Causes of Variation in the Rate of Molecular Evolution

Bromham, Lindell

doi:10.1007/978-3-030-60181-2_4

Cited by 13 publications

(11 citation statements)

References 133 publications

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“…Large intraspecific divergences have been observed in stylommatophoran land snails since very early studies of their mitochondrial variation (Thomaz et al, 1996), but the value found here for M. incarnatus is particularly high. This may be due to a higher substitution rate, which is supposed to be associated with smaller body size and shorter generation time (Bromham, 2020; Mortz et al, 2021; Nabholz et al, 2008). In H. pomatia it takes at least 2–4 years to reach maturity (Frömming, 1954; Ligaszewski et al, 2016; Pollard, 1975) and the same may be assumed for H. thessalica .…”

Section: Discussionmentioning

confidence: 99%

In both directions: Expansions of European land snails to the north and south from glacial refugia

Korábek

Adamcová

Proćków

et al. 2022

Journal of Biogeography

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Aim: Were postglacial recolonizations facilitated by persistence close to the colonized areas rather than by dispersal ability allowing for colonization from distant sources? This question is particularly relevant for organisms with low active dispersal abilities and lacking specialized propagules. Here we identified glacial refugia of four Central European land snail species, including one for which a northern glacial refugium in the region was indicated by indirectly dated fossils.Location: Central Europe and the Balkans.Taxon: Pulmonate land snails: Monachoides incarnatus (Hygromiidae) and Helix pomatia, Helix thessalica and Caucasotachea vindobonensis (Helicidae). Methods:We used continuous phylogeographic analysis of mitochondrial sequence data to trace the origin of postglacially expanding lineages. We assessed the credibility of results from our focal species, M. incarnatus, by comparison to three other broadly sympatric land snail species. In addition, we performed direct radiocarbon dating of fossil shells to verify the presumed glacial presence of M. incarnatus on the territories of Czechia and Slovakia and to test the reliability of the available fossil data. Results:In three of the four species, the molecular data supported refugia located south of the Pannonian Basin, from the south-eastern Alps to the south-western Carpathians, but not more northerly. The direct radiocarbon dating resulted in younger dates than previously assumed. However, the molecular data also revealed unexpected, yet substantial postglacial southward expansions of M. incarnatus and C. vindobonensis into the Balkans.Main Conclusions: Neither the phylogeographic analyses nor the direct radiocarbon dating provided evidence for the glacial survival of studied land snail species in Central Europe. The refugia located adjacent to the Pannonian Basin were the most important source of postglacial expansions to Central Europe, but were also the source of the expansion southwards. Both climatic factors and biological interactions might explain why such southward expansions seem rather rare in Europe.

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Section: Discussionmentioning

confidence: 99%

In both directions: Expansions of European land snails to the north and south from glacial refugia

Korábek

Adamcová

Proćków

et al. 2022

Journal of Biogeography

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“…While many mechanisms link substitution rates to the life-history spectrum [15], we have limited intuition about how the mode of molecular evolution may relate to life-history variation. One idea that has been proposed to explain variation in DNA compositional heterogeneity links a recombination process known as GC-biased gene conversion (gBGC) to generation length, effective population size, and co-varying life-history traits [34,[74][75][76][77][78][79].…”

Section: A Novel Dimension Of Avian Adaptive Radiationmentioning

confidence: 99%

“…Given that life-history parameters such as body mass, generation length, and metabolic rates have been linked to different aspects of molecular sequence evolution [14,15], convergent patterns of life-history evolution are expected to leave an imprint of the K-Pg extinction event in the genomes of surviving lineages [16,17]. Only a few studies of animal taxa have attempted to directly investigate how the aftermath of the K-Pg mass extinction event shaped genome evolution (e.g., [17][18][19][20][21][22]).…”

Section: Introductionmentioning

confidence: 99%

Molecular early burst associated with the diversification of birds at the K–Pg boundary

Berv

Singhal

Field

et al. 2022

Preprint

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Complex patterns of genome and life-history evolution associated with the end-Cretaceous (K– Pg) mass extinction event limit our understanding of the early evolutionary history of crown group birds. Here, we assess molecular heterogeneity across living birds using a technique enabling inferred sequence substitution models to transition across the history of a clade. Our approach identifies contrasting patterns among exons, introns, untranslated regions, and mitochondrial genomes that reflect distinct regimes of molecular evolution. Up to fifteen shifts in the mode of avian molecular evolution map to rapidly diversifying clades near the Cretaceous-Palaeogene boundary, demonstrating a burst of genomic disparity early in the evolutionary history of crown birds. Using simulation and machine learning techniques, we show that shifts in developmental mode or adult body mass best explain transitions in the mode of nucleotide substitution. These patterns are related, in turn, to macroevolutionary shifts in the allometric scaling relationship between basal metabolic rate and body mass. In agreement with theoretical predictions, we show that this scaling relationship became weaker across the end-Cretaceous transition. Ultimately, our study provides evidence that the Chicxulub bolide impact triggered integrated patterns of evolution across avian genomes, physiology, and life history that structured the evolutionary potential of modern birds.

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“…It may also be possible to weight genes according to their inferred rate of evolution (Klopfstein et al, 2017). Sequences evolving more slowly might be better suited for exploring differences between major groups and higher taxa, while those with faster rates might be more appropriate for more closely related species (although these rates themselves often vary across taxa; Bromham, 2021). Such considerations are analogous to those encountered in molecular phylogenetics and phylogenomics (Philippe et al, 2011; Young & Gillung, 2020).…”

Section: Discussionmentioning

confidence: 99%

Why should we compare morphological and molecular disparity?

et al. 2023

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Indices of morphological disparity seek to summarise the highly multivariate morphological variation across groups of species within clades, time bins or other groups. Morphological variation can be quantified using geometric morphometric, outline or surface‐based methods. These are most effective when morphological differences are relatively modest and there are numerous ubiquitous landmarks and phase aligned features of shape variation. The most disparate samples, such as those across classes and phyla, typically necessitate the use of discrete characters. Unfortunately, such characters are often compiled subjectively in a manner reflecting the level of morphological and taxonomic focus and the intensity of taxon sampling. Sampling intensity is often highly variable within a single data set, especially in repurposed and amalgamated cladistic matrices. Here, we propose indices of molecular disparity analogous to those of morphological disparity. Despite numerous shortcomings discussed here, molecular sequence data can be obtained in a more objective, automated and scalable manner than morphological data. Comparisons of the morphological and molecular disparity of subclades in 16 large data sets suggest that molecular disparity is less susceptible to sampling biases than morphological disparity. Moreover, distance matrices inferred from individual genes tend to correlate strongly with each other and with distances from all concatenated genes. By contrast, morphological and molecular disparity are typically not significantly correlated across subclades, such that comparisons for groups can help to give a fuller picture of their evolution. For example, within mammals, Afrotheria have conspicuously high morphological disparity but modest molecular disparity, suggesting unusually high morphological plasticity. Even more strikingly, the molecular disparity of rodents is over five times that for Artiodactyla, despite having only half of their morphological disparity. These contrasts suggest the differential operation of geometric, biomechanical, ontogenetic and environmental constraints on form. Given the increasing abundance of total evidence datasets in the literature and the widespread and sometimes uncritical repurposing of discrete morphological matrices, we propose the comparison of morphological and molecular disparity as a useful tool to understand subclade evolution more fully.

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Causes of Variation in the Rate of Molecular Evolution

Cited by 13 publications

References 133 publications

In both directions: Expansions of European land snails to the north and south from glacial refugia

In both directions: Expansions of European land snails to the north and south from glacial refugia

Molecular early burst associated with the diversification of birds at the K–Pg boundary

Why should we compare morphological and molecular disparity?

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