1
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Lamont BB, He T, Cowling RM. Fossil pollen resolves origin of the South African Proteaceae as transcontinental not transoceanic. ANNALS OF BOTANY 2024; 133:649-658. [PMID: 37076271 PMCID: PMC11082520 DOI: 10.1093/aob/mcad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS The prevailing view from the areocladogenesis of molecular phylogenies is that the iconic South African Cape Proteaceae (subfamily Proteoideae) arrived from Australia across the Indian Ocean during the Late Cretaceous (100-65 million years ago, Ma). Since fossil pollen indicates that the family probably arose in North-West Africa during the Early Cretaceous, an alternative view is that it migrated to the Cape from North-West-Central Africa. The plan therefore was to collate fossil pollen records throughout Africa to determine if they are consistent with an African (para-autochthonous) origin for the Cape Proteaceae, and to seek further support from other palaeo-disciplines. METHODS We used palynology (identity, date and location of records), molecular phylogeny and chronogram preparation, biogeography of plate tectonics, and palaeo-atmospheric and ocean circulation models. KEY RESULTS Our collation of the rich assemblage of Proteaceae palynomorphs stretching back to 107 Ma (Triorites africaensis) in North-West Africa showed its progressive overland migration to the Cape by 75-65 Ma. No key palynomorphs recorded in Australia-Antarctica have morphological affinities with African fossils but specific clade assignment of the pre-Miocene records is not currently possible. The Cape Proteaceae encompass three molecular-based clades (tribes) whose most recent apparent ancestors are sisters to those in Australia. However, our chronogram shows that the major Adenanthos/Leucadendron-related clade, originating 54-34 Ma, would have 'arrived' too late as species with Proteaceae affinities were already present ~20 million years earlier. The Franklandia/Protea-related clade arose 118-81 Ma so its distinctive pollen should have been the foundation for the scores of palynomorphs recorded at 100-80 Ma, but it was not. Also, the prevailing winds and ocean currents trended away from South Africa rather than towards, as the 'out-of-Australia' hypothesis requires. Based on the evidence assembled here, we list three points favouring an Australian origin and nine against; four points favouring an Antarctic origin and seven against; and nine points favouring a North-West-Central African origin and three against. CONCLUSIONS We conclude that a gradual migration of the Proteaceae from North-West-Central Africa southeast→south→southwest to the Cape and its surroundings occurred via adaptation and speciation during the period 95-70 Ma. We caution that incorrect conclusions may be drawn from literal interpretations of molecular phylogenies that neglect the fossil record and do not recognize the possible confounding effects of selection under matched environments leading to parallel evolution and extinction of bona fide sister clades.
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Affiliation(s)
- Byron B Lamont
- Ecology Section, School of Molecular and Life Sciences, Curtin University, Perth, WA 6845, Australia
| | - Tianhua He
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Richard M Cowling
- African Centre for Coastal Palaeoscience, Nelson Mandela University, Eastern Cape, South Africa
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2
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Aylward J, Roets F, Dreyer LL, Wingfield MJ. Unseen fungal biodiversity and complex inter-organismal interactions in Protea flower heads. FUNGAL BIOL REV 2023. [DOI: 10.1016/j.fbr.2023.100317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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3
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Johnson SD, Govender K. Rodent responses to volatile compounds provide insights into the function of floral scent in mammal-pollinated plants. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210167. [PMID: 35491600 DOI: 10.1098/rstb.2021.0167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Flowers pollinated by mammals have evolved in many plant families. Several scent compounds that attract bats to flowers have been identified, but the chemical ecology of pollination mutualisms between plants and ground-dwelling mammals is poorly understood. Rodents are key pollinators in South Africa and rely heavily on olfaction to locate food. Our aim was to identify compounds that may function to attract rodents to flowers. Eighteen volatile compounds, including 14 that are prominent in the scent of rodent-pollinated flowers, were used in choice experiments involving wild-caught individuals of four native rodent species. Rodents were generally attracted to oxygenated aliphatic compounds, specifically ketones and esters, but not to some aromatic compounds common in floral scents of insect-pollinated species, nor to a sulfide compound that is attractive to bats. Associative conditioning using sugar solution as a reward had only weak effects on the attractiveness of compounds to rodents. The attractive effect of some compounds disappeared when they were blended with compounds that did not attract rodents. We conclude that aliphatic ketones and esters are likely to play a key role in attracting rodents to flowers. Deployment of these compounds may allow plants to exploit rodent sensory bias that evolved in other contexts such as intra-specific communication and searching for seeds. This article is part of the theme issue 'Natural processes influencing pollinator health: from chemistry to landscapes'.
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Affiliation(s)
- Steven D Johnson
- Centre for Functional Biodiversity, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg 3209, South Africa
| | - Keeveshnee Govender
- Centre for Functional Biodiversity, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg 3209, South Africa
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4
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Katayama N, Koi S, Sassa A, Kurata T, Imaichi R, Kato M, Nishiyama T. Elevated mutation rates underlie the evolution of the aquatic plant family Podostemaceae. Commun Biol 2022; 5:75. [PMID: 35058542 PMCID: PMC8776956 DOI: 10.1038/s42003-022-03003-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/23/2021] [Indexed: 12/18/2022] Open
Abstract
Molecular evolutionary rates vary among lineages and influence the evolutionary process. Here, we report elevated genome-wide mutation rates in Podostemaceae, a family of aquatic plants with a unique body plan that allows members to live on submerged rocks in fast-flowing rivers. Molecular evolutionary analyses using 1640 orthologous gene groups revealed two historical increases in evolutionary rates: the first at the emergence of the family and the second at the emergence of Podostemoideae, which is the most diversified subfamily. In both branches, synonymous substitution rates were elevated, indicating higher mutation rates. On early branches, mutations were biased in favour of AT content, which is consistent with a role for ultraviolet light-induced mutation and habitat shift. In ancestors of Podostemoideae, DNA-repair genes were enriched in genes under positive selection, which may have responded to the meristem architectural changes.
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Affiliation(s)
- Natsu Katayama
- Graduate School of Science, Chiba University, Chiba, 263-8522, Japan.
- Research Fellow of Japan Society for the Promotion of Science, Tokyo, 102-0083, Japan.
| | - Satoshi Koi
- Botanical Gardens, Osaka City University, Osaka, 575-0004, Japan
| | - Akira Sassa
- Graduate School of Science, Chiba University, Chiba, 263-8522, Japan
| | - Tetsuya Kurata
- Division of Biological Science, Nara Institute of Science and Technology, Nara, 630-0192, Japan
| | - Ryoko Imaichi
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Tokyo, 112-8681, Japan
| | - Masahiro Kato
- Department of Botany, National Museum of Nature and Science, Tsukuba, 305-0005, Japan
| | - Tomoaki Nishiyama
- Division of Integrated Omics Research, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, 920-0934, Japan.
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5
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Mitchell N, Whitney KD. Limited evidence for a positive relationship between hybridization and diversification across seed plant families. Evolution 2021; 75:1966-1982. [PMID: 34156712 DOI: 10.1111/evo.14291] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 05/18/2021] [Accepted: 05/26/2021] [Indexed: 01/09/2023]
Abstract
Hybridization has experimental and observational ties to evolutionary processes and outcomes such as adaptation, speciation, and radiation. Although it has been hypothesized that hybridization and diversification are positively correlated, this idea remains largely untested empirically, and hybridization can also potentially reduce diversity. Here, we use a hybridization database on 170 seed plant families, life history information, and a time-calibrated phylogeny to test for phylogenetically-corrected associations between hybridization and diversification rates, while also taking into account life-history traits that may be correlated with both processes. We use three methods to estimate diversification rates and two metrics of hybridization. Although hybridization explains only a small amount of overall variation in diversification rates, we show that diversification and hybridization are sometimes positively correlated, although the effect sizes are very small. Moreover, the relationship remains detectable when incorporating the correlations between diversification and two other life history characteristics, perenniality and woodiness. We discuss potential mechanisms for this association under four different scenarios: hybridization may drive diversification, diversification may drive hybridization, both hybridization and diversification may jointly be driven by other factors, or, as an alternative, that there is in fact no relationship between the two. We suggest future studies to disentangle the causal structure.
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Affiliation(s)
- Nora Mitchell
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, 87131.,Department of Biology, University of Wisconsin - Eau Claire, Eau Claire, Wisconsin, 54701
| | - Kenneth D Whitney
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, 87131
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6
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Martín-Hernanz S, Albaladejo RG, Lavergne S, Rubio E, Grall A, Aparicio A. Biogeographic history and environmental niche evolution in the palearctic genus Helianthemum (Cistaceae). Mol Phylogenet Evol 2021; 163:107238. [PMID: 34197899 DOI: 10.1016/j.ympev.2021.107238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/27/2021] [Accepted: 06/24/2021] [Indexed: 11/30/2022]
Abstract
The biogeographic history and the degree of environmental niche conservatism provide essential clues to decipher the underlying macroevolutionary processes of species diversification and to understand contemporary patterns of biodiversity. The genus Helianthemum constitutes an excellent case study to investigate the impact of the geo-climatic changes and the environmental niche shifts on the origins of plant species diversity in the Mediterranean hotspot. It is a palearctic species-rich lineage with c. 140 species and subspecies mostly belonging to three distinct evolutionary radiations, almost confined to the Mediterranean region and occurring across varied environmental conditions. In this work, we studied the ample and rapid diversification of the genus Helianthemum across its whole distribution range by performing phylogenetic reconstructions of ancestral ranges and environmental niche evolution. We observed a striking synchrony of biogeographic movements with niche shifts between the three major clades of the genus Helianthemum, likely related to the geo-climatic events occurred in the Mediterranean Basin since the Upper Miocene. In particular, Late Miocene and Early Pliocene were dominated by episodes of range expansions, the Late Pliocene by range contraction and vicariance events, and Pleistocene by most intense environmental niche shifts and in-situ diversification. Our study also provides evidence for four main environmental niches in Helianthemum (i.e., Mediterranean, subdesert, humid-montane and subtropical-insular) and a tendency toward environmental niche conservatism within different subclades, with few niche shifts mostly occurring from Mediterranean ancestors. The relative longer time spent in Mediterranean areas by the ancestors of Helianthemum suggests that the larger species diversity observed in the Mediterranean (i.e. Northern Africa and Southern Europe) may have been generated by a time-for-speciation effect reinforced by environmental niche conservatism. Overall, our work highlights the role of the Mediterranean Basin as a 'cradle of diversity' and an 'evolutionary hub', facilitating the environmental transitions and determining the building up of a global plant biodiversity hotspot.
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Affiliation(s)
- Sara Martín-Hernanz
- Departamento de Biología Vegetal y Ecología, Facultad de Farmacia, Universidad de Sevilla, Sevilla, Spain.
| | - Rafael G Albaladejo
- Departamento de Biología Vegetal y Ecología, Facultad de Farmacia, Universidad de Sevilla, Sevilla, Spain
| | - Sébastien Lavergne
- Laboratoire d'Ecologie Alpine (LECA), CNRS - Université Grenoble Alpes - Université Savoie Mont Blanc, FR-38000 Grenoble, France
| | - Encarnación Rubio
- Departamento de Biología Vegetal y Ecología, Facultad de Farmacia, Universidad de Sevilla, Sevilla, Spain
| | - Aurélie Grall
- Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Abelardo Aparicio
- Departamento de Biología Vegetal y Ecología, Facultad de Farmacia, Universidad de Sevilla, Sevilla, Spain
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7
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Tassone EE, Miles LS, Dyer RJ, Rosenberg MS, Cowling RM, Verrelli BC. Evolutionary stability, landscape heterogeneity, and human land-usage shape population genetic connectivity in the Cape Floristic Region biodiversity hotspot. Evol Appl 2021; 14:1109-1123. [PMID: 33897824 PMCID: PMC8061270 DOI: 10.1111/eva.13185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 01/06/2023] Open
Abstract
As human-induced change eliminates natural habitats, it impacts genetic diversity and population connectivity for local biodiversity. The South African Cape Floristic Region (CFR) is the most diverse extratropical area for plant biodiversity, and much of its habitat is protected as a UNESCO World Heritage site. There has long been great interest in explaining the underlying factors driving this unique diversity, especially as much of the CFR is endangered by urbanization and other anthropogenic activity. Here, we use a population and landscape genetic analysis of SNP data from the CFR endemic plant Leucadendron salignum or "common sunshine conebush" as a model to address the evolutionary and environmental factors shaping the vast CFR diversity. We found that high population structure, along with relatively deeper and older genealogies, is characteristic of the southwestern CFR, whereas low population structure and more recent lineage coalescence depict the eastern CFR. Population network analyses show genetic connectivity is facilitated in areas of lower elevation and higher seasonal precipitation. These population genetic signatures corroborate CFR species-level patterns consistent with high Pleistocene biome stability and landscape heterogeneity in the southwest, but with coincident instability in the east. Finally, we also find evidence of human land-usage as a significant gene flow barrier, especially in severely threatened lowlands where genetic connectivity has been historically the highest. These results help identify areas where conservation plans can prioritize protecting high genetic diversity threatened by contemporary human activities within this unique cultural UNESCO site.
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Affiliation(s)
| | - Lindsay S. Miles
- Center for the Study of Biological ComplexityVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Rodney J. Dyer
- Center for Environmental StudiesVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Michael S. Rosenberg
- School of Life SciencesArizona State UniversityTempeArizonaUSA
- Center for the Study of Biological ComplexityVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Richard M. Cowling
- African Centre for Coastal PalaeoscienceBotany DepartmentNelson Mandela UniversityPort ElizabethSouth Africa
| | - Brian C. Verrelli
- School of Life SciencesArizona State UniversityTempeArizonaUSA
- Center for the Study of Biological ComplexityVirginia Commonwealth UniversityRichmondVirginiaUSA
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8
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Nolting KM, Prunier R, Midgley GF, Holsinger KE. Intraspecific trait variation influences physiological performance and fitness in the South Africa shrub genus Protea (Proteaceae). ANNALS OF BOTANY 2021; 127:519-531. [PMID: 32249291 PMCID: PMC7988518 DOI: 10.1093/aob/mcaa060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 04/03/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS Global plant trait datasets commonly identify trait relationships that are interpreted to reflect fundamental trade-offs associated with plant strategies, but often these trait relationships are not identified when evaluating them at smaller taxonomic and spatial scales. In this study we evaluate trait relationships measured on individual plants for five widespread Protea species in South Africa to determine whether broad-scale patterns of structural trait (e.g. leaf area) and physiological trait (e.g. photosynthetic rates) relationships can be detected within natural populations, and if these traits are themselves related to plant fitness. METHODS We evaluated the variance structure (i.e. the proportional intraspecific trait variation relative to among-species variation) for nine structural traits and six physiological traits measured in wild populations. We used a multivariate path model to evaluate the relationships between structural traits and physiological traits, and the relationship between these traits and plant size and reproductive effort. KEY RESULTS While intraspecific trait variation is relatively low for structural traits, it accounts for between 50 and 100 % of the variation in physiological traits. Furthermore, we identified few trait associations between any one structural trait and physiological trait, but multivariate regressions revealed clear associations between combinations of structural traits and physiological performance (R2 = 0.37-0.64), and almost all traits had detectable associations with plant fitness. CONCLUSIONS Intraspecific variation in structural traits leads to predictable differences in individual-level physiological performance in a multivariate framework, even though the relationship of any particular structural trait to physiological performance may be weak or undetectable. Furthermore, intraspecific variation in both structural and physiological traits leads to differences in plant size and fitness. These results demonstrate the importance of considering measurements of multivariate phenotypes on individual plants when evaluating trait relationships and how trait variation influences predictions of ecological and evolutionary outcomes.
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Affiliation(s)
- Kristen M Nolting
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Rachel Prunier
- Department of Biological and Environmental Sciences, Western Connecticut State University, Danbury, CT, USAand
| | - Guy F Midgley
- Department of Botany and Zoology, Stellenbosch University, Matieland, South Africa
| | - Kent E Holsinger
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
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9
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Mismatches between demographic niches and geographic distributions are strongest in poorly dispersed and highly persistent plant species. Proc Natl Acad Sci U S A 2020; 117:3663-3669. [PMID: 32029599 PMCID: PMC7035498 DOI: 10.1073/pnas.1908684117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Forecasts of global change impacts on biodiversity often assume that the current geographical distributions of species match their ecological niches. Here we examine this assumption using an extensive dataset of large-scale variation in demographic rates that enables us to quantify demography-based ecological niches of 26 plant species. Contrasting these niches with the species’ geographic distributions reveals that niche–distribution mismatches can be large and depend on key life-history traits: poorly dispersed species are absent from suitable sites, and species with high persistence ability are present in sites that are currently unsuitable for them. Such niche–distribution mismatches need to be accounted for to improve forecasts of biodiversity dynamics under environmental change. The ecological niche of a species describes the variation in population growth rates along environmental gradients that drives geographic range dynamics. Niches are thus central for understanding and forecasting species’ geographic distributions. However, theory predicts that migration limitation, source–sink dynamics, and time-lagged local extinction can cause mismatches between niches and geographic distributions. It is still unclear how relevant these niche–distribution mismatches are for biodiversity dynamics and how they depend on species life-history traits. This is mainly due to a lack of the comprehensive, range-wide demographic data needed to directly infer ecological niches for multiple species. Here we quantify niches from extensive demographic measurements along environmental gradients across the geographic ranges of 26 plant species (Proteaceae; South Africa). We then test whether life history explains variation in species’ niches and niche–distribution mismatches. Niches are generally wider for species with high seed dispersal or persistence abilities. Life-history traits also explain the considerable interspecific variation in niche–distribution mismatches: poorer dispersers are absent from larger parts of their potential geographic ranges, whereas species with higher persistence ability more frequently occupy environments outside their ecological niche. Our study thus identifies major demographic and functional determinants of species’ niches and geographic distributions. It highlights that the inference of ecological niches from geographical distributions is most problematic for poorly dispersed and highly persistent species. We conclude that the direct quantification of ecological niches from demographic responses to environmental variation is a crucial step toward a better predictive understanding of biodiversity dynamics under environmental change.
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10
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Kahnt B, Hattingh WN, Theodorou P, Wieseke N, Kuhlmann M, Glennon KL, Niet T, Paxton R, Cron GV. Should I stay or should I go? Pollinator shifts rather than cospeciation dominate the evolutionary history of South African
Rediviva
bees and their
Diascia
host plants. Mol Ecol 2019; 28:4118-4133. [DOI: 10.1111/mec.15154] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 06/19/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Belinda Kahnt
- General Zoology Institute of Biology Martin‐Luther‐University Halle‐Wittenberg Halle (Saale) Germany
| | - Wesley N. Hattingh
- School of Animal, Plant and Environmental Sciences University of the Witwatersrand Braamfontein South Africa
| | - Panagiotis Theodorou
- General Zoology Institute of Biology Martin‐Luther‐University Halle‐Wittenberg Halle (Saale) Germany
| | - Nicolas Wieseke
- Institute for Informatics University of Leipzig Leipzig Germany
| | - Michael Kuhlmann
- Zoological Museum Kiel University Kiel Germany
- Department of Life Sciences Natural History Museum London UK
| | - Kelsey L. Glennon
- School of Animal, Plant and Environmental Sciences University of the Witwatersrand Braamfontein South Africa
| | - Timotheüs Niet
- School of Life Sciences Centre for Functional Biodiversity University of Kwazulu‐Natal Pietermaritzburg South Africa
| | - Robert Paxton
- General Zoology Institute of Biology Martin‐Luther‐University Halle‐Wittenberg Halle (Saale) Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
| | - Glynis V. Cron
- School of Animal, Plant and Environmental Sciences University of the Witwatersrand Braamfontein South Africa
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11
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Skeels A, Cardillo M. Equilibrium and non‐equilibrium phases in the radiation of
Hakea
and the drivers of diversity in Mediterranean‐type ecosystems. Evolution 2019; 73:1392-1410. [DOI: 10.1111/evo.13769] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 03/05/2019] [Accepted: 04/29/2019] [Indexed: 01/10/2023]
Affiliation(s)
- Alexander Skeels
- Macroevolution and Macroecology Group Research School of Biology Australian National University Canberra 0200 Australia
| | - Marcel Cardillo
- Macroevolution and Macroecology Group Research School of Biology Australian National University Canberra 0200 Australia
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12
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Martín‐Hernanz S, Martínez‐Sánchez S, Albaladejo RG, Lorite J, Arroyo J, Aparicio A. Genetic diversity and differentiation in narrow versus widespread taxa of Helianthemum (Cistaceae) in a hotspot: The role of geographic range, habitat, and reproductive traits. Ecol Evol 2019; 9:3016-3029. [PMID: 30962878 PMCID: PMC6434548 DOI: 10.1002/ece3.4481] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/13/2018] [Accepted: 08/03/2018] [Indexed: 11/14/2022] Open
Abstract
Unraveling the relationships between ecological, functional traits and genetic diversity of narrow endemic plants provide opportunities for understanding how evolutionary processes operate over local spatial scales and ultimately how diversity is created and maintained. To explore these aspects in Sierra Nevada, the core of the Mediterranean Betic-Rifean hotspot, we have analyzed nuclear DNA microsatellite diversity and a set of biological and environmental factors (physicochemical soil parameters, floral traits, and community composition) in two strictly endemic taxa from dolomite outcrops of Sierra Nevada (Helianthemum pannosum and H. apenninum subsp. estevei) and two congeneric widespread taxa (H. cinereum subsp. rotundifolium and H. apenninum subsp. apenninum) that further belong to two different lineages (subgenera) of Helianthemum. We obtained rather unexpected results contrasting with the theory: (a) The narrow endemic taxa showed higher values of genetic diversity as well as higher average values of pollen production per flower and pollen-to-ovule ratio than their widespread relatives; and (b) the two taxa of subg. Helianthemum, with larger corollas, approach herkogamy and higher pollen production than the two taxa of subg. Plectolobum, displayed lower genetic diversity and higher values of inbreeding. Altogether, these results disclose how genetic diversity may be affected simultaneously by a large number of intrinsic and extrinsic factors, especially in Pleistocene glacial refugia in mountains where the spatial context harbors a great ecological heterogeneity. On the other hand, differences in mating system and the significant effect of the substrate profile, both being highly diverse in the genus Helianthemum, in the genetic variability illustrate about the importance of these two factors in the diversification and species differentiation of this paradigmatic genus in the Mediterranean and open the field to formulate and test new hypotheses of local adaptation, trait evolution, and habitat diversification.
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Affiliation(s)
- Sara Martín‐Hernanz
- Departamento de Biología Vegetal y EcologíaUniversidad de SevillaSevillaSpain
| | - Sara Martínez‐Sánchez
- Departamento de Biología Vegetal y EcologíaUniversidad de SevillaSevillaSpain
- Present address:
Departamento de Tecnología de la Alimentación y NutriciónUniversidad Católica de MurciaMurciaSpain
| | | | - Juan Lorite
- Departamento de BotánicaUniversidad de GranadaGranadaSpain
| | - Juan Arroyo
- Departamento de Biología Vegetal y EcologíaUniversidad de SevillaSevillaSpain
| | - Abelardo Aparicio
- Departamento de Biología Vegetal y EcologíaUniversidad de SevillaSevillaSpain
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13
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Mitchell N, Holsinger KE. Microscale trait-environment associations in two closely-related South African shrubs. AMERICAN JOURNAL OF BOTANY 2019; 106:211-222. [PMID: 30768876 DOI: 10.1002/ajb2.1234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
PREMISE OF THE STUDY Plant traits are often associated with the environments in which they occur, but these associations often differ across spatial and phylogenetic scales. Here we study the relationship between microenvironment, microgeographical location, and traits within populations using co-occurring populations of two closely related evergreen shrubs in the genus Protea. METHODS We measured a suite of functional traits on 147 plants along a single steep mountainside where both species occur, and we used data-loggers and soil analyses to characterize the environment at 10 microsites spanning the elevational gradient. We used Bayesian path analyses to detect trait-environment relationships in the field for each species. We used complementary data from greenhouse grown seedlings derived from wild collected seed to determine whether associations detected in the field are the result of genetic differentiation. KEY RESULTS Microenvironmental variables differed substantially across our study site. We found strong evidence for six trait-environment associations, although these differed between species. We were unable to detect similar associations in greenhouse-grown seedlings. CONCLUSIONS Several leaf traits were associated with temperature and soil variation in the field, but the inability to detect these in the greenhouse suggests that differences in the field are not the result of genetic differentiation.
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Affiliation(s)
- Nora Mitchell
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, 06269, USA
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, 87131, USA
| | - Kent E Holsinger
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, 06269, USA
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14
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Skeels A, Cardillo M. Reconstructing the Geography of Speciation from Contemporary Biodiversity Data. Am Nat 2019; 193:240-255. [DOI: 10.1086/701125] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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15
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Lamont BB, He T, Yan Z. Evolutionary history of fire‐stimulated resprouting, flowering, seed release and germination. Biol Rev Camb Philos Soc 2018; 94:903-928. [DOI: 10.1111/brv.12483] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/23/2018] [Accepted: 11/01/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Byron B. Lamont
- School of Molecular and Life Sciences Curtin University PO Box U1987, Perth, WA 6845 Australia
| | - Tianhua He
- School of Molecular and Life Sciences Curtin University PO Box U1987, Perth, WA 6845 Australia
| | - Zhaogui Yan
- College of Horticulture and Forestry Sciences Huazhong Agricultural University Wuhan 430070 China
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16
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Aylward J, Wingfield BD, Dreyer LL, Roets F, Wingfield MJ, Steenkamp ET. Genomic overview of closely related fungi with different Protea host ranges. Fungal Biol 2018; 122:1201-1214. [PMID: 30449358 DOI: 10.1016/j.funbio.2018.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/06/2018] [Accepted: 10/04/2018] [Indexed: 11/28/2022]
Abstract
Genome comparisons of species with distinctive ecological traits can elucidate genetic divergence that influenced their differentiation. The interaction of a microorganism with its biotic environment is largely regulated by secreted compounds, and these can be predicted from genome sequences. In this study, we considered Knoxdaviesia capensis and Knoxdaviesia proteae, two closely related saprotrophic fungi found exclusively in Protea plants. We investigated their genome structure to compare their potential inter-specific interactions based on gene content. Their genomes displayed macrosynteny and were approximately 10 % repetitive. Both species had fewer secreted proteins than pathogens and other saprotrophs, reflecting their specialized habitat. The bulk of the predicted species-specific and secreted proteins coded for carbohydrate metabolism, with a slightly higher number of unique carbohydrate-degrading proteins in the broad host-range K. capensis. These fungi have few secondary metabolite gene clusters, suggesting minimal competition with other microbes and symbiosis with antibiotic-producing bacteria common in this niche. Secreted proteins associated with detoxification and iron sequestration likely enable these Knoxdaviesia species to tolerate antifungal compounds and compete for resources, facilitating their unusual dominance. This study confirms the genetic cohesion between Protea-associated Knoxdaviesia species and reveals aspects of their ecology that have likely evolved in response to their specialist niche.
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Affiliation(s)
- Janneke Aylward
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Léanne L Dreyer
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Francois Roets
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
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17
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Miles LS, Johnson JC, Dyer RJ, Verrelli BC. Urbanization as a facilitator of gene flow in a human health pest. Mol Ecol 2018; 27:3219-3230. [PMID: 29972610 DOI: 10.1111/mec.14783] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/16/2018] [Accepted: 04/11/2018] [Indexed: 01/04/2023]
Abstract
Urban fragmentation can reduce gene flow that isolates populations, reduces genetic diversity and increases population differentiation, all of which have negative conservation implications. Alternatively, gene flow may actually be increased among urban areas consistent with an urban facilitation model. In fact, urban adapter pests are able to thrive in the urban environment and may be experiencing human-mediated transport. Here, we used social network theory with a population genetic approach to investigate the impact of urbanization on genetic connectivity in the Western black widow spider, as an urban pest model of human health concern. We collected genomewide single nucleotide polymorphism variation from mitochondrial and nuclear double-digest RAD (ddRAD) sequence data sets from 210 individuals sampled from 11 urban and 10 nonurban locales across its distribution of the Western United States. From urban and nonurban contrasts of population, phylogenetic, and network analyses, urban locales have higher within-population genetic diversity, lower between-population genetic differentiation and higher estimates of genetic connectivity. Social network analyses show that urban locales not only have more connections, but can act as hubs that drive connectivity among nonurban locales, which show signatures of historical isolation. These results are consistent with an urban facilitation model of gene flow and demonstrate the importance of sampling multiple cities and markers to identify the role that urbanization has had on larger spatial scales. As the urban landscape continues to grow, this approach will help determine what factors influence the spread and adaptation of pests, like the venomous black widow spider, in building policies for human and biodiversity health.
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Affiliation(s)
- Lindsay S Miles
- Center for Life Sciences Education, Virginia Commonwealth University, Richmond, Virginia
- Integrative Life Sciences Doctoral Program, Virginia Commonwealth University, Richmond, Virginia
| | - J Chadwick Johnson
- Division of Mathematical and Natural Sciences, Arizona State University at the West Campus, Glendale, Arizona
| | - Rodney J Dyer
- Center for Environmental Studies, Virginia Commonwealth University, Richmond, Virginia
| | - Brian C Verrelli
- Center for Life Sciences Education, Virginia Commonwealth University, Richmond, Virginia
- Department of Biology, Virginia Commonwealth University, Richmond, Virginia
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18
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Rundel PW, Arroyo MTK, Cowling RM, Keeley JE, Lamont BB, Pausas JG, Vargas P. Fire and Plant Diversification in Mediterranean-Climate Regions. FRONTIERS IN PLANT SCIENCE 2018; 9:851. [PMID: 30018621 PMCID: PMC6038726 DOI: 10.3389/fpls.2018.00851] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 05/31/2018] [Indexed: 05/29/2023]
Abstract
Despite decades of broad interest in global patterns of biodiversity, little attention has been given to understanding the remarkable levels of plant diversity present in the world's five Mediterranean-type climate (MTC) regions, all of which are considered to be biodiversity hotspots. Comprising the Mediterranean Basin, California, central Chile, the Cape Region of South Africa, and southwestern Australia, these regions share the unusual climatic regime of mild wet winters and warm dry summers. Despite their small extent, covering only about 2.2% of world land area, these regions are home to approximately one-sixth of the world vascular plant flora. The onset of MTCs in the middle Miocene brought summer drought, a novel climatic condition, but also a regime of recurrent fire. Fire has been a significant agent of selection in assembling the modern floras of four of the five MTC regions, with central Chile an exception following the uplift of the Andes in the middle Miocene. Selection for persistence in a fire-prone environment as a key causal factor for species diversification in MTC regions has been under-appreciated or ignored. Mechanisms for fire-driven speciation are diverse and may include both directional (novel traits) and stabilizing selection (retained traits) for appropriate morphological and life-history traits. Both museum and nursery hypotheses have important relevance in explaining the extant species richness of the MTC floras, with fire as a strong stimulant for diversification in a manner distinct from other temperate floras. Spatial and temporal niche separation across topographic, climatic and edaphic gradients has occurred in all five regions. The Mediterranean Basin, California, and central Chile are seen as nurseries for strong but not spectacular rates of Neogene diversification, while the older landscapes of southwestern Australia and the Cape Region show significant components of both Paleogene and younger Neogene speciation in their diversity. Low rates of extinction suggesting a long association with fire more than high rates of speciation have been key to the extant levels of species richness.
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Affiliation(s)
- Philip W. Rundel
- Department of Ecology and Evolutionary Biology and Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, United States
| | - Mary T. K. Arroyo
- Department of Ecological Science, Faculty of Sciences, Institute of Ecology and Biodiversity, University of Chile, Santiago, Chile
| | - Richard M. Cowling
- African Centre for Coastal Palaeoscience, Nelson Mandela University, Port Elizabeth, South Africa
| | - Jon E. Keeley
- Sequoia Field Station, Western Ecological Research Center, United States Geological Survey, Reston, VA, United States
| | - Byron B. Lamont
- School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Juli G. Pausas
- Centro de Investigaciones sobre Desertificación, University of Valencia, CSIC, Valencia, Spain
| | - Pablo Vargas
- Department of Biodiversity and Conservation, Royal Botanical Garden of Madrid, CSIC, Madrid, Spain
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19
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Mitchell N, Carlson JE, Holsinger KE. Correlated evolution between climate and suites of traits along a fast-slow continuum in the radiation of Protea. Ecol Evol 2018; 8:1853-1866. [PMID: 29435259 PMCID: PMC5792567 DOI: 10.1002/ece3.3773] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/31/2017] [Accepted: 12/06/2017] [Indexed: 12/18/2022] Open
Abstract
Evolutionary radiations are responsible for much of Earth's diversity, yet the causes of these radiations are often elusive. Determining the relative roles of adaptation and geographic isolation in diversification is vital to understanding the causes of any radiation, and whether a radiation may be labeled as "adaptive" or not. Across many groups of plants, trait-climate relationships suggest that traits are an important indicator of how plants adapt to different climates. In particular, analyses of plant functional traits in global databases suggest that there is an "economics spectrum" along which combinations of functional traits covary along a fast-slow continuum. We examine evolutionary associations among traits and between trait and climate variables on a strongly supported phylogeny in the iconic plant genus Protea to identify correlated evolution of functional traits and the climatic-niches that species occupy. Results indicate that trait diversification in Protea has climate associations along two axes of variation: correlated evolution of plant size with temperature and leaf investment with rainfall. Evidence suggests that traits and climatic-niches evolve in similar ways, although some of these associations are inconsistent with global patterns on a broader phylogenetic scale. When combined with previous experimental work suggesting that trait-climate associations are adaptive in Protea, the results presented here suggest that trait diversification in this radiation is adaptive.
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Affiliation(s)
- Nora Mitchell
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsCTUSA
| | - Jane E. Carlson
- Inventory and Monitoring ProgramGulf Coast NetworkNational Park ServiceLafayetteLAUSA
| | - Kent E. Holsinger
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsCTUSA
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20
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Ngubane NP, Dreyer LL, Oberlander KC, Roets F. Two new Sporothrix species from Protea flower heads in South African Grassland and Savanna. Antonie Van Leeuwenhoek 2017; 111:965-979. [PMID: 29214366 DOI: 10.1007/s10482-017-0995-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 12/01/2017] [Indexed: 11/29/2022]
Abstract
The inflorescences and infructescences of African Protea trees provide habitat for a large diversity of Sporothrix species. Here we describe two additional members, Sporothrix nsini sp. nov. and Sporothrix smangaliso sp. nov., that are associated with the infructescences of various Protea species from grasslands and savannas in the KwaZulu-Natal, North-West, Gauteng and Mpumalanga provinces of South Africa. Their description raises the number of described Protea-associated Sporothrix species to twelve. S. smangaliso sp. nov. is distantly related to other Protea-associated species and, in phylogenies using multiple markers (ITS, beta-tubulin and calmodulin), groups with taxa such as Sporothrix bragantina from Brazil and Sporothrix curviconia from the Ivory Coast. S. nsini sp. nov. resolved as sister to a clade containing four other Protea-associated species within the Sporothrix stenoceras complex. S. nsini sp. nov. was collected from within the same infructescences of Protea caffra that also contained the closely related S. africana and S. protearum. This highlights the need to study and understand the factors that influence host selection and speciation of Sporothrix in this atypical niche.
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Affiliation(s)
- Nombuso P Ngubane
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Stellenbosch, 7600, South Africa
| | - Leanne L Dreyer
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Stellenbosch, 7600, South Africa.,DST/NRF Centre of Excellence in Tree Health Biotechnology (CTHB), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Kenneth C Oberlander
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Stellenbosch, 7600, South Africa
| | - Francois Roets
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Stellenbosch, 7600, South Africa. .,DST/NRF Centre of Excellence in Tree Health Biotechnology (CTHB), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa.
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21
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Bouchenak-Khelladi Y, Linder HP. Frequent and parallel habitat transitions as driver of unbounded radiations in the Cape flora. Evolution 2017; 71:2548-2561. [PMID: 28884804 DOI: 10.1111/evo.13364] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 08/25/2017] [Accepted: 08/29/2017] [Indexed: 01/20/2023]
Abstract
The enormous species richness in the Cape Floristic Region (CFR) of Southern Africa is the result of numerous radiations, but the temporal progression and possible mechanisms of these radiations are still poorly understood. Here, we explore the macroevolutionary dynamics of the Restionaceae, which include 340 species that are found in all vegetation types in the Cape flora and are ecologically dominant in fynbos. Using an almost complete (i.e., 98%) species-level time calibrated phylogeny and models of diversification dynamics, we show that species diversification is constant through the Cenozoic, with no evidence of an acceleration with the onset of the modern winter-wet climate, or a recent density-dependent slowdown. Contrary to expectation, species inhabiting the oldest (montane) and most extensive (drylands) habitats did not undergo higher diversification rates than species in the younger (lowlands) and more restricted (wetland) habitats. We show that the rate of habitat transitions is more closely related to the speciation rate than to time, and that more than a quarter of all speciation events are associated with habitat transitions. This suggests that the unbounded Restionaceae diversification resulted from numerous, parallel, habitat shifts, rather than persistence in a habitat stimulating speciation. We speculate that this could be one of the mechanisms resulting in the hyperdiverse Cape flora.
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Affiliation(s)
- Yanis Bouchenak-Khelladi
- Department of Systematic and Evolutionary Botany, University of Zurich, CH 8008 Zurich, Switzerland
| | - H Peter Linder
- Department of Systematic and Evolutionary Botany, University of Zurich, CH 8008 Zurich, Switzerland
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22
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Cardillo M, Weston PH, Reynolds ZKM, Olde PM, Mast AR, Lemmon EM, Lemmon AR, Bromham L. The phylogeny and biogeography of
Hakea
(Proteaceae) reveals the role of biome shifts in a continental plant radiation. Evolution 2017; 71:1928-1943. [DOI: 10.1111/evo.13276] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 05/04/2017] [Indexed: 01/21/2023]
Affiliation(s)
- Marcel Cardillo
- Macroevolution and Macroecology Group, Research School of Biology Australian National University Canberra 0200 Australia
| | - Peter H. Weston
- National Herbarium of New South Wales Royal Botanic Gardens and Domain Trust Sydney NSW 2000 Australia
| | - Zoe K. M. Reynolds
- Macroevolution and Macroecology Group, Research School of Biology Australian National University Canberra 0200 Australia
| | - Peter M. Olde
- National Herbarium of New South Wales Royal Botanic Gardens and Domain Trust Sydney NSW 2000 Australia
| | - Austin R. Mast
- Department of Biological Science Florida State University Tallahassee Florida 32306
| | - Emily M. Lemmon
- Department of Biological Science Florida State University Tallahassee Florida 32306
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University Dirac Science Library Tallahassee Florida 32306
| | - Lindell Bromham
- Macroevolution and Macroecology Group, Research School of Biology Australian National University Canberra 0200 Australia
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23
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24
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Prunier R, Akman M, Kremer CT, Aitken N, Chuah A, Borevitz J, Holsinger KE. Isolation by distance and isolation by environment contribute to population differentiation in Protea repens (Proteaceae L.), a widespread South African species. AMERICAN JOURNAL OF BOTANY 2017; 104:674-684. [PMID: 28500229 DOI: 10.3732/ajb.1600232] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 04/03/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY The Cape Floristic Region (CFR) of South Africa is renowned for its botanical diversity, but the evolutionary origins of this diversity remain controversial. Both neutral and adaptive processes have been implicated in driving diversification, but population-level studies of plants in the CFR are rare. Here, we investigate the limits to gene flow and potential environmental drivers of selection in Protea repens L. (Proteaceae L.), a widespread CFR species. METHODS We sampled 19 populations across the range of P. repens and used genotyping by sequencing to identify 2066 polymorphic loci in 663 individuals. We used a Bayesian FST outlier analysis to identify single-nucleotide polymorphisms (SNPs) marking genomic regions that may be under selection; we used those SNPs to identify potential drivers of selection and excluded them from analyses of gene flow and genetic structure. RESULTS A pattern of isolation by distance suggested limited gene flow between nearby populations. The populations of P. repens fell naturally into two or three groupings, which corresponded to an east-west split. Differences in rainfall seasonality contributed to diversification in highly divergent loci, as do barriers to gene flow that have been identified in other species. CONCLUSIONS The strong pattern of isolation by distance is in contrast to the findings in the only other widespread species in the CFR that has been similarly studied, while the effects of rainfall seasonality are consistent with well-known patterns. Assessing the generality of these results will require investigations of other CFR species.
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Affiliation(s)
- Rachel Prunier
- Department of Biological and Environmental Sciences, Western Connecticut State University, 190 White Street, Danbury, Connecticut 06810, USA
| | - Melis Akman
- Department of Plant Sciences, University of California Davis, 387 N. Quad Avenue, Davis, California 95616, USA
| | - Colin T Kremer
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, Connecticut 06520-8106, USA
| | - Nicola Aitken
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Aaron Chuah
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Justin Borevitz
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Kent E Holsinger
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, U-3043, Storrs, Connecticut 06268, USA
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25
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He T, Lamont BB. Baptism by fire: the pivotal role of ancient conflagrations in evolution of the Earth's flora. Natl Sci Rev 2017. [DOI: 10.1093/nsr/nwx041] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Fire became a defining feature of the Earth's processes as soon as land plants evolved 420 million years ago and has played a major role in shaping the composition and physiognomy of many ecosystems ever since. However, there remains a general lack of appreciation of the place of fire in the origin, evolution, ecology and conservation of the Earth's biodiversity. We review the literature on the presence of fire throughout the Earth's history following the evolution of land plants and examine the evidence for the origin and evolution of adaptive functional traits, biomes and major plant groups in relation to fire. We show that: (1) fire activities have fluctuated throughout geological time due to variations in climate, and more importantly in atmospheric oxygen, as these affected fuel levels and flammability; (2) fire promoted the early evolution and spread of major terrestrial plant groups; (3) fire has shaped the floristics, structure and function of major global biomes; and (4) fire has initiated and maintained the evolution of a wide array of fire-adapted functional traits since the evolution of land plants. We conclude that fire has been a fundamental agent of natural selection on terrestrial plants throughout the history of life on the Earth's land surface. We suggest that a paradigm shift is required to reassess ecological and evolutionary theories that exclude a role for fire, and also there is a need to review fire-suppression policies on ecosystem management and biodiversity conservation in global fire-prone regions.
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Affiliation(s)
- Tianhua He
- Department of Environment and Agriculture, Curtin University, Perth, WA 6845, Australia
| | - Byron B Lamont
- Department of Environment and Agriculture, Curtin University, Perth, WA 6845, Australia
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26
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Aylward J, Dreyer LL, Laas T, Smit L, Roets F. Knoxdaviesia capensis : dispersal ecology and population genetics of a flower-associated fungus. FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2016.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Skeels A, Cardillo M. Environmental niche conservatism explains the accumulation of species richness in Mediterranean-hotspot plant genera. Evolution 2017; 71:582-594. [DOI: 10.1111/evo.13179] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 01/10/2017] [Accepted: 01/10/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Alexander Skeels
- Macroevolution and Macroecology Group, Research School of Biology; Australian National University; Canberra 0200 Australia
| | - Marcel Cardillo
- Macroevolution and Macroecology Group, Research School of Biology; Australian National University; Canberra 0200 Australia
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28
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Mitchell N, Lewis PO, Lemmon EM, Lemmon AR, Holsinger KE. Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L. AMERICAN JOURNAL OF BOTANY 2017; 104:102-115. [PMID: 28104589 DOI: 10.3732/ajb.1600227] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 11/30/2016] [Indexed: 05/05/2023]
Abstract
PREMISE OF THE STUDY Estimating phylogenetic relationships in relatively recent evolutionary radiations is challenging, especially if short branches associated with recent divergence result in multiple gene tree histories. We combine anchored enrichment next-generation sequencing with species tree analyses to produce a robust estimate of phylogenetic relationships in the genus Protea (Proteaceae), an iconic radiation in South Africa. METHODS We sampled multiple individuals within 59 out of 112 species of Protea and 6 outgroup species for a total of 163 individuals, and obtained sequences for 498 low-copy, orthologous nuclear loci using anchored phylogenomics. We compare several approaches for building species trees, and explore gene tree-species tree discrepancies to determine whether poor phylogenetic resolution reflects a lack of informative sites, incomplete lineage sorting, or hybridization. KEY RESULTS Phylogenetic estimates from species tree approaches are similar to one another and recover previously well-supported clades within Protea, in addition to providing well-supported phylogenetic hypotheses for previously poorly resolved intrageneric relationships. Individual gene trees are markedly different from one another and from species trees. Nonetheless, analyses indicate that differences among gene trees occur primarily concerning clades supported by short branches. CONCLUSIONS Species tree methods using hundreds of nuclear loci provided strong support for many previously unresolved relationships in the radiation of the genus Protea. In cases where support for particular relationships remains low, these appear to arise from few informative sites and lack of information rather than strongly supported disagreement among gene trees.
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Affiliation(s)
- Nora Mitchell
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269 United States
| | - Paul O Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269 United States
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306 United States
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, Florida 32306 United States
| | - Kent E Holsinger
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269 United States
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29
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Klak C, Hanáček P, Bruyns PV. Out of southern Africa: Origin, biogeography and age of the Aizooideae (Aizoaceae). Mol Phylogenet Evol 2016; 109:203-216. [PMID: 27998816 DOI: 10.1016/j.ympev.2016.12.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 12/07/2016] [Accepted: 12/12/2016] [Indexed: 01/28/2023]
Abstract
The Aizooideae is an early-diverging lineage within the Aizoaceae. It is most diverse in southern Africa, but also has endemic species in Australasia, Eurasia and South America. We derived a phylogenetic hypothesis from Bayesian and Maximum Likelihood analyses of plastid DNA-sequences. We find that one of the seven genera, the fynbos-endemic Acrosanthes, does not belong to the Aizooideae, but is an ancient sister-lineage to the subfamilies Mesembryanthemoideae & Ruschioideae. Galenia and Plinthus are embedded inside Aizoon and Aizoanthemum is polyphyletic. The Namibian endemic Tetragonia schenckii is sister to Tribulocarpus of the Sesuvioideae. For the Aizooideae, we explored their possible age by means of relaxed Bayesian dating and used Bayesian Binary MCMC reconstruction of ancestral areas to investigate their area of origin. Early diversification occurred in southern Africa in the Eocene-Oligocene, with a split into a mainly African lineage and an Eurasian-Australasian-African-South American lineage. These subsequently radiated in the early Miocene. For Tetragonia, colonisation of Australasia via long-distance dispersal from Eurasia gave rise to the Australasian lineage from which there were subsequent dispersals to South America and Southern Africa. Despite the relatively old age of the Aizooideae, more than half the species have radiated since the Pleiocene, coinciding with the large and rapid diversification of the Ruschioideae. The lineage made up of Tetragonia schenckii &Tribulocarpus split from the remainder of the Sesuvioideae already in the mid Oligocene and its disjunct distribution between Namibia and north-east Africa may be the result of a previously wider distribution within an early Arid African flora. Our reconstruction of ancestral character-states indicates that the expanding keels giving rise to hygrochastic fruits originated only once, i.e. after the split of the Sesuvioideae from the remainder of the Aizoaceae and that they were subsequently lost many times. Variously winged and spiky fruits, adapted to dispersal by wind and animals, have evolved independently in the Aizooideae and the Sesuvioideae. There is then a greater diversity of dispersal systems in the earlier lineages than in the Mesembryanthemoideae and Ruschioideae, where dispersal is mainly achieved by rain.
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Affiliation(s)
- Cornelia Klak
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, 7701 Rondebosch, South Africa.
| | - Pavel Hanáček
- Department of Plant Biology, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic
| | - Peter V Bruyns
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, 7701 Rondebosch, South Africa
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30
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Rundel PW, Arroyo MT, Cowling RM, Keeley JE, Lamont BB, Vargas P. Mediterranean Biomes: Evolution of Their Vegetation, Floras, and Climate. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032330] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Philip W. Rundel
- Department of Ecology and Evolutionary Biology and Institute of the Environment and Sustainability, University of California, Los Angeles, California 90095;
| | - Mary T.K. Arroyo
- Institute of Ecology and Biodiversity, Department of Ecological Sciences, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile;
| | - Richard M. Cowling
- Centre for Coastal Palaeosciences, Nelson Mandela Metropolitan University, Port Elizabeth 6031, South Africa;
| | - Jon E. Keeley
- Sequoia Field Station, Western Ecological Research Center, U.S. Geological Survey, Three Rivers, California 93271;
| | - Byron B. Lamont
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6845, Australia;
| | - Pablo Vargas
- Department of Biodiversity and Conservation, Royal Botanical Garden of Madrid, CSIC, 28014 Madrid, Spain;
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Pirie MD, Oliver EGH, Mugrabi de Kuppler A, Gehrke B, Le Maitre NC, Kandziora M, Bellstedt DU. The biodiversity hotspot as evolutionary hot-bed: spectacular radiation of Erica in the Cape Floristic Region. BMC Evol Biol 2016; 16:190. [PMID: 27639849 PMCID: PMC5027107 DOI: 10.1186/s12862-016-0764-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 09/08/2016] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The disproportionate species richness of the world's biodiversity hotspots could be explained by low extinction (the evolutionary "museum") and/or high speciation (the "hot-bed") models. We test these models using the largest of the species rich plant groups that characterise the botanically diverse Cape Floristic Region (CFR): the genus Erica L. We generate a novel phylogenetic hypothesis informed by nuclear and plastid DNA sequences of c. 60 % of the c. 800 Erica species (of which 690 are endemic to the CFR), and use this to estimate clade ages (using RELTIME; BEAST), net diversification rates (GEIGER), and shifts in rates of diversification in different areas (BAMM; MuSSE). RESULTS The diversity of Erica species in the CFR is the result of a single radiation within the last c. 15 million years. Compared to ancestral lineages in the Palearctic, the rate of speciation accelerated across Africa and Madagascar, with a further burst of speciation within the CFR that also exceeds the net diversification rates of other Cape clades. CONCLUSIONS Erica exemplifies the "hotbed" model of assemblage through recent speciation, implying that with the advent of the modern Cape a multitude of new niches opened and were successively occupied through local species diversification.
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Affiliation(s)
- M D Pirie
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa.
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099, Mainz, Germany.
| | - E G H Oliver
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - A Mugrabi de Kuppler
- INRES Pflanzenzüchtung, Rheinische Friedrich-Wilhelms-Universität Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - B Gehrke
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099, Mainz, Germany
| | - N C Le Maitre
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - M Kandziora
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099, Mainz, Germany
| | - D U Bellstedt
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
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Oberlander KC, Dreyer LL, Goldblatt P, Suda J, Linder HP. Species-rich and polyploid-poor: Insights into the evolutionary role of whole-genome duplication from the Cape flora biodiversity hotspot. AMERICAN JOURNAL OF BOTANY 2016; 103:1336-47. [PMID: 27352831 DOI: 10.3732/ajb.1500474] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 04/22/2016] [Indexed: 05/18/2023]
Abstract
PREMISE OF THE STUDY Whole-genome duplication (WGD) in angiosperms has been hypothesized to be advantageous in unstable environments and/or to increase diversification rates, leading to radiations. Under the first hypothesis, floras in stable environments are predicted to have lower proportions of polyploids than highly, recently disturbed floras, whereas species-rich floras would be expected to have higher than expected proportions of polyploids under the second. The South African Cape flora is used to discriminate between these two hypotheses because it features a hyperdiverse flora predominantly generated by a limited number of radiations (Cape clades), against a backdrop of climatic and geological stability. METHODS We compiled all known chromosome counts for species in 21 clades present in the Cape (1653 species, including 24 Cape clades), inferred ploidy levels for these species by inspection or derived from the primary literature, and compared Cape to non-Cape ploidy levels in these clades (17,520 species) using G tests. KEY RESULTS The Cape flora has anomalously low proportions of polyploids compared with global levels. This pattern is consistently observed across nearly half the clades and across global latitudinal gradients, although individual lineages seem to be following different paths to low levels of WGD and to differing degrees. CONCLUSIONS This pattern shows that the diversity of the Cape flora is the outcome of primarily diploid radiations and supports the hypothesis that WGD may be rare in stable environments.
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Affiliation(s)
- Kenneth C Oberlander
- Institute of Botany, The Czech Academy of Sciences, Průhonice, CZ-25243, Czech Republic Department Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Léanne L Dreyer
- Department Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Peter Goldblatt
- Missouri Botanical Garden, P.O. Box 299, St. Louis, Missouri 63166 USA
| | - Jan Suda
- Institute of Botany, The Czech Academy of Sciences, Průhonice, CZ-25243, Czech Republic Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, CZ - 128 01, Czech Republic
| | - H Peter Linder
- Institute of Systematic Botany, University of Zurich, Zollikerstrasse 107, Zurich CH8008, Switzerland
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Akman M, Carlson JE, Holsinger KE, Latimer AM. Transcriptome sequencing reveals population differentiation in gene expression linked to functional traits and environmental gradients in the South African shrub Protea repens. THE NEW PHYTOLOGIST 2016; 210:295-309. [PMID: 26618926 DOI: 10.1111/nph.13761] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 10/15/2015] [Indexed: 05/11/2023]
Abstract
Understanding the environmental and genetic mechanisms underlying locally adaptive trait variation across the ranges of species is a major focus of evolutionary biology. Combining transcriptome sequencing with common garden experiments on populations spanning geographical and environmental gradients holds promise for identifying such mechanisms. The South African shrub Protea repens displays diverse phenotypes in the wild along drought and temperature gradients. We grew plants from seeds collected at 19 populations spanning this species' range, and sequenced the transcriptomes of these plants to reveal gene pathways associated with adaptive trait variation. We related expression in co-expressed gene networks to trait phenotypes measured in the common garden and to source population climate. We found that expression in gene networks correlated with source-population environment and with plant traits. In particular, the activity of gene networks enriched for growth related pathways correlated strongly with source site minimum winter temperature and with leaf size, stem diameter and height in the garden. Other gene networks with enrichments for photosynthesis related genes showed associations with precipitation. Our results strongly suggest that this species displays population-level differences in gene expression that have been shaped by source population site climate, and that are reflected in trait variation along environmental gradients.
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Affiliation(s)
- Melis Akman
- Department of Plant Sciences, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Jane E Carlson
- Department of Biological Sciences, Nicholls State University, PO Box 2021, Thibodaux, LA, 70310, USA
| | - Kent E Holsinger
- Department of Ecology & Evolutionary Biology, University of Connecticut, U-3043, Storrs, CT, 06269-3043, USA
| | - Andrew M Latimer
- Department of Plant Sciences, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
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Strelin MM, Benitez-Vieyra S, Ackermann M, Cocucci AA. Flower reshaping in the transition to hummingbird pollination in Loasaceae subfam. Loasoideae despite absence of corolla tubes or spurs. Evol Ecol 2016. [DOI: 10.1007/s10682-016-9826-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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Padayachee AL, Procheş Ş. Patterns in the diversity and endemism of extant Eocene age lineages across southern Africa. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12688] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Ashlyn L. Padayachee
- Disicipline of Geography; University of KwaZulu-Natal; Westville Campus Durban 4000 South Africa
| | - Şerban Procheş
- Disicipline of Geography; University of KwaZulu-Natal; Westville Campus Durban 4000 South Africa
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36
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Hoffmann V, Verboom GA, Cotterill FPD. Dated Plant Phylogenies Resolve Neogene Climate and Landscape Evolution in the Cape Floristic Region. PLoS One 2015; 10:e0137847. [PMID: 26422465 PMCID: PMC4589284 DOI: 10.1371/journal.pone.0137847] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 08/22/2015] [Indexed: 11/18/2022] Open
Abstract
In the context of molecularly-dated phylogenies, inferences informed by ancestral habitat reconstruction can yield valuable insights into the origins of biomes, palaeoenvironments and landforms. In this paper, we use dated phylogenies of 12 plant clades from the Cape Floristic Region (CFR) in southern Africa to test hypotheses of Neogene climatic and geomorphic evolution. Our combined dataset for the CFR strengthens and refines previous palaeoenvironmental reconstructions based on a sparse, mostly offshore fossil record. Our reconstructions show remarkable consistency across all 12 clades with regard to both the types of environments identified as ancestral, and the timing of shifts to alternative conditions. They reveal that Early Miocene land surfaces of the CFR were wetter than at present and were dominated by quartzitic substrata. These conditions continue to characterize the higher-elevation settings of the Cape Fold Belt, where they have fostered the persistence of ancient fynbos lineages. The Middle Miocene (13-17 Ma) saw the development of perennial to weakly-seasonal arid conditions, with the strongly seasonal rainfall regime of the west coast arising ~6.5-8 Ma. Although the Late Miocene may have seen some exposure of the underlying shale substrata, the present-day substrate diversity of the CFR lowlands was shaped by Pliocene-Pleistocene events. Particularly important was renewed erosion, following the post-African II uplift episode, and the reworking of sediments on the coastal platform as a consequence of marine transgressions and tectonic uplift. These changes facilitated adaptive radiations in some, but not all, lineages studied.
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Affiliation(s)
- Vera Hoffmann
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
- * E-mail:
| | - G. Anthony Verboom
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
| | - Fenton P. D. Cotterill
- Africa Earth Observatory Network (AEON), Geoecodynamics Research Hub, Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
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37
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Reyes E, Morlon H, Sauquet H. Presence in Mediterranean hotspots and floral symmetry affect speciation and extinction rates in Proteaceae. THE NEW PHYTOLOGIST 2015; 207:401-410. [PMID: 25537140 DOI: 10.1111/nph.13244] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 11/24/2014] [Indexed: 06/04/2023]
Abstract
The Proteaceae is a large angiosperm family displaying the common pattern of uneven distribution of species among genera. Previous studies have shown that this disparity is a result of variation in diversification rates across lineages, but the reasons for this variation are still unclear. Here, we tested the impact of floral symmetry and occurrence in Mediterranean climate regions on speciation and extinction rates in the Proteaceae. A rate shift analysis was conducted on dated genus-level phylogenetic trees of the Proteaceae. Character-dependent analyses were used to test for differences in diversification rates between actinomorphic and zygomorphic lineages and between lineages located within or outside Mediterranean climate regions. The rate shift analysis identified 5-10 major diversification rate shifts in the Proteaceae tree. The character-dependent analyses showed that speciation rates, extinction rates and net diversification rates of the Proteaceae were significantly higher for lineages occurring in Mediterranean hotspots. Higher speciation and extinction rates were also detected for zygomorphic species, but net diversification rates appeared to be similar in actinomorphic and zygomorphic Proteaceae. Presence in Mediterranean hotspots favors Proteaceae diversification. In contrast with observations at the scale of angiosperms, floral symmetry is not a trait that strongly influences their evolutionary success.
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Affiliation(s)
- Elisabeth Reyes
- Laboratoire Écologie, Systématique, Évolution, CNRS UMR 8079, Université Paris-Sud, 91405, Orsay, France
- CMAP, École Polytechnique, CNRS UMR 7641, Route de Saclay, 91128, Palaiseau, France
| | - Hélène Morlon
- CMAP, École Polytechnique, CNRS UMR 7641, Route de Saclay, 91128, Palaiseau, France
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197, 46 rue d'Ulm, 75005, Paris, France
| | - Hervé Sauquet
- Laboratoire Écologie, Systématique, Évolution, CNRS UMR 8079, Université Paris-Sud, 91405, Orsay, France
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38
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Cook LG, Hardy NB, Crisp MD. Three explanations for biodiversity hotspots: small range size, geographical overlap and time for species accumulation. An Australian case study. THE NEW PHYTOLOGIST 2015; 207:390-400. [PMID: 25442328 DOI: 10.1111/nph.13199] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 10/28/2014] [Indexed: 06/04/2023]
Abstract
To understand the generation and maintenance of biodiversity hotspots, we tested three major hypotheses: rates of diversification, ecological limits to diversity, and time for species accumulation. Using dated molecular phylogenies, measures of species' range size and geographical clade overlap, niche modelling, and lineages-through-time plots of Australian Fabaceae, we compared the southwest Australia Floristic Region (SWAFR; a global biodiversity hotspot) with a latitudinally equivalent non-hotspot, southeast Australia (SEA). Ranges of species (real and simulated) were smaller in the SWAFR than in SEA. Geographical overlap of clades was significantly greater for Daviesia in the SWAFR than in SEA, but the inverse for Bossiaea. Lineage diversification rates over the past 10 Myr did not differ between the SWAFR and SEA in either genus. Interaction of multiple factors probably explains the differences in measured diversity between the two regions. Steeper climatic gradients in the SWAFR probably explain the smaller geographical ranges of both genera there. Greater geographical overlap of clades in the SWAFR, combined with a longer time in the region, can explain why Daviesia is far more species-rich there than in SEA. Our results indicate that the time for speciation and ecological limits hypotheses, in concert, can explain the differences in biodiversity.
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Affiliation(s)
- Lyn G Cook
- School of Biological Sciences, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Nate B Hardy
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA
| | - Michael D Crisp
- Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
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39
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Donoghue MJ, Sanderson MJ. Confluence, synnovation, and depauperons in plant diversification. THE NEW PHYTOLOGIST 2015; 207:260-274. [PMID: 25778694 DOI: 10.1111/nph.13367] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/14/2015] [Indexed: 05/02/2023]
Abstract
We review the empirical phylogenetic literature on plant diversification, highlighting challenges in separating the effects of speciation and extinction, in specifying diversification mechanisms, and in making convincing arguments. In recent discussions of context dependence, key opportunities and landscapes, and indirect effects and lag times, we see a distinct shift away from single-point/single-cause 'key innovation' hypotheses toward more nuanced explanations involving multiple interacting causal agents assembled step-wise through a tree. To help crystalize this emerging perspective we introduce the term 'synnovation' (a hybrid of 'synergy' and 'innovation') for an interacting combination of traits with a particular consequence ('key synnovation' in the case of increased diversification rate), and the term 'confluence' for the sequential coming together of a set of traits (innovations and synnovations), environmental changes, and geographic movements along the branches of a phylogenetic tree. We illustrate these concepts using the radiation of Bromeliaceae. We also highlight the generality of these ideas by considering how rate heterogeneity associated with a confluence relates to the existence of particularly species-poor lineages, or 'depauperons.' Many challenges are posed by this re-purposed research framework, including difficulties associated with partial taxon sampling, uncertainty in divergence time estimation, and extinction.
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Affiliation(s)
- Michael J Donoghue
- Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, New Haven, CT, 06520, USA
| | - Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
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40
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Verboom GA, Bergh NG, Haiden SA, Hoffmann V, Britton MN. Topography as a driver of diversification in the Cape Floristic Region of South Africa. THE NEW PHYTOLOGIST 2015; 207:368-376. [PMID: 25708902 DOI: 10.1111/nph.13342] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 01/22/2015] [Indexed: 06/04/2023]
Abstract
The rugged topography of the Cape Floristic Region (CFR), South Africa, is frequently invoked to explain the spectacular radiation of the Cape flora, but the mechanisms involved remain unclear. Where recent authors emphasize the importance of elevation gradients as stimuli for ecological speciation, earlier workers stressed the role of topography as an isolating mechanism, particularly in montane lineages. Using six Cape plant lineages, we tested whether elevation niches are phylogenetically conserved. We then assessed whether high-elevation species are more consistently range-restricted than low-elevation species, and whether high-elevation sisters show stronger range exclusivity (allopatry) and weaker ecological and phenotypic differentiation, suggestive of nonecological speciation. Elevation niches tend to be phylogenetically conserved. Also, high-elevation species are more consistently range-restricted than low-elevation species, potentially explaining the generally stronger range exclusivity of high-elevation sisters. While the high-elevation zone is less homogeneous ecologically, more data are required to demonstrate that high-elevation sister species show generally weaker ecological and phenotypic differentiation. Topographic complexity promotes geographical isolation at high elevations, thereby providing opportunities for nonecological, vicariant speciation. While recognizing the need for additional data, we suggest that the upland and lowland floras of the CFR may differ with regard to predominant speciation mode.
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Affiliation(s)
- G Anthony Verboom
- Bolus Herbarium and Department of Biological Sciences, University of Cape Town, Private Bag, 7701, Rondebosch, South Africa
| | - Nicola G Bergh
- Compton Herbarium, South African National Biodiversity Institute, Private Bag X7, 7735, Claremont, South Africa
| | - Sarah A Haiden
- Bolus Herbarium and Department of Biological Sciences, University of Cape Town, Private Bag, 7701, Rondebosch, South Africa
| | - Vera Hoffmann
- Bolus Herbarium and Department of Biological Sciences, University of Cape Town, Private Bag, 7701, Rondebosch, South Africa
| | - Matthew N Britton
- Bolus Herbarium and Department of Biological Sciences, University of Cape Town, Private Bag, 7701, Rondebosch, South Africa
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41
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Bai K, He C, Wan X, Jiang D. Leaf economics of evergreen and deciduous tree species along an elevational gradient in a subtropical mountain. AOB PLANTS 2015; 7:plv064. [PMID: 26056133 PMCID: PMC4571104 DOI: 10.1093/aobpla/plv064] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Accepted: 05/20/2015] [Indexed: 05/02/2023]
Abstract
The ecophysiological mechanisms underlying the pattern of bimodal elevational distribution of evergreen tree species remain incompletely understood. Here we used leaf economics spectrum (LES) theory to explain such patterns. We measured leaf economic traits and constructed an LES for the co-existing 19 evergreen and 15 deciduous species growing in evergreen broad-leaved forest at low elevation, beech-mixed forest at middle elevation and hemlock-mixed forest at high elevation in Mao'er Mountain, Guangxi, Southern China (25°50'N, 110°49'E). Leaf economic traits presented low but significant phylogenetic signal, suggesting trait similarity between closely related species. After considering the effects of phylogenetic history, deciduous species in general showed a more acquisitive leaf strategy with a higher ratio of leaf water to dry mass, higher leaf nitrogen and phosphorous contents, higher photosynthetic and respiratory rates and greater photosynthetic nitrogen-use efficiency. In contrast, evergreen species exhibited a more conservative leaf strategy with higher leaf mass per area, greater construction costs and longer leaf life span. With the elevation-induced decreases of temperature and soil fertility, both evergreen and deciduous species showed greater resource conservation, suggesting the increasing importance of environmental filtering to community assembly with increasing elevation. We found close inter-specific correlations between leaf economic traits, suggesting that there are strong genetic constraints limiting the independent evolution of LES traits. Phylogenetic signal increased with decreasing evolutionary rate across leaf economic traits, suggesting that genetic constraints are important for the process of trait evolution. We found a significantly positive relationship between primary axis species score (PASS) distance and phylogenetic distance across species pairs and an increasing average PASS distance between evergreen and deciduous species with increasing elevation, implying that the frequency of distantly related evergreen and deciduous pairs with wide spreading of leaf economic values increases with increasing elevation. Our findings thus suggest that elevation acts as an environmental filter to both select the locally adapted evergreen and deciduous species with sufficient phylogenetic variation and regulate their distribution along the elevational gradient based on their coordinated spreading of phylogenetic divergence and leaf economic variation.
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Affiliation(s)
- Kundong Bai
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Chinese Academy of Sciences, Guilin 541006, China Institute of New Forest Technology, Chinese Academy of Forestry, Beijing 100091, China
| | - Chengxin He
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Chinese Academy of Sciences, Guilin 541006, China
| | - Xianchong Wan
- Institute of New Forest Technology, Chinese Academy of Forestry, Beijing 100091, China
| | - Debing Jiang
- Guangxi Mao'er Mountain National Nature Reserve, Guilin 541316, China
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42
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Carlson JE, Holsinger KE. Extrapolating from local ecological processes to genus-wide patterns in colour polymorphism in South African Protea. Proc Biol Sci 2015; 282:20150583. [PMID: 25876847 PMCID: PMC4426637 DOI: 10.1098/rspb.2015.0583] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 03/20/2015] [Indexed: 11/12/2022] Open
Abstract
Polymorphic traits are central to many fundamental discoveries in evolution, yet why they are found in some species and not others remains poorly understood. We use the African genus Protea-within which more than 40% of species have co-occurring pink and white floral colour morphs-to ask whether convergent evolution and ecological similarity could explain the genus-wide pattern of polymorphism. First, we identified environmental correlates of pink morph frequency across 28 populations of four species. Second, we determined whether the same correlates could predict species-level polymorphism and monomorphism across 31 species. We found that pink morph frequency increased with elevation in Protea repens and three section Exsertae species, increased eastward in P. repens, and increased with seed predation intensity in section Exsertae. For cross-species comparisons, populations of monomorphic pink species occurred at higher elevations than populations of monomorphic white species, and 18 polymorphic species spanned broader elevational gradients than 13 monomorphic species. These results suggest that divergent selection along elevational clines has repeatedly favoured polymorphism, and that more uniform selection in altitudinally restricted species may promote colour monomorphism. Our findings are, to our knowledge, the first to link selection acting within species to the presence and absence of colour polymorphism at broader phylogenetic scales.
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Affiliation(s)
- Jane E Carlson
- Department of Ecology and Evolutionary Biology, University of Connecticut, U-3043, Storrs, CT 06269, USA
| | - Kent E Holsinger
- Department of Ecology and Evolutionary Biology, University of Connecticut, U-3043, Storrs, CT 06269, USA
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43
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Cadotte MW. Phylogenetic diversity–ecosystem function relationships are insensitive to phylogenetic edge lengths. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12429] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marc W. Cadotte
- Department of Biological Sciences University of Toronto Scarborough 1265 Military TrailScarborough ON Canada
- Department of Ecology and Evolutionary Biology University of Toronto 25 Willcocks Street, Toronto Scarborough ON Canada
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Mitchell N, Moore TE, Mollmann HK, Carlson JE, Mocko K, Martinez-Cabrera H, Adams C, Silander JA, Jones CS, Schlichting CD, Holsinger KE. Functional Traits in Parallel Evolutionary Radiations and Trait-Environment Associations in the Cape Floristic Region of South Africa. Am Nat 2015; 185:525-37. [DOI: 10.1086/680051] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Onstein RE, Carter RJ, Xing Y, Richardson JE, Linder HP. Do Mediterranean-type ecosystems have a common history?-Insights from the Buckthorn family (Rhamnaceae). Evolution 2015; 69:756-71. [DOI: 10.1111/evo.12605] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 12/30/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Renske E. Onstein
- Institute of Systematic Botany; University of Zurich; Zollikerstrasse 107 8008 Zurich Switzerland
| | - Richard J. Carter
- Institute of Systematic Botany; University of Zurich; Zollikerstrasse 107 8008 Zurich Switzerland
- Cottage Science; Carterton New Zealand
| | - Yaowu Xing
- Institute of Systematic Botany; University of Zurich; Zollikerstrasse 107 8008 Zurich Switzerland
- Department of Botany; Field Museum of Natural History; 1400 South Lake Shore Drive Chicago Illinois 60605
| | - James E. Richardson
- Royal Botanic Garden Edinburgh; 20a Inverleith Row Edinburgh EH3 5LR United Kingdom
- Universidad de Los Andes; Apartado Aéreo 4976 Bogotá Colombia
| | - H. Peter Linder
- Institute of Systematic Botany; University of Zurich; Zollikerstrasse 107 8008 Zurich Switzerland
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46
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Jordan GJ, Carpenter RJ, Koutoulis A, Price A, Brodribb TJ. Environmental adaptation in stomatal size independent of the effects of genome size. THE NEW PHYTOLOGIST 2015; 205:608-17. [PMID: 25266914 PMCID: PMC4301182 DOI: 10.1111/nph.13076] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 08/20/2014] [Indexed: 05/18/2023]
Abstract
Cell sizes are linked across multiple tissues, including stomata, and this variation is closely correlated with genome size. These associations raise the question of whether generic changes in cell size cause suboptimal changes in stomata, requiring subsequent evolution under selection for stomatal size. We tested the relationships among guard cell length, genome size and vegetation type using phylogenetically independent analyses on 67 species of the ecologically and structurally diverse family, Proteaceae. We also compared how genome and stomatal sizes varied at ancient (among genera) and more recent (within genus) levels. The observed 60-fold range in genome size in Proteaceae largely reflected the mean chromosome size. Compared with variation among genera, genome size varied much less within genera (< 6% of total variance) than stomatal size, implying evolution in stomatal size subsequent to changes in genome size. Open vegetation and closed forest had significantly different relationships between stomatal and genome sizes. Ancient changes in genome size clearly influenced stomatal size in Proteaceae, but adaptation to habitat strongly modified the genome-stomatal size relationship. Direct adaptation to the environment in stomatal size argues that new proxies for past concentrations of atmospheric CO2 that incorporate stomatal size are superior to older models based solely on stomatal frequency.
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Affiliation(s)
- Gregory J Jordan
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia
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Experimental climate warming enforces seed dormancy in South African Proteaceae but seedling drought resilience exceeds summer drought periods. Oecologia 2014; 177:1103-16. [PMID: 25502439 DOI: 10.1007/s00442-014-3173-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 11/25/2014] [Indexed: 10/24/2022]
Abstract
Two hypotheses-that elevated night-time temperatures due to climate warming would enforce post-fire dormancy of Proteaceae seed due to low moisture, and that periods without rain during summer would exceed desiccation periods tolerated by Proteaceae seedlings-were tested empirically. Enforced dormancy, i.e., the inability to germinate due to an environmental restraint, was tested by measuring seed germination in 11 Proteaceae species in experimental mesocosms whose soils were artificially elevated by 1.4 and 3.5 °C above ambient by far-red wavelength filtered infrared lamps. Diminished totality of germination and velocities were observed in 91 and 64%, respectively, of the Proteaceae species tested. Drought resilience was tested in one-year-old seedlings of 16 Proteaceae species by withholding water from potted plants during summer in a greenhouse. The most drought-resilient Proteaceae species displayed the lowest initial transpiration rates at field capacity, the smallest declines in transpiration rate with decreasing soil water content, and the lowest water losses by transpiration. Projected drought periods leading to the complete cessation of transpiration in all Proteaceae species greatly exceeded the number of days without rain per month during summer in the current distribution ranges of those species. It was therefore concluded that enforced seed dormancy induced by elevated night-time temperatures is the post-fire recruitment stage of Proteaceae that is most sensitive to climate warming.
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Nock CJ, Baten A, King GJ. Complete chloroplast genome of Macadamia integrifolia confirms the position of the Gondwanan early-diverging eudicot family Proteaceae. BMC Genomics 2014; 15 Suppl 9:S13. [PMID: 25522147 PMCID: PMC4290595 DOI: 10.1186/1471-2164-15-s9-s13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Sequence data from the chloroplast genome have played a central role in elucidating the evolutionary history of flowering plants, Angiospermae. In the past decade, the number of complete chloroplast genomes has burgeoned, leading to well-supported angiosperm phylogenies. However, some relationships, particulary among early-diverging lineages, remain unresolved. The diverse Southern Hemisphere plant family Proteaceae arose on the ancient supercontinent Gondwana early in angiosperm history and is a model group for adaptive radiation in response to changing climatic conditions. Genomic resources for the family are limited, and until now it is one of the few early-diverging 'basal eudicot' lineages not represented in chloroplast phylogenomic analyses. RESULTS The chloroplast genome of the Australian nut crop tree Macadamia integrifolia was assembled de novo from Illumina paired-end sequence reads. Three contigs, corresponding to a collapsed inverted repeat, a large and a small single copy region were identified, and used for genome reconstruction. The complete genome is 159,714 bp in length and was assembled at deep coverage (3.29 million reads; ~2000 x). Phylogenetic analyses based on 83-gene and inverted repeat region alignments, the largest sequence-rich datasets to include the basal eudicot family Proteaceae, provide strong support for a Proteales clade that includes Macadamia, Platanus and Nelumbo. Genome structure and content followed the ancestral angiosperm pattern and were highly conserved in the Proteales, whilst size differences were largely explained by the relative contraction of the single copy regions and expansion of the inverted repeats in Macadamia. CONCLUSIONS The Macadamia chloroplast genome presented here is the first in the Proteaceae, and confirms the placement of this family with the morphologically divergent Plantanaceae (plane tree family) and Nelumbonaceae (sacred lotus family) in the basal eudicot order Proteales. It provides a high-quality reference genome for future evolutionary studies and will be of benefit for taxon-rich phylogenomic analyses aimed at resolving relationships among early-diverging angiosperms, and more broadly across the plant tree of life.
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Donoghue MJ, Edwards EJ. Biome Shifts and Niche Evolution in Plants. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2014. [DOI: 10.1146/annurev-ecolsys-120213-091905] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Michael J. Donoghue
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520;
| | - Erika J. Edwards
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912;
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Ng J, Smith SD. How traits shape trees: new approaches for detecting character state-dependent lineage diversification. J Evol Biol 2014; 27:2035-45. [PMID: 25066512 DOI: 10.1111/jeb.12460] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 07/07/2014] [Accepted: 07/08/2014] [Indexed: 12/30/2022]
Abstract
Biologists have long sought to understand the processes underlying disparities in clade size across the tree of life and the extent to which such clade size differences can be attributed to the evolution of particular traits. The association of certain character states with species-rich clades suggests that trait evolution can lead to increased diversification, but such a pattern could also arise due other processes, such as directional trait evolution. Recent advances in phylogenetic comparative methods have provided new statistical approaches for distinguishing between these intertwined and potentially confounded macroevolutionary processes. Here, we review the historical development of methods for detecting state-dependent diversification and explore what new methods have revealed about classic examples of traits that affect diversification, including evolutionary dead ends, key innovations and geographic traits. Applications of these methods thus far collectively suggest that trait diversity commonly arises through the complex interplay between transition, speciation and extinction rates and that long hypothesized evolutionary dead ends and key innovations are instead often cases of directional trends in trait evolution.
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Affiliation(s)
- J Ng
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
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