Paralogs and Off-Target Sequences Improve Phylogenetic Resolution in a Densely Sampled Study of the Breadfruit Genus (Artocarpus, Moraceae)
We present a 517-gene phylogenetic framework for the breadfruit genusArtocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. Although codon partitioning did not result in any substantial topological differences, the inclusion of flanking noncoding sequence in analyses significantly increased the resolution of gene trees. We also found th...
Source: Systematic Biology - September 24, 2020 Category: Biology Source Type: research
Inferring the Effect of Species Interactions on Trait Evolution
AbstractModels of trait evolution form an important part of macroevolutionary biology. The Brownian motion model and Ornstein –Uhlenbeck models have become classic (null) models of character evolution, in which species evolve independently. Recently, models incorporating species interactions have been developed, particularly involving competition where abiotic factors pull species toward an optimal trait value and compet itive interactions drive the trait values apart. However, these models assume a fitness function rather than derive it from population dynamics and they do not consider dynamics of the trait variance. He...
Source: Systematic Biology - September 22, 2020 Category: Biology Source Type: research
Phylogenomic Data Reveal Widespread Introgression Across the Range of an Alpine and Arctic Specialist
We present whole-genome sequence data for an avian species group with an alpine and arctic tundra distribution to examine the role that different population genetic processes have played in their evolutionary history. Rosy-finches inhabit high elevation mountaintop sky islands and high-latitude island and continental tundra. They exhibit extensive plumage variation coupled with low levels of genetic variation. Additionally, the number of species within the complex is debated, making them excellent for studying the forces involved in the process of diversification, as well as an important species group in which to investiga...
Source: Systematic Biology - September 17, 2020 Category: Biology Source Type: research
An Evolving View of Phylogenetic Support
AbstractIf all nucleotide sites evolved at the same rate within molecules and throughout the history of lineages, if all nucleotides were in equal proportion, if any nucleotide or amino acid evolved to any other with equal probability, if all taxa could be sampled, if diversification happened at well-spaced intervals, and if all gene segments had the same history, then tree building would be easy. But of course, none of those conditions are true. Hence, the need for evaluating the information content and accuracy of phylogenetic trees. The symposium for which this historical essay and presentation were developed focused on...
Source: Systematic Biology - September 11, 2020 Category: Biology Source Type: research
A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data
AbstractPhylogenomic and paleontological data constitute complementary resources for unraveling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthesizing approaches, including a remarkable fossil record that can be incorporated into explicit phylogenetic hypotheses. We revisit the phylogeny of crown group Echinoidea using a total-evidence dating approach that combines the largest phylogenomic data set for the clade, a large-scale morphological matrix with a de...
Source: Systematic Biology - September 3, 2020 Category: Biology Source Type: research
Is Sexual Conflict a Driver of Speciation? A Case Study With a Tribe of Brush-footed Butterflies
AbstractUnderstanding the evolutionary mechanisms governing the uneven distribution of species richness across the tree of life is a great challenge in biology. Scientists have long argued that sexual conflict is a key driver of speciation. This hypothesis, however, has been highly debated in light of empirical evidence. Recent advances in the study of macroevolution make it possible to test this hypothesis with more data and increased accuracy. In the present study, we use phylogenomics combined with four different diversification rate analytical approaches to test whether sexual conflict is a driver of speciation in brus...
Source: Systematic Biology - September 3, 2020 Category: Biology Source Type: research
The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous –Paleogene (K–Pg) Mass Extinction Event
AbstractThe consequences of the Cretaceous –Paleogene (K–Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes a...
Source: Systematic Biology - August 31, 2020 Category: Biology Source Type: research
Congruence and Conflict in the Higher-Level Phylogenetics of Squamate Reptiles: An Expanded Phylogenomic Perspective
AbstractGenome-scale data have the potential to clarify phylogenetic relationships across the tree of life but have also revealed extensive gene tree conflict. This seeming paradox, whereby larger data sets both increase statistical confidence and uncover significant discordance, suggests that understanding sources of conflict is important for accurate reconstruction of evolutionary history. We explore this paradox in squamate reptiles, the vertebrate clade comprising lizards, snakes, and amphisbaenians. We collected an average of 5103 loci for 91 species of squamates that span higher-level diversity within the clade, whic...
Source: Systematic Biology - August 28, 2020 Category: Biology Source Type: research
Modeling Phylogenetic Biome Shifts on a Planet with a Past
AbstractThe spatial distribution of biomes has changed considerably over deep time, so the geographical opportunity for an evolutionary lineage to shift into a new biome may depend on how the availability and connectivity of biomes has varied temporally. To better understand how lineages shift between biomes in space and time, we developed a phylogenetic biome shift model in which each lineage shifts between biomes and disperses between regions at rates that depend on the lineage ’s biome affinity and location relative to the spatial distribution of biomes at any given time. To study the behavior of the biome shift model...
Source: Systematic Biology - August 28, 2020 Category: Biology Source Type: research
Nothing Wrong with the Analysis of Clades in Comparative Evolutionary Studies: A Reply to Poe et al
AbstractIn a recent paper, Poe et al. assert that scientists should abandon clade-based approaches, particularly those using named taxonomic ranks. Poe et al. attempt to demonstrate that clade selection can have effects on the results of evolutionary analyses but unfortunately fall short of making any robust conclusions. Here, we demonstrate that the assertions made by Poe et al. have two important flaws: (i) an erroneous view of modern phylogenetic comparative methods; and (ii) a lack of statistical rigor in their analyses. We repeat Poe et al. ’s analysis but using appropriate phylogenetic comparative approaches. We de...
Source: Systematic Biology - August 26, 2020 Category: Biology Source Type: research
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Source: Systematic Biology - August 20, 2020 Category: Biology Source Type: research
Formal Links between Feature Diversity and Phylogenetic Diversity
AbstractThe extent to which phylogenetic diversity (PD) captures feature diversity (FD) is a topical and controversial question in biodiversity conservation. In this short paper, we formalize this question and establish a precise mathematical condition for FD (based on discrete characters) to coincide with PD. In this way, we make explicit the two main reasons why the two diversity measures might disagree for given data; namely, the presence of certain patterns of feature evolution and loss, and using temporal branch lengths for PD in settings that may not be appropriate (e.g., due to rapid evolution of certain features ov...
Source: Systematic Biology - August 14, 2020 Category: Biology Source Type: research
Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses?
AbstractAlignment is a crucial issue in molecular phylogenetics because different alignment methods can potentially yield very different topologies for individual genes. But it is unclear if the choice of alignment methods remains important in phylogenomic analyses, which incorporate data from hundreds or thousands of genes. For example, problematic biases in alignment might be multiplied across many loci, whereas alignment errors in individual genes might become irrelevant. The issue of alignment trimming (i.e., removing poorly aligned regions or missing data from individual genes) is also poorly explored. Here, we test t...
Source: Systematic Biology - August 14, 2020 Category: Biology Source Type: research
Phylogenomics of Piranhas and Pacus (Serrasalmidae) Uncovers How Dietary Convergence and Parallelism Obfuscate Traditional Morphological Taxonomy
AbstractThe Amazon and neighboring South American river basins harbor the world ’s most diverse assemblages of freshwater fishes. One of the most prominent South American fish families is the Serrasalmidae (pacus and piranhas), found in nearly every continental basin. Serrasalmids are keystone ecological taxa, being some of the top riverine predators as well as the primary se ed dispersers in the flooded forest. Despite their widespread occurrence and notable ecologies, serrasalmid evolutionary history and systematics are controversial. For example, the sister taxon to serrasalmids is contentious, the relationships of ma...
Source: Systematic Biology - August 12, 2020 Category: Biology Source Type: research
Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction
AbstractUltraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here, we characterized UCEs from 11 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated four different sets of UCE markers by ...
Source: Systematic Biology - August 4, 2020 Category: Biology Source Type: research
