Date of Degree

9-2019

Document Type

Dissertation

Degree Name

Ph.D.

Program

Biology

Advisor

Robert Naczi

Committee Members

Amy Berkov

Ana Carnaval

Damon Little

Lena Struwe

Subject Categories

Biodiversity | Botany | Evolution | Integrative Biology | Molecular Biology | Plant Biology

Keywords

Phylogenetics, Conservation and Biodiversity, Taxonomy, Sedges, Morphomertics, Next generation sequencing

Abstract

Carex, with more than 2100 species, is the most species-rich genus of flowering plants in temperate regions of the world. Members of the family Cyperaceae are colloquially known as sedges, and members of the genus Carex are called “true sedges.” Carex occur on every continent except for Antarctica, they thrive in a panoply of habitats, and are ecologically important as a forage source for wildlife, carbon sequestration, prevention of soil erosion, and providing habitat for fresh water invertebrates. Despite their importance many sedges are still poorly known, such as the woodland sedges in Carex section Laxiflorae, which is comprised of about 16 species in North America. Laxiflorae are difficult to identify because there are multiple widespread species complexes in the section that display high phenotypic plasticity within species, and have overlapping measurements for diagnostic characters. Species identification is also confounded by numerous conflicting historical circumscriptions, and poor type material for some taxa. Ten of the sixteen species currently placed in sect. Laxiflorae are included on state endangered or state threatened lists. Here, I contribute five research chapters that employ varied methods in the field of systematics in order to advance knowledge of sect. Laxiflorae. The goal of this dissertation is to test and improve existing taxonomic classifications of the section through nomenclatural review, morphometrics, and molecular phylogenetics. The scope of this work includes sectionlevel analyses that test the boundaries of sect. Laxiflorae, as well as systematic studies of species complexes.

Chapter 2 is a nomenclatural review of all species-level names in Carex sect. Laxiflorae. Multiple names in the section had never been typified prior to this dissertation research. In order to confirm that the current application of names is correct and to fix the application of names that were never typified, R. F. C. Naczi and I conducted a thorough literature review and examined specimens or photographs all of the original type material. We identified 25 species-level names in Carex sect. Laxiflorae, sixteen of which were accepted names prior to the work conducted for this dissertation.We also found that six names in sect. Laxiflorae were never typified, and two names were only first-step lectotypified. In Chapter 2, we designate seven new lectotypes for C. acuminata (nom. illeg.), C. albursina, C. anceps, C. blanda, C. hendersonii, C. leptonervia, C. protracta, and C. styloflexa, and a new epitype for C. laxiflora. We provide type citations for all species-level names, including syntype and isotype citations when possible, and justification for new typifications. Note that nomenclatural actions in this dissertation do not count as effectively published.

The third chapter uses a combination of molecular sequencing methods and phylogenetic approaches to reconstruct the phylogeny of Carex sect. Laxiflorae. The analysis includes two nuclear ribosomal markers (ETS and ITS) and four plastid markers (trnL-trnF, atpB-rbcL, rps16 and rpl16), hereafter called ‘six-region’ data set, separately and as a concatenated data set using maximum likelihood, Bayesian inference, and parsimony methods. In addition, analysis of Double Digest Restriction Associated DNA Sequencing (ddRAD-seq) loci incorporates both quartet-based phylogenetic reconstruction and maximum likelihood inference of all concatenated loci as a single matrix. Phylogenies inferred from ddRAD-seq data and the six-region data set both recovered sect. Laxiflorae as paraphyletic. Phylogenetic reconstruction of the six-region data set, which included broader taxonomic sampling, recovered members of sect. Bicolores and predominantly North American species of sect. Paniceae embedded within sect. Laxiflorae. This clade was recovered as sister to a clade of predominantly Eurasian species of sect. Paniceae. Phylogenetic reconstruction of ddRAD-seq loci resolved species-level relationships with high support, whereas analyses of the six-region data set and separate analysis of the concatenated nuclear markers ETS and ITS did not. Incongruence between the ddRAD-seq phylogeny and the phylogeny inferred from the four plastid markers suggests hybrid origins for some species of Laxiflorae, a highly significant finding because hybrid speciation has only been detected in Carex a few times.

Chapter four is a systematic study of Carex striatula and C. ignota, the latter of which has been ignored or treated as a synonym of C. striatula since its description in 1849 by Chester Dewey. In this chapter, I present results of statistical analyses that support C. ignota as morphologically and taxonomically distinct from C. striatula, and designate a lectotype for C. ignota. Carex ignota is distinguished from C. striatula by its narrower leaves on vegetative shoots, more loosely-flowered pistillate spikes, staminate spike with longer peduncles, and narrower perigynia. I also present the distributions of C. ignota and C. striatula, and results of maximum likelihood phylogenetic reconstruction of ddRAD-seq loci that recover C. ignota and C. striatula as sister species. Carex ignota occurs mostly on the Coastal Plain in the southeastern United States, but inland in a few areas, and grows in sandy to loamy soils in ravines and on slopes in mesic deciduous or mixed hardwood-conifer forests. Carex striatula occurs in similar habitats, and overlaps in geographic range with C. ignota on the southern Coastal Plain as for east as Mississippi, but also occurs on the Coastal Plain in the northeastern United States and inland in the Midwest U.S. Based on strong morphologic and molecular evidence, I argue that C. ignota should be resurrected and treated as a distinct species.

The fifth chapter employs molecular phylogenetics to circumscribe taxa within the Carex blanda complex (including C. congestiflora). Goals of this work are to determine whether C. blanda and C. congestiflora are distinct species, and to search for morphologic characters to distinguish putative taxa. This study employs maximum likelihood (ML) phylogenetic inference of six markers (ETS, ITS, trnL-trnF, atpB-rbcL, rps16, and rpl16), as well as ML phylogenetic inference of ddRAD-seq loci. Both methods recover two clades of C. blanda, which are not sister taxa. Futher, the ddRAD-seq phylogeny recovered C. congestiflora embedded within one of these clades of C. blanda. Topological incongruences between the phyogenetic reconstruction of four plastid loci and ddRAD-seq loci suggest a hybrid origin for one of the clades of C. blanda. Both clades of C. blanda seem to be widely sympatric across eastern North America. Morphometric analyses uncovered some characters that may be useful for separating taxa, but expanded molecular sampling is required to confirm and refine these results. This study demonstrates the utility of ddRAD-seq for detecting cryptic taxa in Carex and identifies important future avenues of research.

SM1-ddradsample_stats.xls (28 kB)
Suppl. Material 1. Summary of nuclear and plastid ddRAD read data stats by sample

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