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: 4.02). 11/2008; 50(1):44-58. DOI: 10.1016/j.ympev.2008.09.023
Source: PubMed

ABSTRACT 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, Jul 30, 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 · 4.02 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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    • "The amplified protein-coding Elongation Factor 1a gene (EF-1a C0) had no introns and consisted of 773 bp. Primers and PCR conditions used are described in Ruiz et al. (2009). PCR products were purified with isopropanol and 5 M ammonium acetate, and sequencing was performed in both directions using the standard protocol for ABI BigDye Terminator v3.1 cycle sequencing kit (Applied Biosystems). "
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    ABSTRACT: A molecular phylogeny of the subtribe Calathina was inferred from DNA sequence data from the mitochondrial cox1-cox2 region and the nuclear genes 28S and EF-1alpha. All lineages within Calathina from the Holarctic region were represented except for the monotypic subgenus Tachalus. Maximum Parsimony and Bayesian analyses of the combined data set showed that the subtribe is a monophyletic lineage that includes a single genus Calathus, where other taxa currently ranked as independent genera (Lindrothius, Synuchidius, Thermoscelis and Acalathus) are nested within this genus.Neocalathus and Lauricalathus, both subgenera of Calathus, were found to be polyphyletic and in need of taxonomic revision. The subtribe appears to have originated in the Mediterranean Basin and thereafter expanded into most parts of the Palearctic region, the Macaronesian archipelagos (at least five independent colonisation events), the Ethiopian highlands and the Nearctic region (at least two independent events).
    Molecular Phylogenetics and Evolution 11/2009; 55(2):358-71. DOI:10.1016/j.ympev.2009.10.026 · 4.02 Impact Factor
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