The Evolutionary History of the Coral Genus Acropora (Scleractinia, Cnidaria) Based on a Mitochondrial and a Nuclear Marker: Reticulation, Incomplete Lineage Sorting, or Morphological Convergence?

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

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The convoluted evolutionary history of the capped-golden langur lineage (Cercopithecidae: Colobinae) – concatenation versus coalescent analyses

10.1101/508929 ◽

2018 ◽

Cited By ~ 2

Author(s):

Kunal Arekar ◽

Abhijna Parigi ◽

K. Praveen Karanth

Keyword(s):

Evolutionary History ◽

Incomplete Lineage Sorting ◽

Phylogenetic Position ◽

Lineage Sorting ◽

Nuclear Markers ◽

Mitochondrial Markers ◽

Multispecies Coalescent ◽

Nuclear Species ◽

History Of ◽

Golden Langur

AbstractEvolutionary studies have traditionally relied on concatenation based methods to reconstruct relationships from multiple markers. However, due to limitations of concatenation analyses, recent studies have proposed coalescent based methods to address evolutionary questions. Results from these methods tend to diverge from each other under situations where there is incomplete lineage sorting or hybridization. Here we used concatenation as well as multispecies coalescent (MSC) methods to understand the evolutionary origin of capped and golden langur (CG) lineage. Previous molecular studies have retrieved conflicting phylogenies, with mitochondrial tree grouping CG lineage with a largely Indian genus Semnopithecus, while nuclear markers support their affinities with a Southeast Asian genus, Trachypithecus. However, as pointed by others, the use of nuclear copies of mitochondrial DNA in the above studies might have generated the discordance. Because of this discordance, the phylogenetic position of CG lineage has been much debated in recent times. In this study, we have used nine nuclear and eight mitochondrial markers. Concatenated nuclear as well as the mitochondrial dataset recovered congruent relationships where CG lineage was sister to Trachypithecus. However nuclear species tree estimated using different MSC methods were incongruent with the above result, suggesting presence of incomplete lineage sorting (ILS)/hybridisation. Furthermore, CG lineage is morphologically intermediate between Semnopithecus and Trachypithecus. Based on this evidence, we argue that CG lineage evolved through hybridisation between Semnopithecus and Trachypithecus. Finally, we reason that both concatenation as well as coalescent methods should be used in conjunction for better understanding of various evolutionary hypotheses.

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Elucidating the Evolutionary History of Oenothera Sect. Pachylophus (Onagraceae): A Phylogenomic Approach

Systematic Botany ◽

10.1600/036364421x16312067913471 ◽

2021 ◽

Author(s):

Amanda Patsis ◽

Rick P. Overson ◽

Krissa A. Skogen ◽

Norman J. Wickett ◽

Matthew G. Johnson ◽

...

Keyword(s):

Evolutionary History ◽

Incomplete Lineage Sorting ◽

Phylogenetic Signal ◽

Morphological Characteristics ◽

Species Trees ◽

Lineage Sorting ◽

Complete Understanding ◽

Protein Coding ◽

History Of ◽

Current Species

Oenothera sect. Pachylophus has proven to be a valuable system in which to study plant-insect coevolution and the drivers of variation in floral morphology and scent. Current species circumscriptions based on morphological characteristics suggest that the section consists of five species, one of which is subdivided into five subspecies. Previous attempts to understand species (and subspecies) relationships at amolecular level have been largely unsuccessful due to high levels of incomplete lineage sorting and limited phylogenetic signal from slowly evolving gene regions. In the present study, target enrichment was used to sequence 322 conserved protein-coding nuclear genes from 50 individuals spanning the geographic range of Oenothera sect. Pachylophus, with species trees inferred using concatenation and coalescentbasedmethods. Our findings concur with previous research in suggesting that O. psammophila and O. harringtonii are nested within a paraphyleticOenothera cespitosa. By contrast, our results show clearly that the two annual species (O. cavernae and O. brandegeei) did not arise from the O. cespitosa lineage, but rather from a common ancestor of Oenothera sect. Pachylophus. Budding speciation as a result of edaphic specializationappears to best explain the evolution of the narrow endemic species O. harringtonii and O. psammophila. Complete understanding of possible introgression among subspecies of O. cespitosa will require broader sampling across the full geographical and ecological ranges of these taxa.

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Out of Sight, Out of Mind: Widespread Nuclear and Plastid-Nuclear Discordance in the Flowering Plant Genus Polemonium (Polemoniaceae) Suggests Widespread Historical Gene Flow Despite Limited Nuclear Signal

Systematic Biology ◽

10.1093/sysbio/syaa049 ◽

2020 ◽

Vol 70 (1) ◽

pp. 162-180

Author(s):

Jeffrey P Rose ◽

Cassio A P Toledo ◽

Emily Moriarty Lemmon ◽

Alan R Lemmon ◽

Kenneth J Sytsma

Keyword(s):

Gene Flow ◽

Evolutionary History ◽

Plastid Genome ◽

Incomplete Lineage Sorting ◽

Nuclear Genome ◽

Reticulate Evolution ◽

Phylogenetic Networks ◽

Flowering Plant ◽

Lineage Sorting ◽

History Of

Abstract Phylogenomic data from a rapidly increasing number of studies provide new evidence for resolving relationships in recently radiated clades, but they also pose new challenges for inferring evolutionary histories. Most existing methods for reconstructing phylogenetic hypotheses rely solely on algorithms that only consider incomplete lineage sorting (ILS) as a cause of intra- or intergenomic discordance. Here, we utilize a variety of methods, including those to infer phylogenetic networks, to account for both ILS and introgression as a cause for nuclear and cytoplasmic-nuclear discordance using phylogenomic data from the recently radiated flowering plant genus Polemonium (Polemoniaceae), an ecologically diverse genus in Western North America with known and suspected gene flow between species. We find evidence for widespread discordance among nuclear loci that can be explained by both ILS and reticulate evolution in the evolutionary history of Polemonium. Furthermore, the histories of organellar genomes show strong discordance with the inferred species tree from the nuclear genome. Discordance between the nuclear and plastid genome is not completely explained by ILS, and only one case of discordance is explained by detected introgression events. Our results suggest that multiple processes have been involved in the evolutionary history of Polemonium and that the plastid genome does not accurately reflect species relationships. We discuss several potential causes for this cytoplasmic-nuclear discordance, which emerging evidence suggests is more widespread across the Tree of Life than previously thought. [Cyto-nuclear discordance, genomic discordance, phylogenetic networks, plastid capture, Polemoniaceae, Polemonium, reticulations.]

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Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives

10.7287/peerj.preprints.377v1 ◽

2014 ◽

Author(s):

Susan R Strickler ◽

Aureliano Bombarely ◽

Jesse D Munkvold ◽

Naama Menda ◽

Gregory B Martin ◽

...

Keyword(s):

Evolutionary History ◽

Common Ancestor ◽

Genomic Sequence ◽

Incomplete Lineage Sorting ◽

Wild Relatives ◽

Lineage Sorting ◽

Phylogenetic Information ◽

Closely Related Species ◽

Phylogenetic Discordance ◽

History Of

Background Studies of ancestry are difficult in tomato because it crosses with many wild relatives and species in the tomato clade have diverged very recently. As a result, the phylogeny in relation to its closest relatives remains uncertain. By using coding sequence from Solanum lycopericum, S. galapagense, S. pimpinellifolium, S. corneliomuelleri, and S. tuberosum and genomic sequence from two of cultivated tomato’s closest relatives, S. galapagense and S. pimpinellifolium, as well as an heirloom line, S. lycopersicum ‘Yellow Pear’, we have aimed to resolve the phylogenies of these closely related species as well as identify phylogenetic discordance in the reference cultivated tomato. Results Divergence date estimates suggest divergence of S. lycopersicum, S. galapagense, and S. pimpinellifolium happened less than 0.5 MYA. Phylogenies based on 8,857 coding sequences support grouping of S. lycopersicum and S. galapagense, although two secondary trees are also highly represented. A total of 29 genes in our analysis showed evidence of selection along the S. lycopersicum lineage. Whole genome phylogenies showed that while incongruence is prevalent in genomic comparisons between these accessions, likely as a result of incomplete lineage sorting and introgression, a primary phylogenetic history was strongly supported. Conclusions Based on analysis of these accessions, S. galapagense appears to be closely related to S. lycopersicum, suggesting they had a common ancestor prior to the arrival of an S. galapagense ancestor to the Galápagos Islands, but after divergence of the sequenced S. pimpinellifolium. Genes showing selection along the S. lycopersicum lineage may be important in domestication. Further analysis of intraspecific data in these species will help to establish the evolutionary history of cultivated tomato. The use of an heirloom line is helpful in deducing true phylogenetic information of S. lycopersicum and identifying regions of introgression from wild species.

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Genomic architecture and introgression shape a butterfly radiation

10.1101/466292 ◽

2018 ◽

Cited By ~ 8

Author(s):

Nathaniel B. Edelman ◽

Paul B. Frandsen ◽

Michael Miyagi ◽

Bernardo Clavijo ◽

John Davey ◽

...

Keyword(s):

Evolutionary History ◽

Incomplete Lineage Sorting ◽

Low Cost ◽

Structural Rearrangement ◽

Color Pattern ◽

Lineage Sorting ◽

Genomic Architecture ◽

History Of ◽

High Gene ◽

High Gene Density

We here pioneer a low-cost assembly strategy for 20 Heliconiini genomes to characterize the evolutionary history of the rapidly radiating genus Heliconius. A bifurcating tree provides a poor fit to the data, and we therefore explore a reticulate phylogeny for Heliconius. We probe the genomic architecture of gene flow, and develop a new method to distinguish incomplete lineage sorting from introgression. We find that most loci with non-canonical histories arose through introgression, and are strongly underrepresented in regions of low recombination and high gene density. This is expected if introgressed alleles are more likely to be purged in such regions due to tighter linkage with incompatibility loci. Finally, we identify a hitherto unrecognized inversion, and show it is a convergent structural rearrangement that captures a known color pattern switch locus within the genus. Our multi-genome assembly approach enables an improved understanding of adaptive radiation.

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Incomplete lineage sorting and hybridization in the evolutionary history of closely related, endemic yellow-flowered Aechmea species of subgenus Ortgiesia (Bromeliaceae)

American Journal of Botany ◽

10.3732/ajb.1700103 ◽

2017 ◽

Vol 104 (7) ◽

pp. 1073-1087 ◽

Cited By ~ 14

Author(s):

Márcia Goetze ◽

Camila M. Zanella ◽

Clarisse Palma-Silva ◽

Miriam V. Büttow ◽

Fernanda Bered

Keyword(s):

Evolutionary History ◽

Incomplete Lineage Sorting ◽

Lineage Sorting ◽

History Of

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Integrative species delimitation based on COI, ITS, and morphological evidence illustrates a unique evolutionary history of the genus Paracercion (Odonata: Coenagrionidae)

PeerJ ◽

10.7717/peerj.11459 ◽

2021 ◽

Vol 9 ◽

pp. e11459

Author(s):

Haiguang Zhang ◽

Xin Ning ◽

Xin Yu ◽

Wen-Jun Bu

Keyword(s):

Species Delimitation ◽

Evolutionary History ◽

Incomplete Lineage Sorting ◽

Molecular Data ◽

Morphological Evidence ◽

Lineage Sorting ◽

Putative Species ◽

Interspecific Divergence ◽

Speciation Event ◽

History Of

Paracercion are common ‘blue and black’ colored damselflies. We explore the species boundaries of Paracercion (Odonata: Coenagrionidae) using ABGD, bPTP, GMYC and Distance-based clustering. We finally got the molecular data of all nine species of Paracercion. P. hieroglyphicum and P. melanotum were combined into one putative species based on cytochrome c oxidase I (COI). However, they were separated into two putative species based on the nuclear segment including ITS1-5.8S-ITS2 (ITS). This suggests the introgression of mtDNA in Paracercion. Paracercion barbatum and Paracercion melanotum can be separated into two species based on COI, whereas they were combined into one putative species based on ITS, which suggests a hybridization event between them. The lower interspecific divergence (COI: 0.49%) between P. barbatum and Paracercion v-nigrum indicates a recent speciation event in Paracercion. Paracercion sieboldii and P. v-nigrum can be separated into two putative species based on COI, while they were frequently merged into the same putative species based on ITS. This can be explained by incomplete lineage sorting in nDNA. Besides, P. pendulum and P. malayanum were synonymized as junior synonyms of P. melanotum. P. luzonicum was confirmed not to belong to Paracercion. The possibility of introgression, hybridization, recent speciation and incomplete lineage sorting makes species delimitation, based on molecular data, difficult and complicates understanding of the evolutionary history of Paracercion. The discordance in COI and ITS also indicates the value of using markers from different sources in species delimitation studies.

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Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives

10.7287/peerj.preprints.377 ◽

2014 ◽

Author(s):

Susan R Strickler ◽

Aureliano Bombarely ◽

Jesse D Munkvold ◽

Naama Menda ◽

Gregory B Martin ◽

...

Keyword(s):

Evolutionary History ◽

Common Ancestor ◽

Genomic Sequence ◽

Incomplete Lineage Sorting ◽

Wild Relatives ◽

Lineage Sorting ◽

Phylogenetic Information ◽

Closely Related Species ◽

Phylogenetic Discordance ◽

History Of

Background Studies of ancestry are difficult in tomato because it crosses with many wild relatives and species in the tomato clade have diverged very recently. As a result, the phylogeny in relation to its closest relatives remains uncertain. By using coding sequence from Solanum lycopericum, S. galapagense, S. pimpinellifolium, S. corneliomuelleri, and S. tuberosum and genomic sequence from two of cultivated tomato’s closest relatives, S. galapagense and S. pimpinellifolium, as well as an heirloom line, S. lycopersicum ‘Yellow Pear’, we have aimed to resolve the phylogenies of these closely related species as well as identify phylogenetic discordance in the reference cultivated tomato. Results Divergence date estimates suggest divergence of S. lycopersicum, S. galapagense, and S. pimpinellifolium happened less than 0.5 MYA. Phylogenies based on 8,857 coding sequences support grouping of S. lycopersicum and S. galapagense, although two secondary trees are also highly represented. A total of 29 genes in our analysis showed evidence of selection along the S. lycopersicum lineage. Whole genome phylogenies showed that while incongruence is prevalent in genomic comparisons between these accessions, likely as a result of incomplete lineage sorting and introgression, a primary phylogenetic history was strongly supported. Conclusions Based on analysis of these accessions, S. galapagense appears to be closely related to S. lycopersicum, suggesting they had a common ancestor prior to the arrival of an S. galapagense ancestor to the Galápagos Islands, but after divergence of the sequenced S. pimpinellifolium. Genes showing selection along the S. lycopersicum lineage may be important in domestication. Further analysis of intraspecific data in these species will help to establish the evolutionary history of cultivated tomato. The use of an heirloom line is helpful in deducing true phylogenetic information of S. lycopersicum and identifying regions of introgression from wild species.

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Molecular systematics and phylogeography of a widespread Neotropical avian lineage: evidence for cryptic speciation with protracted gene flow throughout the Late Quaternary

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blaa193 ◽

2020 ◽

Author(s):

Leonardo S Miranda ◽

Bernardo O Prestes ◽

Alexandre Aleixo

Keyword(s):

Gene Flow ◽

Incomplete Lineage Sorting ◽

Late Quaternary ◽

Integrative Approach ◽

Lineage Sorting ◽

Distribution Models ◽

The North ◽

History Of ◽

Andean South America ◽

Spatio Temporal

Abstract Here we use an integrative approach, including coalescent-based methods, isolation–migration and species distribution models, to infer population structure, divergence times and diversification in the two species of the genus Cymbilaimus (Aves, Thamnophilidae). Our results support a recent and rapid diversification with both incomplete lineage sorting and gene flow shaping the evolutionary history of Cymbilaimus. The spatio-temporal pattern of cladogenesis suggests that Cymbilaimus originated in the north/western portion of cis-Andean South America and then diversified into the Brazilian Shield and Central America after consolidation of the modern Amazonian drainage and the Andean range. This evolutionary scenario is explained by cycles of range expansion and dispersal, followed by isolation, and recurrent gene flow, during the last 1.2 Myr. Our results agree with those recently reported for other closely related suboscine lineages, whereby the window of introgression between closely related taxa remains open for up to a few million years after their original split. In Cymbilaimus, introgression was recurrent between C. lineatus and C. sanctaemariae, even after they acquired vocal and ecological differentiation, supporting the claim that at least in Neotropical suboscines, full reproductive compatibility may take millions of years to evolve and cannot be interpreted as synonymous with a lack of speciation.

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