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1. Habitat quality or quantity? Niche marginality across 21 plants and animals suggests differential responses between highland and lowland species to past climatic changes

   https://doi.org/10.1111/ecog.07391  

   Araya‐Donoso, Raúl; Biddy, Austin; Munguía‐Vega, Adrián; Lira‐Noriega, Andrés; Dolby, Greer A (June 2024, Ecography)

   Warren, Dan (Ed.)

   Climatic changes can affect species distributions, population abundance, and evolution. Such organismal responses could be determined by the amount and quality of available habitats, which can vary independently. In this study, we assessed changes in habitat quantity and quality independently to generate explicit predictions of the species' responses to climatic changes between Last Glacial Maximum (LGM) and present day. We built ecological niche models for genetic groups within 21 reptile, mammal, and plant taxa from the Baja California peninsula inhabiting lowland or highland environments. Significant niche divergence was detected for all clades within species, along with significant differences in the niche breadth and area of distribution between northern and southern clades. We quantified habitat quantity from the distribution models, and most clades showed a reduction in distribution area towards LGM. Further, niche marginality (used as a measure of habitat quality) was higher during LGM for most clades, except for northern highland species. Our results suggest that changes in habitat quantity and quality can affect organismal responses independently. This allows the prediction of genomic signatures associated with changes in effective population size and selection pressure that could be explicitly tested from our models. 

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2. Trophic niche dynamics of two fish mesoconsumers in adjacent coastal habitats with varying nutrient regimes

   https://doi.org/10.1007/s00442-025-05680-w  

   Santos, Rolando O; James, W Ryan; Rehage, Jennifer S; Eggenberger, Cody W; Lesser, Justin S; Madden, Christopher J (March 2025, Oecologia)

   Changes of consumers’ trophic niches, the n-dimensional biotic space that allows a species to satisfy its minimum requirements for population growth, are driven in part by shifts in the degree of individual resource use specialization within a population. Individual specialization results from complex trade-offs in inter- and intraspecific competition as organisms reduce niche overlap within a population or with heterospecifics. It is vital to build empirical knowledge on the trophic niche dynamics of consumers, given the role that niche dynamics play in food web stability, species coexistence, and population resilience, especially quantifying the trophic niche’s expansion and contraction of coastal fish populations experiencing increasing frequency of environmental disturbance and habitat transformation. In coastal ecosystems, disturbances alter the connectivity, productivity, and nutrient regimes of aquatic habitats, which could lead to significant shifts in consumers’ trophic niches. We investigated the trophic niche dynamics of two fish species Centropomus undecimalis (Common Snook) and Megalops atlanticus (Atlantic Tarpon), across two adjacent coastal lake systems of varying nutrient regimes (eutrophic vs. mesotrophic) and hydrological connectivity. In both systems, Snook had larger trophic niches than Tarpon. Also, the trophic niche size in the eutrophic system was larger than the mesotrophic system for both species. Snook and Tarpon used different prey resources, resulting in low niche overlap between species in both systems. Our results highlight how altered hydrological connectivity, and nutrient regimes can shift trophic niche dynamics of higher trophic-level consumers, likely due to changes in prey landscapes and shifts in the foraging ecology of species. 

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3. Multidimensional specialization and generalization are pervasive in soil prokaryotes

   https://doi.org/10.1038/s41559-023-02149-y  

   Hernandez, Damian J.; Kiesewetter, Kasey N.; Almeida, Brianna K.; Revillini, Daniel; Afkhami, Michelle E. (September 2023, Nature Ecology & Evolution)

   Habitat specialization underpins biological processes from species distributions to speciation. However, organisms are often described as specialists or generalists based on a single niche axis, despite facing complex, multidimensional environments. Here, we analysed 236 environmental soil microbiomes across the United States and demonstrate that 90% of >1,200 prokaryotes followed one of two trajectories: specialization on all niche axes (multidimensional specialization) or generalization on all axes (multidimensional generalization). We then documented that this pervasive multidimensional specialization/generalization had many ecological and evolutionary consequences. First, multidimensional specialization and generalization are highly conserved with very few transitions between these two trajectories. Second, multidimensional generalists dominated communities because they were 73 times more abundant than specialists. Lastly, multidimensional specialists played important roles in community structure with ~220% more connections in microbiome networks. These results indicate that multidimensional generalization and specialization are evolutionarily stable with multidimensional generalists supporting larger populations and multidimensional specialists playing important roles within communities, probably stemming from their overrepresentation among pollutant detoxifiers and nutrient cyclers. Taken together, we demonstrate that the vast majority of soil prokaryotes are restricted to one of two multidimensional niche trajectories, multidimensional specialization or multidimensional generalization, which then has far-reaching consequences for evolutionary transitions, microbial dominance and community roles. 

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4. The pan-genome of Aspergillus fumigatus provides a high-resolution view of its population structure revealing high levels of lineage-specific diversity driven by recombination

   https://doi.org/10.1371/journal.pbio.3001890  

   Lofgren, Lotus A.; Ross, Brandon S.; Cramer, Robert A.; Stajich, Jason E. (November 2022, PLOS Biology)

   Sil, Anita (Ed.)

   Aspergillus fumigatus is a deadly agent of human fungal disease where virulence heterogeneity is thought to be at least partially structured by genetic variation between strains. While population genomic analyses based on reference genome alignments offer valuable insights into how gene variants are distributed across populations, these approaches fail to capture intraspecific variation in genes absent from the reference genome. Pan-genomic analyses based on de novo assemblies offer a promising alternative to reference-based genomics with the potential to address the full genetic repertoire of a species. Here, we evaluate 260 genome sequences of A . fumigatus including 62 newly sequenced strains, using a combination of population genomics, phylogenomics, and pan-genomics. Our results offer a high-resolution assessment of population structure and recombination frequency, phylogenetically structured gene presence–absence variation, evidence for metabolic specificity, and the distribution of putative antifungal resistance genes. Although A . fumigatus disperses primarily via asexual conidia, we identified extraordinarily high levels of recombination with the lowest linkage disequilibrium decay value reported for any fungal species to date. We provide evidence for 3 primary populations of A . fumigatus , with recombination occurring only rarely between populations and often within them. These 3 populations are structured by both gene variation and distinct patterns of gene presence–absence with unique suites of accessory genes present exclusively in each clade. Accessory genes displayed functional enrichment for nitrogen and carbohydrate metabolism suggesting that populations may be stratified by environmental niche specialization. Similarly, the distribution of antifungal resistance genes and resistance alleles were often structured by phylogeny. Altogether, the pan-genome of A . fumigatus represents one of the largest fungal pan-genomes reported to date including many genes unrepresented in the Af293 reference genome. These results highlight the inadequacy of relying on a single-reference genome-based approach for evaluating intraspecific variation and the power of combined genomic approaches to elucidate population structure, genetic diversity, and putative ecological drivers of clinically relevant fungi. 

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5. Plant richness and blooming cover affect abundance of flower visitors and network structure in Colombian orchards

   https://doi.org/10.1111/afe.12460  

   Vaca‐Uribe, Jessica_L; Figueroa, Laura_L; Santamaría, Maikol; Poveda, Katja (July 2021, Agricultural and Forest Entomology)

   Abstract Pollination is essential to fruit production. How plant diversity and blooming events in and around orchards affect the pollinator community and the plant‐flower‐visitor network in neotropical systems remains largely unknown.We surveyed the flower visitors in deciduous fruit trees and alternative blooming resources (other crops, hedgerows and weeds) in Colombia across 6 orchards over 12 months. We evaluated whether plant species richness and blooming cover influenced abundance and richness of flower visitors, as well as network‐level connectance and specialization. We also assessed the role of alternative blooming resources for the flower visitors of deciduous fruit trees.Overall, we found 66 taxa of flower visitors, 35 of which visited deciduous fruit trees. There was a greater abundance of flower visitors when there was higher richness of weedy species and greater blooming cover of deciduous fruit trees. Networks were less connected when there was lower crop and weedy species richness. Finally, flower visitor abundance and specialization increased when there were multiple hedgerow species in bloom with a high blooming cover.We highlight the importance of maintaining alternative blooming resources in and around the orchards to support deciduous fruit tree pollinators and diversity in the plant flower‐visitor network. 

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