scholarly journals The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds

PLoS Biology ◽  
2015 ◽  
Vol 13 (8) ◽  
pp. e1002224 ◽  
Author(s):  
Alexander Suh ◽  
Linnéa Smeds ◽  
Hans Ellegren
Keyword(s):  
Adaptive Radiation ◽  
Incomplete Lineage Sorting ◽  
Lineage Sorting

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 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 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.

Insights into the Evolutionary History of the Hawaiian Bidens (Asteraceae) Adaptive Radiation Revealed Through Phylogenomics

2020 ◽  
Vol 111 (1) ◽  
pp. 119-137 ◽  
Author(s):  
Matthew L Knope ◽  
M Renee Bellinger ◽  
Erin M Datlof ◽  
Timothy J Gallaher ◽  
Melissa A Johnson
Keyword(s):  
Adaptive Radiation ◽  
Incomplete Lineage Sorting ◽  
Divergence Time ◽  
Lineage Sorting ◽  
Crown Group ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Biogeographic History ◽  
History Of ◽  
Phylogenomic Analyses

Abstract Hawaiian plant radiations often result in lineages with exceptionally high species richness and extreme morphological and ecological differentiation. However, they typically display low levels of genetic variation, hindering the use of classic DNA markers to resolve their evolutionary histories. Here we utilize a phylogenomic approach to generate the first generally well-resolved phylogenetic hypothesis for the evolution of the Hawaiian Bidens (Asteraceae) adaptive radiation, including refined initial colonization and divergence time estimates. We sequenced the chloroplast genome (plastome) and nuclear ribosomal complex for 18 of the 19 endemic species of Hawaiian Bidens and 4 outgroup species. Phylogenomic analyses based on the concatenated dataset (plastome and nuclear) resulted in identical Bayesian and Maximum Likelihood trees with high statistical support at most nodes. Estimates from dating analyses were similar across datasets, with the crown group emerging ~1.76–1.82 Mya. Biogeographic analyses based on the nuclear and concatenated datasets indicated that colonization within the Hawaiian Islands generally followed the progression rule with 67–80% of colonization events from older to younger islands, while only 53% of events followed the progression rule in the plastome analysis. We find strong evidence for nuclear-plastome conflict indicating a potentially important role for hybridization in the evolution of the group. However, incomplete lineage sorting cannot be ruled out due to the small number of independent loci analyzed. This study contributes new insights into species relationships and the biogeographic history of the explosive Hawaiian Bidens adaptive radiation.

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.

Shallow genetic divergence and distinct phenotypic differences between two Andean hummingbirds: Speciation with gene flow?

The Auk ◽  
2019 ◽  
Vol 136 (4) ◽  
Author(s):  
Catalina Palacios ◽  
Silvana García-R ◽  
Juan Luis Parra ◽  
Andrés M Cuervo ◽  
F Gary Stiles ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Incomplete Lineage Sorting ◽  
Lineage Sorting ◽  
Phenotypic Differences ◽  
Adaptive Mechanisms ◽  
The Face ◽  
Gloger’S Rule ◽  
Divergence With Gene Flow ◽  
Neutral Markers

Abstract Ecological speciation can proceed despite genetic interchange when selection counteracts the homogenizing effects of migration. We tested predictions of this divergence-with-gene-flow model in Coeligena helianthea and C. bonapartei, 2 parapatric Andean hummingbirds with marked plumage divergence. We sequenced putatively neutral markers (mitochondrial DNA [mtDNA] and nuclear ultraconserved elements [UCEs]) to examine genetic structure and gene flow, and a candidate gene (MC1R) to assess its role underlying divergence in coloration. We also tested the prediction of Gloger’s rule that darker forms occur in more humid environments, and examined morphological variation to assess adaptive mechanisms potentially promoting divergence. Genetic differentiation between species was low in both ND2 and UCEs. Coalescent estimates of migration were consistent with divergence with gene flow, but we cannot reject incomplete lineage sorting reflecting recent speciation as an explanation for patterns of genetic variation. MC1R variation was unrelated to phenotypic differences. Species did not differ in macroclimatic niches but were distinct in morphology. Although we reject adaptation to variation in macroclimatic conditions as a cause of divergence, speciation may have occurred in the face of gene flow driven by other ecological pressures or by sexual selection. Marked phenotypic divergence with no neutral genetic differentiation is remarkable for Neotropical birds, and makes C. helianthea and C. bonapartei an appropriate system in which to search for the genetic basis of species differences employing genomics.

Sign in / Sign up

Export Citation Format

Share Document