Ricardo J Pereira

• Doctor of Philosophy
• Group Leader at State Museum of Natural History Stuttgart

Assessing genetic diversity within species is key for conservation strategies in the context of human-induced biotic changes. This is important in marine systems, where many species remain undescribed while being overfished, and conflicts between resource-users and conservation agencies are common. Combining niche modelling with population genomics...

Hybridization, or interbreeding between different taxa, was traditionally considered to be rare and to have a largely detrimental impact on biodiversity, sometimes leading to the breakdown of reproductive isolation and even to the reversal of speciation. However, modern genomic and analytical methods have shown that hybridization is common in some...

Coastal marine ecosystems are highly productive and important for global fisheries. To mitigate over exploitation and to establish efficient conservation management plans for species of economic interest, it is necessary to identify the oceanographic barriers that condition divergence and gene flow between populations with those species, and that d...

The level of habitat availability influences genetic divergence among populations and the genetic diversity within populations. In the marine environment, near-shore species are among the most sensitive to habitat changes. Knowledge of how historical environmental change affected habitat availability and genetic variation can be applied to the deve...

Vector‐borne pathogens exist in obligate transmission cycles between vector and reservoir host species. Host and vector shifts can lead to geographic expansion of infectious agents and the emergence of new diseases in susceptible individuals. Three bacterial genospecies (Borrelia afzelii, Borrelia bavariensis, and Borrelia garinii) predominantly ut...

The availability of population genomic data through new sequencing technologies gives unprecedented opportunities for estimating important evolutionary forces such as genetic drift, selection and mutation biases across organisms. Yet, analytical methods that can handle polymorphisms jointly with sequence divergence across species are rare and not e...

Temporal variation of effective population size and gene flow determine current patterns of genetic diversity within species, and hence the genetic variation upon which natural selection can act. Although such demographic processes are well understood in terrestrial organisms, they remain largely unknown in the ocean, where species diversity is sti...

The phylogeny of many groups of Orthoptera remains poorly understood. Previous phylogenetic studies largely restricted to few mitochondrial markers found many species in the grasshopper subfamily Gomphocerinae to be para- or polyphyletic, presumably because of incomplete lineage sorting and ongoing hybridization between putatively young lineages. R...

The process of species formation is characterised by the accumulation of multiple reproductive barriers. The evolution of hybrid male sterility, or Haldane’s rule, typically characterises later stages of species formation, when reproductive isolation is strongest. Yet, understanding how quickly reproductive barriers evolve and their consequences fo...

The availability of population genomic data through new sequencing technologies gives unprecedented opportunities for estimating important evolutionary forces such as genetic drift, selection, and mutation biases across organisms. Yet, analytical methods that can handle polymorphisms jointly with sequence divergence across species are rare and not...

Popular science book livro electrónico é distribuído gratuitamente. Para mais informações consulte o blogue “Um livro sobre evolução” (http://umlivrosobreevolucao.blogspot.com) ou escreva para ritacampos@cibio.up.pt.

In 1859, Charles Darwin proposed that species are not fundamentally different from subspecies or the varieties from which they evolve. A century later, Dobzhansky (1958) suggested that many such lineages are ephemeral and are likely to revert differentiation through introgression (Fig. 1A); only a few evolve complete reproductive isolation and pers...

Although the process of species formation is notoriously idiosyncratic, the observation of pervasive patterns of reproductive isolation across species pairs suggests that generalities, or “rules”, underlie species formation in all animals. Haldane’s rule states that whenever a sex is absent, rare or sterile in a cross between two taxa, that sex is...

In 1859, Charles Darwin proposed that species are not fundamentally different from subspecies or the varieties from which they evolve. A century later, Dobzhansky (1958) suggested that many such lineages are ephemeral and are likely to revert differentiation through introgression (Fig. 1A); only a few evolve complete reproductive isolation and pers...

Human overexploitation of natural resources has placed conservation and management as one of the most pressing challenges in modern societies, especially in regards to highly vulnerable marine ecosystems. In this context, cryptic species are particularly challenging to conserve because they are hard to distinguish based on morphology alone, and thu...

Vector-borne pathogens exist in obligate transmission cycles between vector and reservoir host species. Host shifts can lead to geographic expansion and the emergence of new diseases. Three etiological agents of human Lyme borreliosis (Borrelia afzelii, Borrelia bavariensis, and Borrelia garinii) predominantly utilize two distinct tick species as v...

Reproductive isolation is often achieved when genes that are neutral or beneficial in their genomic background become functionally incompatible in a foreign genomic background, causing inviability, sterility or other forms of low fitness in hybrids. Recent studies suggest that mitonuclear interactions are among the initial incompatibilities to evol...

Landscape features shape patterns of gene flow among populations, ultimately determining where taxa lay along the continuum between panmixia to complete reproductive isolation. Gene flow can be restricted, leading to population differentiation in two non-exclusive ways: “physical isolation”, in which geographic distance in combination with the land...

The barcoding of the mitochondrial COX1 gene has been instrumental in cataloguing the tree of life, and in providing insights in the phylogeographic history of species. Yet, this strategy has encountered difficulties in major clades characterized by large genomes, which contain a high frequency of nuclear pseudogenes originating from the mitochondr...

Theoretical and empirical studies have shown that species radiations are facilitated when a trait under divergent natural selection is also involved in sexual selection. It is yet unclear how quick and effective radiations are where assortative mating is unrelated to the ecological environment and primarily results from sexual selection. We address...

Reproductive isolation is often achieved when genes that are neutral or beneficial in their genomic background become functionally incompatible in a foreign genome, causing inviability, sterility or low fitness in hybrids. Recent studies suggest that mitonuclear interactions are among the initial incompatibilities to evolve at early stages of popul...

The biodiversity crisis has had particularly harsh impacts on marine environments. However, there is still considerable uncertainty about how many species have been seriously impacted and the effectiveness of protection measures (e.g., marine protected areas or MPAs) due to high levels of cryptic species in many taxa. Here, we employ an integrative...

The Neotropics host the highest number of species of the biological realms, but the roles of Pleistocene climatic oscillations and longstanding geographic barriers on the origins of this remarkable biodiversity remains debated. Here, we test the relative contribution of these evolutionary mechanisms on the genetic and phenotypic diversification of...

Morphological conservatism among closely related species often results in incongruent taxonomic classification between studies, leading to disagreements about the inferred evolutionary history of the species. This is the case in Mugil fishes, where extreme morphologic conservatism contrasts with wide distributions and high genetic divergence. To un...

Understanding how populations adapt to heterogeneous thermal regimes is essential for comprehending how latitudinal gradients in species diversification are formed, and how taxa will respond to ongoing climate change. Adaptation can occur by innate genetic factors, by phenotypic plasticity, or by a combination of both mechanisms. Yet, the relative...

The Tropical Southwestern Atlantic is characterized by prominent ecosystems with large-scale oceanographic complexity. Yet, the evolutionary processes underlying genetic differentiation and connectivity in this region remain largely unknown. Entomacrodus vomerinus (Valenciennes, 1836) is a demersal fish with planktonic larvae endemic to this marine...

Bayesian Skyline Plot of the North ESU (SS), Central ESU (FE+RA) and Coastal ESU (RN+BA) of Entomacrodus vomerinus individuals. (TIF)

Entomacrodus vomerinus specimens included in this study, sampling site, geographic coordinates and sequence accession number. (DOCX)

Analysis of Molecular Variance (AMOVA) of Entomacrodus vomerinus. (DOCX)

As sequencing technologies become more affordable, it is now realistic to propose studying the evolutionary history of virtually any organism on a genomic scale. However, when dealing with non-model organisms it is not always easy to choose the best approach given a specific biological question, a limited budget, and challenging sample material. Fu...

Recent studies have revealed repeated patterns of genomic divergence associated with species formation. Such patterns suggest that natural selection tends to target a set of available genes, but is also indicative that closely related taxa share evolutionary constraints that limit genetic variability. Studying patterns of genomic divergence among p...

Ecological models predict that, in the face of climate change, taxa occupying steep altitudinal gradients will shift their distributions, leading to the contraction or extinction of the high-elevation (cold-adapted) taxa. However, hybridization between eco-morphologically divergent taxa commonly occurs in nature and may lead to alternative evolutio...

In the mid-20th century, Ernst Mayr (1942) and Theodosius Dobzhansky (1958) championed the significance of ‘circular overlaps’ or ‘ring species’ as the perfect demonstration of the gradual nature of species formation. As an ancestral species expands its range, wrapping around a geographic barrier, derived taxa within the ring display interactions t...

The formation of new species is often a consequence of genetic incompatibilities accumulated between populations during allopatric divergence. When divergent taxa interbreed, these incompatibilities impact physiology and have a direct cost resulting in reduced hybrid fitness. Recent surveys of gene regulation in interspecific hybrids have revealed...

The analysis of introgression of genomic regions between divergent populations provides an excellent opportunity to determine the genetic basis of reproductive isolation during the early stages of speciation. However, hybridization and subsequent gene flow must be relatively common in order to localize individual loci that resist introgression. In...

The formation of stable genetic boundaries between emerging species is often diagnosed by reduced hybrid fitness relative to parental taxa. This reduced fitness can arise from endogenous and/or exogenous barriers to gene flow. Although detecting exogenous barriers in nature is difficult, we can estimate the role of ecological divergence in driving...

Early generations of hybrids can express both genetic incompatibilities and phenotypic novelty. Insights into whether these conflicting interactions between intrinsic and extrinsic selection persist after a few generations of recombination require experimental studies. To address this question, we use interpopulation crosses and recombinant inbred...

Reduced fitness in interpopulation hybrids can be a first indication of genetic incompatibilities that may ultimately lead to reproductive isolation and speciation. A growing number of cases of hybrid breakdown have been traced to incompatibilities between the nuclear genome and the organellar genomes of the mitochondria and chloroplasts. Although...

O resultado do projecto "Tenho uma pergunta... e talvez tenha a resposta! - Um livro sobre evolução", este manual é um recurso apelativo e útil para todos os interessados em biologia evolutiva e no ensino sobre evolução. Nele, a evolução é explicada com base em respostas simples mas precisas a perguntas colocadas pelo público-alvo (estudantes com i...

Un resultado del proyecto "Tengo una pregunta ... ¡y quizá también la respuesta! - Un libro sobre evolución", este manual es una herramienta muy atractiva y útil para aquellos que están interesados en la biología evolutiva y la enseñanza de la evolución. En él, la evolución se explica a partir de respuestas simples pero precisas a las preguntas for...

In the mid 20th century, Ernst Mayr and Theodosius Dobzhansky championed the significance of circular overlaps or ring species as the perfect demonstration of speciation, yet in the over 50 years since, only a handful of such taxa are known. We developed a topographic model to evaluate whether the geographic barriers that favor processes leading to...

Barrier permeability as measured by fragmentation and shape. Left: barrier permeability (fragmentation) vs. size (area). Right: barrier permeability (shape as measured by the perimeter-to-area ratio) vs. size (area). Vertical lines identify barriers that are 50,000 km2. Gray points identify all barriers on the planet, as defined by the topographic...

Use of the topographic ring model to identify candidate taxa for ring diversification around a focal barrier in the Iberian Peninsula (southern Europe) that is topographically similar to the reference barrier for the Drakensberg Massif (South Africa), which has promoted ring diversification in a tree species, Acacia karroo. Extensive field-based st...

Use of the topographic ring model to identify candidate taxa for ring diversification around a focal barrier on the island of New Guinea that is topographically similar to the reference barrier for the Central Valley (California, USA), which has promoted ring diversification in a salamander, Ensatina eschscholtzii. The focal barrier (upper right pa...

Use of the topographic ring model to identify candidate taxa for ring diversification around a focal barrier near the Baja California Peninsula (USA and Mexico) that is topographically similar to the reference barrier for the Drakensberg Massif (South Africa), which has promoted ring diversification in a tree species, Acacia karroo. The focal barri...

Use of the topographic ring model to identify candidate taxa for ring diversification around a focal barrier in Costa Rica and Panama that is topographically similar to the reference barrier for the Central Valley (California, USA), which has promoted ring diversification in a salamander, Ensatina eschscholtzii. A: The focal barrier is a long-stand...

Use of the topographic ring model to identify candidate taxa for ring diversification around a focal barrier in Madagascar that is topographically "in between" (Figure 3) reference barriers for the Drakensberg Massif (South Africa), which has promoted ring diversification in a tree species, Acacia karroo, and the Tibetan Plateau (Central Asia), whi...

Reproductive isolation (RI) is widely accepted as an important "check point" in the diversification process, since it defines irreversible evolutionary trajectories. Much less consensus exists about the processes that might drive RI. Here, we employ a formal quantitative analysis of genetic interactions at several stages of divergence within the ri...

Principal component analysis on 19 climatic variables for spatially unique observations of Ensatina within California. PC1 is responsible for 41.2% of the climatic variation and reflects wet and cold gradients (Mean Temperature of Coldest Quarter, Mean Temperature of Wettest Quarter, Min Temperature of Coldest Period, and Precipitation Seasonality;...

Collecting localities for mtDNA data, geographic location and GenBank Accession numbers.

Additional ring-distributed taxa surrounding reference barriers. A: The bird species complex Alauda (sp. arvensis and gulgula): Central Asia. B: The bird species Parus major: Central Asia. C: The bird species complex Charadrius (sp. hiaticula and semipalmatus): Arctic Ocean. Barriers are shown by the red polygons, species' distributions by the blac...

Pleistocene glaciations often resulted in differentiation of taxa in southern European peninsulas, producing the high levels of endemism characteristic of these regions (e.g. the Iberian Peninsula). Despite their small ranges, endemic species often exhibit high levels of intraspecific differentiation as a result of a complex evolutionary history do...