scholarly journals A Genomic Perspective on the Evolutionary Diversification of Turtles

2021 ◽  
Author(s):  
Simone M Gable ◽  
Michael I Byars ◽  
Robert Literman ◽  
Marc Tollis
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Single Copy ◽  
Lineage Sorting ◽  
Turtle Species ◽  
Evolutionary Diversification ◽  
Multispecies Coalescent ◽  
Dna Substitution ◽  
Genomic Regions ◽  
Genome Assemblies

To examine phylogenetic heterogeneity in turtle evolution, we collected thousands of high-confidence single-copy orthologs from 19 genome assemblies representative of extant turtle diversity and estimated a phylogeny with multispecies coalescent and concatenated partitioned methods. We also collected next-generation sequences from 26 turtle species and assembled millions of biallelic markers to reconstruct phylogenies from annotated regions (coding regions, introns, untranslated regions, intergenic, and others) of the western painted turtle (Chrysemys picta bellii) genome. We then measured gene tree-species tree discordance, as well as gene and site heterogeneity at each node in the inferred trees, and tested for incomplete lineage sorting and temporal patterns in phylogenomic heterogeneity across turtle evolution. We found 100% support for all bifurcations in the inferred turtle species phylogenies. However, a number of genes, sites, and genomic features supported alternate relationships between turtle taxa, and some nodes in the turtle phylogeny were well-explained by incomplete lineage sorting. There was no clear pattern between site concordance, node age, and DNA substitution rate across most annotated genomic regions, suggesting a relatively uniform proportion of informative sites drive phylogenetic inference across the evolution of turtles. We found more gene concordance at older nodes in the turtle phylogeny, and suggest that, in addition to incomplete lineage sorting, an overall lack of gene informativeness stemming from a slow rate of evolution can confound inferred patterns in turtle phylogenomics, particularly at more recent divergences. Our study demonstrates that heterogeneity is to be expected even in well resolved clades such as turtles, and that future phylogenomic studies should aim to sample as much of the genome as possible.

scholarly journals Detecting destabilizing species in the phylogenetic backbone of Potentilla (Rosaceae) using low-copy nuclear markers

AoB Plants ◽  
2020 ◽  
Vol 12 (3) ◽  
Author(s):  
Nannie L Persson ◽  
Ingrid Toresen ◽  
Heidi Lie Andersen ◽  
Jenny E E Smedmark ◽  
Torsten Eriksson
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Data Sets ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Nuclear Markers ◽  
Data Set ◽  
Multispecies Coalescent ◽  
Single Marker ◽  
Named Groups

Abstract The genus Potentilla (Rosaceae) has been subjected to several phylogenetic studies, but resolving its evolutionary history has proven challenging. Previous analyses recovered six, informally named, groups: the Argentea, Ivesioid, Fragarioides, Reptans, Alba and Anserina clades, but the relationships among some of these clades differ between data sets. The Reptans clade, which includes the type species of Potentilla, has been noticed to shift position between plastid and nuclear ribosomal data sets. We studied this incongruence by analysing four low-copy nuclear markers, in addition to chloroplast and nuclear ribosomal data, with a set of Bayesian phylogenetic and Multispecies Coalescent (MSC) analyses. A selective taxon removal strategy demonstrated that the included representatives from the Fragarioides clade, P. dickinsii and P. fragarioides, were the main sources of the instability seen in the trees. The Fragarioides species showed different relationships in each gene tree, and were only supported as a monophyletic group in a single marker when the Reptans clade was excluded from the analysis. The incongruences could not be explained by allopolyploidy, but rather by homoploid hybridization, incomplete lineage sorting or taxon sampling effects. When P. dickinsii and P. fragarioides were removed from the data set, a fully resolved, supported backbone phylogeny of Potentilla was obtained in the MSC analysis. Additionally, indications of autopolyploid origins of the Reptans and Ivesioid clades were discovered in the low-copy gene trees.

scholarly journals Species Tree Inference under the Multispecies Coalescent on Data with Paralogs is Accurate

2018 ◽  
Author(s):  
Zhi Yan ◽  
Peng Du ◽  
Matthew W. Hahn ◽  
Luay Nakhleh
Keyword(s):  
Incomplete Lineage Sorting ◽  
Single Copy ◽  
Species Tree ◽  
Biological Data ◽  
Lineage Sorting ◽  
Multispecies Coalescent ◽  
Gene Copies ◽  
Tree Inference ◽  
Inference Methods ◽  
Species Tree Inference

AbstractThe multispecies coalescent (MSC) has emerged as a powerful and desirable framework for species tree inference in phylogenomic studies. Under this framework, the data for each locus is assumed to consist of orthologous, single-copy genes, and heterogeneity across loci is assumed to be due to incomplete lineage sorting (ILS). These assumptions have led biologists that use ILS-aware inference methods, whether based directly on the MSC or proven to be statistically consistent under it (collectively referred to here as MSC-based methods), to exclude all loci that are present in more than a single copy in any of the studied genomes. Furthermore, such analyses entail orthology assignment to avoid the potential of hidden paralogy in the data. The question we seek to answer in this study is: What happens if one runs such species tree inference methods on data where paralogy is present, in addition to or without ILS being present? Through simulation studies and analyses of two biological data sets, we show that running such methods on data with paralogs provide very accurate results, either by treating all gene copies within a family as alleles from multiple individuals or by randomly selecting one copy per species. Our results have significant implications for the use of MSC-based phylogenomic analyses, demonstrating that they do not have to be restricted to single-copy loci, thus greatly increasing the amount of data that can be used. [Multispecies coalescent; incomplete lineage sorting; gene duplication and loss; orthology; paralogy.]

scholarly journals Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes

2021 ◽  
Vol 12 ◽  
Author(s):  
Jeffrey P. Rose ◽  
Ricardo Kriebel ◽  
Larissa Kahan ◽  
Alexa DiNicola ◽  
Jesús G. González-Gallegos ◽  
...  
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Divergence Time ◽  
Time Estimation ◽  
Single Copy ◽  
Lineage Sorting ◽  
Divergence Time Estimation ◽  
Sequencing Technologies ◽  
Plastid Genomes ◽  
Gene Tree Discordance

Next-generation sequencing technologies have facilitated new phylogenomic approaches to help clarify previously intractable relationships while simultaneously highlighting the pervasive nature of incongruence within and among genomes that can complicate definitive taxonomic conclusions. Salvia L., with ∼1,000 species, makes up nearly 15% of the species diversity in the mint family and has attracted great interest from biologists across subdisciplines. Despite the great progress that has been achieved in discerning the placement of Salvia within Lamiaceae and in clarifying its infrageneric relationships through plastid, nuclear ribosomal, and nuclear single-copy genes, the incomplete resolution has left open major questions regarding the phylogenetic relationships among and within the subgenera, as well as to what extent the infrageneric relationships differ across genomes. We expanded a previously published anchored hybrid enrichment dataset of 35 exemplars of Salvia to 179 terminals. We also reconstructed nearly complete plastomes for these samples from off-target reads. We used these data to examine the concordance and discordance among the nuclear loci and between the nuclear and plastid genomes in detail, elucidating both broad-scale and species-level relationships within Salvia. We found that despite the widespread gene tree discordance, nuclear phylogenies reconstructed using concatenated, coalescent, and network-based approaches recover a common backbone topology. Moreover, all subgenera, except for Audibertia, are strongly supported as monophyletic in all analyses. The plastome genealogy is largely resolved and is congruent with the nuclear backbone. However, multiple analyses suggest that incomplete lineage sorting does not fully explain the gene tree discordance. Instead, horizontal gene flow has been important in both the deep and more recent history of Salvia. Our results provide a robust species tree of Salvia across phylogenetic scales and genomes. Future comparative analyses in the genus will need to account for the impacts of hybridization/introgression and incomplete lineage sorting in topology and divergence time estimation.

scholarly journals Target enrichment improves phylogenetic resolution in the genus Zanthoxylum (Rutaceae) and indicates both incomplete lineage sorting and hybridization events

2021 ◽  
Author(s):  
Niklas Reichelt ◽  
Jun Wen ◽  
Claudia Paetzold ◽  
Marc Appelhans
Keyword(s):  
High Throughput Sequencing ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Gene Tree ◽  
Single Copy ◽  
Reticulate Evolution ◽  
Gene Trees ◽  
Target Enrichment ◽  
Lineage Sorting ◽  
Phylogenetic Resolution

Background and aims: Zanthoxylum L. is the only pantropical genus within Rutaceae, with a few species native to temperate eastern Asia and North America. Efforts using Sanger sequencing failed to resolve the backbone phylogeny of Zanthoxylum. In this study, we employed target enrichment high-throughput sequencing to improve resolution. Gene trees were examined for concordance and sectional classifications of Zanthoxylum were evaluated. Off-target reads were investigated to identify putative single-copy markers for bait refinement, and low-copy markers for evidence of putative hybridization events. Methods: We developed a custom bait set for target enrichment of 745 exons in Zanthoxylum and applied it to 45 Zanthoxylum species and one Tetradium species as the outgroup. Illumina reads were processed via the HybPhyloMaker pipeline. Phylogenetic inferences were conducted using coalescent and concatenated methods. Concordance was assessed using quartet sampling. Off-target reads were assembled and putative single- and low-copy genes were extracted. Additional phylogenetic analyses were performed based on these alignments. Key results: Four major clades are supported within Zanthoxylum: the African clade, the Z. asiaticum clade, the Asian-Pacific-Australian clade, and the American-eastern Asian clade. While overall support has improved, regions of conflict are similar to those previously observed. Gene tree discordances indicate a hybridization event in the ancestor of the Hawaiian lineage, and incomplete lineage sorting for the American backbone. Off-target putative single-copy genes largely confirm on-target results, and putative low-copy genes provide additional evidence for hybridization in the Hawaiian lineage. Only two of the five sections of Zanthoxylum are resolved as monophyletic. Conclusion: Target enrichment is suitable to assess phylogenetic relationships in Zanthoxylum. Our phylogenetic analyses reveal that current sectional classifications need revision. Quartet tree concordance indicates several instances of reticulate evolution. Off-target reads are proven useful to identify additional phylogenetically informative regions for bait refinement or gene tree based approaches.

scholarly journals The Multilocus Multispecies Coalescent: A Flexible New Model of Gene Family Evolution

2020 ◽  
Author(s):  
Qiuyi Li ◽  
Celine Scornavacca ◽  
Nicolas Galtier ◽  
Yao-Ban Chan
Keyword(s):  
Gene Family ◽  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Gene Family Evolution ◽  
Gene Copy ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
New Model ◽  
Multispecies Coalescent

Abstract 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. Here we consider the joint action of ILS and DTL on the gene tree/species tree problem in all its complexity. In particular, we show that the interaction between ILS and duplications/transfers (without losses) can result in patterns usually interpreted as resulting from gene loss, and that the realised rate of D, T and L becomes non-homogeneous in time when ILS is taken into account. We introduce algorithmic solutions to these problems. Our new model, the multilocus multispecies coalescent (MLMSC), which also accounts for any level of linkage between loci, generalises the multispecies coalescent model and offers a versatile, powerful framework for proper simulation and inference of gene family evolution.

scholarly journals Gene tree discord, simplex plots, and statistical tests under the coalescent

2020 ◽  
Author(s):  
Elizabeth S. Allman ◽  
Jonathan D. Mitchell ◽  
John A. Rhodes
Keyword(s):  
Incomplete Lineage Sorting ◽  
Statistical Tests ◽  
Gene Tree ◽  
Complex Model ◽  
Species Tree ◽  
Data Sets ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Multispecies Coalescent ◽  
Tree Inference

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 is not in accord with the MSC, and thus either gene tree inference error is substantial or a more complex model such as that on a network may be required. If the collection of gene trees appears to be in accord with the MSC, the plots may reveal when substantial incomplete lineage sorting is present and coalescent based species tree inference is preferred over concatenation approaches. Applications to both simulated and empirical multilocus data sets illustrate the insights provided.

scholarly journals Gene Tree Discord, Simplex Plots, and Statistical Tests under the Coalescent

2021 ◽  
Author(s):  
Elizabeth S Allman ◽  
Jonathan D Mitchell ◽  
John A Rhodes
Keyword(s):  
Incomplete Lineage Sorting ◽  
Hypothesis Test ◽  
Statistical Tests ◽  
Gene Tree ◽  
Complex Model ◽  
Species Tree ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Coalescent Model ◽  
Multispecies Coalescent

Abstract A 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 complex model such as that on a network may be required. If the collection of gene trees is in accord with the MSC, the plots reveal when substantial incomplete lineage sorting is present. Applications to both simulated and empirical multilocus data sets illustrate the insights provided. [Gene tree discordance; hypothesis test; multispecies coalescent model; quartet concordance factor; simplex plot; species tree].

scholarly journals The Multilocus Multispecies Coalescent: A Flexible New Model of Gene Family Evolution

2020 ◽  
Author(s):  
Qiuyi Li ◽  
Celine Scornavacca ◽  
Nicolas Galtier ◽  
Yao-Ban Chan
Keyword(s):  
Gene Family ◽  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Gene Family Evolution ◽  
Gene Copy ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
New Model ◽  
Multispecies Coalescent

AbstractIncomplete 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. Here we consider the joint action of ILS and DTL on the gene tree/species tree problem in all its complexity. In particular, we show that the interaction between ILS and duplications/transfers (without losses) can result in patterns usually interpreted as resulting from gene loss, and that the realised rate of D, T and L becomes non-homogeneous in time when ILS is taken into account. We introduce algorithmic solutions to these problems. Our new model, the multilocus multispecies coalescent (MLMSC), which also accounts for any level of linkage between loci, generalises the multispecies coalescent model and offers a versatile, powerful framework for proper simulation and inference of gene family evolution.

scholarly journals Statistical inconsistency of the unrooted minimize deep coalescence criterion

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0251107
Author(s):  
Ayed A. R. Alanzi ◽  
James H. Degnan
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Species Tree ◽  
Evolutionary Relationships ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
Input Gene ◽  
Multispecies Coalescent ◽  
Deep Coalescence

Species trees, which describe the evolutionary relationships between species, are often inferred from gene trees, which describe the ancestral relationships between sequences sampled at different loci from the species of interest. A common approach to inferring species trees from gene trees is motivated by supposing that gene tree variation is due to incomplete lineage sorting, also known as deep coalescence. One of the earliest methods motivated by deep coalescence is to find the species tree that minimizes the number of deep coalescent events needed to explain discrepancies between the species tree and input gene trees. This minimize deep coalescence (MDC) criterion can be applied in both rooted and unrooted settings. where either rooted or unrooted gene trees can be used to infer a rooted species tree. Previous work has shown that MDC is statistically inconsistent in the rooted setting, meaning that under a probabilistic model for deep coalescence, the multispecies coalescent, for some species trees, increasing the number of input gene trees does not make the method more likely to return a correct species tree. Here, we obtain analogous results in the unrooted setting, showing conditions leading to inconsistency of the MDC criterion using the multispecies coalescent model with unrooted gene trees for four taxa and five taxa.

scholarly journals Addressing incomplete lineage sorting and paralogy in the inference of uncertain salmonid phylogenetic relationships

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9389
Author(s):  
Matthew A. Campbell ◽  
Thaddaeus J. Buser ◽  
Michael E. Alfaro ◽  
J. Andrés López
Keyword(s):  
Evolutionary History ◽  
Molecular Phylogenetics ◽  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Complex Model ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Fish Family ◽  
Multispecies Coalescent ◽  
Analytical Strategies

Recent and continued progress in the scale and sophistication of phylogenetic research has yielded substantial advances in knowledge of the tree of life; however, segments of that tree remain unresolved and continue to produce contradicting or unstable results. These poorly resolved relationships may be the product of methodological shortcomings or of an evolutionary history that did not generate the signal traits needed for its eventual reconstruction. Relationships within the euteleost fish family Salmonidae have proven challenging to resolve in molecular phylogenetics studies in part due to ancestral autopolyploidy contributing to conflicting gene trees. We examine a sequence capture dataset from salmonids and use alternative strategies to accommodate the effects of gene tree conflict based on aspects of salmonid genome history and the multispecies coalescent. We investigate in detail three uncertain relationships: (1) subfamily branching, (2) monophyly of Coregonus and (3) placement of Parahucho. Coregoninae and Thymallinae are resolved as sister taxa, although conflicting topologies are found across analytical strategies. We find inconsistent and generally low support for the monophyly of Coregonus, including in results of analyses with the most extensive dataset and complex model. The most consistent placement of Parahucho is as sister lineage of Salmo.

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