Molecular systematics: A synthesis of the common methods and the state of knowledge

Mauro, Diego San; Agorreta, Ainhoa

doi:10.2478/s11658-010-0010-8

Cited by 56 publications

(38 citation statements)

References 209 publications

(233 reference statements)

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“…These discrepancies could be due to differences of both programs in methodological assumptions of rate change (auto-correlated in MultiDivtime, uncorrelated in BEAST), implementation of evolutionary models and prior calibrations, and techniques to calculate credibility intervals [104]. Moreover, molecular dating estimates are much older than the first neobatrachian fossils (dated in the Early Cretaceous; [105]), indicating either that currently available fossils might be a poor indicator of this particular branching event [105] or that the molecular dating could be overestimated [106].…”

Section: Resultsmentioning

confidence: 99%

The origin of modern frogs (Neobatrachia) was accompanied by acceleration in mitochondrial and nuclear substitution rates

et al. 2012

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BackgroundUnderstanding the causes underlying heterogeneity of molecular evolutionary rates among lineages is a long-standing and central question in evolutionary biology. Although several earlier studies showed that modern frogs (Neobatrachia) experienced an acceleration of mitochondrial gene substitution rates compared to non-neobatrachian relatives, no further characterization of this phenomenon was attempted. To gain new insights on this topic, we sequenced the complete mitochondrial genomes and nine nuclear loci of one pelobatoid (Pelodytes punctatus) and five neobatrachians, Heleophryne regis (Heleophrynidae), Lechriodus melanopyga (Limnodynastidae), Calyptocephalella gayi (Calyptocephalellidae), Telmatobius bolivianus (Ceratophryidae), and Sooglossus thomasseti (Sooglossidae). These represent major clades not included in previous mitogenomic analyses, and most of them are remarkably species-poor compared to other neobatrachians.ResultsWe reconstructed a fully resolved and robust phylogeny of extant frogs based on the new mitochondrial and nuclear sequence data, and dated major cladogenetic events. The reconstructed tree recovered Heleophryne as sister group to all other neobatrachians, the Australasian Lechriodus and the South American Calyptocephalella formed a clade that was the sister group to Nobleobatrachia, and the Seychellois Sooglossus was recovered as the sister group of Ranoides. We used relative-rate tests and direct comparison of branch lengths from mitochondrial and nuclear-based trees to demonstrate that both mitochondrial and nuclear evolutionary rates are significantly higher in all neobatrachians compared to their non-neobatrachian relatives, and that such rate acceleration started at the origin of Neobatrachia.ConclusionsThrough the analysis of the selection coefficient (ω) in different branches of the tree, we found compelling evidence of relaxation of purifying selection in neobatrachians, which could (at least in part) explain the observed higher mitochondrial and nuclear substitution rates in this clade. Our analyses allowed us to discard that changes in substitution rates could be correlated with increased mitochondrial genome rearrangement or diversification rates observed in different lineages of neobatrachians.

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Section: Resultsmentioning

confidence: 99%

The origin of modern frogs (Neobatrachia) was accompanied by acceleration in mitochondrial and nuclear substitution rates

et al. 2012

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“…The resulting alignment was analyzed using maximum likelihood (ML; Felsenstein, 1981) and Bayesian inference (BI; Huelsenbeck et al, 2001), which are currently the standard methods for molecular phylogenetic inference (reviewed in San Mauro and Agorreta, 2010). Analyses were run on the CIPRES Science Gateway (Miller et al, 2010).…”

Section: Methodsmentioning

confidence: 99%

Müller glia reactivity follows retinal injury despite the absence of the glial fibrillary acidic protein gene in Xenopus

Luna

Aruck

et al. 2017

Developmental Biology

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Intermediate filament proteins are structural components of the cellular cytoskeleton with cell-type specific expression and function. Glial fibrillary acidic protein (GFAP) is a type III intermediate filament protein and is up-regulated in glia of the nervous system in response to injury and during neurodegenerative diseases. In the retina, GFAP levels are dramatically increased in Müller glia and are thought to play a role in the extensive structural changes resulting in Müller cell hypertrophy and glial scar formation. In spite of similar changes to the morphology of Xenopus Müller cells following injury, we found that Xenopus lack a gfap gene. Other type III intermediate filament proteins were induced following rod photoreceptor ablation and retinal ganglion cell axotomy. The recently available X. tropicalis and X. laevis genomes indicate a small deletion most likely resulted in the loss of the gfap gene during evolution. Lastly, a survey of representative species from all three extant amphibian orders including the Anura (frogs, toads), Caudata (salamanders, newts), and Gymnophiona (caecilians) suggests that deletion of the gfap locus occurred after the common ancestor of the Anura and Caudata. Our results demonstrate that extensive changes in Müller cell morphology following retinal injury do not require GFAP in Xenopus, and other type III intermediate filament proteins may be involved in the gliotic response.

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“…This widely used method for dating phylogenies [70] assumes a relaxed uncorrelated clock with rates drawn from a lognormal distribution across branches. The ML optimal topology was used as a starting tree, and the birth-death process [71] was used to describe diversification.…”

Section: Methodsmentioning

confidence: 99%

Integrative analyses of speciation and divergence in Psammodromus hispanicus (Squamata: Lacertidae)

et al. 2011

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BackgroundGenetic, phenotypic and ecological divergence within a lineage is the result of past and ongoing evolutionary processes, which lead ultimately to diversification and speciation. Integrative analyses allow linking diversification to geological, climatic, and ecological events, and thus disentangling the relative importance of different evolutionary drivers in generating and maintaining current species richness.ResultsHere, we use phylogenetic, phenotypic, geographic, and environmental data to investigate diversification in the Spanish sand racer (Psammodromus hispanicus). Phylogenetic, molecular clock dating, and phenotypic analyses show that P. hispanicus consists of three lineages. One lineage from Western Spain diverged 8.3 (2.9-14.7) Mya from the ancestor of Psammodromus hispanicus edwardsianus and P. hispanicus hispanicus Central lineage. The latter diverged 4.8 (1.5-8.7) Mya. Molecular clock dating, together with population genetic analyses, indicate that the three lineages experienced northward range expansions from southern Iberian refugia during Pleistocene glacial periods. Ecological niche modelling shows that suitable habitat of the Western lineage and P. h. edwardsianus overlap over vast areas, but that a barrier may hinder dispersal and genetic mixing of populations of both lineages. P. h. hispanicus Central lineage inhabits an ecological niche that overlaps marginally with the other two lineages.ConclusionsOur results provide evidence for divergence in allopatry and niche conservatism between the Western lineage and the ancestor of P. h. edwardsianus and P. h. hispanicus Central lineage, whereas they suggest that niche divergence is involved in the origin of the latter two lineages. Both processes were temporally separated and may be responsible for the here documented genetic and phenotypic diversity of P. hispanicus. The temporal pattern is in line with those proposed for other animal lineages. It suggests that geographic isolation and vicariance played an important role in the early diversification of the group, and that lineage diversification was further amplified through ecological divergence.

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Molecular systematics: A synthesis of the common methods and the state of knowledge

Cited by 56 publications

References 209 publications

The origin of modern frogs (Neobatrachia) was accompanied by acceleration in mitochondrial and nuclear substitution rates

The origin of modern frogs (Neobatrachia) was accompanied by acceleration in mitochondrial and nuclear substitution rates

Müller glia reactivity follows retinal injury despite the absence of the glial fibrillary acidic protein gene in Xenopus

Integrative analyses of speciation and divergence in Psammodromus hispanicus (Squamata: Lacertidae)

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