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Considering decoupled phenotypic diversification between ontogenetic phases in macroevolution: An example using Triggerfishes (Balistidae) Syst. Biol. (IF 6.5) Pub Date : 2024-03-15 Alex Dornburg, Katerina L Zapfe, Rachel Williams, Michael E Alfaro, Richard Morris, Haruka Adachi, Joseph Flores, Francesco Santini, Thomas J Near, Bruno Frédérich
Across the Tree of Life, most studies of phenotypic disparity and diversification have been restricted to adult organisms. However, many lineages have distinct ontogenetic phases that differ from their adult forms in morphology and ecology. Focusing disproportionately on the evolution of adult forms unnecessarily hinders our understanding of the pressures shaping evolution over time. Non-adult disparity
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Distinguishing cophylogenetic signal from phylogenetic congruence clarifies the interplay between evolutionary history and species interactions Syst. Biol. (IF 6.5) Pub Date : 2024-03-12 Benoît Perez-Lamarque, Hélène Morlon
Interspecific interactions, including host-symbiont associations, can profoundly affect the evolution of the interacting species. Given the phylogenies of host and symbiont clades and knowledge of which host species interact with which symbiont, two questions are often asked: “Do closely related hosts interact with closely related symbionts?” and “Do host and symbiont phylogenies mirror one another
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Phylogenomics of Neogastropoda: the backbone hidden in the bush Syst. Biol. (IF 6.5) Pub Date : 2024-03-08 Alexander E Fedosov, Paul Zaharias, Thomas Lemarcis, Maria Vittoria Modica, Mandë Holford, Marco Oliverio, Yuri I Kantor, Nicolas Puillandre
The molluscan order Neogastropoda encompasses over 15,000 almost exclusively marine species playing important roles in benthic communities and in the economies of coastal countries. Neogastropoda underwent intensive cladogenesis in early stages of diversification, generating a ‘bush’ at the base of their evolutionary tree, that has been hard to resolve even with high throughput molecular data. In the
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Ecological predictors of organelle genome evolution: Phylogenetic correlations with taxonomically broad, sparse, unsystematized data Syst. Biol. (IF 6.5) Pub Date : 2024-03-06 Konstantinos Giannakis, Luke Richards, Iain G Johnston
Comparative analysis of variables across phylogenetically linked observations can reveal mechanisms and insights in evolutionary biology. As the taxonomic breadth of the sample of interest increases, challenges of data sparsity, poor phylogenetic resolution, and complicated evolutionary dynamics emerge. Here, we investigate a cross-eukaryotic question where all these problems exist: which organismal
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MAST: Phylogenetic Inference with Mixtures Across Sites and Trees Syst. Biol. (IF 6.5) Pub Date : 2024-02-27 Thomas K F Wong, Caitlin Cherryh, Allen G Rodrigo, Matthew W Hahn, Bui Quang Minh, Robert Lanfear
Hundreds or thousands of loci are now routinely used in modern phylogenomic studies. Concatenation approaches to tree inference assume that there is a single topology for the entire dataset, but different loci may have different evolutionary histories due to incomplete lineage sorting, introgression, and/or horizontal gene transfer; even single loci may not be treelike due to recombination. To overcome
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The Effect of Copy Number Hemiplasy on Gene Family Evolution Syst. Biol. (IF 6.5) Pub Date : 2024-02-08 Qiuyi Li, Yao-ban Chan, Nicolas Galtier, Celine Scornavacca
The evolution of gene families is complex, involving gene-level evolutionary events such as gene duplication, horizontal gene transfer, and gene loss (DTL), and other processes such as incomplete lineage sorting (ILS). Because of this, topological differences often exist between gene trees and species trees. A number of models have been recently developed to explain these discrepancies, the most realistic
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Dating in the Dark: Elevated Substitution Rates in Cave Cockroaches (Blattodea: Nocticolidae) Have Negative Impacts on Molecular Date Estimates Syst. Biol. (IF 6.5) Pub Date : 2024-02-06 Toby G L Kovacs, James Walker, Simon Hellemans, Thomas Bourguignon, Nikolai J Tatarnic, Jane M McRae, Simon Y W Ho, Nathan Lo
Rates of nucleotide substitution vary substantially across the Tree of Life, with potentially confounding effects on phylogenetic and evolutionary analyses. A large acceleration in mitochondrial substitution rate occurs in the cockroach family Nocticolidae, which predominantly inhabit subterranean environments. To evaluate the impacts of this among-lineage rate heterogeneity on estimates of phylogenetic
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The evolution of multiple colour mechanisms is correlated with diversification in sunbirds (Nectariniidae) Syst. Biol. (IF 6.5) Pub Date : 2024-01-30 Michaël P J Nicolaï, Bert Van Hecke, Svana Rogalla, Gerben Debruyn, Rauri C K Bowie, Nicholas J Matzke, S J Hackett, Liliana D’Alba, Matthew D Shawkey
How and why certain groups become speciose is a key question in evolutionary biology. Novel traits that enable diversification by opening new ecological niches are likely important mechanisms. However, ornamental traits can also promote diversification by opening up novel sensory niches and thereby creating novel inter-specific interactions. More specifically, ornamental colours may enable more precise
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Bayesian Phylogenetic Analysis on multi-core Compute Architectures: Implementation and evaluation of BEAGLE in RevBayes with MPI Syst. Biol. (IF 6.5) Pub Date : 2024-01-29 Killian Smith, Daniel Ayres, Rene Neumaier, Gert Worheide, Sebastian Hohna
Phylogenies are central to many research areas in biology and commonly estimated using likelihood based methods. Unfortunately, any likelihood based method, including Bayesian inference, can be restrictively slow for large datasets —with many taxa and/or many sites in the sequence alignment— or complex substitutions models. The primary limiting factor when using large datasets and/or complex models
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Tropical Origin, Global Diversification and Dispersal in the Pond Damselflies (Coenagrionoidea) Revealed by a New Molecular Phylogeny Syst. Biol. (IF 6.5) Pub Date : 2024-01-23 B Willink, J Ware, E I Svensson
The processes responsible for the formation of Earth’s most conspicuous diversity pattern, the latitudinal diversity gradient (LDG), remain unexplored for many clades in the Tree of Life. Here, we present a densely-sampled and dated molecular phylogeny for the most speciose clade of damselflies worldwide (Odonata: Coenagrionoidea), and investigate the role of time, macroevolutionary processes and biome-shift
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Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information Syst. Biol. (IF 6.5) Pub Date : 2024-01-15 Xiao-Xu Pang, Da-Yong Zhang
In recent years, the study of hybridization and introgression has made significant progress, with ghost introgression—the transfer of genetic material from extinct or unsampled lineages to extant species—emerging as a key area for research. Accurately identifying ghost introgression, however, presents a challenge. To address this issue, we focused on simple cases involving three species with a known
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Deep learning and likelihood approaches for viral phylogeography converge on the same answers whether the inference model is right or wrong Syst. Biol. (IF 6.5) Pub Date : 2024-01-08 Ammon Thompson, Benjamin Liebeskind, Erik J Scully, Michael Landis
Analysis of phylogenetic trees has become an essential tool in epidemiology. Likelihood-based methods fit models to phylogenies to draw inferences about the phylodynamics and history of viral transmission. How- ever, these methods are often computationally expensive, which limits the complexity and realism of phylodynamic models and makes them ill-suited for informing policy decisions in real-time
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Gene Flow and Isolation in the Arid Nearctic Revealed by Genomic Analyses of Desert Spiny Lizards Syst. Biol. (IF 6.5) Pub Date : 2024-01-05 Carlos J Pavón-Vázquez, Qaantah Rana, Keaka Farleigh, Erika Crispo, Mimi Zeng, Jeevanie Liliah, Daniel Mulcahy, Alfredo Ascanio, Tereza Jezkova, Adam D Leaché, Tomas Flouri, Ziheng Yang, Christopher Blair
The opposing forces of gene flow and isolation are two major processes shaping genetic diversity. Understanding how these vary across space and time is necessary to identify the environmental features that promote diversification. The detection of considerable geographic structure in taxa from the arid Nearctic has prompted research into the drivers of isolation in the region. Several geographic features
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Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A museomic case study from the Andean flora Syst. Biol. (IF 6.5) Pub Date : 2024-01-03 Laura Frost, Ana M Bedoya, Laura Lagomarsino
The Andes mountains of western South America are a globally important biodiversity hotspot, yet there is a paucity of resolved phylogenies for plant clades from this region. Filling an important gap to our understanding of the World’s richest flora, we present the first phylogeny of Freziera (Pentaphylacaceae), an Andean-centered, cloud forest radiation. Our dataset was obtained via yrid-enriched target
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Phylogenetic conflict between species tree and maternally inherited gene trees in a clade of Emberiza buntings (Aves: Emberizidae) Syst. Biol. (IF 6.5) Pub Date : 2023-12-29 Dezhi Zhang, Huishang She, Shangyu Wang, Haitao Wang, Shi Li, Yalin Cheng, Gang Song, Chenxi Jia, Yanhua Qu, Frank E Rheindt, Urban Olsson, Per Alström, Fumin Lei
Different genomic regions may reflect conflicting phylogenetic topologies primarily due to incomplete lineage sorting and/or gene flow. Genomic data are necessary to reconstruct the true species tree and explore potential causes of phylogenetic conflict. Here, we investigate the phylogenetic relationships of four Emberiza species (Aves: Emberizidae) and discuss the potential causes of the observed
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The limits of the constant-rate birth-death prior for phylogenetic tree topology inference Syst. Biol. (IF 6.5) Pub Date : 2023-12-28 Mark P Khurana, Neil Scheidwasser-Clow, Matthew J Penn, Samir Bhatt, David A Duchêne
Birth-death models are stochastic processes describing speciation and extinction through time and across taxa, and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under the constant-rate birth-death (crBD) model tend to differ from empirical trees, for example with respect to the amount of phylogenetic imbalance. However
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Alpine Extremophytes in Evolutionary Turmoil: Complex Diversification Patterns and Demographic Responses of a Halophilic Grass in a Central Asian Biodiversity Hotspot Syst. Biol. (IF 6.5) Pub Date : 2023-12-23 Anna Wróbel, Ewelina Klichowska, Arkadiusz Nowak, Marcin Nobis
Diversification and demographic responses are key processes shaping species evolutionary history. Yet we still lack a full understanding of ecological mechanisms that shape genetic diversity at different spatial scales upon rapid environmental changes. In this study, we examined genetic differentiation in an extremophilic grass Puccinellia pamirica and factors affecting its population dynamics among
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Fast Bayesian inference of phylogenies from multiple continuous characters Syst. Biol. (IF 6.5) Pub Date : 2023-12-12 Rong Zhang, Alexei J Drummond, Fábio K Mendes
Time-scaled phylogenetic trees are an ultimate goal of evolutionary biology and a necessary ingredient in comparative studies. The accumulation of genomic data has resolved the tree of life to a great extent, yet timing evolutionary events remains challenging if not impossible without external information such as fossil ages and morphological characters. Methods for incorporating morphology in tree
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Bayesian total-evidence dating revisits sloth phylogeny and biogeography: a cautionary tale on morphological clock analyses Syst. Biol. (IF 6.5) Pub Date : 2023-12-02 Julia V Tejada, Pierre-Olivier Antoine, Philippe Münch, Guillaume Billet, Lionel Hautier, Frédéric Delsuc, Fabien L Condamine
Combining morphological and molecular characters through Bayesian total-evidence dating allows inferring the phylogenetic and timescale framework of both extant and fossil taxa, while accounting for the stochasticity and incompleteness of the fossil record. Such an integrative approach is particularly needed when dealing with clades such as sloths (Mammalia: Folivora), for which developmental and biomechanical
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Robust phylogenetic regression Syst. Biol. (IF 6.5) Pub Date : 2023-12-01 Richard Adams, Zoe Cain, Raquel Assis, Michael DeGiorgio
Modern comparative biology owes much to phylogenetic regression. At its conception, this technique sparked a revolution that armed biologists with phylogenetic comparative methods (PCMs) for disentangling evolutionary correlations from those arising from hierarchical phylogenetic relationships. Over the past few decades, the phylogenetic regression framework has become a paradigm of modern comparative
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DNA sequences from type specimens and type strains – how to increase their number and improve their annotation in NCBI GenBank and related databases Syst. Biol. (IF 6.5) Pub Date : 2023-11-13 Susanne S Renner, Mark D Scherz, Conrad L Schoch, Marc Gottschling, Miguel Vences
Scientific names permit humans and search engines to access knowledge about the biodiversity that surrounds us, and names linked to DNA sequences are playing an ever-greater role in search-and-match identification procedures. Here, we analyze how users and curators of the National Center for Biotechnology Information (NCBI) are flagging and curating sequences derived from nomenclatural type material
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Reference genome choice and filtering thresholds jointly influence phylogenomic analyses Syst. Biol. (IF 6.5) Pub Date : 2023-10-26 Jessica A Rick, Chad D Brock, Alexander L Lewanski, Jimena Golcher-Benavides, Catherine E Wagner
Molecular phylogenies are a cornerstone of modern comparative biology and are commonly employed to investigate a range of biological phenomena, such as diversification rates, patterns in trait evolution, biogeography, and community assembly. Recent work has demonstrated that significant biases may be introduced into downstream phylogenetic analyses from processing genomic data; however, it remains
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River drainage reorganization and reticulate evolution in the Two-Lined Salamander (Eurycea bislineata) species complex. Syst. Biol. (IF 6.5) Pub Date : 2023-10-25 Todd W Pierson,Kenneth H Kozak,Travis C Glenn,Benjamin M Fitzpatrick
The origin and eventual loss of biogeographic barriers can create alternating periods of allopatry and secondary contact, facilitating gene flow among distinct metapopulations and generating reticulate evolutionary histories that are not adequately described by a bifurcating evolutionary tree. One such example may exist in the two-lined salamander (Eurycea bislineata) species complex, where discordance
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Gene Transfer-based Phylogenetics: Analytical Expressions and Additivity via Birth–Death Theory Syst. Biol. (IF 6.5) Pub Date : 2023-10-20 Guy Katriel, Udi Mahanaymi, Shelly Brezner, Noor Kezel, Christoph Koutschan, Doron Zeilberger, Mike Steel, Sagi Snir
The genomic era has opened up vast opportunities in molecular systematics, one of which is deciphering the evolutionary history in fine detail. Under this mass of data, analyzing the point mutations of standard markers is often too crude and slow for fine-scale phylogenetics. Nevertheless, genome dynamics (GD) events provide alternative, often richer information. The synteny index (SI) between a pair
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Is Over-parameterization a Problem for Profile Mixture Models? Syst. Biol. (IF 6.5) Pub Date : 2023-10-16 Hector Baños, Edward Susko, Andrew J Roger
Biochemical constraints on the admissible amino acids at specific sites in proteins lead to heterogeneity of the amino acid substitution process over sites in alignments. It is well known that phylogenetic models of protein sequence evolution that do not account for site heterogeneity are prone to long-branch attraction (LBA) artifacts. Profile mixture models were developed to model heterogeneity of
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Introgression underlies phylogenetic uncertainty but not parallel plumage evolution in a recent songbird radiation Syst. Biol. (IF 6.5) Pub Date : 2023-10-06 Loïs Rancilhac, Erik D Enbody, Rebecca Harris, Takema Saitoh, Martin Irestedt, Yang Liu, Fumin Lei, Leif Andersson, Per Alström
Instances of parallel phenotypic evolution offer great opportunities to understand the evolutionary processes underlying phenotypic changes. However, confirming parallel phenotypic evolution and studying its causes requires a robust phylogenetic framework. One such example is the “black-and-white wagtails”, a group of five species in the songbird genus Motacilla: one species, Motacilla alba, shows
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Geogenomic predictors of genetree heterogeneity explain phylogeographic and introgression history: a case study in an Amazonian bird (Thamnophilus aethiops) Syst. Biol. (IF 6.5) Pub Date : 2023-10-04 Lukas J Musher, Glaucia Del-Rio, Rafael S Marcondes, Robb T Brumfield, Gustavo A Bravo, Gregory Thom
Can knowledge about genome architecture inform biogeographic and phylogenetic inference? Selection, drift, recombination, and gene flow interact to produce a genomic landscape of divergence wherein patterns of differentiation and genealogy vary nonrandomly across the genomes of diverging populations. For instance, genealogical patterns that arise due to gene flow should be more likely to occur on smaller
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Cophylogeny Reconstruction Allowing for Multiple Associations Through Approximate Bayesian Computation Syst. Biol. (IF 6.5) Pub Date : 2023-09-13 Blerina Sinaimeri, Laura Urbini, Marie-France Sagot, Catherine Matias
Phylogenetic tree reconciliation is extensively employed for the examination of coevolution between host and symbiont species. An important concern is the requirement for dependable cost values when selecting event-based parsimonious reconciliation. Although certain approaches deduce event probabilities unique to each pair of host and symbiont trees, which can subsequently be converted into cost values
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Fast and Accurate Maximum-Likelihood Estimation of Multi-Type Birth-Death Epidemiological Models from Phylogenetic Trees Syst. Biol. (IF 6.5) Pub Date : 2023-09-11 Anna Zhukova, Frédéric Hecht, Yvon Maday, Olivier Gascuel
Multi-type birth-death (MTBD) models are phylodynamic analogies of compartmental models in classical epidemiology. They serve to infer such epidemiological parameters as the average number of secondary infections Re and the infectious time from a phylogenetic tree (a genealogy of pathogen sequences). The representatives of this model family focus on various aspects of pathogen epidemics. For instance
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Skyline fossilized birth-death model is robust to violations of sampling assumptions in total-evidence dating Syst. Biol. (IF 6.5) Pub Date : 2023-08-22 Chi Zhang, Fredrik Ronquist, Tanja Stadler
Several total-evidence dating studies under the fossilized birth-death (FBD) model have produced very old age estimates, which are not supported by the fossil record. This phenomenon has been termed “deep root attraction (DRA)”. For two specific data sets, involving divergence time estimation for the early radiations of ants, bees and wasps (Hymenoptera) and of placental mammals (Eutheria), it has
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The Cauchy Process on Phylogenies: a Tractable Model for Pulsed Evolution Syst. Biol. (IF 6.5) Pub Date : 2023-08-21 Paul Bastide, Gilles Didier
Phylogenetic comparative methods use random processes, such as the Brownian Motion, to model the evolution of continuous traits on phylogenetic trees. Growing evidence for non-gradual evolution motivated the development of complex models, often based on Lévy processes. However, their statistical inference is computationally intensive, and currently relies on approximations, high dimensional sampling
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How important is budding speciation for comparative studies? Syst. Biol. (IF 6.5) Pub Date : 2023-08-16 Daniel S Caetano, Tiago Bosisio Quental
The acknowledgment of evolutionary dependence among species has fundamentally changed how we ask biological questions. Phylogenetic models became the standard approach for studies with three or more lineages, in particular those using extant species. Most phylogenetic comparative methods (PCMs) translate relatedness into covariance, meaning that evolutionary changes before lineages split should be
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Multiple Routes to Color Convergence in a Radiation of Neotropical Poison Frogs Syst. Biol. (IF 6.5) Pub Date : 2023-08-09 Evan Twomey, Paulo Melo-Sampaio, Lisa M Schulte, Franky Bossuyt, Jason L Brown, Santiago Castroviejo-Fisher
Convergent evolution is defined as the independent evolution of similar phenotypes in different lineages. Its existence underscores the importance of external selection pressures in evolutionary history, revealing how functionally similar adaptations can evolve in response to persistent ecological challenges through a diversity of evolutionary routes. However, many examples of convergence, particularly
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Robustness of Felsenstein’s versus Transfer Bootstrap Supports with respect to Taxon Sampling Syst. Biol. (IF 6.5) Pub Date : 2023-08-09 Paul Zaharias, Frédéric Lemoine, Olivier Gascuel
The bootstrap method is based on resampling sequence alignments and re-estimating trees. Felsenstein’s bootstrap proportions (FBP) is the most common approach to assess the reliability and robustness of sequence-based phylogenies. However, when increasing taxon sampling (i.e., the number of sequences) to hundreds or thousands of taxa, FBP tends to return low supports for deep branches. The Transfer
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Deep Learning from Phylogenies for Diversification Analyses Syst. Biol. (IF 6.5) Pub Date : 2023-08-09 Sophia Lambert, Jakub Voznica, Hélène Morlon
Birth-death models are widely used in combination with species phylogenies to study past diversification dynamics. Current inference approaches typically rely on likelihood-based methods. These methods are not generalizable, as a new likelihood formula must be established each time a new model is proposed; for some models such formula is not even tractable. Deep learning can bring solutions in such
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Speciation-by-Extinction Syst. Biol. (IF 6.5) Pub Date : 2023-08-05 Glenn F Seeholzer, Robb T Brumfield
Extinction is a dominant force shaping patterns of biodiversity through time; however its role as a catalyst of speciation through its interaction with intraspecific variation has been overlooked. Here, we synthesize ideas alluded to by Darwin and others into the model of ‘speciation-by-extinction’ in which speciation results from the extinction of intermediate populations within a single geographically
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Burma Terrane Amber Fauna Shows Connections to Gondwana and Transported Gondwanan Lineages to the Northern Hemisphere (Araneae: Palpimanoidea) Syst. Biol. (IF 6.5) Pub Date : 2023-08-01 Hannah M Wood, Jörg Wunderlich
Burmese amber is a significant source of fossils that documents the mid-Cretaceous biota. This deposit was formed around 99 Ma on the Burma Terrane, which broke away from Gondwana and later collided with Asia, although the timing is disputed. Palpimanoidea is a dispersal-limited group that was a dominant element of the Mesozoic spider fauna, and has an extensive fossil record, particularly from Burmese
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Populating a Continent: Phylogenomics Reveal the Timing of Australian Frog Diversification Syst. Biol. (IF 6.5) Pub Date : 2023-08-01 Ian G Brennan, Alan R Lemmon, Emily Moriarty Lemmon, Conrad J Hoskin, Stephen C Donnellan, J Scott Keogh
The Australian continent’s size and isolation make it an ideal place for studying the accumulation and evolution of biodiversity. Long separated from the ancient supercontinent Gondwana, most of Australia’s plants and animals are unique and endemic, including the continent’s frogs. Australian frogs comprise a remarkable ecological and morphological diversity categorized into a small number of distantly
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Online tree expansion could help solve the problem of scalability in Bayesian phylogenetics Syst. Biol. (IF 6.5) Pub Date : 2023-07-27 Jakub Truszkowski, Allison Perrigo, David Broman, Fredrik Ronquist, Alexandre Antonelli
Bayesian phylogenetics is now facing a critical point. Over the last 20 years, Bayesian methods have reshaped phylogenetic inference and gained widespread popularity due to their high accuracy, the ability to quantify the uncertainty of inferences and the possibility of accommodating multiple aspects of evolutionary processes in the models that are used. Unfortunately, Bayesian methods are computationally
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The Artefactual Branch Effect and Phylogenetic Conflict: Species Delimitation with Gene Flow in Mangrove Pit Vipers (Trimeresurus purpureomaculatus-erythrurus complex) Syst. Biol. (IF 6.5) Pub Date : 2023-07-21 Kin Onn Chan, Daniel G Mulcahy, Shahrul Anuar
Mangrove pit vipers of the Trimeresurus purpureomaculatus-erythrurus complex are the only species of viper known to inhabit mangroves. Despite serving integral ecological functions in mangrove ecosystems, the evolutionary history, distribution, and species boundaries of mangrove pit vipers remain poorly understood, partly due to overlapping distributions, confusing phenotypic variations, and the lack
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The non-dereliction in evolution: Trophic specialisation drives convergence in the radiation of red devil spiders (Araneae: Dysderidae) in the Canary Islands Syst. Biol. (IF 6.5) Pub Date : 2023-07-19 Adrià Bellvert, Silvia Adrián-Serrano, Nuria Macías-Hernández, Søren Toft, Antigoni Kaliontzopoulou, Miquel A Arnedo
Natural selection plays a key role in deterministic evolution, as clearly illustrated by the multiple cases of repeated evolution of ecomorphological characters observed in adaptive radiations. Unlike most spiders, Dysdera species display a high variability of cheliceral morphologies, which has been suggested to reflect different levels of specialisation to feed on isopods. In this study, we integrate
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Scalable Bayesian divergence time estimation with ratio transformations Syst. Biol. (IF 6.5) Pub Date : 2023-07-17 Xiang Ji, Alexander A Fisher, Shuo Su, Jeffrey L Thorne, Barney Potter, Philippe Lemey, Guy Baele, Marc A Suchard
Divergence time estimation is crucial to provide temporal signals for dating biologically important events, from species divergence to viral transmissions in space and time. With the advent of high-throughput sequencing, recent Bayesian phylogenetic studies have analyzed hundreds to thousands of sequences. Such large-scale analyses challenge divergence time reconstruction by requiring inference on
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Espalier: Efficient tree reconciliation and ARG reconstruction using maximum agreement forests Syst. Biol. (IF 6.5) Pub Date : 2023-07-17 David A Rasmussen, Fangfang Guo
In the presence of recombination individuals may inherit different regions of their genome from different ancestors, resulting in a mosaic of phylogenetic histories across their genome. Ancestral recombination graphs (ARGs) can capture how phylogenetic relationships vary across the genome due to recombination, but reconstructing ARGs from genomic sequence data is notoriously difficult. Here we present
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Nucleotide Substitution Model Selection is not Necessary for Bayesian Inference of Phylogeny with Well Behaved Priors Syst. Biol. (IF 6.5) Pub Date : 2023-07-17 Luiza Guimarães Fabreti, Sebastian Höhna
Model selection aims to choose the most adequate model for the statistical analysis at hand. The model must be complex enough to capture the complexity of the data but should be simple enough not to overfit. In phylogenetics, the most common model selection scenario concerns selecting an adequate substitution and partition model for sequence evolution to infer a phylogenetic tree. Previously, several
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Phylogenomics reveals patterns ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives Syst. Biol. (IF 6.5) Pub Date : 2023-07-13 Brian J Sanderson, Diksha Ghambir, Guanqiao Feng, Nan Hu, Quentin C Cronk, Diana M Percy, Francisco Molina Freaner, Matthew G Johnson, Lawrence B Smart, Ken Keefover-Ring, Tongming Yin, Tao Ma, Stephen P DiFazio, Jianquan Liu, Matthew S Olson
Despite the economic, ecological, and scientific importance of the genera Salix L. (willows) and Populus L. (poplars, cottonwoods, and aspens) Salicaceae, we know little about the sources of differences in species diversity between the genera and of the phylogenetic conflict that often confounds estimating phylogenetic trees. Salix subgenera and sections, in particular, have been difficult to classify
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DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies. Syst. Biol. (IF 6.5) Pub Date : 2023-11-01 Paschalia Kapli,Ioanna Kotari,Maximilian J Telford,Nick Goldman,Ziheng Yang
Inference of deep phylogenies has almost exclusively used protein rather than DNA sequences based on the perception that protein sequences are less prone to homoplasy and saturation or to issues of compositional heterogeneity than DNA sequences. Here, we analyze a model of codon evolution under an idealized genetic code and demonstrate that those perceptions may be misconceptions. We conduct a simulation
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Resolving marine–freshwater transitions by diatoms through a fog of gene tree discordance Syst. Biol. (IF 6.5) Pub Date : 2023-06-17 Wade R Roberts, Elizabeth C Ruck, Kala M Downey, Eveline Pinseel, Andrew J Alverson
Despite the obstacles facing marine colonists, most lineages of aquatic organisms have colonized and diversified in freshwaters repeatedly. These transitions can trigger rapid morphological or physiological change and, on longer timescales, lead to increased rates of speciation and extinction. Diatoms are a lineage of ancestrally marine microalgae that have diversified throughout freshwater habitats
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Correction to: Modeling phylogenetic biome shifts on a planet with a past. Syst. Biol. (IF 6.5) Pub Date : 2023-11-01
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A k-mer-Based Approach for Phylogenetic Classification of Taxa in Environmental Genomic Data. Syst. Biol. (IF 6.5) Pub Date : 2023-11-01 Julia Van Etten,Timothy G Stephens,Debashish Bhattacharya
In the age of genome sequencing, whole-genome data is readily and frequently generated, leading to a wealth of new information that can be used to advance various fields of research. New approaches, such as alignment-free phylogenetic methods that utilize k-mer-based distance scoring, are becoming increasingly popular given their ability to rapidly generate phylogenetic information from whole-genome
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Speciation in Coastal Basins Driven by Staggered Headwater Captures: Dispersal of a Species Complex, Leporinus bahiensis, as Revealed by Genome-wide SNP Data Syst. Biol. (IF 6.5) Pub Date : 2023-05-31 Jorge L Ramirez, Carolina B Machado, Paulo Roberto Antunes de Mello Affonso, Pedro M Galetti
Past sea level changes and geological instability along watershed boundaries have largely influenced fish distribution across coastal basins, either by dispersal via palaeodrainages now submerged or by headwater captures, respectively. Accordingly, the South American Atlantic coast encompasses several small and isolated drainages that share a similar species composition, representing a suitable model
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PhyloCoalSimulations: A simulator for network multispecies coalescent models, including a new extension for the inheritance of gene flow Syst. Biol. (IF 6.5) Pub Date : 2023-05-31 John Fogg, Elizabeth S Allman, Cécile Ané
We consider the evolution of phylogenetic gene trees along phylogenetic species networks, according to the network multispecies coalescent process, and introduce a new network coalescent model with correlated inheritance of gene flow. This model generalizes two traditional versions of the network coalescent: with independent or common inheritance. At each reticulation, multiple lineages of a given
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Inferring historical introgression with deep learning Syst. Biol. (IF 6.5) Pub Date : 2023-05-31 Yubo Zhang, Qingjie Zhu, Yi Shao, Yanchen Jiang, Yidan Ouyang, Li Zhang, Wei Zhang
Resolving phylogenetic relationships among taxa remains a challenge in the era of big data due to the presence of genetic admixture in a wide range of organisms. Rapidly developing sequencing technologies and statistical tests enable evolutionary relationships to be disentangled at a genome-wide level, yet many of these tests are computationally intensive and rely on phased genotypes, large sample
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Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Implementations Syst. Biol. (IF 6.5) Pub Date : 2023-05-26 Alexander M Kramer, Bryan Thornlow, Cheng Ye, Nicola De Maio, Jakob McBroome, Angie S Hinrichs, Robert Lanfear, Yatish Turakhia, Russell Corbett-Detig
Phylogenetics has been foundational to SARS-CoV-2 research and public health policy, assisting in genomic surveillance, contact tracing, and assessing emergence and spread of new variants. However, phylogenetic analyses of SARS-CoV-2 have often relied on tools designed for de novo phylogenetic inference, in which all data are collected before any analysis is performed and the phylogeny is inferred
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A Cautionary Note on “A Cautionary Note on the Use of Ornstein Uhlenbeck Models in Macroevolutionary Studies” Syst. Biol. (IF 6.5) Pub Date : 2023-05-25 Mark Grabowski, Jason Pienaar, Kjetil L Voje, Staffan Andersson, Jesualdo Fuentes-González, Bjørn T Kopperud, Daniel S Moen, Masahito Tsuboi, Josef Uyeda, Thomas F Hansen
Models based on the Ornstein–Uhlenbeck process have become standard for the comparative study of adaptation. Cooper et al. (2016) have cast doubt on this practice by claiming statistical problems with fitting Ornstein–Uhlenbeck models to comparative data. Specifically, they claim that statistical tests of Brownian motion may have too high Type I error rates and that such error rates are exacerbated
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PARNAS: Objectively Selecting the Most Representative Taxa on a Phylogeny Syst. Biol. (IF 6.5) Pub Date : 2023-05-20 Alexey Markin, Sanket Wagle, Siddhant Grover, Amy L Vincent Baker, Oliver Eulenstein, Tavis K Anderson
The use of next-generation sequencing technology has enabled phylogenetic studies with hundreds of thousands of taxa. Such large-scale phylogenies have become a critical component in genomic epidemiology in pathogens such as SARS-CoV-2 and influenza A virus. However, detailed phenotypic characterization of pathogens or generating a computationally tractable dataset for detailed phylogenetic analyses
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Increasing Information Content and Diagnosability in Family-Level Classifications Syst. Biol. (IF 6.5) Pub Date : 2023-05-11 Matjaž Kuntner, Klemen Čandek, Matjaž Gregorič, Eva Turk, Chris A Hamilton, Lisa Chamberland, James Starrett, Ren-Chung Cheng, Jonathan A Coddington, Ingi Agnarsson, Jason E Bond
Higher-level classifications often must account for monotypic taxa representing depauperate evolutionary lineages and lacking synapomorphies of their better-known, well-defined sister clades. In a ranked (Linnean) or unranked (phylogenetic) classification system, discovering such a depauperate taxon does not necessarily invalidate the rank classification of sister clades. Named higher taxa must be
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The ClaDS rate-heterogeneous birth-death prior for full phylogenetic inference in BEAST2 Syst. Biol. (IF 6.5) Pub Date : 2023-05-11 Joëlle Barido-Sottani, Hélène Morlon
Bayesian phylogenetic inference requires a tree prior, which models the underlying diversification process which gives rise to the phylogeny. Existing birth-death diversification models include a wide range of features, for instance lineage-specific variations in speciation and extinction rates. While across-lineage variation in speciation and extinction rates is widespread in empirical datasets, few
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Phylogenomic Analyses Reveal an Allopolyploid Origin of Core Didymocarpinae (Gesneriaceae) Followed by Rapid Radiation Syst. Biol. (IF 6.5) Pub Date : 2023-05-11 Lihua Yang, A J Harris, Fang Wen, Zheng Li, Chao Feng, Hanghui Kong, Ming Kang
Allopolyploid plants have long been regarded as possessing genetic advantages under certain circumstances due to the combined effects of their hybrid origins and duplicated genomes. However, the evolutionary consequences of allopolyploidy in lineage diversification remain to be fully understood. Here, we investigate the evolutionary consequences of allopolyploidy using 138 transcriptomic sequences
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Hybridization and Transgressive Evolution Generate Diversity in an Adaptive Radiation of Anolis Lizards Syst. Biol. (IF 6.5) Pub Date : 2023-04-25 Guinevere O U Wogan, Michael L Yuan, D Luke Mahler, Ian J Wang
Interspecific hybridization may act as a major force contributing to the evolution of biodiversity. Although generally thought to reduce or constrain divergence between two species, hybridization can, paradoxically, promote divergence by increasing genetic variation or providing novel combinations of alleles that selection can act upon to move lineages toward new adaptive peaks. Hybridization may,
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Complex Patterns of Diversification in the Gray Zone of Speciation: Model-Based Approaches Applied to Patagonian Liolaemid Lizards (Squamata: Liolaemus kingii clade) Syst. Biol. (IF 6.5) Pub Date : 2023-04-25 Kevin I Sánchez, Emilce G Diaz Huesa, María F Breitman, Luciano J Avila, Jack W Sites Jr., Mariana Morando
In this study we detangled the evolutionary history of the Patagonian lizard clade Liolaemus kingii, coupling dense geographic sampling and novel computational analytical approaches. We analyzed nuclear and mitochondrial data (restriction site-associated DNA sequencing and cytochrome b) to hypothesize and evaluate species limits, phylogenetic relationships, and demographic histories. We complemented