Alexandre Aleixo

• PhD
• Researcher at University of Helsinki

South American savannas are a disjunct biome with an unclear evolutionary history. We tested hypotheses about their Quaternary history and the evolution of savanna cores through fragmentation or dispersal from the Cerrado. We used genomic data (genotyping‐by‐sequencing) and ecological niche models of the Burnished‐buff Tanager (Stilpnia cayana Linn...

The Needle-billed Hermit Phaethornis philippii is a monotypic species of hummingbird, endemic to the humid forests of western and Central Amazonia. It occurs in eastern Peru, northern Bolivia and part of Brazil, south of the Solimões and the Amazon rivers and west of the Tapajós River. Despite being included in some previous works, the evolutionary...

This study aims to enhance our understanding of the temporal and spatial processes scales governing the evolutionary diversification of Neotropical birds with Trans‐ and Cis‐Andean populations of the species Attila spadiceus from South and Central America. Through a multilocus analysis of the mitochondrial (CytB and ND2) and nuclear genes (I7BF, I5...

We combined mitochondrial DNA sequence data and paleoclimatic distribution models to document phylogeographic patterns and investigate the historical demography of two manakins, Ceratopipra rubrocapilla and Pseudopipra pipra, as well as to explore connections between Amazonia and the Atlantic Forest. ND2 sequences of C. rubrocapilla (75 individuals...

The live link for the pre print is https://www.authorea.com/doi/full/10.22541/au.173200576.61620921/v1

Estimates of current genetic diversity and population connectivity are especially important for endangered species that are subject to illegal harvesting and trafficking. Genetic monitoring can also ensure that management units are sustaining viable populations, while estimating genetic structure and population dynamics can influence genetic rescue...

National, subnational, and supranational entities are creating biodiversity strategy and action plans (BSAPs) to develop concrete commitments and actions to curb biodiversity loss, meet international obligations, and achieve a society in harmony with nature. In light of policymakers' increasing recognition of genetic diversity in species and ecosys...

Analisar a biodiversidade não é uma tarefa fácil devido à sua complexidade, evolução e interações entre seus componentes. No entanto, a perda de biodiversidade e a temperatura média global estão aumentando rapidamente, tornando urgentes as avaliações sobre a biodiversidade. A biodiversidade é uma característica-chave do capital natural, definido c...

Motivation: With increasing initiatives to study biodiversity through high-quality reference genomes and the growing capacity of sequencing a wide range of organisms, there is a pressing need for an accessible, reproducible, and user-friendly tool that incorporates state-of-the-art methodologies for large genome assembly. Results: We introduce Pipe...

The biodiversity crisis is a global phenomenon, and measures to monitor, stop, and revert the impacts on species’ extinction risk are urgently needed. Megadiverse countries, especially in the Global South, are responsible for managing and protecting Earth’s biodiversity. Various initiatives have started to sequence reference-level genomes or perfor...

Aim The Amazon rainforest is one of the most biodiverse regions on earth, but our understanding of the processes that have shaped its patterns of diversity remains incomplete. One hypothesis for Amazonian speciation is the river‐refuge hypothesis, which suggests that retraction of forests away from the periphery of Amazonia, where rivers are narrow...

The Harpy Eagle (Harpia harpyja) is an iconic species that inhabits forested landscapes in Neotropical regions, with decreasing population trends mainly due to habitat loss, and currently classified as vulnerable. Here, we report on a chromosome-scale genome assembly for a female individual combining long reads, optical mapping, and chromatin confo...

Biodiversity conservation, especially in megadiverse regions like Brazil, faces challenges that demand the implementation of innovative approaches. In this context, a partnership agreement was signed between the Chico Mendes Institute for Biodiversity Conservation (ICMBio) and the Vale Institute ofTechnology (ITV), named GBB (Genomics of the Brazil...

Ever since Alfred Russel Wallace’s nineteenth-century observation that related terrestrial species are often separated on opposing riverbanks, major Amazonian rivers have been recognized as key drivers of speciation. However, rivers are dynamic entities whose widths and courses may vary through time. It thus remains unknown how effective rivers are...

The Caatinga is the largest patch of Seasonal Dry Tropical Forest in the Neotropics, located in northeastern Brazil and characterized mainly by deciduous vegetation and extreme rainfall seasonality. It has historically been treated as a biologically impoverished domain, but recent studies uncovered new diversification patterns and several new taxa...

A avifauna do estado do Tocantins foi inicialmente sumarizada a partir das coleções ornitológicas conduzidas por José Hidasi, entre as décadas de 1960 e 1990, sendo recompiladas em 2009. Após 15 anos, apresentamos uma nova listagem das espécies de aves ocorrentes no estado, considerando riqueza e composição, status migratório, perfil de endemismo,...

The reduced temporal validity of species lists made available in a traditional manner in scientific publications has always represented a problem. These lists are invariably limited to a few taxonomic groups and do not represent the up-to-date knowledge of all species and classifications. The Catálogo Taxonômico da Fauna do Brasil (CTFB), made publ...

The "Amazon tipping point" is a global change scenario resulting in replacement of up-land terra-firme forests by large-scale "savannization" of mostly southern and eastern Amazon. Reduced rainfall accompanying the Last Glacial Maximum (LGM) has been proposed to have acted as such a tipping point in the past, with the prediction that terra-firme in...

Catálogo Taxonômico da Fauna do Brasil: se ng the baseline knowledge on the animal diversity in Brazil

Incomplete lineage sorting (ILS) and introgression increase genealogical discordance across the genome, which complicates phylogenetic inference. In such cases, identifying orthologs that result in gene trees with low estimation error is crucial because phylogenomic methods rely on accurate gene histories. We sequenced whole genomes for the tinamou...

Geographic barriers are frequently invoked to explain genetic structuring across the landscape. However, inferences on the spatial and temporal origins of population variation have been largely limited to evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known as genomic architecture in pr...

Our understanding of Amazonian biogeography is quickly increasing, catalyzed by the growing use of genomic datasets, improved knowledge of species distributions, and the accumulation of new data on the geological and climatic history of the region. The high number of species in Amazonia and their intricate patterns of geographic distribution trigge...

Rivers frequently delimit the geographic ranges of species in the Amazon Basin. These rivers also define the boundaries between genetic clusters within many species, yet river boundaries have been documented to break down in headwater regions where rivers are narrower. To explore the evolutionary implications of headwater contact zones in Amazonia,...

The natural world is under unprecedented and accelerating pressure. Much work on understanding resilience to local and global environmental change has, so far, focussed on ecosystems. However, understanding a system’s behaviour requires knowledge of its component parts and their interactions. Here we call for increased efforts to understand ‘biolog...

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...

Graphical abstract Highlights d Ecological metadata were compiled for 7,694 sites across the Brazilian Amazon d Accessibility and proximity to research facilities influenced research probability d Knowledge gaps are greater in uplands than in wetlands and aquatic habitats d Undersampled areas overlap predicted hotspots of climate change and defores...

We reconstruct the species-level phylogenetic relationship among toucans, toucan-barbets, New World barbets using phylogenomic data to assess the monophyly and relationships at the family, generic, and specific levels. Our analyses confirmed (1) the monophyly of toucans (Aves: Ramphastidae), toucan-barbets (Aves: Semnornithidae), and New World barb...

Guia para as três etapas principais da identificação de SNPs usando genomas completos de baixa cobertura: (i) avaliação da qualidade do sequenciamento; (ii) mapeamento de genomas de baixa cobertura em um genoma de referência e (iii) seleção de SNPs para as análises populacionais e de conservação. Futuros estudos com genomas dentro e fora do projeto...

Understanding the factors that govern variation in genetic structure across species is key to the study of speciation and population genetics. Genetic structure has been linked to several aspects of life history, such as foraging strategy, habitat association, migration distance, and dispersal ability, all of which might influence dispersal and gen...

Birds are the vertebrate group most used in studies that attempts to decipher the events that have molded the diversification of the Amazonian biota. However, inconsistencies related to the existence of polytypic species, associated with the limited samples available for many regions, hamper the accurate reconstruction of phylogeographic patterns....

In a recent commentary, Lima (Ornithol Res 30:225–228, 2022a) claims that the Brazilian Ornithological Records Committee (CBRO) bases its species ranking decisions on a misinterpretation of the general lineage species concept (GLSC), with two major detrimental consequences: (1) misinform the Brazilian ornithological community about the nature of in...

Although vicariant processes are expected to leave similar genomic signatures among codistributed taxa, ecological traits such as habitat and stratum can influence genetic divergence within species. Here, we combined landscape history and habitat specialization to understand the historical and ecological factors responsible for current levels of ge...

Phylogeographical studies of the most species‐rich region of the planet—the Amazon basin—have repeatedly uncovered genetically distinctive, allopatric lineages within currently named species, but understanding whether such lineages are reproductively isolated species is challenging. Here we harness the power of genome‐wide data sets together with d...

Few phylogeographic studies have focused on understanding the role of the Tocantins–Araguaia Interfluve (TAI) in the diversification of Amazonian biodiversity. Herein we evaluate the phylogeographic relationships of 14 avian lineages present in the TAI and its two neighboring Amazonian Areas of Endemism: the Xingu (XAE) and Belém (BAE). Four altern...

Aim Biotic interchange, speciation and extinction processes drive biotas assembling. However, the evolutionary outcomes of those mechanisms are complex and difficult to discriminate. Here, we investigate how these processes affect avian diversification in tropical forest regions and test the relative roles of vicariant speciation and biotic interch...

The genus Willisornis is endemic to the Amazon Basin, inhabiting upland terra firme forest, with two species and seven subspecies currently recognized. Despite numerous systematic studies, a taxonomically-dense sampled phylogeny for Willisornis is still lacking, which, combined with evidence of paraphyly and gene flow between its recognized species...

The genus Willisornis is endemic to the Amazon Basin, inhabiting upland terra firme forest, with two species and seven subspecies currently recognized. Despite numerous systematic studies, a taxonomically-dense sampled phylogeny for Willisornis is still lacking, which, combined with evidence of paraphyly and gene flow between its recognized species...

Large Amazonian rivers impede dispersal for many species, but lowland river networks frequently rearrange, thereby altering the location and effectiveness of river barriers through time. These rearrangements may promote biotic diversification by facilitating episodic allopatry and secondary contact among populations. We sequenced genome-wide marker...

The cover image is based on the Letter AVONET: morphological, ecological and geographical data for all birds by Tobias et al., https://doi.org/10.1111/ele.13898. The sword‐billed hummingbird (Ensifera ensifera) is exquisitely adapted to its trophic niche as an aerial pollinator of flowerings plants (angiosperms) in the high Andes. A new global data...

Functional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models of global change can only be fully realised when species‐level information is complete. Here we present the AVON...

Large rivers are ubiquitously invoked to explain the distributional limits and speciation of the Amazon Basin's mega-diversity. However, inferences on the spatial and temporal origins of Amazonian species have narrowly focused on evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known to p...

Background Thamnophilidae birds are the result of a monophyletic radiation of insectivorous Passeriformes. They are a diverse group of 225 species and 45 genera and occur in lowlands and lower montane forests of Neotropics. Despite the large degree of diversity seen in this family, just four species of Thamnophilidae have been karyotyped with a dip...

Large Amazonian rivers impede dispersal for many species, but lowland river networks frequently rearrange, thereby altering the location and effectiveness of river-barriers through time. These rearrangements may promote biotic diversification by facilitating episodic allopatry and secondary contact among populations. We sequenced genome-wide marker...

Integrative taxonomic studies continue to reveal that many current polytypic species of birds are in fact constituted by two or more species and therefore have been central in uncovering ‘hidden’ or ‘cryptic’ biodiversity. The Olivaceous Flatbill (Aves: Tyrannidae: Rhynchocyclus olivaceus) currently has nine recognized subspecies distributed throug...

Aim Amazonian floodplains include distinct types of seasonally flooded habitats, determined by the flooding regime and sedimentation dynamics. Some bird species prefer specific habitat types within the floodplains. To investigate whether distinct habitats are differentially affected by geologic and climatic history, we compare population history in...

Aim Ecological, climatic and palaeogeographical processes drive biological diversification. However, the evolutionary outcomes of those mechanisms are complex and difficult to discriminate. Here, we test how alternative drivers affected connectivity along the Amazonian floodplains generating current patterns of population structure and diversity wi...

Aim: We tested if historical demographic changes of populations occurring on the floodplains of a major Amazon Basin tributary could be associated with range expansions from upper and middle sections of the river, following the establishment of widespread river-created environments during the Late Pleistocene and Holocene. Location: Solimoes River,...

We describe the phylogeographic structure of Attila spadiceus, a neotropical bird with 12 recognized subspecies, through the analysis for partial Cytb amplicon region obtained from 11 subspecies. The topology recovered from the analysis indicated the existence of two principal molecular lineages and that the morphological variation underlying the d...

We assessed population structure and the spatio‐temporal pattern of diversification in the Glossy Antshrike Sakesphorus luctuosus (Aves, Thamnophilidae) to understand the processes shaping the evolutionary history of Amazonian floodplains and address unresolved taxonomic controversies surrounding its species limits. By targeting ultraconserved elem...

An updated version of the checklist of birds of Brazil is presented, along with a summary of the changes approved by the Brazilian Ornithological Records Committee’s Taxonomy Subcommittee since the first edition, published in 2015. In total, 1971 bird species occurring in Brazil are supported by documentary evidence and are admitted to the Primary...

Molecular studies have shown that many polytypic species of birds are paraphyletic and may actually consist of multiple independent species, some of them phenotypically cryptic. One of such cases is Dendrocolaptes picumnus, which was found to be a paraphyletic species, with Dendrocolaptes hoffmannsi nested in it. Recent evidence also showed that mu...

The family Thamnophilidae is a species-rich Neotropical radiation of passerine birds. Current classification of its 235 species is mostly based on morphological similarities, but recent studies integrating comprehensive phenotypic and phylogenetic data have redefined taxonomic limits of several taxa. Here, we assess generic relationships of Herpsil...

Several bird taxa have been recently described or elevated to full species and almost twice as many bird species than are currently recognized may exist. Defining species is one of the most basic and important issues in biological science because unknown or poorly defined species hamper subsequent studies. Here, we evaluate the species limits and e...

A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03473-8.

Megascops is the most species-rich owl genus in the New World, with 21 species currently recognized. Phylogenetic relationships within this genus are notoriously difficult to establish due to the considerable plumage similarity among species and polymorphism within species. Previous studies have suggested that the widespread lowland Amazonian M. wa...

Aim Neotropical savanna birds occur north and south of, but mostly not in the Amazon Basin, except for a few isolated savanna patches. Here, we investigate the phylogeography of 23 taxa of Neotropical savanna birds co‐distributed across multiple isolated savanna patches to assess to what extent these species have a shared history of spatial diversi...

The Genomic Resources Collection is a separate, independently managed part of the natural history collections of the Finnish Museum of Natural History Luomus specifically intended for consumptive research. The GRC policy deals with the materials that are archived for the very purpose of enabling the study of biological diversity at the genome level...

Diversity does not drive speciation The role of the environment in the origin of new species has long been debated. Harvey et al. examined the evolutionary history and species diversity of suboscine birds in the tropics (see the Perspective by Morlon). Contrary to expectations that the tropics have higher rates of speciation, the authors observed t...

Here we use an integrative approach, including coalescent-based methods, isolation–migration and species distribution models, to infer population structure, divergence times and diversification in the two species of the genus Cymbilaimus (Aves, Thamnophilidae). Our results support a recent and rapid diversification with both incomplete lineage sort...

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1,2,3,4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic...

Target capture sequencing effectively generates molecular marker arrays useful for molecular systematics. These extensive data sets are advantageous where previous studies using a few loci have failed to resolve relationships confidently. Moreover, target capture is well-suited to fragmented source DNA, allowing data collection from species that la...

Ecosystems are under unprecedented and accelerating pressures. Much work on understanding resilience to these pressures has, so far, focussed on the ecosystem. However, understanding a system’s behaviour also requires knowledge of its component parts and their interactions. Here we present a framework for understanding ‘biological resilience’, or t...

How species evolve reproductive isolation in the species-rich Amazon basin is poorly understood in vertebrates. Here we sequenced a reference genome and used a genome-wide sample of SNPs to analyze a hybrid zone between two highly cryptic species of Hypocnemis warbling-antbirds - the Rondonia warbling-antbird (H. ochrogyna) and Spix's warbling-antb...

Based on a phylogeographic and niche model analyses of the Narrow-billed Woodcreeper (Lepidocolaptes angustirostris), we evaluated the predictions of two diversification hypotheses related to the dry diagonal of South America: (I) isolation by distance (IBD) and (II) landscape heterogeneity. We also investigated the influence of the Pleistocene cli...

The true diversity and interspecific limits in the Neotropical endemic avian genus Dendrocolaptes (Furnariidae) remain a highly controversial subject, with previous genus‐wide assessments, based mostly on morphological characters, producing poorly resolved phylogenies. The lack of well‐resolved, robust, and taxonomically densely sampled phylogenies...

Hybridization is a relatively common phenomenon in birds, but it is probably underestimated due to our poor knowledge on the reproductive biology of several species. Here, we present the second case of intergeneric hybrid in the family Momotidae and the first case between Amazonian Motmot (Momotus momota) and Rufous Motmot (Baryphthengus martii). I...

We identify key interdisciplinary questions and approaches to understanding the paleogeographic and biotic history of Amazonia. We discuss the importance of comparing evolutionary taxonomic units across groups and considering their particular environmental affinities as a framework for a mechanistic understanding of how the diversity of Amazonia wa...

White sand ecosystems (WSE) occur in nutrient-poor sandy soils patchily distributed throughout the lowlands of Amazonia. The diversification and current patterns of diversity of birds and plants specialized to the WSE were likely affected by abiotic conditions in very different ways relative to those in the upland Terra Firme forest, which has been...