An Overview to the Index to Chromosome Numbers in Asteraceae Database: Revisiting Base Chromosome Numbers, Polyploidy, Descending Dysploidy, and Hybridization.

A brief overview to the Index to Chromosome Numbers in Asteraceae database is provided. The database contains karyological information on Asteraceae and has been repeatedly improved and updated and is now hosted at the National Bioscience Database center. Also, we take the opportunity to revisit the evolution of base chromosome numbers in Asteraceae, emphasizing the phenomena of polyploidy, descending dysploidy, and hybridization, common in the family. Chromosome numbers for species included in one of the most recent phylogenetic treatments of the Asteraceae were obtained from the Index to Chromosome Numbers in Asteraceae database were mapped on to the modified phylogeny diagram, and base chromosome numbers were determined for each branch of the phylogeny. Results for tribal base numbers were the same as those hypothesized in our previous work with additional base numbers added for tribes not previously recognized but supported by newer phylogenetic methods. The Asteraceae show an ancestral base chromosome number of x = 9 and originated in the Antarctica (Gondowanaland) in Cretaceous (80 Mys ago). The x = 9 number has been retained through successive South American lineages of the Barnadesieeae, Gochnatieae, Stiffieae, Wunderlichieae, Astereae, and Senecioneae following northward migration. Northward migration to Africa was accompanied with x = 10 becoming the dominant base chromosome number as the family evolved multiple additional tribes. Northward migration to Australasia with x = 9 was in Astereae and the families Goodeneaseae, Menyanthaceae, and Stylydiaceae. The evolution of the North American Heliantheae alliance began with the appearance of x2 = 19 which persisted in multiple additional new tribes. Frequent dysploidy decreases, polyploidy and hybridization occurred throughout the history of the family.

Goldenrod herbariomics: Hybrid-sequence capture reveals the phylogeny of Solidago.

PREMISE: The phylogenetic relationships among the ca. 138 species of goldenrods (Solidago; Asteraceae) have been difficult to infer due to species richness, and shallow interspecific genetic divergences. This study aims to overcome these obstacles by combining extensive sampling of goldenrod herbarium specimens with the use of a custom Solidago hybrid-sequence capture probe set. METHODS: A set of tissues from herbarium samples comprising ca. 90% of Solidago species was assembled and DNA was extracted. A custom hybrid-sequence capture probe set was designed, and data from 854 nuclear regions were obtained and analyzed from 209 specimens. Maximum likelihood and coalescent approaches were used to estimate the genus phylogeny for 157 diploid samples. RESULTS: Although DNAs from older specimens were both more fragmented and produced fewer sequencing reads, there was no relationship between specimen age and our ability to obtain sufficient data at the target loci. The Solidago phylogeny was generally well-supported, with 88/155 (57%) nodes receiving ≥95% bootstrap support. Solidago was supported as monophyletic, with Chrysoma pauciflosculosa identified as sister. A clade comprising Solidago ericameriodes, Solidago odora, and Solidago chapmanii was identified as the earliest diverging Solidago lineage. The previously segregated genera Brintonia and Oligoneuron were identified as placed well within Solidago. These and other phylogenetic results were used to establish four subgenera and fifteen sections within the genus. CONCLUSIONS: The combination of expansive herbarium sampling and hybrid-sequence capture data allowed us to quickly and rigorously establish the evolutionary relationships within this difficult, species-rich group.

Two cytotype niche shifts are of different magnitude in Solidago gigantea.

PREMISE: Polyploidy may serve to contribute to range size if autopolyploid cytotypes are adapted to differing ecological conditions. This study aims to establish the geographic distribution of cytotypes within the giant goldenrod (Solidago gigantea), and to assess whether cytotypes exhibit differing ecological tolerances and morphology. METHODS: A range-wide set of 629 Solidago gigantea individuals was obtained through field collecting, sampling from herbarium specimens, and incorporating existing chromosome counts. Cytotype of each unknown sample was estimated by observing allele numbers at twelve microsatellite loci, a strategy that was assessed by comparing estimated to known cytotype in 20 chromosome-counted samples. Abiotic ecological differentiation was assessed for two transitions: diploid-tetraploid and tetraploid-hexaploid. Morphological differentiation among cytotypes was assessed. RESULTS: Microsatellite repeat variation accurately estimated cytotype in 85% of samples for which ploidy was known. Applying this approach to samples of unknown ploidy established that the three cytotypes are non-randomly distributed. Although niche modeling and MANOVA approaches identified significant differences in macro-climatic conditions for both cytotype transitions, the tetraploid to hexaploid transition was more substantial. Leaf length and width did not differ among cytotypes. Although leaf vestiture exhibited strong trends, no absolute differences were observed among cytotypes. CONCLUSIONS: With the largest such study to date, we established niche transitions among giant goldenrod cytotypes of differing magnitudes. Collectively, this suggests that whole-genome duplication has contributed to Solidago gigantea's large range.

Next-generation sampling: Pairing genomics with herbarium specimens provides species-level signal in Solidago (Asteraceae).

PREMISE OF THE STUDY: The ability to conduct species delimitation and phylogeny reconstruction with genomic data sets obtained exclusively from herbarium specimens would rapidly enhance our knowledge of large, taxonomically contentious plant genera. In this study, the utility of genotyping by sequencing is assessed in the notoriously difficult genus Solidago (Asteraceae) by attempting to obtain an informative single-nucleotide polymorphism data set from a set of specimens collected between 1970 and 2010. METHODS: Reduced representation libraries were prepared and Illumina-sequenced from 95 Solidago herbarium specimen DNAs, and resulting reads were processed with the nonreference Universal Network-Enabled Analysis Kit (UNEAK) pipeline. Multidimensional clustering was used to assess the correspondence between genetic groups and morphologically defined species. RESULTS: Library construction and sequencing were successful in 93 of 95 samples. The UNEAK pipeline identified 8470 single-nucleotide polymorphisms, and a filtered data set was analyzed for each of three Solidago subsections. Although results varied, clustering identified genomic groups that often corresponded to currently recognized species or groups of closely related species. DISCUSSION: These results suggest that genotyping by sequencing is broadly applicable to DNAs obtained from herbarium specimens. The data obtained and their biological signal suggest that pairing genomics with large-scale herbarium sampling is a promising strategy in species-rich plant groups.

Genus-wide microsatellite primers for the goldenrods (Solidago; Asteraceae).

PREMISE OF THE STUDY: Microsatellite primers were developed for studies of polyploid evolution, ecological genetics, conservation genetics, and species delimitation in the genus Solidago. • METHODS AND RESULTS: Illumina sequencing of a shotgun library from S. gigantea identified ca. 1900 putative single-copy loci. Fourteen loci were subsequently shown to be amplifiable, single-copy, and variable in a broad range of Solidago species. • CONCLUSIONS: The utility of these markers both across the genus and in herbarium specimens of a wide age range will facilitate numerous inter- and intraspecific studies in the ca. 120 Solidago species.