Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis

Platt, Roy N.; Zhang, Yuhua; Witherspoon, David J.; Xing, Jinchuan; Suh, Alexander; Keith, Megan S.; Jorde, Lynn B.; Stevens, Richard D.; Ray, David A.

doi:10.1093/gbe/evv099

Cited by 23 publications

(20 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…74, 93, and 94) than L1 (95) or SVA (SINE/VNTR/Alu) (96) elements, which occur at much lower density in primate genomes. Thus, it is tempting to speculate that the explosive amplification of one or a few TE families, such as CR1 elements in woodpeckers (46) and Ves SINEs in bats (97,98), led to an increase opportunity for NAHR, thereby facilitating the extreme degree of DNA loss that we observed in these two lineages (Figs. 2 and 3 and Fig.…”

Section: Dna Gain and Loss Analysis Reveals The Elasticity Of Avian Amentioning

confidence: 99%

Dynamics of genome size evolution in birds and mammals

Kapusta

Suh

Feschotte

2017

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

357

358

View full text Add to dashboard Cite

Genome size in mammals and birds shows remarkably little interspecific variation compared with other taxa. However, genome sequencing has revealed that many mammal and bird lineages have experienced differential rates of transposable element (TE) accumulation, which would be predicted to cause substantial variation in genome size between species. Thus, we hypothesize that there has been covariation between the amount of DNA gained by transposition and lost by deletion during mammal and avian evolution, resulting in genome size equilibrium. To test this model, we develop computational methods to quantify the amount of DNA gained by TE expansion and lost by deletion over the last 100 My in the lineages of 10 species of eutherian mammals and 24 species of birds. The results reveal extensive variation in the amount of DNA gained via lineage-specific transposition, but that DNA loss counteracted this expansion to various extents across lineages. Our analysis of the rate and size spectrum of deletion events implies that DNA removal in both mammals and birds has proceeded mostly through large segmental deletions (>10 kb). These findings support a unified "accordion" model of genome size evolution in eukaryotes whereby DNA loss counteracting TE expansion is a major determinant of genome size. Furthermore, we propose that extensive DNA loss, and not necessarily a dearth of TE activity, has been the primary force maintaining the greater genomic compaction of flying birds and bats relative to their flightless relatives.genome size evolution | DNA loss | transposable elements | amniotes | flight T he nature and relative importance of the molecular mechanisms and evolutionary forces underlying genome size variation has been the subject of intense research and debate (1-7). Variation in genome sizes may not always occur at a level where natural selection is strong enough to prevent genetic drift to determine their fate (neutral or effectively neutral variation) (3). Additionally, the fixation probability of slightly deleterious deletions or insertions would be higher in species with smaller effective population sizes, where natural selection acts less efficiently (3,8). On the other hand, a number of correlative associations between genome size and phenotypic traits, such as cell size (9, 10) and metabolic rate associated with powered flight (11, 12), suggest that natural selection and adaptive processes also shape genome size evolution. Teasing apart the relative importance of these two forces (drift and selection) requires a better understanding of the mode and processes by which DNA is gained and lost over long evolutionary periods in different taxa. Thus, establishing an integrated view of the contribution of gain and loss of DNA to genome size variation (or lack thereof) remains an important goal in genome biology (e.g., refs. 1, 2, 13, and 14).Most studies of genome size evolution have focused on taxa with extensive variation in genome sizes, such as flowering plants (15)(16)(17)(18)(19)(20), conifers (21), insects (22-...

show abstract

Section: Dna Gain and Loss Analysis Reveals The Elasticity Of Avian Amentioning

confidence: 99%

Dynamics of genome size evolution in birds and mammals

Kapusta

Suh

Feschotte

2017

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

357

358

View full text Add to dashboard Cite

show abstract

“…It is difficult to draw major conclusions from studies limited in the number of characters (Ruedi 73 and Mayer 2001; Stadelmann, et al 2007;Larsen, et al 2012; Ruedi, et al 2013;Haynie, et al 2016) or 74 taxa (Platt, et al 2015). Current data seem to indicate that nuclear and mitochondrial markers recover 75 similar topologies.…”

Section: Introductionmentioning

confidence: 95%

“…Current data seem to indicate that nuclear and mitochondrial markers recover 75 similar topologies. Platt et al (2015) generated a phylogeny based entirely on nuclear data using 85,028 76 shared transposable element insertions. Their results generally confirmed the mitochondrial phylogenies 77 of Myotis, but only included seven taxa in their analysis.…”

Section: Introductionmentioning

confidence: 99%

Conflicting evolutionary histories of the mitochondrial and nuclear genomes in New WorldMyotisbats

Platt

Faircloth

Sullivan

et al. 2017

Preprint

Self Cite

View full text Add to dashboard Cite

The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial genomes of 37 representative Myotis, primarily from the New World, in conjunction with targeted sequencing of 3,648 ultraconserved elements (UCEs). We inferred the phylogeny and explored the effects of concatenation and summary phylogenetic methods, as well as combinations of markers based on informativeness or levels of missing data, on our results. Of the 294 phylogenies generated from the nuclear UCE data, all are significantly different from phylogenies inferred using mitochondrial genomes. Even within the nuclear data, quartet frequencies indicate that around half of all UCE loci conflict with the estimated species tree. Several factors can drive such conflict, including incomplete lineage sorting, introgressive hybridization, or even phylogenetic error. Despite the degree of discordance between nuclear UCE loci and the mitochondrial genome and among UCE loci themselves, the most common nuclear topology is recovered in one quarter of all analyses with strong nodal support. Based on these results, we re-examine the evolutionary history of Myotis to better understand the phenomena driving their unique nuclear, mitochondrial, and biogeographic histories.

show abstract

“…However, I predict that more examples of hard polytomies will be discovered once various types of densely sampled genome-scale data are available for other super-rapid radiations. These might include, for example, gibbons (Veeramah et al 2015), Hawaiian honeycreepers (Lerner et al 2011), Lake Malawi cichlids (Takahashi et al 2001), Lake Tanganyika cichlids (Meyer et al 2015), Myotis bats (Platt et al 2015), sylvioid songbirds (Fregin et al 2012), thrushes (Nylander et al 2008) and white eyes (Moyle et al 2009).…”

Section: Why Is the Root Of Neoaves Unresolved?mentioning

confidence: 99%

The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves

2016

Self Cite

View full text Add to dashboard Cite

Suh, A. (2016). The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves. -Zoologica Scripta, 45, 50-62. Birds have arguably been the most intensely studied animal group for their phylogenetic relationships. However, the recent advent of genome-scale phylogenomics has made the forest of bird phylogenies even more complex and confusing. Here, in this perspective piece, I show that most parts of the avian Tree of Life are now firmly established as reproducible phylogenetic hypotheses. This is to the exception of the deepest relationships among Neoaves. Using phylogenetic networks and simulations, I argue that the very onset of the super-rapid neoavian radiation is irresolvable because of eight near-simultaneous speciation events. Such a hard polytomy of nine taxa translates into 2 027 025 possible rooted bifurcating trees. Accordingly, recent genome-scale phylogenies show extremely complex conflicts in this (and only this) part of the avian Tree of Life. I predict that the upcoming years of avian phylogenomics will witness many more, highly conflicting tree topologies regarding the early neoavian polytomy. I further caution against bootstrapping in the era of genomics and suggest to instead use reproducibility (e.g. independent methods or data types) as support for phylogenetic hypotheses. The early neoavian polytomy coincides with the Cretaceous-Paleogene (K-Pg) mass extinction and is, to my knowledge, the first empirical example of a hard polytomy.

show abstract

Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis

Cited by 23 publications

References 50 publications

Dynamics of genome size evolution in birds and mammals

Dynamics of genome size evolution in birds and mammals

Conflicting evolutionary histories of the mitochondrial and nuclear genomes in New WorldMyotisbats

The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves

Contact Info

Product

Resources

About