Izeni Pires Farias

Federal University of Amazonas | UFAM · Department of Genetics

The Yanomami are one of the oldest indigenous tribes in the Amazon and are direct descendants of the first people to colonize South America 12,000 years ago. They are located on the border between Venezuela and Brazil, with the Venezuelan side remaining uncontacted. While they maintain a hunter-gatherer society, they are currently experiencing cont...

Presently, Myloplus schomburgkii is the most easily recognized species among the serrasalmids by having a vertical black bar in the middle of the body. However, through a broad taxonomic review, including DNA barcoding and morphological analyses, we were able to identify and describe two new species that also share a dark vertical bar on the flank....

Landscape characteristics can influence gene flow depending on the species ability to disperse. This imposes different levels of resistance to movement, determining the genetic structure and diversity of populations. Waterfalls and rapids in the Amazon basin have been suggested as contributing factors to the diversification and genetic structure of...

Aim The central and western Amazonia underwent several landscape changes during the Quaternary. Whereas the Riverine Barrier Hypothesis is traditionally used to explain the influence of rivers on speciation, processes such as river rearrangements have been overlooked to explain the geographic distribution and evolutionary history of Amazonia biota....

Despite the current disjoint distribution of Amazonian and Atlantic forests, evidence suggests past historical connections. Here we investigated the historical connections between three didelphid mammal species from Amazonian and Atlantic forests (Caluromys philander, Marmosa demerarae, and M. murina) using comparative phylogeography and paleodistr...

The accumulation of studies delimiting species in Amazonia has not only shed light on the patterns of its outstanding species richness but also allowed a better understanding of the processes of diversification within this immense region. Nevertheless, vast knowledge gaps remain even for prominent anuran species complexes, such as the Rhinella marg...

The so-called arc of deforestation is a major agricultural and industrial frontier in southern Amazonia and northern Cerrado of Brazil. As arboreal mammals, the primates in this region are therefore threatened by forest loss and fragmentation. At the same time, knowledge about the taxonomic diversity and distribution ranges of these taxa is incompl...

Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3–9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by...

COLE TCH, FARIAS IP (2023) Filogenia dos PRIMATAS © Cole, Farias 2023 (CC-BY), Portuguese version of: COLE (2023) Phylogeny of PRIMATES • pôster educativo com árvore hipotética baseada em dados filogenéticos moleculares • filogenia e classificação de acordo com as referências abaixo • comprimentos dos ramos deliberados, não expressando a escala de...

The primary (PSR), secondary (SSR) and adult (ASR) sex ratios of sexually reproducing organisms influence their life histories. Species exhibiting reversed sexual size dimorphism (RSD) may imply a higher cost of female production or lower female survival, thus generating biases in PSR, SSR and/or ASR towards males. The Harpy Eagle is the world's la...

Investigating parallel roles of geography and environmental heterogeneity in diversification provides insights on how neutral and selective forces drive evolution of biological systems. Here, we investigate whether geographic and climatic distances explain either genetic or phenotypic variation in Blue-crowned Manakins (Lepidothrix coronata), a pol...

Platyrrhinus guianensis is bat with a distribution restricted to the Guiana Region of South America in Guyana and Suriname. Herein, we report the southernmost record of this species, extending its distribution to Brazil in Brazilian Amazon. Our record indicates that the species have a larger geographical range that previously thought. Platyrrhinus...

Currently, 15 species of Amazon marmosets (genus Mico) are known to science. The Amazon marmosets occur primarily in southern Brazilian Amazonia, the arc of deforestation, and are among the least studied primates of the neotropics. This is particularly the case for M. acariensis and M. chrysoleucos, both endemic to the Aripuanã–Sucundurí interfluve...

Uakari monkeys (genus Cacajao ) are endemic to the Amazon rainforest. These have been divided into two main groups: bald and black, mainly based on phenotypic and ecological differences, for which eight taxonomic species have been described. We present 48 geo-localized high coverage whole genomes from uakaris in wild populations across their habita...

The genus Saguinus comprises three principal clades that diverged in the Middle to Late Miocene. Their taxa are ecologically differentiated and allopatrically distributed. These clades were recently recognized as different genera, Saguinus, Tamarinus and Oedipomidas. In Tamarinus, the phylogenetic relationships among species/subspecies are poorly u...

Aim Western Amazonia is a region that underwent several landscape changes during the Quaternary. While Riverine Barrier Hypothesis is traditionally used to explain the influence of rivers on speciation, processes such as river rearrangements have been overlooked to explain the geographic distribution and evolutionary history of the Amazonia biota....

Pitheciines have unique dental specializations among New World monkeys that allow them to feed on fruits with hard pericarps, thus playing a major role as seed predators. The three extant pitheciine genera, Pithecia, Cacajao and Chiropotes, are all endemic to the Amazon region. Because of the uncertainties about interspecific relationships, we revi...

Background Semaprochilodus insignis is a migratory fish of commercial and subsistence importance to communities in the Amazon. Despite the high intensity of exploitation, recent studies have not been carried out to assess the genetic status of its stocks. Methods This study is the first to estimate genetic diversity and to test the existence of sp...

Marmosets, with a total of 24 species classified into four genera ( Callithrix , Cebuella , Mico and Callibella ), are the smallest of the anthropoids and one of the most diverse and widespread groups of primates in South America. In contrast, the Goeldi's monkey ( Callimico goeldii ) is represented by a single species of black, small, fungi-eating...

The arc of deforestation, located between the southern Amazonia and the northern Cerrado of Brazil, is a top deforestation frontier worldwide. The high deforestation rates in this region are caused by human activities and threatens a rich diversity of primates that are still poorly-known and therefore investments into taxonomy and distribution rese...

The Neotropics contain one of the most diverse assemblages of freshwater fishes worldwide. Part of this diversity is shared between the Orinoco and Amazon basins. These basins have been separated for a long time due to the Vaupes Arch, rising between 10–11 Ma. Today, there is only one permanent connection between the Orinoco and Negro (Amazon) basi...

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 mill...

The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats the...

The discovery and characterization of cryptic diversity is important for conservation and management, especially for ichthyofauna, whose diversity is underestimated and understudied. Cryptic diversity is especially common in widely distributed species, and Pellona flavipinnis is one such species. Thus, the aim of the present study was to investigat...

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 mil...

The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology, and is urgent given severe threats th...

Landscape features can influence gene flow detected in genetic structure and diversity. The effect will depend on the ability to disperse and may vary between species. Waterfalls and rapids in the Amazon basin have been suggested as causing the diversification and genetic structure of freshwater species, including turtles. Thus, we evaluated the sp...

Despite the disjunct distribution of Amazonian and Atlantic forests, evidence suggests historical connections. Here we investigated the historical connections between three didelphid mammal species from Amazonian and Atlantic forests ( Caluromys philander , Marmosa murina and Marmosa demerarae ) to uncover these connections using a comparative phyl...

Although the Amazon has the greatest diversity of primates, there are still taxonomic uncertainties for many taxa, such as the species of the Saguinus mystax group. The most geographically broadly distributed and phenotypically diverse species in this group is S. mystax, and its phenotypic diversity has been recognized as three subspecies—S. mystax...

The brown or pouchless four-eyed opossums or jupatis represent the genus Metachirus with a wide geographical range in the Neotropics. Recent studies show distinct monophyletic clades with high genetic divergence and recognized two species, Metachirus nudicaudatus and Metachirus myosuros. Nevertheless, there is a need for systematic revision with mu...

Amazonian mammal diversity is exceptionally high, yet new taxonomic discoveries continue to be made and many questions remain for understanding its diversification through time and space. Here we investigate the diversification of spiny rats in the genus Makalata , whose species are strongly associated with seasonally flooded forests, watercourses...

Recently, the large migratory fishes of the family Serrasalmidae (Piaractus brachypomus and P. orinoquensis) were described as restricted to the Orinoco and Amazon basins. Both species provide important ecosystem services. They also are an important fisheries resource, which has caused that their populations have decreased in recent years. National...

Categoria: Menos Preocupante (LC) Data da avaliação: Ago/2016 Paleosuchus palpebrosus ocorre em dez países da América do Sul, porém, a maior parte de sua distribuição está no Brasil, ocorrendo em quase todos os Estados. Sua extensão de ocorrência estimada para o território brasileiro é de 7.536.119 km². Ocorre naturalmente em baixas densidades, ocu...

Justificativa Nomes comuns Jacaré-coroa , jacaré-de-cara-lisa , Schneider's smooth-fronted caiman , Cachirre , Keilkopf-Glattstirnkaimans Nomes antigos Paleosuchus trigonatus (Schneider, 1801) Categoria: Menos Preocupante (LC) Data da avaliação: Ago/2016 Paleosuchus trigonatus é encontrado em grande parte da Amazônia brasileira e em outros nove paí...

Justificativa Caiman crocodilus (Linnaeus, 1758) Categoria: Menos Preocupante (LC) Data da avaliação: Ago/2016 Caiman crocodilus habita praticamente todos os tipos de ambientes de zonas úmidas de baixa altitude na região Neotropical, sendo a espécie dentre os crocodilianos com maior distribuição na América Latina. No Brasil, ocorre naturalmente na...

Justificativa Caiman yacare (Daudin, 1802) Categoria: Menos Preocupante (LC) Data da avaliação: Ago/2016 Caiman yacare é encontrado nas regiões alagadas do nordeste e leste da Bolívia, no Pantanal brasileiro e afluentes do rio Madeira, no Paraguai e no nordeste da Argentina. Sua extensão de ocorrência estimada para o território brasileiro é de 547....

Colour variation in crocodilians is associated with size, environment and genetic structure, but little is known about colour variation in the genus Paleosuchus (Alligatoridae). Different genetic lineages of Paleosuchus palpebrosus (Dwarf caiman) occupy different environments throughout the species extensive distribution, and all are cryptically co...

The spread of non-native fish species is increasing globally and threatening aquatic ecosystems. Identifying the origins, the pathways, and vectors is crucial for managing biological invasions. We conducted a genetic characterization of Arapaima gigas from the Madeira River, considering native and non-native populations, to elucidate the invasion o...

Based on morphological and molecular analysis of Astronotus species, a new species is described from the Orinoco River and Gulf of Paria basins in Venezuela and Colombia. Morphologically, it differs from As-tronotus crassipinnis and Astronotus ocellatus in pre-orbital depth, caudal peduncle depth, head width, and caudal peduncle length, with signif...

Mico schneideri was recently described by scientists, and currently there is no information on habitat availability and population sizes. Given high deforestation rates across its range, it is suspected that this marmoset's extent of occurrence (EOO) and area of occupancy (AOO) are both undergoing ongoing decline. From 2001 to 2020, the Mato Grosso...

We describe two new species of Rhinella (Anura: Bufonidae) from the department of Loreto, Peru. We integrate morphological and phylogenetic analyses to provide evidence of new species. R. angeli sp. nov. is diagnosable from all congeners by its pronounced fleshy proboscis and R. unapensis sp. nov. by the small size (mean snout-vent length=37.7 ± 4....

Context Waterfalls and rapids of Amazon basin have been suggested as causing the speciation and genetic structure of many freshwater species, including turtles. The species behavior affects the way waterfalls and rapids limit gene flow. The Yellow-spotted River Turtle ( Podocnemis unifilis ), a widely distributed and endangered Amazonian turtle, do...

Turtles are one of the most threatened groups of vertebrates, with about 60% of species classified at some level of extinction risk. Compounding this extinction crisis are cryptic species and species complexes that are evaluated under a single species epithet but harbor multiple species, each of which needs to be evaluated independently. The Phryno...

Traditionally, Saguinus has been organized into six taxonomic groups: bicolor, inustus, midas, mystax, nigricollis, and oedipus. After recent revisions, taxonomic reclassifications were proposed, including (1) the recognition of Leontocebus as a new genus, and (2) the subdivision of Saguinus into three subgenera. Nonetheless, the contradictory natu...

Mitochondrial DNA remains a cornerstone for molecular ecology, especially for study species from which high‐quality tissue samples cannot be easily obtained. Methods using mitochondrial markers are usually reliant on reference databases, but these are often incomplete. Furthermore, available mitochondrial genomes often lack crucial metadata, such a...

Night monkeys (Aotus, Cebidae) are a widely distributed genus of Neotropical primates with a poorly understood taxonomy and biogeography. The number of species in the genus varies from one to nine, depending on the author, and there are at least 18 known karyotypes, varying from 2n = 46 to 2n = 58. Historically, night monkeys are divided into two s...

en Morphology has been used to establish interspecific limits in echimyid rodents. However, using only morphology can be problematic, especially for polymorphic or morphologically cryptic species. Recently, combined data sources have been used to recognize and delimit species and have proven to be especially useful for taxonomic resolutions. Makala...

South American freshwater ichthyofauna is taxonomically the most diverse on the planet, yet its diversity is still vastly underestimated. The Amazon basin alone holds more than half of this diversity. The evidence of this underestimation comes from the backlog of morphologically distinct, yet undescribed forms deposited in museum collections, and f...

Platyrrhine primate taxonomy is a rapidly evolving area of research. The recent description of the Parecis titi monkey, Plecturocebus parecis, has raised substantial questions regarding the taxonomy, distribution, and evolutionary history of titi taxa from south-central Amazonia. There is only a single documented record of P. parecis, which is the...

The large catfish Pseudoplatystoma punctifer plays an important role as a top predator in the Amazonian Basin ecosystem. The Madeira River is the largest tributary of the Amazon River marked by a series of rapids and waterfalls. Between 2011 and 2012 some of the rapids were submerged by two hydroelectric dams. Upstream and downstream of the rapids...

Está ocorrendo uma revolução na pesquisa de crocodilianos, possibilitada pelo uso de ferramentas moleculares, que aprimoram nosso conhecimento sobre a diversidade de espécies e consequentemente a delimitação de estratégias de conservação para as mesmas. Neste capítulo, abordamos os avanços no conhecimento da genética da conservação de cada uma das...

Amazonia has the richest primate fauna in the world. Nonetheless, the diversity and distribution of Amazonian primates remain little known and the scarcity of baseline data challenges their conservation. These challenges are especially acute in the Amazonian arc of deforestation, the 2500 km long southern edge of the Amazonian biome that is rapidly...

The state of Florida has the world's highest diversity of established nonnative reptiles, including snakes, lizards, turtles, and crocodilians, most of them introduced from the pet trade. The Spectacled Caiman (Caiman crocodilus) is the only nonnative crocodilian established in Florida, with the earliest date of introduction in 1950. Despite its li...

Subsistence hunting of Paleosuchus species is widely practiced by rural and indigenous communities throughout the Brazilian Amazon and the Cerrado-Caatinga transition, and it is considered one of the threats to the species. This take an overview of the poaching of Paleosuchus species in northern Brazilian Amazon by reporting local densities close t...

Geographical and environmental distances influence the divergence of characters among biological populations, especially on a macro spatial scale, making it difficult to interpret the individual contribution of these predictor variables in the process of population differentiation. Anurans are excellent models for multi-character evolutionary studi...

Boana hobbsi is a poorly known hylid frog currently placed within the Boana punctata group. Yet, morphological, ecological and bioacoustic traits do not support this placement, with no molecular data being available to date to test this hypothesis. Based on newly collected mitochondrial DNA sequences, morphological data review and field observation...

Biogeography is an area of study dedicated to understanding the evolutionary processes that resulted in current organismal distribution patterns. In general, exclusively terrestrial and exclusively aquatic vertebrates have well-studied and defned biogeographic patterns in the New World, but the biogeography of semiaquatic organisms is still poorly...

This book aims to be a comprehensive review of the literature on the conservation genetics of the New World crocodilians, from the biological and demographical aspects of the living species to the application of molecular techniques for conservation purposes. It covers the current status of the molecular genetics applied to phylogenetics, phylogeog...

Genetic diversity is one of the most important attributes of any population; it is defined as the variation in the amount of genetic information within and among individuals of a population, species, assemblage, or community. It can be expressed as differences between individuals at different levels, such as morphological features, structure and ch...

The subject of this chapter is addressed seeking to establish a balanced relationship of deepening, trying to be interesting for those who are looking for information on molecular markers, while not intending to be too long in the descriptions of the techniques and providing an indication of application in molecular ecology of crocodilians that are...

Supplementary data _Erickson_et_al-1367.pdf

Temperature-dependent sex determination occurs in many species of turtles. Because substrates differ in their heat retention capacities, a relatively small change in ambient temperature can exert great influence on sex ratios of hatchlings from clutches deposited in different substrates even within the same geographical area. Since Podocnemis unifi...

Nesting site selection is of great ecological and evolutionary importance for turtles, because it is a key determinant of individual reproductive success. In this study we evaluated the effects of two types of nesting substrate (sand bank and clay banks) on the incubation success of a generalist nesting species, Podocnemis unifilis, in a floodplain...

Neotropical toads from the Rhinella margaritifera species group have been considered a taxonomic puzzle for a long time. Because of the high morphological similarity and an unknown number of undescribed taxa among the species of this group, we did an extensive search for character distribution within all nominal taxa. Herein we describe Rhinella pa...

Species of Neacomys are small cricetid rodents that occur in forested habitats of Central and South America, from eastern Panama to central Bolivia and central/western Brazil. In order to assess species diversity of this poorly known genus, we obtained cytochrome b gene sequences from the most comprehensive taxonomic and geographic sampling analyze...

Cheracebus is a new genus of New World primate of the family Pitheciidae, subfamily Callicebinae. Until recently, Cheracebus was classified as the torquatus species group of the genus Callicebus . The genus Cheracebus has six species: C. lucifer, C. lugens, C. regulus, C. medemi, C. torquatus , and C. purinus , which are all endemic to the Amazon b...

Neon tetras (Paracheirodon spp.) are three colorful characid species with a complicated taxonomic history, and relationships among the species are poorly known. Molecular data resolved the relationships among the three neon tetras, and strongly supported monophyly of the genus and its sister taxon relationship to Brittanichthys. Additionally, the s...

Species discovery methods utilizing coalescent-based approaches are powerful tools for detecting cryptic lineages within morphological conservative groups, thus being an important methodology of integrative taxonomic research. Crocodilians are a classic example of morphologically conserved group where coalescence-based species delimitation analyses...

The matamata is one of the most charismatic turtles on earth, widely distributed in northern South America. Debates have occurred over whether or not there should be two subspecies or species recognized due to its geographic variation in morphology. Even though the matamata is universally known, its natural history, conservation status and biogeogr...

Pacus of the genus Myloplus represent a formidable taxonomic challenge, and particularly so for the case of M. asterias and M. rubripinnis, two widespread and common species that harbor considerable morphological diversity. Here we apply DNA barcoding and multiple species discovery methods to find candidate species in this complex group. We report...

Humpback whales have a cosmopolitan distribution and undertake annual migrations between low and high latitudes where breeding and feeding takes place, respectively. In Brazil, the main breeding area encompasses the Abrolhos Bank at the Eastern Brazilian Coast and the feeding area of this population is located in South Georgia and South Sandwich Is...

Arapaima, pirarucu or paiche (Arapaima gigas) is one of the largest freshwater fish in the world, and has a long history of commercial exploitation in the Amazon region. To estimate levels of genetic variability and historical and recent connectivity in Arapaima, we examined variation in eleven microsatellite DNA markers in individuals from 22 loca...

Although the Atlantic Forest marmosets (Callithrix spp.) are among the best studied Neotropical primates, the Amazonian marmosets (Callibella humilis, Cebuella spp. and Mico spp.) are much less well-known. Even species diversity and distributions are yet to be properly determined because field data and materials currently available in scientific co...