Latest Articles
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Section: Registered Reports ; Topics: Ecology, Evolution, Psychological and cognitive sciences
Behavioral flexibility is similar in two closely related species where only one is rapidly expanding its geographic range
10.24072/pcjournal.582 - Peer Community Journal, Volume 5 (2025), article no. e75
Get full text PDFHuman-modified environments are rapidly increasing, which puts other species in the precarious position of either adapting to the new challenges or, if they are not able to adapt, shifting their range to a more suitable environment. It is generally thought that behavioral flexibility, the ability to change behavior when circumstances change, plays an important role in the ability of a species to rapidly expand their geographic range. To determine whether species differences in range expansion propensity are linked to differences in behavioral flexibility, we compared two closely related species, great-tailed grackles (Quiscalus mexicanus; GTGR) and boat-tailed grackles (Quiscalus major; BTGR). GTGR are rapidly expanding their geographic range by settling in new areas, whereas BTGR are not. We previously found that GTGR are behaviorally flexible, however not much is known about BTGR behavior. Using the comparative method thus provides an ideal way to test the hypothesis that behavioral flexibility plays a key role in the GTGR rapid range expansion. We compared the behavioral flexibility of two GTGR populations (an older population where they have been breeding since 1951 in the middle of the northern expansion front: Tempe, Arizona, and a more recent population where they have been breeding since 2004 on the northern edge of the expansion front: Woodland, California) with one BTGR population from Venus, Florida (the age of the population is unknown, but likely thousands of years old), to investigate whether the rapidly expanding GTGR, particularly the more recent population, are more flexible. We found that both species, and both GTGR populations, have similar levels of flexibility (measured as food type switching rates during focal follows). Our results elucidate that, while GTGR are highly flexible, flexibility in foraging behavior may not be the primary factor involved in their successful range expansion. If this were the case, we would expect to see a rapid range expansion in BTGR as well. This comparative perspective adds further support to our previous intraspecific findings that persistence and the variance in flexibility (rather than population average flexibility) play a larger role in the edge GTGR population than in the GTGR population away from the edge. Our research indicates that the hypothesis that higher average levels of flexibility are the primary facilitators of rapid geographic range expansions into new areas needs to be revisited.
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Section: Ecology ; Topics: Ecology, Evolution, Systems biology
Behavioral flexibility is related to foraging, but not social or habitat use behaviors, in a species that is rapidly expanding its range
Logan, Corina;
Lukas, Dieter;
Geng, Xuewen;
Hardy, Kristin;
LeGrande, Christa;
Marfori, Zara;
MacPherson, Maggie;
Rowney, Carolyn;
Smith, Caroline;
McCune, Kelsey
10.24072/pcjournal.573 - Peer Community Journal, Volume 5 (2025), article no. e74
Get full text PDFThe ability of other species to adapt to human modified environments is increasingly crucial because of the rapid expansion of this landscape type. Behavioral flexibility, the ability to change behavior in the face of a changing environment by packaging information and making it available to other cognitive processes, is hypothesized to be a key factor in a species’ ability to successfully adapt to new environments, including human modified environments, and expand its geographic range. However, most tests of this hypothesis confound behavioral flexibility with the specific proxy aspect of foraging, social, or habitat use behavior that was feasible to measure. This severely limits the power of predictions about whether and how a species uses flexibility to adapt behavior to new environments. To begin to resolve this issue, we directly tested flexibility using two measures (reversal learning and puzzlebox solution switching) and investigated its relationship with foraging, social, and habitat use behaviors in a flexible species that is rapidly expanding its geographic range: the great-tailed grackle. We found relationships between flexibility and foraging breadth and foraging techniques, with the less flexible individuals using a higher proportion of human foods and having more human food sources within their home range, suggesting that they specialize on human foods. These relationships were only detectable after a flexibility manipulation where some individuals were trained to be more flexible via serial reversal learning and compared with control individuals who were not, but not when using data from outside of the flexibility manipulation. There were no strong relationships between flexibility and social or habitat use behaviors. Given that this species is rapidly expanding its geographic range and recently shifting more toward urban and arid environments, our findings could suggest that foraging breadth and foraging technique breadth are factors in facilitating such an expansion. Overall, this evidence indicates that cross-species correlations between flexibility and foraging, social, and habitat use behaviors based on proxies have a high degree of uncertainty, resulting in an insufficient ability to draw conclusions.
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Section: Ecology ; Topics: Biology of interactions, Ecology, Statistics
Trait matching without traits: using correspondence analysis to investigate the latent structure of interaction networks
10.24072/pcjournal.580 - Peer Community Journal, Volume 5 (2025), article no. e73
Get full text PDFSpecies interactions in ecological communities are often represented as networks, the structure of which is thought to be linked to species' interaction niches (or Eltonian niches). Interaction niches are intimately related to the notion of trait matching, which posits that a species interacts preferentially with partners whose traits are complementary to their own. Multivariate methods are commonly used to quantify species environmental niches (or Grinnellian niches). More recently, some of these methods have also been used to study the interaction niche, but they consider only the niche optimum and require trait data. In this article, we use the correspondence analysis (CA) framework to study interaction networks and investigate trait matching without requiring trait data, using the notion of latent traits. We use reciprocal scaling, a method related to CA, to estimate niche optima and breadths, defined respectively as the mean and standard deviation of the latent traits of species' interacting partners. We present the method, test its performance using a simulation model we designed, and analyze a real frugivory network between birds and plants. The simulation study shows that the method is able to recover niche breadths and optima for data generated with parameters typical of ecological networks. The birds-plants network analysis shows strong relationships between species latent traits and niche breadths: a posteriori correlation with measured traits suggests that birds and plants of intermediate size tend to have the broadest niches. Additionally, birds preferentially foraging in the understory have broader niches than birds preferentially foraging in the canopy. CA and reciprocal scaling are described as fruitful exploratory methods to characterize species interaction profiles, provide an ecologically meaningful graphical representation of interaction niches, and explore the effect of latent traits on network structure.
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Section: Mathematical & Computational Biology ; Topics: Evolution, Genetics/genomics, Microbiology
A systematic assessment of phylogenomic approaches for microbial species tree reconstruction
10.24072/pcjournal.579 - Peer Community Journal, Volume 5 (2025), article no. e72
Get full text PDFA key challenge in microbial phylogenomics is that microbial gene families are often affected by extensive horizontal gene transfer (HGT). As a result, most existing methods for microbial phylogenomics can only make use of a small subset of the gene families present in the microbial genomes under consideration, potentially biasing their results and affecting their accuracy. To address this challenge, several methods have recently been developed for inferring microbial species trees from genome-scale datasets of gene families affected by evolutionary events such as HGT, gene duplication, and gene loss. In this work, we use extensive simulated and real biological datasets to systematically assess the accuracies of four recently developed methods for microbial phylogenomics, SpeciesRax, ASTRAL-Pro 2, PhyloGTP, and AleRax, under a range of different conditions. Our analysis reveals important insights into the relative performance of these methods on datasets with different characteristics, identifies shared weaknesses when analyzing complex biological datasets, and demonstrates the importance of accounting for gene tree inference error/uncertainty for improved species tree reconstruction. Among other results, we find that (i) AleRax, the only method that explicitly accounts for gene tree inference error/uncertainty, shows the best species tree reconstruction accuracy among all tested methods, (ii) PhyloGTP (developed previously by the authors of this paper) shows the best overall accuracy among methods that do not account for gene tree error and uncertainty, (iii) ASTRAL-Pro 2 is less accurate than the other methods across nearly all tested conditions, and (iv) explicitly accounting for gene tree inference error/uncertainty can lead to substantial improvements in species tree reconstruction accuracy. Importantly, we also find that all methods, including AleRax and PhyloGTP, are susceptible to biases present in complex real biological datasets and can sometimes yield misleading phylogenies.
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The network image was drawn by Martin Grandjean: A force-based network visualization CC BY-SA