staff

Ilham Bahechar

Research assistant in Vertebrate evolution

  • T: +41 22 379 67 98
  • office 4067a (Sciences III)
  • Evolutionary units delimitation and continental multilocus phylogeny of the hyperdiverse catfish genus Hypostomus. Mol. Phylogenet. Evol. 2019 Dec;():106711. S1055-7903(19)30305-7. 10.1016/j.ympev.2019.106711.

    abstract

    With 149 currently recognized species, Hypostomus is one of the most species-rich catfish genera in the world, widely distributed over most of the Neotropical region. To clarify the evolutionary history of this genus, we reconstructed a comprehensive phylogeny of Hypostomus based on four nuclear and two mitochondrial markers. A total of 206 specimens collected from the main Neotropical rivers were included in the present study. Combining morphology and a Bayesian multispecies coalescent (MSC) approach, we recovered 85 previously recognized species plus 23 putative new species, organized into 118 'clusters'. We presented the Cluster Credibility (CC) index that provides numerical support for every hypothesis of cluster delimitation, facilitating delimitation decisions. We then examined the correspondence between the morphologically identified species and their inter-specific COI barcode pairwise divergence. The mean COI barcode divergence between morphological sisters species was 1.3±1.2%, and only in 11% of the comparisons the divergence was ≥ 2%. This indicates that the COI barcode threshold of 2% classically used to delimit fish species would seriously underestimate the number of species in Hypostomus, advocating for a taxon-specific COI-based inter-specific divergence threshold to be used only when approximations of species richness are needed. The phylogeny of the 108 Hypostomus species, together with 35 additional outgroup species, confirms the monophyly of the genus. Four well-supported main lineages were retrieved, hereinafter called super-groups: Hypostomus cochliodon, H. hemiurus, H. auroguttatus, and H. plecostomus super-groups. We present a compilation of diagnostic characters for each super-group. Our phylogeny lays the foundation for future studies on biogeography and on macroevolution to better understand the successful radiation of this Neotropical fish genus.

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  • The contribution of neutral evolution and adaptive processes in driving phenotypic divergence in a model mammalian species, the Andean fox Lycalopex culpaeus Journal of Biogeography. 2018;45:1114–1125

    abstract

    Understanding the mechanisms that drive phenotypic divergence along climatic gradients is a long‐standing goal of biogeography. To fulfil this objective, we tested if neutral and/or adaptive effects drive phenotypic diversification. We quantified the effects of neutral evolution and natural selection on morphological variability of a well‐suited mammalian species, the fox, Lycalopex culpaeus.

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  • Transcriptome screen for fast evolving genes by Inter-Specific Selective Hybridization (ISSH). BMC Genomics 2010 ;11():126. 1471-2164-11-126. 10.1186/1471-2164-11-126. PMC2838844.

    abstract

    Fast evolving genes are targets of an increasing panel of biological studies, from cancer research to population genetics and species specific adaptations. Yet, their identification and isolation are still laborious, particularly for non-model organisms. We developed a method, named the Inter-Specific Selective Hybridization (ISSH) method, for generating cDNA libraries enriched in fast evolving genes. It utilizes transcripts of homologous tissues of distinct yet related species. Experimental hybridization conditions are monitored in order to discard transcripts that do not find their homologous counterparts in the two species sets as well as transcripts that display a strong complementarity between the two species. Only heteroduplexes that disanneal at low stringency are used for constructing the resulting cDNA library.

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