Early genome size increase in urodeles

Laurin, Michel; Canoville, Aurore; Struble, Mikayla; Organ, Chris L.; Buffrénil, Vivian de

doi:10.1016/j.crpv.2014.12.006

Cited by 21 publications

(20 citation statements)

References 45 publications

(65 reference statements)

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“…The presence of multiple character acquisitions in a restricted region of the tree, coupled with the apparent absence of similar events in other clades, may best be explained by a variable‐rate model. Similar general patterns can be seen in the evolution of genome size in amphibians (Laurin et al, ; Organ et al, ).…”

Section: Macroevo‐devo With Fossils and Phylogenetic Comparative Methodssupporting

confidence: 67%

Macroevolutionary developmental biology: Embryos, fossils, and phylogenies

Organ

Cooper

Hieronymus

2015

Developmental Dynamics

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The field of evolutionary developmental biology is broadly focused on identifying the genetic and developmental mechanisms underlying morphological diversity. Connecting the genotype with the phenotype means that evo-devo research often considers a wide range of evidence, from genetics and morphology to fossils. In this commentary, we provide an overview and framework for integrating fossil ontogenetic data with developmental data using phylogenetic comparative methods to test macroevolutionary hypotheses. We survey the vertebrate fossil record of preserved embryos and discuss how phylogenetic comparative methods can integrate data from developmental genetics and paleontology. Fossil embryos provide limited, yet critical, developmental data from deep time. They help constrain when developmental innovations first appeared during the history of life and also reveal the order in which related morphologies evolved. Phylogenetic comparative methods provide a powerful statistical approach that allows evo-devo researchers to infer the presence of nonpreserved developmental traits in fossil species and to detect discordant evolutionary patterns and processes across levels of biological organization.

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Section: Macroevo‐devo With Fossils and Phylogenetic Comparative Methodssupporting

confidence: 67%

Macroevolutionary developmental biology: Embryos, fossils, and phylogenies

Organ

Cooper

Hieronymus

2015

Developmental Dynamics

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“…The ancestral amphibia genome (C‐value ~ 3 pg) has experienced massive amplification during the evolution of the Urodela (Liedtke, Gower, Wilkinson, & Gomez‐Mestre, ; Organ, Canoville, Reisz, & Laurin, ; Organ, Struble, Canoville, Bruffénil, & Laurin, ). An early ancestor of salamanders, for example, has been estimated to have a large genome size of approximately 33.1 pg, which is similar to the reconstructed ancestral genome size of 32–43 pg (Laurin, Canoville, Struble, & Buffrénil, ; Liedtke et al., ; Sessions, ). An earlier study suggested that genome size in salamanders has increased with time, although the exact rate of increase remains unclear (Martin & Gordon, ; Sessions, ).…”

Section: Introductionmentioning

confidence: 71%

“…An early ancestor of salamanders, for example, has been estimated to have a large genome size of approximately 33.1 pg, which is similar to the reconstructed ancestral genome size of 32-43 pg (Laurin, Canoville, Struble, & Buffrénil, 2015;Liedtke et al, 2018;Sessions, 2008). An earlier study suggested that genome size in salamanders has increased with time, although the exact rate of increase remains unclear (Martin & Gordon, 1995;Sessions, 2008).…”

Section: Introductionmentioning

confidence: 73%

Genome size variation and species diversity in salamanders

Sclavi

Herrick

2019

J of Evolutionary Biology

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Salamanders (Urodela) have among the largest vertebrate genomes, ranging in size from 10 to 120 pg. Although changes in genome size often occur randomly and in the absence of selection pressure, nonrandom patterns of genome size variation are evident among specific vertebrate lineages. Several reports suggest a relationship between species richness and genome size, but the exact nature of that relationship remains unclear both within and across different taxonomic groups. Here, we report (a) a negative relationship between haploid genome size (C‐value) and species richness at the family taxonomic level in salamander clades; (b) a correlation of C‐value and species richness with clade crown age but not with diversification rates; (c) strong associations between C‐value and both geographic area and climatic‐niche rate. Finally, we report a relationship between C‐value diversity and species diversity at both the family‐ and genus‐level clades in urodeles.

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“…The large genomes in all extant salamanders examined to date, as well as one of the earliest known stem salamanders, suggest that salamander genomes have been gigantic for at least 150-200 million years (Thomson and Muraszko 1978;Laurin et al 2016;Gregory 2016). Since this initial expansion, genome size has increased and decreased within the clade, with increases outnumbering decreases at least threefold (Sessions and Larson 1987;Sessions 2008).…”

Section: Discussionmentioning

confidence: 99%

“…Salamanders and frogs last shared a common ancestor ß300 mya (Zhang et al 2005;Hedges et al 2006;Roelants et al 2007;San Mauro 2010). Fossil evidence, along with the nested phylogenetic position of salamanders within vertebrates, indicates that large genome size is derived in salamanders (Thomson and Muraszko 1978;Organ et al 2011;Laurin et al 2016).…”

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confidence: 99%

Genetic drift and mutational hazard in the evolution of salamander genomic gigantism

Mohlhenrich

Mueller

2016

Evolution

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GENETIC DRIFT AND MUTATIONAL HAZARD IN THE EVOLUTION OF SALAMANDER GENOMIC GIGANTISMSalamanders have the largest nuclear genome sizes among tetrapods and, with the exception of lungfishes, among vertebrates as a whole. Lynch and Conery (2003) have proposed the mutational hazard hypothesis to explain variation in genome size and complexity. Under this hypothesis, non-coding DNA imposes a selective cost by increasing the target for degenerative mutations, i.e. the mutational hazard. Expansion of non-coding DNA, and thus genome size, is expected to be driven by increased levels of genetic drift and/or decreased mutation rates; the former determines the efficiency with which excess non-coding DNA can be selected against, while the latter determines the level of mutational hazard. Here, we test the hypothesis that salamanders have experienced stronger long-term, persistent genetic drift than frogs, a clade with more typically sized vertebrate genomes. To test this hypothesis, we compared dN/dS and Kr/Kc values between these clades. Our results reject this hypothesis; we find that salamanders have not experienced stronger genetic drift than frogs. Additionally, we find evidence consistent with a lower nucleotide substitution rate in salamanders. This result, along with previous work showing lower rates of small deletions and ectopic recombination in salamanders, suggests that a lower mutational hazard may contribute to genome expansion in this clade. Taken together, these results further underscore the importance of studying large genomes and indicate that salamanders provide an important model system for the study of how non-drift processes (i.e. mutation, natural selection) shape the evolution of genome size.iii ACKNOWLEDGEMENTS I would like to thank my parents, Roger and Susan. My father instilled in me the sense of wonder and curiosity that guide my life and work. My mother has been my biggest supporter since day one (literally), and none of this would have been possible without her love.

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Early genome size increase in urodeles

Cited by 21 publications

References 45 publications

Macroevolutionary developmental biology: Embryos, fossils, and phylogenies

Macroevolutionary developmental biology: Embryos, fossils, and phylogenies

Genome size variation and species diversity in salamanders

Genetic drift and mutational hazard in the evolution of salamander genomic gigantism

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