Juan Montoya-burgos | Université de Genève (original) (raw)

Papers by Juan Montoya-burgos

Journal of Fish Biology

This study confirms the presence of two species of the non-native mosquitofish Gambusia in Argent... more This study confirms the presence of two species of the non-native mosquitofish Gambusia in Argentina. The risks that they represent to native biota, their potential dispersal in the region, and their effectiveness in mosquito larvae control are discussed.

Molecular Biology and Evolution, 2016

Phylogenetic inference artifacts can occur when sequence evolution deviates from assumptions made... more Phylogenetic inference artifacts can occur when sequence evolution deviates from assumptions made by the models used to analyze them. The combination of strong model assumption violations and highly heterogeneous lineage evolutionary rates can become problematic in phylogenetic inference, and lead to the well-described long branch attraction (LBA) artifact. Here, we define an objective criterion for assessing lineage evolutionary rate heterogeneity among predefined lineages: the result of a likelihood ratio test between a model in which the lineages evolve at the same rate (homogeneous model) and a model in which different lineage rates are allowed (heterogeneous model). We implement this criterion in the algorithm Lineage Specific Sequence Subsampling (LS(3)), aimed at reducing the effects of LBA in multi-gene datasets. For each gene, LS(3) sequentially removes the fastest-evolving taxon of the ingroup and tests for lineage rate homogeneity until all lineages have uniform evolutionary rates. The sequences excluded from the homogeneously evolving taxon subset are flagged as potentially problematic. The software provides the user with the possibility to remove the flagged sequences for generating a new concatenated alignment. We tested LS(3) with simulations and two real datasets containing LBA artifacts: a nucleotide dataset regarding the position of Glires within mammals and an amino-acid dataset concerning the position of nematodes within bilaterians. The initially incorrect phylogenies were corrected in all cases upon removing data flagged by LS(3).

Molecular Phylogenetics and Evolution

The Neotropics possess the greatest freshwater fish diversity of the world, rendering the study o... more The Neotropics possess the greatest freshwater fish diversity of the world, rendering the study of their evolutionary history extremely challenging. Loricariidae catfishes are one of the most diverse components of the Neotropical ichthyofauna and despite a long history of classification, major issues still need elucidation. Based on a nuclear gene, we present a robust phylogeny of two former loricariid subfamilies: Hypoptopomatinae and Neoplecostominae. Our results show that Neoplecostominae is nested within Hypoptopomatinae, and is the sister group to the former Otothyrini tribe. According to our results, supplemented by morphological observations, we erect two new subfamilies, the Otothyrinae and a new Hypoptopomatinae, and modify the Neoplecostominae by including the genus Pseudotocinclus. The uncovered evolutionary relationships allow a detailed analysis of their historical biogeography. We tested two Dispersal-Extinction-Cladogenesis models for inferring the distribution range evolution of the new subfamilies, and show that the model having no constrains performs better than a model constraining long-range dispersal. The Maximum Likelihood reconstructions of ancestral ranges showed a marked division between the Amazonian origin of the Hypoptopomatinae and the eastern coastal Brazil+Upper Paraná origin of the Neoplecostominae and Otothyrinae. Markedly few instances of dispersal across the border separating the Amazon basin and the Paraná-Paraguay+eastern coastal Brazil+Uruguay were reconstructed. This result is in clear contrast with the historical biogeography of many Neotropical fishes, including other Loricariidae. Part of the dispersal limitation may be explained by divergent ecological specialization: lowland rivers versus mountain streams habitats. Moreover, because most species of the new subfamilies are small, we hypothesize that body size-related effects might limit their dispersal, like predation and energetic cost to migration. Finally, morphological and anatomical features are presented that limit or, to the contrary, enhance dispersal capability in these small and fascinating catfishes.

Molecular Phylogenetics and Evolution, 2015

The Loricariinae belong to the Neotropical mailed catfish family Loricariidae, the most species-r... more The Loricariinae belong to the Neotropical mailed catfish family Loricariidae, the most species-rich catfish family. Among loricariids, members of the Loricariinae are united by a long and flattened caudal peduncle and the absence of an adipose fin. Despite numerous studies of the Loricariidae, there is no comprehensive phylogeny of this morphologically highly diversified subfamily. To fill this gap, we present a molecular phylogeny of this group, including 350 representatives, based on the analysis of mitochondrial and nuclear genes (8426 positions). The resulting phylogeny indicates that Loricariinae are distributed into two sister tribes: Harttiini and Loricariini. The Harttiini tribe, as classically defined, constitutes a paraphyletic assemblage and is here restricted to the three genera Harttia, Cteniloricaria, and Harttiella. Two subtribes are distinguished within Loricariini: Farlowellina and Loricariina. Within Farlowellina, the nominal genus formed a paraphyletic group, as did Sturisoma and Sturisomatichthys. Within Loricariina, Loricaria, Crossoloricaria, and Apistoloricaria are also paraphyletic. To solve these issues, and given the lack of clear morphological diagnostic features, we propose here to synonymize several genera (Quiritixys with Harttia; East Andean members of Crossoloricaria, and Apistoloricaria with Rhadinoloricaria; Ixinandria, Hemiloricaria, Fonchiiichthys, and Leliella with Rineloricaria), to restrict others (Crossoloricaria, and Sturisomatichthys to the West Andean members, and Sturisoma to the East Andean species), and to revalidate the genus Proloricaria.

PLoS ONE, 2011

Recent genome-wide analyses have revealed patterns of positive selection acting on protein-coding... more Recent genome-wide analyses have revealed patterns of positive selection acting on protein-coding genes in humans and mammals. To assess whether the conclusions drawn from these analyses are valid for other vertebrates and to identify mammalian specificities, I have investigated the selective pressure acting on protein-coding genes of the puffer fishes Tetraodon and Takifugu. My results indicate that the strength of purifying selection in puffer fishes is similar to previous reports for murids but stronger in hominids, which have a smaller population size. Gene ontology analyses show that more than half of the biological processes targeted by positive selection in mammals are also targeted in puffer fishes, highlighting general patterns for vertebrates. Biological processes enriched with positively selected genes that are shared between mammals and fishes include immune and defense responses, signal transduction, regulation of transcription and several of their descendent terms. Mammalian-specific processes displaying an excess of positively selected genes are related to sensory perception and neurological processes. The comparative analyses also revealed that, for both mammals and fishes, genes encoding extracellular proteins are preferentially targeted by positive selection, indicating that adaptive evolution occurs more often in the extra-cellular environment rather than inside the cell. Moreover, I present here the first genome-wide characterization of neutrally-evolving regions of protein-coding genes. This analysis revealed an unexpectedly high proportion of genes containing both positively selected motifs and neutrally-evolving regions, uncovering a strong link between neutral evolution and positive selection. I speculate that neutrally-evolving regions are a major source of novelties screened by natural selection.

Molecular Ecology, 2003

Tropical South America possesses the largest ichthyofauna of any continental region. To test whet... more Tropical South America possesses the largest ichthyofauna of any continental region. To test whether palaeohydrological changes may have been the causes of such diversification, the 'hydrogeological' hypothesis, the phylogenetic relationships of 51 representatives of the catfish genus Hypostomus (Siluriformes: Loricariidae) were inferred using mitochondrial D-loop haplotype sequences. Specimens were collected in all main tropical South American rivers systems east to the Andes. The major interrelationships found with the D-loop data were confirmed with a subset of 21 species using complete internal transcribed spacer (ITS) region sequences. The phylogenetic analysis indicate that the genus Hypostomus can be divided into four monophyletic clades. The historical biogeographical analysis of each of these clades allows the identification of seven major cladogenetic events. Using calibrated D-loop and ITS molecular clocks, date estimations were attributed to each of these cladogenetic events allowing a linkage between four of them with documented hydrogeological changes. Comparisons with published distribution patterns of unrelated fish groups indicate that several of the reconstructed and dated hydrogeological-cladogenetic events may have acted at a large scale on the diversification of Neotropical freshwater fish fauna during late Tertiary.

Molecular Ecology, Jan 1, 2009

Neotropical freshwater fishes have reached an unrivalled diversity, organized into several areas ... more Neotropical freshwater fishes have reached an unrivalled diversity, organized into several
areas of endemism, yet the underlying processes are still largely unknown. The topographical
and ecological characteristics of the Guyanas Region make it an ideal area of endemism in
which to investigate the forces that have shaped this great diversity. This region is thought
to be inhabited by species descending from Amazonian ancestors, which would have used
two documented routes that, however, hardly explain the entrance of species adapted to
running waters. Here, we investigate the evolutionary history of Pseudancistrus brevispinis,
a catfish endemic to this region and exclusively found in running waters, thus making it an
ideal model for investigating colonization routes and dispersal in such habitats. Our analyses,
based on mitochondrial and nuclear markers, revealed an unexpected diversity consisting
of six monophyletic lineages within P. brevispinis, showing a disjoint distribution pattern.
The lineages endemic to Guyanas coastal rivers form a monophyletic group that originated
via an ancestral colonization event from the Amazon basin. Evidence given favours a
colonization pathway through river capture between an Amazonian tributary and the Upper
Maroni River. Population genetic analyses of the most widespread species indicate that
subsequent dispersal among Guyanas coastal rivers occurred principally by temporary
connections between adjacent rivers during periods of lower sea level, yet instances of
dispersal via interbasin river captures are not excluded. During high sea level intervals, the
isolated populations would have diverged leading to the observed allopatric species. This
evolutionary process is named the sea level fluctuation (SLF) hypothesis of diversification.

A novel mycobacterial species is described in this study. The strain was isolated from the cerebr... more A novel mycobacterial species is described in this study. The strain was isolated from the cerebrospinal fluid of a severely immunocompromised AIDS patient. It was scotochromogenic and slow-growing. Characteristic features for its differentiation from other mycobacteria are its lipid pattern and the unique gene sequences within the hypervariable regions of the 16S rDNA. The strain shows susceptibility to current antimycobacterial

Chromosoma, 2006

The Drosophila protein SU(VAR)3-7 is essential for fly viability, chromosome structure, and heter... more The Drosophila protein SU(VAR)3-7 is essential for fly viability, chromosome structure, and heterochromatin formation. We report that searches in silico and in vitro for homologues of SU(VAR)3-7 were successful within, but not outside, the Drosophila genus. Protein sequence homology between the distant sibling species Drosophila melanogaster and Drosophila virilis is low, except for the general organization of the protein and three conserved motives: seven widely spaced zinc fingers in the N-terminal half and the BESS and BoxA motives in the C-terminal half of the protein. We have undertaken a fine functional dissection of SU(VAR)3-7 in vivo using transgenes encoding truncations of the protein. BESS mediates interaction of SU(VAR)3-7 with itself, and BoxA is required for specific heterochromatin association. Both are necessary for the silencing properties of SU(VAR)3-7. The seven zinc fingers, widely spaced over the N-terminal half of SU(VAR)3-7, are required for binding to polytene chromosomes. One finger is necessary and sufficient to determine the appropriate chromatin association of the C-terminal half of the protein. Conferring a function to each of the conserved motives allows us to better understand the mode of action of SU(VAR)3-7 in triggering heterochromatin formation and subsequent genomic silencing.

Annales de Limnologie - International Journal of Limnology, 2013

Fish assemblages inhabiting the mountain streams of the Guiana shield have scarcely been studied.... more Fish assemblages inhabiting the mountain streams of the Guiana shield have scarcely been studied. Here we investigated fish assemblages in eight headwater mountain streams of the Mount Itoupe( French Guiana), and tested how local freshwater fish assemblages are shaped by environmental characteristics. We show that Mount Itoupe´streams host uneven species assemblages, characterized by low species richness (less than ten species per site) and a high proportion of small Siluriform species. Differences in fish assemblage composition between the sites were mainly due to basin identity, but regional climate and position of the site in the river gradient also had a significant effect, although of lower magnitude. In contrast, local habitat hardly affected fish richness, abundances or assemblage composition. Species richness increased along the upstream-downstream gradient, whereas fish abundance depended mainly on the slope orientation of Mount Itoupe´. Although these results need confirmation on a larger amount of sampling sites, located on other Guianese mountains, this preliminary study shows that the mountain streams of the Guiana Shield, although rarely investigated, host not only uneven species assemblages, but also present an original combination of environmental determinants shaping fish assemblage structure. Those rare and original ecosystems hence deserve more attention and should be preserved from human disturbances.

Within the Loricariidae, the genus Hypostomus is one of the most diversified freshwater catfish g... more Within the Loricariidae, the genus Hypostomus is one of the most diversified freshwater catfish groups. Using new sequence data from the mitochondrial Control Region (D-loop) we examined the phylogeny of this genus. Our phylogenetic analyses suggest that, in the Paraná river basin, species diversity in the genus Hypostomus has been shaped by two processes: 1) by inter-basin diversification, generating groups of species that inhabit different basins, as a result of dispersal events; and 2) via intra-basin speciation as a result of basin fragmentation due to past marine transgressions, which produced groups of species within a basin. Using the D-loop as a molecular clock, each event of diversification was dated and linked with documented hydrological events or sea level changes. We also assessed the possible dispersal routes between the Paraná and Uruguay rivers, in addition to the obvious dispersal route via the Río de la Plata estuary. Finally, we describe a new species of Hypostomus inhabiting Middle Paraná river, Hypostomus arecuta n. sp. This species can be separated from all other Hypostomus by having light roundish dots on a darker background and by number of premaxillary/ dentary teeth.

Trends in genetics : TIG, 2003

The mouse Fxy gene was translocated into the highly recombining pseudoautosomal region comparativ... more The mouse Fxy gene was translocated into the highly recombining pseudoautosomal region comparatively recently in evolutionary terms. This event resulted in a rapid increase of GC content. We investigated the consequences of the translocation further by sequencing exons and introns of Fxy in various rodent species. We found that the DNA fragment newly located in a highly recombining context has acquired every property of a GC-rich isochore, namely increased GC content (especially at the third codon positions of exons), shorter introns and high density of minisatellites. These results strongly suggest that recombination is the primary determinant of the isochore organization of mammalian genomes.

then compared development of three muroid species: mouse (9 rugae), rat (8) and golden hamster . ... more then compared development of three muroid species: mouse (9 rugae), rat (8) and golden hamster . We showed that palatal growth rate, spacing and addition rate in mouse/rat were remarkably similar (with respect to the embryo size difference), and that increase to 9 rugae in mouse is achieved by postponing the end of the addition process (hypermorphosis). Such a heterochronic

PLOS Genetics, 2007

Understanding the early evolution of placental mammals is one of the most challenging issues in m... more Understanding the early evolution of placental mammals is one of the most challenging issues in mammalian phylogeny. Here, we addressed this question by using the sequence data of the ENCODE consortium, which include 1% of mammalian genomes in 18 species belonging to all main mammalian lineages. Phylogenetic reconstructions based on an unprecedented amount of coding sequences taken from 218 genes

Evolutionary Applications, 2015

Interspecific hybridization occurs in nature but can also be caused by human actions. It often le... more Interspecific hybridization occurs in nature but can also be caused by human actions. It often leads to infertile or fertile hybrids that exclude one parental genome during gametogenesis, escaping genetic recombination and introgression. The threat that genome-exclusion hybridization might represent on parental species is poorly understood, especially when invasive species are involved. Here, we show how to assess the effects of genome-exclusion hybridization and how to elaborate conservation actions by simulating scenarios using a model of nonintrogressive hybridization. We examine the case of the frog Pelophylax ridibundus, introduced in Western Europe, which can hybridize with the native Pelophylax lessonae and the pre-existing hybrid Pelophylax esculentus, maintained by hybridogenesis. If translocated from Southern Europe, P. ridibundus produces new sterile hybrids and we show that it mainly threatens P. esculentus. Translocation from Central Europe leads to new fertile hybrids, threatening all native waterfrogs. Local extinction is demographically mediated via wasted reproductive potential or via demographic flow through generations towards P. ridibundus. We reveal that enlarging the habitat size of the native P. lessonae relative to that of the invader is a promising conservation strategy, avoiding the difficulties of fighting the invader. We finally stress that nonintrogressive hybridization is to be considered in conservation programmes.

PLoS ONE, 2014

Interspecific hybridization is common in nature but can be increased in frequency or even origina... more Interspecific hybridization is common in nature but can be increased in frequency or even originated by human actions, such as species introduction or habitat modification, which may threaten species persistence. When hybridization occurs between distantly related species, referred to as ''distant hybridization,'' the resulting hybrids are generally infertile or fertile but do not undergo chromosomal recombination during gametogenesis. Here, we present a model describing this frequent but poorly studied interspecific hybridization to assess its consequences on parental species and to anticipate the conditions under which they can reach extinction. Our general model fully incorporates three important processes: densitydependent competition, dominance/recessivity inheritance of traits and assortative mating. We demonstrate its use and flexibility by assessing population extinction risk between Atlantic salmon and brown trout in Norway, whose interbreeding has recently increased due to farmed fish releases into the wild. We identified the set of conditions under which hybridization may threaten salmonid species. Thanks to the flexibility of our model, we evaluated the effect of an additional risk factor, a parasitic disease, and showed that the cumulative effects dramatically increase the extinction risk. The consequences of distant hybridization are not genetically, but demographically mediated. Our general model is useful to better comprehend the evolution of such hybrid systems and we demonstrated its importance in the field of conservation biology to set up management recommendations when this increasingly frequent type of hybridization is in action.

Copeia, 2001

A new species of the mailed catfish genus Harttia is described from the Sao Francisco River drain... more A new species of the mailed catfish genus Harttia is described from the Sao Francisco River drainage, States of Minas Gerais and Bahia, Brazil. The new species is distinguished from congeners by the combination of an abdominal region covered by small bony plates, plates 3-4 times in eye diameter; interorbital width 3.1-4.0 in head length and greater than eye diameter; body width at anal fin origin 6.3-8.3 in standard length; margins of the head and pectoral fin spine of mature males with elongate and conspicuous odontodes; anal fin of males longer than of females. A key to Harttia species and a comparison with other species are provided. Uma nova especie de cascudos do genero Harttia edescrita da drenagem do rio Sao Francisco, nos estados de Minas Gerais e Bahia, Brasil. A nova especie epron- tamente diferenciada das demais especies por possuir a seguinte combinacao de caracteres: regiao abdominal revestida por placas osseas pequenas (3-4 vezes o diametro do olho), desde a cintura e...

Molecular Phylogenetics and Evolution - MOL PHYLOGENET EVOL, 2008

Proceedings of the National Academy of Sciences, 2007

A comprehensive phylogenetic framework is indispensable for investigating the evolution of genomi... more A comprehensive phylogenetic framework is indispensable for investigating the evolution of genomic features in mammals as a whole, and particularly in humans. Using the ENCODE sequence data, we estimated mammalian neutral evolutionary rates and selective pressures acting on conserved coding and noncoding elements. We show that neutral evolutionary rates can be explained by the generation time (GT) hypothesis. Accordingly, primates (especially humans), having longer GTs than other mammals, display slower rates of neutral evolution. The evolution of constrained elements, particularly of nonsynonymous sites, is in agreement with the expectations of the nearly neutral theory of molecular evolution. We show that rates of nonsynonymous substitutions (dN) depend on the population size of a species. The results are robust to the exclusion of hypermutable CpG prone sites. The average rate of evolution in conserved noncoding sequences (CNCs) is 1.7 times higher than in nonsynonymous sites. Despite this, CNCs evolve at similar or even lower rates than nonsynonymous sites in the majority of basal branches of the eutherian tree. This observation could be the result of an overall gradual or, alternatively, lineage-specific relaxation of CNCs. The latter hypothesis was supported by the finding that 3 of the 20 longest CNCs displayed significant relaxation of individual branches. This observation may explain why the evolution of CNCs fits the expectations of the nearly neutral theory less well than the evolution of nonsynonymous sites.