William Russell Anderson (1942–2013)

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/147021/1/tax63114.pd

Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: A case study in Carex sect. Racemosae

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141466/1/ajb20337-sup-0001.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/141466/2/ajb20337.pd

Burton V. Barnes as a forest botanist

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/120432/1/Dick2016_Barnes_Tribute.pdfDescription of Dick2016_Barnes_Tribute.pdf : Main articl

Polyploidy, infraspecific cytotype variation, and speciation in Goldenrods: The cytogeography of Solidago subsect. Humiles (Asteraceae) in North America

Polyploidy is an important evolutionary mechanism in plants, and in some genera (e.g., Solidago in Asteraceae) it is particularly widespread and is hypothesized to have played a major role in diversification. Goldenrods are notorious for their ploidy variation, with roughly 14% and 32% of recognized North American species being polyploid or including multiple cytotypes, respectively. We used traditional chromosome counts and flow cytometry to examine cytogeographic patterns, biogeographic and evolutionary hypotheses, and species boundaries in S. subsect. Humiles. Chromosome numbers and DNA ploidy determinations are reported for 337 individuals, including 148 new reports. Cytotypes show significant geographic structuring. Solidago simplex and S. spathulata were uniformly diploid (2n = 18) in western North America, while cytogeographic patterns in eastern North America were regionally complex and included 2n, 4n, and 6n cytotypes. Cytotypes within S. simplex were ecogeographically segregated and mixed‐ploidy populations were rare. Data from this study and additional biosystematic data indicate that cytotypes in S. simplex fulfill the requirements of multiple species concepts and should best be treated as distinct species. Polyploid cytotypes possibly formed recurrently, however, and evolution and species boundaries within poly ploid S. simplex will require additional study. Results from this study and accumulated data from other studies suggest that biological species diversity in Solidago is considerably higher than currently recognized taxonomically.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/147108/1/tax611014-sup-001-PDF.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/147108/2/tax611014.pd

Three newly described species of carex sect. fecundae (cyperaceae) from Central America and typification of two related names

Three new species of Carex sect. Fecundae (Cyperaceae) are described from Central America. Carex orothanatica from Costa Rica, Carex siguanabae occurring in El Salvador and Honduras, and Carex via-aquae from Costa Rica and Panama. The three new species are compared with relatives. In addition, two related names, Carex lehmanniana Boott, and C. lehmaniana var. simplex Kük., are lectotypifie

Chromosome Number Changes Associated with Speciation in Sedges: a Phylogenetic Study in Carex section Ovales (Cyperaceae) Using AFLP Data

Phylogenetic analysis of amplified fragment length polymorphisms (AFLP) was used to infer patterns of morphologic and chromosomal evolution in an eastern North American group of sedges (ENA clade I of Carex sect. Ovales). Distance analyses of AFLP data recover a tree that is topologically congruent with previous phylogenetic estimates based on nuclear ribosomal DNA (nrDNA) sequences and provide support for four species groups within ENA clade I. A maximum likelihood method designed for analysis of restriction site data is used to evaluate the strength of support for alternative topologies. While there is little support for the precise placement of the root, the likelihood of topologies in which any of the four clades identified within the ENA clade I is forced to be paraphyletic is much lower than the likelihood of the optimal tree. Chromosome counts for a sampling of species from throughout sect. Ovales are mapped onto the tree, as well as counts for all species in ENA clade I. Parsimony reconstruction of ancestral character states suggest that: (1) Heilborn’s hypothesis that more highly derived species in Carex have higher chromosome counts does not apply within sect. Ovales, (2) the migration to eastern North America involved a decrease in average chromosome count within sect. Ovales, and (3) intermediate chromosome counts are ancestral within ENA clade I. A more precise understanding of chromosomal evolution in Carex should be possible using likelihood analyses that take into account the intraspecific polymorphism and wide range of chromosome counts that characterize the genus

Slender False Brome (Brachypodium sylvaticum, Poaceae), an Invasive Grass New to Ontario, Canada

Brachypodium sylvaticum, Slender False Brome, an invasive Eurasian grass, is reported for the first time in Ontario and eastern Canada from Grey County, southern Ontario. The only previous Canadian record is from Vancouver Island, British Columbia. The species is widespread in the U.S. Pacific Northwest, where it is spreading aggressively throughout much of western Oregon. In the eastern U.S.A., known populations are few and localized, although the species will likely spread

Allozyme variation and genetic relationships among species in the Carex willdenowii complex (Cyperaceae)

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142149/1/ajb20546.pd

Incentivising Use of Structured Language in Biological Descriptions: Author-Driven Phenotype Data and Ontology Production

Phenotypes are used for a multitude of purposes such as defining species, reconstructing phylogenies, diagnosing diseases or improving crop and animal productivity, but most of this phenotypic data is published in free-text narratives that are not computable. This means that the complex relationship between the genome, the environment and phenotypes is largely inaccessible to analysis and important questions related to the evolution of organisms, their diseases or their response to climate change cannot be fully addressed. It takes great effort to manually convert free-text narratives to a computable format before they can be used in large-scale analyses. We argue that this manual curation approach is not a sustainable solution to produce computable phenotypic data for three reasons: 1) it does not scale to all of biodiversity; 2) it does not stop the publication of free-text phenotypes that will continue to need manual curation in the future and, most importantly, 3) It does not solve the problem of inter-curator variation (curators interpret/convert a phenotype differently from each other). Our empirical studies have shown that inter-curator variation is as high as 40% even within a single project. With this level of variation, it is difficult to imagine that data integrated from multiple curation projects can be of high quality. The key causes of this variation have been identified as semantic vagueness in original phenotype descriptions and difficulties in using standardised vocabularies (ontologies). We argue that the authors describing phenotypes are the key to the solution. Given the right tools and appropriate attribution, the authors should be in charge of developing a project’s semantics and ontology. This will speed up ontology development and improve the semantic clarity of phenotype descriptions from the moment of publication. A proof of concept project on this idea was funded by NSF ABI in July 2017. We seek readers input or critique of the proposed approaches to help achieve community-based computable phenotype data production in the near future. Results from this project will be accessible through https://biosemantics.github.io/author-driven-production

Incentivising Use of Structured Language in Biological Descriptions: Author-Driven Phenotype Data and Ontology Production

Phenotypes are used for a multitude of purposes such as defining species, reconstructing phylogenies, diagnosing diseases or improving crop and animal productivity, but most of this phenotypic data is published in free-text narratives that are not computable. This means that the complex relationship between the genome, the environment and phenotypes is largely inaccessible to analysis and important questions related to the evolution of organisms, their diseases or their response to climate change cannot be fully addressed. It takes great effort to manually convert free-text narratives to a computable format before they can be used in large-scale analyses. We argue that this manual curation approach is not a sustainable solution to produce computable phenotypic data for three reasons: 1) it does not scale to all of biodiversity; 2) it does not stop the publication of free-text phenotypes that will continue to need manual curation in the future and, most importantly, 3) It does not solve the problem of inter-curator variation (curators interpret/convert a phenotype differently from each other). Our empirical studies have shown that inter-curator variation is as high as 40% even within a single project. With this level of variation, it is difficult to imagine that data integrated from multiple curation projects can be of high quality. The key causes of this variation have been identified as semantic vagueness in original phenotype descriptions and difficulties in using standardised vocabularies (ontologies). We argue that the authors describing phenotypes are the key to the solution. Given the right tools and appropriate attribution, the authors should be in charge of developing a project’s semantics and ontology. This will speed up ontology development and improve the semantic clarity of phenotype descriptions from the moment of publication. A proof of concept project on this idea was funded by NSF ABI in July 2017. We seek readers input or critique of the proposed approaches to help achieve community-based computable phenotype data production in the near future. Results from this project will be accessible through https://biosemantics.github.io/author-driven-production