Population and phylogenomic decomposition via genotyping‐by‐sequencing in Australian <i>Pelargonium</i>

Nicotra, Adrienne B.; Chong, Caroline; Bragg, Jason G.; Ong, Chong Ren; Aitken, Nicola; Chuah, Aaron; Lepschi, Brendan J.; Borevitz, Justin O.

doi:10.1111/mec.13584

Cited by 28 publications

(33 citation statements)

References 79 publications

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“…In such species SNPs are identified by using the reference sequence of a different, but closely related species (Maughan et al, 2009), or the de novo assembly of sequencing reads (Catchen et al, 2011(Catchen et al, , 2013. Despite these limitations, GBS and related RADseq approaches have been used for phylogenetic analyses of both closely and distantly related taxa (Ariani et al, 2016;Eaton and Ree, 2013;Harvey et al, 2016;Nicotra et al, 2016) Several software tools were developed for phylogenetic analyses based on biallelic markers. For example, SNAPP (SNP and AFLP Package for Phylogenetic analysis) infers species trees directly from biallelic markers by implementing a full multispecies coalescent model (Bryant et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Analysis of phylogenetic relationships and genome size evolution of theAmaranthusgenus using GBS indicates the ancestors of an ancient crop

Stetter

Schmid

2016

Preprint

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The genus Amaranthus consists of 50 to 70 species and harbors several cultivated and weedy species of great economic importance. A small number of suitable traits, phenotypic plasticity, gene flow and hybridization made it difficult to establish the taxonomy and phylogeny of the whole genus despite various studies using molecular markers. We inferred the phylogeny of the Amaranthus genus using genotyping by sequencing (GBS) of 94 genebank accessions representing 35 Amaranthus species and measured their genome sizes. SNPs were called by de novo and reference-based methods, for which we used the distant sugarbeet Beta vulgaris and the closely related Amaranthus hypochondriacus as references. SNP counts and proportions of missing data differed between methods, but the resulting phylogenetic trees were highly similar. A distance-based neighbor joing tree of individual accessions and a species tree calculated with the multispecies coalescent supported a previous taxonomic classification into three subgenera although the subgenus A. Acnida consists of two highly differentiated clades. The analysis of the Hybridus complex within the A. Amaranthus subgenus revealed insights on the history of cultivated grain amaranths. The complex includes the three cultivated grain amaranths and their wild relatives and was well separated from other species in the subgenus. Wild and cultivated amaranth accessions did not differentiate according to the species assignment but clustered by their geographic origin from South and Central America. Different geographically separated populations of Amaranthus hybridus appear to be the common ancestors of the three cultivated grain species and A. quitensis might be additionally be involved in the evolution of South American grain amaranth (A. caudatus). We also measured genome sizes of the species and observed little variation with the exception of two lineages that showed evidence for a recent polyploidization. With the exception of two lineages, genome sizes are quite similar and indicate that polyploidization did not play a major role in the history of the genus. A. floridanus A. tuberculatus A. fimbriatus A. tucsonensis

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Section: Introductionmentioning

confidence: 99%

Analysis of phylogenetic relationships and genome size evolution of theAmaranthusgenus using GBS indicates the ancestors of an ancient crop

Stetter

Schmid

2016

Preprint

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“…For simulated data, this approach consistently inferred the correct phylogeny, and often with the best fit to the true branch length distribution. In the case of Pelargonium, however, it did not retrieve one of the clades strongly supported by SNAPP (Nicotra et al, 2016), and for Craspedia locus-wise scoring resulted in poorly resolved and poorly supported relationships.…”

Section: Choice Of Scoring Approachmentioning

confidence: 87%

“…We generated empirical SNP data used in this study with Genotyping-by-Sequencing (Elshire et al, 2011) as described in detail by Nicotra et al (2016). Briefly, genomic DNA was digested with PstI and ligated to uniquely barcoded sequencing adaptor pairs.…”

Section: Snp Data Setsmentioning

confidence: 99%

“…We also used a published dataset of Australian native Pelargonium L'Her. ex Aiton (Geraniaceae) (Nicotra et al, 2016) which provides an accepted phylogeny inferred with SNAPP to compare against other approaches. The dataset comprised 463 SNPs for 23 samples representing eight species, sub-sampled from an original 29,531 SNPs for 177 samples to decrease the amount of missing data and computation time.…”

Section: Snp Data Setsmentioning

confidence: 99%

“…In other analyses, trees for simulated data were rooted on the known outgroup, and the phylogeny of Australian Pelargonium was, where possible, outgroup-rooted on P. havlasae Domin and P. littorale Hügel following the results of Nicotra et al (2016). The Craspedia dataset lacks an outgroup because no high quality sample of C. haplorrhiza was available, and consequently we focused on comparing the topologies of unrooted trees.…”

Section: Rootingmentioning

confidence: 99%

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Species trees from consensus single nucleotide polymorphism (SNP) data: Testing phylogenetic approaches with simulated and empirical data

Schmidt‐Lebuhn

Aitken

Chuah

2017

Molecular Phylogenetics and Evolution

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Datasets of hundreds or thousands of SNPs (Single Nucleotide Polymorphisms) from multiple individuals per species are increasingly used to study population structure, species delimitation and shallow phylogenetics. The principal software tool to infer species or population trees from SNP data is currently the BEAST template SNAPP which uses a Bayesian coalescent analysis. However, it is computationally extremely demanding and tolerates only small amounts of missing data. We used simulated and empirical SNPs from plants (Australian Craspedia, Asteraceae, and Pelargonium, Geraniaceae) to compare species trees produced (1) by SNAPP, (2) using SVD quartets, and (3) using Bayesian and parsimony analysis with several different approaches to summarising data from multiple samples into one set of traits per species. Our aims were to explore the impact of tree topology and missing data on the results, and to test which data summarising and analyses approaches would best approximate the results obtained from SNAPP for empirical data. SVD quartets retrieved the correct topology from simulated data, as did SNAPP except in the case of a very unbalanced phylogeny. Both methods failed to retrieve the correct topology when large amounts of data were missing. Bayesian analysis of species level summary data scoring the two alleles of each SNP as independent characters and parsimony analysis of data scoring each SNP as one character produced trees with branch length distributions closest to the true trees on which SNPs were simulated. For empirical data, Bayesian inference and Dollo parsimony analysis of data scored allele-wise produced phylogenies most congruent with the results of SNAPP. In the case of study groups divergent enough for missing data to be phylogenetically informative (because of additional mutations preventing amplification of genomic fragments or bioinformatic establishment of homology), scoring of SNP data as a presence/absence matrix irrespective of allele content might be an additional option. As this depends on sampling across species being reasonably even and a random distribution of non-informative instances of missing data, however, further exploration of this approach is needed. Properly chosen data summary approaches to inferring species trees from SNP data may represent a potential alternative to currently available individual-level coalescent analyses especially for quick data exploration and when dealing with computationally demanding or patchy datasets.

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Analysis of phylogenetic relationships and genome size evolution of the Amaranthus genus using GBS indicates the ancestors of an ancient crop

Stetter

Schmid

2017

Molecular Phylogenetics and Evolution

108

104

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The genus Amaranthus consists of 50-70 species and harbors several cultivated and weedy species of great economic importance. A small number of suitable traits, phenotypic plasticity, gene flow and hybridization made it difficult to establish the taxonomy and phylogeny of the whole genus despite various studies using molecular markers. We inferred the phylogeny of the Amaranthus genus using genotyping by sequencing (GBS) of 94 genebank accessions representing 35 Amaranthus species and measured their genome sizes. SNPs were called by de novo and reference-based methods, for which we used the distant sugarbeet Beta vulgaris and the closely related Amaranthus hypochondriacus as references. SNP counts and proportions of missing data differed between methods, but the resulting phylogenetic trees were highly similar. A distance-based neighbor joining tree of individual accessions and a species tree calculated with the multispecies coalescent supported a previous taxonomic classification into three subgenera although the subgenus A. Acnida consists of two highly differentiated clades. The analysis of the Hybridus complex within the A. Amaranthus subgenus revealed insights on the history of cultivated grain amaranths. The complex includes the three cultivated grain amaranths and their wild relatives and was well separated from other species in the subgenus. Wild and cultivated amaranth accessions did not differentiate according to the species assignment but clustered by their geographic origin from South and Central America. Different geographically separated populations of Amaranthus hybridus appear to be the common ancestors of the three cultivated grain species and A. quitensis might be additionally be involved in the evolution of South American grain amaranth (A. caudatus). We also measured genome sizes of the species and observed little variation with the exception of two lineages that showed evidence for a recent polyploidization. With the exception of two lineages, genome sizes are quite similar and indicate that polyploidization did not play a major role in the history of the genus.

show abstract

Population and phylogenomic decomposition via genotyping‐by‐sequencing in Australian Pelargonium

Cited by 28 publications

References 79 publications

Analysis of phylogenetic relationships and genome size evolution of theAmaranthusgenus using GBS indicates the ancestors of an ancient crop

Analysis of phylogenetic relationships and genome size evolution of theAmaranthusgenus using GBS indicates the ancestors of an ancient crop

Species trees from consensus single nucleotide polymorphism (SNP) data: Testing phylogenetic approaches with simulated and empirical data

Analysis of phylogenetic relationships and genome size evolution of the Amaranthus genus using GBS indicates the ancestors of an ancient crop

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