Friday, August 27, 2021

RESEARCH PROJECT: Parasite Community Assembly and Disassembly

Students interested in conducting undergraduate and graduate thesis research for Spring-Fall semesters 2022 feel free to contact me at:

The project aims to understand the succession and assembly process of both hosts (vertebrate) and parasite (blood parasites) communities using long term research at the USF Forest Preserve, and across an urbanization gradient in the Tampa area. 

For more information on the forest preserve visit:

The main vertebrate group to study is birds and the parasites are the group of malarias and related haemosporidians (vector-borne blood parasites).

Thursday, February 4, 2021

How Quantum Mechanics Can Explain Evolutionary Adaptations and Novelty?

Quantum biology seeks to explain biological phenomena via quantum

mechanisms, such as enzyme reaction rates via tunnelling and photosynthesis

energy efficiency via coherent superposition of states. However, less

effort has been devoted to study the role of quantum mechanisms in biological

evolution. In this paper, we used transcription factor networks with two

and four different phenotypes, and used classical random walks (CRW) and

quantum walks (QW) to compare network search behaviour and efficiency

at finding novel phenotypes between CRW and QW. In the network with

two phenotypes, at temporal scales comparable to decoherence time TD,

QW are as efficient as CRW at finding new phenotypes. In the case of the

network with four phenotypes, the QW had a higher probability of mutating

to a novel phenotype than the CRW, regardless of the number of mutational

steps (i.e. 1, 2 or 3) away from the new phenotype. Before quantum decoherence,

the QW probabilities become higher turning the QW effectively more

efficient than CRW at finding novel phenotypes under different starting conditions.

Thus, our results warrant further exploration of the QW under more

realistic network scenarios (i.e. larger genotype networks) in both closed and

open systems (e.g. by considering Lindblad terms).

J. R. Soc. Interface 17: 20200567.

Wednesday, October 21, 2020

NEW BOOK! Avian Malaria and Related Parasites in the Tropics: Ecology, Evolution and Systematics

The Tropics are home to the greatest biodiversity in the world, but tropical species are at risk due to anthropogenic activities, mainly land use change, habitat loss, invasive species, and pathogens. Over the past 20 years, the avian malaria and related parasites (Order: Haemosporida) systems have received increased attention in the tropical regions from a diverse array of research perspectives. However, to date no attempts have been made to synthesize the available information and to propose new lines of research. This book provides such a synthesis by not only focusing on the antagonistic interactions, but also by providing conceptual chapters on topics going from avian haemosporidians life cycles and study techniques, to chapters addressing current concepts on ecology and evolution. For example, a chapter synthesizing basic biogeography and ecological niche model concepts is presented, followed by one on the island biogeography of avian haemosporidians. Accordingly, researchers and professionals interested in these antagonistic interaction systems will find both an overview of the field with special emphasis on the tropics, and access to the necessary conceptual framework for various topics in ecology, evolution and systematics. Given its conceptual perspective, the book will appeal not only to readers interested in avian haemosporidians, but also to those more generally interested in the ecology, evolution and systematics of host-parasite interactions.
 You can buy it at:

Saturday, June 13, 2020

Parasite Richness Decreases With Urbanization

Effects of land use change (rural-urban) on the diversity and epizootiological
parameters of avian Haemosporida in a widespread neotropical bird

Transformation of natural environments for livestock, agriculture and human settlements modifies the diversity of organisms, usually decreasing in highly disturbed land uses. Like their hosts, parasites have to adapt to novel human impacted landscapes, in which the abiotic and biotic conditions are radically different from those of conserved natural environments. We evaluated the diversity (alpha and beta taxonomic and phylogenetic diversity) of haemosporidians (mtDNA cyt b lineages) in the common chlorospingus (Chlorospingus flavopectus) at five land use types. We further analyzed the response of prevalence, parasitaemia and parasite aggregation to and use types and seasonality. Parasite lineage richness (i.e., haplotypes) and abundance (no. infected hosts) decreased with disturbance. Parasite assemblages were commonly dominated by either one of two lineages, one dominant in the urban greenspace (pBAEBIC02) and the other dominant in well-preserved mountain cloud forest (hCHLFLA01). Beta diversity was mainly explained by lineage turnover. Phylo beta diversity was low (i.e., lineages are closely related). Overall prevalence increased in wet season that coincides with host's breeding season. Haemoproteus and Plasmodium prevalence presented the opposite response to urbanization (negative and positive, respectively). Parasitaemia presented similar values across land uses for both genera and seasons, while Plasmodium aggregation decreased with urbanization. Thus, some parasite lineages (pBAEBIC02) will benefit from the urbanization process, while others will entirely disappear from cities (hCHLFLA01).

Hernández-Lara C, Carbó-Ramírez P, Santiago-Alarcon D. 2020. Effects of land use change (rural-urban) on the diversity and epizootiological parameters of avian Haemosporida in a widespread neotropical bird. Acta Tropica209: 105542
To download for free until August 01, 2020:,2Uvj2LY

Thursday, April 2, 2020

House Sparrows Are City Gangsters!

Biological invasions are the second most important cause of species extinction. Aided by processes such as transportation and urbanization, exotic species can establish and spread to new locations, causing changes in the function and structure of ecosystems. The House Sparrow is a widespread and highly abundant landbird associated to human presence. Previous studies performed in urban landscapes have suggested that this species could be acting, in synergy with urbanization, as a potential threat to native urban avian assemblages. In this study we assessed the relationship between House Sparrow density and native bird species richness in a region where the sparrows are scarce and sparsely distributed. We surveyed bird assemblages in and around four small-sized human settlements, considering three conditions in relation to House Sparrow presence: urban invaded,
urban non-invaded, and non-urban non-invaded. To assess the potential detrimental role of House Sparrows on native bird species richness, we measured, additionally to sparrow densities, 20 predictor variables that describe vegetation structure and complexity, as well as urban infrastructure and human activities across four seasons of 1 year. Our results show that maximum shrub height was positively related to bird species richness, built cover was negatively associated with it, and House Sparrow invaded sites were related to a significant decrease of bird species richness, with increasing richness loss when more sparrows were present. Thus, we here provide evidence that urban areas can act in synergy with the presence of House Sparrows (even in low densities) in the urban-related species richness decline pattern.
García-Arroyo M, Santiago-Alarcon D, Quesada J, MacGregor-Fors I. 2020. Are invasive House Sparrows a nuisance for native avifauna when scarce? Urban Ecosystems

City Is Less Risky For House Sparrows Infection

Urbanization affects the ecology of wildlife diseases and although it has been suggested that there are lower risks of infection in urban areas, there have been no experiments to support this conclusion. We assessed haemosporidian prevalence and intensity in House Sparrows Passer domesticus using field and experimental data under contrasting conditions (i.e. urban vs. non-urban). For experimental data, we kept 32 male House Sparrows in captivity as a proxy of stress, and for field data we sampled 49 House Sparrows (17 females). We made use of microscopy to determine the relative intensity and used the polymerase chain reaction to estimate infection prevalence. We obtained total leucocyte counts, leucocyte differentials, heterophil/lymphocyte ratio (H/L) as a measure of stress, and the Polychromatic Index as a measure of physiological condition (erythropoiesis). We identified a total of 10 haemosporidian lineages. For field samples (both males and females), we found a significantly higher prevalence of infection in non-urban House Sparrows than in urban ones. Under experimental conditions, non-urban House Sparrows showed a higher prevalence than urban ones both before and after captivity, with a significant increase in parasite intensity. The number of infected birds increased after captivity for both urban (~ 32%) and non-urban House Sparrows (~ 19%), indicating either a recrudescence of chronic and relapses of latent infections or the appearance of infections that had been acquired earlier. The H/L ratio was significantly higher for non-urban than for urban male House Sparrows before captivity. No difference in H/L was found for urban House Sparrows before and after captivity, indicating tolerance to city stressors. Our results showed a significant decrease in H/L for non-urban birds after captivity, suggesting higher stress in the non-urban agricultural environment. Haemosporidian infections were not associated with the H/L ratio. Our study provides evidence that highly urbanized areas within cities represent lower haemosporidian infection risks than do non-urban areas for House Sparrows.
Santiago-Alarcon D, Carbó-Ramírez P, MacGregor-Fors I., Chávez-Zichinelli C.A., Yeh P.J. 2020. Avian malaria prevalence of an invasive urban bird is lower in urban than non-urban environments. Ibis162: 201-214. doi:10.1111/ibi.12699