Alexandre Aleixo

University of Helsinki | HY · Finnish Museum of Natural History

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...

Phylogeographic studies of the most species rich region of the planet – the Amazon basin – repeatedly uncover 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 datasets together with detaile...

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...

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 interchange...

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...

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...

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: 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...

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 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...

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...

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...

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...