scholarly journals Genomic data reveals potential for hybridization, introgression, and incomplete lineage sorting to confound phylogenetic relationships in an adaptive radiation of narrow-mouth frogs

Evolution ◽  
2016 ◽  
Vol 71 (2) ◽  
pp. 475-488 ◽  
Author(s):  
Alana M. Alexander ◽  
Yong-Chao Su ◽  
Carl H. Oliveros ◽  
Karen V. Olson ◽  
Scott L. Travers ◽  
...  
Keyword(s):  
Adaptive Radiation ◽  
Phylogenetic Relationships ◽  
Incomplete Lineage Sorting ◽  
Genomic Data ◽  
Lineage Sorting

scholarly journals Genomic architecture and introgression shape a butterfly radiation

Science ◽  
2019 ◽  
Vol 366 (6465) ◽  
pp. 594-599 ◽  
Author(s):  
Nathaniel B. Edelman ◽  
Paul B. Frandsen ◽  
Michael Miyagi ◽  
Bernardo Clavijo ◽  
John Davey ◽  
...  
Keyword(s):  
Gene Flow ◽  
Adaptive Radiation ◽  
Phylogenetic Relationships ◽  
De Novo ◽  
Incomplete Lineage Sorting ◽  
Color Pattern ◽  
Lineage Sorting ◽  
Genome Sequences ◽  
Genomic Architecture ◽  
Genome Assemblies

We used 20 de novo genome assemblies to probe the speciation history and architecture of gene flow in rapidly radiating Heliconius butterflies. Our tests to distinguish incomplete lineage sorting from introgression indicate that gene flow has obscured several ancient phylogenetic relationships in this group over large swathes of the genome. Introgressed loci are underrepresented in low-recombination and gene-rich regions, consistent with the purging of foreign alleles more tightly linked to incompatibility loci. Here, we identify a hitherto unknown inversion that traps a color pattern switch locus. We infer that this inversion was transferred between lineages by introgression and is convergent with a similar rearrangement in another part of the genus. These multiple de novo genome sequences enable improved understanding of the importance of introgression and selective processes in adaptive radiation.

scholarly journals Comparative Performance of Popular Methods for Hybrid Detection using Genomic Data

2020 ◽  
Author(s):  
Sungsik Kong ◽  
Laura S. Kubatko
Keyword(s):  
Statistical Power ◽  
Evolutionary Dynamics ◽  
Mean Squared Error ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Genomic Data ◽  
Lineage Sorting ◽  
Comparative Performance ◽  
Pattern Frequency ◽  
Hybrid Detection

AbstractInterspecific hybridization is an important evolutionary phenomenon that generates genetic variability in a population and fosters species diversity in nature. The availability of large genome scale datasets has revolutionized hybridization studies to shift from the examination of the presence or absence of hybrids in nature to the investigation of the genomic constitution of hybrids and their genome-specific evolutionary dynamics. Although a handful of methods have been proposed in an attempt to identify hybrids, accurate detection of hybridization from genomic data remains a challenging task. The available methods can be classified broadly as site pattern frequency based and population genetic clustering approaches, though the performance of the two classes of methods under different hybridization scenarios has not been extensively examined. Here, we use simulated data to comparatively evaluate the performance of four tools that are commonly used to infer hybridization events: the site pattern frequency based methods HyDe and the D-statistic (i.e., the ABBA-BABA test), and the population clustering approaches structure and ADMIXTURE. We consider single hybridization scenarios that vary in the time of hybridization and the amount of incomplete lineage sorting (ILS) for different proportions of parental contributions (γ); introgressive hybridization; multiple hybridization scenarios; and a mixture of ancestral and recent hybridization scenarios. We focus on the statistical power to detect hybridization, the false discovery rate (FDR) for the D-statistic and HyDe, and the accuracy of the estimates of γ as measured by the mean squared error for HyDe, structure, and ADMIXTURE. Both HyDe and the D-statistic demonstrate a high level of detection power in all scenarios except those with high ILS, although the D-statistic often has an unacceptably high FDR. The estimates of γ in HyDe are impressively robust and accurate whereas structure and ADMIXTURE sometimes fail to identify hybrids, particularly when the proportional parental contributions are asymmetric (i.e., when γ is close to 0). Moreover, the posterior distribution estimated using structure exhibits multimodality in many scenarios, making interpretation difficult. Our results provide guidance in selecting appropriate methods for identifying hybrid populations from genomic data.

Phylogenetic relationships based on nuclear and plastid DNA sequences reveal recent diversification and discordant patterns of morphological evolution of the Chilean genera of Gilliesieae (Amaryllidaceae: Allioideae)

2020 ◽  
Vol 194 (1) ◽  
pp. 84-99
Author(s):  
Inelia Escobar ◽  
Eduardo Ruiz-Ponce ◽  
Paula J Rudall ◽  
Michael F Fay ◽  
Oscar Toro-Núñez ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Incomplete Lineage Sorting ◽  
Morphological Evolution ◽  
Strong Support ◽  
Plastid Dna ◽  
Lineage Sorting ◽  
Generic Level ◽  
Molecular Analyses ◽  
Floral Diversity

Abstract Gilliesieae are a South American tribe of Amaryllidaceae characterized by high floral diversity. Given different taxonomic interpretations and proposals for generic and specific relationships, a representative phylogenetic analysis is required to clarify the systematics of this group. The present study provides a framework for understanding phylogenetic relationships and contributing to the development of an appropriate taxonomic treatment of Gilliesieae. Molecular analyses, based on nuclear (ITS) and plastid DNA sequences (trnL-F and rbcL), resolve with strong support the monophyly of the tribe and the differentiation of two major clades. Clade I comprises the genera Gilliesia, Gethyum and Solaria and Clade II includes Miersia and Speea. These well-supported clades are mostly congruent with vegetative and karyotype characters rather than, e.g., floral symmetry. At the generic level, all molecular analyses reveal the paraphyly of Gilliesia and Miersia. Gethyum was found to be paraphyletic, resulting in the confirmation of Ancrumia as a distinct genus. Several instances of incongruent phylogenetic signals were found among data sets. The calibrated tree suggests a recent diversification of the tribe (Pliocene–Pleistocene), a contemporary process of speciation in which instances of hybridization and incomplete lineage sorting could explain patterns of paraphyly and incongruence of floral morphology.

scholarly journals Interrogating Genomic Data in the Phylogenetic Placement of Treeshrews Reveals Potential Sources of Conflict

2021 ◽  
Author(s):  
Alexander Knyshov ◽  
Yana Hrytsenko ◽  
Robert Literman ◽  
Rachel S Schwartz
Keyword(s):  
Incomplete Lineage Sorting ◽  
Phylogenetic Signal ◽  
Strong Support ◽  
Genomic Data ◽  
Phylogenetic Position ◽  
Lineage Sorting ◽  
Mammal Species ◽  
Small Magnitude ◽  
Locus Selection ◽  
Alternative Hypotheses

The position of some taxa on the Tree of Life remains controversial despite the increase in genomic data used to infer phylogenies. While analyzing large datasets alleviates stochastic errors, it does not prevent systematic errors in inference, caused by both biological (e.g., incomplete lineage sorting, hybridization) and methodological (e.g., incorrect modeling, erroneous orthology assessments) factors. In our study, we systematically investigated factors that could result in these controversies, using the treeshrew (Scandentia, Mammalia) as a study case. Recent studies have narrowed the phylogenetic position of treeshrews to three competing hypotheses: sister to primates and flying lemurs (Primatomorpha), sister to rodents and lagomorphs (Glires), or sister to a clade comprising all of these. We sampled 50 mammal species including three treeshrews, a selection of taxa from the potential sister groups, and outgroups. Using a large diverse set of loci, we assessed support for the alternative phylogenetic position of treeshrews. A plurality of loci support treeshrews as sister to rodents and lagomorphs; however, only a few loci exhibit strong support for any hypothesis. Surprisingly, we found that a subset of loci that strongly support the monophyly of Primates, support treeshrews as sister to primates and flying lemurs. The overall small magnitude of differences in phylogenetic signal among the alternative hypotheses suggests that these three groups diversified nearly simultaneously. However, with our large dataset and approach to examining support, we provide evidence for the hypothesis of treeshrews as sister to rodents and lagomorphs, while demonstrating why support for alternate hypotheses has been seen in prior work. We also suggest that locus selection can unwittingly bias results.

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.

scholarly journals Phylogenomic Analyses Clarify True Species within the Butterfly Genus Speyeria despite Evidence of a Recent Adaptive Radiation

Insects ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 209
Author(s):  
Erin Thompson ◽  
Jason Baumsteiger ◽  
Ryan I. Hill
Keyword(s):  
Adaptive Radiation ◽  
North American ◽  
Incomplete Lineage Sorting ◽  
Legal Protection ◽  
Evolutionary Model ◽  
Morphological Characters ◽  
Anthropogenic Factors ◽  
Lineage Sorting ◽  
The North ◽  
Phylogenetic Resolution

When confronted with an adaptive radiation, considerable evidence is needed to resolve the evolutionary relationships of these closely related lineages. The North American genus Speyeria is one especially challenging radiation of butterflies due to potential signs of incomplete lineage sorting, ongoing hybridization, and similar morphological characters between species. Previous studies have found species to be paraphyletic and have been unable to disentangle taxa, often due to a lack of data and/or incomplete sampling. As a result, Speyeria remains unresolved. To achieve phylogenetic resolution of the genus, we conducted phylogenomic and population genomic analyses of all currently recognized North American Speyeria species, as well as several subspecies, using restriction-site-associated DNA sequencing (RADseq). Together, these analyses confirm the 16 canonical species, and clarify many internal relationships. However, a few relationships within Speyeria were poorly supported depending on the evolutionary model applied. This lack of resolution among certain taxa corroborates Speyeria is experiencing an ongoing adaptive radiation, with incomplete lineage sorting and lack of postzygotic reproductive barriers contributing to hybridization and further ambiguity. Given that many Speyeria taxa are under duress from anthropogenic factors, their legal protection must be viewed cautiously and on a case by case basis in order to properly conserve the diversity being generated.

scholarly journals Phylogenetic Trees and Networks Can Serve as Powerful and Complementary Approaches for Analysis of Genomic Data

2019 ◽  
Vol 69 (3) ◽  
pp. 593-601 ◽  
Author(s):  
Christopher Blair ◽  
Cécile Ané
Keyword(s):  
Gene Flow ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Phylogenetic Network ◽  
Genomic Data ◽  
Point Of View ◽  
Phylogenetic Networks ◽  
Lineage Sorting

Abstract Genomic data have had a profound impact on nearly every biological discipline. In systematics and phylogenetics, the thousands of loci that are now being sequenced can be analyzed under the multispecies coalescent model (MSC) to explicitly account for gene tree discordance due to incomplete lineage sorting (ILS). However, the MSC assumes no gene flow post divergence, calling for additional methods that can accommodate this limitation. Explicit phylogenetic network methods have emerged, which can simultaneously account for ILS and gene flow by representing evolutionary history as a directed acyclic graph. In this point of view, we highlight some of the strengths and limitations of phylogenetic networks and argue that tree-based inference should not be blindly abandoned in favor of networks simply because they represent more parameter rich models. Attention should be given to model selection of reticulation complexity, and the most robust conclusions regarding evolutionary history are likely obtained when combining tree- and network-based inference.

Phylogeny and evolution of the green lizards, Lacerta spp. (Squamata: Lacertidae) based on mitochondrial and nuclear DNA sequences

2005 ◽  
Vol 26 (3) ◽  
pp. 271-285 ◽  
Author(s):  
D. James Harris ◽  
Nuno Ferrand ◽  
Eduardo Crespo ◽  
Raquel Godinho
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Nuclear Dna ◽  
Incomplete Lineage Sorting ◽  
Bird Species ◽  
Rrna Genes ◽  
12S Rrna ◽  
Lineage Sorting ◽  
Extant Species ◽  
Mitochondrial Cytochrome B

AbstractPartial DNA sequences from three mitochondrial (cytochrome b, 12S rRNA and 16S rRNA) and two nuclear (β-fibrinogen intron 7 and C-mos) genes were used to estimate the phylogenetic relationships among all eight extant species of green lizards, Lacerta sensu stricto, and many currently recognized subspecies. All eight species form a monophyletic group. L. agilis, L. schreiberi and L. strigata are genetically well differentiated species. L. trilineata and L. pamphylica are not monophyletic units based on analyses of the β-fibrinogen intron 7. Lacerta media is closely related to some Lacerta trilineata. L. bilineata and L. viridis are closely related, and recognition of L. bilineata as a distinct species makes L. viridis paraphyletic also. For both L. bilineata and L. viridis, some subspecies appear to remain in their southern glacial refugia, while a single genetic entity shows successfully postglacial expansion. The topology derived from C-mos variation is concordant with that derived from mtDNA, with substitutions occurring at a similar rate to that of transversions in the rRNA genes. Although C-mos is typically used at deeper taxonomic levels it is also phylogenetically informative within green lizards. β-fibrinogen intron 7, typically used for assessing phylogenetic relationships among bird species, is a useful phylogenetic marker for reptiles also, showing considerable variation between species. There is not complete concordance between estimates of relationships derived from the mtDNA and nuclear markers, probably because rapid diversification led to incomplete lineage sorting in the green lizards. Introgression could also be occuring between some species.

scholarly journals Plastome data reveal multiple geographic origins of Quercus Group Ilex

2015 ◽  
Author(s):  
Marco Cosimo Simeone ◽  
Guido W Grimm ◽  
Alessio Papini ◽  
Federico Vessella ◽  
Simone Cardoni ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Nuclear Genome ◽  
Sequence Divergence ◽  
Geographic Area ◽  
Geographic Region ◽  
Tectonic Activity ◽  
Lineage Sorting ◽  
Distribution Ranges

Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One exception is the large and economically important genus Quercus (oaks). Whereas differentiation patterns of the nuclear genome are in agreement with morphology and the fossil record, diversity patterns in the plastome are at odds with established taxonomic and phylogenetic relationships. However, the extent and evolutionary implications of this incongruence has yet to be fully uncovered. The DNA sequence divergence of four Euro-Mediterranean Group Ilex oak species (Quercus ilex L., Q. coccifera L., Q. aucheri Jaub. & Spach., Q. alnifolia Poech.) was explored at three chloroplast markers (rbcL, trnK-matK, trnH-psbA). Phylogenetic relationships were reconstructed including worldwide members of additional 55 species representing all Quercus subgeneric groups. Family and order sequence data were harvested from gene banks to better frame the observed divergence in larger taxonomic contexts. We found a strong geographic sorting in the focal group and the genus in general that is entirely decoupled from species boundaries. Main plastid haplotypes shared by distinct oak lineages from the same geographic region and high plastid diversity in members of Group Ilex are indicative for a polyphyletic origin of their plastomes. The results suggest that incomplete lineage sorting and repeated phases of unidirectional introgression among ancestral lineages of Group Ilex and two other main Groups of Eurasian oaks (Cyclobalanopsis and Cerris) caused this complex pattern. Comparison with the current phylogenetic synthesis also suggests an initial high- versus mid-latitude biogeographic split within Quercus. High plastome plasticity of Group Ilex reflects geographic area disruptions, possibly linked with high tectonic activity of past and modern distribution ranges, that did not leave imprints in the nuclear genome of modern species and infrageneric lineages.

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