Dissertations, Theses, and Capstone Projects

Date of Degree

2-2025

Document Type

Dissertation

Degree Name

Ph.D.

Program

Biology

Advisor

Damon Little

Committee Members

Robert Naczi

Ana Carnaval

Christopher Blair

Alejandra Gandolfo

Subject Categories

Biodiversity | Biology | Botany | Ecology and Evolutionary Biology | Genomics | Plant Sciences

Keywords

new york city, botany, larch, urban botany, phylogenetics, historical ecology

Abstract

Part 1: the Spontaneous Flora of New York City

New York City is often celebrated for its cultural diversity, but its rich biodiversity is frequently overlooked. The city hosts hundreds of plant species across a variety of habitats, from urban cracks to saltwater marshes and old-growth forests. This diversity provides countless ecosystem services, but is threatened by the effects of urbanization, particularly habitat transformation and fragmentation, urban environmental conditions, and human preference.

Over two centuries, many devoted individuals have contributed to the documentation, study, and conservation of the flora of NYC. In Chapter 1, A History of Botany in New York City, I outline the history of the study of the flora of New York City from prehistory to current day. It examines how social, political, and scientific trends have influenced the study of the city's flora, and identifies key conditions for the continued engagement with and stewardship of the plants of the city, including collaboration between field and academic botanists, engagement of amateur and avocational botanists in data collection, and an emphasis on the inspiration and cultivation of the next generation of local botanists.

This long-term endeavor to document the city's flora has resulted in a large but fragmented body of literature. In Chapter 2, Index to New York City Botanical Literature, I present a collection of 359 works published on the vascular and non-vascular flora of New York City between 1811 and 2023, and explore spatial, temporal, and thematic patterns among them. The results of these analyses highlight the pivotal role of individual authors and organizations in the documentation and understanding of New York City's flora, identify emerging fields of research, and highlight opportunities for future researchers to close gaps in knowledge.

In Chapter 3, Taxonomic and Functional Diversity of New York City's Contemporary and Historical Flora, I make my own contribution to this endeavor. Based on historical and contemporary resources, I compiled a list of plants that occur or have occurred within the city, along with values for 10 functional traits previously shown to react to effects of urbanization. These data were used to explore changes in taxonomic and functional diversity over time, and further to identify traits potentially associated with persistence and loss of native and introduced taxa in an increasingly urban environment.

Part 2: Systematics of Larix Mill. (Pinaceae)

The genus Larix Mill. (larch), known for its striking golden foliage in fall, includes 10-20 species of deciduous conifers found across North America, Europe, and Asia. Larches are key components of the circumboreal forest and are successful pioneer species that thrive at treeline and in other inhospitable locations. They provide numerous ecosystem services but face a number of anthropogenic threats like deforestation and shifting climate.

Despite its ecological and economic importance, the systematics of Larix remain unresolved. Early morphological classifications focused on seed cone traits, but molecular studies have identified three clades based on geography and revealed inconsistent genetic signals across nuclear, plastid, and mitochondrial markers. Recent advancements in DNA sequencing offer a new opportunity to clarify the phylogenetic relationships between larch species.

In Chapter 4, I use target capture sequencing to reconstruct the phylogeny of the genus using 2,073 nuclear loci and partial plastid genomes. A custom bait set was designed due to limited genetic resources, supplemented by the popular GoFlag451 bait set. Phylogenetic analysis revealed three geographic clades: a Tibetan Plateau clade sister to the North American and Eurasian clades. Relationships within the North American and Tibetan Plateau clades was strongly supported, but relationships between Eurasian taxa remain unresolved, due to poor sampling and potential incidence of hybridization. A notable incongruency between the nuclear and plastid trees included the placement of L. decidua (European larch), nested within the Eurasian clade in the nuclear tree, but sister to the North American clade in the plastid phylogeny.

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