Angulo-Perez, D. | Search bioRxiv

bioRxiv2024

Advances and applications of the closest-tree algorithm and Hadamard conjugation in phylogenetic inference

In phylogenetic inference Hadamard methods and the closest-tree algorithm have been a promising alternative to likelihood-based methods. However, applications to actual biological problems have been limited so far. In the early nineties, Hendy and Penny (1993) developed the two-state closest-tree algorithm for estimating the optimal branch lengths of a phylogenetic tree, whose parameters correspond to the Cavenders molecular evolution model (CFN). Steel et al. (1992) then developed the four-state version of this method, whose parameters correspond to the Kimura 3STs molecular evolution model (K3ST). In both cases, formulas for solving the optimization problems were provided. Here, we do not only contribute with proofs for these formulas, but we also adapt this methodology to the orchid genus Lophiarella, whose phylogenetic relationships remain unclear. With this biological application, we show the efficacy of the closest-tree algorithm coupled with Hadamard conjugation, phylogenetic invariants and edge-parameter inequalities (in Fourier coordinates) in jointly inferring the tree topology and the molecular evolution model that best explains the data. Finally, we reconcile this phylogeny with biogeographical and morphological aspects within this genus.

evolutionary biology↗

bioRxiv2019

The effect of alien species on plant-pollinator network structure across a gradient of plant species invasion

The interactions between pairs of native and alien plants via shared use of pollinators have been widely studied. Studies of invasive species effects at the community level on the other hand are still scarce. Few community level studies, however, have considered how differences in the intensity of invasion, and degree of floral trait similarity between native and invasive species, can mediated effects on native plant-pollinator communities. Here, we evaluated the effect of alien species on overall plant-pollinator network structure, and species-level network parameters, across nine coastal communities distributed along 205 km at Yucatan, Mexico that vary in alien species richness and flower abundance. We further assessed the effect of alien plant species on plant-pollinator network structure and robustness via computational simulation of native and invasive plant extinction scenarios. We did not find significant differences between native and alien species in functional floral phenotypes, the visitation rate and species composition of the pollinator community. Variation in the proportion of alien plant species and flower abundance across sites did not affect plant-pollinator networks structure. Species-level network parameters (i.e., normalized degree and nestedness contribution) did not differ between native and alien species. Furthermore, our simulation analyses revealed that alien species are functionally equivalent to native species and contribute equally to network structure and robustness. Overall, our results suggest that alien species are well integrated into native coastal plant-pollinator networks which may be facilitated by high levels of floral trait similarity and pollinator use overlap. As a result, alien species may play a similar role than that of natives in the structure and stability of native plant and pollinator communities in the studied coastal sand dune ecosystem.

ecology↗