Biodiversity Commons^™

A Framework For Near-Real Time Monitoring Of Diversity Patterns Based On Indirect Remote Sensing, With An Application In The Brazilian Atlantic Rainforest, Andrea Paz, Thiago S. Silva, Ana C. Carnaval

Publications and Research

Monitoring biodiversity change is key to effective conservation policy. While it is difficult to establish in situ biodiversity monitoring programs at broad geographical scales, remote sensing advances allow for near-real time Earth observations that may help with this goal. We combine periodical and freely available remote sensing information describing temperature and precipitation with curated biological information from several groups of animals and plants in the Brazilian Atlantic rainforest to design an indirect remote sensing framework that monitors potential loss and gain of biodiversity in near-real time. Using data from biological collections and information from repeated field inventories, we demonstrate that …

Population Structure Of The Lizard Ecpleopus Gaudichaudii Coincides With A Biogeographic Barrier - The Doce River, Alexander J. Garretson

Dissertations and Theses

Intraspecific genetic variation is an integral component of diversification and the accumulation of biodiversity. The degree to which isolated populations of the same species are genetically structured in geographical space is impacted by a variety of mechanisms. In this study, I document patterns and discuss possible drivers of genetic structure within Ecpleopus gaudichaudii, a lizard species endemic to the Atlantic Forest of Brazil. For that, I assembled ddRadseq sequences from 48 individuals across much of the range of the E. gaudichaudii and analyzed its population structure. I created an intraspecific phylogeny for this group utilizing RAxML and conducted a …

Phylogenomics Of Alligator Lizards Elucidate Diversification Patterns Across The Mexican Transition Zone And Support The Recognition Of A New Genus, Christopher Blair, Robert W. Bryson Jr, Uri O. García-Vázquez, Adrián Nieto-Montes De Oca, David Lazcano, John E. Mccormack, John Klicka

Publications and Research

Genomic data continue to advance our understanding of species limits and biogeographic patterns. However, there is still no consensus regarding appropriate methods of phylogenomic analysis that make the best use of these heterogeneous data sets. In this study, we used thousands of ultraconserved element (UCE) loci from alligator lizards in the genus Gerrhonotus to compare and contrast species trees inferred using multiple contemporary methods and provide a time frame for biological diversification across the Mexican Transition Zone (MTZ). Concatenated maximum likelihood (ML) and Bayesian analyses provided highly congruent results, with differences limited to poorly supported nodes. Similar topologies were inferred …

Vertebrate Scavenger Diversity And Ecosystem Services Along An Elevational Gradient In Central Nepal, Aishwarya Bhattacharjee

Dissertations, Theses, and Capstone Projects

A growing number of studies recognize the ecological significance of vertebrate scavengers, and several species belonging to this diverse, functional guild are of high conservation importance around the globe. Studies on taxonomic and functional components of biodiversity often use elevation gradients to comprehensively examine patterns and drivers across multiple spatial scales. Yet, there are relatively few elevational studies on large vertebrates or multi-taxa guilds, and the related variation of their ecosystem services. In particular, scavenger research has largely focused on local-scale studies or regional/global comparisons of local-scale investigations. Moreover, these studies primarily consider taxonomic community characteristics and the patterns of …

Dna Barcoding Of The High-Altitude Artemisia And Nepeta Species, Vyacheslav Dushenkov, Csanad Gurdon, Shukhratdzhon Satorov

Publications and Research

DNA barcoding was performed for four medicinal plant species from the mountain region of Tajikistan. The nucleotide sequences for Artemisia sieberi, Artemisia scoparia, Artemisia vulgaris, and Nepeta glutinosa were deposited into the GenBank at the National Center for Biotechnology Information.

Genomic And Ecological Dimensions Of Malagasy Reptile And Amphibian Biodiversity, Arianna L. Kuhn

Dissertations, Theses, and Capstone Projects

A long history of isolation coupled with complex topographic and ecological landscapes makes Madagascar ideal for exploring the historical factors that have shaped patterns of population diversity and endemism. Many species-level studies have suggested Late Quaternary climate change may have influenced population dynamics in the tropics, but Madagascar’s ecologically unique biomes or individual species properties may have driven idiosyncratic responses to these shifts. Using community-scale population genetic data I implement a hierarchical approximate Bayesian computation (hABC) approach to evaluate the degree of synchronous population expansion during glacial cycles across herpetofaunal assemblages both within and across discrete biomes and taxonomic groups. …

Understanding And Predicting The Distribution Of Biodiversity In The Atlantic Forest, Andrea Paz Velez

Dissertations, Theses, and Capstone Projects

Understanding how biodiversity is distributed in geography is essential for conservation. This requires an understanding of the multiple dimensions of biodiversity: species, their ecological functions, and their evolutionary history. For my Ph.D. dissertation, I devised a study to explore the environmental drivers of biodiversity patterns in Neotropical species. I first investigated broad macroecological patterns in the Brazilian Atlantic Forest, combining occurrence data and phylogenetic information from multiple clades of animals and plants (Chapter 1). I discovered that one can accurately predict the accumulation of species richness and phylogenetic diversity based on current climatic descriptors – particularly precipitation – but not …

The Paradox Of Retained Genetic Diversity Of Hippocampus Guttulatus In The Face Of Demographic Decline, Rupert Stacy, Jorge Palma, Miguel Correia, Anthony B. Wilson, José Pedro Andrade, Rita Castilho

Publications and Research

Genetic diversity is the raw foundation for evolutionary potential. When genetic diversity is significantly reduced, the risk of extinction is heightened considerably. The long-snouted seahorse (Hippocampus guttulatus) is one of two seahorse species occurring in the North-East Atlantic. The population living in the Ria Formosa (South Portugal) declined dramatically between 2001 and 2008, prompting fears of greatly reduced genetic diversity and reduced effective population size, hallmarks of a genetic bottleneck. This study tests these hypotheses using samples from eight microsatellite loci taken from 2001 and 2013, on either side of the 2008 decline. The data suggest that the population has …

Intangible Cultural Heritage: A Benefit To Climate-Displaced And Host Communities, Gül Aktürk, Martha B. Lerski

Publications and Research

Climate change is borderless, and its impacts are not shared equally by all communities. It causes an imbalance between people by creating a more desirable living environment for some societies while erasing settlements and shelters of some others. Due to floods, sea level rise, destructive storms, drought, and slow-onset factors such as salinization of water and soil, people lose their lands, homes, and natural resources. Catastrophic events force people to move voluntarily or involuntarily. The relocation of communities is a debatable climate adaptation measure which requires utmost care with human rights, ethics, and psychological well-being of individuals upon the issues …

Species In Vernal Pools: Anova, Lisa Manne

Open Educational Resources

A one-way analysis of variance exercise using data on species diversities from vernal pools.Data are from vernal pools in Willowbrook Park (adjacent to College of Staten Island's campus) in spring.

The typical ANOVA gives a straightforward result (significant anova, easily-interpreted Tukey-Kramer analysis). This data set requires more nuanced interpretation, as the ANOVA is marginally significant, and Tukey-Kramer yields one significant pairwise comparison between groups. Relative lack of variation within groups explains this apparent enigma.

Earth Law And The Rights Of Nature A New Generation Of Laws Built For Nature, Lindsey Kayman, Paul Bartlett, Milena Popov, Grant Wilson

Open Educational Resources

Earth Law and the Rights of Nature: A New Generation of Laws Built for Nature

Wilson, Grant, Kayman, Lindsey, Bartlett, Paul, and Milena Popov John Jay College of Criminal Justice, Earth Law Center, Environmental Education Fund

Forget doom and gloom. Let’s educate students about the Rights of Nature, an inspiring, evolving legal development which is gaining traction in the US and around the world, and which can promote the cultural shift needed to address our overlapping intersecting environmental crises — climate change, accelerating species extinction, and ecosystem collapse. The Rights of Nature is one aspect of Earth Law. Some of …

The Insular Herpetofauna Of Mexico: Composition, Conservation, And Biogeographic Patterns, Juan Valentín Pliego‐Sánchez, Christopher Blair, Aníbal H. Díaz De La Vega‐Pérez, Víctor H. Jiménez‐Arcos

Publications and Research

We compile a Mexican insular herpetofaunal checklist to estimate endemism, conservation status, island threats, net taxonomic turnover among six biogeographic provinces belonging to the Nearctic and Neotropical regions, and the relationships between island area and mainland distance versus species richness. We compile a checklist of insular herpetofaunal through performing a literature and collection review. We define the conservation status according to conservation Mexican law, the Red List of International Union for Conservation of Nature, and Environmental Vulnerability Scores. We determine threat percentages on islands according to the 11 major classes of threats to biodiversity. We estimate the net taxonomic turnover …

Not Withering On The Evolutionary Vine: Systematic Revision Of The Brown Vine Snake (Reptilia: Squamata: Oxybelis) From Its Northern Distribution, Robert C. Jadin, Christopher Blair, Sarah A. Orlofske, Michael J. Jowers, Gilson A. Rivas, Laurie J. Vitt, Julie M. Ray, Eric N. Smith, John C. Murphy

Publications and Research

The genus Oxybelis currently is composed of four taxa despite numerous studies suggesting and describing multiple taxa within the O. aeneus complex. Here, we utilize a multilocus molecular dataset (i.e. cyt b, ND4, 12S, 16S, cmos, PRLR, 3663 bp) to conduct phylogenetic analyses to assess the evolutionary history of Oxybelis. Our molecular analyses find three major lineages of Oxybelis (i.e. O. aeneus complex, O. brevirostris, O. fulgidus complex) with a sister relationship between O. brevirostris and the O. aeneus complex to the exclusion of the O. fulgidus complex. More specifically, O. aeneus appears to harbor at least …

Assessment Of Wild Ring-Tailed Lemur (Lemur Catta) Populations In Southwestern Madagascar With Implications For The Illegal Pet Trade, Samantha D. Calkins

Theses and Dissertations

Accurate population estimates are critical to inform conservation management of species. Incomplete sampling can lead to population underestimates and lacking conservation efforts. Population surveys are important for assessing human and animal welfare to allow for targeted conservation action. Recent ring-tailed lemur (Lemur catta) surveys have led researchers to conclude that L. catta populations are crashing. This has generated much attention and alarm, but may also be based on incomplete information. To better understand population dynamics, more thorough sampling is needed. Here, we survey five such sites to reassess the presence and abundance of L. catta in these locations. …

16s Rrna Amplicon Sequencing Of Urban Prokaryotic Communities In The South Bronx River Estuary, Eugenia Naro-Maciel, Melissa R. Ingala, Irena E. Werner, Allison M. Fitzgerald

Publications and Research

Biodiversity monitoring is an essential component of restoration efforts. We sequenced 16S rRNA gene amplicons from sediments and waters of Hunts Point Riverside Park and Soundview Park, located in a historically degraded but recovering urban estuary in New York. In total, 16,165 unique amplicon sequence variants were recovered, and Proteobacteria was the dominant phylum.

On The Distribution Of Genetic Variation In Ecological Communities, Isaac Overcast

Dissertations, Theses, and Capstone Projects

Biodiversity in ecological communities is structured hierarchically across spatial and temporal scales. Many open questions remain as to how this structure accumulates. For example, what are the relative contributions of dispersal versus in situ speciation? Or, how important are stochastic drift versus deterministic processes? Up to this point, these questions have been investigated by isolated disciplines (e.g. macroecology, comparative phylogeography, macroevolution) using tools and data that tend to focus on only one axis of community scale data (e.g. phylogenies, relative abundances, and/or trait information). Yet we know that there are feedbacks among processes that respond on short, medium, and long …

More Than Meets The Eye: A Taxonomic Revision Of The Nearctic Species In The Eye-Gnat Genus Amiota Loew (Diptera: Drosophilidae), Lance E. Jones

Dissertations and Theses

Thorough biotic inventories are still needed even in families as seemingly well-studied as fruit flies (Diptera: Drosophilidae). Drosophilidae have had an outsize effect on the history of biology because of their pivotal role in the study of genetics, development, and evolution. Even with more than a century of intensive study, large gaps remain in our understanding of diversity in this fly family, including well-studied areas such as North America. This thesis presents a taxonomic revision of the Nearctic species of the genus Amiota Loew. Twenty-three species are identified as being new to science for publication at a later date. This …

Systematics Of Carex Section Laxiflorae (Cyperaceae), Jenna Dorey

Dissertations, Theses, and Capstone Projects

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 …

Cultural Heritage Preservation In The Context Of Climate Change Adaptation Or Relocation: Barbuda As A Case Study, Martha B. Lerski

Dissertations, Theses, and Capstone Projects

This case study introduces an arts camp methodology of engaging communities in identifying their key cultural heritage features, thus serving as a meta study. It presents original research based on field studies on the climate-vulnerable Caribbean island of Barbuda during 2017 and 2018. Its Valued Cultural Elements survey, enabling precise identification of key tangible and intangible art forms and biocultural practices, may serve as a basis for further studies. Such approaches may facilitate future research or planning as climate-vulnerable communities harness Local or Indigenous Knowledge for purposes of biocultural heritage preservation, or towards adaptation or relocation. I report on findings …

Zero Textbook Cost Syllabus For Env 3009/4900 (Conservation Biology And Sustainable Development), Stephen Gosnell

Open Educational Resources

Conservation biology is an interdisciplinary topic that explores how we can protect and maintain natural areas. Due to the resources we take and impacts we have on natural environments, this field is directly related to restoration ecology (restoring natural areas) and sustainable development/natural resource management. We will explore the basis for these related fields from an ecological, social, legal, and cultural perspective, as all conservation and management projects take place in the larger human landscape. We will consider how we measure biodiversity, why it matters, why is it is threatened, and how we can manage (protect, restore, maintain, use) it …

Distribution And Population Structure Of The Invasive Nitellopsis Obtusa (Desv. In Loisel.) J. Groves And Native Species Of Characeae In The Northeast U.S.A., Robin Sleith

Dissertations, Theses, and Capstone Projects

Freshwater ecosystems are some of the most biologically diverse environments on Earth. Billions of humans rely on functioning freshwater ecosystems for drinking water and many other services. These ecosystems are increasingly threatened by human impacts including nutrient pollution, invasive species, and climate change. Here I contribute four research chapters that investigate freshwater diversity and ecosystem threats using the Characeae, a family of freshwater green macroalgae, as a study system. Characeae are a diverse and ancient group with more than 500 extant species and a fossil history spanning at least 250 million years. These algae are macrophytes in freshwater ecosystems, and …

Standards For Distribution Models In Biodiversity Assessments, Miguel B. Araújo, Robert P. Anderson, A. Márcia Barbosa, Colin M. Beale, Carsten F. Dormann, Regan Early, Raquel A. Garcia, Antoine Guisan, Luigi Maiorano, Babak Naimi, Robert B. O'Hara, Niklaus E. Zimmermann, Carsten Rahbek

Publications and Research

Demand for models in biodiversity assessments is rising, but which models are adequate for the task? We propose a set of best-practice standards and detailed guidelines enabling scoring of studies based on species distribution models for use in biodiversity assessments. We reviewed and scored 400 modeling studies over the past 20 years using the proposed standards and guidelines. We detected low model adequacy overall, but with a marked tendency of improvement over time in model building and, to a lesser degree, in biological data and model evaluation. We argue that implementation of agreed-upon standards for models in biodiversity assessments would …

Cryptic Diversity In The Mexican Highlands: Thousands Of Uce Loci Help Illuminate Phylogenetic Relationships, Species Limits And Divergence Times Of Montane Rattlesnakes (Viperidae: Crotalus ), Christopher Blair, Robert W. Bryson Jr, Charles W. Linkem, David Lazcano, John Klicka, John E. Mccormack

Publications and Research

With the continued adoption of genome‐scale data in evolutionary biology comes the challenge of adequately harnessing the information to make accurate phylogenetic inferences. Coalescent‐based methods of species tree inference have become common, and concatenation has been shown in simulation to perform well, particularly when levels of incomplete lineage sorting are low. However, simulation conditions are often overly simplistic, leaving empiricists with uncertainty regarding analytical tools. We use a large ultraconserved element data set (>3,000 loci) from rattlesnakes of the Crotalus triseriatus group to delimit lineages and estimate species trees using concatenation and several coalescent‐based methods. Unpartitioned and partitioned maximum …

A Contribution Toward A Global Monograph Of Gyroporus: Taxonomy, Phylogeny, Biogeography, Naveed Davoodian

Dissertations, Theses, and Capstone Projects

Gyroporus (Sclerodermatineae, Boletales, Agaricomycetes, Basidiomycota, Fungi) is a genus of ectomycorrhizal mushroom-forming fungi distributed throughout the world in suitable habitats. Previous attempts to untangle the diversity of this genus proved difficult due to the presence of semi-cryptic species and equivocal results from phylogenetic analysis of ribosomal RNA markers. To overcome these obstacles, a combined taxonomic and phylogenetic (emphasizing protein-coding genes) approach is used here to delimit species and elucidate geographic and evolutionary patterns of Gyroporus. Careful study of relevant literature and herbarium specimens was augmented by field work in North America, Australia, and East Asia for observation and collection …

Facebook As A Social Outreach And Advocacy Tool In Intersex/Dsd Groups, Emelie J. Ali Ms

Publications and Research

My project includes a netnography of a Facebook intersex group called Families and Friends of Intersex People. I observed the group’s forms of communication within the group and which topics they discussed. It appears one of the major concerns the group has is the use of nonconsensual, sex assignment surgery on infants to “correct” their body to match a gender identity. I have also discovered a link between being intersex and affiliated with the LGBT+ community. Since the 20th century, intersex people have been stigmatized due to their assumed ability to engage in sexual, same-sex relations. I have concluded that …

Using Molecular Markers To Trace The Population History Of Volant Organisms At Differing Temporal Scales, Noah A. Burg

Dissertations, Theses, and Capstone Projects

Using molecular markers to test phylogenetic and phylogeographic hypotheses is critical for tracking the population origin of invasive, introduced species (Chapter 2, Chapter 4) and to identify the systematic relationships of disparate lineages at both shallow and deep evolutionary time scales (Chapters 3, Chapter 4). In this thesis, Sanger Sequencing was used to generate datasets based on fresh and preserved tissue from specimens collected in the field, as well as museum tissue vouchers granted from various institutions in the US and Europe. In combining these source materials, data were generated for three focal studies: 1) In the first research section …

Niche Shifts, Species Distributions, And Genetic Diversity In Gymnophthalminae Lizards, With A Focus On Microclimates And Thermophysiology, Maria Strangas

Dissertations, Theses, and Capstone Projects

The environmental niche is a central organizing concept in the study of ecology and evolution, as the environmental conditions in which species can persist (their fundamental niches) and the conditions in which they occur (their realized niches) can shape spatial and temporal patterns of biodiversity at multiple scales. How organisms at different levels of biological organization are affected by environmental heterogeneity has consequences for the distribution of genetic and phenotypic diversity, yet the mechanisms through which this occurs are poorly studied. In this dissertation, I present three research chapters that explore how species’ traits and their microclimatic environments shape biodiversity …

Militarization Of Conservation, Daniel Ryan Michel

Dissertations, Theses, and Capstone Projects

The world is facing biological diversity extinction of its wildlife solely caused by humans. One of the leading causes of the extinction crisis is attributed to poaching and the illegal trade of wildlife products. In search of finding suitable methods to curb the crisis, a dichotomy of overarching solutions has arisen: those who have advocated for community-based natural resource management and those who support militarized conservation. The focus of this paper is to delineate which method is, if any, the most appropriate when combatting poaching and the illegal wildlife trade. Concentrating on elephants (both African and Asian) and the rhinoceros, …

In Anthropocene Air: Deleuze's Encounter With Shakespeare, Steven Swarbrick

Publications and Research

No abstract provided.

Evolution Of Floral Morphology And Symmetry In The Miconieae (Melastomataceae), Maria Gavrutenko

Dissertations and Theses

Analyses of evolution of floral morphology and symmetry broaden our understanding of the drivers of angiosperm diversification. Integrated within a flower, labile floral characters produce different phenotypes that promote variable interactions with pollinators. Thus, investigation of floral evolution may help infer potential historic transitions in pollinator modes and ecological pressures that generated present diversity. This study aims to explore morphological evolution of flowers in Miconieae, a species-rich Neotropical tribe within family Melastomataceae. Despite a constrained floral plan, Melastomataceae manage to achieve a variety of floral traits appealing to diverse pollinator types, with majority of the species requiring specialized “buzz pollination” …