Science Enabled by Specimen Data

Marcussen, T., H. E. Ballard, J. Danihelka, A. R. Flores, M. V. Nicola, and J. M. Watson. 2022. A Revised Phylogenetic Classification for Viola (Violaceae). Plants 11: 2224. https://doi.org/10.3390/plants11172224

The genus Viola (Violaceae) is among the 40–50 largest genera among angiosperms, yet its taxonomy has not been revised for nearly a century. In the most recent revision, by Wilhelm Becker in 1925, the then-known 400 species were distributed among 14 sections and numerous unranked groups. Here, we provide an updated, comprehensive classification of the genus, based on data from phylogeny, morphology, chromosome counts, and ploidy, and based on modern principles of monophyly. The revision is presented as an annotated global checklist of accepted species of Viola, an updated multigene phylogenetic network and an ITS phylogeny with denser taxon sampling, a brief summary of the taxonomic changes from Becker’s classification and their justification, a morphological binary key to the accepted subgenera, sections and subsections, and an account of each infrageneric subdivision with justifications for delimitation and rank including a description, a list of apomorphies, molecular phylogenies where possible or relevant, a distribution map, and a list of included species. We distribute the 664 species accepted by us into 2 subgenera, 31 sections, and 20 subsections. We erect one new subgenus of Viola (subg. Neoandinium, a replacement name for the illegitimate subg. Andinium), six new sections (sect. Abyssinium, sect. Himalayum, sect. Melvio, sect. Nematocaulon, sect. Spathulidium, sect. Xanthidium), and seven new subsections (subsect. Australasiaticae, subsect. Bulbosae, subsect. Clausenianae, subsect. Cleistogamae, subsect. Dispares, subsect. Formosanae, subsect. Pseudorupestres). Evolution within the genus is discussed in light of biogeography, the fossil record, morphology, and particular traits. Viola is among very few temperate and widespread genera that originated in South America. The biggest identified knowledge gaps for Viola concern the South American taxa, for which basic knowledge from phylogeny, chromosome counts, and fossil data is virtually absent. Viola has also never been subject to comprehensive anatomical study. Studies into seed anatomy and morphology are required to understand the fossil record of the genus.

Chevalier, M. 2022. <i>crestr</i>: an R package to perform probabilistic climate reconstructions from palaeoecological datasets. Climate of the Past 18: 821–844. https://doi.org/10.5194/cp-18-821-2022

Abstract. Statistical climate reconstruction techniques are fundamental tools to study past climate variability from fossil proxy data. In particular, the methods based on probability density functions (or PDFs) can be used in various environments and with different climate proxies because they rely on elementary calibration data (i.e. modern geolocalised presence data). However, the difficulty of accessing and curating these calibration data and the complexity of interpreting probabilistic results have often limited their use in palaeoclimatological studies. Here, I introduce a new R package (crestr) to apply the PDF-based method CREST (Climate REconstruction SofTware) on diverse palaeoecological datasets and address these problems. crestr includes a globally curated calibration dataset for six common climate proxies (i.e. plants, beetles, chironomids, rodents, foraminifera, and dinoflagellate cysts) associated with an extensive range of climate variables (20 terrestrial and 19 marine variables) that enables its use in most terrestrial and marine environments. Private data collections can also be used instead of, or in combination with, the provided calibration dataset. The package includes a suite of graphical diagnostic tools to represent the data at each step of the reconstruction process and provide insights into the effect of the different modelling assumptions and external factors that underlie a reconstruction. With this R package, the CREST method can now be used in a scriptable environment and thus be more easily integrated with existing workflows. It is hoped that crestr will be used to produce the much-needed quantified climate reconstructions from the many regions where they are currently lacking, despite the availability of suitable fossil records. To support this development, the use of the package is illustrated with a step-by-step replication of a 790 000-year-long mean annual temperature reconstruction based on a pollen record from southeastern Africa.

Liang, S., X. Zhang, and R. Wei. 2022. Ecological adaptation shaped the genetic structure of homoploid ferns against strong dispersal capacity. Molecular Ecology 31: 2679–2697. https://doi.org/10.1111/mec.16420

The formation of spatial genetic structure with the presence of extensive gene flow, an evolutionary force which is generally expected to eliminate population-specific variation and maintain genetic homogeneity, remains poorly understood. Homosporous ferns, which spread by spores through wind and possess long-distance dispersal capacity, provide an ideal system to investigate such a process. Here, using a homoploid fern lineage, the Athyrium sinense complex, we used reduced-representation genomic data to examine spatial genetic structure and explored potential driving forces including geographical distance, environment, climatic history and external dispersal constraints. Our findings showed a clear north-south divergence at the genetic, morphological and ecological levels between both sides of 35°N in East Asia. Fluctuant and heterogeneous climatic condition was demonstrated to play a crucial role during the formation of the divergence. Our results suggested that this lineage was able to migrate southward and colonize new habitat as a result of the Quaternary climatic fluctuation. Furthermore, the present genetic structure is attributed to adaptation to heterogeneous environments, especially temperature difference. In addition to ecological adaptation, we found clues showing that canopy density, wind direction as well as habitat continuity were all likely to constrain the effect of gene flow. These results demonstrated a diversification process without ploidy changes in ferns providing new insights for our present knowledge on ferns’ spatio-temporal evolutionary pattern. In particular, our study highlights the influence of environmental heterogeneity in driving genetic divergence against strong dispersal capacity.

Filartiga, A. L., A. Klimeš, J. Altman, M. P. Nobis, A. Crivellaro, F. Schweingruber, and J. Doležal. 2022. Comparative anatomy of leaf petioles in temperate trees and shrubs: the role of plant size, environment and phylogeny. Annals of Botany 129: 567–582. https://doi.org/10.1093/aob/mcac014

Background and Aims Petioles are important plant organs connecting stems with leaf blades and affecting light-harvesting ability of the leaf as well as transport of water, nutrients and biochemical signals. Despite the high diversity in petiole size, shape and anatomy, little information is availabl…

Vasconcelos, T., J. D. Boyko, and J. M. Beaulieu. 2021. Linking mode of seed dispersal and climatic niche evolution in flowering plants. Journal of Biogeography. https://doi.org/10.1111/jbi.14292

Aim: Due to the sessile nature of flowering plants, movements to new geographical areas occur mainly during seed dispersal. Frugivores tend to be efficient dispersers because animals move within the boundaries of their preferable niches, so seeds are more likely to be transported to environments tha…

Christiansen, D. M., L. L. Iversen, J. Ehrlén, and K. Hylander. 2021. Changes in forest structure drive temperature preferences of boreal understorey plant communities. Journal of Ecology 110: 631–643. https://doi.org/10.1111/1365-2745.13825

The local climate in forest understories can deviate substantially from ambient conditions. Moreover, forest microclimates are often characterized by cyclic changes driven by management activities such as clear-cutting and subsequent planting. To understand how and why understorey plant communities …

Alban, D. M., E. M. Biersma, J. W. Kadereit, and M. S. Dillenberger. 2021. Colonization of the Southern Hemisphere by Sagina and Colobanthus (Caryophyllaceae). Plant Systematics and Evolution 308. https://doi.org/10.1007/s00606-021-01793-w

Colobanthus (23 species) and Sagina (30–33 species) together are sister to Facchinia. Whereas Facchinia is distributed in western Eurasia, Colobanthus is almost exclusively distributed in the Southern Hemisphere, and Sagina is distributed in both hemispheres with the highest species diversity in wes…

Xue, T., S. R. Gadagkar, T. P. Albright, X. Yang, J. Li, C. Xia, J. Wu, and S. Yu. 2021. Prioritizing conservation of biodiversity in an alpine region: Distribution pattern and conservation status of seed plants in the Qinghai-Tibetan Plateau. Global Ecology and Conservation 32: e01885. https://doi.org/10.1016/j.gecco.2021.e01885

The Qinghai-Tibetan Plateau (QTP) harbors abundant and diverse plant life owing to its high habitat heterogeneity. However, the distribution pattern of biodiversity hotspots and their conservation status remain unclear. Based on 148,283 high-resolution occurrence coordinates of 13,450 seed plants, w…

Rock, B. M., and B. H. Daru. 2021. Impediments to Understanding Seagrasses’ Response to Global Change. Frontiers in Marine Science 8. https://doi.org/10.3389/fmars.2021.608867

Uncertainties from sampling biases present challenges to ecologists and evolutionary biologists in understanding species sensitivity to anthropogenic climate change. Here, we synthesize possible impediments that can constrain research to assess present and future seagrass response from climate chang…

Allstädt, F. J., A. Koutsodendris, E. Appel, W. Rösler, T. Reichgelt, S. Kaboth-Bahr, A. A. Prokopenko, and J. Pross. 2021. Late Pliocene to early Pleistocene climate dynamics in western North America based on a new pollen record from paleo-Lake Idaho. Palaeobiodiversity and Palaeoenvironments 101: 177–195. https://doi.org/10.1007/s12549-020-00460-1

Marked by the expansion of ice sheets in the high latitudes, the intensification of Northern Hemisphere glaciation across the Plio/Pleistocene transition at ~ 2.7 Ma represents a critical interval of late Neogene climate evolution. To date, the characteristics of climate change in North America duri…