High density, genome-wide markers and intra-specific replication yield an unprecedented phylogenetic reconstruction of a globally significant, speciose lineage of Eucalyptus

Jones, Rebecca C.; Nicolle, Dean; Steane, Dorothy A.; Vaillancourt, René E.; Potts, Brad M.

doi:10.1016/j.ympev.2016.08.009

Cited by 31 publications

(76 citation statements)

References 77 publications

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“…We reconstructed the phylogeny of the Tasmanian eucalypts using a set of 3,881 parsimony informative Diversity Array Technology (DArT) markers (Jaccoud et al 2001) and Metropolis-coupled Markov chain Monte Carlo in MrBayes v3.2 (Ronquist and Huelsenbeck 2003). We used DArT markers because they perform well at resolving phylogenetic relationships among Eucalyptus species (Jones et al 2016). Genetic material for DArT markers was collected from individuals grown from seeds purchased from Forestry Tasmania (http://www.forestrytas.com.au/; see Appendix S1: Table S1 for information on seed collection zones), including the 23 species in the greenhouse experiment (described herein), plus four Tasmanian natives not included in the greenhouse experiment (E. johnstonii, E. nitida, E. perriniana, and E. vernicosa), and one non-native (E. nitens).…”

Section: Phylogenetic Reconstructionmentioning

confidence: 99%

“…We used these groupings to address whether phylogenetic groups differ in responses to N enrichment. Because the placement of E. globulus (the Tasmanian Blue Gum) into either of the gum lineages is uncertain (for this and other phylogenetic reconstructions, e.g., Steane et al 2011, Senior et al 2013, Jones et al 2016, we excluded it from the lineage-level comparisons described herein.…”

Section: Phylogenetic Reconstructionmentioning

confidence: 99%

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Phylogeny is a powerful tool for predicting plant biomass responses to nitrogen enrichment

Wooliver

Marion

Peterson

et al. 2017

Ecology

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Abstract. Increasing rates of anthropogenic nitrogen (N) enrichment to soils often lead to the dominance of nitrophilic plant species and reduce plant diversity in natural ecosystems. Yet, we lack a framework to predict which species will be winners or losers in soil N enrichment scenarios, a framework that current literature suggests should integrate plant phylogeny, functional tradeoffs, and nutrient co-limitation. Using a controlled fertilization experiment, we quantified biomass responses to N enrichment for 23 forest tree species within the genus Eucalyptus that are native to Tasmania, Australia. Based on previous work with these species' responses to global change factors and theory on the evolution of plant resource-use strategies, we hypothesized that (1) growth responses to N enrichment are phylogenetically structured, (2) species with more resource-acquisitive functional traits have greater growth responses to N enrichment, and (3) phosphorus (P) limits growth responses to N enrichment differentially across species, wherein P enrichment increases growth responses to N enrichment more in some species than others. We built a hierarchical Bayesian model estimating effects of functional traits (specific leaf area, specific stem density, and specific root length) and P fertilization on species' biomass responses to N, which we then compared between lineages to determine whether phylogeny explains variation in responses to N. In concordance with literature on N limitation, a majority of species responded strongly and positively to N enrichment. Mean responses ranged three-fold, from 6.21 (E. pulchella) to 16.87 (E. delegatensis) percent increases in biomass per g NÁm À2 Áyr À1 added. We identified a strong difference in responses to N between two phylogenetic lineages in the Eucalyptus subgenus Symphyomyrtus, suggesting that shared ancestry explains variation in N limitation. However, our model indicated that after controlling for phylogenetic non-independence, eucalypt responses to N were not associated with functional traits (although post-hoc analyses show a phylogenetic pattern in specific root length similar to that of responses to N), nor were responses differentially limited by P. Overall, our model results suggest that phylogeny is a powerful predictor of winners and losers in anthropogenic N enrichment scenarios in Tasmanian eucalypts, which may have implications for other species.

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Section: Phylogenetic Reconstructionmentioning

confidence: 99%

Section: Phylogenetic Reconstructionmentioning

confidence: 99%

Phylogeny is a powerful tool for predicting plant biomass responses to nitrogen enrichment

Wooliver

Marion

Peterson

et al. 2017

Ecology

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“…many nearly simultaneous speciation events resulting in fast changes of morphological characters, which are not equally accompanied by changes in the (neutral) marker regions we used for our study. Here using next-generation sequencing approaches to screen for genome-wide DNA differences seems a more suitable approach to us for resolving such narrow species groups 39–41 . Moreover, these methods could simultaneously identify genome regions contributing to fast morphological changes.…”

Section: Discussionmentioning

confidence: 99%

Molecular phylogeny and divergence times of Astragalus section Hymenostegis: An analysis of a rapidly diversifying species group in Fabaceae

Bagheri

Maassoumi

Rahiminejad

et al. 2017

Sci Rep

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The taxa of Astragalus section Hymenostegis are an important element of mountainous and steppe habitats in Southwest Asia. A phylogenetic hypothesis of sect. Hymenostegis has been obtained from nuclear ribosomal DNA internal transcribed spacer (ITS) and plastid ycf1 sequences of up to 303 individuals from 106 species, including all 89 taxa currently assigned to sect. Hymenostegis, 14 species of other Astragalus sections, and two species of Oxytropis and one Biserrula designated as outgroups. Bayesian phylogenetic inference and parsimony analyses reveal that three species from two other closely related sections group within sect. Hymenostegis, making the section paraphyletic. DNA sequence diversity is generally very low among Hymenostegis taxa, which is consistent with recent diversification of the section. We estimate that diversification in sect. Hymenostegis occurred in the middle to late Pleistocene, with many species arising only during the last one million years, when environmental conditions in the mountain regions of Southwest and Central Asia cycled repeatedly between dry and more humid conditions.Astragalus is with about 2500-3000 species in 250 sections the largest genus of flowering plants [1][2][3][4][5][6][7] . It belongs to the legume family (Leguminosae or Fabaceae) that is, after Orchidaceae and Asteraceae, the third largest family of flowering plants 5 consisting of about 730 genera and nearly 19,300 species. Also its subfamily Papilionoideae, with about 478 genera and 13,800 species 5 , is very species rich. Astragalus belongs within this subfamily together with genera like Oxytropis and Colutea to the Astragalean clade of the so-called Inverted Repeat Lacking Clade (IRLC). Its members are all characterized by the loss of one copy of the two 25-kb inverted repeat regions in the chloroplast genome 2,[8][9][10] .Although species richness seems to be a general characteristic of the legumes, this feature is not evenly distributed among the groups within this family. Thus, Sanderson and Wojciechowski 11 found that Astragalus itself is not significantly more speciose compared to its close relatives, but that species richness is a feature of the entire Astragalean clade in comparison to the other groups of the IRLC. High species numbers can originate through constant accumulation of diversity through time or following a punctuated pattern, where bursts of diversification rates alternate with times of stasis 12 . The latter pattern often results from the evolution of a key innovation that provides the possibility to fill a new ecological niche, or from a key opportunity, i.e. the colonization of a new, formerly not inhabited area and speciation therein [12][13][14][15] . For Astragalus and the entire Astragalean clade the reason(s) for the high species numbers are still unclear. In an effort to better understand reasons for and timing of species diversification in Astragalus we here analyze a large section of the genus, where we put some effort into arriving at a complete species sample.

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“…Subsequent studies, including Steane et al (2011) suggested that the 'MEL+5' lineage is certainly monophyletic, and that Brooker's (2000) embedding of sections Bisectae, Dumaria, Platysperma, Inclusae and Bolites within this lineage was not an accurate reflection of the phylogeny as now understood. Jones et al (2016) used genome-wide markers and an unprecedented scale of sampling to construct a robust phylogeny for this lineage. The study used 3109 DArT markers distributed throughout the genome and 540 samples covering 185 terminal taxa in sections Maidenaria, Exsertaria, Latoangulatae and related smaller sections Racemus (one species), Inclusae (one species), Similares (one species), Incognitae (two species), Liberivalvae (five species), Platysperma (seven species) and Pumilio (one species), all of which were hypothesised to be sister sections to, or embedded within, the Exsertaria, Latoangulatae and Maidenaria lineage (Brooker 2000;Nicolle 2015;Steane et al 2007).…”

Section: Introductionmentioning

confidence: 99%

“…The study used 3109 DArT markers distributed throughout the genome and 540 samples covering 185 terminal taxa in sections Maidenaria, Exsertaria, Latoangulatae and related smaller sections Racemus (one species), Inclusae (one species), Similares (one species), Incognitae (two species), Liberivalvae (five species), Platysperma (seven species) and Pumilio (one species), all of which were hypothesised to be sister sections to, or embedded within, the Exsertaria, Latoangulatae and Maidenaria lineage (Brooker 2000;Nicolle 2015;Steane et al 2007). Of the 153 species that we recognise in the 'MEL+5' lineage, Jones et al (2016) included samples of all species except for E. cupularis (a close relative of E. herbertiana and E. gregoriensis), E. mooreana (the sample labeled as E. mooreana in Jones et al 2016 is actually the recently named E. revelata, see Nicolle and Barrett 2018), and E. sp. Arnhem Land (a close relative of E. bigalerita).…”

Section: Introductionmentioning

confidence: 99%

A revised classification for the predominantly eastern Australian Eucalyptus subgenus Symphyomyrtus sections Maidenaria, Exsertaria, Latoangulatae and related smaller sections (Myrtaceae).

Nicolle¹,

Jones

2018

Telopea

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A revised classification for the predominantly eastern Australian Eucalyptus subgenus Symphyomyrtus sections Maidenaria, Exsertaria, Latoangulatae and related smaller sections (Myrtaceae). Abstract A revised classification for Eucalyptus subgenus Symphyomyrtus sections Maidenaria, Exsertaria, Latoangulatae and five related smaller sections (Liberivalvae, Racemus, Incognitae, Similares and Pumilio) (herein referred to as 'MEL+5' lineage for convenience) is provided, based on evidence from a recent phylogenetic study of this group (Jones et al. 2016) and on observations and data from other sources, including our extensive field observations, study of herbarium collections, common garden trials and the findings of other phylogenetic studies. We recognise 153 species and 184 terminal taxa in the 'MEL+5' lineage, and classify this group into 6 sections, 23 series and 8 subseries. This new classification mainly involved the repositioning of various terminal taxa into existing higher-level taxonomic groups (sections, series and subseries), as we have attempted to achieve an accurate and useful classification while minimising taxonomic disruption of existing names. Nevertheless, nine new higher-level taxa (eight series and one subseries) are newly described. A full classification of the 'MEL+5' lineage is provided, which includes all terminal taxa, taxon authorships, type species, the natural distribution of recognised terminal taxa, and taxonomic and nomenclatural synonyms. ser. Sturgissianae L.A.S.Johnson ex Brooker (T = E. sturgissiana) E. sturgissiana L.A.S.Johnson & Blaxell NSW ser. Viminales Blakely (T = E. viminalis) E. ser. Acaciiformes L.A.S.Johnson ex Brooker & Slee (T = E. acaciiformis), E. ser. Argyrophyllae Blakely (T = E. cinerea), E. ser. Benthamianae Brooker (T = E. benthamii), E. ser. Compactae Brooker (T = E. badjensis), E. ser. Confines Brooker (T = E. kartzoffiana), E. ser. Kitsonianae L.A.S.Johnson ex Brooker & Slee (T = E. kitsoniana), E. ser. Microcarpae Blakely (T = E. scoparia), E. ser. Orbiculares Brooker & Slee (T = E. perriniana), E. ser. Saxicola Brooker (T = E. baeuerlenii) subser. Circulares Brooker (T = E. rubida)

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High density, genome-wide markers and intra-specific replication yield an unprecedented phylogenetic reconstruction of a globally significant, speciose lineage of Eucalyptus

Cited by 31 publications

References 77 publications

Phylogeny is a powerful tool for predicting plant biomass responses to nitrogen enrichment

Phylogeny is a powerful tool for predicting plant biomass responses to nitrogen enrichment

Molecular phylogeny and divergence times of Astragalus section Hymenostegis: An analysis of a rapidly diversifying species group in Fabaceae

A revised classification for the predominantly eastern Australian Eucalyptus subgenus Symphyomyrtus sections Maidenaria, Exsertaria, Latoangulatae and related smaller sections (Myrtaceae).

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