journal
https://read.qxmd.com/read/33169797/the-perfect-storm-gene-tree-estimation-error-incomplete-lineage-sorting-and-ancient-gene-flow-explain-the-most-recalcitrant-ancient-angiosperm-clade-malpighiales
#1
Liming Cai, Zhenxiang Xi, Emily Moriarty Lemmon, Alan R Lemmon, Austin Mast, Christopher E Buddenhagen, Liang Liu, Charles C Davis
The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent (MSC) model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci from 64 taxa representing 39 families to infer the species tree of the flowering plant order Malpighiales...
November 10, 2020: Systematic Biology
https://read.qxmd.com/read/33169795/the-multilocus-multispecies-coalescent-a-flexible-new-model-of-gene-family-evolution
#2
Qiuyi Li, Celine Scornavacca, Nicolas Galtier, Yao-Ban Chan
Incomplete lineage sorting (ILS), the interaction between coalescence and speciation, can generate incongruence between gene trees and species trees, as can gene duplication (D), transfer (T) and loss (L). These processes are usually modelled independently, but in reality, ILS can affect gene copy number polymorphism, i.e., interfere with DTL. This has been previously recognised, but not treated in a satisfactory way, mainly because DTL events are naturally modelled forward-in-time, while ILS is naturally modelled backwards-in-time with the coalescent...
November 10, 2020: Systematic Biology
https://read.qxmd.com/read/33104202/do-meristic-characters-used-in-phylogenetic-analysis-evolve-in-an-ordered-manner
#3
Neil Brocklehurst, Yara Haridy
The use of ordered characters in phylogenetic analysis has been inconsistent throughout the history of phylogenetic inference. It has become more widespread in recent years, and some have advocated that all characters representing continuous or meristic traits should be ordered as a matter of course. Here, using the example of dental evolution, we examine two factors that may impact on whether meristic characters actually evolve in an ordered manner: the regulatory hierarchy governing the development of teeth that allows large sections of the entire tooth-row to be supressed in a single transition, and regionalisation of the tooth row where different modules have a degree of independence in their evolution...
October 26, 2020: Systematic Biology
https://read.qxmd.com/read/33084875/a-cautionary-note-on-the-use-of-genotype-callers-in-phylogenomics
#4
Pablo Duchen, Nicolas Salamin
Next-generation-sequencing genotype callers are commonly used in studies to call variants from newly-sequenced species. However, due to the current availability of genomic resources, it is still common practice to use only one reference genome for a given genus, or even one reference for an entire clade of a higher taxon. The problem with traditional genotype callers, such as the one from GATK, is that they are optimized for variant calling at the population level. However, when these callers are used at the phylogenetic level, the consequences for downstream analyses can be substantial...
October 21, 2020: Systematic Biology
https://read.qxmd.com/read/33057723/the-phylogeny-and-evolution-of-the-flashiest-of-the-armored-harvestmen-arachnida-opiliones
#5
Ligia R Benavides, Ricardo Pinto-da-Rocha, Gonzalo Giribet
Gonyleptoidea, largely restricted to the Neotropics, constitutes the most diverse superfamily of Opiliones and includes the largest and flashiest representatives of this arachnid order. However, the relationships among its main lineages (families and superfamilies) and the timing of their origin are not sufficiently understood to explain how this tropical clade has been able to colonize the temperate zone. Here we used transcriptomics and divergence time dating to investigate the phylogeny of Gonyleptoidea...
October 15, 2020: Systematic Biology
https://read.qxmd.com/read/33057686/parallel-ddrad-and-genome-skimming-analyses-reveal-a-radiative-and-reticulate-evolutionary-history-of-the-temperate-bamboos
#6
Cen Guo, Peng-Fei Ma, Guo-Qian Yang, Xia-Ying Ye, Ying Guo, Jing-Xia Liu, Yun-Long Liu, Deren A R Eaton, Zhen-Hua Guo, De-Zhu Li
Rapid evolutionary radiations are among the most challenging phylogenetic problems, wherein different types of data (e.g., morphology, molecular) or genetic markers (e.g., nuclear, organelle) often yield inconsistent results. The tribe Arundinarieae i.e., the temperate bamboos, is a clade of tetraploid originated 22 million years ago and subsequently radiated in East Asia. Previous studies of Arundinarieae have found conflicting relationships and/or low support. Here, we obtain nuclear markers from ddRAD data for 213 Arundinarieae taxa and parallel sampling of chloroplast genomes from genome-skimming for 147 taxa...
October 15, 2020: Systematic Biology
https://read.qxmd.com/read/33057674/mind-the-outgroup-and-bare-branches-in-total-evidence-dating-a-case-study-of-pimpliform-darwin-wasps-hymenoptera-ichneumonidae
#7
Tamara Spasojevic, Gavin R Broad, Ilari E Sääksjärvi, Martin Schwarz, Masato Ito, Stanislav Korenko, Seraina Klopfstein
Taxon sampling is a central aspect of phylogenetic study design, but it has received limited attention in the context of total-evidence dating, a widely used dating approach that directly integrates molecular and morphological information from extant and fossil taxa. We here assess the impact of commonly employed outgroup sampling schemes and missing morphological data in extant taxa on age estimates in a total-evidence dating analysis under the uniform tree prior. Our study group is Pimpliformes, a highly diverse, rapidly radiating group of parasitoid wasps of the family Ichneumonidae...
October 15, 2020: Systematic Biology
https://read.qxmd.com/read/32979270/phylogenomics-of-parasitic-and-non-parasitic-lice-insecta-psocodea-combining-sequence-data-and-exploring-compositional-bias-solutions-in-next-generation-datasets
#8
Robert S de Moya, Kazunori Yoshizawa, Kimberly K O Walden, Andrew D Sweet, Christopher H Dietrich, Kevin P Johnson
The insect order Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and non-parasitic members (Psocoptera). The extreme age and ecological diversity of the group may be associated with major genomic changes, such as base compositional biases expected to affect phylogenetic inference. Divergent morphology between parasitic and non-parasitic members has also obscured the origins of parasitism within the order. We conducted a phylogenomic analysis on the order Psocodea utilizing both transcriptome and genome sequencing to obtain a data set of 2,370 orthologous genes...
September 26, 2020: Systematic Biology
https://read.qxmd.com/read/32979264/the-origins-of-coca-museum-genomics-reveals-multiple-independent-domestications-from-progenitor-erythroxylum-gracilipes
#9
Dawson M White, Jen-Pan Huang, Orlando Adolfo Jara-Muñoz, Santiago Madriñán, Richard H Ree, Roberta J Mason-Gamer
Coca is the natural source of cocaine as well as a sacred and medicinal plant farmed by South American Amerindians and mestizos. The coca crop comprises four closely related varieties classified into two species (Amazonian and Huánuco varieties within Erythroxylum coca Lam., and Colombian and Trujillo varieties within E. novogranatense (D.Morris) Hieron.) but our understanding of the domestication and evolutionary history of these taxa is nominal. In this study we use genomic data from natural history collections to estimate the geographic origins and genetic diversity of this economically and culturally important crop in the context of its wild relatives...
September 26, 2020: Systematic Biology
https://read.qxmd.com/read/32970819/paralogs-and-off-target-sequences-improve-phylogenetic-resolution-in-a-densely-sampled-study-of-the-breadfruit-genus-artocarpus-moraceae
#10
Elliot M Gardner, Matthew G Johnson, Joan T Pereira, Aida Shafreena Ahmad Puad, Deby Arifiani, Norman J Wickett, Nyree J C Zerega
We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (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. While codon partitioning did not result in any substantial topological differences, the inclusion of flanking non-coding sequence in analyses significantly increased the resolution of gene trees...
September 24, 2020: Systematic Biology
https://read.qxmd.com/read/32960972/inferring-the-effect-of-species-interactions-on-trait-evolution
#11
Liang Xu, Sander van Doorn, Hanno Hildenbrandt, Rampal S Etienne
Models 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 competitive 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...
September 22, 2020: Systematic Biology
https://read.qxmd.com/read/32941630/phylogenomic-data-reveal-widespread-introgression-across-the-range-of-an-alpine-and-arctic-specialist
#12
Erik R Funk, Garth M Spellman, Kevin Winker, Jack J Withrow, Kristen C Ruegg, Erika Zavaleta, Scott A Taylor
Understanding how gene flow affects population divergence and speciation remains challenging. Differentiating one evolutionary process from another can be difficult because multiple processes can produce similar patterns, and more than one process can occur simultaneously. While simple population models produce predictable results, how these processes balance in taxa with patchy distributions and complicated natural histories is less certain. These types of populations might be highly connected through migration (gene flow), but can experience stronger effects of genetic drift and inbreeding, or localized selection...
September 17, 2020: Systematic Biology
https://read.qxmd.com/read/32915964/an-evolving-view-of-phylogenetic-support
#13
Chris Simon
If 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...
September 11, 2020: Systematic Biology
https://read.qxmd.com/read/32882040/a-total-evidence-dated-phylogeny-of-echinoidea-combining-phylogenomic-and-paleontological-data
#14
Nicolás Mongiardino Koch, Jeffrey R Thompson
Phylogenomic and paleontological data constitute complementary resources for unravelling 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 synthetizing 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 dataset for the clade, a large-scale morphological matrix with a dense fossil sampling, and a novel compendium of tip and node age constraints...
September 3, 2020: Systematic Biology
https://read.qxmd.com/read/32882028/is-sexual-conflict-a-driver-of-speciation-a-case-study-with-a-tribe-of-brush-footed-butterflies
#15
Ana Paula S Carvalho, Ryan A St Laurent, Emmanuel F A Toussaint, Caroline Storer, Kelly M Dexter, Kwaku Aduse-Poku, Akito Y Kawahara
Understanding 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 brush-footed butterflies of the tribe Acraeini...
September 3, 2020: Systematic Biology
https://read.qxmd.com/read/32845334/nothing-wrong-with-the-analysis-of-clades-in-comparative-evolutionary-studies-a-reply-to-poe-et-al
#16
Joanna Baker, Andrew Meade, Mark Pagel, Chris Venditti
In a recent paper, Poe et al. (2020) assert that scientists should abandon clade-based approaches, particularly those using named taxonomic ranks. Poe et al (2020) 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. (2020) have two important flaws: (i) an erroneous view of modern phylogenetic comparative methods; and (ii) a lack of statistical rigour in their analyses...
August 26, 2020: Systematic Biology
https://read.qxmd.com/read/32797209/formal-links-between-feature-diversity-and-phylogenetic-diversity
#17
Kristina Wicke, Arne Mooers, Mike Steel
The extent to which phylogenetic diversity (PD) captures feature diversity (FD) is a topical and controversial question in biodiversity conservation. In this short paper, we formalise 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...
August 14, 2020: Systematic Biology
https://read.qxmd.com/read/32797207/do-alignment-and-trimming-methods-matter-for-phylogenomic-uce-analyses
#18
Daniel M Portik, John J Wiens
Alignment 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 dozens, 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...
August 14, 2020: Systematic Biology
https://read.qxmd.com/read/32785686/disentangling-sources-of-gene-tree-discordance-in-phylogenomic-datasets-testing-ancient-hybridizations-in-amaranthaceae-s-l
#19
Diego F Morales-Briones, Gudrun Kadereit, Delphine T Tefarikis, Michael J Moore, Stephen A Smith, Samuel F Brockington, Alfonso Timoneda, Won C Yim, John C Cushman, Ya Yang
Gene tree discordance in large genomic datasets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s...
August 12, 2020: Systematic Biology
https://read.qxmd.com/read/32785670/phylogenomics-of-piranhas-and-pacus-serrasalmidae-uncovers-how-dietary-convergence-and-parallelism-obfuscate-traditional-morphological-taxonomy
#20
M A Kolmann, L C Hughes, L P Hernandez, D Arcila, R Betancur-R, M H Sabaj, H López-Fernández, G Ortí
The 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 seed dispersers in the flooded forest. Despite their widespread occurrence and notable ecologies, serrasalmid evolutionary history and systematics are controversial...
August 12, 2020: Systematic Biology
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