionsEnslaved peoples brought from a wide variety of African locations were major carriers of P. falciparum mitochondrial lineages into the Americas, but additional human migration waves are likely to have contributed to the extensive genetic diversity of present-day New World populations of P. vivax. The reduced genetic diversity of vivax-like monkey parasites, compared with human P. vivax from across this country, argues for a recent human-to-monkey transfer of these lineages in the Atlantic Forest of Brazil.\n\nAuthor summaryMalaria is currently endemic to the Americas, with over 400,000 laboratory-confirmed infections reported annually, but how and when human malaria parasites entered this continent remains largely unknown. To determine the geographic origins of malaria parasites currently circulating in the Americas, we examined a global collection of Plasmodium falciparum and P. vivax mitochondrial genomes, including those from understudied isolates of P. vivax and P. simium, a vivax-like species that infect platyrrhini monkeys, from the Atlantic Forest of Brazil. We found evidence of significant historical migration to the New World of malaria parasites from Africa and, to a lesser extent, South Asia, with further genetic contribution of Melanesian lineages to South American P. vivax populations. Importantly, mitochondrial haplotypes of P. simium are shared by monkeys and humans from the Atlantic Forest, most likely as a result of a recent human-to-monkey transfer. Interestingly, these potentially zoonotic lineages are not found in the Amazon Basin, the main malaria-endemic area in the Americas. We conclude that enslaved Africans were the main carriers of P. falciparum mitochondrial lineages into the Americas, whereas additional migration waves of Australasian peoples and parasites may have contributed to the genetic makeup of present-day New World populations of P. vivax.

microbiology↗