Raul Ernesto Sedano-Cruz

This study examines the genetic variation and structure of the spectacled caiman (Caiman crocodilus) on Gorgona Island, Colombia, compared to continental populations. We analyzed 178 partial Cytochrome b gene sequences, most of which were obtained from GenBank, and identified 23 haplogroups, with five of these specifically found on the Island. Phylogenetic analysis using maximum likelihood placed C. crocodilus, including the Gorgona Island population, in a distinct monophyletic group. Genetic structure analysis identified two main clusters, with Gorgona Island caimans primarily assigned to the Trans-Andean cluster. The haplogroup network illustrates the two major groups, with a maximum of 12 mutational steps between them. Additionally, Tajima’s D statistic suggests an excess of rare alleles in the spectacled caiman. Genetic differentiation across regions suggests historical isolation, likely shaped by geographical barriers and limited gene flow. The distinct genetic patterns of island populations highlight their disparity in terms of evolutionary dynamics and conservation importance. Further genomic analysis is recommended to explore demographic history. Conservation strategies should prioritize the maintenance of genetic diversity to mitigate the effects of isolation, while also incorporating insights from the species’ biogeographic history. Our findings highlight the unique contribution of the small population in Gorgona Island to the species’ spatial genetic structure.

This exploratory study presents the first metagenomic assessment of the gut microbiome in domestic cats from Cali, Colombia. Fecal samples were collected from 10 healthy, sterilized domestic cats, aged 8 months to over 2 years, with variation in sex (7 females, 3 males), diet (processed or raw), and outdoor access (5 with, 5 without). Using 16S rRNA gene metabarcoding and pooled shotgun metagenomic sequencing, the study characterized the taxonomic composition and functional potential of the feline gut microbiome. Dominant phyla included Bacillota and Bacteroidota, with substantial inter-individual variation. Peptoclostridium was the most consistently abundant genus, while Megamonas and Megasphaera showed higher variability. Shotgun analysis detected antibiotic resistance genes (ErmG, ErmQ) and virulence factors (pfoA, plc, colA, nanJ, nagI) in Clostridium perfringens, highlighting potential zoonotic risk. The composition of the gut microbiota was influenced primarily by diet and outdoor access, while age and gender had more moderate effects. The study concludes that lifestyle and environmental factors play a key role in shaping the gut microbiome of domestic cats. We recommend further longitudinal and larger-scale studies to better understand the dynamics of feline microbiota and their implications for animal and public health within a One Health framework.

Island-mainland systems serve as natural laboratories for studying communication signals. We explored potential divergence in the song of the black-crowned antshrike between Gorgona Island, a land-bridge island off the Pacific coast of Colombia, and several mainland populations. We found that the perching song of this species, the so called loudsong, was distinctly different on Gorgona Island. This differentiation encompassed an increase in frequency bandwidth, a decrease in vocal performance, and a reduction in song duration. All are consistent with documented patterns of divergence observed in avian acoustic signals on oceanic islands. The observed distinctions in loudsong acoustics, including variations in frequency and temporal features, led to the inference that the population on Gorgona Island produces the least complex loudsong dialect across the entire species range. This pattern of how an innate vocalization manifests within a land-bridge island, which was connected to the mainland not long ago, lends support to the Character Release Hypothesis. To ensure an unbiased comparison, we considered genetic clusters and analyzed them by comparing ten acoustic signals between the land-bridge island and several mainland populations. Combined with the gene genealogy, this finding supports the validity of two geographic forms: Thamnophilus atrinucha atrinucha and Thamnophilus atrinucha gorgonae (island). However, they also reveal the existence of additional unrecognized dialects of loudsong that transcend current taxonomic classifications. We provide evidence that challenges the long-standing presumption suggesting minimal intraspecific geographic variation in the vocalization among non-vocal learning species. Significance statement: Significant evolutionary implications exist for an intriguing pattern of variation of the loudsong behavior in the Black-crowned Antshrike over a land-bridge island. Our gene tree does provide evidence of the enormous haplotypic diversity accumulated in the trans-Andean region long after the final uplift of the northern Andes. The acoustic divergence of the loudsong suggests substantial geographic variation within a non-vocal learning suboscine. Genetic and loudsong divergence on a land-bridge island add to document that evolution of acoustic traits may be relaxed in islands as compared to those observed on the species-rich mainland. The island-mainland system is one of the few definitive biogeographic contexts for understanding evolution of acoustic behavior.

Wildlife mortality caused by domestic cats is evident where free-roaming house cats are present in the tropical Andes region, a phenomenon for which there is a lack of scientific reports. Our goal is to present plausible range estimates of the potential avoidable number of birds killed by domestic cats in Colombia. We calculated estimates of the number of birds killed as the product of the number of cats, the proportion of cats with at least some outdoor access, the proportion of cats that hunt wildlife, the annual predation probability, and adjustments for estimates of total prey killed by cats. We extracted such data not only from public records, but also from a citizen science study, for which we circulated a questionnaire to examine cat owners’ attitudes toward the impact of domestic cats on wildlife during the 2020 and 2021 COVID-19 lockdowns in Colombia. We estimated that three to 12 million birds are killed annually by domestic cats in urban and suburban areas. In addition, we estimated that cats kill eight to 29 million vertebrate fauna in the Andes of Colombia. The total kill estimate provides a first figure on the magnitude of the impact of an anthropogenic cause of wildlife mortality for Colombia. These estimates would be more rigorous if the unowned or feral cat population size in Colombia was better known. Because most pet cats in Colombia roam outdoors without supervision and their population is growing, they pose an increasing threat to wildlife. Intervention is urgent to mitigate bird mortality by domestic cats.

To better understand the processes that may lead to potentially avoidable extinction events, it is important to identify the influence of change in the communities at the local scale. We compiled bird lists from a field station with an artificial wetland system and a history of drastic changes in land use in the Colombian Andes. This data expands from 1974 to 2018. Our assessment uses three criteria to recognize local extinction: looking at the short-term (last 5 years) variation, a comparison between baseline and the most recent data, and the time in between. These criteria also allowed us to quantify substantial colonization and recolonization events. We found that 5.9% of previously recorded species had become extirpated, 5.2% can be considered probably extirpated, and 6.7% are possibly extirpated. Moreover, there was an important turnover in foraging guilds which implies a transition in the community's functional diversity. The loss of artificial wetlands in addition to the local afforestation plan in the mid-90s at the study site likely constitute the leading factors for the observed gains and losses of species in the agroecosystem. We highlight the importance of multicriteria assessment in community-level studies to distinguish between an apparent persistence and an actual extirpation event over the long term. Artificial wetlands and agroecosystems should be better studied as they could complement regional conservation targets.

La estructura genética de poblaciones de mariposas con distribución en islas y sus pares continentales ha sido poco documentada para el neotrópico. Este estudio presenta la caracterización de una población de Heliconius sara con distribución en la Isla Gorgona, ubicada en la región del Pacífico Oriental Colombiano. Para esto se examinaron secuencias parciales de un marcador mitocondrial incluyendo información obtenida del GenBank. Se comparó la diversidad y estructura genética con sus conespecíficos continentales y también con congéneres, con los que comparte un ancestro común cercano en el clado Sapho-Sara. Para el análisis de diversidad y estructura genética se realizó un análisis molecular de varianza. Este análisis muestra que la distancia entre la población de la isla y sus pares en el continente es consistente con la variación intraespecífica observada en otras especies del género Heliconius. Para la reconstrucción de la genealogía y datación reciente en el Pleistoceno superior del grupo monofilético de secuencias de H. sara, se realizó un análisis de inferencia bayesiana, así como una de máxima verosimilitud. Del análisis demográfico se seleccionó un modelo histórico de flujo asimétrico desde la isla hacia el continente que sugiere baja resistencia de la discontinuidad geográfica a la dispersión de esta mariposa diurna desde la isla. Este es el primer estudio en examinar un posible evento de aislamiento de una población insular de mariposas en Colombia.

Melanism in plumage color is often associated to the single nucleotide polymorphism of the melanocortin-1-receptor (MC1R). Despite the striking association between the substitution of a Glutamic-acid by for a Lysine at position 92 on the MC1R protein and a completely black plumage, an in-depth understanding of the effect of missense mutations on the conformational change and behavior of the MC1R in the lipid bilayer caused by the absence of a crystal structure is lacking. We examine the structural basis for receptor activation using DNA sequences from the GenBank to perform in silicoprotein homology-based modeling. Our tridimensional model shows that the Alanine for a 179-Threoninesubstitution is a structural complement of the charge-reversing effect associated to the substitution of a Glutamic-acid by for a Lysine at position 92 on the MC1R. We proposed the possibility of gradual evolution in stability and electrostatic properties of the MC1R by the sequential accumulation of these two rare substitutions. These two rare substitutions further perturb physical-chemical properties that may be necessary folding requirements of the constitutively active MC1R forms without altering of ligand binding affinity. The computational coarse-grained molecular dynamics of the MC1R binding affinities to the melanocyte-stimulating hormone predicted the disparity in ligand binding amongalleles. We speculate that the disparity in structural constraints and ligand binding among the alleles within heterozygous individuals may contribute as a mechanism to the plumage color variation in the Coereba flaveola.

La variación genética entre las poblaciones insulares y continentales de la hormiga cortadora de hojas Atta cephalotes ha sido poco estudiada, a pesar de su importancia para comprender su capacidad de dispersión, la estructura regional y la distribución de una de las especies más abundantes en el neotrópico. Objetivo: Analizar la variación genética de una población insular de esta hormiga cortadora de hojas en un contexto regional más amplio para América Central y del Sur. Métodos: Se secuenció el gen de la Citocromo oxidasa I de Atta cephalotes para las poblaciones de la isla Gorgona y el continente para realizar un análisis de la varianza molecular, la selección de modelos del flujo de genes, así como para calcular el tiempo de divergencia de los haplogrupos que circulan en la isla. Se realizó una prueba de asignación de individuos para estimar la conectividad genética espacial y la distribución de esta hormiga en el Pacífico Oriental Tropical. Resultados: un total de 33 muestras de la isla y el continente colombiano se compararon con 389 accesiones de Genebank de Atta cephalotes de América Central y del Sur. La hormiga cortadora de hojas en la isla Gorgona está estrechamente relacionada con el continente colombiano a pesar de que la separación entre la isla y el continente probablemente constituya una barrera para el flujo de genes. Los haplogrupos más comunes en el continente probablemente llegaron a la isla en algún momento hacia final del Pleistoceno. Sin embargo, no se puede excluir la influencia antropogénica en la reciente colonización de la isla por esta hormiga cortadora de hojas. Un mapa de conectividad muestra que esta población tiene límites geográficos que se superponen en gran medida con una región biogeográfica dentro del Pacífico Oriental Tropical. Esta población trans-andina acumula el 23% de la diversidad de herencia matrilineal de Atta cephalotes. Conclusiones: la hormiga cortadora de hojas en la isla Gorgona y el Pacífico colombiano está estrechamente relacionada con la población centroamericana y toda esta región alberga un segmento significativo de la diversidad genética de Atta cephalotes en América del Sur.

Avian haemosporidia are obligate blood parasites with an ample range of hosts worldwide. To understand how host communities may influence the diversity of parasites of the neotropics, the spatial genetic variation of avian Plasmodium, Haemoproteus, and Leucocytozoon was examined between areas of host endemism and along the elevational gradient in the tropical Andes. A total of 1686 accessions of the cytochrome b gene of avian haemosporidia were selected from 43 publications, that further provides additional information on 14.2% of bird species in the Neotropics. Haplotype groups were identified using a similarity-based clustering of sequences using a cut-off level ≥ 99.3% of sequence identity. Phylogenetic-based analyses were implemented to examine the spatial genetic structure of avian haemosporidia among areas of host endemism and the elevation gradient in the tropical Andes. The areas of avian endemism, including the tropical Andes, can explain the differential distribution of the haemosporidia cytochrome b gene variation. In the tropical Andes region, the total number of avian haemosporidia haplotypes follows a unimodal pattern that peaks at mid-elevation between 2000 and 2500 m above sea level. Furthermore, the haplotype assemblages of obligate blood parasites tend to overlap towards mid-elevation, where avian host diversity tends to be maximized. Spatial analyses revealed that richness and turnover in haemosporidia suggest an association with montane host diversity, according to elevation in the tropical Andes. In addition, the spatial distribution of haemosporidia diversity is closely associated with patterns of host assemblages over large geographical scale in the tropical Andes and areas of avian endemism nearby.