Eduardo Eizirik

Pontifícia Universidade Católica do Rio Grande do Sul | PUCRS · Escola de Ciências da Saúde e da Vida

Estimates of de novo mutation rates are essential for phylogenetic and demographic analyses, but their inference has previously been impeded by high error rates in sequence data and uncertainty in the fossil record. Here, we directly estimate de novo germline mutation rates for all extant members of Panthera, as well as the closely related outgroup...

Effective conservation management depends on the maintenance of key areas that allow population connectivity across the landscape. However, the lack of knowledge of how habitat conversion affects species movement hinders the identification of these areas. Here, we analyzed the impact of habitat fragmentation on landscape connectivity for Leopardus...

Cryptic biodiversity continues to be revealed worldwide, even in apparently well-known groups such as carnivorans. The Neotropical Otter (Lontra longicaudis) presents shape variation in its nose pad, a character that has been used to differentiate species in this group. Based on this, 3 subspecies are recognized: L. l. annectens (Mexico, Central Am...

Vocal production learning is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical and neurophysiological data from the Egyptian fruit-bat with analyses of the genomes of 215 placental mammals. First, we identified a set of proteins evolving more s...

The hoary fox (Lycalopex vetulus) is the only species of the Canidae (Mammalia: Carnivora) endemic to Brazil, and so far has been the target of few genetic studies. Using microsatellites and mtDNA markers, we investigated its present genetic diversity and population structure. We also tested the hypothesis that this species currently hybridizes wit...

Recently, the tiger-cat species complex was split into Leopardus tigrinus and Leopardus guttulus, along with other proposed schemes. We performed a detailed analysis integrating ecological modeling, biogeography, and phenotype of the four originally recognized subspecies-tigrinus, oncilla, pardinoides, guttulus-and presented a new multidimensional...

Even in the genomics era, the phylogeny of Neotropical small felids comprised in the genus Leopardus remains contentious. We used whole-genome resequencing data to construct a time-calibrated consensus phylogeny of this group, quantify phylogenomic discordance, test for inter-species introgression, and assess patterns of genetic diversity and demog...

Poster presenting the research published as Lescroart J, Bonilla-Sánchez A, Napolitano C, Buitrago-Torres DL, Ramírez-Chaves HE, Pulido-Santacruz P, Murphy WJ, Svardal H, Eizirik E. Extensive phylogenomic discordance and the complex evolutionary history of the Neotropical cat genus Leopardus. Molecular Biology and Evolution. 2023:msad255. https:/...

The common name of pampas cat includes a complex of small Neotropical felid species found in various habitats of South America. Recently several species of this complex were proposed, but there are few records in the northernmost distribution of the continent, and reports of the pampas cat’s presence in Colombia have been ambiguous. Current norther...

The chapter addresses the current state of the field of conservation genomics focused on neotropical carnivores (Mammalia, Carnivora), the history of its development in the last decade, and its prospects for the future. It describes the genomic resources that have been developed so far for these species, and their applications in conservation effor...

The success of translocation as a management tool is based on reversing the factors that led to a population becoming threatened or locally extinct. We assessed whether translocating a jaguar Panthera onca into the surroundings of a protected area in the Brazilian Atlantic Forest with a resident jaguar population was effective. We captured a male j...

Current knowledge of cancer genomics remains biased against noncoding mutations. To systematically search for regulatory noncoding mutations, we assessed mutations in conserved positions in the genome under the assumption that these are more likely to be functional than mutations in positions with low conservation. To this end, we use whole-genome...

Geoffroy’s cat (Leopardus geoffroyi) is a small neotropical felid that has been the focus of a few dietary studies in the Brazilian Pampa. In order to better understand its trophic ecology, it is essential to accurately determine its diet and to evaluate potential relationships between prey composition and habitat suitability. To achieve this, we e...

The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral...

Biologists currently have an assortment of high-throughput sequencing techniques allowing the study of population dynamics in increasing detail. The utility of genetic estimates depends on their ability to recover meaningful approximations while filtering out noise produced by artifacts. We empirically compared the congruence of two reduced represe...

Aim The use of landscape resistance maps to model connectivity has become an indispensable tool for species conservation. However, different methods can be used to estimate landscape resistance, but there is no consensus on which is the most reliable one. Therefore, comparing the performance of those methods in predicting resistance can be quite us...

The remarkable radiation of South American (SA) canids produced 10 extant species distributed across diverse habitats, including disparate forms such as the short-legged, hypercarnivorous bush dog and the long-legged, largely frugivorous maned wolf. Despite considerable research spanning nearly two centuries, many aspects of their evolutionary hist...

Comparative whole-genome analyses hold great power to illuminate commonalities and differences in the evolution of related species that share similar ecologies. The mustelid subfamily Lutrinae includes 13 currently recognized extant species of otters,1, 2, 3, 4, 5 a semiaquatic group whose evolutionary history is incompletely understood. We assembl...

The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral...

The canid genus Lycalopex comprises six recently diversified South American species whose evolutionary relationships have been remarkably challenging to resolve. We analyzed 6000 bp of mitochondrial DNA (mtDNA) from 55 Lycalopex individuals (L. sechurae = 4, L. culpaeus = 7, L.griseus = 8, L.gymnocercus = 17, L.vetulus = 13 and L. fulvipes = 6), an...

Recording of presentation at Evolution 2022. The same presentation was given at ASM 2022. Abstract: The phylogeny and other aspects of the evolutionary history of the Neotropical cat genus Leopardus have long been shrouded in uncertainty, partly owing to an overwhelming abundance of genealogical discordance in this group. We employ whole-genome s...

The phylogeny and taxonomy of the Neotropical genus Leopardus (Felidae) has always been controversial, owing to the cryptic morphology, rapid diversification and instances of hybridization in this clade. We employ whole-genome sequencing data of 15 samples spanning all 8 recognized Leopardus species (IUCN/SSC Cat Specialist Group) to address how sp...

Ecological differentiation among diverging species is an important component of the evolutionary process and can be investigated in rapid and recent radiations. Here we use whole genome sequences of five species from the genus Leopardus, a recently diversified Neotropical lineage with species bearing distinctive morphological, ecological and behavi...

A classificação de sequências de DNA usando algoritmos de aprendizado de máquina ainda tem espaço para evoluir, tanto na qualidade do resultado quanto na eficiência computacional dos algoritmos. Nesse trabalho, realizou-se uma avaliação de desempenho em dois algoritmos de aprendizado de máquina da ferramenta Qiime2 para classificação de sequências...

El jaguar, bestia majestuosa reverenciada por nuestros antepasados e icono de las selvas tropicales, es un animal con una historia fascinante. Los estudios científicos nos ayudan a develar los detalles de su épica travesía a través del tiempo y la geografía del continente americano.

Periphyton communities in freshwater systems play an essential role in biogeochemical processes, but knowledge of their structure and dynamics lags far behind other environments. We used eDNA metabarcoding of 16S and 18S rRNA markers to investigate the formation and establishment of a periphytic community, in addition to morphology-based analyses o...

A remarkable paraphyly in the northern tiger cat (Leopardus tigrinus) was recently detected with genome-wide SNPs by Trindade and colleagues (2021). Despite strong support for the existence of multiple cryptic tiger cat species, other key aspects of Leopardus phylogeny remain unresolved with SNP array data. An overwhelming abundance of genealogical...

Phylogenetic reconstruction and species delimitation are often challenging in the case of recent evolutionary radiations, especially when post-speciation gene flow is present. Leopardus is a Neotropical cat genus that has a long history of recalcitrant taxonomic problems, along with both ancient and current episodes of interspecies admixture. Here...

Habitat loss and fragmentation are important threats to carnivores worldwide and are especially intense for large predators. Jaguars have been extirpated from over half of their original distribution, and few regions still maintain large populations. The Pantanal is among the best examples of such regions and can be used to better understand severa...

Fig. 1. Ensemble Spatial distribution model (SDM) of Muñoa’s pampas cat. A) General ensemble SDM showing medium (pink) and low (grey) suitability pixels outside this felid’s distribution range. B) Map showing the ensemble SDM exclusively inside Muñoa’s pampas cat geographic distribution and categorized by levels of suitability.

Muñoa’s pampas cat (recently proposed to be a distinct species, Leopardus munoai) is a small felid that is endemic to the Uruguayan Savanna ecoregion (encompassing southern Brazil, north-eastern Argentina and Uruguay). Previous studies have suggested that it is threatened, but its conservation assessment has been hampered by the scarcity of data on...

The vast amount of data contained in a single genome represents a detailed record of past events in that lineage and may forecast its evolutionary potential in the face of environmental changes. Here we employed whole-genome sequence (WGS) data to infer the demographic history and assess signals of recent inbreeding in jaguar (Panthera onca) popula...

The diversity of mammalian coat colors, and their potential adaptive significance, have long fascinated scientists as well as the general public. The recent decades have seen substantial improvement in our understanding of their genetic bases and evolutionary relevance, revealing novel insights into the complex interplay of forces that influence th...

Stranded cetaceans (whales, dolphins, and porpoises) are frequently used to obtain data on species occurrence and demographic trends. Accurate species-level identification of these individuals is crucial, but often challenging or impossible when relying solely on morphological features (e.g., for highly decayed specimens). To aid in the development...

Identifying factors that create and maintain a hybrid zone is of great interest to ecology, evolution and, more recently, conservation biology. Here, we investigated the role of environmental features in shaping the spatial dynamics of a hybrid zone between the southern tigrina, Leopardus guttulus, and Geoffroy’s cat, L. geoffroyi, testing for exog...

Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1, 2, 3, 4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predati...

Mammalian carnivores are considered a key group in maintaining ecological health and can indicate potential ecological integrity in landscapes where they occur. Carnivores also hold high conservation value and their habitat requirements can guide management and conservation plans. The order Carnivora has 84 species from 8 families in the Neotropica...

Tracing the evolutionary origin of species can be a challenging task, especially when these species cross-breed and thereby cloud the genetic record of their evolution. Fast- developing techniques in acquiring genetic information have improved to the point where complete genomes can be routinely sequenced. One of the upcoming questions is how to ma...

Penguins are the only extant family of flightless diving birds. They currently comprise at least 18 species, distributed from polar to tropical environments in the Southern Hemisphere. The history of their diversification and adaptation to these diverse environments remains controversial. We used 22 new genomes from 18 penguin species to reconstruc...

To investigate patterns of biotic community composition at different spatial scales and biological contexts, we used environmental DNA metabarcoding to characterize eukaryotic and prokaryotic assemblages present in the phytotelmata of three bromeliad species (Aechmea gamosepala, Vriesea friburgensis and Vriesea platynema) at a single Atlantic Fores...

The margay (Leopardus wiedii) is a small Neotropical arboreal wild cat. This species is thought to be forest-dependent, although few studies so far have directly evaluated the relationships between spatiotemporal aspects of its ecology and landscape characteristics. The aim of this study was to estimate margay population density and activity patter...

Lions are one of the world’s most iconic megafauna, yet little is known about their temporal and spatial demographic history and population differentiation. We analyzed a genomic dataset of 20 specimens: two ca. 30,000-y-old cave lions ( Panthera leo spelaea ), 12 historic lions ( Panthera leo leo/Panthera leo melanochaita ) that lived between the...

Assessing trends in abundance and density of species of conservation concern is vital to inform conservation and management strategies. The remaining population of the cheetah (Acinonyx jubatus) largely exists outside of protected areas, where they are often in conflict with humans. Despite this, the population status and dynamics of cheetah outsid...

S1 Video. Typical alert display showing the white marks on the posterior surface of the ears in Southern tigrina

Melanism in the cat family has been associated with functions including camouflage, ther-moregulation and parasite resistance. Here we investigate a new hypothesis proposing that the evolution of melanism in cats has additionally been influenced by communication functions of body markings. To evaluate this hypothesis, we assembled a species-level d...

Melanism in the cat family has been associated with functions including camouflage, ther-moregulation and parasite resistance. Here we investigate a new hypothesis proposing that the evolution of melanism in cats has additionally been influenced by communication functions of body markings. To evaluate this hypothesis, we assembled a species-level d...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Deep subsurface microbial communities are more abundant in coarse-grained sedimentary rocks such as sandstones than in fine-grained mudstones. The low porosity and low permeability of mudstones are believed to restrict microbial life. Then, it is expected that distinct, isolated microbial communities may form in sandstones separated by mudstones. I...

Geoffroy’s cat is a small Neotropical felid, seemingly abundant throughout most of its range and exhibiting considerable ecological plasticity. In Brazil, the species is restricted to the Pampas, one of the most threatened biomes in the country, where information on its ecology is scarce. Here we report the first assessments of its density, habitat...

Pumas are the most widely distributed felid in the Western Hemisphere. Increasingly, however, human persecution and habitat loss are isolating puma populations. To explore the genomic consequences of this isolation, we assemble a draft puma genome and a geographically broad panel of resequenced individuals. We estimate that the lineage leading to p...

In this study we present a record of an antagonistic interaction potentially resulting from intraguild predation or elimination of competitor within the Carnivora, in which an individual of Leopardus pardalis carries an individual of Cerdocyon thous. This record was obtained through camera trapping at the Pró-Mata Center for Research and Nature Con...

The ecology of complex microhabitats remains poorly characterized in most tropical and subtropical biomes, and holds potential to help understand the structure and dynamics of different biodiversity components in these ecosystems. We assessed nutritional and metabolic parameters of two bromeliad species (Aechmea gamosepala and Vriesea platynema) at...

Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of post-speciation gene flow that can produce a mosaic of phylogenetic signals that interact with recombinational variation. Here we tested the vali...

Transboundary conservation of northern pampas carnivores of northeastern Argentina, southern Brazil and Uruguay.

Mortality from collision with vehicles is the most visible impact of road traffic on wildlife. Mortality due to roads (hereafter road-kill) can affect the dynamic of populations of many species and can, therefore, increase the risk of local decline or extinction. This is especially true in Brazil, where plans for road network upgrading and expansio...

In this study we present a record of an antagonistic interaction potentially resulting from intraguild predation or elimination of competitor within the Carnivora, in which an individual of Leopardus pardalis carries an individual of Cerdocyon thous. This record was obtained through camera trapping at the Pró-Mata Center for Research and Nature Con...

Accurate identification of predator species is a critical requirement to investigate their diet using faecal samples. We used non-invasive sampling and two methods of predator identification to investigate the diets of sympatric carnivores in a highly deforested region of the Brazilian Amazon. Of 108 scats, 81 could be identified at the species lev...

Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of gene flow that result in a mosaic of phylogenetic signals that interact with recombinational variation. Here we tested the validity of this assum...

Introduction paragraph/Abstract Across the geographic range of mountain lions, which includes much of North and South America, populations have become increasingly isolated due to human persecution and habitat loss. To explore the genomic consequences of these processes, we assembled a high-quality mountain lion genome and analyzed a panel of reseq...

The systematics and phylogeny of Otariidae have been extensively studied for over two centuries. Yet, several relationships, in particular, the monophyly within Arctocephalus, remain unclear. Recent molecular phylogenies only used few concatenated mitochondrial or nuclear genes. Here we reconstructed the Otariidae phylogeny based on whole-genome se...

The peritrich ciliates Vorticella veloxiiforme n.sp. and Vorticella ampullaria n.sp. were found as epibionts on the ampullarid mollusk Pomacea canaliculata collected from Patos Lagoon, Rio Grande do Sul state, Brazil. The detailed morphology of both species was investigated using live and stained specimens, as well as scanning electron microscopy....

The southern tigrina (Leopardus guttulus) has recently been separated from little spotted cat (L. tigrinus) and recognized as a valid species. This cat categorized globally as "vulnerable" is one of the least studied wild cats in the Neotropics. Additionally, most of its geographic distribution lies in Atlantic Forest biome, one of the world's most...

The margay (Leopardus wiedii) is a small and arboreal wild cat from the Neotropics. The main area of margay distribution is the Atlantic Forest, a highly threatened biome. Few studies have focused the ecological characteristics of this species, a wild cat that seems to be forest-dependent. The present project aims to investigate the occupancy and a...

Mortality from collision with vehicles is the most visible impact of road traffic on wildlife. Mortality due to roads (hereafter road‐kill) can affect the dynamic of populations of many species and can, therefore, increase the risk of local decline or extinction. This is especially true in Brazil, where plans for road network upgrading and expansio...

Mortality from collision with vehicles is the most visible impact of road traffic on wildlife. Mortality due to roads (hereafter road-kill) can affect the dynamic of populations of many species and can, therefore, increase the risk of local decline or extinction. This is especially true in Brazil, where plans for road network upgrading and expansio...

Mortality from collision with vehicles is the most visible impact of road traffic on wildlife. Mortality due to roads (hereafter road-kill) can affect the dynamic of populations of many species and can, therefore, increase the risk of local decline or extinction. This is especially true in Brazil, where plans for road network upgrading and expansio...

Geoffroy’s cat (Leopardus geoffroyi) is a small Neotropical felid whose social behavior remains poorly understood. We used simultaneous radiotelemetry (4 males and 3 females) and camera trapping to examine the spatial structure and dynamics of a population of this species in the Brazilian pampas (part of the Uruguayan Savannah ecoregion), including...

Many carnivore species, particularly felids, are sensitive to land use changes and may disappear from landscapes with reduced natural habitat and increased fragmentation. The jaguar (Panthera onca) is highly affected by these factors and is particularly endangered in the Atlantic Forest (AF) of South America, one of the most threatened biomes in th...

As the depth increases and the light fades in oceanic cold seeps, a variety of chemosynthetic-based benthic communities arise. Previous assessments reported polychaete annelids belonging to the family Siboglinidae as part of the fauna at cold seeps, with the 'Vestimentifera' clade containing specialists that depend on microbial chemosynthetic endos...

Genetic research is a well-recognized component of understanding biodiversity and is an invaluable approach for documenting and mitigating increasingly high rates of loss. Here we present a quantitative synthesis of conservation genetics science in Latin America and its progress, focusing on evolving trends on different taxonomic groups, environmen...

The Neotropical region currently harbors 8 recognized species of small cats, including the margay (Leopardus wiedii) and jaguarundi (Puma yagouaroundi). These similar-sized species have broad geographic distributions and commonly occur in sympatry. We constructed species occurrence databases and used the maximum entropy (Maxent) modeling approach t...

The pampas cat is a small felid that occurs in open habitats throughout much of South America. Previous studies have revealed intriguing patterns of morphological differentiation and genetic structure among its populations, as well as molecular evidence for hybridization with the closely related L. tigrinus. Here we report phylogeographic analyses...

- Samples and sequences analyzed in the present study.

- Analysis of the pairwise nucleotide differences distribution (Mismatch Distribution) of mtDNA haplotypes assessed in this study.

- Correlation between genetic and geographic distance for L. colocola and L. tigrinus haplotypes.

Tema/Meio de apresentação: Evolução/Oral Polymorphic phenotypes have often been inferred to play some adaptive roles in ecological, physiological and behavioral processes. Melanism is a coloration polymorphism that is present in various groups of organisms and it is rather common in the Felidae family. The Geoffroy's Cat (Leopardus geoffroyi) is a...

Conspicuous physicochemical vertical stratification in the deep sea is one of the main forces driving microbial diversity in the oceans. Oxygen and sunlight availability are key factors promoting microbial diversity throughout the water column. Ocean currents also play a major role in the physicochemical stratification, carrying oxygen down to deep...

Geoffroy's cat is the most abundant felid of the temperate Neotropics. We investigated which factors influence its persistence in one of the most threatened biomes in Brazil, the Pampas. Our study area was a mosaic of open-grassland with pasture, croplands and riparian vegetation. We recorded 516 camera-trap images of Geoffroy's cat and nine indivi...

http://imc12-2017.p.promaco.currinda.com/days/2017-07-13/abstract/162

The great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar...

Bromeliads are a diverse group of plants that includes many species whose individuals are capable of retaining water, forming habitats called phytotelmata. These habitats harbor a diversity of organisms including prokaryotes, unicellular eukaryotes, metazoans, and fungi. Among single-celled eukaryotic organisms, ciliates are generally the most abun...

The geographic distribution and habitat association of most mammalian polymorphic phenotypes are still poorly known, hampering assessments of their adaptive significance. Even in the case of the black panther, an iconic melanistic variant of the leopard (Panthera pardus), no map exists describing its distribution. We constructed a large database of...

Panthera pardus location records used in the present study. (PDF)

Environmental predictors used in the initial analysis and selected with Pearson's test (in red). (PDF)