Variation Across Mitochondrial Gene Trees Provides Evidence for Systematic Error: How Much Gene Tree Variation Is Biological?

ABSTRACTThe use of large genomic datasets in phylogenetics has highlighted extensive topological variation across genes. Much of this discordance is assumed to result from biological processes. However, variation among gene trees can also be a consequence of systematic error driven by poor model fit, and the relative importance of these biological versus methodological factors in explaining gene tree variation is a major unresolved question in phylogenetics. Using mitochondrial genomes to control for biological causes of gene tree variation, we estimate the extent of gene tree discordance driven by systematic error and employ posterior prediction to highlight the role of model fit. We find that the amount of discordance among mitochondrial gene trees is similar to the amount of discordance found in other studies that assume only biological causes of variation. This similarity suggests that the role of systematic error in generating gene tree variation is underappreciated and that critical evaluation of the fit between assumed models and the data used for inference is important for the resolution of unresolved phylogenetic questions.

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A new living species of degu, genus Octodon (Hystricomorpha: Octodontidae)

Journal of Mammalogy ◽

10.1093/jmammal/gyaa143 ◽

2020 ◽

Author(s):

Guillermo D’Elía ◽

Pablo Teta ◽

Diego H Verzi ◽

Richard Cadenillas ◽

James L Patton

Keyword(s):

New Species ◽

Mitochondrial Gene ◽

Gene Tree ◽

Nuclear Gene ◽

Qualitative Assessment ◽

Large Set ◽

Gene Trees ◽

Cranial Measurements ◽

Living Species ◽

Gene Data

Abstract We combine morphological (qualitative and quantitative data) and genetic (one mitochondrial and one nuclear gene) data from a large set of specimens of Octodon from the four currently recognized living species of the genus. The integration of the results (qualitative assessment, multivariate analysis of cranial measurements, and gene trees) allows us to state that 1) the current taxonomic scheme does not reflect the species diversity of Octodon; 2) in particular, as currently understood O. bridgesii likely is a complex of three species; 3) one of these, encompassing the southern populations of the genus, in the Araucanía Region (Chile) and Neuquén Province (Argentina), is named and described here as a new species; and 4) the mitochondrial gene tree departs from the nuclear gene tree with respect to O. pacificus and the new species here described.

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Novel Intron Phylogeny Supports Plumage Convergence in Orioles (Icterus)

The Auk ◽

10.1093/auk/120.4.961 ◽

2003 ◽

Vol 120 (4) ◽

pp. 961-969 ◽

Cited By ~ 3

Author(s):

Eva Sanders Allen ◽

Kevin E. Omland

Keyword(s):

New World ◽

Mitochondrial Gene ◽

Gene Tree ◽

Nuclear Gene ◽

Gene Trees ◽

Mt Dna ◽

Single Linkage ◽

Mitochondrial Data ◽

Phylogenetic Resolution ◽

Phylogenetic Hypotheses

Abstract A recent study of New World orioles (Icterus spp.), which traced a large number of plumage characters onto a mitochondrial DNA phylogeny, reported high frequencies of evolutionary convergence and reversal of plumage characters (Omland and Lanyon 2000). Although those results are consistent with other smaller scale studies that have documented plumage homoplasy, the mitochondrial genome is inherited as a single linkage group, so mitochondrial data represent only one gene tree. The mitochondrial (mt) DNA tree may not reflect the true evolutionary history of a lineage; therefore, it remains possible that the plumage characters could reflect the true species phylogeny. Other rapidly evolving regions of DNA can provide independent phylogenetic hypotheses useful for evaluating mitochondrial gene trees. A novel phylogenetic marker, a region of the nuclear gene ornithine decarboxylase (ODC) spanning from exon 6 to exon 8, was sequenced in 10 oriole species. The resultant nuclear gene tree reconstructs the same three major oriole clades as the mtDNA tree (Omland et al. 1999), supporting the conclusion that plumage evolution in the New World orioles has been highly homoplastic. Although most phylogenetic studies that have employed introns report greatest resolution at the genus or family level, ODC appears to offer some degree of phylogenetic resolution for infrageneric analyses. However, that intron has clearly not sorted to monophyly within or between closely related species.

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Different behaviour of mitochondrial and nuclear markers: introgression and the evolutionary history of Chrysocarabus (Coleoptera: Carabidae)

Entomologica Fennica ◽

10.33338/ef.84330 ◽

2006 ◽

Vol 17 (3) ◽

Cited By ~ 3

Author(s):

Andreas Düring ◽

Martina Brückner ◽

Dietrich Mossakowski

Keyword(s):

Phylogenetic Trees ◽

Evolutionary History ◽

Phylogenetic Analyses ◽

Mitochondrial Gene ◽

Gene Tree ◽

Gene Trees ◽

Nuclear Markers ◽

Mitochondrial Haplotypes ◽

History Of ◽

Mitochondrial And Nuclear Markers

Phylogenetic analyses of Chrysocarabus taxa using different markers result in different phylogenetic trees. In particular, the mitochondrial gene tree contradicts the results of morphological and inbreeding studies. Two very different haplotypes of Carabus splendens Olivier, 1790 do not form a clade within this phylogenetic tree. We have earlier proposed that contradictory results are due to introgression. To verify our hypothesis, we analysed the internal transcribed spacer 2. No substitutions were observed in these nuclear sequences between the individuals of Carabus splendens, which contain the different mitochondrial haplotypes in question. The differences in the gene trees based on mitochondrial and nuclear sequences can be explained with at least two introgression events.

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Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci

Genetics ◽

10.1093/genetics/164.4.1645 ◽

2003 ◽

Vol 164 (4) ◽

pp. 1645-1656 ◽

Cited By ~ 3

Author(s):

Bruce Rannala ◽

Ziheng Yang

Keyword(s):

Dna Sequences ◽

Gene Tree ◽

Species Tree ◽

Bayes Estimation ◽

Ancestral Population ◽

Divergence Times ◽

Gene Trees ◽

Species Divergence ◽

Multiple Loci ◽

Population Sizes

Abstract The effective population sizes of ancestral as well as modern species are important parameters in models of population genetics and human evolution. The commonly used method for estimating ancestral population sizes, based on counting mismatches between the species tree and the inferred gene trees, is highly biased as it ignores uncertainties in gene tree reconstruction. In this article, we develop a Bayes method for simultaneous estimation of the species divergence times and current and ancestral population sizes. The method uses DNA sequence data from multiple loci and extracts information about conflicts among gene tree topologies and coalescent times to estimate ancestral population sizes. The topology of the species tree is assumed known. A Markov chain Monte Carlo algorithm is implemented to integrate over uncertain gene trees and branch lengths (or coalescence times) at each locus as well as species divergence times. The method can handle any species tree and allows different numbers of sequences at different loci. We apply the method to published noncoding DNA sequences from the human and the great apes. There are strong correlations between posterior estimates of speciation times and ancestral population sizes. With the use of an informative prior for the human-chimpanzee divergence date, the population size of the common ancestor of the two species is estimated to be ∼20,000, with a 95% credibility interval (8000, 40,000). Our estimates, however, are affected by model assumptions as well as data quality. We suggest that reliable estimates have yet to await more data and more realistic models.

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Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere

Systematic Biology ◽

10.1093/sysbio/syaa099 ◽

2020 ◽

Author(s):

Fernando Lopes ◽

Larissa R Oliveira ◽

Amanda Kessler ◽

Yago Beux ◽

Enrique Crespo ◽

...

Keyword(s):

Incomplete Lineage Sorting ◽

Gene Tree ◽

Molecular Data ◽

Species Tree ◽

Gene Trees ◽

Lineage Sorting ◽

Data Types ◽

High Coverage ◽

Sea Lions ◽

The Family

Abstract The phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance because of strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here we used high-coverage genome-wide sequencing for 14 of the 15 species of Otariidae to elucidate the phylogeny of the family and its bearing on the taxonomy and biogeographical history. Despite extreme topological discordance among gene trees, we found a fully supported species tree that agrees with the few well-accepted relationships and establishes monophyly of the genus Arctocephalus. Our data support a relatively recent trans-hemispheric dispersal at the base of a southern clade, which rapidly diversified into six major lineages between 3 to 2.5 Ma. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be non-monophyletic, with California (Z. californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Z. wollebaeki) with evidence for introgression between the two genera. Overall, the high degree of genealogical discordance was best explained by incomplete lineage sorting resulting from quasi-simultaneous speciation within the southern clade with introgresssion playing a subordinate role in explaining the incongruence among and within prior phylogenetic studies of the family.

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How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow Using Loricaria (Asteraceae) as an Example

Frontiers in Plant Science ◽

10.3389/fpls.2021.765719 ◽

2022 ◽

Vol 12 ◽

Author(s):

Martha Kandziora ◽

Petr Sklenář ◽

Filip Kolář ◽

Roswitha Schmickl

Keyword(s):

Incomplete Lineage Sorting ◽

Gene Tree ◽

Species Tree ◽

Secondary Contact ◽

Gene Trees ◽

Species Trees ◽

Lineage Sorting ◽

Phylogenetic Discordance ◽

Gene Tree Discordance ◽

High Degree

A major challenge in phylogenetics and -genomics is to resolve young rapidly radiating groups. The fast succession of species increases the probability of incomplete lineage sorting (ILS), and different topologies of the gene trees are expected, leading to gene tree discordance, i.e., not all gene trees represent the species tree. Phylogenetic discordance is common in phylogenomic datasets, and apart from ILS, additional sources include hybridization, whole-genome duplication, and methodological artifacts. Despite a high degree of gene tree discordance, species trees are often well supported and the sources of discordance are not further addressed in phylogenomic studies, which can eventually lead to incorrect phylogenetic hypotheses, especially in rapidly radiating groups. We chose the high-Andean Asteraceae genus Loricaria to shed light on the potential sources of phylogenetic discordance and generated a phylogenetic hypothesis. By accounting for paralogy during gene tree inference, we generated a species tree based on hundreds of nuclear loci, using Hyb-Seq, and a plastome phylogeny obtained from off-target reads during target enrichment. We observed a high degree of gene tree discordance, which we found implausible at first sight, because the genus did not show evidence of hybridization in previous studies. We used various phylogenomic analyses (trees and networks) as well as the D-statistics to test for ILS and hybridization, which we developed into a workflow on how to tackle phylogenetic discordance in recent radiations. We found strong evidence for ILS and hybridization within the genus Loricaria. Low genetic differentiation was evident between species located in different Andean cordilleras, which could be indicative of substantial introgression between populations, promoted during Pleistocene glaciations, when alpine habitats shifted creating opportunities for secondary contact and hybridization.

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Deep-Time Demographic Inference Suggests Ecological Release as Driver of Neoavian Adaptive Radiation

Diversity ◽

10.3390/d12040164 ◽

2020 ◽

Vol 12 (4) ◽

pp. 164 ◽

Cited By ~ 2

Author(s):

Peter Houde ◽

Edward L. Braun ◽

Lawrence Zhou

Keyword(s):

Evolutionary Biology ◽

Gene Tree ◽

Difficult Problem ◽

Gene Trees ◽

Effective Population ◽

Deep Time ◽

Ecological Release ◽

Population Sizes ◽

Demographic Inference ◽

Gene Tree Discordance

Assessing the applicability of theory to major adaptive radiations in deep time represents an extremely difficult problem in evolutionary biology. Neoaves, which includes 95% of living birds, is believed to have undergone a period of rapid diversification roughly coincident with the Cretaceous–Paleogene (K-Pg) boundary. We investigate whether basal neoavian lineages experienced an ecological release in response to ecological opportunity, as evidenced by density compensation. We estimated effective population sizes (Ne) of basal neoavian lineages by combining coalescent branch lengths (CBLs) and the numbers of generations between successive divergences. We used a modified version of Accurate Species TRee Algorithm (ASTRAL) to estimate CBLs directly from insertion–deletion (indel) data, as well as from gene trees using DNA sequence and/or indel data. We found that some divergences near the K-Pg boundary involved unexpectedly high gene tree discordance relative to the estimated number of generations between speciation events. The simplest explanation for this result is an increase in Ne, despite the caveats discussed herein. It appears that at least some early neoavian lineages, similar to the ancestor of the clade comprising doves, mesites, and sandgrouse, experienced ecological release near the time of the K-Pg mass extinction.

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

AoB Plants ◽

10.1093/aobpla/plaa017 ◽

2020 ◽

Vol 12 (3) ◽

Cited By ~ 1

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.

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Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction

Systematic Biology ◽

10.1093/sysbio/syaa063 ◽

2020 ◽

Author(s):

Matthew H Van Dam ◽

James B Henderson ◽

Lauren Esposito ◽

Michelle Trautwein

Keyword(s):

Marine Invertebrates ◽

Phylogenetic Analyses ◽

Single Gene ◽

Gene Tree ◽

Single Copy ◽

Species Tree ◽

Bootstrap Support ◽

Gene Trees ◽

Species Trees ◽

Tree Reconstruction

Abstract Ultraconserved 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 genomic category from five different studies including: birds, mammals, fish, Hymenoptera (ants, wasps, and bees), and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by two or more UCEs, corresponding to nonoverlapping segments of a single gene. We considered these UCEs to be nonindependent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging cogenic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees was significantly improved across all data sets apparently driven by the increase in loci length. Additionally, we conducted simulations and found that gene trees generated from merged UCEs were more accurate than those generated by unmerged UCEs. As loci length improves gene tree accuracy, this modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses. [Anchored hybrid enrichment; ants; ASTRAL; bait capture; carangimorph; Coleoptera; conserved nonexonic elements; exon capture; gene tree; Hymenoptera; mammal; phylogenomic markers; songbird; species tree; ultraconserved elements; weevils.]

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