Mitochondrial pseudogenes: evolution's misplaced witnesses

Bensasson, Douda; Zhang, Dexing; Hartl, Daniel L.; Hewitt, Godfrey M.

doi:10.1016/s0169-5347(01)02151-6

Cited by 980 publications

(910 citation statements)

References 48 publications

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“…We also suspect that the sequences obtained from the amplification of the 5 0 end of the cytb fragment in T. italicus is from a pseudogene or numt gene. We reached this conclusion on the basis of a phylogenetic criterion to check for spurious positions of putative pseudogene sequences in an otherwise well-established clade (Bensasson et al, 2001). This is the only species for which we could not amplify the whole 800 bp in a single PCR reaction.…”

Section: Authenticity Of Cytb Sequencesmentioning

confidence: 97%

A Bayesian approach on molecules and behavior: reconsidering phylogenetic and evolutionary patterns of the Salamandridae with emphasis on Triturus newts

et al. 2006

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The monophyly of European newts of the genus Triturus within the family Salamandridae has for decades rested on presumably homologous behavioral and morphological characters. Molecular data challenge this hypothesis, but the phylogenetic position of Triturus within the Salamandridae has not yet been convincingly resolved. We addressed this issue and the temporal divergence of Triturus within the Salamandridae with novel Bayesian approaches applied to DNA sequence data from three mitochondrial genes (12S, 16S and cytb). We included 38 salamandrid species comprising all 13 recognized species of Triturus and 16 out of 17 salamandrid genera. A clade comprising all the ''Newts'' can be separated from the ''True Salamanders'' and Salamandrina clades. Within the ''Newts'' well-supported clades are: Tylototriton-Pleurodeles, the ''New World Newts'' (Notophthalmus-Taricha), and the ''Modern Eurasian Newts'' (Cynops, Pachytriton, Paramesotriton 5 together the ''Modern Asian Newts'', Calotriton, Euproctus, Neurergus and Triturus species). We found that Triturus is a non-monophyletic species assemblage, which includes four groups that are themselves monophyletic: (i) the ''Large-Bodied Triturus'' (six species), (ii) the ''Small-Bodied Triturus'' (five species), (iii) T. alpestris and (iv) T. vittatus. We estimated that the last common ancestor of Triturus existed around 64 million years ago (mya) while the root of the Salamandridae dates back to 95 mya. This was estimated using a fossil-based molecular dating approach and an explicit framework to select calibration points that least underestimated their corresponding nodes. Using the molecular phylogeny we mapped the evolution of life history and courtship traits in Triturus and found that several Triturus-specific courtship traits evolved independently. J. Exp. Zool. (Mol. Dev. Evol.) 308B:139-162, 2007. r 2006 How to cite this article: Steinfartz S, Vicario S, Arntzen JW, Caccone A. 2007. A Bayesian approach on molecules and behavior: reconsidering phylogenetic and evolutionary patterns of the salamandridae with emphasis on Triturus newts. J. Exp. Zool. (Mol. Dev. Evol.) 308B:139-162.Salamanders and newts of the family Salamandridae are at present distributed over North America and Eurasia. Despite a profound diversity in life history traits, including courtship and reproductive modes, the monophyly of the Salamandridae is strongly supported (Weisrock et al., 2005). Among the 17 extant salamandrid genera, the genus Triturus has the widest distribution and the highest number of species, since it is found throughout Europe except for northern Scandina- 308B:139-162 (2007) via and the Mediterranean islands (Fig. 1). The monophyly of Triturus was generally assumed on the basis of overall similarity in morphology and traits of courtship behavior. Triturus newts display a biphasic life style with aquatic reproduction, typically taking place in ponds and stagnant waters during spring and early summer, and a subsequent terrestrial phase until the next reproductive eve...

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Section: Authenticity Of Cytb Sequencesmentioning

confidence: 97%

A Bayesian approach on molecules and behavior: reconsidering phylogenetic and evolutionary patterns of the Salamandridae with emphasis on Triturus newts

et al. 2006

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“…Chromatogram output was checked by eye 12 using Sequencher 4.1 (Gene Codes) or ProSeq (Filatov, 2002). Direct sequencing of a small proportion of the cytb PCR products revealed mixtures of multiple cytb-like fragments, or 290 sequences possessing reading frames containing stop codons or indels, suggesting the possible presence of nuclear pseudogenes (Bensasson et al 2001, Rokas et al, 2003a. In these cases, individual PCR products were amplified by cloning (TA cloning, Invitrogen) and only specimens for which a single, correct open reading frame (ORF) bearing sequence was identified have been included in the following analyses.…”

Section: Dna Extraction and Sequencingmentioning

confidence: 99%

Phylogeny and DNA barcoding of inquiline oak gallwasps (Hymenoptera: Cynipidae) of the Western Palaearctic

Ács

Challis

Bihari

et al. 2010

Molecular Phylogenetics and Evolution

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The NERC and CEH trade marks and logos ('the Trademarks') are registered trademarks of NERC in the UK and other countries, and may not be used without the prior written consent of the Trademark owner. We examine phylogenetic relationships within the Synergus complex of herbivorous 50 inquiline gallwasps associated with (Hymenoptera; Cynipidae; Synergini) associated with cynipid host galls on oak, a biologically diverse group whose genus-level morphological taxonomy has long been considered stable but whose species level taxonomy is problematic.We incorporate data for over 80% of recognised Western Palaearctic species in 5 morphology-based genera (Ceroptres, Saphonecrus, Synergus, Synophrus, Ufo), comprising 55 sequence for two mitochondrial two mitochondrial loci (coxI, cytb) and one nuclear locus (28S D2). In particular, we assess the evidence for monophyly of two long-established, morphology-defined sections within the genus Synergus that differ in a range of biological traits between-generation polymorphism and impact on the host gall inducer (lethal versus non-lethal). To aid analyses of ecological interactions within oak cynipid communities, we 60 also consider the utility of cytochrome oxidase I (coxI) DNA barcodes in the oak inquilines.In this assessment, we do not assume that species are delineated at a single threshold value of sequence divergence for a single gene, but examine concordance in the composition of molecular operational Taxonomic units (MOTUs) across a range of sequence divergences in each gene and across genes. We also assess the impact of sampling effort on MOTU stability. 65Phylogenetic reconstructions for all three loci support monophyly for Synergus and Synophrus, but reject monophyly for Saphonecrus and for the two sections within Synergus.The suites of traits associated with the two sections of the genus Synergus are thus homoplasious. All three loci also reject monophyly for three Synergus species (S. hayneanus, S. pallipes, S. umbraculus). Sequences for each locus identify robust MOTUs that are largely 70 concordant across loci for a range of cut-off values. Though many MOTU's correspond to recognised Linnean species, there is significant, multigene disagreement between groupings supported by morphology and sequence data, with both allocation of different morphospecies to the same MOTU and allocation of the same morphospecies to multiple MOTUs, regardless 3 of cutoff value. Our results imply that while DNA barcoding has considerable utility within 75 this group, morphology-based identification needs major revision at both genus and species levels. Further, lifehistory traits currently attributed to single morphospecies probably confound attributes of multiple lineages. Revealing patterns of character state evolution in Synergus requires collection of new host association and life history data explicitly linked to DNA barcode data for the specimens concerned. 80

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“…MEGA5 was then also used to perform phylogenetic estimations (complete deletion of gaps and missing data). No gaps, stopcodons or discrepancies between forward and reverse strands were contained in the coxI alignment, so that the amplification of nuclear pseudogenes (Bensasson et al 2001) could be excluded. Based on the lowest Bayesian Information Criterion score, a General Time Reversible (GTR) model + G (Gamma shape parameter = 0.23) was selected as best-fitting nucleotide substitution model for the data to construct a Maximum Likelihood (ML) phylogenetic tree using the nearest neighbor interchange algorithm (Nei and Kumar 2000;Tamura et al 2011;Hall 2013).…”

Section: Methodsmentioning

confidence: 99%

“…Additional sequencing of the coxI genetic barcoding region with the primers LepF/LepR (Hebert et al 2004;Smith et al 2014) yielded multiple peaks in the sequence chromatograms of colonies Cac2, Tap and TC indicating nuclear pseudogenes (Bensasson et al 2001) of this fragment. We, therefore, used our CI13/CI14 fragments, which partially overlap with the barcoding region, to achieve a final alignment of 490 bp with eight barcoding fragments from GenBank (Smith et al 2014) of L. praedator from Costa Rica, including variant JTL-001 and five more variants for which no morphological description is available yet.…”

Section: Methodsmentioning

confidence: 99%

Genetic differentiation at species level in the Neotropical army ant Labidus praedator

2015

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The nomadic, swarm-raiding army ant Labidus praedator (Smith, 1858) is an important arthropod predator in the Neotropics with a strong ecological impact on invertebrate communities. However, despite its high abundance and ubiquity over a large distribution range, it received relatively little scientific attention. Moreover, the taxonomic status is confusing because some morphological descriptions point towards the co-occurrence of several distinct taxa which are lumped together as L. praedator in most classical keys. Yet, clarifying genetic studies are lacking. Here, we show strong genetic differentiation within an L. praedator population in Mexico. Both microsatellite genotype patterns and phylogenetic analyses (concatenated nuclear and mtDNA sequences, including the coxI genetic barcoding region), reveal the occurrence of two strongly isolated lineages. Colonies from the very same location, clearly identified as the same species (L. praedator) according to classical morphological keys, exhibit an extremely high average sequence divergence (9.7-12.8 %), which was well in the range of divergence among GenBank sequences from other Labidus species. Thus, our data very likely show genetic differentiation at species level or cryptic speciation within L. praedator, which should be recognized when investigating biodiversity and ecological importance of army ants (or other arthropods) in the Neotropics.

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Mitochondrial pseudogenes: evolution's misplaced witnesses

Cited by 980 publications

References 48 publications

A Bayesian approach on molecules and behavior: reconsidering phylogenetic and evolutionary patterns of the Salamandridae with emphasis on Triturus newts

A Bayesian approach on molecules and behavior: reconsidering phylogenetic and evolutionary patterns of the Salamandridae with emphasis on Triturus newts

Phylogeny and DNA barcoding of inquiline oak gallwasps (Hymenoptera: Cynipidae) of the Western Palaearctic

Genetic differentiation at species level in the Neotropical army ant Labidus praedator

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