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1. Common, showy, and perennial species dominate a restoration species pool

   https://doi.org/10.1111/rec.13969  

   Kaul, Andrew D.; Barash, Michael; Albrecht, Matthew A. (June 2023, Restoration Ecology)

   Native seed vendors are a primary source of germplasm for restoration projects; however, most plant species are not commercially available. Preferences in the types of species that vendors grow and sell may limit the similarity between reference communities and reconstructed ones established from seed mixes. We tested whether a restoration species pool shows preference for certain groups of species, focusing on the Ozark Highland Ecoregion (midcontinent United States). We identified the pool of 1,082 candidate herbaceous plant species appropriate for restoration projects on upland habitats in this region, and then surveyed nine regional seed vendors to assess their commercial availability. Commercially available species were more likely to be forbs over graminoids, perennials over annuals, and common species with larger ranges and moderate conservatism scores. Within forbs, taller species and those with longer bloom durations were favored. Species with affinity to open habitats (e.g. grassland) were more likely to be available from multiple vendors than those from woodlands and forests. Encouragingly, 454 (42%) of the species in this regional pool were available. However, this means that most species in the region are not likely to be included in seed mixes, unless they are hand‐collected from remnant populations. This restoration pool favors common and showy species, which is consistent with previous studies showing these kinds of species tend to dominate seed mixes and restored plant communities. We identified 39 species that were not available from any of the vendors surveyed, which we recommend as candidates for expansion of the Ozark restoration species pool. 

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2. Species Diversity Associated with Foundation Species in Temperate and Tropical Forests

   https://doi.org/10.3390/f10020128  

   Ellison, Aaron; Buckley, Hannah; Case, Bradley; Cardenas, Dairon; Duque, Álvaro; Lutz, James; Myers, Jonathan; Orwig, David; Zimmerman, Jess (February 2019, Forests)

   Foundation species define and structure ecological communities but are difficult to identify before they are declining. Yet, their defining role in ecosystems suggests they should be a high priority for protection and management while they are still common and abundant. We used comparative analyses of six large forest dynamics plots spanning a temperate-to-tropical gradient in the Western Hemisphere to identify statistical “fingerprints” of potential foundation species based on their size-frequency and abundance-diameter distributions, and their spatial association with five measures of diversity of associated woody plant species. Potential foundation species are outliers from the common “reverse-J” size-frequency distribution, and have negative effects on alpha diversity and positive effects on beta diversity at most spatial lags and directions. Potential foundation species also are more likely in temperate forests, but foundational species groups may occur in tropical forests. As foundation species (or species groups) decline, associated landscape-scale (beta) diversity is likely to decline along with them. Preservation of this component of biodiversity may be the most important consequence of protecting foundation species while they are still common. 

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3. Epidemics in native species influence the outcome of a species invasion

   https://doi.org/10.1007/s00442-023-05444-4  

   Blackwood, Paradyse E.; Jonasen, Kacie L.; Hoenig, Brandon D.; Heil, Brittany N.; Searle, Catherine L. (February 2024, Oecologia)
4. Neural basis of acoustic species recognition in a cryptic species complex

   https://doi.org/10.1242/jeb.243405  

   Gupta, Saumya; Alluri, Rishi K.; Rose, Gary J.; Bee, Mark A. (December 2021, Journal of Experimental Biology)

   ABSTRACT Sexual traits that promote species recognition are important drivers of reproductive isolation, especially among closely related species. Identifying neural processes that shape species differences in recognition is crucial for understanding the causal mechanisms of reproductive isolation. Temporal patterns are salient features of sexual signals that are widely used in species recognition by several taxa, including anurans. Recent advances in our understanding of temporal processing by the anuran auditory system provide an opportunity to investigate the neural basis of species-specific recognition. The anuran inferior colliculus consists of neurons that are selective for temporal features of calls. Of potential relevance are auditory neurons known as interval-counting neurons (ICNs) that are often selective for the pulse rate of conspecific advertisement calls. Here, we tested the hypothesis that ICNs mediate acoustic species recognition by exploiting the known differences in temporal selectivity in two cryptic species of gray treefrog (Hyla chrysoscelis and Hyla versicolor). We examined the extent to which the threshold number of pulses required to elicit behavioral responses from females and neural responses from ICNs was similar within each species but potentially different between the two species. In support of our hypothesis, we found that a species difference in behavioral pulse number thresholds closely matched the species difference in neural pulse number thresholds. However, this relationship held only for ICNs that exhibited band-pass tuning for conspecific pulse rates. Together, these findings suggest that differences in temporal processing of a subset of ICNs provide a mechanistic explanation for reproductive isolation between two cryptic treefrog species. 

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5. Clustering Species With Residual Covariance Matrix in Joint Species Distribution Models

   https://doi.org/10.3389/fevo.2021.601384  

   Bystrova, Daria; Poggiato, Giovanni; Bektaş, Billur; Arbel, Julyan; Clark, James S.; Guglielmi, Alessandra; Thuiller, Wilfried (March 2021, Frontiers in Ecology and Evolution)

   null (Ed.)

   Modeling species distributions over space and time is one of the major research topics in both ecology and conservation biology. Joint Species Distribution models (JSDMs) have recently been introduced as a tool to better model community data, by inferring a residual covariance matrix between species, after accounting for species' response to the environment. However, these models are computationally demanding, even when latent factors, a common tool for dimension reduction, are used. To address this issue, Taylor-Rodriguez et al. ( 2017 ) proposed to use a Dirichlet process, a Bayesian nonparametric prior, to further reduce model dimension by clustering species in the residual covariance matrix. Here, we built on this approach to include a prior knowledge on the potential number of clusters, and instead used a Pitman–Yor process to address some critical limitations of the Dirichlet process. We therefore propose a framework that includes prior knowledge in the residual covariance matrix, providing a tool to analyze clusters of species that share the same residual associations with respect to other species. We applied our methodology to a case study of plant communities in a protected area of the French Alps (the Bauges Regional Park), and demonstrated that our extensions improve dimension reduction and reveal additional information from the residual covariance matrix, notably showing how the estimated clusters are compatible with plant traits, endorsing their importance in shaping communities. 

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