Phylogenetic signal of genomic repeat abundances can be distorted by random homoplasy: a case study from hominid primates

Martín-Peciña, María; Ruiz‐Ruano, Francisco J.; Camacho, Juan Pedro M.; Dodsworth, Steven

doi:10.1093/zoolinnean/zly077

Cited by 13 publications

(10 citation statements)

References 51 publications

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“…The method proved to be useful in reconstructing the evolutionary history of several plant and animal groups (e.g. Dodsworth et al 2014;Martín-Peciña et al 2018;Bolsheva et al 2019), yielding as well additional data for comparative studies of genome evolution. More recently, other authors have also proposed more or less analogous phylogenetic approaches based on the genomic abundance of repetitive elements (Piednöel et al 2015;Harkess et al 2016;Doronina et al 2017), which emphasize the interest of evolutionary researchers on this topic.…”

Section: Introductionmentioning

confidence: 99%

Reconstructing Phylogenetic Relationships Based on Repeat Sequence Similarities

Vitales

Garcia

Dodsworth

2019

Preprint

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A recent phylogenetic method based on genome-wide abundance of different repeat types proved to be useful in reconstructing the evolutionary history of several plant and animal groups. Here, we demonstrate that an alternative information source from the repeatome can also be employed to infer phylogenetic relationships among taxa. Specifically, this novel approach makes use of the repeat sequence similarity matrices obtained from the comparative clustering analyses of RepeatExplorer 2, which are subsequently transformed to between-taxa distance matrices. These pairwise matrices are used to construct neighbour-joining trees for each of the top most-abundant clusters and they are finally summarized in a consensus network. This methodology was tested on three groups of angiosperms and one group of insects, resulting in congruent evolutionary hypotheses compared to more standard systematic analyses based on commonly used DNA markers. We propose that the combined application of these phylogenetic approaches based on repeat abundances and repeat sequence similarities could be helpful to understand mechanisms governing genome and repeatome evolution.

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Section: Introductionmentioning

confidence: 99%

Reconstructing Phylogenetic Relationships Based on Repeat Sequence Similarities

Vitales

Garcia

Dodsworth

2019

Preprint

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“…These rapid evolutionary dynamics can be useful for understanding species boundaries, but repetitive sequences are rarely used in this context. Our approach expands on previous findings (Sproul, Barton, et al, 2020) Previous studies show that patterns of repeat abundance hold phylogenetic signal (Dodsworth et al, 2015); however, repeat abundance can evolve so dynamically (even between sister taxa, let alone across deep phylogenetic splits) that homoplasy can present a major challenge when encoding phylogenetic characters from raw abundance (Martín-Peciña et al, 2019). Rather than use repeat abundance as the character of interest, our approach encodes the signature of abundant variants relative to a common reference sequence.…”

Section: Discussionmentioning

confidence: 72%

“…Within species, this variation may be largely caused by expansion and contraction of repeats due to unequal exchange of recombining repeat clusters (Smith, 1976). Dynamic variation in repeat abundance may add noise when comparing patterns across samples, which can confound signals that may be present (Martín-Peciña, Ruiz-Ruano, Camacho, & Dodsworth, 2019). Development of approaches that can extract evolutionary signal despite repeat abundance variation can potentially increase the resolution of evolutionary studies among populations and species (Sproul, Barton, & Maddison, 2020).…”

Section: Introductionmentioning

confidence: 99%

RepeatProfiler: a pipeline for visualization and comparative analysis of repetitive DNA profiles

Negm

Greenberg

Larracuente

et al. 2020

Preprint

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Study of DNA repeats in model organisms highlights the role of repetitive DNA in many processes that drive genome evolution and phenotypic change. Because repetitive DNA is much more dynamic than single-copy DNA, repetitive sequences can reveal signals of evolutionary history over short time scales that may not be evident in sequences from slower-evolving genomic regions. Many tools for studying repeats are directed toward organisms with existing genomic resources, including genome assemblies and repeat libraries. However, signals in repeat variation may prove especially valuable in disentangling evolutionary histories in diverse non-model groups, for which genomic resources are limited. Here we introduce RepeatProfiler, a tool for generating, visualizing, and comparing repetitive DNA profiles from low-coverage, shortread sequence data. RepeatProfiler automates the generation and visualization of repetitive DNA coverage depth profiles and allows for statistical comparison of profile shape across samples. In addition, RepeatProfiler facilitates comparison of profiles by extracting signal from sequence variants across profiles which can then be analyzed as molecular morphological characters using phylogenetic analysis. We validate RepeatProfiler with data sets from ground beetles (Bembidion), flies (Drosophila), and tomatoes (Solanum). We highlight the potential of repetitive DNA profiles as a high-resolution data source for studies in species delimitation, comparative genomics, and repeat biology.

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“…The maximum likelihood principle and its derivatives are currently the most frequently used methods (Tsantes and Steiper, 2009;Moorjani et al, 2016), whereas in most of the early studies on the rates of substitution the neighbor-joining algorithm was used (Elango et al, 2006;Kim et al, 2006;Perry et al, 2011). It is remarkable that virtually all recent studies on the phylogeny of primates are based on the maximum likelihood and Bayesian approaches (Chatterjee et al, 2009;Perelman et al, 2011;Finstermeier et al, 2013;Pozzi et al, 2014;Wu et al, 2017), although the maximum parsimony method was also used (Martín-Peciña et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Negative correlation between mean female age at first birth and rates of molecular evolution in primates, with predictions of the reproductive age in early hominins

Bajdek

2020

Preprint

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mtDNA-based phylogenetic trees of the order Primates were constructed by the minimum evolution (ME) and maximum likelihood (ML) methods. Branch lengths were compared with the mean female age at first birth in the taxa studied. Higher reproductive age in females triggers a lower number of generations through time and, on average, at the molecular level smaller evolutionary distances between related taxa. However, this relationship is significant when the phylogeny is resolved by the ME method rather than the ML method. Reliability of the minimum evolution approach is discussed. In contrast to most studies, the ME tree recovers Tarsius bancanus (Tarsiiformes) as a member of the Strepsirrhini, which phylogeny is supported by a strong branch length−reproductive age relationship and which is proposed as a novel heuristic method to test phylogeny. However, branches of certain taxa on the constructed phylogenetic tree show anomalous lengths relative to the mean female age at first birth, such as e.g. the human branch. As estimated in this paper, early members of the human lineage have likely reproduced at higher rates than modern humans, some forms possibly giving first birth at the mean age of 10−12 years, which is more comparable to the mean age at first birth in extant gorillas than to that typical of living humans and chimpanzees. Probable early reproduction in human ancestors is also supported by the comparably more evolved mitochondrial DNA in Denisovans than in modern humans, and by a smaller body mass in most fossil hominins, which often triggers fast maturation in primates.

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Phylogenetic signal of genomic repeat abundances can be distorted by random homoplasy: a case study from hominid primates

Cited by 13 publications

References 51 publications

Reconstructing Phylogenetic Relationships Based on Repeat Sequence Similarities

Reconstructing Phylogenetic Relationships Based on Repeat Sequence Similarities

RepeatProfiler: a pipeline for visualization and comparative analysis of repetitive DNA profiles

Negative correlation between mean female age at first birth and rates of molecular evolution in primates, with predictions of the reproductive age in early hominins

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