https://www.cell.com/trends/parasitology/pdf/S1471-4922(12)00121-3.pdf

Ticks and tick-borne diseases: a One Health perspective.

As a result of climate change, many plants are now flowering measurably earlier than they did in the past. However, some species' flowering times have changed much more than others. Data at the community level can clarify the variation in flowering responses to climate change. In order to determine how North American species' flowering times respond to climate, we analyzed a series of previously unstudied records of the dates of first flowering for over 500 plant taxa in Concord, Massachusetts, USA. These records began with six years of observations by the famous naturalist Henry David Thoreau from 1852 to 1858, continued with 16 years of observations by the botanist Alfred Hosmer in 1878 and 1888-1902, and concluded with our own observations in 2004, 2005, and 2006. From 1852 through 2006, Concord warmed by 2.4 degrees C due to global climate change and urbanization. Using a subset of 43 common species, we determined that plants are now flowering seven days earlier on average than they did in Thoreau's times. Plant flowering times were most correlated with mean temperatures in the one or two months just before flowering and were also correlated with January temperatures. Summer-flowering species showed more interannual variation in flowering time than did spring-flowering species, but the flowering times of spring-flowering species correlated more strongly to mean monthly temperatures. In many cases, such as within the genera Betula and Solidago, closely related, co-occurring species responded to climate very differently from one another. The differences in flowering responses to warming could affect relationships in plant communities as warming continues. Common St. John's wort (Hypericum perforatum) and highbush blueberry (Vaccinium corymbosum) are particularly responsive to changes in climate, are common across much of the United States, and could serve as indicators of biological responses to climate change. We discuss the need for researchers to be aware, when using data sets involving multiple observers, of how varying methodologies, sample sizes, and sampling intensities affect the results. Finally, we emphasize the importance of using historical observations, like those of Thoreau and Hosmer, as sources of long-term data and to increase public awareness of biological responses to climate change.

https://www.jstor.org/stable/pdfplus/27651546.pdf

Global warming and flowering times in thoreau's concord: a community perspective

S ociety has a growing need for credible taxonomic information in order to allow us to conserve, manage, understand, and enjoy the natural world. At the same time, support for taxonomy and collections is failing to keep pace. Funds nominally allocated to taxonomy go largely to reconstruct molecular phylogenies, while thousands of species are threatened by imminent extinction. Ecologists working in the tropics have felt this lack of taxonomic knowledge as an impediment that inhibits their ability to analyze community-level phenomena. It is time to evaluate the sources of this impediment and address them. Taxonomy must facilitate, not obstruct, biodiversity studies and conservation.

Existing taxonomic practices have served us well for centuries but are clearly inadequate for the challenge at hand. The taxonomic community must rally around a common vision, critically evaluate its needs, set an ambitious research agenda, embrace emerging technologies, and univocally communicate its aspirations. This will require a major change in approach, engaging individual scholars, professional societies, and institutions.

Molecular data, abundant and inexpensive, have revolutionized phylogenetics but not diminished the importance of traditional work. Morphology links living and fossil species, is the object of natural selection, inspires the search for causal explanations, and democratizes science. Visual morphological knowledge is ideally suited to Internet communication. The need for this research has been masked, because molecular researchers could draw on centuries of banked morphology knowledge. That knowledge, however, is limited to a fraction of Earth's species and will very soon be exhausted. Fashionable DNA bar-coding methods are a breakthrough for identification, but they will not supplant the need to formulate and rigorously test species hypotheses. Predicted advances in cyber-infrastructure suggest that the time is right to re-envisage taxonomy.

Some naively see the information technology challenge as liberating data from cabinets. The reality is that for all but a few taxa, much data is outdated or unreliable. Many specimens represent undescribed or misidentified species. Rapid access to bad data is unacceptable; the challenge is not merely to speed data access but to expedite taxonomic research. We can envision virtual monographs, revisions, floras, and faunas that are living dynamic works rather than static documents.

It is time to approach taxonomy as large-scale international science. The goal of discovering, describing, and classifying the species of our planet assuredly qualifies as big science. In the face of the biodiversity crisis, the need for urgency could not be greater. Imagine a taxonomic renaissance built on a foundation of cyber-infrastructure. A taxonomist in her laboratory examines a type specimen in another city in real time with remote microscopy. She sets priorities for teams of collectors in several countries who are also using such tools to evaluate the day's catch. Turned around, the same digital microscope electronically brings a taxonomist into a classroom. Aspiring taxonomists in developing countries have full access to taxonomic literature formerly reserved for a few great libraries. Peer-reviewed species descriptions are published electronically and made instantly available. Teams of taxonomists speed species exploration, as in the recent National Science Foundation Planetary Biodiversity Inventories.

Taxonomy is planetary-scale science and deserves a planetary-scale tool. This virtual instrument could vastly accelerate taxonomic research and education. Taxonomic understanding of biodiversity, constrained only by evolutionary history, complements long-term and place-based studies of the role of biodiversity in ecosystem functions. Both perspectives are necessary. This tool would be a biodiversity observatory, permitting scientists to “see” across continents and geologic time.

Our generation is the first to fully comprehend the threat of the biodiversity crisis and the last with the opportunity to explore and document the species diversity of our planet. Time is rapidly running out. Society's investment for centuries in great natural history collections can now be repaid through a powerful taxonomic research platform connecting researchers, educators, and decision-makers. The grand biological challenge of our age is to create a legacy of knowledge for a planet that is soon to be biologically decimated. To meet it, 21st-century taxonomists and museums must have the right tools.

https://science.sciencemag.org/content/sci/303/5656/285.full.pdf

Taxonomy: impediment or expedient?

Contents
 	Summary	367	
I.	Introduction	367	
II.	Background on isotopes	368	
III.	Patterns of soil δ15N	370	
IV.	Patterns of fungal δ15N	372	
V.	Biochemical basis for the influence of fungi on δ15N patterns in plant–soil systems	373	
VI.	Patterns of δ15N in plant and fungal culture studies	374	
VII.	Mycoheterotrophic and parasitic plants	375	
VIII.	Patterns of foliar δ15N in autotrophic plants	376	
IX.	Controls over plant δ15N	377	
X.	Conclusions and research needs	378	
 	Acknowledgements	379	
 	References	379	


Summary
In this review, we synthesize field and culture studies of the 15N/14N (expressed as δ15N) of autotrophic plants, mycoheterotrophic plants, parasitic plants, soil, and mycorrhizal fungi to assess the major controls of isotopic patterns. One major control for plants and fungi is the partitioning of nitrogen (N) into either 15N-depleted chitin, ammonia, or transfer compounds or 15N-enriched proteinaceous N. For example, parasitic plants and autotrophic hosts are similar in δ15N (with no partitioning between chitin and protein), mycoheterotrophic plants are higher in δ15N than their fungal hosts, presumably with preferential assimilation of fungal protein, and autotrophic, mycorrhizal plants are lower in 15N than their fungal symbionts, with saprotrophic fungi intermediate, because mycorrhizal fungi transfer 15N-depleted ammonia or amino acids to plants. Similarly, nodules of N2-fixing bacteria transferring ammonia are often higher in δ15N than their plant hosts. N losses via denitrification greatly influence bulk soil δ15N, whereas δ15N patterns within soil profiles are influenced both by vertical patterns of N losses and by N transfers within the soil–plant system. Climate correlates poorly with soil δ15N; climate may primarily influence δ15N patterns in soils and plants by determining the primary loss mechanisms and which types of mycorrhizal fungi and associated vegetation dominate across climatic gradients.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-8137.2012.04300.x

Nitrogen isotopes link mycorrhizal fungi and plants to nitrogen dynamics

Plants are a hyperdiverse clade that plays a key role in maintaining ecological and evolutionary processes as well as human livelihoods. Biases, gaps and uncertainties in plant occurrence information remain a central problem in ecology and conservation, but these limitations remain largely unassessed globally. In this synthesis, we propose a conceptual framework for analysing gaps in information coverage, information uncertainties and biases in these metrics along taxonomic, geographical and temporal dimensions, and apply it to all c. 370 000 species of land plants. To this end, we integrated 120 million point-occurrence records with independent databases on plant taxonomy, distributions and conservation status. We find that different data limitations are prevalent in each dimension. Different metrics of information coverage and uncertainty are largely uncorrelated, and reducing taxonomic, spatial or temporal uncertainty by filtering out records would usually come at great costs to coverage. In light of these multidimensional data limitations, we discuss prospects for global plant ecological and biogeographical research, monitoring and conservation and outline critical next steps towards more effective information usage and mobilisation. Our study provides an empirical baseline for evaluating and improving global floristic knowledge, along with a conceptual framework that can be applied to study other hyperdiverse clades.

Multidimensional biases, gaps and uncertainties in global plant occurrence information

Summary
•Humans are increasing both the deposition of reactive nitrogen (N) and concentrations of atmospheric CO2 on Earth, but the combined effects on terrestrial ecosystems are not clear. In the absence of historical records, it is difficult to know if N availability is currently increasing or decreasing on regional scales.
•To determine the nature and timing of past changes in grassland ecosystem dynamics, we measured the composition of stable carbon (C) and N isotopes in leaf tissue from 545 herbarium specimens of 24 vascular plant species collected in Kansas, USA from 1876 to 2008. We also parameterized a simple model of the terrestrial N cycle coupled with a stable isotope simulator to constrain processes consistent with observed patterns.
•A prolonged decline in foliar N concentrations began in 1926, while a prolonged decline in foliar δ15N values began in 1940. Changes in the difference between foliar and atmospheric C isotopes reveal slightly increased photosynthetic water use efficiency since 1876.
•The declines in foliar N concentrations and foliar δ15N suggest declining N availability in these grasslands during the 20th century despite decades of anthropogenic N deposition. Our results are consistent with progressive-nitrogen-limitation-type hypotheses where declines in N availability are driven by increased ecosystem N storage as a result of increased atmospheric CO2.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-8137.2010.03322.x

Thirteen decades of foliar isotopes indicate declining nitrogen availability in central North American grasslands.

Collections of plant specimens are the basic infrastructure for all studies of plant diversity, but there is concern that plant collecting is in decline. We acquired collection data from a diverse sample of 71 herbaria to test whether there is a decrease in rates of local collecting in the United States. The recorded data were the decade of collection for all specimens of nine exemplar genera from the local region of the herbarium. All analyses showed evidence of a decline in local collecting. We found that the temporal pattern of collecting varied considerably from herbarium to herbarium, but that more herbaria showed a decreasing trend than an increasing trend. The total accumulation of specimens is in decline and only 21% of the sampled herbaria reached their peaks in local collecting activity in the last 20 years. Furthermore, two thirds of the herbaria acquired fewer locally-collected specimens in the last two decades than in the prior two. These trends were consistent over all size classes of herbaria and over herbaria from all regions, though they were less severe in the Mountain region herbaria. Tests for bias indicated that our sample of herbaria was more active than typical, thus our conclusions should be considered a conservative estimate of decline.

The Decline of Plant Collecting in the United States: A Threat to the Infrastructure of Biodiversity Studies

Morus (Tribe Moreae, Moraceae) consists of ca. 13 species of trees distributed in Asia, Africa, Europe, and North, Central, and South America. The broad geographical distribution of the genus, overlapping ranges of many taxa, and documented hybridization between some species present interesting questions of taxonomy, phylogeny, and biogeography. Phylogenetic data for Morus also contribute to higher level taxonomic work in the family. We used sequence data from ITS of the nrDNA and the chloroplast trnL-trnF intergenic spacer to study phylogenetic relationships of Morus. Phylogenies based on separate data sets were not statistically incongruent, and the combined tree reveals that Morus, as currently circumscribed, is non-monophyletic. Subgenus Morus (sensu Leroy) is resolved as a clade and consists of two well-supported clades: one of Asian taxa and one of North American taxa. Sampled members of the genus Trophis (two, including the type) form a clade sister to subgenus Morus. Morus mesozygia (Afri...

https://bioone.org/journals/systematic-botany/volume-37/issue-2/036364412X635485/Phylogenetics-of-Morus-Moraceae-Inferred-from-ITS-and-trnL-trnF/10.1600/036364412X635485.pdf

Phylogenetics of Morus (Moraceae) Inferred from ITS and trnL-trnF Sequence Data

Blood samples from dogs with clinical signs compatible with ehrlichiosis were examined for infection of Ehrlichia canis using PCR, multiplex real-time PCR, and DNA sequencing analysis. Eleven of 25 samples were positive for a new strain of E. canis. This is the first molecular identification of E. canis infection in dogs from Peru.

Molecular Evidence of a New Strain of Ehrlichia canis from South America

The comparison of independent phylogenies is a valuable approach to the study of evolutionary pattern and process. Available data on eastern North American Phlox, including our recent ITS phylogeny, suggest that relationships are complicated in the group and that hybridization may have been a contributing factor. We used restriction site data from the chloroplast genome to develop a second phylogeny for eastern Phlox. Sampling was the same as that for the ITS study and consisted of 79 samples (including all 22 eastern Phlox species and most eastern subspecies, as well as multiple populations of many taxa). The resulting cpDNA phylogeny agrees with the ITS phylogeny in many respects, strengthening earlier conclusions. Nevertheless, incongruence between the trees is noteworthy: many samples, particularly of members of the P. pilosa and P. glaberrima complexes, are placed in different clades. A variety of tests were carried out to assess congruence in terms of topological patterns, character congruence, and homogeneity of data sets. Significant conflict between the phylogenies is discussed in light of the hypothesis that hybridization has affected relationships in this genus.

Carolyn J. Ferguson

Papers

Thirteen decades of foliar isotopes indicate declining nitrogen availability in central North American grasslands.

The Decline of Plant Collecting in the United States: A Threat to the Infrastructure of Biodiversity Studies

Phylogenetics of Morus (Moraceae) Inferred from ITS and trnL-trnF Sequence Data

Molecular Evidence of a New Strain of Ehrlichia canis from South America

A chloroplast DNA phylogeny of eastern Phlox (Polemoniaceae): implications of congruence and incongruence with the ITS phylogeny