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Zhang X, Ekwealor JTB, Mishler BD, Silva AT, Yu L, Jones AK, Nelson ADL, Oliver MJ. Syntrichia ruralis: emerging model moss genome reveals a conserved and previously unknown regulator of desiccation in flowering plants. New Phytol 2024. [PMID: 38415863 DOI: 10.1111/nph.19620] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/05/2024] [Indexed: 02/29/2024]
Abstract
Water scarcity, resulting from climate change, poses a significant threat to ecosystems. Syntrichia ruralis, a dryland desiccation-tolerant moss, provides valuable insights into survival of water-limited conditions. We sequenced the genome of S. ruralis, conducted transcriptomic analyses, and performed comparative genomic and transcriptomic analyses with existing genomes and transcriptomes, including with the close relative S. caninervis. We took a genetic approach to characterize the role of an S. ruralis transcription factor, identified in transcriptomic analyses, in Arabidopsis thaliana. The genome was assembled into 12 chromosomes encompassing 21 169 protein-coding genes. Comparative analysis revealed copy number and transcript abundance differences in known desiccation-associated gene families, and highlighted genome-level variation among species that may reflect adaptation to different habitats. A significant number of abscisic acid (ABA)-responsive genes were found to be negatively regulated by a MYB transcription factor (MYB55) that was upstream of the S. ruralis ortholog of ABA-insensitive 3 (ABI3). We determined that this conserved MYB transcription factor, uncharacterized in Arabidopsis, acts as a negative regulator of an ABA-dependent stress response in Arabidopsis. The new genomic resources from this emerging model moss offer novel insights into how plants regulate their responses to water deprivation.
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Affiliation(s)
- Xiaodan Zhang
- The Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Jenna T B Ekwealor
- Department of Biology, Utah State University, Logan, UT, 84322, USA
- Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA
| | - Brent D Mishler
- University and Jepson Herbaria, Berkeley, CA, 94720-2465, USA
- Department of Integrative Biology, University of California, Berkeley, CA, 94720-2465, USA
| | | | - Li'ang Yu
- The Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Andrea K Jones
- The Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Andrew D L Nelson
- The Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Melvin J Oliver
- Division of Plant Sciences and Technology and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
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Jauregui-Lazo J, Wilson M, Mishler BD. The dynamics of external water conduction in the dryland moss Syntrichia. AoB Plants 2023; 15:plad025. [PMID: 37292250 PMCID: PMC10244898 DOI: 10.1093/aobpla/plad025] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/16/2023] [Indexed: 06/10/2023]
Abstract
Syntrichia relies on external water conduction for photosynthesis, survival, and reproduction, a condition referred to as ectohydry. Capillarity spaces are abundant in Syntrichia, but the link between function and morphology is complex. The aim of this study was to provide a better understanding of species-specific morphological traits underlying the functions of water conduction and storage. We used an environmental scanning electron microscope and confocal microscopy for observing anatomical characters in the leaves of Syntrichia species. We also measured hydration/dehydration curves to understand the rate of conduction and dehydration by experimental approaches. Syntrichia is an ectohydric moss that can externally transport and store water from the base of the stem using capillary action. We propose a new framework to study ectohydric capabilities, which incorporates three morphological scales and the timing of going from completely dehydrated to fully hydrated. Characters of interest in this model include cell anatomy (papillae development, hyaline basal cells and laminar cells), architecture of the stem (concavity and orientation) and whole clump characteristics (density of stems). We report significant variations in the speed of conduction, water holding capacity and hydration associated with each species studied (11 in total). All Syntrichia species are capable of external water conduction and storage, but the relevant traits differ among species. These results help to understand potential evolutionary and ecological trade-offs among speed of water conduction, water holding capacity, ontogeny, and differing habitat requirements. An integrative view of ectohydry in Syntrichia contributes to understanding the water relationships of mosses.
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Affiliation(s)
| | - Marielle Wilson
- Department of Integrative Biology, and University and Jepson Herbaria, 1001 Valley Life Sciences Building, University of California, Berkeley, CA 94720-2465, USA
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Brent D Mishler
- Department of Integrative Biology, and University and Jepson Herbaria, 1001 Valley Life Sciences Building, University of California, Berkeley, CA 94720-2465, USA
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Jauregui-Lazo J, Brinda JC, Mishler BD. The phylogeny of Syntrichia: An ecologically diverse clade of mosses with an origin in South America. Am J Bot 2023; 110:e16103. [PMID: 36576338 DOI: 10.1002/ajb2.16103] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
PREMISE To address the biodiversity crisis, we need to understand the evolution of all organisms and how they fill geographic and ecological space. Syntrichia is one of the most diverse and dominant genera of mosses, ranging from alpine habitats to desert biocrusts, yet its evolutionary history remains unclear. METHODS We present a comprehensive phylogenetic analysis of Syntrichia, based on both molecular and morphological data, with most of the named species and closest outgroups represented. In addition, we provide ancestral-state reconstructions of water-related traits and a global biogeographic analysis. RESULTS We found 10 major well-resolved subclades of Syntrichia that possess geographical or morphological coherence, in some cases representing previously accepted genera. We infer that the extant species diversity of Syntrichia likely originated in South America in the early Eocene (56.5-43.8 million years ago [Mya]), subsequently expanded its distribution to the neotropics, and finally dispersed to the northern hemisphere. There, the clade experienced a recent diversification (15-12 Mya) into a broad set of ecological niches (e.g., the S. caninervis and S. ruralis complexes). The transition from terricolous to either saxicolous or epiphytic habitats occurred more than once and was associated with changes in water-related traits. CONCLUSIONS Our study provides a framework for understanding the evolutionary history of Syntrichia through the combination of morphological and molecular characters, revealing that migration events that shaped the current distribution of the clade have implications for morphological character evolution in relation to niche diversity.
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Affiliation(s)
- Javier Jauregui-Lazo
- Department of Integrative Biology, and University and Jepson Herbaria, 1001 Valley Life Sciences Building, University of California Berkeley, CA, 94720-2465, USA
| | - John C Brinda
- Missouri Botanical Garden, 4344 Shaw Boulevard, Saint Louis, MO, 63110, USA
| | - Brent D Mishler
- Department of Integrative Biology, and University and Jepson Herbaria, 1001 Valley Life Sciences Building, University of California Berkeley, CA, 94720-2465, USA
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Antoninka A, Chuckran PF, Mau RL, Slate ML, Mishler BD, Oliver MJ, Coe KK, Stark LR, Fisher KM, Bowker MA. Responses of Biocrust and Associated Soil Bacteria to Novel Climates Are Not Tightly Coupled. Front Microbiol 2022; 13:821860. [PMID: 35572693 PMCID: PMC9096946 DOI: 10.3389/fmicb.2022.821860] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/16/2022] [Indexed: 11/13/2022] Open
Abstract
Climate change is expanding drylands even as land use practices degrade them. Representing ∼40% of Earth’s terrestrial surface, drylands rely on biological soil crusts (biocrusts) for key ecosystem functions including soil stability, biogeochemical cycling, and water capture. Understanding how biocrusts adapt to climate change is critical to understanding how dryland ecosystems will function with altered climate. We investigated the sensitivity of biocrusts to experimentally imposed novel climates to track changes in productivity and stability under both warming and cooling scenarios. We established three common gardens along an elevational-climate gradient on the Colorado Plateau. Mature biocrusts were collected from each site and reciprocally transplanted intact. Over 20 months we monitored visible species composition and cover, chlorophyll a, and the composition of soil bacterial communities using high throughput sequencing. We hypothesized that biocrusts replanted at their home site would show local preference, and biocrusts transplanted to novel environments would maintain higher cover and stability at elevations higher than their origin, compared to at elevations lower than their origin. We expected responses of the visible biocrust cover and soil bacterial components of the biocrust community to be coupled, with later successional taxa showing higher sensitivity to novel environments. Only high elevation sourced biocrusts maintained higher biocrust cover and community stability at their site of origin. Biocrusts from all sources had higher cover and stability in the high elevation garden. Later successional taxa decreased cover in low elevation gardens, suggesting successional reversal with warming. Visible community composition was influenced by both source and transplant environment. In contrast, soil bacterial community composition was not influenced by transplant environments but retained fidelity to the source. Thus, responses of the visible and soil bacterial components of the biocrust community were not coupled. Synthesis: Our results suggest biocrust communities are sensitive to climate change, and loss of species and function can be expected, while associated soil bacteria may be buffered against rapid change.
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Affiliation(s)
- Anita Antoninka
- School of Forestry, Northern Arizona University, Flagstaff, AZ, United States
| | - Peter F Chuckran
- Department of Biological Sciences, Center for Ecosystem Science and Society (ECOSS), Northern Arizona University, Flagstaff, AZ, United States
| | - Rebecca L Mau
- Department of Biological Sciences, Center for Ecosystem Science and Society (ECOSS), Northern Arizona University, Flagstaff, AZ, United States
| | - Mandy L Slate
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States
| | - Brent D Mishler
- Department of Integrative Biology, University and Jepson Herbaria, University of California, Berkeley, Berkeley, CA, United States
| | - Melvin J Oliver
- Interdisciplinary Plant Group, Division of Plant Sciences, University of Missouri, Columbia, MO, United States
| | - Kirsten K Coe
- Department of Biology, Middlebury College, Middlebury, VT, United States
| | - Llo R Stark
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Kirsten M Fisher
- Department of Biological Sciences, California State University, Los Angeles, CA, United States
| | - Matthew A Bowker
- School of Forestry, Northern Arizona University, Flagstaff, AZ, United States
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Nitta JH, Mishler BD, Iwasaki W, Ebihara A. Spatial phylogenetics of Japanese ferns: Patterns, processes, and implications for conservation. Am J Bot 2022; 109:727-745. [PMID: 35435239 PMCID: PMC9325522 DOI: 10.1002/ajb2.1848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 03/11/2022] [Accepted: 03/11/2022] [Indexed: 06/02/2023]
Abstract
PREMISE Biodiversity is often only measured with species richness; however, this metric ignores evolutionary history and is not sufficient for making conservation decisions. Here, we characterize multiple facets and drivers of biodiversity to understand how these relate to bioregions and conservation status in the ferns of Japan. METHODS We compiled a community data set of 1239 grid cells (20 × 20 km each) including 672 taxa based on >300,000 specimen records. We combined the community data with a phylogeny and functional traits to analyze taxonomic, phylogenetic, and functional diversity and modeled biodiversity metrics in response to environmental factors and reproductive mode. Hierarchical clustering was used to delimit bioregions. Conservation status and threats were assessed by comparing the overlap of significantly diverse grid cells with conservation zones and range maps of native Japanese deer. RESULTS Taxonomic richness was highest at mid-latitudes. Phylogenetic and functional diversity and phylogenetic endemism were highest in small southern islands. Relative phylogenetic and functional diversity were high at high and low latitudes, and low at mid-latitudes. Grid cells were grouped into three (phylogenetic) or four (taxonomic) major bioregions. Temperature and apomixis were identified as drivers of biodiversity patterns. Conservation status was generally high for grid cells with significantly high biodiversity, but the threat due to herbivory by deer was greater for taxonomic richness than other metrics. CONCLUSIONS Our integrative approach reveals previously undetected patterns and drivers of biodiversity in the ferns of Japan. Future conservation efforts should recognize that threats can vary by biodiversity metric and consider multiple metrics when establishing conservation priorities.
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Affiliation(s)
- Joel H. Nitta
- Department of Biological Sciences, Graduate School of ScienceThe University of TokyoTokyoJapan
| | - Brent D. Mishler
- University and Jepson Herbaria, and Department of Integrative BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of ScienceThe University of TokyoTokyoJapan
- Department of Integrated Biosciences, Graduate School of Frontier SciencesThe University of TokyoChibaJapan
| | - Atsushi Ebihara
- Department of BotanyNational Museum of Nature and ScienceTsukubaJapan
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Ekwealor JTB, Benjamin SD, Jomsky JZ, Bowker MA, Stark LR, McLetchie DN, Mishler BD, Fisher KM. Genotypic confirmation of a biased phenotypic sex ratio in a dryland moss using restriction fragment length polymorphisms. Appl Plant Sci 2022; 10:e11467. [PMID: 35495199 PMCID: PMC9039795 DOI: 10.1002/aps3.11467] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 02/09/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
PREMISE In dioicous mosses, sex is determined by a single U (female, ♀) or V (male, ♂) chromosome. Although a 1 : 1 sex ratio is expected following meiosis, phenotypic sex ratios based on the production of gametangia are often female-biased. The dryland moss Syntrichia caninervis (Pottiaceae) is notable for its low frequency of sex expression and strong phenotypic female bias. Here we present a technique to determine genotypic sex in a single shoot of S. caninervis, and report results of a case study examining genotypic and phenotypic sex ratios. METHODS We reanalyzed 271 non-expressing gametophyte shoots from a previous study on S. caninervis sex expression across microhabitats using a restriction fragment length polymorphism (RFLP) method. RESULTS We recovered a genotypic sex ratio in non-expressing shoots of 18.4♀ : 1♂, which exceeds the female bias of the phenotypic ratio (5.3♀ : 1♂; P = 0.013). We also found that the distribution of male and female genotypes across microsites with different levels of sun exposure was not predicted by patterns of sex expression in these microsites. DISCUSSION These findings contribute to our understanding of how the environment may modulate sex ratios in S. caninervis, either through its direct influence on sex expression or through selection on genotypes with particular sex expression phenotypes.
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Affiliation(s)
- Jenna T. B. Ekwealor
- Department of Integrative Biology and University and Jepson HerbariaUniversity of CaliforniaBerkeleyUSA
- Data Science Lab, Office of the Chief Information OfficerSmithsonian InstitutionWashingtonD.C.USA
| | - Simone D. Benjamin
- Department of Biological SciencesCalifornia State UniversityLos Angeles, CaliforniaUSA
| | - Jordan Z. Jomsky
- Department of Integrative Biology and University and Jepson HerbariaUniversity of CaliforniaBerkeleyUSA
| | | | - Lloyd R. Stark
- School of Life SciencesUniversity of NevadaLas VegasNevadaUSA
| | | | - Brent D. Mishler
- Department of Integrative Biology and University and Jepson HerbariaUniversity of CaliforniaBerkeleyUSA
| | - Kirsten M. Fisher
- Department of Biological SciencesCalifornia State UniversityLos Angeles, CaliforniaUSA
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Zhang XX, Ye JF, Laffan SW, Mishler BD, Thornhill AH, Lu LM, Mao LF, Liu B, Chen YH, Lu AM, Miller JT, Chen ZD. Spatial phylogenetics of the Chinese angiosperm flora provides insights into endemism and conservation. J Integr Plant Biol 2022; 64:105-117. [PMID: 34773376 DOI: 10.1111/jipb.13189] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 07/16/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
The flora of China is well known for its high diversity and endemism. Identifying centers of endemism and designating conservation priorities are essential goals for biodiversity studies. However, there is no comprehensive study from a rigorous phylogenetic perspective to understand patterns of diversity and endemism and to guide biodiversity conservation in China. We conducted a spatial phylogenetic analysis of the Chinese angiosperm flora at the generic level to identify centers of neo- and paleo-endemism. Our results indicate that: (i) the majority of grid cells in China with significantly high phylogenetic endemism (PE) were located in the mountainous regions; (ii) four of the nine centers of endemism recognized, located in northern and western China, were recognized for the first time; (iii) arid and semiarid regions in Northwest China were commonly linked to significant PE, consistent with other spatial phylogenetic studies worldwide; and (iv) six high-priority conservation gaps were detected by overlaying the boundaries of China's nature reserves on all significant PE cells. Overall, we conclude that the mountains of southern and northern China contain both paleo-endemics (ancient relictual lineages) and neo-endemics (recently diverged lineages). The areas we highlight as conservation priorities are important for broad-scale planning, especially in the context of evolutionary history preservation.
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Affiliation(s)
- Xiao-Xia Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Jian-Fei Ye
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- Beijing Botanical Garden, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Shawn W Laffan
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Brent D Mishler
- University and Jepson Herbaria, and Department of Integrative Biology, University of California, Berkeley, CA, 94720-2465, USA
| | - Andrew H Thornhill
- University and Jepson Herbaria, and Department of Integrative Biology, University of California, Berkeley, CA, 94720-2465, USA
- The University of Adelaide, Environment Institute, Adelaide, SA, 5005, Australia
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Department for Environment and Water, Adelaide, SA, 5001, Australia
| | - Li-Min Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Ling-Feng Mao
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Bing Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- Sino-Africa Joint Research Center, the Chinese Academy of Sciences, Wuhan, 430074, China
| | - You-Hua Chen
- Chengdu Institute of Biology, the Chinese Academy of Sciences, Chengdu, 610041, China
| | - An-Ming Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Joseph T Miller
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Department for Environment and Water, Adelaide, SA, 5001, Australia
- Global Biodiversity Information Facility, Copenhagen, Denmark
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- Sino-Africa Joint Research Center, the Chinese Academy of Sciences, Wuhan, 430074, China
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Ekwealor JTB, Mishler BD. Transcriptomic Effects of Acute Ultraviolet Radiation Exposure on Two Syntrichia Mosses. Front Plant Sci 2021; 12:752913. [PMID: 34777431 PMCID: PMC8581813 DOI: 10.3389/fpls.2021.752913] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
Ultraviolet radiation (UVR) is a major environmental stressor for terrestrial plants. Here we investigated genetic responses to acute broadband UVR exposure in the highly desiccation-tolerant mosses Syntrichia caninervis and Syntrichia ruralis, using a comparative transcriptomics approach. We explored whether UVR protection is physiologically plastic and induced by UVR exposure, addressing the following questions: (1) What is the timeline of changes in the transcriptome with acute UVR exposure in these two species? (2) What genes are involved in the UVR response? and (3) How do the two species differ in their transcriptomic response to UVR? There were remarkable differences between the two species after 10 and 30 min of UVR exposure, including no overlap in significantly differentially abundant transcripts (DATs) after 10 min of UVR exposure and more than twice as many DATs for S. caninervis as there were for S. ruralis. Photosynthesis-related transcripts were involved in the response of S. ruralis to UVR, while membrane-related transcripts were indicated in the response of S. caninervis. In both species, transcripts involved in oxidative stress and those important for desiccation tolerance (such as late embryogenesis abundant genes and early light-inducible protein genes) were involved in response to UVR, suggesting possible roles in UVR tolerance and cross-talk with desiccation tolerance in these species. The results of this study suggest potential UVR-induced responses that may have roles outside of UVR tolerance, and that the response to URV is different in these two species, perhaps a reflection of adaptation to different environmental conditions.
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Affiliation(s)
- Jenna T. B. Ekwealor
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
- The University and Jepson Herbaria, University of California, Berkeley, Berkeley, CA, United States
| | - Brent D. Mishler
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
- The University and Jepson Herbaria, University of California, Berkeley, Berkeley, CA, United States
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Bowker MA, Rengifo‐Faiffer MC, Antoninka AJ, Grover HS, Coe KK, Fisher K, Mishler BD, Oliver M, Stark LR. Community composition influences ecosystem resistance and production more than species richness or intraspecific diversity. OIKOS 2021. [DOI: 10.1111/oik.08473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
| | | | | | | | | | - Kirsten Fisher
- Dept of Biological Sciences, California State Univ. Los Angeles CA USA
| | - Brent D. Mishler
- Dept of Integrative Biology, Univ. of California Berkeley CA USA
| | - Mel Oliver
- Plant Sciences, Univ. of Missouri Columbia MO USA
| | - Lloyd R. Stark
- School of Life Sciences, Univ. of Nevada Las Vegas NV USA
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10
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Ekwealor JTB, Clark TA, Dautermann O, Russell A, Ebrahimi S, Stark LR, Niyogi KK, Mishler BD. Natural ultraviolet radiation exposure alters photosynthetic biology and improves recovery from desiccation in a desert moss. J Exp Bot 2021; 72:4161-4179. [PMID: 33595636 DOI: 10.1093/jxb/erab051] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Plants in dryland ecosystems experience extreme daily and seasonal fluctuations in light, temperature, and water availability. We used an in situ field experiment to uncover the effects of natural and reduced levels of ultraviolet radiation (UV) on maximum PSII quantum efficiency (Fv/Fm), relative abundance of photosynthetic pigments and antioxidants, and the transcriptome in the desiccation-tolerant desert moss Syntrichia caninervis. We tested the hypotheses that: (i) S. caninervis plants undergo sustained thermal quenching of light [non-photochemical quenching (NPQ)] while desiccated and after rehydration; (ii) a reduction of UV will result in improved recovery of Fv/Fm; but (iii) 1 year of UV removal will de-harden plants and increase vulnerability to UV damage, indicated by a reduction in Fv/Fm. All field-collected plants had extremely low Fv/Fm after initial rehydration but recovered over 8 d in lab-simulated winter conditions. UV-filtered plants had lower Fv/Fm during recovery, higher concentrations of photoprotective pigments and antioxidants such as zeaxanthin and tocopherols, and lower concentrations of neoxanthin and Chl b than plants exposed to near natural UV levels. Field-grown S. caninervis underwent sustained NPQ that took days to relax and for efficient photosynthesis to resume. Reduction of solar UV radiation adversely affected recovery of Fv/Fm following rehydration.
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Affiliation(s)
- Jenna T B Ekwealor
- Department of Integrative Biology, and University and Jepson Herbaria, University of California, Berkeley, CA, USA
| | - Theresa A Clark
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - Oliver Dautermann
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | | | - Sotodeh Ebrahimi
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - Lloyd R Stark
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Brent D Mishler
- Department of Integrative Biology, and University and Jepson Herbaria, University of California, Berkeley, CA, USA
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11
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Earl C, Belitz MW, Laffan SW, Barve V, Barve N, Soltis DE, Allen JM, Soltis PS, Mishler BD, Kawahara AY, Guralnick R. Spatial phylogenetics of butterflies in relation to environmental drivers and angiosperm diversity across North America. iScience 2021; 24:102239. [PMID: 33997666 PMCID: PMC8101049 DOI: 10.1016/j.isci.2021.102239] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/13/2020] [Accepted: 02/23/2021] [Indexed: 11/25/2022] Open
Abstract
Broad-scale, quantitative assessments of insect biodiversity and the factors shaping it remain particularly poorly explored. Here we undertook a spatial phylogenetic analysis of North American butterflies to test whether climate stability and temperature gradients have shaped their diversity and endemism. We also performed the first quantitative comparisons of spatial phylogenetic patterns between butterflies and flowering plants. We expected concordance between the two groups based on shared historical environmental drivers and presumed strong butterfly-host plant specializations. We instead found that biodiversity patterns in butterflies are strikingly different from flowering plants, especially warm deserts. In particular, butterflies show different patterns of phylogenetic clustering compared with flowering plants, suggesting differences in habitat conservation between the two groups. These results suggest that shared biogeographic histories and trophic associations do not necessarily assure similar diversity outcomes. The work has applied value in conservation planning, documenting warm deserts as a North American butterfly biodiversity hotspot.
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Affiliation(s)
- Chandra Earl
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Michael W. Belitz
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
| | - Shawn W. Laffan
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Vijay Barve
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Narayani Barve
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Douglas E. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
| | - Julie M. Allen
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, USA
| | - Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
| | - Brent D. Mishler
- University of Jepson Herbaria, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Akito Y. Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Robert Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
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12
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Silva AT, Gao B, Fisher KM, Mishler BD, Ekwealor JTB, Stark LR, Li X, Zhang D, Bowker MA, Brinda JC, Coe KK, Oliver MJ. To dry perchance to live: Insights from the genome of the desiccation-tolerant biocrust moss Syntrichia caninervis. Plant J 2021; 105:1339-1356. [PMID: 33277766 DOI: 10.1111/tpj.15116] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/30/2020] [Indexed: 05/24/2023]
Abstract
With global climate change, water scarcity threatens whole agro/ecosystems. The desert moss Syntrichia caninervis, an extremophile, offers novel insights into surviving desiccation and heat. The sequenced S. caninervis genome consists of 13 chromosomes containing 16 545 protein-coding genes and 2666 unplaced scaffolds. Syntenic relationships within the S. caninervis and Physcomitrella patens genomes indicate the S. caninervis genome has undergone a single whole genome duplication event (compared to two for P. patens) and evidence suggests chromosomal or segmental losses in the evolutionary history of S. caninervis. The genome contains a large sex chromosome composed primarily of repetitive sequences with a large number of Copia and Gypsy elements. Orthogroup analyses revealed an expansion of ELIP genes encoding proteins important in photoprotection. The transcriptomic response to desiccation identified four structural clusters of novel genes. The genomic resources established for this extremophile offer new perspectives for understanding the evolution of desiccation tolerance in plants.
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Affiliation(s)
- Anderson T Silva
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, 65211, USA
| | - Bei Gao
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Science, Urumqi, 830011, China
| | - Kirsten M Fisher
- Department of Biological Sciences, California State University, Los Angeles, California, 90032, USA
| | - Brent D Mishler
- Department of Integrative Biology, University and Jepson Herbaria, University of California, Berkeley, California, 94720-2465, USA
| | - Jenna T B Ekwealor
- Department of Integrative Biology, University and Jepson Herbaria, University of California, Berkeley, California, 94720-2465, USA
| | - Lloyd R Stark
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, 89154-4004, USA
| | - Xiaoshuang Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Science, Urumqi, 830011, China
| | - Daoyuan Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Science, Urumqi, 830011, China
| | - Matthew A Bowker
- School of Forestry, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - John C Brinda
- Missouri Botanical Garden, St. Louis, Missouri, 63110-0299, USA
| | - Kirsten K Coe
- Department of Biology, Middlebury College, Middlebury, Vermont, 40506-0225, USA
| | - Melvin J Oliver
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, 65211, USA
- USDA-ARS-MWA, Plant Genetics Research Unit, Columbia, Missouri, 65211, USA
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13
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Coe KK, Greenwood JL, Slate ML, Clark TA, Brinda JC, Fisher KM, Mishler BD, Bowker MA, Oliver MJ, Ebrahimi S, Stark LR. Strategies of desiccation tolerance vary across life phases in the moss Syntrichia caninervis. Am J Bot 2021; 108:249-262. [PMID: 33249553 DOI: 10.1002/ajb2.1571] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 07/22/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Desiccation tolerance (DT) is a widespread phenomenon among land plants, and variable ecological strategies for DT are likely to exist. Using Syntrichia caninervis, a dryland moss and model system used in DT studies, we hypothesized that DT is lowest in juvenile (protonemal) tissues, highest in asexual reproductive propagules (gemmae), and intermediate in adults (shoots). We tested the long-standing hypothesis of an inherent constitutive strategy of DT in this species. METHODS Plants were rapidly dried to levels of equilibrating relative humidity (RHeq) ranging from 0 to 93%. Postrehydration recovery was assessed using chlorophyll fluorescence, regeneration rates, and visual tissue damage. For each life phase, we estimated the minimum rate of drying (RoDmin ) at RHeq = 42% that did not elicit damage 24 h postrehydration. RESULTS DT strategy varied with life phase, with adult shoots having the lowest RoDmin (10-25 min), followed by gemmae (3-10 h) and protonema (14-20 h). Adult shoots exhibited no detectable damage 24 h postrehydration following a rapid-dry only at the highest RHeq used (93%), but when dried to lower RHs the response declined to <50% of control fluorescence values. Notably, immediately following rehydration (0 h postrehydration), shoots were damaged below control levels of fluorescence regardless of the RHeq, thus implicating damage. CONCLUSIONS Life phases of the moss S. caninervis had a range of strategies from near constitutive (adult shoots) to demonstrably inducible (protonema). A new response variable for assessing degree of DT is introduced as the minimum rate of drying from which full recovery occurs.
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Affiliation(s)
- Kirsten K Coe
- Department of Biology, Middlebury College, Middlebury, VT, 40506-0225, USA
| | - Joshua L Greenwood
- School of Life Sciences, University of Nevada, 4505 Maryland Parkway, Las Vegas, NV, 89154-4004, USA
| | - Mandy L Slate
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, CO, 80309, USA
| | - Theresa A Clark
- School of Life Sciences, University of Nevada, 4505 Maryland Parkway, Las Vegas, NV, 89154-4004, USA
| | - John C Brinda
- Missouri Botanical Garden, Bryophyte Herbarium, 4344 Shaw Blvd, St. Louis, MO, 63110-0299, USA
| | - Kirsten M Fisher
- Department of Biological Sciences, California State University, 5151 State University Drive, Los Angeles, CA, 90032, USA
| | - Brent D Mishler
- Department of Integrative Biology, University and Jepson Herbaria and University of California, 1001 Valley Life Sciences Bld #2465, Berkeley, CA, 94720-2465, USA
| | - Matthew A Bowker
- School of Forestry, Northern Arizona University, 200 East Pine Knoll Drive, P.O. Box 15018, Flagstaff, AZ, 86011, USA
| | - Melvin J Oliver
- USDA ARS MWA PGRU, University of Missouri, 206 Curtis Hall, Columbia, MO, 65211, USA
| | - Sotodeh Ebrahimi
- School of Life Sciences, University of Nevada, 4505 Maryland Parkway, Las Vegas, NV, 89154-4004, USA
| | - Lloyd R Stark
- School of Life Sciences, University of Nevada, 4505 Maryland Parkway, Las Vegas, NV, 89154-4004, USA
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14
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Knapp WM, Frances A, Noss R, Naczi RFC, Weakley A, Gann GD, Baldwin BG, Miller J, McIntyre P, Mishler BD, Moore G, Olmstead RG, Strong A, Kennedy K, Heidel B, Gluesenkamp D. Vascular plant extinction in the continental United States and Canada. Conserv Biol 2021; 35:360-368. [PMID: 32860266 PMCID: PMC8151872 DOI: 10.1111/cobi.13621] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 05/11/2023]
Abstract
Extinction rates are expected to increase during the Anthropocene. Current extinction rates of plants and many animals remain unknown. We quantified extinctions among the vascular flora of the continental United States and Canada since European settlement. We compiled data on apparently extinct species by querying plant conservation databases, searching the literature, and vetting the resulting list with botanical experts. Because taxonomic opinion varies widely, we developed an index of taxonomic uncertainty (ITU). The ITU ranges from A to F, with A indicating unanimous taxonomic recognition and F indicating taxonomic recognition by only a single author. The ITU allowed us to rigorously evaluate extinction rates. Our data suggest that 51 species and 14 infraspecific taxa, representing 33 families and 49 genera of vascular plants, have become extinct in our study area since European settlement. Seven of these taxa exist in cultivation but are extinct in the wild. Most extinctions occurred in the west, but this outcome may reflect the timing of botanical exploration relative to settlement. Sixty-four percent of extinct plants were single-site endemics, and many occurred outside recognized biodiversity hotspots. Given the paucity of plant surveys in many areas, particularly prior to European settlement, the actual extinction rate of vascular plants is undoubtedly much higher than indicated here.
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Affiliation(s)
- Wesley M. Knapp
- North Carolina Natural Heritage ProgramAshevilleNC28805U.S.A.
| | - Anne Frances
- NatureServe2550 South Clark Street, Suite 930ArlingtonVA22202‐3926U.S.A.
| | - Reed Noss
- Florida Institute for Conservation Science112 Half Moon TrailMelroseFL32666U.S.A.
| | - Robert F. C. Naczi
- Institute of Systematic Botany, New York Botanical Garden2900 Southern Blvd.BronxNY10458‐5126U.S.A.
| | - Alan Weakley
- Biology Department, North Carolina Botanical GardenUniversity of North Carolina at Chapel HillCampus Box 3280Chapel HillNC27599‐3280U.S.A.
| | - George D. Gann
- The Institute for Regional Conservation100 E. Linton Blvd. #302BDelray BeachFL33483U.S.A.
| | - Bruce G. Baldwin
- Jepson Herbarium & Department of Integrative BiologyUniversity of California1001 Valley Life Sciences Bldg. #2465BerkeleyCA94720‐2465U.S.A.
| | - James Miller
- Missouri Botanical Garden4344 Shaw Blvd.St. LouisMO63110U.S.A.
| | - Patrick McIntyre
- NatureServe2550 South Clark Street, Suite 930ArlingtonVA22202‐3926U.S.A.
| | - Brent D. Mishler
- University and Jepson Herbaria & Department of Integrative BiologyUniversity of California1001 Valley Life Sciences Bldg. #2465BerkeleyCA94720‐2465U.S.A.
| | - Gerry Moore
- National Plant Data TeamUnited States Department of Agriculture2901 East Gate City Blvd., Suite 2100GreensboroNC27041U.S.A.
| | - Richard G. Olmstead
- Department of Biology and Burke MuseumUniversity of WashingtonSeattleWA98195U.S.A.
| | - Anna Strong
- Texas Parks and Wildlife Department4200 Smith School RoadAustinTX78744U.S.A.
| | - Kathryn Kennedy
- United States Forest Service333 Broadway Blvd. SEAlbuquerqueNM87102U.S.A.
| | - Bonnie Heidel
- Wyoming Natural Diversity DatabaseUniversity of Wyoming1000 E. University AvenueLaramieWY82071U.S.A.
| | - Daniel Gluesenkamp
- California Native Plant Society2707 K Street, Suite 1SacramentoCA95816U.S.A.
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15
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Knapp WM, Frances A, Noss R, Naczi RFC, Weakley A, Gann GD, Baldwin BG, Miller J, McIntyre P, Mishler BD, Moore G, Olmstead RG, Strong A, Gluesenkamp D, Kennedy K. Regional records improve data quality in determining plant extinction rates. Nat Ecol Evol 2020. [PMID: 32152535 DOI: 10.5061/dryad.xsj3tx99n] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Wesley M Knapp
- North Carolina Natural Heritage Program, Asheville, NC, USA.
| | | | - Reed Noss
- Florida Institute for Conservation Science, Sarasota, FL, USA
| | - Robert F C Naczi
- Institute of Systematic Botany, New York Botanical Garden, Bronx, NY, USA
| | - Alan Weakley
- Biology Department, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - George D Gann
- The Institute for Regional Conservation, Delray Beach, FL, USA
| | - Bruce G Baldwin
- University and Jepson Herbaria & Department of Integrative Biology, University of California, Berkeley, CA, USA
| | | | | | - Brent D Mishler
- University and Jepson Herbaria & Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Gerry Moore
- National Plant Data Team, Natural Resources Conservation Service, United States Department of Agriculture, Greensboro, NC, USA
| | - Richard G Olmstead
- Department of Biology and Burke Museum, University of Washington, Seattle, WA, USA
| | - Anna Strong
- Texas Parks and Wildlife Department, Austin, TX, USA
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16
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Knapp WM, Frances A, Noss R, Naczi RFC, Weakley A, Gann GD, Baldwin BG, Miller J, McIntyre P, Mishler BD, Moore G, Olmstead RG, Strong A, Gluesenkamp D, Kennedy K. Regional records improve data quality in determining plant extinction rates. Nat Ecol Evol 2020; 4:512-514. [PMID: 32152535 DOI: 10.1038/s41559-020-1146-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 02/10/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Wesley M Knapp
- North Carolina Natural Heritage Program, Asheville, NC, USA.
| | | | - Reed Noss
- Florida Institute for Conservation Science, Sarasota, FL, USA
| | - Robert F C Naczi
- Institute of Systematic Botany, New York Botanical Garden, Bronx, NY, USA
| | - Alan Weakley
- Biology Department, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - George D Gann
- The Institute for Regional Conservation, Delray Beach, FL, USA
| | - Bruce G Baldwin
- University and Jepson Herbaria & Department of Integrative Biology, University of California, Berkeley, CA, USA
| | | | | | - Brent D Mishler
- University and Jepson Herbaria & Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Gerry Moore
- National Plant Data Team, Natural Resources Conservation Service, United States Department of Agriculture, Greensboro, NC, USA
| | - Richard G Olmstead
- Department of Biology and Burke Museum, University of Washington, Seattle, WA, USA
| | - Anna Strong
- Texas Parks and Wildlife Department, Austin, TX, USA
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17
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Coe KK, Howard NB, Slate ML, Bowker MA, Mishler BD, Butler R, Greenwood J, Stark LR. Morphological and physiological traits in relation to carbon balance in a diverse clade of dryland mosses. Plant Cell Environ 2019; 42:3140-3151. [PMID: 31306496 DOI: 10.1111/pce.13613] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/18/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
Plant functional trait analyses have focused almost exclusively on vascular plants, but bryophytes comprise ancient and diverse plant lineages that have widespread global distributions and important ecological functions in terrestrial ecosystems. We examined a diverse clade of dryland mosses, Syntrichia, and studied carbon balance during a precipitation event (C-balance), a functional trait related to physiological functioning, desiccation tolerance, survival, and ecosystem carbon and nitrogen cycling. We examined variability in C-balance among 14 genotypes of Syntrichia and measured an additional 10 physiological and 13 morphological traits at the cell, leaf, shoot, and clump level. C-balance varied 20-fold among genotypes, and highest C-balances were associated with long, narrow leaves with awns, and small cells with thick cell walls, traits that may influence water uptake and retention during a precipitation event. Ordination analyses revealed that the axis most strongly correlated with C-balance included the maximum chlorophyll fluorescence, Fm , indicating the importance of photosystem II health for C exchange. C-balance represents a key functional trait in bryophytes, but its measurement is time intensive and not feasible to measure on large scales. We propose two models (using physiological and morphological traits) to predict C-balance, whereby identifying simpler to measure traits for trait databases.
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Affiliation(s)
- Kirsten K Coe
- Department of Biology, St. Mary's College of Maryland, St. Mary's, City, MD, 20653, USA
| | - Nora B Howard
- Department of Biology, St. Mary's College of Maryland, St. Mary's, City, MD, 20653, USA
| | - Mandy L Slate
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Matthew A Bowker
- School of Forestry, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Brent D Mishler
- University and Jepson Herbaria, and Department of Integrative Biology, University of California Berkeley, Berkeley, CA, 94720-2465, USA
| | - Riley Butler
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Joshua Greenwood
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Lloyd R Stark
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
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18
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Kling MM, Mishler BD, Thornhill AH, Baldwin BG, Ackerly DD. Facets of phylodiversity: evolutionary diversification, divergence and survival as conservation targets. Philos Trans R Soc Lond B Biol Sci 2018; 374:rstb.2017.0397. [PMID: 30455214 DOI: 10.1098/rstb.2017.0397] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2018] [Indexed: 11/12/2022] Open
Abstract
Biodiversity is often described as having multiple facets, including species richness, functional diversity and phylogenetic diversity. In this paper, we argue that phylogenetic diversity itself has three distinct facets-lineage diversification, character divergence and survival time-that can be quantified using distinct branch length metrics on an evolutionary tree. Each dimension is related to different processes of macroevolution, has different spatial patterns and is tied to distinct goals for conserving biodiversity and protecting its future resilience and evolutionary potential. We compared the landscapes identified as top conservation priorities by each of these three metrics in a conservation gap analysis for California, a world biodiversity hotspot, using herbarium data on the biogeography and evolutionary relationships of more than 5000 native plant species. Our analysis incorporated a novel continuous metric of current land protection status, fine-scale data on landscape intactness and an optimization algorithm used to identify complementary priority sites containing concentrations of taxa that are evolutionarily unique, vulnerable due to small range size and/or poorly protected across their ranges. Top conservation priorities included pockets of coastal and northern California that ranked highly for all three phylodiversity dimensions and for species richness, as well as sites uniquely identified by each metric whose value may depend on whether properties such as genetic divergence, high net diversification or independent survival experience are most desirable in an Anthropocene flora.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
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Affiliation(s)
- Matthew M Kling
- Department of Integrative Biology, University and Jepson Herbaria/University of California, Berkeley, CA 94720-3200, USA
| | - Brent D Mishler
- Department of Integrative Biology, University and Jepson Herbaria/University of California, Berkeley, CA 94720-3200, USA
| | - Andrew H Thornhill
- Department of Integrative Biology, University and Jepson Herbaria/University of California, Berkeley, CA 94720-3200, USA
| | - Bruce G Baldwin
- Department of Integrative Biology, University and Jepson Herbaria/University of California, Berkeley, CA 94720-3200, USA
| | - David D Ackerly
- Department of Integrative Biology, University and Jepson Herbaria/University of California, Berkeley, CA 94720-3200, USA
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19
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Yost JM, Sweeney PW, Gilbert E, Nelson G, Guralnick R, Gallinat AS, Ellwood ER, Rossington N, Willis CG, Blum SD, Walls RL, Haston EM, Denslow MW, Zohner CM, Morris AB, Stucky BJ, Carter JR, Baxter DG, Bolmgren K, Denny EG, Dean E, Pearson KD, Davis CC, Mishler BD, Soltis PS, Mazer SJ. Digitization protocol for scoring reproductive phenology from herbarium specimens of seed plants. Appl Plant Sci 2018; 6:e1022. [PMID: 29732253 PMCID: PMC5851559 DOI: 10.1002/aps3.1022] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/02/2018] [Indexed: 05/13/2023]
Abstract
PREMISE OF THE STUDY Herbarium specimens provide a robust record of historical plant phenology (the timing of seasonal events such as flowering or fruiting). However, the difficulty of aggregating phenological data from specimens arises from a lack of standardized scoring methods and definitions for phenological states across the collections community. METHODS AND RESULTS To address this problem, we report on a consensus reached by an iDigBio working group of curators, researchers, and data standards experts regarding an efficient scoring protocol and a data-sharing protocol for reproductive traits available from herbarium specimens of seed plants. The phenological data sets generated can be shared via Darwin Core Archives using the Extended MeasurementOrFact extension. CONCLUSIONS Our hope is that curators and others interested in collecting phenological trait data from specimens will use the recommendations presented here in current and future scoring efforts. New tools for scoring specimens are reviewed.
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Affiliation(s)
- Jennifer M. Yost
- Department of Biological SciencesCalifornia Polytechnic State University1 Grand AvenueSan Luis ObispoCalifornia93407USA
| | - Patrick W. Sweeney
- Division of BotanyPeabody Museum of Natural HistoryYale UniversityP.O. Box 208118New HavenConnecticut06520USA
| | - Ed Gilbert
- Arizona State UniversitySchool of Life SciencesP.O. Box 874501TempeArizona85287‐4501USA
| | - Gil Nelson
- iDigBioCollege of Communication and InformationFlorida State UniversityTallahasseeFlorida32306USA
| | - Robert Guralnick
- Florida Museum of Natural History and Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611USA
| | - Amanda S. Gallinat
- Boston UniversityDepartment of Biology5 Cummington MallBostonMassachusets02215USA
| | | | - Natalie Rossington
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraCalifornia93106‐9620USA
| | - Charles G. Willis
- Department of Organismic and Evolutionary BiologyHarvard University Herbaria22 Divinity AvenueCambridgeMassachusetts02138USA
- University of MinnesotaDepartment of Biology Teaching and Learning515 Delaware Street SEMinneapolisMinnesota55455USA
| | - Stanley D. Blum
- Biodiversity Information Standards (TDWG)1342 34th AvenueSan FranciscoCalifornia94122USA
| | - Ramona L. Walls
- CyVerseUniversity of Arizona1657 East Helen StreetTucsonArizona85721USA
| | - Elspeth M. Haston
- Royal Botanic Garden Edinburgh20a Inverleith RowEdinburghEH3 5LRUnited Kingdom
| | - Michael W. Denslow
- Florida Museum of Natural History and Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611USA
- Department of BiologyAppalachian State UniversityBooneNorth Carolina28608USA
| | - Constantin M. Zohner
- Systematic Botany and MycologyDepartment of BiologyMunich University (LMU)80638MunichGermany
| | - Ashley B. Morris
- Department of BiologyMiddle Tennessee State UniversityMurfreesboroTennessee37138USA
| | - Brian J. Stucky
- Florida Museum of Natural History and Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611USA
| | | | - David G. Baxter
- University and Jepson HerbariaUniversity of California Berkeley1001 Valley Life Sciences BuildingBerkeleyCalifornia94720USA
| | - Kjell Bolmgren
- Swedish University of Agricultural SciencesUnit for Field‐based Forest Research360 30LammhultSweden
| | - Ellen G. Denny
- USA National Phenology NetworkUniversity of ArizonaTucsonArizona85721USA
| | - Ellen Dean
- UC Davis Center for Plant DiversityPlant Sciences M.S. 7, One Shields AvenueDavisCalifornia95616USA
| | - Katelin D. Pearson
- Department of Biological ScienceFlorida State UniversityTallahasseeFlorida32304USA
| | - Charles C. Davis
- Department of Organismic and Evolutionary BiologyHarvard University Herbaria22 Divinity AvenueCambridgeMassachusetts02138USA
| | - Brent D. Mishler
- University and Jepson HerbariaUniversity of California Berkeley1001 Valley Life Sciences BuildingBerkeleyCalifornia94720USA
- Department of Integrative BiologyUniversity of CaliforniaBerkeleyCalifornia94720‐2465USA
| | - Pamela S. Soltis
- Florida Museum of Natural History and Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611USA
| | - Susan J. Mazer
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraCalifornia93106‐9620USA
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20
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Thornhill AH, Baldwin BG, Freyman WA, Nosratinia S, Kling MM, Morueta-Holme N, Madsen TP, Ackerly DD, Mishler BD. Spatial phylogenetics of the native California flora. BMC Biol 2017; 15:96. [PMID: 29073895 PMCID: PMC5658987 DOI: 10.1186/s12915-017-0435-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/05/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND California is a world floristic biodiversity hotspot where the terms neo- and paleo-endemism were first applied. Using spatial phylogenetics, it is now possible to evaluate biodiversity from an evolutionary standpoint, including discovering significant areas of neo- and paleo-endemism, by combining spatial information from museum collections and DNA-based phylogenies. Here we used a distributional dataset of 1.39 million herbarium specimens, a phylogeny of 1083 operational taxonomic units (OTUs) and 9 genes, and a spatial randomization test to identify regions of significant phylogenetic diversity, relative phylogenetic diversity, and phylogenetic endemism (PE), as well as to conduct a categorical analysis of neo- and paleo-endemism (CANAPE). RESULTS We found (1) extensive phylogenetic clustering in the South Coast Ranges, southern Great Valley, and deserts of California; (2) significant concentrations of short branches in the Mojave and Great Basin Deserts and the South Coast Ranges and long branches in the northern Great Valley, Sierra Nevada foothills, and the northwestern and southwestern parts of the state; (3) significant concentrations of paleo-endemism in Northwestern California, the northern Great Valley, and western Sonoran Desert, and neo-endemism in the White-Inyo Range, northern Mojave Desert, and southern Channel Islands. Multiple analyses were run to observe the effects on significance patterns of using different phylogenetic tree topologies (uncalibrated trees versus time-calibrated ultrametric trees) and using different representations of OTU ranges (herbarium specimen locations versus species distribution models). CONCLUSIONS These analyses showed that examining the geographic distributions of branch lengths in a statistical framework adds a new dimension to California floristics that, in comparison with climatic data, helps to illuminate causes of endemism. In particular, the concentration of significant PE in more arid regions of California extends previous ideas about aridity as an evolutionary stimulus. The patterns seen are largely robust to phylogenetic uncertainty and time calibration but are sensitive to the use of occurrence data versus modeled ranges, indicating that special attention toward improving geographic distributional data should be top priority in the future for advancing understanding of spatial patterns of biodiversity.
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Affiliation(s)
- Andrew H Thornhill
- University and Jepson Herbaria and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, CA, 94720, USA.
| | - Bruce G Baldwin
- University and Jepson Herbaria and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, CA, 94720, USA
| | - William A Freyman
- University and Jepson Herbaria and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, CA, 94720, USA
| | - Sonia Nosratinia
- University and Jepson Herbaria and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, CA, 94720, USA
| | - Matthew M Kling
- University and Jepson Herbaria and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, CA, 94720, USA
| | - Naia Morueta-Holme
- University and Jepson Herbaria and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, CA, 94720, USA
| | - Thomas P Madsen
- University and Jepson Herbaria and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, CA, 94720, USA
| | - David D Ackerly
- University and Jepson Herbaria and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, CA, 94720, USA
| | - Brent D Mishler
- University and Jepson Herbaria and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, CA, 94720, USA
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Baldwin BG, Thornhill AH, Freyman WA, Ackerly DD, Kling MM, Morueta-Holme N, Mishler BD. Species richness and endemism in the native flora of California. Am J Bot 2017; 104:487-501. [PMID: 28341628 DOI: 10.3732/ajb.1600326] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 02/23/2017] [Indexed: 05/22/2023]
Abstract
PREMISE OF THE STUDY California's vascular flora is the most diverse and threatened in temperate North America. Previous studies of spatial patterns of Californian plant diversity have been limited by traditional metrics, non-uniform geographic units, and distributional data derived from floristic descriptions for only a subset of species. METHODS We revisited patterns of sampling intensity, species richness, and relative endemism in California based on equal-area spatial units, the full vascular flora, and specimen-based distributional data. We estimated richness, weighted endemism (inverse range-weighting of species), and corrected weighted endemism (weighted endemism corrected for richness), and performed a randomization test for significantly high endemism. KEY RESULTS Possible biases in herbarium data do not obscure patterns of high richness and endemism at the spatial resolution studied. High species richness was sometimes associated with significantly high endemism (e.g., Klamath Ranges) but often not. In Stebbins and Major's (1965) main endemism hotspot, Southwestern California, species richness is high across much of the Peninsular and Transverse ranges but significantly high endemism is mostly localized to the Santa Rosa and San Bernardino mountains. In contrast, species richness is low in the Channel Islands, where endemism is significantly high, as also found for much of the Death Valley region. CONCLUSIONS Measures of taxonomic richness, even with greater weighting of range-restricted taxa, are insufficient for identifying areas of significantly high endemism that warrant conservation attention. Differences between our findings and those in previous studies appear to mostly reflect the source and scale of distributional data, and recent analytical refinements.
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Affiliation(s)
- Bruce G Baldwin
- University and Jepson Herbaria and Department of Integrative Biology, 1001 Valley Life Sciences Building #2465, University of California, Berkeley, California 94720-2465 USA
| | - Andrew H Thornhill
- University and Jepson Herbaria and Department of Integrative Biology, 1001 Valley Life Sciences Building #2465, University of California, Berkeley, California 94720-2465 USA
| | - William A Freyman
- University and Jepson Herbaria and Department of Integrative Biology, 1001 Valley Life Sciences Building #2465, University of California, Berkeley, California 94720-2465 USA
| | - David D Ackerly
- University and Jepson Herbaria and Department of Integrative Biology, 1001 Valley Life Sciences Building #2465, University of California, Berkeley, California 94720-2465 USA
| | - Matthew M Kling
- University and Jepson Herbaria and Department of Integrative Biology, 1001 Valley Life Sciences Building #2465, University of California, Berkeley, California 94720-2465 USA
| | - Naia Morueta-Holme
- University and Jepson Herbaria and Department of Integrative Biology, 1001 Valley Life Sciences Building #2465, University of California, Berkeley, California 94720-2465 USA
| | - Brent D Mishler
- University and Jepson Herbaria and Department of Integrative Biology, 1001 Valley Life Sciences Building #2465, University of California, Berkeley, California 94720-2465 USA
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Laffan SW, Rosauer DF, Di Virgilio G, Miller JT, González‐Orozco CE, Knerr N, Thornhill AH, Mishler BD. Range‐weighted metrics of species and phylogenetic turnover can better resolve biogeographic transition zones. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12513] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Shawn W. Laffan
- Centre for Ecosystem Science School of Biological, Earth and Environmental Sciences University of New South Wales Sydney NSW 2052 Australia
| | - Dan F. Rosauer
- Research School of Biology and Centre for Biodiversity Analysis Australian National University Canberra ACT Australia
| | - Giovanni Di Virgilio
- Centre for Ecosystem Science School of Biological, Earth and Environmental Sciences University of New South Wales Sydney NSW 2052 Australia
| | - Joseph T. Miller
- National Research Collections Australia CSIRO National Facilities and Collections Canberra ACT Australia
- Division of Environmental Biology National Science Foundation Arlington Virginia USA
| | - Carlos E. González‐Orozco
- Institute for Applied Ecology and Collaborative Research Network for Murray‐Darling Basin Futures, University of Canberra Canberra ACT Australia
| | - Nunzio Knerr
- National Research Collections Australia CSIRO National Facilities and Collections Canberra ACT Australia
| | - Andrew H. Thornhill
- National Research Collections Australia CSIRO National Facilities and Collections Canberra ACT Australia
- Australian Tropical Herbarium James Cook University Cairns QLD 4870 Australia
- Department of Integrative Biology University and Jepson Herbaria University of California Berkeley California USA
| | - Brent D. Mishler
- Department of Integrative Biology University and Jepson Herbaria University of California Berkeley California USA
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González-Orozco CE, Mishler BD, Miller JT, Laffan SW, Knerr N, Unmack P, Georges A, Thornhill AH, Rosauer DF, Gruber B. Assessing biodiversity and endemism using phylogenetic methods across multiple taxonomic groups. Ecol Evol 2015; 5:5177-5192. [PMID: 30151122 PMCID: PMC6102556 DOI: 10.1002/ece3.1747] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/21/2015] [Accepted: 08/24/2015] [Indexed: 11/13/2022] Open
Abstract
Identifying geographical areas with the greatest representation of the tree of life is an important goal for the management and conservation of biodiversity. While there are methods available for using a single phylogenetic tree to assess spatial patterns of biodiversity, there has been limited exploration of how separate phylogenies from multiple taxonomic groups can be used jointly to map diversity and endemism. Here, we demonstrate how to apply different phylogenetic approaches to assess biodiversity across multiple taxonomic groups. We map spatial patterns of phylogenetic diversity/endemism to identify concordant areas with the greatest representation of biodiversity across multiple taxa and demonstrate the approach by applying it to the Murray–Darling basin region of southeastern Australia. The areas with significant centers of phylogenetic diversity and endemism were distributed differently for the five taxonomic groups studied (plant genera, fish, tree frogs, acacias, and eucalypts); no strong shared patterns across all five groups emerged. However, congruence was apparent between some groups in some parts of the basin. The northern region of the basin emerges from the analysis as a priority area for future conservation initiatives focused on eucalypts and tree frogs. The southern region is particularly important for conservation of the evolutionary heritage of plants and fishes.
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Affiliation(s)
- Carlos E González-Orozco
- Institute for Applied Ecology and Collaborative Research Network for Murray-Darling Basin Futures University of Canberra Canberra Australian Capital Territory 2601 Australia
| | - Brent D Mishler
- University and Jepson Herbaria Department of Integrative Biology University of California Berkeley California 94720-2465
| | - Joseph T Miller
- Centre for Australian National Biodiversity Research CSIRO Plant Industry GPO Box 1600 Canberra Australian Capital Territory 2601 Australia.,Division of Environmental Biology National Science Foundation Arlington Virginia 22230
| | - Shawn W Laffan
- Centre for Ecosystem Science School of Biological, Earth and Environmental Sciences University of New South Wales Kensington New South Wales 2052
| | - Nunzio Knerr
- Centre for Australian National Biodiversity Research CSIRO Plant Industry GPO Box 1600 Canberra Australian Capital Territory 2601 Australia
| | - Peter Unmack
- Institute for Applied Ecology and Collaborative Research Network for Murray-Darling Basin Futures University of Canberra Canberra Australian Capital Territory 2601 Australia
| | - Arthur Georges
- Institute for Applied Ecology and Collaborative Research Network for Murray-Darling Basin Futures University of Canberra Canberra Australian Capital Territory 2601 Australia
| | - Andrew H Thornhill
- University and Jepson Herbaria Department of Integrative Biology University of California Berkeley California 94720-2465.,Centre for Australian National Biodiversity Research CSIRO Plant Industry GPO Box 1600 Canberra Australian Capital Territory 2601 Australia.,Australian Tropical Herbarium James Cook University Cairns QLD 4870 Australia
| | - Dan F Rosauer
- Division of Ecology, Evolution and Genetics Australian National University Canberra Australian Capital Territory 0200 Australia
| | - Bernd Gruber
- Institute for Applied Ecology and Collaborative Research Network for Murray-Darling Basin Futures University of Canberra Canberra Australian Capital Territory 2601 Australia
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Nagalingum NS, Knerr N, Laffan SW, González-Orozco CE, Thornhill AH, Miller JT, Mishler BD. Continental scale patterns and predictors of fern richness and phylogenetic diversity. Front Genet 2015; 6:132. [PMID: 25926846 PMCID: PMC4396410 DOI: 10.3389/fgene.2015.00132] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 03/19/2015] [Indexed: 12/02/2022] Open
Abstract
Because ferns have a wide range of habitat preferences and are widely distributed, they are an ideal group for understanding how diversity is distributed. Here we examine fern diversity on a broad-scale using standard and corrected richness measures as well as phylogenetic indices; in addition we determine the environmental predictors of each diversity metric. Using the combined records of Australian herbaria, a dataset of over 60,000 records was obtained for 89 genera to infer richness. A molecular phylogeny of all the genera was constructed and combined with the herbarium records to obtain phylogenetic diversity patterns. A hotspot of both taxic and phylogenetic diversity occurs in the Wet Tropics of northeastern Australia. Although considerable diversity is distributed along the eastern coast, some important regions of diversity are identified only after sample-standardization of richness and through the phylogenetic metric. Of all of the metrics, annual precipitation was identified as the most explanatory variable, in part, in agreement with global and regional fern studies. However, precipitation was combined with a different variable for each different metric. For corrected richness, precipitation was combined with temperature seasonality, while correlation of phylogenetic diversity to precipitation plus radiation indicated support for the species-energy hypothesis. Significantly high and significantly low phylogenetic diversity were found in geographically separate areas. These separate areas correlated with different climatic conditions such as seasonality in precipitation. The phylogenetic metrics identified additional areas of significant diversity, some of which have not been revealed using traditional taxonomic analyses, suggesting that different ecological and evolutionary processes have operated over the continent. Our study demonstrates that it is possible and vital to incorporate evolutionary metrics when inferring biodiversity hotspots from large compilations of data.
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Affiliation(s)
- Nathalie S. Nagalingum
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain TrustSydney, NSW, Australia
| | - Nunzio Knerr
- Centre for Australian National Biodiversity Research, Commonwealth Scientific and Industrial Research Organisation Plant IndustryCanberra, ACT, Australia
| | - Shawn W. Laffan
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South WalesSydney, NSW, Australia
| | - Carlos E. González-Orozco
- Centre for Australian National Biodiversity Research, Commonwealth Scientific and Industrial Research Organisation Plant IndustryCanberra, ACT, Australia
- Institute for Applied Ecology and Collaborative Research Network for Murray-Darling Basin Futures, University of CanberraACT, Australia
| | - Andrew H. Thornhill
- Centre for Australian National Biodiversity Research, Commonwealth Scientific and Industrial Research Organisation Plant IndustryCanberra, ACT, Australia
- Australian Tropical Herbarium, James Cook UniversityCairns, QLD, Australia
| | - Joseph T. Miller
- Centre for Australian National Biodiversity Research, Commonwealth Scientific and Industrial Research Organisation Plant IndustryCanberra, ACT, Australia
| | - Brent D. Mishler
- University and Jepson Herbaria, and Department of Integrative Biology, University of CaliforniaBerkeley, CA, USA
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Abstract
Oleosins form a steric barrier surface on lipid droplets in cytoplasm, preventing them from contacting and coalescing with adjacent droplets. Oleosin genes have been detected in numerous plant species. However, the presence of oleosin genes in the most basally diverging lineage of land plants, liverworts, has not been reported previously. Thus we explored whether liverworts have an oleosin gene. In Marchantia polymorpha L., a thalloid liverwort, one predicted sequence was found that could encode oleosin, possessing the hallmark of oleosin, a proline knot (-PX5SPX3P-) motif. The phylogeny of the oleosin gene family in land plants was reconstructed based on both nucleotide and amino acid sequences of oleosins, from 31 representative species covering almost all the main lineages of land plants. Based on our phylogenetic trees, oleosin genes were classified into three groups: M-oleosins (defined here as a novel group distinct from the two previously known groups), low molecular weight isoform (L-oleosin), and high molecular weight isoform (H-oleosin), according to their amino-acid organization, phylogenetic relationships, expression tissues, and immunological characteristics. In liverworts, mosses, lycophytes, and gymnosperms, only M-oleosins have been described. In angiosperms, however, while this isoform remains and is highly expressed in the gametophyte pollen tube, two other isoforms also occur, L-oleosins and H-oleosins. Phylogenetic analyses suggest that the M-oleosin isoform is the precursor to the ancestor of L-oleosins and H-oleosins. The later two isoforms evolved by successive gene duplications in ancestral angiosperms. At the genomic level, most oleosins possess no introns. If introns are present, in both the L-isoform and the M-isoform a single intron inserts behind the central region, while in the H-isoform, a single intron is located at the 5'-terminus. This study fills a major gap in understanding functional gene evolution of oleosin in land plants, shedding new light on evolutionary transitions of lipid storage strategies.
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Affiliation(s)
- Yuan Fang
- School of Life Science, East China Normal University, Shanghai, China
- University and Jepson Herbaria, and Department of Integrative Biology, University of California, Berkeley, California, United State of America
| | - Rui-Liang Zhu
- School of Life Science, East China Normal University, Shanghai, China
| | - Brent D. Mishler
- University and Jepson Herbaria, and Department of Integrative Biology, University of California, Berkeley, California, United State of America
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27
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Abstract
BACKGROUND Mosses are the largest of the three extant clades of gametophyte-dominant land plants and remain poorly studied using comparative genomic methods. Major monophyletic moss lineages are characterised by different types of a spore dehiscence apparatus called the peristome, and the most important unsolved problem in higher-level moss systematics is the branching order of these peristomate clades. Organellar genome sequencing offers the potential to resolve this issue through the provision of both genomic structural characters and a greatly increased quantity of nucleotide substitution characters, as well as to elucidate organellar evolution in mosses. We publish and describe the chloroplast and mitochondrial genomes of Tetraphis pellucida, representative of the most phylogenetically intractable and morphologically isolated peristomate lineage. RESULTS Assembly of reads from Illumina SBS and Pacific Biosciences RS sequencing reveals that the Tetraphis chloroplast genome comprises 127,489 bp and the mitochondrial genome 107,730 bp. Although genomic structures are similar to those of the small number of other known moss organellar genomes, the chloroplast lacks the petN gene (in common with Tortula ruralis) and the mitochondrion has only a non-functional pseudogenised remnant of nad7 (uniquely amongst known moss chondromes). CONCLUSIONS Structural genomic features exist with the potential to be informative for phylogenetic relationships amongst the peristomate moss lineages, and thus organellar genome sequences are urgently required for exemplars from other clades. The unique genomic and morphological features of Tetraphis confirm its importance for resolving one of the major questions in land plant phylogeny and for understanding the evolution of the peristome, a likely key innovation underlying the diversity of mosses. The functional loss of nad7 from the chondrome is now shown to have occurred independently in all three bryophyte clades as well as in the early-diverging tracheophyte Huperzia squarrosa.
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Affiliation(s)
- Neil E Bell
- />Botanical Museum, Finnish Museum of Natural History, University of Helsinki, PO Box 7, FI-00014 Helsinki, Finland
- />Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, FI-00014 Helsinki, Finland
| | - Jeffrey L Boore
- />Department of Integrative Biology, University of California Berkeley, 1005 Valley Life Sciences Building, Berkeley, CA 94720-3140 USA
| | - Brent D Mishler
- />Department of Integrative Biology and University and Jepson Herbaria, University of California, 1001 Valley Life Sciences Bldg, Berkeley, CA 94720-2465 USA
| | - Jaakko Hyvönen
- />Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, FI-00014 Helsinki, Finland
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González-Orozco CE, Ebach MC, Laffan S, Thornhill AH, Knerr NJ, Schmidt-Lebuhn AN, Cargill CC, Clements M, Nagalingum NS, Mishler BD, Miller JT. Quantifying phytogeographical regions of Australia using geospatial turnover in species composition. PLoS One 2014; 9:e92558. [PMID: 24658356 PMCID: PMC3962426 DOI: 10.1371/journal.pone.0092558] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 02/25/2014] [Indexed: 11/18/2022] Open
Abstract
The largest digitized dataset of land plant distributions in Australia assembled to date (750,741 georeferenced herbarium records; 6,043 species) was used to partition the Australian continent into phytogeographical regions. We used a set of six widely distributed vascular plant groups and three non-vascular plant groups which together occur in a variety of landscapes/habitats across Australia. Phytogeographical regions were identified using quantitative analyses of species turnover, the rate of change in species composition between sites, calculated as Simpson's beta. We propose six major phytogeographical regions for Australia: Northern, Northern Desert, Eremaean, Eastern Queensland, Euronotian and South-Western. Our new phytogeographical regions show a spatial agreement of 65% with respect to previously defined phytogeographical regions of Australia. We also confirm that these new regions are in general agreement with the biomes of Australia and other contemporary biogeographical classifications. To assess the meaningfulness of the proposed phytogeographical regions, we evaluated how they relate to broad scale environmental gradients. Physiographic factors such as geology do not have a strong correspondence with our proposed regions. Instead, we identified climate as the main environmental driver. The use of an unprecedentedly large dataset of multiple plant groups, coupled with an explicit quantitative analysis, makes this study novel and allows an improved historical bioregionalization scheme for Australian plants. Our analyses show that: (1) there is considerable overlap between our results and older biogeographic classifications; (2) phytogeographical regions based on species turnover can be a powerful tool to further partition the landscape into meaningful units; (3) further studies using phylogenetic turnover metrics are needed to test the taxonomic areas.
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Affiliation(s)
- Carlos E González-Orozco
- Centre for Australian National Biodiversity Research, Commonwealth Scientific and Industrial Research Organisation, Plant Industry, Canberra, Australian Capital Territory, Australia
| | - Malte C Ebach
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Shawn Laffan
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Andrew H Thornhill
- Centre for Australian National Biodiversity Research, Commonwealth Scientific and Industrial Research Organisation, Plant Industry, Canberra, Australian Capital Territory, Australia; Australian Tropical Herbarium, James Cook University, Cairns, Queensland, Australia
| | - Nunzio J Knerr
- Centre for Australian National Biodiversity Research, Commonwealth Scientific and Industrial Research Organisation, Plant Industry, Canberra, Australian Capital Territory, Australia
| | - Alexander N Schmidt-Lebuhn
- Centre for Australian National Biodiversity Research, Commonwealth Scientific and Industrial Research Organisation, Plant Industry, Canberra, Australian Capital Territory, Australia
| | - Christine C Cargill
- Centre for Australian National Biodiversity Research, Commonwealth Scientific and Industrial Research Organisation, Plant Industry, Canberra, Australian Capital Territory, Australia
| | - Mark Clements
- Centre for Australian National Biodiversity Research, Commonwealth Scientific and Industrial Research Organisation, Plant Industry, Canberra, Australian Capital Territory, Australia
| | - Nathalie S Nagalingum
- National Herbarium of New South Wales, Botanic Gardens Trust, Sydney, New South Wales, Australia
| | - Brent D Mishler
- University and Jepson Herbaria, Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Joseph T Miller
- Centre for Australian National Biodiversity Research, Commonwealth Scientific and Industrial Research Organisation, Plant Industry, Canberra, Australian Capital Territory, Australia
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Oliver MJ, Velten J, Mishler BD. Desiccation tolerance in bryophytes: a reflection of the primitive strategy for plant survival in dehydrating habitats? Integr Comp Biol 2012; 45:788-99. [PMID: 21676830 DOI: 10.1093/icb/45.5.788] [Citation(s) in RCA: 172] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bryophytes are a non-monophyletic group of three major lineages (liverworts, hornworts, and mosses) that descend from the earliest branching events in the phylogeny of land plants. We postulate that desiccation tolerance is a primitive trait, thus mechanisms by which the first land plants achieved tolerance may be reflected in how extant desiccation-tolerant bryophytes survive drying. Evidence is consistent with extant bryophytes employing a tolerance strategy of constitutive cellular protection coupled with induction of a recovery/repair mechanism upon rehydration. Cellular structures appear intact in the desiccated state but are disrupted by rapid uptake of water upon rehydration, but cellular integrity is rapidly regained. The photosynthetic machinery appears to be protected such that photosynthetic activity recovers quickly. Gene expression responds following rehydration and not during drying. Gene expression is translationally controlled and results in the synthesis of a number of proteins, collectively called rehydrins. Some prominent rehydrins are similar to Late Embryogenesis Abundant (LEA) proteins, classically ascribed a protection function during desiccation. The role of LEA proteins in a rehydrating system is unknown but data indicates a function in stabilization and reconstitution of membranes. Phylogenetic studies using a Tortula ruralis LEA-like rehydrin led to a re-examination of the evolution of desiccation tolerance. A new phylogenetic analysis suggests that: (i) the basic mechanisms of tolerance seen in modern day bryophytes have changed little from the earliest manifestations of desiccation tolerance in land plants, and (ii) vegetative desiccation tolerance in the early land plants may have evolved from a mechanism present first in spores.
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Affiliation(s)
- Melvin J Oliver
- USDA-ARS, Cropping Systems Research Laboratory, 3810 4th St, Lubbock, Texas 79415
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30
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Affiliation(s)
- Nico Cellinese
- Florida Museum of Natural History, University of Florida, 354 Dickinson Hall, Gainesville, FL 32611-7800; 2Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA; and 3University and Jepson Herbaria and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - David A. Baum
- Florida Museum of Natural History, University of Florida, 354 Dickinson Hall, Gainesville, FL 32611-7800; 2Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA; and 3University and Jepson Herbaria and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Brent D. Mishler
- Florida Museum of Natural History, University of Florida, 354 Dickinson Hall, Gainesville, FL 32611-7800; 2Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA; and 3University and Jepson Herbaria and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
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31
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Karol KG, Arumuganathan K, Boore JL, Duffy AM, Everett KDE, Hall JD, Hansen SK, Kuehl JV, Mandoli DF, Mishler BD, Olmstead RG, Renzaglia KS, Wolf PG. Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages. BMC Evol Biol 2010; 10:321. [PMID: 20969798 PMCID: PMC3087542 DOI: 10.1186/1471-2148-10-321] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Accepted: 10/23/2010] [Indexed: 11/17/2022] Open
Abstract
Background Despite considerable progress in our understanding of land plant phylogeny, several nodes in the green tree of life remain poorly resolved. Furthermore, the bulk of currently available data come from only a subset of major land plant clades. Here we examine early land plant evolution using complete plastome sequences including two previously unexamined and phylogenetically critical lineages. To better understand the evolution of land plants and their plastomes, we examined aligned nucleotide sequences, indels, gene and nucleotide composition, inversions, and gene order at the boundaries of the inverted repeats. Results We present the plastome sequences of Equisetum arvense, a horsetail, and of Isoetes flaccida, a heterosporous lycophyte. Phylogenetic analysis of aligned nucleotides from 49 plastome genes from 43 taxa supported monophyly for the following clades: embryophytes (land plants), lycophytes, monilophytes (leptosporangiate ferns + Angiopteris evecta + Psilotum nudum + Equisetum arvense), and seed plants. Resolution among the four monilophyte lineages remained moderate, although nucleotide analyses suggested that P. nudum and E. arvense form a clade sister to A. evecta + leptosporangiate ferns. Results from phylogenetic analyses of nucleotides were consistent with the distribution of plastome gene rearrangements and with analysis of sequence gaps resulting from insertions and deletions (indels). We found one new indel and an inversion of a block of genes that unites the monilophytes. Conclusions Monophyly of monilophytes has been disputed on the basis of morphological and fossil evidence. In the context of a broad sampling of land plant data we find several new pieces of evidence for monilophyte monophyly. Results from this study demonstrate resolution among the four monilophytes lineages, albeit with moderate support; we posit a clade consisting of Equisetaceae and Psilotaceae that is sister to the "true ferns," including Marattiaceae.
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Affiliation(s)
- Kenneth G Karol
- The Lewis B, and Dorothy Cullman Program for Molecular Systematics Studies, The New York Botanical Garden, Bronx, NY 10458, USA.
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Oliver MJ, Murdock AG, Mishler BD, Kuehl JV, Boore JL, Mandoli DF, Everett KDE, Wolf PG, Duffy AM, Karol KG. Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes. BMC Genomics 2010; 11:143. [PMID: 20187961 PMCID: PMC2841679 DOI: 10.1186/1471-2164-11-143] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Accepted: 02/27/2010] [Indexed: 11/21/2022] Open
Abstract
Background Tortula ruralis, a widely distributed species in the moss family Pottiaceae, is increasingly used as a model organism for the study of desiccation tolerance and mechanisms of cellular repair. In this paper, we present the chloroplast genome sequence of T. ruralis, only the second published chloroplast genome for a moss, and the first for a vegetatively desiccation-tolerant plant. Results The Tortula chloroplast genome is ~123,500 bp, and differs in a number of ways from that of Physcomitrella patens, the first published moss chloroplast genome. For example, Tortula lacks the ~71 kb inversion found in the large single copy region of the Physcomitrella genome and other members of the Funariales. Also, the Tortula chloroplast genome lacks petN, a gene found in all known land plant plastid genomes. In addition, an unusual case of nucleotide polymorphism was discovered. Conclusions Although the chloroplast genome of Tortula ruralis differs from that of the only other sequenced moss, Physcomitrella patens, we have yet to determine the biological significance of the differences. The polymorphisms we have uncovered in the sequencing of the genome offer a rare possibility (for mosses) of the generation of DNA markers for fine-level phylogenetic studies, or to investigate individual variation within populations.
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Affiliation(s)
- Melvin J Oliver
- USDA-ARS-MWA, Plant Genetics Research Unit, University of Missouri, 205 Curtis Hall, Columbia, MO 65211, USA.
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Stark LR, Oliver MJ, Mishler BD, McLetchie DN. Generational differences in response to desiccation stress in the desert moss Tortula inermis. Ann Bot 2007; 99:53-60. [PMID: 17098752 PMCID: PMC2802979 DOI: 10.1093/aob/mcl238] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Revised: 08/30/2006] [Accepted: 09/19/2006] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS Active growth in post-embryonic sporophytes of desert mosses is restricted to the cooler, wetter months. However, most desert mosses have perennial gametophytes. It is hypothesized that these life history patterns are due, in part, to a reduced desiccation tolerance for sporophytes relative to gametophytes. METHODS Gametophytes with attached post-embryonic sporophytes of Tortula inermis (early seta elongation phenophase) were exposed to two levels of desiccation stress, one rapid-dry cycle and two rapid-dry cycles, then moistened and allowed to recover, resume development, and/or regenerate for 35 d in a growth chamber. KEY RESULTS Gametophytes tolerated the desiccation treatments well, with 93 % survival through regenerated shoot buds and/or protonemata. At the high stress treatment, a significantly higher frequency of burned leaves and browned shoots occurred. Sporophytes were far more sensitive to desiccation stress, with only 23 % surviving after the low desiccation stress treatment, and 3 % surviving after the high desiccation stress treatment. While the timing of protonemal production and sporophytic phenophases was relatively unaffected by desiccation stress, shoots exposed to one rapid-dry cycle produced shoots more rapidly than shoots exposed to two rapid-dry cycles. CONCLUSIONS It is concluded that sporophytes of Tortula inermis are more sensitive to rapid drying than are maternal gametophytes, and that sporophyte abortion in response to desiccation results from either reduced desiccation tolerance of sporophytes relative to gametophytes, or from a termination of the sporophyte on the part of the gametophyte in response to stress.
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Affiliation(s)
- Lloyd R Stark
- School of Life Sciences, University of Nevada, 4505 Maryland Parkway, Las Vegas, NV 89154-4004, USA.
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Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, dePamphilis C, deSalle R, Doyle JJ, Eisen JA, Gu X, Harshman J, Jansen RK, Kellogg EA, Koonin EV, Mishler BD, Philippe H, Pires JC, Qiu YL, Rhee SY, Sjölander K, Soltis DE, Soltis PS, Stevenson DW, Wall K, Warnow T, Zmasek C. Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS 2006; 10:231-7. [PMID: 16901231 PMCID: PMC3167193 DOI: 10.1089/omi.2006.10.231] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In the eight years since phylogenomics was introduced as the intersection of genomics and phylogenetics, the field has provided fundamental insights into gene function, genome history and organismal relationships. The utility of phylogenomics is growing with the increase in the number and diversity of taxa for which whole genome and large transcriptome sequence sets are being generated. We assert that the synergy between genomic and phylogenetic perspectives in comparative biology would be enhanced by the development and refinement of minimal reporting standards for phylogenetic analyses. Encouraged by the development of the Minimum Information About a Microarray Experiment (MIAME) standard, we propose a similar roadmap for the development of a Minimal Information About a Phylogenetic Analysis (MIAPA) standard. Key in the successful development and implementation of such a standard will be broad participation by developers of phylogenetic analysis software, phylogenetic database developers, practitioners of phylogenomics, and journal editors.
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Affiliation(s)
- Jim Leebens-Mack
- Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA.
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Affiliation(s)
- Kipling W Will
- ESPM Department-Insect Biology, University of California, Berkeley, California 94720, USA
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Wolf PG, Karol KG, Mandoli DF, Kuehl J, Arumuganathan K, Ellis MW, Mishler BD, Kelch DG, Olmstead RG, Boore JL. The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae). Gene 2005; 350:117-28. [PMID: 15788152 DOI: 10.1016/j.gene.2005.01.018] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2004] [Revised: 11/29/2004] [Accepted: 01/24/2005] [Indexed: 10/25/2022]
Abstract
We used a unique combination of techniques to sequence the first complete chloroplast genome of a lycophyte, Huperzia lucidula. This plant belongs to a significant clade hypothesized to represent the sister group to all other vascular plants. We used fluorescence-activated cell sorting (FACS) to isolate the organelles, rolling circle amplification (RCA) to amplify the genome, and shotgun sequencing to 8x depth coverage to obtain the complete chloroplast genome sequence. The genome is 154,373 bp, containing inverted repeats of 15,314 bp each, a large single-copy region of 104,088 bp, and a small single-copy region of 19,657 bp. Gene order is more similar to those of mosses, liverworts, and hornworts than to gene order for other vascular plants. For example, the Huperzia chloroplast genome possesses the bryophyte gene order for a previously characterized 30 kb inversion, thus supporting the hypothesis that lycophytes are sister to all other extant vascular plants. The lycophyte chloroplast genome data also enable a better reconstruction of the basal tracheophyte genome, which is useful for inferring relationships among bryophyte lineages. Several unique characters are observed in Huperzia, such as movement of the gene ndhF from the small single copy region into the inverted repeat. We present several analyses of evolutionary relationships among land plants by using nucleotide data, inferred amino acid sequences, and by comparing gene arrangements from chloroplast genomes. The results, while still tentative pending the large number of chloroplast genomes from other key lineages that are soon to be sequenced, are intriguing in themselves, and contribute to a growing comparative database of genomic and morphological data across the green plants.
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Affiliation(s)
- Paul G Wolf
- Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84322-5305, USA.
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Mishler BD. The Origin and Early Diversification of Land Plants: A Cladistic Study.—Paul Kenrick and Peter Crane. Syst Biol 2001. [DOI: 10.1080/106351501753328875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
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Stark LR, Mishler BD, McLetchie DN. The cost of realized sexual reproduction: assessing patterns of reproductive allocation and sporophyte abortion in a desert moss. Am J Bot 2000; 87:1599-1608. [PMID: 11080110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The desert moss Syntrichia caninervis exhibits one of the most skewed sex ratios in the plant kingdom, with female individuals far outnumbering male individuals (exceeding 14♀:1♂). The "cost of sex hypothesis" derives from allocational theory and predicts that the sex which is most expensive should be the rarer sex. This hypothesis, which, as considered here represents the realized cost of sexual reproduction, is contingent upon two assumptions that are explored: (1) that male sex expression is more expensive than female sex expression, and (2) that sexual reproduction is resource limited. Using inflorescence biomass and discounting sperm, male sex expression was found to be in the neighborhood of one order of magnitude more expensive than female sex expression, and this difference is reflected in higher numbers of gametangia per male inflorescence, presence of paraphyses in male inflorescences, and a much longer developmental time for male inflorescences. The realized cost of female reproduction from two communities dominated by S. caninervis was found to be lower than the realized cost of male sexual reproduction. Resource-limited reproduction was assessed by determining the frequency of sporophyte abortion, the age distribution of sporophyte abortions, and patterns of sporophyte abortion that may be density dependent. Among ten sexually reproducing populations, abortive sporophytes occurred at a frequency of 0.64. Abortive sporophytes averaged 8% the mass of mature sporophytes, and cohort sporophytes from the same individual female were found to abort in a density-dependent pattern. We conclude that the two assumptions, upon which the cost of sex hypothesis depends, are supported.
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Affiliation(s)
- L R Stark
- Department of Biological Sciences, University of Nevada, 4505 Maryland Parkway, Box 454004, Las Vegas, Nevada 89154-4004 USA
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Bowker MA, Stark LR, McLetchie DN, Mishler BD. Sex expression, skewed sex ratios, and microhabitat distribution in the dioecious desert moss Syntrichia caninervis (Pottiaceae). Am J Bot 2000; 87:517-526. [PMID: 10766723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The moss Syntrichia caninervis is the dominant soil bryophyte in a blackbrush (Coleogyne ramosissima) community in the southern Nevada Mojave Desert, with a mean cover of 6.3%. A survey of the 10-ha study site revealed an expressed ramet sex ratio of 14♀ : 1♂ (N = 890), with 85% of ramets not expressing sex over their life span, and an expressed population sex ratio of 40♀ : 2♂ : 1♀♂ (female : male : mixed-sex, N = 89), with 52% of populations not expressing sex. A greater incidence of sex expression was associated with shaded microsites, higher soil moisture content, and taller ramets. Shaded microsites had higher surface soil moisture levels than exposed microsites. In the exposed microhabitat, surface soil moisture was positively correlated with ramet height but not with sex expression. Male ramets and populations were restricted to shaded microhabitats, whereas female ramets and populations were found in both shaded and exposed microhabitats, suggesting gender specialization. The rarity of mature sporophytes, found in 0% of the ramets sampled and in only 3% of the populations, is probably due to the rarity of mixed-sex populations. We hypothesize that mixed-sex populations are rare because of factors relating to male rarity and that the differential cost of sex expression reduces the clonal growth capacity of male individuals.
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Affiliation(s)
- M A Bowker
- Department of Biological Sciences, University of Nevada, 4505 Maryland Parkway, Box 454004, Las Vegas, Nevada 89154-4004 USA
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Lewis LA, Mishler BD, Vilgalys R. Phylogenetic relationships of the liverworts (Hepaticae), a basal embryophyte lineage, inferred from nucleotide sequence data of the chloroplast gene rbcL. Mol Phylogenet Evol 1997; 7:377-93. [PMID: 9187096 DOI: 10.1006/mpev.1996.0395] [Citation(s) in RCA: 133] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Sequence data from the chloroplast-encoded gene rbcL were obtained for 24 liverworts, a basal group of embryophytes. Maximum likelihood and parsimony analyses of these data, along with data from other major green plant lineages, confirm hypotheses based on morphological data, such as the paraphyly of bryophytes, and the basal position of liverworts. Molecular data corroborate the deep separation between the complex thalloid and leafy/simple thalloid liverworts implied by morphological data, but the monophyly of liverworts could not be rejected. The effects of accounting for site-to-site rate heterogeneity in these data were examined using maximum likelihood methods. Comparison of trees obtained with and without rate heterogeneity showed that simply allowing for heterogeneity had a greater improvement on likelihood score than optimization of transition/transversion bias. Incorporation of site-to-site rate heterogeneity in the larger analysis, however, did not necessarily change which topology was favored. Properties of rbcL sequences from the two liverwort groups were compared. Significantly different substitution rates were found between leafy/simple thalloid and complex thalloid liverwort taxa, with rates of rbcL sequence evolution in leafy/simple thalloid taxa being higher and more indicative of those of vascular plants, and with those of complex thalloid taxa (such as Marchantia) being slower. Codon usage in rbcL in complex thalloid liverworts was biased toward NNU and NNA, compared to the leafy/simple thalloid liverworts. Although base composition and relative substitution rates differed between the two groups, no significant differences were detected within each of the two groups of liverworts. The signal present in first and second codon sites versus third codon sites was compared. While the third codon positions in rbcL across this taxon sampling are highly variable (with only 15 constant sites of 439), the trees obtained were in general agreement with trees from the entire data set and with trees obtained from independent sources of data. The presence of signal in third codon positions across greater than 400 MY of plant evolution means that definitions of saturation based on pair-wise comparisons of sequences inadequately assess phylogenetic signal.
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Affiliation(s)
- L A Lewis
- Department of Botany, Duke University, Durham, North Carolina 27708, USA
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Mishler BD, Albert VA, Chase MW, Karis PO, Bremer K. CHARACTER-STATE WEIGHTING FOR DNA RESTRICTION SITE DATA: ASYMMETRY, ANCESTORS AND THE ASTERACEAE. Cladistics 1996. [DOI: 10.1111/j.1096-0031.1996.tb00190.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Abstract
Considerable progress has been made recently in phylogenetic reconstruction in a number of groups of organisms. This progress coincides with two major advances in systematics: new sources have been found for potentially informative characters (i.e., molecular data) and (more importantly) new approaches have been developed for extracting historical information from old or new characters (i.e., Hennigian phylogenetic systematics or cladistics). The basic assumptions of cladistics (the existence and splitting of lineages marked by discrete, heritable, and independent characters, transformation of which occurs at a rate slower than divergence of lineages) are discussed and defended. Molecular characters are potentially greater in quantity than (and usually independent of) more traditional morphological characters, yet their great simplicity (i.e., fewer potential character states; problems with determining homology), and difficulty of sufficient sampling (particularly from fossils) can lead to special difficulties. Expectations of the phylogenetic behavior of different types of data are investigated from a theoretical standpoint, based primarily on variation in the central parameter lambda (branch length in terms of expected number of character changes per segment of a tree), which also leads to possibilities for character and character state weighting. Also considered are prospects for representing diverse yet clearly monophyletic clades in larger-scale cladistic analyses, e.g., the exemplar method vs. "compartmentalization" (a new approach involving substituting an inferred "archetype" for a large clade accepted as monophyletic based on previous analyses). It is concluded that parsimony is to be preferred for synthetic, "total evidence" analyses because it appears to be a robust method, is applicable to all types of data, and has an explicit and interpretable evolutionary basis.
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Affiliation(s)
- B D Mishler
- Department of Integrative Biology, University and Jepson Herbaria, University of California, Berkeley 94720
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Chase MW, Soltis DE, Olmstead RG, Morgan D, Les DH, Mishler BD, Duvall MR, Price RA, Hills HG, Qiu YL, Kron KA, Rettig JH, Conti E, Palmer JD, Manhart JR, Sytsma KJ, Michaels HJ, Kress WJ, Karol KG, Clark WD, Hedren M, Gaut BS, Jansen RK, Kim KJ, Wimpee CF, Smith JF, Furnier GR, Strauss SH, Xiang QY, Plunkett GM, Soltis PS, Swensen SM, Williams SE, Gadek PA, Quinn CJ, Eguiarte LE, Golenberg E, Learn GH, Graham SW, Barrett SCH, Dayanandan S, Albert VA. Phylogenetics of Seed Plants: An Analysis of Nucleotide Sequences from the Plastid Gene rbcL. Annals of the Missouri Botanical Garden 1993; 80:528. [PMID: 0 DOI: 10.2307/2399846] [Citation(s) in RCA: 632] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
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