Challenges of comprehensive taxon sampling in comparative biology: Wrestling with rosids

Using phylogenetic approaches to test hypotheses on a large scale, in terms of both species sampling and associated species traits and occurrence data—and doing this with rigor despite all the attendant challenges—is critical for addressing many broad questions in evolution and ecology. However, application of such approaches to empirical systems is hampered by a lingering series of theoretical and practical bottlenecks. The community is still wrestling with the challenges of how to develop species‐level, comprehensively sampled phylogenies and associated geographic and phenotypic resources that enable global‐scale analyses. We illustrate difficulties and opportunities using the rosids as a case study, arguing that assembly of biodiversity data that is scale‐appropriate—and therefore comprehensive and global in scope—is required to test global‐scale hypotheses. Synthesizing comprehensive biodiversity data sets in clades such as the rosids will be key to understanding the origin and present‐day evolutionary and ecological dynamics of the angiosperms.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143800/1/ajb21059.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143800/2/ajb21059_am.pd

Can Low-Severity Fire Reverse Compositional Change in Montane Forests of the Sierra Nevada, California, USA?

Throughout the Sierra Nevada, nearly a century of fire suppression has altered the tree species composition, forest structure, and fire regimes that were previously characteristic of montane forests. Species composition is fundamentally important because species differ in their tolerances to fire and environmental stressors, and these differences dictate future forest structure and influence fire regime attributes. In some lower montane stands, shade-tolerant, fire-sensitive species have driven a threefold increase in tree density that may intensify the risk of high-severity fire. In upper montane forests, which were historically characterized by longer fire return intervals, the effects of fire exclusion are both less apparent and less studied. Although land managers have been reintroducing fire to lower and upper montane forests for \u3e4 decades, the potentially restorative effects of these actions on species composition remain largely unassessed. We used tree diameter and species data from 51 recently burned and 46 unburned plots located throughout lower and upper montane forests in Yosemite National Park and Sequoia & Kings Canyon National Parks to examine the effects of low-to moderate-severity (hereafter, lower-severity)fire on the demography of seven prevalent tree species. The density of Abies concolor concolor 30–45 cm dbh, A. magnifica Calocedrus decurrens concolor but not for C. decurrens, and (2) variability in tree density among plots that burned at lower severity exceeded the range of tree densities reported in historical data sets. High proportions of shade-tolerant species in some postfire stands may increase the prevalence of shade-tolerant species in the future, a potential concern for managers who seek to minimize ladder fuels and promote forest structure that is less prone to high-severity fire

Character evolution and missing (morphological) data across Asteridae

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143691/1/ajb21050-sup-0007-AppendixS7.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143691/2/ajb21050_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143691/3/ajb21050-sup-0019-AppendixS19.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143691/4/ajb21050-sup-0013-AppendixS13.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143691/5/ajb21050-sup-0014-AppendixS14.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143691/6/ajb21050-sup-0012-AppendixS12.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143691/7/ajb21050-sup-0009-AppendixS9.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143691/8/ajb21050-sup-0018-AppendixS18.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143691/9/ajb21050.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143691/10/ajb21050-sup-0004-AppendixS4.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143691/11/ajb21050-sup-0008-AppendixS8.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143691/12/ajb21050-sup-0005-AppendixS5.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143691/13/ajb21050-sup-0017-AppendixS17.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143691/14/ajb21050-sup-0006-AppendixS6.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143691/15/ajb21050-sup-0011-AppendixS11.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143691/16/ajb21050-sup-0016-AppendixS16.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143691/17/ajb21050-sup-0015-AppendixS15.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143691/18/ajb21050-sup-0010-AppendixS10.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143691/19/ajb21050-sup-0003-AppendixS3.pd

An endemic plant and the plant-insect visitor network of a dune ecosystem

Network theory increasingly is used to quantify and evaluate mutualistic interactions, such as those among plants and their flower-visiting insects or pollinators. Some plant species have been shown to be important in community structure using network metrics; however, the roles of plant taxa, particularly rare species, are not well understood. Pitcher's thistle (Cirsium pitcheri), a threatened endemic of Great Lakes shorelines, flowers late-June to early-August, when other floral resources may be less abundant or unavailable. We performed 10 min insect visitor observations on all insect pollinated plants in 44–10 m by 10 m plots at Sturgeon Bay, northern lower MI, USA, during C. pitcheri flowering and recorded plant species, number of open flowers, species of insect visiting, and number of visits by insects. Pitcher's thistle received 18.2% of all 600 recorded visits, 61.1% more than the next most visited plant. Pitcher's thistle also received visits from 22 of the 59 different insect species in the network, twice as many as the next most visited plant species. Species-level network analysis metrics showed that Pitcher's thistle was most generalized, with greatest species strength, betweenness, and connectance scores of any other plant taxon, demonstrating network topological importance. Pitcher's thistle received significantly more insect visits relative to its abundance that did any other plant species. Therefore, conservation of C. pitcheri and of other rare taxa, particularly in xeric and low diversity systems, can be significant beyond species-level management and may extend to conservation of the plant-insect community.Joyner Open Access Publishing Support Fun

The US Virtual Herbarium: working with individual herbaria to build a national resource

Volume: 209Start Page: 55End Page: 7

Extraction of phenotypic traits from taxonomic descriptions for the tree of life using natural language processing

Premise of the StudyPhenotypic data sets are necessary to elucidate the genealogy of life, but assembling phenotypic data for taxa across the tree of life can be technically challenging and prohibitively time consuming. We describe a semi-automated protocol to facilitate and expedite the assembly of phenotypic character matrices of plants from formal taxonomic descriptions. This pipeline uses new natural language processing (NLP) techniques and a glossary of over 9000 botanical terms. Methods and ResultsOur protocol includes the Explorer of Taxon Concepts (ETC), an online application that assembles taxon-by-character matrices from taxonomic descriptions, and MatrixConverter, a Java application that enables users to evaluate and discretize the characters extracted by ETC. We demonstrate this protocol using descriptions from Araucariaceae. ConclusionsThe NLP pipeline unlocks the phenotypic data found in taxonomic descriptions and makes them usable for evolutionary analyses.U.S. National Science Foundation [DEB-1208256, DEB-1541506, DBI-1147266]Open access journal.This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]