On Defining and Finding Islands of Trees and Mitigating Large Island Bias
AbstractHow best can we summarize sets of phylogenetic trees? Systematists have relied heavily on consensus methods, but if tree distributions can be partitioned into distinct subsets, it may be helpful to provide separate summaries of these rather than relying entirely upon a single consensus tree. How sets of trees can most helpfully be partitioned and represented leads to many open questions, but one natural partitioning is provided by the islands of trees found during tree searches. Islands that are of dissimilar size have been shown to yield majority-rule consensus trees dominated by the largest sets We illustrate thi...
Source: Systematic Biology - March 22, 2021 Category: Biology Source Type: research
Evolutionary Sample Size and Consilience in Phylogenetic Comparative Analysis
AbstractPhylogenetic comparative methods (PCMs) are commonly used to study evolution and adaptation. However, frequently used PCMs for discrete traits mishandle single evolutionary transitions. They erroneously detect correlated evolution in these situations. For example, hair and mammary glands cannot be said to have evolved in a correlated fashion because each evolved only once in mammals, but a commonly used model (Pagel ’s Discrete) statistically supports correlated (dependent) evolution. Using simulations, we find that rate parameter estimation, which is central for model selection, is poor in these scenarios due to...
Source: Systematic Biology - March 15, 2021 Category: Biology Source Type: research
A New Method for Integrating Ecological Niche Modeling with Phylogenetics to Estimate Ancestral Distributions
We present a new method for phylogenetic niche modeling, implemented in R. Given past and present climate data, taxon occurrence data, and a time-calibrated phylogeny, our method constructs niche models for each extant taxon, uses ancestral character estimation to reconstruct ancestral niche models, and projects these models into paleoclimate data to provide a historical estimate of the geographic range of a lineage. Models either at nodes or along branches of the phylogeny can be estimated. We demonstrate our method on a small group of dendrobatid frogs and show that it can make inferences given species with restricted ra...
Source: Systematic Biology - March 15, 2021 Category: Biology Source Type: research
Interrogating Phylogenetic Discordance Resolves Deep Splits in the Rapid Radiation of Old World Fruit Bats (Chiroptera: Pteropodidae)
AbstractThe family Pteropodidae (Old World fruit bats) comprises $>$200 species distributed across the Old World tropics and subtropics. Most pteropodids feed on fruit, suggesting an early origin of frugivory, although several lineages have shifted to nectar-based diets. Pteropodids are of exceptional conservation concern with $>$50% of species considered threatened, yet the systematics of this group has long been debated, with uncertainty surrounding early splits attributed to an ancient rapid diversification. Resolving the relationships among the main pteropodid lineages is essential if we are to fully understand t...
Source: Systematic Biology - March 4, 2021 Category: Biology Source Type: research
QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution
AbstractAmino acid substitution models play a crucial role in phylogenetic analyses. Maximum likelihood (ML) methods have been proposed to estimate amino acid substitution models; however, they are typically complicated and slow. In this article, we propose QMaker, a new ML method to estimate a general time-reversible $Q$ matrix from a large protein data set consisting of multiple sequence alignments. QMaker combines an efficient ML tree search algorithm, a model selection for handling the model heterogeneity among alignments, and the consideration of rate mixture models among sites. We provide QMaker as a user-friendly fu...
Source: Systematic Biology - February 22, 2021 Category: Biology Source Type: research
Dissecting Incongruence between Concatenation- and Quartet-Based Approaches in Phylogenomic Data
We examined incongruence stemming from conflict the between likelihood-based signal (quantified by the difference in gene-wise log-likelihood score or $\Delta $GLS) and quartet-based topological signal (quantified by the difference in gene-wise quartet score or $\Delta $GQS) for every gene in three phylogenomic studies in animals, fungi, and plants, which were chosen because their concatenation-based IQ-TREE (T1) and quartet-based ASTRAL (T2) phylogenies are known to produce eight conflicting internal branches (bipartitions). By comparing the types of phylogenetic signal for all genes in these three data matrices, we found...
Source: Systematic Biology - February 22, 2021 Category: Biology Source Type: research
Of Traits and Trees: Probabilistic Distances under Continuous Trait Models for Dissecting the Interplay among Phylogeny, Model, and Data
AbstractStochastic models of character trait evolution have become a cornerstone of evolutionary biology in an array of contexts. While probabilistic models have been used extensively for statistical inference, they have largely been ignored for the purpose of measuring distances between phylogeny-aware models. Recent contributions to the problem of phylogenetic distance computation have highlighted the importance of explicitly considering evolutionary model parameters and their impacts on molecular sequence data when quantifying dissimilarity between trees. By comparing two phylogenies in terms of their induced probabilit...
Source: Systematic Biology - February 15, 2021 Category: Biology Source Type: research
Corrigendum to: Phylogenomics of piranhas and pacus (Serrasalmidae) uncovers how dietary convergence and parallelism obfuscate traditional morphological taxonomy
M A Kolmann, L C Hughes, L P Hernandez, D Arcila, R Betancur-R, M H Sabaj, H L ópez-Fernández, G Ortí (Source: Systematic Biology)
Source: Systematic Biology - February 11, 2021 Category: Biology Source Type: research
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Source: Systematic Biology - February 10, 2021 Category: Biology Source Type: research
Gene Tree Discord, Simplex Plots, and Statistical Tests under the Coalescent
AbstractA simple graphical device, the simplex plot of quartet concordance factors, is introduced to aid in the exploration of a collection of gene trees on a common set of taxa. A single plot summarizes all gene tree discord and allows for visual comparison to the expected discord from the multispecies coalescent model (MSC) of incomplete lineage sorting on a species tree. A formal statistical procedure is described that can quantify the deviation from expectation for each subset of four taxa, suggesting when the data are not in accord with the MSC, and thus that either gene tree inference error is substantial or a more c...
Source: Systematic Biology - February 9, 2021 Category: Biology Source Type: research
Incorporating Hierarchical Characters into Phylogenetic Analysis
AbstractPopular optimality criteria for phylogenetic trees focus on sequences of characters that are applicable to all the taxa. As studies grow in breadth, it can be the case that some characters are applicable for a portion of the taxa and inapplicable for others. Past work has explored the limitations of treating inapplicable characters as missing data, noting that this strategy may favor trees where internal nodes are assigned impossible states, where the arrangement of taxa within subclades is unduly influenced by variation in distant parts of the tree, and/or where taxa that otherwise share most primary characters ar...
Source: Systematic Biology - February 9, 2021 Category: Biology Source Type: research
Segmental Series and Size: Clade-Wide Investigation of Molar Proportions Reveals a Major Evolutionary Allometry in the Dentition of Placental Mammals
AbstractIterative segments such as teeth or limbs are a widespread characteristic of living organisms. While their proportions may be governed by similar developmental rules in vertebrates, there is no emerging pattern as regards their relation to size. Placental mammals span eight orders of magnitude in body size and show a wide spectrum of dietary habits associated with size and reflected in their dentitions, especially molars. Although variation in size constitutes an important determinant for variation in biological traits, few major allometric trends have been documented on placental molars so far. Molar proportions h...
Source: Systematic Biology - February 9, 2021 Category: Biology Source Type: research
Impact of Pleistocene Eustatic Fluctuations on Evolutionary Dynamics in Southeast Asian Biodiversity Hotspots
AbstractPleistocene climatic fluctuations (PCF) are frequently highlighted as important evolutionary engines that triggered cycles of biome expansion and contraction. Although there is ample evidence of the impact of PCF on biodiversity of continental biomes, the consequences in insular systems depend on the geology of the islands and the ecology of the taxa inhabiting them. The idiosyncratic aspects of insular systems are exemplified by the islands of the Sunda Shelf in Southeast Asia (Sundaland), where PCF-induced eustatic fluctuations had complex interactions with the geology of the region, resulting in high species div...
Source: Systematic Biology - February 9, 2021 Category: Biology Source Type: research
Phylogenomic Analysis of Ultraconserved Elements Resolves the Evolutionary and Biogeographic History of Segmented Trapdoor Spiders
AbstractThe segmented trapdoor spiders (Liphistiidae) are the sole surviving family of the suborder Mesothelae, which forms the sister lineage to all other living spiders. Liphistiids have retained a number of plesiomorphic traits and their present-day distribution is limited to East and Southeast Asia. Studying this group has the potential to shed light on the deep evolutionary history of spiders, but the phylogeny and divergence times of the family have not been resolved with confidence. We performed phylogenomic and molecular dating analyses of 2765 ultraconserved element loci from 185 liphistiid taxa. Our analyses show...
Source: Systematic Biology - February 8, 2021 Category: Biology Source Type: research
Integrating Sequence Capture and Restriction Site-Associated DNA Sequencing to Resolve Recent Radiations of Pelagic Seabirds
AbstractThe diversification of modern birds has been shaped by a number of radiations. Rapid diversification events make reconstructing the evolutionary relationships among taxa challenging due to the convoluted effects of incomplete lineage sorting (ILS) and introgression. Phylogenomic data sets have the potential to detect patterns of phylogenetic incongruence, and to address their causes. However, the footprints of ILS and introgression on sequence data can vary between different phylogenomic markers at different phylogenetic scales depending on factors such as their evolutionary rates or their selection pressures. We s...
Source: Systematic Biology - February 6, 2021 Category: Biology Source Type: research
