The relative abundance of languages: Neutral and non-neutral dynamics

Credible estimates suggest that a large number of the nearly 7000 languages in the world could go extinct this century, a prospect with profound cultural, socioeconomic, and political ramifications. Despite its importance, we still have little predictive theory for language dynamics and richness. Critical to the language extinction problem, however, is to understand the dynamics of the number of speakers of languages, the dynamics of language abundance distributions (LADs). Many regional LADs are very similar to the bell-shaped distributions of relative species abundance predicted by neutral theory in ecology. Using the tenets of neutral theory, here we show that LADs can be understood as an equilibrium or disequilibrium between stochastic rates of origination and extinction of languages. However, neutral theory does not fit some regional LADs, which can be explained if the number of speakers has grown systematically faster in some languages than others, due to cultural factors and other non-neutral processes. Only the LADs of Australia and the United States, deviate from a bell-shaped pattern. These deviations are due to the documented higher, non-equilibrium extinction rates of low-abundance languages in these countries.

Hidden-state-only speciation and extinction models provide accurate tip estimates of diversification rates

1. State-dependent speciation and extinction (SSE) models provide a framework for testing potential correlations between the evolution of an observed trait and speciation and extinction rates. Recent expansions of these models allow for the inclusion of "hidden states" that, among other things, allow for rate heterogeneity often observed among lineages sharing a particular character state. However, in reality, multiple circumstances and interacting traits related to a focal character play a role in changing diversification dynamics of a lineage over time, restricting the use of available SSE models that require trait information to be assigned at the tips. 2. Here we introduce MiSSE, an SSE approach that infers diversification rate differences from hidden states only. It can be used similarly to other trait-free methods to estimate varying speciation, extinction, but also different functions of these parameters such as net-diversification, turnover rates, and extinction fraction. Given the size of the model space, we also describe an algorithm designed for efficiently searching through a reasonably large set of models without having to be exhaustive. 3. We compare the accuracy of rates inferred at the tips of the tree by MiSSE against popular character-free methods and demonstrate that the error associated with tip estimates is generally low. Due to certain characteristics of the SSE models, this method avoids some of the recent concerns with parameter identifiability in diversification analyses and can be used alongside regular phylogenetic comparative methods in trait-related diversification hypotheses. 4. Finally, we apply MiSSE, with a renewed focus on classic comparative methods, to understand processes happening near the present, rather than deep in the past, to examine how variation in plant height has impacted turnover rates in eucalypts, a species-rich lineage of flowering plants.

Pulled Diversification Rates, Lineages-Through-Time Plots and Modern Macroevolutionary Modelling

Estimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary, is key to understanding how ecological and evolutionary processes shape biodiversity. Due to an increasing availability of phylogenetic trees, a growing number of process-based methods relying on the birth-death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticised such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineages-through-time (LTT) plots, a recent study (Louca and Pennell, 2020) has shown that there are an infinite number of equally likely diversification scenarios that can generate any timetree. This has led to questioning whether or not diversification rates should be estimated at all. Here we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models to disentangle diversification histories. Using simulations we illustrate the characteristics of newly-proposed “pulled rates” and their utility. We recognize that the recent findings are a step forward in understanding the behavior of macroevolutionary modelling, but they in no way suggest we should abandon diversification modelling altogether. On the contrary, the study of macroevolution using phylogenetic trees has never been more exciting and promising than today. We still face important limitations in regard to data availability and methods, but by acknowledging them we can better target our joint efforts as a scientific community.

Decreasing Phanerozoic extinction intensity as a consequence of Earth surface oxygenation and metazoan ecophysiology

The decline in background extinction rates of marine animals through geologic time is an established but unexplained feature of the Phanerozoic fossil record. There is also growing consensus that the ocean and atmosphere did not become oxygenated to near-modern levels until the mid-Paleozoic, coinciding with the onset of generally lower extinction rates. Physiological theory provides us with a possible causal link between these two observations—predicting that the synergistic impacts of oxygen and temperature on aerobic respiration would have made marine animals more vulnerable to ocean warming events during periods of limited surface oxygenation. Here, we evaluate the hypothesis that changes in surface oxygenation exerted a first-order control on extinction rates through the Phanerozoic using a combined Earth system and ecophysiological modeling approach. We find that although continental configuration, the efficiency of the biological carbon pump in the ocean, and initial climate state all impact the magnitude of modeled biodiversity loss across simulated warming events, atmospheric oxygen is the dominant predictor of extinction vulnerability, with metabolic habitat viability and global ecophysiotype extinction exhibiting inflection points around 40% of present atmospheric oxygen. Given this is the broad upper limit for estimates of early Paleozoic oxygen levels, our results are consistent with the relative frequency of high-magnitude extinction events (particularly those not included in the canonical big five mass extinctions) early in the Phanerozoic being a direct consequence of limited early Paleozoic oxygenation and temperature-dependent hypoxia responses.

Earth history events shaped the evolution of uneven biodiversity across tropical moist forests

Far from a uniform band, the biodiversity found across Earth’s tropical moist forests varies widely between the high diversity of the Neotropics and Indomalaya and the relatively lower diversity of the Afrotropics. Explanations for this variation across different regions, the “pantropical diversity disparity” (PDD), remain contentious, due to difficulty teasing apart the effects of contemporary climate and paleoenvironmental history. Here, we assess the ubiquity of the PDD in over 150,000 species of terrestrial plants and vertebrates and investigate the relationship between the present-day climate and patterns of species richness. We then investigate the consequences of paleoenvironmental dynamics on the emergence of biodiversity gradients using a spatially explicit model of diversification coupled with paleoenvironmental and plate tectonic reconstructions. Contemporary climate is insufficient in explaining the PDD; instead, a simple model of diversification and temperature niche evolution coupled with paleoaridity constraints is successful in reproducing the variation in species richness and phylogenetic diversity seen repeatedly among plant and animal taxa, suggesting a prevalent role of paleoenvironmental dynamics in combination with niche conservatism. The model indicates that high biodiversity in Neotropical and Indomalayan moist forests is driven by complex macroevolutionary dynamics associated with mountain uplift. In contrast, lower diversity in Afrotropical forests is associated with lower speciation rates and higher extinction rates driven by sustained aridification over the Cenozoic. Our analyses provide a mechanistic understanding of the emergence of uneven diversity in tropical moist forests across 110 Ma of Earth’s history, highlighting the importance of deep-time paleoenvironmental legacies in determining biodiversity patterns.

Conserved ancestral tropical niche but different continental histories explain the latitudinal diversity gradient in brush-footed butterflies

The global increase in species richness toward the tropics across continents and taxonomic groups, referred to as the latitudinal diversity gradient, stimulated the formulation of many hypotheses to explain the underlying mechanisms of this pattern. We evaluate several of these hypotheses to explain spatial diversity patterns in a butterfly family, the Nymphalidae, by assessing the contributions of speciation, extinction, and dispersal, and also the extent to which these processes differ among regions at the same latitude. We generate a time-calibrated phylogeny containing 2,866 nymphalid species (~45% of extant diversity). Neither speciation nor extinction rate variations consistently explain the latitudinal diversity gradient among regions because temporal diversification dynamics differ greatly across longitude. The Neotropical diversity results from low extinction rates, not high speciation rates, and biotic interchanges with other regions are rare. Southeast Asia is also characterized by a low speciation rate but, unlike the Neotropics, is the main source of dispersal events through time. Our results suggest that global climate change throughout the Cenozoic, combined with tropical niche conservatism, played a major role in generating the modern latitudinal diversity gradient of nymphalid butterflies.

When fossil clades ‘compete’: local dominance, global diversification dynamics and causation

Examining the supposition that local-scale competition drives macroevolutionary patterns has become a familiar goal in fossil biodiversity studies. However, it is an elusive goal, hampered by inadequate confirmation of ecological equivalence and interactive processes between clades, patchy sampling, few comparative analyses of local species assemblages over long geological intervals, and a dearth of appropriate statistical tools. We address these concerns by reevaluating one of the classic examples of clade displacement in the fossil record, in which cheilostome bryozoans surpass the once dominant cyclostomes. Here, we analyse a newly expanded and vetted compilation of 40 190 fossil species occurrences to estimate cheilostome and cyclostome patterns of species proportions within assemblages, global genus richness and genus origination and extinction rates while accounting for sampling. Comparison of time-series models using linear stochastic differential equations suggests that inter-clade genus origination and extinction rates are causally linked to each other in a complex feedback relationship rather than by simple correlations or unidirectional relationships, and that these rates are not causally linked to changing within-assemblage proportions of cheilostome versus cyclostome species.

Phanerozoic parasitism and marine metazoan diversity: dilution versus amplification

Growing evidence suggests that biodiversity mediates parasite prevalence. We have compiled the first global database on occurrences and prevalence of marine parasitism throughout the Phanerozoic and assess the relationship with biodiversity to test if there is support for amplification or dilution of parasitism at the macroevolutionary scale. Median prevalence values by era are 5% for the Paleozoic, 4% for the Mesozoic, and a significant increase to 10% for the Cenozoic. We calculated period-level shareholder quorum sub-sampled (SQS) estimates of mean sampled diversity, three-timer (3T) origination rates, and 3T extinction rates for the most abundant host clades in the Paleobiology Database to compare to both occurrences of parasitism and the more informative parasite prevalence values. Generalized linear models (GLMs) of parasite occurrences and SQS diversity measures support both the amplification (all taxa pooled, crinoids and blastoids, and molluscs) and dilution hypotheses (arthropods, cnidarians, and bivalves). GLMs of prevalence and SQS diversity measures support the amplification hypothesis (all taxa pooled and molluscs). Though likely scale-dependent, parasitism has increased through the Phanerozoic and clear patterns primarily support the amplification of parasitism with biodiversity in the history of life. This article is part of the theme issue ‘Infectious disease macroecology: parasite diversity and dynamics across the globe’.

Long-Term Colony Dynamics and Fitness in a Colonial Tent-Web Spider Cyrtophora citricola

Social animals are expected to experience a positive effect of conspecific number or density on fitness (an Allee effect) because of the benefits of group living. However, social animals also often disperse to live either solitarily or in small groups, so to understand why social animals leave their groups it is necessary to understand how group size affects both average fitness and the expected fitness outcomes of individuals. We examined the relationships between group size and fitness in the colonial spider Cyrtophora citricola using long-term observations of colony demographics. We censused colonies, recording the number of juveniles, large females, and egg sacs, approximately every 2 months for 2 years. We also recorded the substrates supporting colony webs, including plant species and size, and the azimuth the colony occupied on the plant. Colonies in all regions showed cyclical patterns of growth and decline; however, regions were not synchronized, and seasonal effects differed between years. Colonies with fewer individuals at the initial observation were less likely to survive over the course of observations, and extinction rates were also influenced by an interaction between region and plant substrate. Small colonies were more likely to be extinct by the next census, but if they survived, they were more likely to have high growth rates compared to larger colonies. Despite the potential for high growth rates, high extinction rates depressed the average fitness of small colonies so that population growth rates peaked at intermediate colony sizes. Variance in egg sac production also peaked at intermediate colony sizes, suggesting that competitive interactions may increase the uneven distribution of resources in larger groups. Even if average fitness is high, if spiders can anticipate poor outcomes in large colonies, they may disperse to live solitarily or in smaller, less competitive groups.