Species-level phylogeny of Allium subgenus Melanocrommyum : Incomplete lineage sorting, hybridization and trnF gene duplication

Taxon ◽  
2010 ◽  
Vol 59 (3) ◽  
pp. 829-840 ◽  
Author(s):  
Maia Gurushidze ◽  
Reinhard M. Fritsch ◽  
Frank R. Blattner
Keyword(s):  
Gene Duplication ◽  
Incomplete Lineage Sorting ◽  
Species Level ◽  
Lineage Sorting

scholarly journals Unifying Gene Duplication, Loss, and Coalescence on Phylogenetic Networks

2019 ◽  
Author(s):  
Peng Du ◽  
Huw A. Ogilvie ◽  
Luay Nakhleh
Keyword(s):  
Gene Duplication ◽  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Phylogenetic Network ◽  
Biological Data ◽  
Phylogenetic Networks ◽  
Lineage Sorting ◽  
Evolutionary Processes ◽  
Domains Of Life ◽  
Gene Duplication And Loss

AbstractStatistical methods were recently introduced for inferring phylogenetic networks under the multispecies network coalescent, thus accounting for both reticulation and incomplete lineage sorting. Two evolutionary processes that are ubiquitous across all three domains of life, but are not accounted for by those methods, are gene duplication and loss (GDL).In this work, we devise a three-piece model—phylogenetic network, locus network, and gene tree—that unifies all the aforementioned processes into a single model of how genes evolve in the presence of ILS, GDL, and introgression within the branches of a phylogenetic network. To illustrate the power of this model, we develop an algorithm for estimating the parameters of a phylogenetic network topology under this unified model. The algorithm consists of a set of moves that allow for stochastic search through the parameter space. The challenges with developing such moves stem from the intricate dependencies among the three pieces of the model. We demonstrate the application of the model and the accuracy of the algorithm on simulated as well as biological data.Our work adds to the biologist’s toolbox of methods for phylogenomic inference by accounting for more complex evolutionary processes.

scholarly journals Polynomial-Time Statistical Estimation of Species Trees under Gene Duplication and Loss

2019 ◽  
Author(s):  
Brandon Legried ◽  
Erin K. Molloy ◽  
Tandy Warnow ◽  
Sébastien Roch
Keyword(s):  
Gene Duplication ◽  
Polynomial Time ◽  
Incomplete Lineage Sorting ◽  
Data Bank ◽  
Polynomial Time Algorithm ◽  
Species Tree ◽  
Species Trees ◽  
Lineage Sorting ◽  
Biological Studies ◽  
Gene Duplication And Loss

AbstractPhylogenomics—the estimation of species trees from multilocus datasets—is a common step in many biological studies. However, this estimation is challenged by the fact that genes can evolve under processes, including incomplete lineage sorting (ILS) and gene duplication and loss (GDL), that make their trees different from the species tree. In this paper, we address the challenge of estimating the species tree under GDL. We show that species trees are identifiable under a standard stochastic model for GDL, and that the polynomial-time algorithm ASTRAL-multi, a recent development in the ASTRAL suite of methods, is statistically consistent under this GDL model. We also provide a simulation study evaluating ASTRAL-multi for species tree estimation under GDL. All scripts and datasets used in this study are available on the Illinois Data Bank: https://doi.org/10.13012/B2IDB-2626814_V1.

A chloroplast phylogeny of Zieria (Rutaceae) in Australia and New Caledonia shows widespread incongruence with species-level taxonomy

2014 ◽  
Vol 27 (6) ◽  
pp. 427 ◽  
Author(s):  
Rosemary A. Barrett ◽  
Michael J. Bayly ◽  
Marco F. Duretto ◽  
Paul I. Forster ◽  
Pauline Y. Ladiges ◽  
...  
Keyword(s):  
Nuclear Dna ◽  
New Caledonia ◽  
Incomplete Lineage Sorting ◽  
Species Level ◽  
Lineage Sorting ◽  
Widespread Species ◽  
Geographic Ranges ◽  
Cpdna Markers ◽  
Insight Into ◽  
Chloroplast Phylogeny

This study presents a molecular phylogeny of Zieria Sm., a genus of shrubs and small trees, with 59 species in Australia and one endemic to New Caledonia. The phylogeny is based on four cpDNA markers and 116 samples representing all species of Zieria except one, and the monotypic outgroup Neobyrnesia suberosa. The New Caledonian species, Z. chevalieri, was resolved as sister to a well supported clade of all Australian taxa. There was widespread incongruence between the cpDNA tree and species-level taxonomy, with 14 species shown as polyphyletic or paraphyletic. These included widespread species (e.g. Z. smithii and Z. arborescens, each falling in at least four well supported clades) and some with narrow geographic ranges (e.g. Z. alata and Z. oreocena). No species represented by three or more samples was resolved as monophyletic. We suggest that a combination of factors explains this incongruence, including regional cpDNA introgression (chloroplast capture), incomplete lineage sorting and inappropriate taxonomic boundaries. The cpDNA phylogeny provides useful insight into the evolution of Zieria but, because of its complexity, does not provide a clear basis for assessing phylogenetic relationships and monophyly of taxa. Better understanding of relationships, taxon limits and evolutionary processes in Zieria will require comparisons with nuclear DNA markers and critical assessment of morphological and genetic variation in widespread species.

Phylogenetic analysis of Zieria (Rutaceae) in Australia and New Caledonia based on nuclear ribosomal DNA shows species polyphyly, divergent paralogues and incongruence with chloroplast DNA

2018 ◽  
Vol 31 (1) ◽  
pp. 16 ◽  
Author(s):  
Rosemary A. Barrett ◽  
Michael J. Bayly ◽  
Marco F. Duretto ◽  
Paul I. Forster ◽  
Pauline Y. Ladiges ◽  
...  
Keyword(s):  
New Caledonia ◽  
Incomplete Lineage Sorting ◽  
Evolutionary Process ◽  
Species Level ◽  
Nuclear Ribosomal Dna ◽  
Species Relationships ◽  
Insufficient Information ◽  
Lineage Sorting ◽  
External Transcribed Spacer ◽  
Underlying Causes

This study presents a phylogeny of Zieria Sm. (Rutaceae) based on sequences of internal transcribed spacer and external transcribed spacer regions of nrDNA, and using Neobyrnesia suberosa J.A.Armstr. as the outgroup. The phylogeny includes 109 samples, representing 58 of the 60 currently recognised species of Zieria, with multiple accessions of most. Ten species were resolved as monophyletic on the basis of two, or in one case four, samples. Monophyly of four species was neither supported nor rejected, and all other species with more than one accession were resolved as polyphyletic or paraphyletic. Results showed that divergent paralogues of nrDNA are present in some individuals, although the underlying evolutionary process that gave rise to those paralogues is uncertain. Divergent paralogues within genomes could predate speciation and be variably retained or variably detected within the species sampled here; alternatively, they could represent novel nrDNA combinations formed through hybridisation after speciation. There was no strong evidence for recombination between paralogues or that paralogues represent pseudogenes. Variation of nrDNA sequences was clearly incongruent with previously published cpDNA variation, with the nrDNA potentially providing a better indication of species relationships in Zieria. Evidence for this comes from the greater level of congruence, in some species at least, between nrDNA and existing species-level taxonomy than between cpDNA and taxonomy. Incomplete lineage sorting is proposed as a plausible cause for much of the conflict between nrDNA and cpDNA in Zieria, although, in most cases, there was insufficient information to identify the underlying causes with confidence. Implications for species-level taxonomy are discussed.

scholarly journals The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales

2020 ◽  
Author(s):  
Liming Cai ◽  
Zhenxiang Xi ◽  
Emily Moriarty Lemmon ◽  
Alan R Lemmon ◽  
Austin Mast ◽  
...  
Keyword(s):  
Gene Flow ◽  
Incomplete Lineage Sorting ◽  
Estimation Error ◽  
Gene Tree ◽  
Species Tree ◽  
Flowering Plant ◽  
Estimation Methods ◽  
Lineage Sorting ◽  
Tree Estimation ◽  
Perfect Storm

Abstract 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. This order includes nine of the top ten most unstable nodes in angiosperms, which have been hypothesized to arise from the rapid radiation during the Cretaceous. Here, we show that coalescent-based methods do not resolve the backbone of Malpighiales and concatenation methods yield inconsistent estimations, providing evidence that gene tree heterogeneity is high in this clade. Despite high levels of ILS and gene tree estimation error, our simulations demonstrate that these two factors alone are insufficient to explain the lack of resolution in this order. To explore this further, we examined triplet frequencies among empirical gene trees and discovered some of them deviated significantly from those attributed to ILS and estimation error, suggesting gene flow as an additional and previously unappreciated phenomenon promoting gene tree variation in Malpighiales. Finally, we applied a novel method to quantify the relative contribution of these three primary sources of gene tree heterogeneity and demonstrated that ILS, gene tree estimation error, and gene flow contributed to 10.0%, 34.8%, and 21.4% of the variation, respectively. Together, our results suggest that a perfect storm of factors likely influence this lack of resolution, and further indicate that recalcitrant phylogenetic relationships like the backbone of Malpighiales may be better represented as phylogenetic networks. Thus, reducing such groups solely to existing models that adhere strictly to bifurcating trees greatly oversimplifies reality, and obscures our ability to more clearly discern the process of evolution.

scholarly journals Morphological, Ecological, and Molecular Divergence of Conogethes pinicolalis from C. punctiferalis (Lepidoptera: Crambidae)

Insects ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 455
Author(s):  
Na Ra Jeong ◽  
Min Jee Kim ◽  
Sung-Soo Kim ◽  
Sei-Woong Choi ◽  
Iksoo Kim
Keyword(s):  
Phylogenetic Analysis ◽  
First Generation ◽  
Incomplete Lineage Sorting ◽  
Divergence Time ◽  
Sequence Divergence ◽  
Lineage Sorting ◽  
Mitochondrial Coi ◽  
Feeding Type ◽  
Pine Trees ◽  
Yellow Peach Moth

Conogethes pinicolalis has long been considered as a Pinaceae-feeding type of the yellow peach moth, C. punctiferalis, in Korea. In this study, the divergence of C. pinicolalis from the fruit-feeding moth C. punctiferalis was analyzed in terms of morphology, ecology, and genetics. C. pinicolalis differs from C. punctiferalis in several morphological features. Through field observation, we confirmed that pine trees are the host plants for the first generation of C. pinicolalis larvae, in contrast to fruit-feeding C. punctiferalis larvae. We successfully reared C. pinicolalis larvae to adults by providing them pine needles as a diet. From a genetic perspective, the sequences of mitochondrial COI of these two species substantially diverged by an average of 5.46%; moreover, phylogenetic analysis clearly assigned each species to an independent clade. On the other hand, nuclear EF1α showed a lower sequence divergence (2.10%) than COI. Overall, EF1α-based phylogenetic analysis confirmed each species as an independent clade, but a few haplotypes of EF1α indicated incomplete lineage sorting between these two species. In conclusion, our results demonstrate that C. pinicolalis is an independent species according to general taxonomic criteria; however, analysis of the EF1α sequence revealed a short divergence time.

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

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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