Coevolution-induced selection for and against phenotypic novelty shapes species richness in clade co-diversification.

Coevolution can occur because of species interactions. However, it remains unclear how coevolutionary processes translate into the accumulation of species richness over macroevolutionary timescales. Assuming speciation occurs as a result of genetic differentiation across space due to dispersal limitation, we examine the effects of coevolution-induced phenotypic selection on species diversification. Based on the idea that dispersers often carry novel phenotypes, we propose and test two hypotheses. (1) Stability hypothesis: selection against phenotypic novelty enhances species diversification by strengthening dispersal limitation. (2) Novelty hypothesis: selection for phenotypic novelty impedes species diversification by weakening dispersal limitation. We simulate clade co-diversification using an individual-based model, considering scenarios where phenotypic selection is shaped by neutral dynamics, mutualistic coevolution, or antagonistic coevolution, where coevolution operates through trait matching or trait difference, and where the strength of coevolutionary selection is symmetrical or asymmetrical. Our key assumption that interactions occur between an independent party (whose individuals can establish or persist independently, e.g. hosts) and a dependent party (whose individuals cannot establish or persist independently, e.g. parasites or obligate mutualists) yields two contrasting results. The stability hypothesis is supported in the dependent clade but not in the independent clade. Conversely, the novelty hypothesis is supported in the independent clade but not in the dependent clade. These results are partially corroborated by empirical dispersal data, suggesting that these mechanisms might potentially explain the diversification of some of the most species-rich clades in the Tree of Life.

Origin and Diversification of the Saguaro Cactus (Carnegiea gigantea): A Within-Species Phylogenomic Analysis.

Reconstructing accurate historical relationships within a species poses numerous challenges, not least in many plant groups in which gene flow is high enough to extend well beyond species boundaries. Nonetheless, the extent of tree-like history within a species is an empirical question on which it is now possible to bring large amounts of genome sequence to bear. We assess phylogenetic structure across the geographic range of the saguaro cactus, an emblematic member of Cactaceae, a clade known for extensive hybridization and porous species boundaries. Using 200 Gb of whole genome resequencing data from 20 individuals sampled from 10 localities, we assembled two data sets comprising 150,000 biallelic single nucleotide polymorphisms (SNPs) from protein coding sequences. From these, we inferred within-species trees and evaluated their significance and robustness using five qualitatively different inference methods. Despite the low sequence diversity, large census population sizes, and presence of wide-ranging pollen and seed dispersal agents, phylogenetic trees were well resolved and highly consistent across both data sets and all methods. We inferred that the most likely root, based on marginal likelihood comparisons, is to the east and south of the region of highest genetic diversity, which lies along the coast of the Gulf of California in Sonora, Mexico. Together with striking decreases in marginal likelihood found to the north, this supports hypotheses that saguaro's current range reflects postglacial expansion from the refugia in the south of its range. We conclude with observations about practical and theoretical issues raised by phylogenomic data sets within species, in which SNP-based methods must be used rather than gene tree methods that are widely used when sequence divergence is higher. These include computational scalability, inference of gene flow, and proper assessment of statistical support in the presence of linkage effects. [Phylogenomics; phylogeography; rooting; Sonoran Desert.].

Species interactions have predictable impacts on diversification.

A fundamental goal of ecology is to reveal generalities in the myriad types of interactions among species, such as competition, mutualism and predation. Another goal is to explain the enormous differences in species richness among groups of organisms. Here, we show how these two goals are intertwined: we find that different types of species interactions have predictable impacts on rates of species diversification, which underlie richness patterns. On the basis of a systematic review, we show that interactions with positive fitness effects for individuals of a clade (e.g. insect pollination for plants) generally increase that clade's diversification rates. Conversely, we find that interactions with negative fitness effects (e.g. predation for prey, competition) generally decrease diversification rates. The sampled clades incorporate all animals and land plants, encompassing 90% of all described species across life. Overall, we show that different types of local-scale species interactions can predictably impact large-scale patterns of diversification and richness.

Do mutualistic interactions last longer than antagonistic interactions?

Species interactions are crucial and ubiquitous across organisms. However, it remains unclear how long these interactions last over macroevolutionary timescales, and whether the nature of these interactions (mutualistic versus antagonistic) helps predict how long they persist. Here, we estimated the ages of diverse species interactions, based on phylogenies from 60 studies spanning the Tree of Life. We then tested if mutualistic interactions persist longer than antagonistic interactions. We found that the oldest mutualisms were significantly older than the oldest antagonisms across all organisms, and within plants, fungi, bacteria and protists. Surprisingly, this pattern was reversed in animals, with the oldest mutualisms significantly younger than the oldest antagonisms. We also found that many mutualisms were maintained for hundreds of millions of years (some greater than 1 billion years), providing strong evidence for the long-term stability of mutualisms and for niche conservatism in species interactions.

Mixed-method study on medicinal herb collection in relation to wildlife conservation: the case of giant pandas in China.

Medicinal herb collection has historical and cultural roots in many rural communities in developing countries. Areas where herb collection occurs may overlap with biodiversity hotspots and crucial habitat of endangered and threatened species. However, impacts of such practices on wildlife are unknown and possibly underestimated, perhaps due to the elusive nature of such activities. We examined this phenomenon in Wolong Nature Reserve, China, a protected area in the South-Central China biodiversity hotspot that also supports a community of Tibetan, Qiang and Han people who use herb collection as a supplementary source of livelihood. We adopted a participatory approach in which we engaged local people in outlining spatial and temporal dynamics of medicinal herb collection practices. We found that the overall spatial extent of herb collection increased in the past two decades. We then overlaid herb collection maps with localities of giant panda (Ailuropoda melanoleuca) feces collected over two time points in the reserve. Using a Bayesian parameter estimation, we found evidence for declined giant panda occurrence in the areas most recently impacted by emerging medicinal herb collection. Our methodology demonstrates the potential power of integrating participatory approaches with quantitative methods for processes like herb collection that may be difficult to examine empirically. We discuss future directions for improving explanatory power and addressing uncertainty in this type of mixed-method, interdisciplinary research. This work has implications for future attempts to understand whether and how prevalent but subtle human activities may affect wildlife conservation.