Macrosystematics of eutherian mammals combining HTS data to expand taxon coverage

Feijoo, Matías; Parada, Andrés

doi:10.1016/j.ympev.2017.05.004

Cited by 9 publications

(7 citation statements)

References 72 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We prepared, enriched and sequenced DNA libraries as described by Esselstyn et al [27] and used the Python package PHYLUCE [39] for subsequent data processing. We assembled cleaned reads into contigs using TRINITY v. r2013.08.14 [40] and extracted contigs for each taxon that matched UCE loci.…”

Section: Methodsmentioning

confidence: 99%

“…Several authors have used hundreds to thousands of nuclear loci to examine topology at the rodent root and recovered all three possible topologies. However, these studies have found low statistical support [26][27][28] or neglected to closely evaluate evidence at this node [29,30]. The latter is problematic as large molecular datasets often have inflated bootstrap values [31], while small numbers of anomalous loci can drive phylogenetic signal [32].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

A phylogenomic rodent tree reveals the repeated evolution of masseter architectures

2019

View full text Add to dashboard Cite

Understanding the number of times a trait has evolved is a necessary foundation for comprehending its potential relationships with selective regimes, developmental constraints and evolutionary diversification. Rodents make up over 40% of extant mammalian species, and their ecological and evolutionary success has been partially attributed to the increase in biting efficiency that resulted from a forward shift of one or two portions of the masseter muscle from the zygomatic arch onto the rostrum. This forward shift has occurred in three discrete ways, but the number of times it has occurred has never been explicitly quantified. We estimated an ultrametric phylogeny, the first to include all rodent families, using thousands of ultraconserved elements. We examined support for evolutionary relationships among the five rodent suborders and then incorporated relevant fossils, fitted models of character evolution, and used stochastic character mapping to determine that a portion of the masseter muscle has moved forward onto the rostrum at least seven times (with one reversal) during the approximately 70 Myr history of rodents. Combined, the repeated evolution of this key innovation, its increasing prevalence through time, and the species diversity of clades with this character underscores the adaptive value of improved biting efficiency and the relative ease with which some advantageous traits arise.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A phylogenomic rodent tree reveals the repeated evolution of masseter architectures

2019

View full text Add to dashboard Cite

show abstract

“…Nevertheless, this does not excuse researchers from assessing the quality of their alignments and gene trees. Indeed, numerous phylogenomic data sets (Struck et al, 2011; Chiari et al, 2012; Song et al, 2012; Kumar et al, 2013; Jarvis et al, 2014; Feijoo and Parada, 2017; Chen et al, 2017; Liu et al, 2017a) contain alignments with homology problems that impact the results and main conclusions of these studies (Struck, 2013; Springer and Gatesy, 2016; Brown and Thomson, 2017; Gatesy and Springer, 2017; Springer and Gatesy, 2018a; Springer and Gatesy, 2018b). These problems could have been avoided with appropriate screening procedures to flag problematic alignments and gene trees.…”

Section: Node Dating and Beyondmentioning

confidence: 99%

Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary

et al. 2019

View full text Add to dashboard Cite

Deciphering the timing of the placental mammal radiation is a longstanding problem in evolutionary biology, but consensus on the tempo and mode of placental diversification remains elusive. Nevertheless, an accurate timetree is essential for understanding the role of important events in Earth history (e.g., Cretaceous Terrestrial Revolution, KPg mass extinction) in promoting the taxonomic and ecomorphological diversification of Placentalia. Archibald and Deutschman described three competing models for the diversification of placental mammals, which are the Explosive, Long Fuse, and Short Fuse Models. More recently, the Soft Explosive Model and Trans-KPg Model have emerged as additional hypotheses for the placental radiation. Here, we review molecular and paleontological evidence for each of these five models including the identification of general problems that can negatively impact divergence time estimates. The Long Fuse Model has received more support from relaxed clock studies than any of the other models, but this model is not supported by morphological cladistic studies that position Cretaceous eutherians outside of crown Placentalia. At the same time, morphological cladistics has a poor track record of reconstructing higher-level relationships among the orders of placental mammals including the results of new pseudoextinction analyses that we performed on the largest available morphological data set for mammals (4,541 characters). We also examine the strengths and weaknesses of different timetree methods (node dating, tip dating, and fossilized birth-death dating) that may now be applied to estimate the timing of the placental radiation. While new methods such as tip dating are promising, they also have problems that must be addressed if these methods are to effectively discriminate among competing hypotheses for placental diversification. Finally, we discuss the complexities of timetree estimation when the signal of speciation times is impacted by incomplete lineage sorting (ILS) and hybridization. Not accounting for ILS results in dates that are older than speciation events. Hybridization, in turn, can result in dates than are younger or older than speciation dates. Disregarding this potential variation in "gene" history across the genome can distort phylogenetic branch lengths and divergence estimates when multiple unlinked genomic loci are combined together in a timetree analysis.

show abstract

“…5D; Meredith et al 2011;dos Reis et al 2012;Emerling et al 2015;Foley et al 2016;Tarver et al 2016). Previous investigations of this systematic problem have employed both genome-scale DNA sequence data and retroposon insertions, yielding highly incongruent results (Nishihara et al 2006;Hallström et al 2011;Meredith et al 2011;Song et al 2012;Tarver et al 2016;Chen et al 2017;Doronina et al 2017a;Feijoo and Parada, 2017;Liu et al 2017). Some of these analyses are further complicated by homology problems with the underlying data (see Gatesy 2016, 2017;Gatesy and Springer 2017).…”

Section: Laurasiatheria Retroposonsmentioning

confidence: 99%

An ABBA-BABA Test for Introgression Using Retroposon Insertion Data

Ms¹,

Gatesy

2019

Preprint

View full text Add to dashboard Cite

DNA sequence alignments provide the majority of data for inferring phylogenetic relationships with both concatenation and coalescence methods. However, DNA sequences are susceptible to extensive homoplasy, especially for deep divergences in the Tree of Life. Retroposon insertions have emerged as a powerful alternative to sequences for deciphering evolutionary relationships because these data are nearly homoplasy-free.In addition, retroposon insertions satisfy the 'no intralocus recombination' assumption of summary coalescence methods because they are singular events and better approximate neutrality relative to DNA sequences commonly applied in phylogenomic work.Retroposons have traditionally been analyzed with phylogenetic methods that ignore incomplete lineage sorting (ILS). Here, we analyze three retroposon data sets for mammals (Placentalia, Laurasiatheria, Balaenopteroidea) with two different ILS-aware methods. The first approach constructs a species tree from retroposon bipartitions with ASTRAL, and the second is a modification of SVD-Quartets. We also develop a χ 2 Quartet-Asymmetry Test to detect hybridization using retroposon data. Both coalescence methods recovered the same topology for each of the three data sets. The ASTRAL species tree for Laurasiatheria has consecutive short branch lengths that are consistent with an anomaly zone situation. For the Balaenopteroidea data set, which includes rorquals (Balaenopteridae) and gray whale (Eschrichtiidae), both coalescence methods recovered a topology that supports the paraphyly of Balaenopteridae. Application of the χ 2 Quartet-Asymmetry Test to this data set detected 16 different quartets of species for which historical hybridization may be inferred, but significant asymmetry was not detected in the placental root and Laurasiatheria analyses.

show abstract

Macrosystematics of eutherian mammals combining HTS data to expand taxon coverage

Cited by 9 publications

References 72 publications

A phylogenomic rodent tree reveals the repeated evolution of masseter architectures

A phylogenomic rodent tree reveals the repeated evolution of masseter architectures

Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary

An ABBA-BABA Test for Introgression Using Retroposon Insertion Data

Contact Info

Product

Resources

About