Population genetic analysis and phylogeny reconstruction in Eucalyptus (Myrtaceae) using high-throughput, genome-wide genotyping

Steane, Dorothy A.; Nicolle, Dean; Sansaloni, Carolina; Petroli, César; Carling, Jason; Kilian, Andrzej; Myburg, Alexander Andrew; Grattapaglia, Dário; Vaillancourt, René E.

doi:10.1016/j.ympev.2011.02.003

Cited by 103 publications

(105 citation statements)

References 89 publications

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“…In addition, closely related co-occurring taxa in subgenus Eucalyptus (sections Aromatica, Capillulus, Cineraceae and Longitudinales) were sampled (often from more than one individual per species from different locations). Eucalyptus cloeziana (subgenus Idiogenes) was included as an out-group to subgenus Eucalyptus on the basis of previous studies (Sale et al 1993;Hill and Johnson 1995;Ladiges et al 1995;Steane et al 1999;Udovicic and Ladiges 2000;Steane et al 2011 …”

Section: Sampling Of Taxamentioning

confidence: 99%

“…Morphological differences among species are often narrowly defined (Hill 1991), and clinal variation and morphological convergence between taxa are common (McKinnon et al 2004). Defining species boundaries is further complicated by interspecific hybridisation, often between distantly related taxa (Griffin et al 1988;Rossetto et al 1997;McKinnon et al 2001;Field et al 2011aField et al , 2011bSteane et al 2011;Pollock et al 2013Pollock et al , 2015. As a result, understanding evolutionary relationships in Eucalyptus, particularly between closely related species, remains a major challenge.…”

Section: Introductionmentioning

confidence: 99%

“…ITS and ETS) in eucalypts because of the functional constraints imposed on neutral change of nucleotides during evolution (Bayly and Ladiges 2007;Ochieng et al 2007a;Bayly et al 2008). Marker systems theoretically representing the whole genome, such as microsatellites and amplified fragment length polymorphisms (AFLPs), have been used to overcome some of these issues (Steane et al 2011). However, although microsatellites have moderate levels of throughput, and are highly polymorphic and transferable across populations, their transferability across species is sometimes poor (Rossetto et al 2000;Semagn et al 2006).…”

Section: Introductionmentioning

confidence: 99%

“…DArT is a microarray hybridisation-based technique that simultaneously assays hundreds to thousands of markers across the genome (Jaccoud et al 2001;Sansaloni et al 2010;Kullan et al 2012). Steane et al (2011) used over 8000 DArT markers (primarily nuclear) to construct a phylogeny of Eucalyptus, where relationships among higher taxa were generally concordant with traditional taxonomy and ITS-based phylogenies, with high resolution within major clades (including between some closely related species) relative to previous techniques.…”

Section: Introductionmentioning

confidence: 99%

“…Eucalyptus regnans, E. obliqua, E. triflora) have been included in molecular Phylogenomics of green ashes Australian Systematic Botanyphylogenies over the past 10 years (Bayly and Ladiges 2007;Steane et al 2011;Bayly et al 2013), there has been no broader study of the green ash eucalypts using these more advanced techniques. Prober et al (1990) used allozyme data to investigate diversity in the green ashes, and this revealed low differentiation among taxa and many relationships that were not consistent with those derived from morphological characters.…”

Section: Introductionmentioning

confidence: 99%

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Phylogenomics of the green ash eucalypts (Myrtaceae): a tale of reticulate evolution and misidentification

Rutherford¹,

Wilson²,

Rossetto³

et al. 2015

Aust. Systematic Bot.

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Abstract. Eucalyptus is a genus that occurs in a range of habitats in Australia, Papua New Guinea, Timor, Sulawesi and the Philippines, with several species being used as sources of timber and fibre. However, despite its ecological and commercial significance, understanding its evolutionary history remains a challenge. The focus of the present study is the green ashes (subgenus Eucalyptus section Eucalyptus). Although previous studies, based primarily on morphology, suggest that the green ashes form a monophyletic group, there has been disagreement concerning the divergence of taxa. The present study aims to estimate the phylogeny of the green ashes and closely related eucalypts (37 taxa from over 50 locations in south-eastern Australia), using genome-wide analyses based on Diversity Arrays Technology (DArT). Results of analyses were similar in topology and consistent with previous phylogenies based on sequence data. Many of the relationships supported those proposed by earlier workers. However, other relationships, particularly of taxa within the Sydney region and Blue Mountains, were not consistent with previous classifications. These findings raise important questions concerning how we define species and discern relationships in Eucalyptus and may have implications for other plant species, particularly those with a complex evolutionary history where hybridisation and recombination have occurred.

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Section: Sampling Of Taxamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Phylogenomics of the green ash eucalypts (Myrtaceae): a tale of reticulate evolution and misidentification

Rutherford¹,

Wilson²,

Rossetto³

et al. 2015

Aust. Systematic Bot.

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Multiple evolutionary processes drive the patterns of genetic differentiation in a forest tree species complex

Jones

Steane

Lavery³

et al. 2013

Ecology and Evolution

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Forest trees frequently form species complexes, complicating taxonomic classification and gene pool management. This is certainly the case in Eucalyptus, and well exemplified by the Eucalyptus globulus complex. This ecologically and economically significant complex comprises four taxa (sspp. bicostata, globulus, maidenii, pseudoglobulus) that are geographically and morphologically distinct, but linked by extensive “intergrade” populations. To resolve their genetic affinities, nine microsatellites were used to genotype 1200 trees from throughout the natural range of the complex in Australia, representing 33 morphological core and intergrade populations. There was significant spatial genetic structure (FST = 0.10), but variation was continuous. High genetic diversity in southern ssp. maidenii indicates that this region is the center of origin. Genetic diversity decreases and population differentiation increases with distance from this area, suggesting that drift is a major evolutionary process. Many of the intergrade populations, along with other populations morphologically classified as ssp. pseudoglobulus or ssp. globulus, belong to a “cryptic genetic entity” that is genetically and geographically intermediate between core ssp. bicostata, ssp. maidenii, and ssp. globulus. Geography, rather than morphology, therefore, is the best predictor of overall genetic affinities within the complex and should be used to classify germplasm into management units for conservation and breeding purposes.

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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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Population genetic analysis and phylogeny reconstruction in Eucalyptus (Myrtaceae) using high-throughput, genome-wide genotyping

Cited by 103 publications

References 89 publications

Phylogenomics of the green ash eucalypts (Myrtaceae): a tale of reticulate evolution and misidentification

Phylogenomics of the green ash eucalypts (Myrtaceae): a tale of reticulate evolution and misidentification

Multiple evolutionary processes drive the patterns of genetic differentiation in a forest tree species complex

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

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