Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high‐Andean diversification (Asteraceae: Astereae: Diplostephium)

On the phylogenetic position of Myzostomida: can 77 genes get it wrong?

Bleidorn, C.
Podsiadlowski, L.
Zhong, M.
Eeckhaut, I.
Hartmann, S.
Halanych, K.
Tiedemann, R.

January 2009

Background: Phylogenomic analyses recently became popular to address questions about deep metazoan p...

Data for Morales et al. Perpendicular axes of incipient speciation in a widespread passerine with mitonuclear discordance (unpublished, submitted to Axios Review, April 2016)

Hernan Morales (2886857)
Paul Sunnucks (182576)
Leo Joseph (114181)
Alexandra Pavlova (182554)

August 2016

<div>Contents:</div><div><br></div><div>SampleInfo:</div><div>Table 1. Samples screened for nuclear ...

Disentangling sources of gene tree discordance in phylogenomic datasets: testing ancient hybridizations in Amaranthaceae s.l.

Morales-Briones, Diego F.
Kadereit, Gudrun
Tefarikis, Delphine
Moore, Michael
Smith, Stephen
Brockington, Samuel
Timoneda, Alfonso
Yim, Won
Cushman, John
Yang, Ya

August 2020

Gene tree discordance in large genomic datasets can be caused by evolutionary processes such as inco...

Data from: Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium)

Vargas, Oscar M.
Ortiz, Edgardo M.
Simpson, Beryl B.

High-throughput sequencing is helping biologists to overcome the difficulties of inferring the phylo...

One thousand plant transcriptomes and the phylogenomics of green plants

One Thousand Plant Transcriptomes Initiative

October 2019

Article describes the results of the One Thousand Plant Transcriptomes Initiative's efforts to seque...

Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages

Stull, Gregory
Soltis, Pamela S.
Soltis, Douglas E.
Gitzendanner, Matthew A.
Smith, Stephen A.

May 2020

Premise : Discordance between nuclear and organellar phylogenies (cytonuclear discordance) is a well...

Phylogenomic analyses in Phrymaceae reveal extensive gene tree discordance in relationships among major clades

Morales-Briones, Diego F.
Lin, Nan
Huang, Eileen
Grossenbacher, Dena
Sobel, James
Gilmore, Caroline
Tank, David
Yang, Ya

April 2022

• Premise of the study: Phylogenomic datasets using genomes and transcriptomes provide rich opportun...

Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

Pease, James B.
Brown, Joseph W.
Walker, Joseph F.
Hinchliff, Cody E.
Smith, Stephen A.

March 2018

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143738/1/ajb21016-sup-0009-AppendixS9....

Data from: Phylogenomic structure and speciation in an emerging model: The Sphagnum magellanicum complex (Bryophyta)

Shaw, A. Jonathan
Duffy, Aaron
Piatkowski, Bryan
Aguero, Blanka
Imwattana, Karn
Nieto-Lugilde, Marta
Healy, Adam
Weston, David
Patel, Megan
Schmutz, Jeremy
Yavitt, Joseph
Hassel, Kristian
Stenøien, Hans
Flatberg, Kjell Ivar

September 2022

The moss genus Sphagnum has unparalleled ecological importance because some 30% of the total terrest...

Data from: Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

Smith, Stephen A.
Yang, Ya
Brown, Joseph W.
Moore, Michael J.

July 2015

Background: The use of transcriptomic and genomic datasets for phylogenetic reconstruction has becom...

Data from: Deep phylogenetic incongruence in the angiosperm clade Rosidae

Sun, Miao
Soltis, Douglas E.
Soltis, Pamela S.
Zhu, Xinyu
Burleigh, J. Gordon
Chen, Zhiduan

November 2014

Analysis of large data sets can help resolve difficult nodes in the tree of life and also reveal com...

Data from: Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

Pease, James B.
Brown, Joseph W.
Walker, Joseph F.
Hinchliff, Cody E.
Smith, Stephen A.

September 2018

Premise of the Study—Phylogenetic support has been difficult to evaluate within the green plant tree...

Data from: Analyzing contentious relationships and outlier genes in phylogenomics

Walker, Joseph F.
Brown, Joseph W.
Smith, Stephen A.

June 2018

Recent studies have demonstrated that conflict is common among gene trees in phylogenomic studies, a...

Molecular systematic perspectives on biome origins and dynamics

Dick, Christopher W.
Pennington, R. Toby

January 2012

invited commentary on the following article:De-Nova JA, Medina R, Montero JC, Weeks A, Rosell JA, Ol...

Refining phylogenetic hypotheses using chloroplast genomics and incomplete data sets in Lasthenia (Madieae, Asteraceae)

Walker, Joseph Frederic

January 2014

The genus Lasthenia (Madieae, Asteraceae), consists of predominantly annual plant species that are l...

On the phylogenetic position of Myzostomida: can 77 genes get it wrong?

Bleidorn, C.
Podsiadlowski, L.
Zhong, M.
Eeckhaut, I.
Hartmann, S.
Halanych, K.
Tiedemann, R.

January 2009

Background: Phylogenomic analyses recently became popular to address questions about deep metazoan p...

Data for Morales et al. Perpendicular axes of incipient speciation in a widespread passerine with mitonuclear discordance (unpublished, submitted to Axios Review, April 2016)

Hernan Morales (2886857)
Paul Sunnucks (182576)
Leo Joseph (114181)
Alexandra Pavlova (182554)

August 2016

<div>Contents:</div><div><br></div><div>SampleInfo:</div><div>Table 1. Samples screened for nuclear ...

Disentangling sources of gene tree discordance in phylogenomic datasets: testing ancient hybridizations in Amaranthaceae s.l.

Morales-Briones, Diego F.
Kadereit, Gudrun
Tefarikis, Delphine
Moore, Michael
Smith, Stephen
Brockington, Samuel
Timoneda, Alfonso
Yim, Won
Cushman, John
Yang, Ya

August 2020

Gene tree discordance in large genomic datasets can be caused by evolutionary processes such as inco...

Data from: Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium)

Vargas, Oscar M.
Ortiz, Edgardo M.
Simpson, Beryl B.

High-throughput sequencing is helping biologists to overcome the difficulties of inferring the phylo...

One thousand plant transcriptomes and the phylogenomics of green plants

One Thousand Plant Transcriptomes Initiative

October 2019

Article describes the results of the One Thousand Plant Transcriptomes Initiative's efforts to seque...

Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages

Stull, Gregory
Soltis, Pamela S.
Soltis, Douglas E.
Gitzendanner, Matthew A.
Smith, Stephen A.

May 2020

Premise : Discordance between nuclear and organellar phylogenies (cytonuclear discordance) is a well...

Phylogenomic analyses in Phrymaceae reveal extensive gene tree discordance in relationships among major clades

Morales-Briones, Diego F.
Lin, Nan
Huang, Eileen
Grossenbacher, Dena
Sobel, James
Gilmore, Caroline
Tank, David
Yang, Ya

April 2022

• Premise of the study: Phylogenomic datasets using genomes and transcriptomes provide rich opportun...

Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

Pease, James B.
Brown, Joseph W.
Walker, Joseph F.
Hinchliff, Cody E.
Smith, Stephen A.

March 2018

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143738/1/ajb21016-sup-0009-AppendixS9....

Data from: Phylogenomic structure and speciation in an emerging model: The Sphagnum magellanicum complex (Bryophyta)

Shaw, A. Jonathan
Duffy, Aaron
Piatkowski, Bryan
Aguero, Blanka
Imwattana, Karn
Nieto-Lugilde, Marta
Healy, Adam
Weston, David
Patel, Megan
Schmutz, Jeremy
Yavitt, Joseph
Hassel, Kristian
Stenøien, Hans
Flatberg, Kjell Ivar

September 2022

The moss genus Sphagnum has unparalleled ecological importance because some 30% of the total terrest...

Data from: Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

Smith, Stephen A.
Yang, Ya
Brown, Joseph W.
Moore, Michael J.

July 2015

Background: The use of transcriptomic and genomic datasets for phylogenetic reconstruction has becom...

Data from: Deep phylogenetic incongruence in the angiosperm clade Rosidae

Sun, Miao
Soltis, Douglas E.
Soltis, Pamela S.
Zhu, Xinyu
Burleigh, J. Gordon
Chen, Zhiduan

November 2014

Analysis of large data sets can help resolve difficult nodes in the tree of life and also reveal com...

Data from: Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

Pease, James B.
Brown, Joseph W.
Walker, Joseph F.
Hinchliff, Cody E.
Smith, Stephen A.

September 2018

Premise of the Study—Phylogenetic support has been difficult to evaluate within the green plant tree...

Data from: Analyzing contentious relationships and outlier genes in phylogenomics

Walker, Joseph F.
Brown, Joseph W.
Smith, Stephen A.

June 2018

Recent studies have demonstrated that conflict is common among gene trees in phylogenomic studies, a...

Molecular systematic perspectives on biome origins and dynamics

Dick, Christopher W.
Pennington, R. Toby

January 2012

invited commentary on the following article:De-Nova JA, Medina R, Montero JC, Weeks A, Rosell JA, Ol...

Refining phylogenetic hypotheses using chloroplast genomics and incomplete data sets in Lasthenia (Madieae, Asteraceae)

Walker, Joseph Frederic

January 2014

The genus Lasthenia (Madieae, Asteraceae), consists of predominantly annual plant species that are l...

On the phylogenetic position of Myzostomida: can 77 genes get it wrong?

Bleidorn, C.
Podsiadlowski, L.
Zhong, M.
Eeckhaut, I.
Hartmann, S.
Halanych, K.
Tiedemann, R.

January 2009

Background: Phylogenomic analyses recently became popular to address questions about deep metazoan p...

Data for Morales et al. Perpendicular axes of incipient speciation in a widespread passerine with mitonuclear discordance (unpublished, submitted to Axios Review, April 2016)

Hernan Morales (2886857)
Paul Sunnucks (182576)
Leo Joseph (114181)
Alexandra Pavlova (182554)

August 2016

<div>Contents:</div><div><br></div><div>SampleInfo:</div><div>Table 1. Samples screened for nuclear ...

Disentangling sources of gene tree discordance in phylogenomic datasets: testing ancient hybridizations in Amaranthaceae s.l.

Morales-Briones, Diego F.
Kadereit, Gudrun
Tefarikis, Delphine
Moore, Michael
Smith, Stephen
Brockington, Samuel
Timoneda, Alfonso
Yim, Won
Cushman, John
Yang, Ya

August 2020

Gene tree discordance in large genomic datasets can be caused by evolutionary processes such as inco...

Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high‐Andean diversification (Asteraceae: Astereae: Diplostephium)

Abstract

Extracted data

Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high‐Andean diversification (Asteraceae: Astereae: Diplostephium)

Abstract

Extracted data

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