Science Enabled by Specimen Data

Bywater‐Reyes, S., Diehl, R. M., Wilcox, A. C., Stella, J. C., & Kui, L. (2022). A Green New Balance: interactions among riparian vegetation plant traits and morphodynamics in alluvial rivers. Earth Surface Processes and Landforms. Portico.

The strength of interactions between plants and river processes is mediated by plant traits and fluvial conditions, including above‐ground biomass, stem density and flexibility, channel and bed material properties, and flow and sediment regimes. In many rivers, concurrent changes in 1) the composition of riparian vegetation communities as a result of exotic species invasion and 2) shifts in hydrology have altered physical and ecological conditions in a manner that has been mediated by feedbacks between vegetation and morphodynamic processes. We review how Tamarix, which has invaded many U.S. Southwest waterways, and Populus species, woody pioneer trees that are native to the region, differentially affect hydraulics, sediment transport, and river morphology. We draw on flume, field, and modeling approaches spanning the individual seedling to river‐corridor scales. In a flume study, we found differences in the crown morphology, stem density, and flexibility of Tamarix compared to Populus influenced near‐bed flow velocities in a manner that favored aggradation associated with Tamarix. Similarly, at the patch and corridor scales, observations confirmed increased aggradation with increased vegetation density. Furthermore, long‐term channel adjustments were different for Tamarix‐ versus Populus‐dominated reaches, with faster and greater geomorphic adjustments for Tamarix. Collectively, our studies show how plant‐trait differences between Tamarix and Populus, from individual seedlings to larger spatial and temporal scales, influence the co‐adjustment of rivers and riparian plant communities. These findings provide a basis for predicting changes in alluvial riverine systems which we conceptualize as a Green New Balance model that considers how channels may adjust to changes in plant traits and community structure in additional to alterations in flow and sediment supply. We offer suggestions regarding how the Green New Balance can be used in management and invasive species management.

Yi, X., & Latch, E. K. (2022). Nuclear phylogeography reveals strong impacts of gene flow in big brown bats. Journal of Biogeography. Portico.

Aim Understanding speciation mechanisms requires disentangling processes that promote and erode population-level divergence. Three hypotheses are raised that contemporary population structure is mainly shaped by refugial isolation, gene flow or both. Testing these hypotheses requires range-wide phylogeography and integrative analyses across scales. Here we aimed to (1) re-estimate the previously unresolved nuclear divergence within a widespread bat; (2) test the above three phylogeographical hypotheses and (3) inform conservation management under climatic change. Location North America including the Caribbean. Taxon The big brown bat (Eptesicus fuscus). Methods We collected range-wide samples and genome-wide markers using restriction site-associated DNA sequencing. Population structure was analysed by clustering methods and spatial estimations. Nuclear phylogeographical divergence was estimated using tree methods (concatenation and coalescence) and network analyses (TreeMix). Phylogeographical hypotheses were tested by comparing alternative evolutionary scenarios using demographic modelling. Species distribution modelling was used to help identify Pleistocene refugia and predict future range shifts under climatic change. Results We identified three populations in the Caribbean, eastern and western North America. The western population further split into three phylogeographical clades: Pacific, southwestern North America and Mexico. Discordance among mitochondrial and nuclear topologies reflected strong impacts of gene flow without sex bias. Demographic modelling supported scenarios of historical isolation followed by secondary gene flow and estimated Holocene divergence times. Species distribution was essentially continuous during glaciation with possible regional isolation, and northward range shifts were predicted under future climatic change. Main Conclusions Contemporary population divergence of big brown bats was shaped by both historical isolation and secondary gene flow, supporting the third phylogeographical hypothesis. While climatic change likely triggered initial divergence, ongoing gene flow has largely impacted the dynamic within-species evolution and generated population divergence without speciation.

Chevalier, M. (2022). <i>crestr</i>: an R package to perform probabilistic climate reconstructions from palaeoecological datasets. Climate of the Past, 18(4), 821–844.

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.

López-Cuamatzi, I. L., Hortelano-Moncada, Y., Ortega, J., Ospina-Garcés, S. M., Zúñiga, G., & Mac Swiney G., M. C. (2022). Extension of the distribution of Townsend’s Big-eared Bat, Corynorhinus townsendii (Cooper, 1837) (Chiroptera, Vespertilionidae), to Chiapas, Mexico. Check List, 18(2), 335–339.

We report the first record of Townsend’s Big-eared Bat, Corynorhinus townsendii (Cooper, 1837) from Chiapas, Mexico, based on three females collected on 29 September 1979 near Ocozocoautla de Espinosa and stored in the Colección Nacional de Mamíferos of the Instituto de Biología at Universidad Nacional Autónoma de México. The Chiapas locality is ~180 km east of the closest previously known occurrence in Tehuantepec, Oaxaca, Mexico. This extends the distribution of C. townsendii through tropical areas of southeastern Mexico and corroborates the capacity of this species to inhabit a diversity of ecosystems.

Llanes-Quevedo, A., Mastretta-Yanes, A., Sánchez-González, L. A., Castillo-Chora, V. J., & Navarro-Sigüenza, A. G. (2022). The tangled evolutionary history of a long-debated Mesoamerican taxon: The Velazquez Woodpecker (Melanerpes santacruzi, Aves: Picidae). Molecular Phylogenetics and Evolution, 170, 107445.

The Velazquez Woodpecker Melanerpes santacruzi is a highly polytypic species distributed from east-central Mexico to northern Nicaragua. The ample variation in body size, barring of the plumage, and the coloration of nasal tufts, neck, and belly have fueled debates about the taxonomy and evolutionar…

Espindola, Vázquez‐Domínguez, E., Nakamura, M., Osorio‐Olvera, L., Martínez‐Meyer, E., Myers, E. A., Overcast, I., Reid, B. N., & Burbrink, F. T. (2022). Complex genetic patterns and distribution limits mediated by native congeners of the worldwide invasive red‐eared slider turtle. Molecular Ecology. Portico.

Non-native (invasive) species offer a unique opportunity to study the geographical distribution and range limits of species, wherein the evolutionary change driven by interspecific interactions between native and non-native closely related species is a key component. The red-eared slider turtle, Tra…

Fell, Osborne, O. G., Jones, M. D., Atkinson, S., Tarr, S., Keddie, S. H., & Algar, A. C. (2022). Biotic factors limit the invasion of the plague pathogen ( Yersinia pestis ) in novel geographical settings. Global Ecology and Biogeography. Portico.

Aim: The distribution of Yersinia pestis, the pathogen that causes plague in humans, is reliant upon transmission between host species; however, the degree to which host species distributions dictate the distribution of Y. pestis, compared with limitations imposed by the environmental niche of Y. pe…

Freitas, C., Brum, F. T., Cássia-Silva, C., Maracahipes, L., Carlucci, M. B., Collevatti, R. G., & Bacon, C. D. (2021). Incongruent Spatial Distribution of Taxonomic, Phylogenetic, and Functional Diversity in Neotropical Cocosoid Palms. Frontiers in Forests and Global Change, 4. doi:10.3389/ffgc.2021.739468

Biodiversity can be quantified by taxonomic, phylogenetic, and functional diversity. Current evidence points to a lack of congruence between the spatial distribution of these facets due to evolutionary and ecological constraints. A lack of congruence is especially evident between phylogenetic and ta…

Zhang, N., Liao, Z., Wu, S., Nobis, M. P., Wang, J., & Wu, N. (2021). Impact of climate change on wheat security through an alternate host of stripe rust. Food and Energy Security. doi:10.1002/fes3.356

In the 21st century, stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is still the most devastating disease of wheat globally. Despite the critical roles of the alternate host plants, the Berberis species, in the sexual reproduction and spread of Pst, the climate change impacts on t…

Vasconcelos, T., Boyko, J. D., & Beaulieu, J. M. (2021). Linking mode of seed dispersal and climatic niche evolution in flowering plants. Journal of Biogeography. doi: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…