scholarly journals Interspecific Gene Exchange Introduces High Genetic Variability in Crop Pathogen

2019 ◽  
Vol 11 (11) ◽  
pp. 3095-3105 ◽  
Author(s):  
Alice Feurtey ◽  
Danielle M Stevens ◽  
Wolfgang Stephan ◽  
Eva H Stukenbrock
Keyword(s):  
Transposable Elements ◽  
Population Genomics ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Length Distribution ◽  
Virulence Determinants ◽  
Lineage Sorting ◽  
Zymoseptoria Tritici ◽  
Variable Regions ◽  
The Impact

Abstract Genome analyses have revealed a profound role of hybridization and introgression in the evolution of many eukaryote lineages, including fungi. The impact of recurrent introgression on fungal evolution however remains elusive. Here, we analyzed signatures of introgression along the genome of the fungal wheat pathogen Zymoseptoria tritici. We applied a comparative population genomics approach, including genome data from five Zymoseptoria species, to characterize the distribution and composition of introgressed regions representing segments with an exceptional haplotype pattern. These regions are found throughout the genome, comprising 5% of the total genome and overlapping with > 1,000 predicted genes. We performed window-based phylogenetic analyses along the genome to distinguish regions which have a monophyletic or nonmonophyletic origin with Z. tritici sequences. A majority of nonmonophyletic windows overlap with the highly variable regions suggesting that these originate from introgression. We verified that incongruent gene genealogies do not result from incomplete lineage sorting by comparing the observed and expected length distribution of haplotype blocks resulting from incomplete lineage sorting. Although protein-coding genes are not enriched in these regions, we identify 18 that encode putative virulence determinants. Moreover, we find an enrichment of transposable elements in these regions implying that hybridization may contribute to the horizontal spread of transposable elements. We detected a similar pattern in the closely related species Zymoseptoria ardabiliae, suggesting that hybridization is widespread among these closely related grass pathogens. Overall, our results demonstrate a significant impact of recurrent hybridization on overall genome evolution of this important wheat pathogen.

scholarly journals Impact of Ghost Introgression on Coalescent-based Species Tree Inference and Estimation of Divergence Time

2022 ◽  
Author(s):  
XiaoXu Pang ◽  
Da-Yong Zhang
Keyword(s):  
Incomplete Lineage Sorting ◽  
Divergence Time ◽  
Species Tree ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
Multispecies Coalescent ◽  
Tree Inference ◽  
Tree Methods ◽  
The Impact

The species studied in any evolutionary investigation generally constitute a very small proportion of all the species currently existing or that have gone extinct. It is therefore likely that introgression, which is widespread across the tree of life, involves "ghosts," i.e., unsampled, unknown, or extinct lineages. However, the impact of ghost introgression on estimations of species trees has been rarely studied and is thus poorly understood. In this study, we use mathematical analysis and simulations to examine the robustness of species tree methods based on a multispecies coalescent model under gene flow sourcing from an extant or ghost lineage. We found that very low levels of extant or ghost introgression can result in anomalous gene trees (AGTs) on three-taxon rooted trees if accompanied by strong incomplete lineage sorting (ILS). In contrast, even massive introgression, with more than half of the recipient genome descending from the donor lineage, may not necessarily lead to AGTs. In cases involving an ingroup lineage (defined as one that diverged no earlier than the most basal species under investigation) acting as the donor of introgression, the time of root divergence among the investigated species was either underestimated or remained unaffected, but for the cases of outgroup ghost lineages acting as donors, the divergence time was generally overestimated. Under many conditions of ingroup introgression, the stronger the ILS was, the higher was the accuracy of estimating the time of root divergence, although the topology of the species tree is more prone to be biased by the effect of introgression.

scholarly journals A test statistic to quantify treelikeness in phylogenetics

2021 ◽  
Author(s):  
Caitlin Cherryh ◽  
Bui Quang Minh ◽  
Rob Lanfear
Keyword(s):  
Evolutionary History ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Phylogenetic Network ◽  
Parametric Bootstrap ◽  
Lineage Sorting ◽  
Test Statistic ◽  
Sequence Alignments ◽  
Wide Range ◽  
History Of

AbstractMost phylogenetic analyses assume that the evolutionary history of an alignment (either that of a single locus, or of multiple concatenated loci) can be described by a single bifurcating tree, the so-called the treelikeness assumption. Treelikeness can be violated by biological events such as recombination, introgression, or incomplete lineage sorting, and by systematic errors in phylogenetic analyses. The incorrect assumption of treelikeness may then mislead phylogenetic inferences. To quantify and test for treelikeness in alignments, we develop a test statistic which we call the tree proportion. This statistic quantifies the proportion of the edge weights in a phylogenetic network that are represented in a bifurcating phylogenetic tree of the same alignment. We extend this statistic to a statistical test of treelikeness using a parametric bootstrap. We use extensive simulations to compare tree proportion to a range of related approaches. We show that tree proportion successfully identifies non-treelikeness in a wide range of simulation scenarios, and discuss its strengths and weaknesses compared to other approaches. The power of the tree-proportion test to reject non-treelike alignments can be lower than some other approaches, but these approaches tend to be limited in their scope and/or the ease with which they can be interpreted. Our recommendation is to test treelikeness of sequence alignments with both tree proportion and mosaic methods such as 3Seq. The scripts necessary to replicate this study are available at https://github.com/caitlinch/treelikeness

scholarly journals Dissecting the basis of novel trait evolution in a radiation with widespread phylogenetic discordance

2017 ◽  
Author(s):  
Meng Wu ◽  
Jamie L. Kostyun ◽  
Matthew W. Hahn ◽  
Leonie Moyle
Keyword(s):  
De Novo ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Gene Tree ◽  
Fruit Color ◽  
Species Tree ◽  
Color Variation ◽  
Lineage Sorting ◽  
Floral Character ◽  
Trait Evolution

ABSTRACTPhylogenetic analyses of trait evolution can provide insight into the evolutionary processes that initiate and drive phenotypic diversification. However, recent phylogenomic studies have revealed extensive gene tree-species tree discordance, which can lead to incorrect inferences of trait evolution if only a single species tree is used for analysis. This phenomenon—dubbed “hemiplasy”—is particularly important to consider during analyses of character evolution in rapidly radiating groups, where discordance is widespread. Here we generate whole-transcriptome data for a phylogenetic analysis of 14 species in the plant genus Jaltomata (the sister clade to Solanum), which has experienced rapid, recent trait evolution, including in fruit and nectar color, and flower size and shape. Consistent with other radiations, we find evidence for rampant gene tree discordance due to incomplete lineage sorting (ILS) and several introgression events among the well-supported subclades. Since both ILS and introgression increase the probability of hemiplasy, we perform several analyses that take discordance into account while identifying genes that might contribute to phenotypic evolution. Despite discordance, the history of fruit color evolution in Jaltomata can be inferred with high confidence, and we find evidence of de novo adaptive evolution at individual genes associated with fruit color variation. In contrast, hemiplasy appears to strongly affect inferences about floral character transitions in Jaltomata, and we identify candidate loci that could arise either from multiple lineage-specific substitutions or standing ancestral polymorphisms. Our analysis provides a generalizable example of how to manage discordance when identifying loci associated with trait evolution in a radiating lineage.

scholarly journals Terraces in Gene Tree Reconciliation-Based Species Tree Inference

2020 ◽  
Author(s):  
Michael J. Sanderson ◽  
Michelle M. McMahon ◽  
Mike Steel
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Solution Space ◽  
Species Tree ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
Data Set ◽  
Tree Reconciliation ◽  
The Impact

AbstractTerraces in phylogenetic tree space are sets of trees with identical optimality scores for a given data set, arising from missing data. These were first described for multilocus phylogenetic data sets in the context of maximum parsimony inference and maximum likelihood inference under certain model assumptions. Here we show how the mathematical properties that lead to terraces extend to gene tree - species tree problems in which the gene trees are incomplete. Inference of species trees from either sets of gene family trees subject to duplication and loss, or allele trees subject to incomplete lineage sorting, can exhibit terraces in their solution space. First, we show conditions that lead to a new kind of terrace, which stems from subtree operations that appear in reconciliation problems for incomplete trees. Then we characterize when terraces of both types can occur when the optimality criterion for tree search is based on duplication, loss or deep coalescence scores. Finally, we examine the impact of assumptions about the causes of losses: whether they are due to imperfect sampling or true evolutionary deletion.

scholarly journals Phylogeny and Species Delimitation of Chinese Medicago (Leguminosae) and Its Relatives Based on Molecular and Morphological Evidence

2021 ◽  
Vol 11 ◽  
Author(s):  
Jinyuan Chen ◽  
Guili Wu ◽  
Nawal Shrestha ◽  
Shuang Wu ◽  
Wei Guo ◽  
...  
Keyword(s):  
Phylogenetic Relationship ◽  
Species Delimitation ◽  
Large Scale ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Population Based ◽  
Integrative Approach ◽  
Morphological Evidence ◽  
Sampling Errors ◽  
Lineage Sorting

Medicago and its relatives, Trigonella and Melilotus comprise the most important forage resources globally. The alfalfa selected from the wild relatives has been cultivated worldwide as the forage queen. In the Flora of China, 15 Medicago, eight Trigonella, and four Melilotus species are recorded, of which six Medicago and two Trigonella species are introduced. Although several studies have been conducted to investigate the phylogenetic relationship within the three genera, many Chinese naturally distributed or endemic species are not included in those studies. Therefore, the taxonomic identity and phylogenetic relationship of these species remains unclear. In this study, we collected samples representing 18 out of 19 Chinese naturally distributed species of these three genera and three introduced Medicago species, and applied an integrative approach by combining evidences from population-based morphological clusters and molecular data to investigate species boundaries. A total of 186 individuals selected from 156 populations and 454 individuals from 124 populations were collected for genetic and morphological analyses, respectively. We sequenced three commonly used DNA barcodes (trnH-psbA, trnK-matK, and ITS) and one nuclear marker (GA3ox1) for phylogenetic analyses. We found that 16 out of 21 species could be well delimited based on phylogenetic analyses and morphological clusters. Two Trigonella species may be merged as one species or treated as two subspecies, and Medicago falcata should be treated as a subspecies of the M. sativa complex. We further found that major incongruences between the chloroplast and nuclear trees mainly occurred among the deep diverging lineages, which may be resulted from hybridization, incomplete lineage sorting and/or sampling errors. Further studies involving a finer sampling of species associated with large scale genomic data should be employed to better understand the species delimitation of these three genera.

scholarly journals Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10896
Author(s):  
José Cerca ◽  
Angel G. Rivera-Colón ◽  
Mafalda S. Ferreira ◽  
Mark Ravinet ◽  
Michael D. Nowak ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Cryptic Species ◽  
Species Complex ◽  
Population Genomics ◽  
Incomplete Lineage Sorting ◽  
Morphological Evolution ◽  
Population Level ◽  
Similar Species ◽  
Lineage Sorting ◽  
Amplification Method

Morphologically similar species, that is cryptic species, may be similar or quasi-similar owing to the deceleration of morphological evolution and stasis. While the factors underlying the deceleration of morphological evolution or stasis in cryptic species remain unknown, decades of research in the field of paleontology on punctuated equilibrium have originated clear hypotheses. Species are expected to remain morphologically identical in scenarios of shared genetic variation, such as hybridization and incomplete lineage sorting, or in scenarios where bottlenecks reduce genetic variation and constrain the evolution of morphology. Here, focusing on three morphologically similar Stygocapitella species, we employ a whole-genome amplification method (WGA) coupled with double-digestion restriction-site associated DNA sequencing (ddRAD) to reconstruct the evolutionary history of the species complex. We explore population structure, use population-level statistics to determine the degree of connectivity between populations and species, and determine the most likely demographic scenarios which generally reject for recent hybridization. We find that the combination of WGA and ddRAD allowed us to obtain genomic-level data from microscopic eukaryotes (∼1 millimetre) opening up opportunities for those working with population genomics and phylogenomics in such taxa. The three species share genetic variance, likely from incomplete lineage sorting and ancient admixture. We speculate that the degree of shared variation might underlie morphological similarity in the Atlantic species complex.

scholarly journals Pollinators drive floral evolution in an Atlantic Forest genus

AoB Plants ◽  
2020 ◽  
Vol 12 (5) ◽  
Author(s):  
Beatriz Neves ◽  
Igor M Kessous ◽  
Ricardo L Moura ◽  
Dayvid R Couto ◽  
Camila M Zanella ◽  
...  
Keyword(s):  
Functional Groups ◽  
Atlantic Forest ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Floral Traits ◽  
Lineage Sorting ◽  
Pollination Syndromes ◽  
Angiosperm Diversification ◽  
Species Complexes ◽  
As Species

Abstract Pollinators are important drivers of angiosperm diversification at both micro- and macroevolutionary scales. Both hummingbirds and bats pollinate the species-rich and morphologically diverse genus Vriesea across its distribution in the Brazilian Atlantic Forest. Here, we (i) determine if floral traits predict functional groups of pollinators as documented, confirming the pollination syndromes in Vriesea and (ii) test if genetic structure in Vriesea is driven by geography (latitudinal and altitudinal heterogeneity) or ecology (pollination syndromes). We analysed 11 floral traits of 58 Vriesea species and performed a literature survey of Vriesea pollination biology. The genealogy of haplotypes was inferred and phylogenetic analyses were performed using chloroplast (rps16-trnk and matK) and nuclear (PHYC) molecular markers. Floral traits accurately predict functional groups of pollinators in Vriesea. Genetic groupings match the different pollination syndromes. Species with intermediate position were found between the groups, which share haplotypes and differ morphologically from the typical hummingbird- and bat-pollinated flowers of Vriesea. The phylogeny revealed moderately to well-supported clades which may be interpreted as species complexes. Our results suggest a role of pollinators driving ecological isolation in Vriesea clades. Incipient speciation and incomplete lineage sorting may explain the overall low genetic divergence within and among morphologically defined species, precluding the identification of clear species boundaries. The intermediate species with mixed floral types likely represent a window into shifts between pollinator syndromes. This study reports the morphological-genetic continuum that may be typical of ongoing pollinator-driven speciation in biodiversity hotspots.

scholarly journals Plastomes of eight Ligusticum species: characterization, genome evolution, and phylogenetic relationships

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Ting Ren ◽  
Zi-Xuan Li ◽  
Deng-Feng Xie ◽  
Ling-Jian Gui ◽  
Chang Peng ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
De Novo ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Purifying Selection ◽  
Repeat Sequence ◽  
Lineage Sorting ◽  
Plastome Evolution ◽  
Tree Topologies

Abstract Background The genus Ligusticum consists of approximately 60 species distributed in the Northern Hemisphere. It is one of the most taxonomically difficult taxa within Apiaceae, largely due to the varied morphological characteristics. To investigate the plastome evolution and phylogenetic relationships of Ligusticum, we determined the complete plastome sequences of eight Ligusticum species using a de novo assembly approach. Results Through a comprehensive comparative analysis, we found that the eight plastomes were similar in terms of repeat sequence, SSR, codon usage, and RNA editing site. However, compared with the other seven species, L. delavayi exhibited striking differences in genome size, gene number, IR/SC borders, and sequence identity. Most of the genes remained under the purifying selection, whereas four genes showed relaxed selection, namely ccsA, rpoA, ycf1, and ycf2. Non-monophyly of Ligusticum species was inferred from the plastomes and internal transcribed spacer (ITS) sequences phylogenetic analyses. Conclusion The plastome tree and ITS tree produced incongruent tree topologies, which may be attributed to the hybridization and incomplete lineage sorting. Our study highlighted the advantage of plastome with mass informative sites in resolving phylogenetic relationships. Moreover, combined with the previous studies, we considered that the current taxonomy system of Ligusticum needs to be improved and revised. In summary, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of Ligusticum species.

Genome skimming provides well resolved plastid and nuclear phylogenies, showing patterns of deep reticulate evolution in the tropical carnivorous plant genus Nepenthes (Caryophyllales)

2019 ◽  
Author(s):  
Lars Nauheimer ◽  
Lujing Cui ◽  
Charles Clarke ◽  
Darren M. Crayn ◽  
Greg Bourke ◽  
...  
Keyword(s):  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Reticulate Evolution ◽  
Carnivorous Plant ◽  
Evolutionary Relationships ◽  
Lineage Sorting ◽  
Molecular Clock Model ◽  
A Genome ◽  
Genome Skimming

Nepenthes is a genus of carnivorous plants consisting of ~160 species that are distributed in the paleotropics. Molecular systematics has so far not been able to resolve evolutionary relationships of most species because of the limited genetic divergence in previous studies. In the present study, we used a genome-skimming approach to infer phylogenetic relationships on the basis of 81 plastid genes and the highly repetitive rRNA (external transcribed spacer (ETS)–26S) for 39 accessions representing 34 species from eight sections. Maximum-likelihood analysis and Bayesian inference were performed separately for the nuclear and the plastid datasets. Divergence-time estimations were conducted on the basis of a relaxed molecular-clock model, using secondary calibration points. The phylogenetic analyses of the nuclear and plastid datasets yielded well resolved and supported phylogenies. Incongruences between the two datasets were detected, suggesting multiple hybridisation events or incomplete lineage sorting in the deeper and more recent evolutionary history of the genus. The inclusion of several known and suspected hybrids in the phylogenetic analysis provided insights into their parentage. Divergence-time estimations placed the crown diversification of Nepenthes in the early Miocene, c. 20 million years ago. This study showed that genome skimming provides well resolved nuclear and plastid phylogenies that provide valuable insights into the complex evolutionary relationships of Nepenthes.

scholarly journals Herzog Vindicated: Integrative Taxonomy Reveals that Trichostomum brachydontium (Pottiaceae, Bryophyta) Comprises Several Species

2021 ◽  
Author(s):  
Rosa M. Ros ◽  
Olaf Werner ◽  
Ron D. Porley
Keyword(s):  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Integrative Taxonomy ◽  
Morphological Data ◽  
Phylogenetic Study ◽  
Lineage Sorting ◽  
New Name ◽  
Molecular Phylogenetic Study ◽  
Molecular Phylogenetic ◽  
Phylogenetic Lineages

The morphologically variable moss Trichostomum brachydontium is very common in south and west Europe, particularly under Mediterranean and Atlantic climates. A morphological study was conducted alongside a molecular phylogenetic study based on nr ITS and cp rbcL regions in order to assess if T. brachydontium is an exceptionally polymorphic species as evidenced by the number of described infraspecific taxa from the last century or, alternatively, if it includes more than one species, and if so, to find the valid name for them. Phylogenetic analyses of both nuclear and chloroplast datasets show that there are four well-supported clades. While the ITS based tree is in good agreement with the morphological data, there are a few inconsistencies with reference to the rbcL tree; this may be explained by incomplete lineage sorting or by hybridization. The morphological survey revealed well-defined discriminate differences between the four phylogenetic lineages. The taxonomic conclusions include the recognition of four species: T. brachydontium s.s., T. herzogii (a new name proposed for var. cuspidatum), T. littorale and T. meridionale (a new name proposed for var. densum). Lectotypes are designated for T. brachydontium and T. littorale. Our results underline the ongoing need of integrative studies to examine further the underestimated diversity of the T. brachydontium complex in other regions.

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