Trait-mediated speciation and human-driven extinctions in proboscideans revealed by unsupervised Bayesian neural networks.

Species life-history traits, paleoenvironment, and biotic interactions likely influence speciation and extinction rates, affecting species richness over time. Birth-death models inferring the impact of these factors typically assume monotonic relationships between single predictors and rates, limiting our ability to assess more complex effects and their relative importance and interaction. We introduce a Bayesian birth-death model using unsupervised neural networks to explore multifactorial and nonlinear effects on speciation and extinction rates using fossil data. It infers lineage- and time-specific rates and disentangles predictor effects and importance through explainable artificial intelligence techniques. Analysis of the proboscidean fossil record revealed speciation rates shaped by dietary flexibility and biogeographic events. The emergence of modern humans escalated extinction rates, causing recent diversity decline, while regional climate had a lesser impact. Our model paves the way for an improved understanding of the intricate dynamics shaping clade diversification.

The reorganization of predator-prey networks over 20 million years explains extinction patterns of mammalian carnivores.

Linking the species interactions occurring at the scale of local communities to their potential impact at evolutionary timescales is challenging. Here, we used the high-resolution fossil record of mammals from the Iberian Peninsula to reconstruct a timeseries of trophic networks spanning more than 20 million years and asked whether predator-prey interactions affected regional extinction patterns. We found that, despite small changes in species richness, trophic networks showed long-term trends, gradually losing interactions and becoming sparser towards the present. This restructuring of the ecological networks was driven by the loss of medium-sized herbivores, which reduced prey availability for predators. The decrease in prey availability was associated with predator longevity, such that predators with less available prey had greater extinction risk. These results not only reveal long-term trends in network structure but suggest that prey species richness in ecological communities may shape large scale patterns of extinction and persistence among predators.

Early Jurassic origin of avian endothermy and thermophysiological diversity in dinosaurs.

A fundamental question in dinosaur evolution is how they adapted to long-term climatic shifts during the Mesozoic and when they developed environmentally independent, avian-style acclimatization, becoming endothermic.1,2 The ability of warm-blooded dinosaurs to flourish in harsher environments, including cold, high-latitude regions,3,4 raises intriguing questions about the origins of key innovations shared with modern birds,5,6 indicating that the development of homeothermy (keeping constant body temperature) and endothermy (generating body heat) played a crucial role in their ecological diversification.7 Despite substantial evidence across scientific disciplines (anatomy,8 reproduction,9 energetics,10 biomechanics,10 osteohistology,11 palaeobiogeography,12 geochemistry,13,14 and soft tissues15,16,17), a consensus on dinosaur thermophysiology remains elusive.1,12,15,17,18,19 Differential thermophysiological strategies among terrestrial tetrapods allow endotherms (birds and mammals) to expand their latitudinal range (from the tropics to polar regions), owing to their reduced reliance on environmental temperature.20 By contrast, most reptilian lineages (squamates, turtles, and crocodilians) and amphibians are predominantly constrained by temperature in regions closer to the tropics.21 Determining when this macroecological pattern emerged in the avian lineage relies heavily on identifying the origin of these key physiological traits. Combining fossils with macroevolutionary and palaeoclimatic models, we unveil distinct evolutionary pathways in the main dinosaur lineages: ornithischians and theropods diversified across broader climatic landscapes, trending toward cooler niches. An Early Jurassic shift to colder climates in Theropoda suggests an early adoption of endothermy. Conversely, sauropodomorphs exhibited prolonged climatic conservatism associated with higher thermal conditions, emphasizing temperature, rather than plant productivity, as the primary driver of this pattern, suggesting poikilothermy with a stronger dependence on higher temperatures in sauropods.

Plio-Pleistocene African megaherbivore losses associated with community biomass restructuring.

Fossil abundance data can reveal ecological dynamics underpinning taxonomic declines. Using fossil dental metrics, we reconstructed body mass and mass-abundance distributions in Late Miocene to recent African large mammal communities. Despite collection biases, fossil and extant mass-abundance distributions are highly similar, with unimodal distributions likely reflecting savanna environments. Above 45 kilograms, abundance decreases exponentially with mass, with slopes close to -0.75, as predicted by metabolic scaling. Furthermore, communities before ~4 million years ago had considerably more large-sized individuals, with a greater proportion of total biomass allocated in larger size categories, than did later communities. Over time, individuals and biomass were redistributed into smaller size categories, reflecting a gradual loss of large-sized individuals from the fossil record paralleling the long-term decline of Plio-Pleistocene large mammal diversity.

A macroevolutionary pathway to megaherbivory.

Several scenarios have been proposed to explain rapid net size increases in some early Cenozoic mammalian lineages: sustained and gradual directional change, successive occupation of adaptive zones associated with progressively larger body sizes, and nondirectional evolution associated with branching events in combination with higher diversification potential of the larger lineages. We test these hypotheses in brontotheres, which are among the first radiations of mammals that consistently evolved multitonne sizes. Body-mass evolution in brontotheres mainly occurred during speciation and had no preferential direction. Long-term directional change stemmed from the higher survival of larger lineages in less-saturated herbivore guilds. Our study emphasizes the role of differential species proliferation in explaining the long-term phenotypic trends observed in the fossil record, which are more than an accumulation of steady microevolutionary changes.

A phylogenetic study to assess the link between biome specialization and diversification in swallowtail butterflies.

The resource-use hypothesis, proposed by E.S. Vrba, states that habitat fragmentation caused by climatic oscillations would affect particularly biome specialists (species inhabiting only one biome), which might show higher speciation and extinction rates than biome generalists. If true, lineages would accumulate biome-specialist species. This effect would be particularly exacerbated for biomes located at the periphery of the global climatic conditions, namely, biomes that have high/low precipitation and high/low temperature such as rainforest (warm-humid), desert (warm-dry), steppe (cold-dry) and tundra (cold-humid). Here, we test these hypotheses in swallowtail butterflies, a clade with more than 570 species, covering all the continents but Antarctica, and all climatic conditions. Swallowtail butterflies are among the most studied insects, and they are a model group for evolutionary biology and ecology studies. Continental macroecological rules are normally tested using vertebrates, this means that there are fewer examples exploring terrestrial invertebrate patterns at global scale. Here, we compiled a large Geographic Information System database on swallowtail butterflies' distribution maps and used the most complete time-calibrated phylogeny to quantify diversification rates (DRs). In this paper, we aim to answer the following questions: (1) Are there more biome-specialist swallowtail butterflies than biome generalists? (2) Is DR related to biome specialization? (3) If so, do swallowtail butterflies inhabiting extreme biomes show higher DRs? (4) What is the effect of species distribution area? Our results showed that swallowtail family presents a great number of biome specialists which showed substantially higher DRs compared to generalists. We also found that biome specialists are unevenly distributed across biomes. Overall, our results are consistent with the resource-use hypothesis, species climatic niche and biome fragmentation as key factors promoting isolation.

Trophic Niche Breadth of Falconidae Species Predicts Biomic Specialisation but Not Range Size.

Trophic niche breadth plays a key role in biogeographic distribution patterns. Theory posits that generalist strategies are favoured in a more heterogeneous set of environments across a spatio-temporal gradient of resources predictability, conferring individuals and species a greater capacity for colonising new habitats and thus expanding their distribution area. Using the family Falconidae (Aves, Falconiformes) as a model study, we tested the prediction that those species with a wider diet spectrum will have larger geographic range sizes and inhabit more biomes. We assessed the relationships between trophic breadth (diet richness and diversity) at different taxonomic resolutions of the prey (class and order), range size and biomic specialisation index (BSI; number of biomes inhabited) for the different species. Despite different diet breadth indexes and taxonomic resolutions defined differently the trophic niche of the clade and species, our findings revealed that trophic breadth was not a good predictor for range size but was for total environmental heterogeneity, with more diet-generalist species occupying a higher number of biomes. Diet breadth at the order taxonomic level showed a higher capacity of predicting BSI than at class level, and can be an important ecological trait explaining biogeographic patterns of the species.

An Italian dinosaur Lagerstätte reveals the tempo and mode of hadrosauriform body size evolution.

During the latest Cretaceous, the European Archipelago was characterized by highly fragmented landmasses hosting putative dwarfed, insular dinosaurs, claimed as fossil evidence of the "island rule". The Villaggio del Pescatore quarry (north-eastern Italy) stands as the most informative locality within the palaeo-Mediterranean region and represents the first, multi-individual Konservat-Lagerstätte type dinosaur-bearing locality in Italy. The site is here critically re-evaluated as early Campanian in age, thus preceding the final fragmentation stages of the European Archipelago, including all other European localities preserving hypothesized dwarfed taxa. New skeletal remains allowed osteohistological analyses on the hadrosauroid Tethyshadros insularis indicating subadult features in the type specimen whereas a second, herein newly described, larger individual is likely somatically mature. A phylogenetic comparative framework places the body-size of T. insularis in range with other non-hadrosaurid Eurasian hadrosauroids, rejecting any significant evolutionary trend towards miniaturisation in this clade, confuting its 'pygmy' status, and providing unmatched data to infer environmentally-driven body-size trends in Mesozoic dinosaurs.

The rise and fall of proboscidean ecological diversity.

Proboscideans were keystone Cenozoic megaherbivores and present a highly relevant case study to frame the timing and magnitude of recent megafauna extinctions against long-term macroevolutionary patterns. By surveying the entire proboscidean fossil history using model-based approaches, we show that the dramatic Miocene explosion of proboscidean functional diversity was triggered by their biogeographical expansion beyond Africa. Ecomorphological innovations drove niche differentiation; communities that accommodated several disparate proboscidean species in sympatry became commonplace. The first burst of extinctions took place in the late Miocene, approximately 7 million years ago (Ma). Importantly, this and subsequent extinction trends showed high ecomorphological selectivity and went hand in hand with palaeoclimate dynamics. The global extirpation of proboscideans began escalating from 3 Ma with further extinctions in Eurasia and then a dramatic increase in African extinctions at 2.4 Ma. Overhunting by humans may have served as a final double jeopardy in the late Pleistocene after climate-triggered extinction trends that began long before hominins evolved suitable hunting capabilities.

Punctuated ecological equilibrium in mammal communities over evolutionary time scales.

The study of deep-time ecological dynamics has the ability to inform conservation decisions by anticipating the behavior of ecosystems millions of years into the future. Using network analysis and an exceptional fossil dataset spanning the past 21 million years, we show that mammalian ecological assemblages undergo long periods of functional stasis, notwithstanding high taxonomic volatility due to dispersal, speciation, and extinction. Higher functional richness and diversity promoted the persistence of functional faunas despite species extinction risk being indistinguishable among these different faunas. These findings, and the large mismatch between functional and taxonomic successions, indicate that although safeguarding functional diversity may or may not minimize species losses, it would certainly enhance the persistence of ecosystem functioning in the face of future disturbances.

Assessing the utility of conserving evolutionary history.

It is often claimed that conserving evolutionary history is more efficient than species-based approaches for capturing the attributes of biodiversity that benefit people. This claim underpins academic analyses and recommendations about the distribution and prioritization of species and areas for conservation, but evolutionary history is rarely considered in practical conservation activities. One impediment to implementation is that arguments related to the human-centric benefits of evolutionary history are often vague and the underlying mechanisms poorly explored. Herein we identify the arguments linking the prioritization of evolutionary history with benefits to people, and for each we explicate the purported mechanism, and evaluate its theoretical and empirical support. We find that, even after 25 years of academic research, the strength of evidence linking evolutionary history to human benefits is still fragile. Most - but not all - arguments rely on the assumption that evolutionary history is a useful surrogate for phenotypic diversity. This surrogacy relationship in turn underlies additional arguments, particularly that, by capturing more phenotypic diversity, evolutionary history will preserve greater ecosystem functioning, capture more of the natural variety that humans prefer, and allow the maintenance of future benefits to humans. A surrogate relationship between evolutionary history and phenotypic diversity appears reasonable given theoretical and empirical results, but the strength of this relationship varies greatly. To the extent that evolutionary history captures unmeasured phenotypic diversity, maximizing the representation of evolutionary history should capture variation in species characteristics that are otherwise unknown, supporting some of the existing arguments. However, there is great variation in the strength and availability of evidence for benefits associated with protecting phenotypic diversity. There are many studies finding positive biodiversity-ecosystem functioning relationships, but little work exists on the maintenance of future benefits or the degree to which humans prefer sets of species with high phenotypic diversity or evolutionary history. Although several arguments link the protection of evolutionary history directly with the reduction of extinction rates, and with the production of relatively greater future biodiversity via increased adaptation or diversification, there are few direct tests. Several of these putative benefits have mismatches between the relevant spatial scales for conservation actions and the spatial scales at which benefits to humans are realized. It will be important for future work to fill in some of these gaps through direct tests of the arguments we define here.

Evolutionary pathways toward gigantism in sharks and rays.

Through elasmobranch (sharks and rays) evolutionary history, gigantism evolved multiple times in phylogenetically distant species, some of which are now extinct. Interestingly, the world's largest elasmobranchs display two specializations found never to overlap: filter feeding and mesothermy. The contrasting lifestyles of elasmobranch giants provide an ideal case study to elucidate the evolutionary pathways leading to gigantism in the oceans. Here, we applied a phylogenetic approach to a global dataset of 459 taxa to study the evolution of elasmobranch gigantism. We found that filter feeders and mesotherms deviate from general relationships between trophic level and body size, and exhibit significantly larger sizes than ectothermic-macropredators. We confirm that filter feeding arose multiple times during the Paleogene, and suggest the possibility of a single origin of mesothermy in the Cretaceous. Together, our results elucidate two main evolutionary pathways that enable gigantism: mesothermic and filter feeding. These pathways were followed by ancestrally large clades and facilitated extreme sizes through specializations for enhancing prey intake. Although a negligible percentage of ectothermic-macropredators reach gigantic sizes, these species lack such specializations and are correspondingly constrained to the lower limits of gigantism. Importantly, the very adaptive strategies that enabled the evolution of the largest sharks can also confer high extinction susceptibility.

Divergent trends in functional and phylogenetic structure in reptile communities across Africa.

Despite extensive research on ecological community compositions, general patterns across large-scale environmental gradients have remained unclear. A widely used explanatory model is the stress dominance hypothesis (SDH), predicting that the relative influence of environmental filtering is greater in stressful habitats while competition is more important in benign environments. Here, we test the SDH using African squamates as a model system to facilitate general predictions on community structures amidst changing global environments. For the first time we investigate changes in functional, phylogenetic and species diversity across continental, environmental gradients within a multidimensional, phylogenetically informed approach. Results suggest that phylogenetic patterns of African squamates were likely shaped by clade-specific biogeographic histories, whereas functional structure reflects SDH predictions. We further detected significant structuring at both local and regional spatial scales, emphasizing the impact of regional-historical processes on local assemblages, and the need for broad conceptual frameworks to detect general patterns of community composition.

Multi-scale interplays of biotic and abiotic drivers shape mammalian sub-continental diversity over millions of years.

The reconstruction of deep-time diversity trends is key to understanding current and future species richness. Studies that statistically evaluate potential factors affecting paleodiversity have focused on continental and global, clade-wide datasets, and thus we ignore how community species richness build-up to generate large-scale patterns over geological timescales. If community diversity is shaped by biotic interactions and continental and global diversities are governed by abiotic events, which are the modulators of diversity in subcontinental regions? To address this question, we model Iberian mammalian species richness over 13 million years (15 to 2 Ma) using exhaustive fossil evidence for subcontinental species' ecomorphology, environmental context, and biogeographic affinities, and quantitatively evaluate their impact on species richness. We find that the diversity of large Iberian mammals has been limited over time, with species richness showing marked fluctuations, undergoing substantial depletions as diversity surpasses a critical limit where a significant part of the niches is unviable. The strength of such diversity-dependence has also shifted. Large faunal dispersals and environmental heterogeneity increased the system's critical diversity limit. Diversity growth rate (net migration and diversification) also oscillated, mainly modulated by functional saturation, patchiness of canopy cover, and local temperature and aridity. Our study provides quantitative support for subcontinental species pools being complex and dynamic systems where diversity is perpetually imbalanced over geological timescales. Subcontinental diversity-dependence dynamics are mainly modulated by a multi-scale interplay of biotic and abiotic factors, with abiotic factors playing a more relevant role.

Correction: Body-size structure of Central Iberian mammal fauna reveals semidesertic conditions during the middle Miocene Global Cooling Event.

[This corrects the article DOI: 10.1371/journal.pone.0186762.].

Differential responses of Miocene rodent metacommunities to global climatic changes were mediated by environmental context.

The study of how long-term changes affect metacommunities is a relevant topic, that involves the evaluation of connections among biological assemblages across different spatio-temporal scales, in order to fully understand links between global changes and macroevolutionary patterns. We applied multivariate statistical analyses and diversity tests using a large data matrix of rodent fossil sites in order to analyse long-term faunal changes. Late Miocene rodent faunas from southwestern Europe were classified into metacommunities, presumably sharing ecological affinities, which followed temporal and environmental non-random assembly and disassembly patterns. Metacommunity dynamics of these faunas were driven by environmental changes associated with temperature variability, but there was also some influence from the aridity shifts described for this region during the late Miocene. Additionally, while variations in the structure of rodent assemblages were directly influenced by global climatic changes in the southern province, the northern sites showed a pattern of climatic influence mediated by diversity-dependent processes.

Body-size structure of Central Iberian mammal fauna reveals semidesertic conditions during the middle Miocene Global Cooling Event.

We developed new quantitative palaeoclimatic inference models based on the body-size structure of mammal faunas from the Old World tropics and applied them to the Somosaguas fossil site (middle Miocene, central Iberian Peninsula). Twenty-six mammal species have been described at this site, including proboscideans, ungulates, carnivores, insectivores, lagomorphs and rodents. Our analyses were based on multivariate and bivariate regression models correlating climatic data and body-size structure of 63 modern mammal assemblages from Sub-Saharan Africa and the Indian subcontinent. The results showed an average temperature of the coldest month higher than 26°C for the Somosaguas fossil site, a mean annual thermal amplitude around 10°C, a drought length of 10 months, and an annual total precipitation greater than 200 mm per year, which are climate conditions typical of an ecotonal zone between the savanna and desert biomes. These results are congruent with the aridity peaks described over the middle Aragonian of Spain and particularly in the local biozone E, which includes Somosaguas. The aridity increase detected in this biozone is associated with the Middle Miocene Global Cooling Event. The environment of Somosaguas around 14 Ma was similar to the current environment in the Sahel region of North Africa, the Horn of Africa, the boundary area between the Kalahari and the Namib in Southern Africa, south-central Arabia, or eastern Pakistan and northwestern India. The distribution of modern vegetation in these regions follows a complex mosaic of plant communities, dominated by scattered xerophilous shrublands, semidesert grasslands, and vegetation linked to seasonal watercourses and ponds.

Systematics and Evolution of the Miocene Three-Horned Palaeomerycid Ruminants (Mammalia, Cetartiodactyla).

Palaeomerycids were strange three-horned Eurasian Miocene ruminants known through fossils from Spain to China. We here study their systematics, offering the first cladistic phylogeny of the best-known species of the group, and also reassess their phylogenetic position among ruminants, which is currently disputed. The beautifully preserved remains of a new palaeomerycid from middle Miocene deposits of Spain, Xenokeryx amidalae gen. et sp. nov., helps us to better understand palaeomerycid anatomy, especially that of the nuchal region in the skull, significantly improving our current knowledge on these enigmatic ruminants. Our results show two main lineages of palaeomerycids, one containing the genus Ampelomeryx diagnosed by a characteristic type of cranium / cranial appendages and some dental derived traits, and another one that clusters those forms more closely related to Triceromeryx than to Ampelomeryx, characterized by a more derived dentition and a set of apomorphic cranial features. Xenokeryx branches as a basal offshoot of this clade. Also, we find that Eurasian palaeomerycids are not closely related to North American dromomerycids, thus rejecting the currently more accepted view of palaeomerycids as the Eurasian part of the dromomerycid lineage. Instead of this, palaeomerycids are nested with the African Miocene pecoran Propalaeoryx and with giraffoids. On the other hand, dromomerycids are closely related to cervids. We define a clade Giraffomorpha that includes palaeomerycids and giraffids, and propose an emended diagnosis of the Palaeomerycidae based on cranial and postcranial characters, including several features of the cranium not described so far. We also define the Palaeomerycidae as the least inclusive clade of pecorans containing Triceromeryx and Ampelomeryx. Finally, we reassess the taxonomy of several palaeomerycid taxa.

Congruent phylogenetic and fossil signatures of mammalian diversification dynamics driven by Tertiary abiotic change.

Computational methods for estimating diversification rates from extant species phylogenetic trees have become abundant in evolutionary research. However, little evidence exists about how their outcome compares to a complementary and direct source of information: the fossil record. Furthermore, there is virtually no direct test for the congruence of evolutionary rates based on these two sources. This task is only achievable in clades with both a well-known fossil record and a complete phylogenetic tree. Here, we compare the evolutionary rates of ruminant mammals as estimated from their vast paleontological record--over 1200 species spanning 50 myr--and their living-species phylogeny. Significantly, our results revealed that the ruminant's fossil record and phylogeny reflect congruent evolutionary processes. The concordance is especially strong for the last 25 myr, when living groups became a dominant part of ruminant diversity. We found empirical support for previous hypotheses based on simulations and neontological data: The pattern captured by the tree depends on how clade specific the processes are and which clades are involved. Also, we report fossil evidence for a postradiation speciation slowdown coupled with constant, moderate extinction in the Miocene. The recent deceleration in phylogenetic rates is connected to rapid extinction triggered by recent climatic fluctuations.

A macroecological glance at the structure of late Miocene rodent assemblages from Southwest Europe.

Deep-time perspectives in macroecology are essential with regard to understanding the impact of climate forcing on faunal communities. Using late Miocene rodent faunas (12 to 5 Ma) from two different biogeographical provinces from southwestern Europe, we asked whether the waxing and waning of faunas with dissimilar ecological affinities tracked climate in different ways. The latest middle Miocene featured a fauna dominated by dormice with forest and mixed-habitat affinities. This group declined towards the Upper Miocene. Rodent taxa with the highest values of richness at the beginning of the Upper Miocene are generalists in the southern province and specialists of forested habitats in the northern province. Finally, we identified a third, increasingly significant group of rodents linked to open landscapes towards the end of the Miocene. These three broad ecological groups showed differential responses to a complex set of interconnected circumstances, including the biogeographic structure of the study area and climatic changes throughout time.