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Kriebel R, Rose JP, Drew BT, González-Gallegos JG, Celep F, Heeg L, Mahdjoub MM, Sytsma KJ. Model selection, hummingbird natural history, and biological hypotheses: a response to Sazatornil et al. Evolution 2023; 77:646-653. [PMID: 36626811 DOI: 10.1093/evolut/qpac023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 10/19/2022] [Accepted: 11/11/2022] [Indexed: 01/12/2023]
Abstract
We have previously suggested that a shift from bee to hummingbird pollination, in concert with floral architecture modifications, occurred at the crown of Salvia subgenus Calosphace in North America ca. 20 mya (Kriebel et al. 2020 and references therein). Sazatornil et al. (2022), using a hidden states model, challenged these assertions, arguing that bees were the ancestral pollinator of subg. Calosphace and claiming that hummingbirds could not have been the ancestral pollinator of subg. Calosphace because hummingbirds were not contemporaneous with crown subg. Calosphace in North America. Here, using a variety of models, we demonstrate that most analyses support hummingbirds as ancestral pollinators of subg. Calosphace and show that Sazatornil et al. (2022) erroneously concluded that hummingbirds were absent from North America ca. 20 mya. We contend that "biological realism" - based on timing and placement of hummingbirds in Mexico ca. 20 mya and the correlative evolution of hummingbird associated floral traits - must be considered when comparing models based on fit and complexity, including hidden states models.
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Affiliation(s)
- Ricardo Kriebel
- Department of Botany, California Academy of Sciences, San Francisco, CA, United States.,Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
| | - Jeffrey P Rose
- Department of Biology, University of Nebraska at Kearney, Kearney, NE, United States
| | - Bryan T Drew
- Department of Biology, University of Nebraska at Kearney, Kearney, NE, United States
| | | | - Ferhat Celep
- Kırıkkale University, Faculty of Arts and Sciences, Department of Biology, Yahşiyan, Turkey
| | - Luciann Heeg
- Department of Botany, California Academy of Sciences, San Francisco, CA, United States
| | - Mohamed M Mahdjoub
- Department of Biology, Faculty of Natural and Life Sciences and Earth Sciences, University of Bouira, Bouira, Algeria
| | - Kenneth J Sytsma
- Department of Botany, California Academy of Sciences, San Francisco, CA, United States
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Rose JP, Kriebel R, Kahan L, DiNicola A, González-Gallegos JG, Celep F, Lemmon EM, Lemmon AR, Sytsma KJ, Drew BT. Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes. Front Plant Sci 2021; 12:767478. [PMID: 34899789 PMCID: PMC8652245 DOI: 10.3389/fpls.2021.767478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/22/2021] [Indexed: 05/13/2023]
Abstract
Next-generation sequencing technologies have facilitated new phylogenomic approaches to help clarify previously intractable relationships while simultaneously highlighting the pervasive nature of incongruence within and among genomes that can complicate definitive taxonomic conclusions. Salvia L., with ∼1,000 species, makes up nearly 15% of the species diversity in the mint family and has attracted great interest from biologists across subdisciplines. Despite the great progress that has been achieved in discerning the placement of Salvia within Lamiaceae and in clarifying its infrageneric relationships through plastid, nuclear ribosomal, and nuclear single-copy genes, the incomplete resolution has left open major questions regarding the phylogenetic relationships among and within the subgenera, as well as to what extent the infrageneric relationships differ across genomes. We expanded a previously published anchored hybrid enrichment dataset of 35 exemplars of Salvia to 179 terminals. We also reconstructed nearly complete plastomes for these samples from off-target reads. We used these data to examine the concordance and discordance among the nuclear loci and between the nuclear and plastid genomes in detail, elucidating both broad-scale and species-level relationships within Salvia. We found that despite the widespread gene tree discordance, nuclear phylogenies reconstructed using concatenated, coalescent, and network-based approaches recover a common backbone topology. Moreover, all subgenera, except for Audibertia, are strongly supported as monophyletic in all analyses. The plastome genealogy is largely resolved and is congruent with the nuclear backbone. However, multiple analyses suggest that incomplete lineage sorting does not fully explain the gene tree discordance. Instead, horizontal gene flow has been important in both the deep and more recent history of Salvia. Our results provide a robust species tree of Salvia across phylogenetic scales and genomes. Future comparative analyses in the genus will need to account for the impacts of hybridization/introgression and incomplete lineage sorting in topology and divergence time estimation.
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Affiliation(s)
- Jeffrey P. Rose
- Department of Biology, University of Nebraska at Kearney, Kearney, NE, United States
- Department of Botany, University of Wisconsin–Madison, Madison, WI, United States
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin–Madison, Madison, WI, United States
| | - Larissa Kahan
- Department of Botany, University of Wisconsin–Madison, Madison, WI, United States
| | - Alexa DiNicola
- Department of Botany, University of Wisconsin–Madison, Madison, WI, United States
| | | | - Ferhat Celep
- Department of Biology, Faculty of Arts and Sciences, Kırıkkale University, Yahşihan, Turkey
| | - Emily M. Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, United States
| | - Kenneth J. Sytsma
- Department of Botany, University of Wisconsin–Madison, Madison, WI, United States
| | - Bryan T. Drew
- Department of Biology, University of Nebraska at Kearney, Kearney, NE, United States
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Kriebel R, Drew B, González-Gallegos JG, Celep F, Heeg L, Mahdjoub MM, Sytsma KJ. Pollinator shifts, contingent evolution, and evolutionary constraint drive floral disparity in Salvia (Lamiaceae): Evidence from morphometrics and phylogenetic comparative methods. Evolution 2020; 74:1335-1355. [PMID: 32484910 DOI: 10.1111/evo.14030] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/21/2020] [Indexed: 12/23/2022]
Abstract
Switches in pollinators have been argued to be key drivers of floral evolution in angiosperms. However, few studies have tested the relationship between floral shape evolution and switches in pollination in large clades. In concert with a dated phylogeny, we present a morphometric analysis of corolla, anther connective, and style shape across 44% of nearly 1000 species of Salvia (Lamiaceae) and test four hypotheses of floral evolution. We demonstrate that floral morphospace of New World (NW) Salvia is largely distinct from that of Old World (OW) Salvia and that these differences are pollinator driven; shifts in floral morphology sometimes mirror shifts in pollinators; anther connectives (key constituents of the Salvia staminal lever) and styles co-evolved from curved to linear shapes following shifts from bee to bird pollination; and morphological differences between NW and OW bee flowers are partly the legacy of constraints imposed by an earlier shift to bird pollination in the NW. The distinctive staminal lever in Salvia is a morphologically diverse structure that has evolved in concert with both the corolla and style, under different pollinator pressures, and in contingent fashion.
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Affiliation(s)
- Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Bryan Drew
- Department of Biology, University of Nebraska at Kearney, Kearney, Nebraska, 68849
| | | | - Ferhat Celep
- Department of Biology, Faculty of Arts and Sciences, Kırıkkale University, Yahşiyan, 71450, Turkey
| | - Luciann Heeg
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Mohamed M Mahdjoub
- Department of Biology, Faculty of Natural and Life Sciences and Earth Sciences, University of Bouira, Bouira, 10000, Algeria
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706
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Kriebel R, Drew BT, Drummond CP, González-Gallegos JG, Celep F, Mahdjoub MM, Rose JP, Xiang CL, Hu GX, Walker JB, Lemmon EM, Lemmon AR, Sytsma KJ. Tracking temporal shifts in area, biomes, and pollinators in the radiation of Salvia (sages) across continents: leveraging anchored hybrid enrichment and targeted sequence data. Am J Bot 2019. [PMID: 30986330 DOI: 10.5061/dryad.8m40rb0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
PREMISE OF THE STUDY A key question in evolutionary biology is why some clades are more successful by being widespread geographically, biome diverse, or species-rich. To extend understanding of how shifts in area, biomes, and pollinators impact diversification in plants, we examined the relationships of these shifts to diversification across the mega-genus Salvia. METHODS A chronogram was developed from a supermatrix of anchored hybrid enrichment genomic data and targeted sequence data for over 500 of the nearly 1000 Salvia species. Ancestral areas and biomes were reconstructed using BioGeoBEARS. Pollinator guilds were scored, ancestral pollinators determined, shifts in pollinator guilds identified, and rates of pollinator switches compared. KEY RESULTS A well-resolved phylogenetic backbone of Salvia and updated subgeneric designations are presented. Salvia originated in Southwest Asia in the Oligocene and subsequently dispersed worldwide. Biome shifts are frequent from a likely ancestral lineage utilizing broadleaf and/or coniferous forests and/or arid shrublands. None of the four species diversification shifts are correlated to shifts in biomes. Shifts in pollination system are not correlated to species diversification shifts, except for one hummingbird shift that precedes a major shift in diversification near the crown of New World subgen. Calosphace. Multiple reversals back to bee pollination occurred within this hummingbird clade. CONCLUSIONS Salvia diversified extensively in different continents, biomes, and with both bee and bird pollinators. The lack of tight correlation of area, biome, and most pollinator shifts to the four documented species diversification shifts points to other important drivers of speciation in Salvia.
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Affiliation(s)
- Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Bryan T Drew
- Department of Biology, University of Nebraska at Kearney, Kearney, NE, 68849, USA
| | - Chloe P Drummond
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Ferhat Celep
- Mehmet Akif Ersoy mah. 269. cad. Urankent Prestij Konutları, C16 Blok, No. 53, Demetevler, Ankara, Turkey
| | - Mohamed M Mahdjoub
- Research Laboratory of Ecology and Environment, Department of Environment Biological Sciences, Faculty of Nature and Life Sciences, Université de Bejaia, Targa Ouzemmour, 06000, Bejaia, Algeria
| | - Jeffrey P Rose
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Chun-Lei Xiang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Guo-Xiong Hu
- College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Jay B Walker
- Union High School, 6636 S. Mingo Road, Tulsa, OK, 74133, USA
| | - Emily M Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, 32306, USA
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
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