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Article ; Online: Green land: Multiple perspectives on green algal evolution and the earliest land plants.

McCourt, Richard M / Lewis, Louise A / Strother, Paul K / Delwiche, Charles F / Wickett, Norman J / de Vries, Jan / Bowman, John L

American journal of botany

2023 Volume 110, Issue 5, Page(s) e16175

Abstract: Green plants, broadly defined as green algae and the land plants (together, Viridiplantae), constitute the primary eukaryotic lineage that successfully colonized Earth's emergent landscape. Members of various clades of green plants have independently ... ...

Abstract	Green plants, broadly defined as green algae and the land plants (together, Viridiplantae), constitute the primary eukaryotic lineage that successfully colonized Earth's emergent landscape. Members of various clades of green plants have independently made the transition from fully aquatic to subaerial habitats many times throughout Earth's history. The transition, from unicells or simple filaments to complex multicellular plant bodies with functionally differentiated tissues and organs, was accompanied by innovations built upon a genetic and phenotypic toolkit that have served aquatic green phototrophs successfully for at least a billion years. These innovations opened an enormous array of new, drier places to live on the planet and resulted in a huge diversity of land plants that have dominated terrestrial ecosystems over the past 500 million years. This review examines the greening of the land from several perspectives, from paleontology to phylogenomics, to water stress responses and the genetic toolkit shared by green algae and plants, to the genomic evolution of the sporophyte generation. We summarize advances on disparate fronts in elucidating this important event in the evolution of the biosphere and the lacunae in our understanding of it. We present the process not as a step-by-step advancement from primitive green cells to an inevitable success of embryophytes, but rather as a process of adaptations and exaptations that allowed multiple clades of green plants, with various combinations of morphological and physiological terrestrialized traits, to become diverse and successful inhabitants of the land habitats of Earth.
MeSH term(s)	Biological Evolution ; Ecosystem ; Embryophyta/genetics ; Phylogeny ; Plants/genetics ; Chlorophyta/genetics ; Evolution, Molecular
Language	English
Publishing date	2023-05-29
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	2935-x
ISSN	1537-2197 ; 0002-9122
ISSN (online)	1537-2197
ISSN	0002-9122
DOI	10.1002/ajb2.16175
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Article ; Online: Green land: Multiple perspectives on green algal evolution and the earliest land plants

McCourt, Richard M. / Lewis, Louise A. / Strother, Paul K. / Delwiche, Charles F. / Wickett, Norman J. / de Vries, Jan / Bowman, John L.

American Journal of Botany. 2023 May, v. 110, no. 5 p.e16175-

2023

Abstract	Green plants, broadly defined as green algae and the land plants (together, Viridiplantae), constitute the primary eukaryotic lineage that successfully colonized Earth's emergent landscape. Members of various clades of green plants have independently made the transition from fully aquatic to subaerial habitats many times throughout Earth's history. The transition, from unicells or simple filaments to complex multicellular plant bodies with functionally differentiated tissues and organs, was accompanied by innovations built upon a genetic and phenotypic toolkit that have served aquatic green phototrophs successfully for at least a billion years. These innovations opened an enormous array of new, drier places to live on the planet and resulted in a huge diversity of land plants that have dominated terrestrial ecosystems over the past 500 million years. This review examines the greening of the land from several perspectives, from paleontology to phylogenomics, to water stress responses and the genetic toolkit shared by green algae and plants, to the genomic evolution of the sporophyte generation. We summarize advances on disparate fronts in elucidating this important event in the evolution of the biosphere and the lacunae in our understanding of it. We present the process not as a step‐by‐step advancement from primitive green cells to an inevitable success of embryophytes, but rather as a process of adaptations and exaptations that allowed multiple clades of green plants, with various combinations of morphological and physiological terrestrialized traits, to become diverse and successful inhabitants of the land habitats of Earth.
Keywords	Viridiplantae ; algae ; autotrophs ; biosphere ; botany ; embryophytes ; evolution ; genomics ; landscapes ; paleontology ; phenotype ; sporophytes ; water stress
Language	English
Dates of publication	2023-05
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	REVIEW
ZDB-ID	2935-x
ISSN	1537-2197 ; 0002-9122
ISSN (online)	1537-2197
ISSN	0002-9122
DOI	10.1002/ajb2.16175
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Article ; Online: Incomplete reproductive isolation and low genetic differentiation despite floral divergence across varying geographic scales in Castilleja.

Wenzell, Katherine E / McDonnell, Angela J / Wickett, Norman J / Fant, Jeremie B / Skogen, Krissa A

American journal of botany

2021 Volume 108, Issue 7, Page(s) 1270–1288

Abstract: Premise: Divergence depends on the strength of selection and frequency of gene flow between taxa, while reproductive isolation relies on mating barriers and geographic distance. Less is known about how these processes interact at early stages of ... ...

Abstract	Premise: Divergence depends on the strength of selection and frequency of gene flow between taxa, while reproductive isolation relies on mating barriers and geographic distance. Less is known about how these processes interact at early stages of speciation. Here, we compared population-level differentiation in floral phenotype and genetic sequence variation among recently diverged Castilleja to explore patterns of diversification under different scenarios of reproductive isolation. Methods: Using target enrichment enabled by the Angiosperms353 probe set, we assessed genetic distance among 50 populations of four Castilleja species. We investigated whether patterns of genetic divergence are explained by floral trait variation or geographic distance in two focal groups: the widespread C. sessiliflora and the more restricted C. purpurea species complex. Results: We document that C. sessiliflora and the C. purpurea complex are characterized by high diversity in floral color across varying geographic scales. Despite phenotypic divergence, groups were not well supported in phylogenetic analyses, and little genetic differentiation was found across targeted Angiosperms353 loci. Nonetheless, a principal coordinate analysis of single nucleotide polymorphisms revealed differentiation within C. sessiliflora across floral morphs and geography and less differentiation among species of the C. purpurea complex. Conclusions: Patterns of genetic distance in C. sessiliflora suggest species cohesion maintained over long distances despite variation in floral traits. In the C. purpurea complex, divergence in floral color across narrow geographic clines may be driven by recent selection on floral color. These contrasting patterns of floral and genetic differentiation reveal that divergence can arise via multiple eco-evolutionary paths.
MeSH term(s)	Biological Evolution ; Genetic Drift ; Orobanchaceae ; Phylogeny ; Reproductive Isolation
Language	English
Publishing date	2021-07-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2935-x
ISSN	1537-2197 ; 0002-9122
ISSN (online)	1537-2197
ISSN	0002-9122
DOI	10.1002/ajb2.1700
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Article: Incomplete reproductive isolation and low genetic differentiation despite floral divergence across varying geographic scales in Castilleja

Wenzell, Katherine E. / McDonnell, Angela J. / Wickett, Norman J. / Fant, Jeremie B. / Skogen, Krissa A.

American journal of botany. 2021 July, v. 108, no. 7

2021

Abstract: PREMISE: Divergence depends on the strength of selection and frequency of gene flow between taxa, while reproductive isolation relies on mating barriers and geographic distance. Less is known about how these processes interact at early stages of ... ...

Abstract	PREMISE: Divergence depends on the strength of selection and frequency of gene flow between taxa, while reproductive isolation relies on mating barriers and geographic distance. Less is known about how these processes interact at early stages of speciation. Here, we compared population‐level differentiation in floral phenotype and genetic sequence variation among recently diverged Castilleja to explore patterns of diversification under different scenarios of reproductive isolation. METHODS: Using target enrichment enabled by the Angiosperms353 probe set, we assessed genetic distance among 50 populations of four Castilleja species. We investigated whether patterns of genetic divergence are explained by floral trait variation or geographic distance in two focal groups: the widespread C. sessiliflora and the more restricted C. purpurea species complex. RESULTS: We document that C. sessiliflora and the C. purpurea complex are characterized by high diversity in floral color across varying geographic scales. Despite phenotypic divergence, groups were not well supported in phylogenetic analyses, and little genetic differentiation was found across targeted Angiosperms353 loci. Nonetheless, a principal coordinate analysis of single nucleotide polymorphisms revealed differentiation within C. sessiliflora across floral morphs and geography and less differentiation among species of the C. purpurea complex. CONCLUSIONS: Patterns of genetic distance in C. sessiliflora suggest species cohesion maintained over long distances despite variation in floral traits. In the C. purpurea complex, divergence in floral color across narrow geographic clines may be driven by recent selection on floral color. These contrasting patterns of floral and genetic differentiation reveal that divergence can arise via multiple eco‐evolutionary paths.
Keywords	Castilleja ; botany ; cohesion ; color ; floral characteristics ; gene flow ; genetic distance ; genetic variation ; geography ; multidimensional scaling ; phenotype ; phenotypic variation ; phylogeny ; reproductive isolation ; sequence diversity
Language	English
Dates of publication	2021-07
Size	p. 1270-1288.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2935-x
ISSN	1537-2197 ; 0002-9122
ISSN (online)	1537-2197
ISSN	0002-9122
DOI	10.1002/ajb2.1700
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Article ; Online: Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta).

Parks, Matthew B / Wickett, Norman J / Alverson, Andrew J

Molecular biology and evolution

2017 Volume 35, Issue 1, Page(s) 80–93

Abstract: Diatoms (Bacillariophyta) are a species-rich group of eukaryotic microbes diverse in morphology, ecology, and metabolism. Previous reconstructions of the diatom phylogeny based on one or a few genes have resulted in inconsistent resolution or low support ...

Abstract	Diatoms (Bacillariophyta) are a species-rich group of eukaryotic microbes diverse in morphology, ecology, and metabolism. Previous reconstructions of the diatom phylogeny based on one or a few genes have resulted in inconsistent resolution or low support for critical nodes. We applied phylogenetic paralog pruning techniques to a data set of 94 diatom genomes and transcriptomes to infer perennially difficult species relationships, using concatenation and summary-coalescent methods to reconstruct species trees from data sets spanning a wide range of thresholds for taxon and column occupancy in gene alignments. Conflicts between gene and species trees decreased with both increasing taxon occupancy and bootstrap cutoffs applied to gene trees. Concordance between gene and species trees was lowest for short internodes and increased logarithmically with increasing edge length, suggesting that incomplete lineage sorting disproportionately affects species tree inference at short internodes, which are a common feature of the diatom phylogeny. Although species tree topologies were largely consistent across many data treatments, concatenation methods appeared to outperform summary-coalescent methods for sparse alignments. Our results underscore that approaches to species-tree inference based on few loci are likely to be misled by unrepresentative sampling of gene histories, particularly in lineages that may have diversified rapidly. In addition, phylogenomic studies of diatoms, and potentially other hyperdiverse groups, should maximize the number of gene trees with high taxon occupancy, though there is clearly a limit to how many of these genes will be available.
MeSH term(s)	Computer Simulation ; Diatoms/classification ; Diatoms/genetics ; Eukaryota/classification ; Eukaryota/genetics ; Genetic Speciation ; Genome/genetics ; Genomics/methods ; Models, Genetic ; Phylogeny ; Sequence Analysis, DNA/methods ; Transcriptome/genetics
Language	English
Publishing date	2017-10-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msx268
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Article: Elucidating the Evolutionary History of Oenothera Sect. Pachylophus (Onagraceae): A Phylogenomic Approach

Patsis, Amanda / Overson, Rick P. / Skogen, Krissa A. / Wickett, Norman J. / Johnson, Matthew G. / Wagner, Warren L. / Raguso, Robert A. / Fant, Jeremie B. / Levin, Rachel A.

Systematic botany. 2021 Oct. 25, v. 46, no. 3

2021

Abstract: 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 ... ...

Abstract	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 a molecular 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 coalescent-based methods. Our findings concur with previous research in suggesting that O. psammophila and O. harringtonii are nested within a paraphyletic Oenothera 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 specialization appears 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.
Keywords	Oenothera ; ancestry ; coevolution ; flower morphology ; genes ; geographical distribution ; indigenous species ; introgression ; odors ; paraphyly
Language	English
Dates of publication	2021-1025
Size	p. 799-811.
Publishing place	American Society of Plant Toxonomists
Document type	Article
ZDB-ID	2052625-8
ISSN	1548-2324 ; 0363-6445
ISSN (online)	1548-2324
ISSN	0363-6445
DOI	10.1600/036364421X16312067913471
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Article ; Online: A phylogeny of the evening primrose family (Onagraceae) using a target enrichment approach with 303 nuclear loci.

Overson, Rick P / Johnson, Matthew G / Bechen, Lindsey L / Kinosian, Sylvia P / Douglas, Norman A / Fant, Jeremie B / Hoch, Peter C / Levin, Rachel A / Moore, Michael J / Raguso, Robert A / Wagner, Warren L / Skogen, Krissa A / Wickett, Norman J

BMC ecology and evolution

2023 Volume 23, Issue 1, Page(s) 66

Abstract: Background: The evening primrose family (Onagraceae) includes 664 species (803 taxa) with a center of diversity in the Americas, especially western North America. Ongoing research in Onagraceae includes exploring striking variation in floral morphology, ...

Abstract	Background: The evening primrose family (Onagraceae) includes 664 species (803 taxa) with a center of diversity in the Americas, especially western North America. Ongoing research in Onagraceae includes exploring striking variation in floral morphology, scent composition, and breeding system, as well as the role of these traits in driving diversity among plants and their interacting pollinators and herbivores. However, these efforts are limited by the lack of a comprehensive, well-resolved phylogeny. Previous phylogenetic studies based on a few loci strongly support the monophyly of the family and the sister relationship of the two largest tribes but fail to resolve several key relationships. Results: We used a target enrichment approach to reconstruct the phylogeny of Onagraceae using 303 highly conserved, low-copy nuclear loci. We present a phylogeny for Onagraceae with 169 individuals representing 152 taxa sampled across the family, including extensive sampling within the largest tribe, Onagreae. Deep splits within the family are strongly supported, whereas relationships among closely related genera and species are characterized by extensive conflict among individual gene trees. Conclusions: This phylogenetic resource will augment current research projects focused throughout the family in genomics, ecology, coevolutionary dynamics, biogeography, and the evolution of characters driving diversification in the family.
MeSH term(s)	Humans ; Phylogeny ; Oenothera biennis/genetics ; Onagraceae ; Plant Breeding ; Genomics
Language	English
Publishing date	2023-11-17
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ISSN	2730-7182
ISSN (online)	2730-7182
DOI	10.1186/s12862-023-02151-9
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Article ; Online: Differential gene expression associated with a floral scent polymorphism in the evening primrose Oenothera harringtonii (Onagraceae).

Bechen, Lindsey L / Johnson, Matthew G / Broadhead, Geoffrey T / Levin, Rachel A / Overson, Rick P / Jogesh, Tania / Fant, Jeremie B / Raguso, Robert A / Skogen, Krissa A / Wickett, Norman J

BMC genomics

2022 Volume 23, Issue 1, Page(s) 124

Abstract: Background: Plant volatiles play an important role in both plant-pollinator and plant-herbivore interactions. Intraspecific polymorphisms in volatile production are ubiquitous, but studies that explore underlying differential gene expression are rare. ... ...

Abstract	Background: Plant volatiles play an important role in both plant-pollinator and plant-herbivore interactions. Intraspecific polymorphisms in volatile production are ubiquitous, but studies that explore underlying differential gene expression are rare. Oenothera harringtonii populations are polymorphic in floral emission of the monoterpene (R)-(-)-linalool; some plants emit (R)-(-)-linalool (linalool+ plants) while others do not (linalool- plants). However, the genes associated with differential production of this floral volatile in Oenothera are unknown. We used RNA-Seq to broadly characterize differential gene expression involved in (R)-(-)-linalool biosynthesis. To identify genes that may be associated with the polymorphism for this trait, we used RNA-Seq to compare gene expression in six different Oenothera harringtonii tissues from each of three linalool+ and linalool- plants. Results: Three clusters of differentially expressed genes were enriched for terpene synthase activity: two were characterized by tissue-specific upregulation and one by upregulation only in plants with flowers that produce (R)-(-)-linalool. A molecular phylogeny of all terpene synthases identified two putative (R)-(-)-linalool synthase transcripts in Oenothera harringtonii, a single allele of which is found exclusively in linalool+ plants. Conclusions: By using a naturally occurring polymorphism and comparing different tissues, we were able to identify candidate genes putatively involved in the biosynthesis of (R)-(-)-linalool. Expression of these genes in linalool- plants, while low, suggests a regulatory polymorphism, rather than a population-specific loss-of-function allele. Additional terpene biosynthesis-related genes that are up-regulated in plants that emit (R)-(-)-linalool may be associated with herbivore defense, suggesting a potential economy of scale between plant reproduction and defense.
MeSH term(s)	Flowers/genetics ; Gene Expression ; Gene Expression Regulation, Plant ; Odorants ; Oenothera ; Oenothera biennis ; Onagraceae
Language	English
Publishing date	2022-02-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2041499-7
ISSN	1471-2164 ; 1471-2164
ISSN (online)	1471-2164
ISSN	1471-2164
DOI	10.1186/s12864-022-08370-6
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Article: Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta)

Parks, Matthew B. / Nakov, Teofil / Ruck, Elizabeth C. / Wickett, Norman J. / Alverson, Andrew J.

American journal of botany. 2018 Mar., v. 105, no. 3

2018

Abstract: PREMISE OF THE STUDY: Diatoms are one of the most species‐rich lineages of microbial eukaryotes. Similarities in clade age, species richness, and primary productivity motivate comparisons to angiosperms, whose genomes have been inordinately shaped by ... ...

Abstract	PREMISE OF THE STUDY: Diatoms are one of the most species‐rich lineages of microbial eukaryotes. Similarities in clade age, species richness, and primary productivity motivate comparisons to angiosperms, whose genomes have been inordinately shaped by whole‐genome duplication (WGD). WGDs have been linked to speciation, increased rates of lineage diversification, and identified as a principal driver of angiosperm evolution. We synthesized a large but scattered body of evidence that suggests polyploidy may be common in diatoms as well. METHODS: We used gene counts, gene trees, and distributions of synonymous divergence to carry out a phylogenomic analysis of WGD across a diverse set of 37 diatom species. KEY RESULTS: Several methods identified WGDs of varying age across diatoms. Determining the occurrence, exact number, and placement of events was greatly impacted by uncertainty in gene trees. WGDs inferred from synonymous divergence of paralogs varied depending on how redundancy in transcriptomes was assessed, gene families were assembled, and synonymous distances (Ks) were calculated. Our results highlighted a need for systematic evaluation of key methodological aspects of Ks‐based approaches to WGD inference. Gene tree reconciliations supported allopolyploidy as the predominant mode of polyploid formation, with strong evidence for ancient allopolyploid events in the thalassiosiroid and pennate diatom clades. CONCLUSIONS: Our results suggest that WGD has played a major role in the evolution of diatom genomes. We outline challenges in reconstructing paleopolyploid events in diatoms that, together with these results, offer a framework for understanding the impact of genome duplication in a group that likely harbors substantial genomic diversity.
Keywords	Angiospermae ; Bacillariophyceae ; allopolyploidy ; botany ; eukaryotic cells ; genes ; genetic variation ; phylogeny ; primary productivity ; species richness ; transcriptome ; uncertainty
Language	English
Dates of publication	2018-03
Size	p. 330-347.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2935-x
ISSN	1537-2197 ; 0002-9122
ISSN (online)	1537-2197
ISSN	0002-9122
DOI	10.1002/ajb2.1056
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Article ; Online: Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).

Gardner, Elliot M / Johnson, Matthew G / Pereira, Joan T / Puad, Aida Shafreena Ahmad / Arifiani, Deby / Wickett, Norman J / Zerega, Nyree J C

Systematic biology

2020

Abstract: We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore ...

Abstract	We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. While codon partitioning did not result in any substantial topological differences, the inclusion of flanking non-coding sequence in analyses significantly increased the resolution of gene trees. We also found that increasing the size of datasets increased convergence between analysis methods but did not reduce gene tree conflict. We optimized the HybPiper targeted-enrichment sequence assembly pipeline for short sequences derived from degraded DNA extracted from museum specimens. While the subgenera of Artocarpus were monophyletic, revision is required at finer scales, particularly with respect to widespread species. We expect our results to provide a basis for further studies in Artocarpus and provide guidelines for future analyses of datasets based on target enrichment data, particularly those using sequences from both fresh and museum material, counseling careful attention to the potential of off-target sequences to improve resolution.
Language	English
Publishing date	2020-09-24
Publishing country	England
Document type	Journal Article
ZDB-ID	1482572-7
ISSN	1076-836X ; 1063-5157
ISSN (online)	1076-836X
ISSN	1063-5157
DOI	10.1093/sysbio/syaa073
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