scholarly journals Resolving Relationships among the Megadiverse Butterflies and Moths with a Novel Pipeline for Anchored Phylogenomics

2017 ◽  
Vol 67 (1) ◽  
pp. 78-93 ◽  
Author(s):  
Jesse W. Breinholt ◽  
Chandra Earl ◽  
Alan R. Lemmon ◽  
Emily Moriarty Lemmon ◽  
Lei Xiao ◽  
...  
Keyword(s):  
Anchored Phylogenomics

Evolution of green lacewings (Neuroptera: Chrysopidae): an anchored phylogenomics approach

2019 ◽  
Vol 44 (3) ◽  
pp. 514-526 ◽  
Author(s):  
Shaun L. Winterton ◽  
Jessica P. Gillung ◽  
Ivonne J. Garzón‐Orduña ◽  
Davide Badano ◽  
Laura C.V. Breitkreuz ◽  
...  
Keyword(s):  
Green Lacewings ◽  
Anchored Phylogenomics

scholarly journals Phylogenomic Reconstruction Sheds Light on New Relationships and Timescale of Rails (Aves: Rallidae) Evolution

Diversity ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 70 ◽  
Author(s):  
Juan C. Garcia-R ◽  
Emily Moriarty Lemmon ◽  
Alan R. Lemmon ◽  
Nigel French
Keyword(s):  
Evolutionary History ◽  
State Of The Art ◽  
Molecular Techniques ◽  
Evolutionary Significance ◽  
Phylogenetic Structure ◽  
Bayesian Approaches ◽  
Phylogenetic Studies ◽  
Anchored Phylogenomics ◽  
History Of ◽  
Phylogenomic Analyses

The integration of state-of-the-art molecular techniques and analyses, together with a broad taxonomic sampling, can provide new insights into bird interrelationships and divergence. Despite their evolutionary significance, the relationships among several rail lineages remain unresolved as does the general timescale of rail evolution. Here, we disentangle the deep phylogenetic structure of rails using anchored phylogenomics. We analysed a set of 393 loci from 63 species, representing approximately 40% of the extant familial diversity. Our phylogenomic analyses reconstruct the phylogeny of rails and robustly infer several previously contentious relationships. Concatenated maximum likelihood and coalescent species-tree approaches recover identical topologies with strong node support. The results are concordant with previous phylogenetic studies using small DNA datasets, but they also supply an additional resolution. Our dating analysis provides contrasting divergence times using fossils and Bayesian and non-Bayesian approaches. Our study refines the evolutionary history of rails, offering a foundation for future evolutionary studies of birds.

scholarly journals Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L.

2017 ◽  
Vol 104 (1) ◽  
pp. 102-115 ◽  
Author(s):  
Nora Mitchell ◽  
Paul O. Lewis ◽  
Emily Moriarty Lemmon ◽  
Alan R. Lemmon ◽  
Kent E. Holsinger
Keyword(s):  
Evolutionary Relationships ◽  
Rapid Radiation ◽  
Anchored Phylogenomics

scholarly journals Anchored phylogenomics of burrowing mayflies (Ephemeroptera) and the evolution of tusks

2018 ◽  
Vol 43 (4) ◽  
pp. 692-701 ◽  
Author(s):  
Dustin B. Miller ◽  
Stephanie Bartlett ◽  
Michel Sartori ◽  
Jesse W. Breinholt ◽  
T. Heath Ogden
Keyword(s):  
Anchored Phylogenomics

scholarly journals Anchored phylogenomics illuminates the skipper butterfly tree of life

2018 ◽  
Vol 18 (1) ◽  
Author(s):  
Emmanuel F. A. Toussaint ◽  
Jesse W. Breinholt ◽  
Chandra Earl ◽  
Andrew D. Warren ◽  
Andrew V. Z. Brower ◽  
...  
Keyword(s):  
Tree Of Life ◽  
Anchored Phylogenomics

Anchored phylogenomics and a revised classification of the planidial larva clade of jewel wasps (Hymenoptera: Chalcidoidea)

2022 ◽  
Author(s):  
Junxia Zhang ◽  
John M. Heraty ◽  
Christopher Darling ◽  
Robert L. Kresslein ◽  
Austin J. Baker ◽  
...  
Keyword(s):  
Anchored Phylogenomics

scholarly journals The limits of Quediini at last (Staphylinidae: Staphylininae): a rove beetle mega‐radiation resolved by comprehensive sampling and anchored phylogenomics

2021 ◽  
Vol 46 (2) ◽  
pp. 396-421
Author(s):  
Adam J. Brunke ◽  
Aslak K. Hansen ◽  
Maria Salnitska ◽  
Janina L. Kypke ◽  
Alexander V. Predeus ◽  
...  
Keyword(s):  
Rove Beetle ◽  
Anchored Phylogenomics

scholarly journals Evolution of lacewings and allied orders using anchored phylogenomics (Neuroptera, Megaloptera, Raphidioptera)

2017 ◽  
Vol 43 (2) ◽  
pp. 330-354 ◽  
Author(s):  
SHAUN L. WINTERTON ◽  
ALAN R. LEMMON ◽  
JESSICA P. GILLUNG ◽  
IVONNE J. GARZON ◽  
DAVIDE BADANO ◽  
...  
Keyword(s):  
Anchored Phylogenomics

scholarly journals Resolving Rapid Radiations Within Angiosperm Families Using Anchored Phylogenomics

2017 ◽  
Author(s):  
Étienne Léveillé-Bourret ◽  
Julian R. Starr ◽  
Bruce A. Ford ◽  
Emily Moriarty Lemmon ◽  
Alan R. Lemmon
Keyword(s):  
Estimation Error ◽  
Gene Tree ◽  
Nuclear Gene ◽  
Nuclear Data ◽  
Pcr Primers ◽  
Nuclear Genes ◽  
Flowering Plant ◽  
Nuclear Ribosomal Dna ◽  
Anchored Phylogenomics ◽  
Rapid Radiations

AbstractDespite the promise that molecular data would provide a seemingly unlimited source of independent characters, many plant phylogenetic studies are based on only two regions, the plastid genome and nuclear ribosomal DNA (nrDNA). Their popularity can be explained by high copy numbers and universal PCR primers that make their sequences easily amplified and converted into parallel datasets. Unfortunately, their utility is limited by linked loci and limited characters resulting in low confidence in the accuracy of phylogenetic estimates, especially when rapid radiations occur. In another contribution on anchored phylogenomics in angiosperms, we presented flowering plant-specific anchored enrichment probes for hundreds of conserved nuclear genes and demonstrated their use at the level of all angiosperms. In this contribution, we focus on a common problem in phylogenetic reconstructions below the family level: weak or unresolved backbone due to rapid radiations (≤ 10 million years) followed by long divergence, using the Cariceae-Dulichieae-Scirpeae clade (CDS, Cyperaceae) as a test case. By comparing our nuclear matrix of 461 genes to a typical Sanger-sequence dataset consisting of a few plastid genes (matK, ndhF) and an nrDNA marker (ETS), we demonstrate that our nuclear data is fully compatible with the Sanger dataset and resolves short backbone internodes with high support in both concatenated and coalescence-based analyses. In addition, we show that nuclear gene tree incongruence is inversely proportional to phylogenetic information content, indicating that incongruence is mostly due to gene tree estimation error. This suggests that large numbers of conserved nuclear loci could produce more accurate trees than sampling rapidly evolving regions prone to saturation and long-branch attraction. The robust phylogenetic estimates obtained here, and high congruence with previous morphological and molecular analyses, are strong evidence for a complete tribal revision of CDS. The anchored hybrid enrichment probes used in this study should be similarly effective in other flowering plant groups. [Carex, coalescent based species tree, flowering plants, low-copy nuclear genes, low-level phylogenetics, universal hybrid enrichment probes]

scholarly journals Owlflies are derived antlions: anchored phylogenomics supports a new phylogeny and classification of Myrmeleontidae (Neuroptera)

2018 ◽  
Vol 44 (2) ◽  
pp. 418-450 ◽  
Author(s):  
Renato J. P. Machado ◽  
Jessica P. Gillung ◽  
Shaun L. Winterton ◽  
Ivonne J. Garzón-Orduña ◽  
Alan R. Lemmon ◽  
...  
Keyword(s):  
Anchored Phylogenomics
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