Molecular phylogeny of the tribe Sphodrini (Coleoptera: Carabidae) based on mitochondrial and nuclear markers

Departamento de Zoología y Antropología Física (Biología Animal), Facultad de Veterinaria, Universidad de Murcia, Campus de Espinardo, 30071 Murcia, Spain.
Molecular Phylogenetics and Evolution (Impact Factor: 3.92). 11/2008; 50(1):44-58. DOI: 10.1016/j.ympev.2008.09.023
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A phylogenetic analysis of 6.4 kb of nucleotide sequence data from seven genes (mitochondrial cox1-cox2 and tRNA(leu), and nuclear Ef-1alpha C0, Ef-1alpha C1, 28S, and 18S) was done to reconstruct the phylogenetic relationships of the ground-beetle tribe Sphodrini. Gene regions of variable nucleotide length were aligned using both a secondary structure model, Clustal W, and a combination of the two. Sensitivity analysis was performed in order to explore the effect of alignment methods. The ribosomal and protein-coding genes were largely congruent based on the ILD test and partitioned Bremer support measures. MtDNA analysis provided high resolution and high support for most clades. The tribe Sphodrini and the related tribes Platynini, Pterostichini and Zabrini made up monophyletic clades, but the relationship between them was weakly resolved and sensitive to alignment strategy. Previously suggested relationships between subtribes of Sphodrini were not corroborated, and only the subtribe Atranopsina revealed high support as the sister clade to the other subtribes. The analyses clearly demonstrated the importance of exploring effects of alignment methods that may become particularly important in resolving polytomies and nodes with low support.

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Available from: Carlos Ruiz, Oct 06, 2015
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    • "The same applies to the use of intron–exon structure in determining copy identity. Previous analyses reported diagnostic introns for different copies within insect orders (Brady et al., 2011; Danforth et al., 2006a; Desjardins et al., 2007; Jordal, 2002; Ruiz et al., 2009), but we here show that at least for Hymenoptera, this conclusion was an artifact of limited taxon sampling. Distance methods using reference sequences might represent an alternative, but even those can be misleading at the nucleotide level because of saturation and heterogeneous base composition. "
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    ABSTRACT: The eukaryotic translation elongation factor-1α gene (eEF1A) has been used extensively in higher level phylogenetics of insects and other groups, despite being present in two or more copies in several taxa. Orthology assessment has relied heavily on the position of introns, but the basic assumption of low rates of intron loss and absence of convergent intron gains has not been tested thoroughly. Here, we study the evolution of eEF1A based on a broad sample of taxa in the insect order Hymenoptera. The gene is universally present in two copies --- F1 and F2 --- both of which apparently originated before the emergence of the order. An elevated ratio of non-synonymous versus synonymous substitutions and differences in rates of amino acid replacements between the copies suggest that they evolve independently, and phylogenetic methods clearly cluster the copies separately. The F2 copy appears to be ancient; it is orthologous with the copy known as F1 in Diptera, and is likely present in most insect orders. The hymenopteran F1 copy, which may or may not be unique to this order, apparently originated through retroposition and was originally intron free. During the evolution of the Hymenoptera, it has successively accumulated introns, at least three of which have appeared at the same position as introns in the F2 copy or in eEF1A copies in other insects. The sites of convergent intron gain are characterized by highly conserved nucleotides that strongly resemble specific intron-associated sequence motifs, so-called proto-splice sites. The significant rate of convergent intron gain renders intron-exon structure unreliable as an indicator of orthology in eEF1A, and probably also in other protein-coding genes.
    Molecular Phylogenetics and Evolution 02/2013; 67(1). DOI:10.1016/j.ympev.2013.01.015 · 3.92 Impact Factor
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    • "Our divergence time estimations are still provisional as more calibration points are needed in the future. However, the two calibration points available, produce plausible results given that they correctly crossdate each other and that the derived mutation rates are well in the range of published mutation rates [46], [47], [53], [54] with the exception of the very fast rates derived for Trechus on the Canary Islands [49]. As the calibration scheme based on this rate produced an unrealistically young age estimate for the Pterostichus clade (see Baltic Amber fossils, mentioned above), these results can be dismissed. "
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    ABSTRACT: The Himalayan mountain arc is one of the hotspots of biodiversity on earth, and species diversity is expected to be especially high among insects in this region. Little is known about the origin of the Himalayan insect fauna. With respect to the fauna of high altitude cloud forests, it has generally been accepted that Himalayan lineages are derived from ancestors that immigrated from Western Asia and from adjacent mountainous regions of East and Southeast Asia (immigration hypothesis). In this study, we sought to test a Tibetan Origin as an alternative hypothesis for groups with a poor dispersal ability through a phylogeographic analysis of the Ethira clade of the genus Pterostichus. We sequenced COI mtDNA and the 18S and 28S rDNA genes in 168 Pterostichini specimens, including 46 species and subspecies of the Ethira clade. In our analysis, we were able to show that the Ethira clade is monophyletic and, thus, represents a Himalayan endemic clade, supporting endemism of two of the basal lineages to the Central Himalaya and documenting large distributional gaps within the phylogeographic structure of the Ethira clade. Furthermore, the molecular data strongly indicate very limited dispersal abilities of species and subspecies of these primary wingless ground beetles. These results are consistent with the hypothesis of a Tibetan Origin, which explains the evolution, diversity and distribution of the Himalayan ground beetle Ethira clade much more parsimoniously than the original immigration hypothesis.
    PLoS ONE 09/2012; 7(9):e45482. DOI:10.1371/journal.pone.0045482 · 3.23 Impact Factor
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    • "Therefore, our analyses resulted in relatively broad ranges of estimated divergence times, in particular for the most basal nodes. The estimated rates in analysis A (1.52% to 1.92%) are congruent with others reported for various Coleopteran groups, with pairwise substitution rates ranging from 0.7% to 2% (Adephaga: Prüser & Mossakowski, 1998; Polyphaga: Gó mez-Zurita et al., 2000; Farrell, 2001; Sota & Hayashi, 2007; Ruiz et al., 2009; Faille et al., 2010). These estimates are slightly lower than the standard 2.3% rate assumed in numerous studies of insect taxa and lower than others recently reported in Coleoptera: cox1, 3–17.6% and cox2, 5.2% (Papadopoulou et al., 2010; Pons et al., 2010; Ribera et al., 2010). "
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    ABSTRACT: The Mediterranean Basin is one of the most diverse biological hotspots in the world (Myers et al., 2000). A rich biota has developed there from the closing of the Tethys Sea in the Oligocene due to complex geological and climatic changes (Krijgsman, 2002; Mannion, 2008). Collisions and splits of tectonic plates have shaped the patterns of dispersal and ABSTRACT Aim To investigate the effects of Pleistocene climatic variations on the diversification rate of the subgenus Calathus (Coleoptera: Carabidae), and to estimate the role of vicariance and dispersal for explaining current distributional patterns. Location Western Palaearctic Region, particularly the Mediterranean Basin. Methods Fragments of the mitochondrial cox1–cox2 and the nuclear 28S and EF1a genes were analysed by Bayesian inference. Lineage divergence times were estimated using a Bayesian relaxed molecular clock. Three diversification rate analyses were conducted, namely gamma (c)-statistic, birth–death likelihood (BDL) test and survival analyses, in order to test departures from a constant rate model of diversification. A Bayesian approach to dispersal–vicariance analysis was developed to reconstruct the most probable ancestral area of subgenus Calathus and subsequent events of dispersal and colonization. Results A constant rate of speciation events from the late Miocene onwards was found for the subgenus Calathus, whereas recent Pleistocene climatic oscillations played an important role only in shaping intraspecific diversity. Overall diversification patterns for the subgenus are best explained by at least four westward dispersal events from the eastern Mediterranean Basin. Three distinct phylogroups were found for the widely distributed Calathus fuscipes. Incongruence between mitochondrial and nuclear loci was found for a number of species.
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