Partitioning Diversity across Scales
Diversity partitioning is an analytical method for decomposing gamma diversity into alpha- and beta-diversity. Gamma-diversity is typically thought of as regional species richness (all species collected within the broadest sampling extent), alpha- diversity is typically thought of as local species richness (species collected within a sample), and beta-diversity is the species not found in a given sample (diversity among samples). Samples may represent a variety of units: an array of Sherman live traps of mammals, pitfall traps of invertebrates, point-counts of birds, dip nets of aquatic invertebrates, etc.
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PARTITION was developed to conduct hypothesis testing for hierarchical analysis of the alpha and beta components of diversity. The diversity partitioning software PARTITION was first developed in 2004 by Joe Veech and Tom Crist with the help of Keith Summerville and Jon Gering. The latest release was PARTITION 3.0 in 2009. Currently, access to the software must be granted by Joe or Tom. To provide open access, improve user-interface, and broaden the applicability of the PARTITION software, I have been leading a team to convert this standalone software into an R package with an updated name (PARTITIONR).
The multi-university team is composed of myself, Michael Cunningham-Minnick, Hannah Penn, Joseph Veech, Keith Summerville, and Thomas Crist. We are happy to announce that the version 0.0.1 of PARTITIONR is available for download on our github page and we are working to upload PARTITIONR to CRAN in the near future.
The multi-university team is composed of myself, Michael Cunningham-Minnick, Hannah Penn, Joseph Veech, Keith Summerville, and Thomas Crist. We are happy to announce that the version 0.0.1 of PARTITIONR is available for download on our github page and we are working to upload PARTITIONR to CRAN in the near future.
Changes in Biodiversity through Time
Recent publications have brought the term "Insect Apocalypse" into the public realm. Insect declines have been reported from purely anecdotal evidence to multidecadal studies on insect biomass in protected areas, rainforests, and a variety of habitats. These studies highlight concerning gradual loss of insect biomass across select areas of the globe. Conversely, other studies have shown neutral and even positive trends of species richness through time.
These studies typically have shortcomings including non-continuous datasets, select ecosystem types (majority of studies are conducted in semi-natural terrestrial habitats), poor taxonomic resolution (either focus on single orders/families or use broad taxonomic groupings), poor diversity metrics, and unreliably identified drivers of insect declines. To give a clearer picture of invertebrate diversity trends, scientists must overcome these shortcomings.
In an effort to monitor how human activities are affecting water quality, the United States Geological Services (USGS) and U.S. Environmental Protection Agency (USEPA) have collaborated over numerous years to standardize the collection of abiotic and biotic samples from streams and rivers across the conterminous U.S., creating numerous data repositories. As part of an international, multi-institutional team lead by Samantha Rumschlag, I am working to quantify changes in community structure and diversity of aquatic macroinvertebrates across time and space. Stay tuned for updates regarding this project.
These studies typically have shortcomings including non-continuous datasets, select ecosystem types (majority of studies are conducted in semi-natural terrestrial habitats), poor taxonomic resolution (either focus on single orders/families or use broad taxonomic groupings), poor diversity metrics, and unreliably identified drivers of insect declines. To give a clearer picture of invertebrate diversity trends, scientists must overcome these shortcomings.
In an effort to monitor how human activities are affecting water quality, the United States Geological Services (USGS) and U.S. Environmental Protection Agency (USEPA) have collaborated over numerous years to standardize the collection of abiotic and biotic samples from streams and rivers across the conterminous U.S., creating numerous data repositories. As part of an international, multi-institutional team lead by Samantha Rumschlag, I am working to quantify changes in community structure and diversity of aquatic macroinvertebrates across time and space. Stay tuned for updates regarding this project.