Ancient tropical extinctions at high latitudes contributed to the latitudinal diversity gradient

The fate of South America's endemic mammalian fauna in response to the most dramatic Cenozoic climate disruption

Around 34 Mya, the Eocene-Oligocene transition (EOT) marked the most dramatic global climatic cooling of the Cenozoic. On a planetary scale, paleontological evidence suggests that this transition was associated with major faunal turnovers, sometimes even regarded as a mass extinction crisis. In South America, there is no consensus on the response of the endemic mammals to this transition. Here, using a vetted fossil dataset and cutting-edge Bayesian methods, we analyzed the dynamics of South American mammal (SAM) diversification and their possible drivers across latitude (tropical vs. extratropical), taxonomic groups, and trophic guilds throughout the Eocene-Oligocene (ca. 56 to 23 Ma). Our results did not evidence any mass extinction among SAM at the EOT. Instead, they experienced a gradual and long-term diversity decline from the middle Eocene to the early Oligocene, followed by a sudden waxing-and-waning diversity associated with a large taxonomic-but not ecological-turnover. Tropical and extratropical lineages have had very distinct macroevolutionary histories. No effective change in the pace at which tropical lineages diversify was found, thus favoring the tropical stability hypothesis proposed by Wallace. Diversity-dependent effects, temperature, and Andean uplift were recovered as probable drivers of SAM diversification across the period. Contrasting evidence casts doubt on the common hypothesis primarily linking Oligocene faunal changes to grassland expansion. Our findings illustrate the uniqueness of the deep-time interplay between endemic SAM and their physical environment in a context of climatic shift, highlighting the need to consider regional idiosyncrasies for understanding the coevolution of life and climate.

Amphibians and Reptiles Exhibit Different Ecological and Evolutionary Spatial Patterns in the Amazon Basin

Understanding spatial variability in ecological and evolutionary patterns is key to Amazonian biodiversity conservation. This study examined taxonomic, phylogenetic, and functional diversity across amphibians and reptiles, assessing the influence of elevation, interrelationships among metrics, and distribution across five Amazon Basin ecoregions, exploring the "cradle" (speciation) and "museum" (lineage preservation) hypotheses. We analyzed 1011 amphibian species from three lineages and 828 reptile species from four lineages. Integrating distribution maps, phylogenies, and trait data, we calculated phylogenetic (PD), functional (FD), and taxonomic (TD) diversity, including mean phylogenetic (PDmntd) and functional (FDmntd) distance to the nearest taxon. We examined spatial regressions between diversity metrics and elevation, assessed correlations among metrics, and compared diversity metrics across ecoregions for each lineage. Diversity metrics across amphibian and reptile lineages reveal distinct geographical patterns related to elevation. Anurans exhibit higher PD, FD, and TD in the western Amazon, while squamates show hotspots at low altitudes. Testudines are linked to major rivers, and crocodilians display high PD near the equator. Anurans and squamates show elevated PDmntd and FDmntd in the Andes, whereas testudines are found in cratonic regions. Significant correlations and notable differences among ecoregions were found, especially in the Andes and low regions of the Amazon Basin. This study highlights the diverse eco-evolutionary patterns among amphibian and reptile lineages in the Amazon Basin, each exhibiting distinct hotspots distributed across ecoregions. The findings align with the cradle-museum hypothesis, suggesting that some regions serve as centers of ongoing diversification, others preserve ancient lineages, or serve as both. The cradle-museum hypothesis should be carefully analyzed, as each taxon presents a distinct pattern. This research underscores the necessity for targeted conservation strategies tailored to distinct ecological and evolutionary dynamics across ecoregions.

Global phylogeny of the family Gomphillaceae (Ascomycota, Graphidales) sheds light on the origin, diversification and endemism in foliicolous lineages

Foliicolous lichens grow on living leaves of vascular plants. They are mostly found in tropical to subtropical or temperate rainforests. Many phenotype-based species are considered as pantropical or even sub-cosmopolitan, either attributed to old ages, having existed prior to continental breakups or long-distance dispersal. We built a much expanded, global phylogeny of Gomphillaceae, the most diverse group of leaf-dwelling lichenised fungi. Our sampling encompassed six major biodiversity hotspots: MIOI (Madagascar and the Indian Ocean Islands), the Caribbean, New Caledonia, the Colombian Chocó, Mesoamerica and the Atlantic coast of Brazil. It was based on multilocus sequence data (mtSSU rDNA, nuLSU rDNA and RPB1), including 2207 sequences of 1256 specimens. Species delimitation methods combined with a phenotype matrix identified 473 putative species. Amongst these, 104 are confirmed as described, 213 are classified as cryptic or near cryptic (hidden diversity), 100 represent new species to science (identified on the basis of phenotype) and 56 remain unidentified. Amongst the 104 species with a valid name, 40.5% are distributed across 2-5 continents (lichenogeographical regions) by applying the phenotype-based species concept. However, using the integrative approach to delineate species, this estimate is reduced to 9%. We estimate the global species richness of Gomphillaceae at 1,861-2,356 species. The timing of species-level divergences suggests that the current distribution of foliicolous lichens is shaped more by long-distance dispersal and rapid diversification than by vicariance. The origin of the family and major clades appears to be in the Neotropics, with subsequent numerous dispersal events. Our results support the separation of three major lineages, corresponding to the former families Asterothyriaceae, Gomphillaceae s.str. and Solorinellaceae, which should be recognised at the subfamily level.

Potential plant extinctions with the loss of the Pleistocene mammoth steppe

During the Pleistocene-Holocene transition, the dominant mammoth steppe ecosystem across northern Eurasia vanished, in parallel with megafauna extinctions. However, plant extinction patterns are rarely detected due to lack of identifiable fossil records. Here, we introduce a method for detection of plant taxa loss at regional (extirpation) to potentially global scale (extinction) and their causes, as determined from ancient plant DNA metabarcoding in sediment cores (sedaDNA) from lakes in Siberia and Alaska over the past 28,000 years. Overall, potential plant extinctions track changes in temperature, in vegetation, and in megafauna extinctions at the Pleistocene-Holocene transition. Estimated potential plant extinction rates were 1.7-5.9 extinctions per million species years (E/MSY), above background extinction rates but below modern estimates. Major potential plant extinction events were detected around 17,000 and 9000 years ago which lag maximum vegetation turnover. Our results indicate that herbaceous taxa and taxa contributing less to beta diversity are more vulnerable to extinction. While the robustness of the estimates will increase as DNA reference libraries and ancient sedaDNA data expand, the available data support that plants are more resilient to environmental changes than mammals.

Reticulate evolution: Detection and utility in the phylogenomics era

Phylogenomics has enriched our understanding that the Tree of Life can have network-like or reticulate structures among some taxa and genes. Two non-vertical modes of evolution - hybridization/introgression and horizontal gene transfer - deviate from a strictly bifurcating tree model, causing non-treelike patterns. However, these reticulate processes can produce similar patterns to incomplete lineage sorting or recombination, potentially leading to ambiguity. Here, we present a brief overview of a phylogenomic workflow for inferring organismal histories and compare methods for distinguishing modes of reticulate evolution. We discuss how the timing of coalescent events can help disentangle introgression from incomplete lineage sorting and how horizontal gene transfer events can help determine the relative timing of speciation events. In doing so, we identify pitfalls of certain methods and discuss how to extend their utility across the Tree of Life. Workflows, methods, and future directions discussed herein underscore the need to embrace reticulate evolutionary patterns for understanding the timing and rates of evolutionary events, providing a clearer view of life's history.

Multiple karyotype differences between populations of the Hoplias malabaricus (Teleostei; Characiformes), a species complex in the gray area of the speciation process

Neotropical fishes exhibit remarkable karyotype diversity, whose evolution is poorly understood. Here, we studied genetic differences in 60 individuals, from 11 localities of one species, the wolf fish Hoplias malabaricus, from populations that include six different "karyomorphs". These differ in Y-X chromosome differentiation, and, in several cases, by fusions with autosomes that have resulted in multiple sex chromosomes. Other differences are also observed in diploid chromosome numbers and morphologies. In an attempt to start understanding how this diversity was generated, we analyzed within- and between-population differences in a genome-wide sequence data set. We detect clear genotype differences between karyomorphs. Even in sympatry, samples with different karyomorphs differ more in sequence than samples from allopatric populations of the same karyomorph, suggesting that they represent populations that are to some degree reproductively isolated. However, sequence divergence between populations with different karyomorphs is remarkably low, suggesting that chromosome rearrangements may have evolved during a brief evolutionary time. We suggest that the karyotypic differences probably evolved in allopatry, in small populations that would have allowed rapid fixation of rearrangements, and that they became sympatric after their differentiation. Further studies are needed to test whether the karyotype differences contribute to reproductive isolation detected between some H. malabaricus karyomorphs.

Tangled webs and spider-flowers: Phylogenomics, biogeography, and seed morphology inform the evolutionary history of Cleomaceae

PREMISE

Cleomaceae is an important model clade for studies of evolutionary processes including genome evolution, floral form diversification, and photosynthetic pathway evolution. Diversification and divergence patterns in Cleomaceae remain tangled as research has been restricted by its worldwide distribution, limited genetic sampling and species coverage, and a lack of definitive fossil calibration points.

METHODS

We used target sequence capture and the Angiosperms353 probe set to perform a phylogenetic study of Cleomaceae. We estimated divergence times and biogeographic analyses to explore the origin and diversification of the family. Seed morphology across extant taxa was documented with multifocal image-stacking techniques and morphological characters were extracted, analyzed, and compared to fossil records.

RESULTS

We recovered a well-supported and resolved phylogenetic tree of Cleomaceae generic relationships that includes 236 (~86%) species. We identified 11 principal clades and confidently placed Cleomella as sister to the rest of the family. Our analyses suggested that Cleomaceae and Brassicaceae diverged ~56 mya, and Cleomaceae began to diversify ~53 mya in the Palearctic and Africa. Multiple transatlantic disjunct distributions were identified. Seeds were imaged from 218 (~80%) species in the family and compared to all known fossil species.

CONCLUSIONS

Our results represent the most comprehensive phylogenetic study of Cleomaceae to date. We identified transatlantic disjunctions and proposed explanations for these patterns, most likely either long-distance dispersals or contractions in latitudinal distributions caused by climate change over geological timescales. We found that seed morphology varied considerably but mostly mirrored generic relationships.

Tropical Origin, Global Diversification, and Dispersal in the Pond Damselflies (Coenagrionoidea) Revealed by a New Molecular Phylogeny

The processes responsible for the formation of Earth's most conspicuous diversity pattern, the latitudinal diversity gradient (LDG), remain unexplored for many clades in the Tree of Life. Here, we present a densely sampled and dated molecular phylogeny for the most speciose clade of damselflies worldwide (Odonata: Coenagrionoidea) and investigate the role of time, macroevolutionary processes, and biome-shift dynamics in shaping the LDG in this ancient insect superfamily. We used process-based biogeographic models to jointly infer ancestral ranges and speciation times and to characterize within-biome dispersal and biome-shift dynamics across the cosmopolitan distribution of Coenagrionoidea. We also investigated temporal and biome-dependent variation in diversification rates. Our results uncover a tropical origin of pond damselflies and featherlegs ~105 Ma, while highlighting the uncertainty of ancestral ranges within the tropics in deep time. Even though diversification rates have declined since the origin of this clade, global climate change and biome-shifts have slowly increased diversity in warm- and cold-temperate areas, where lineage turnover rates have been relatively higher. This study underscores the importance of biogeographic origin and time to diversify as important drivers of the LDG in pond damselflies and their relatives, while diversification dynamics have instead resulted in the formation of ephemeral species in temperate regions. Biome-shifts, although limited by tropical niche conservatism, have been the main factor reducing the steepness of the LDG in the last 30 Myr. With ongoing climate change and increasing northward range expansions of many damselfly taxa, the LDG may become less pronounced. Our results support recent calls to unify biogeographic and macroevolutionary approaches to improve our understanding of how latitudinal diversity gradients are formed and why they vary across time and among taxa.

Poleward migration of tropical corals inhibited by future trends of seawater temperature and calcium carbonate (CaCO3) saturation

Poleward range expansion of marine organisms is commonly attributed to anthropogenic ocean warming. However, the extent to which a single species can migrate poleward remains unclear. In this study, we used molecular data to examine the current distribution of the Pocillopora damicornis species complex in Taiwan waters and applied niche modeling to predict its potential range through the end of the 21st Century. The P. damicornis species complex is widespread across shallow, tropical and subtropical waters of the Indo-Pacific regions. Our results revealed that populations from subtropical nonreefal coral communities are P. damicornis, whose native geographical ranges are approximately between 23°N and 35°N. In contrast, those from tropical reefs are P. acuta. Our analysis of 50 environmental data layers demonstrated that the concentrations of CaCO3 polymorphs had the greatest contributions to the distributions of the two species. Future projections under intermediate shared socioeconomic pathways (SSP) 2-4.5 and very high (SSP5-8.5) scenarios of greenhouse gas emissions showed that while sea surface temperature (SST) isotherms would shift northwards, saturation isolines of two CaCO3 polymorphs, calcite (Ωcal) and aragonite (Ωarag), would shift southwards by 2100. Subsequent predictions of future suitable habitats under those conditions indicated that distinct delimitation of geographical ranges for the two species would persist, and neither would extend beyond its native geographical zones, indicating that tropical Taiwan waters are the northern limit for P. acuta. In contrast, subtropical waters are the southern limit for P. damicornis. We concluded that the decline in CaCO3 saturation would make high latitudes less inhabitable, which could be one of the boundary elements that limit poleward range expansion driven by rising SSTs and preserve the latitudinal diversity gradient (LDG) on Earth. Consequently, poleward migration of tropical reef corals to cope with warming oceans should be reevaluated.

The origin and speciation of orchids

Orchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up-to-date phylogeographic analysis. We present a new Orchidaceae phylogeny based on combined high-throughput and Sanger sequencing data, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and c. 7% (1921) of the 29 524 accepted species, and use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distributions from the World Checklist of Vascular Plants. The orchids' most recent common ancestor is inferred to have lived in Late Cretaceous Laurasia. The modern range of Apostasioideae, which comprises two genera with 16 species from India to northern Australia, is interpreted as relictual, similar to that of numerous other groups that went extinct at higher latitudes following the global climate cooling during the Oligocene. Despite their ancient origin, modern orchid species diversity mainly originated over the last 5 Ma, with the highest speciation rates in Panama and Costa Rica. These results alter our understanding of the geographic origin of orchids, previously proposed as Australian, and pinpoint Central America as a region of recent, explosive speciation.

Reconciling fossils with phylogenies reveals the origin and macroevolutionary processes explaining the global cycad biodiversity

The determinants of biodiversity patterns can be understood using macroevolutionary analyses. The integration of fossils into phylogenies offers a deeper understanding of processes underlying biodiversity patterns in deep time. Cycadales are considered a relict of a once more diverse and globally distributed group but are restricted to low latitudes today. We still know little about their origin and geographic range evolution. Combining molecular data for extant species and leaf morphological data for extant and fossil species, we study the origin of cycad global biodiversity patterns through Bayesian total-evidence dating analyses. We assess the ancestral geographic origin and trace the historical biogeography of cycads with a time-stratified process-based model. Cycads originated in the Carboniferous on the Laurasian landmass and expanded in Gondwana in the Jurassic. Through now-vanished continental connections, Antarctica and Greenland were crucial biogeographic crossroads for cycad biogeography. Vicariance is an essential speciation mode in the deep and recent past. Their latitudinal span increased in the Jurassic and restrained toward subtropical latitudes in the Neogene in line with biogeographic inferences of high-latitude extirpations. We show the benefits of integrating fossils into phylogenies to estimate ancestral areas of origin and to study evolutionary processes explaining the global distribution of present-day relict groups.

Climate change and land use threaten global hotspots of phylogenetic endemism for trees

Across the globe, tree species are under high anthropogenic pressure. Risks of extinction are notably more severe for species with restricted ranges and distinct evolutionary histories. Here, we use a global dataset covering 41,835 species (65.1% of known tree species) to assess the spatial pattern of tree species' phylogenetic endemism, its macroecological drivers, and how future pressures may affect the conservation status of the identified hotspots. We found that low-to-mid latitudes host most endemism hotspots, with current climate being the strongest driver, and climatic stability across thousands to millions of years back in time as a major co-determinant. These hotspots are mostly located outside of protected areas and face relatively high land-use change and future climate change pressure. Our study highlights the risk from climate change for tree diversity and the necessity to strengthen conservation and restoration actions in global hotspots of phylogenetic endemism for trees to avoid major future losses of tree diversity.

Numbers of fish species, higher taxa, and phylogenetic similarity decrease with latitude and depth, and deep-sea assemblages are unique

Species richness has been found to increase from the poles to the tropics but with a small dip near the equator over all marine fishes. Phylogenetic diversity measures offer an alternative perspective on biodiversity linked to evolutionary history. If phylogenetic diversity is standardized for species richness, then it may indicate places with relatively high genetic diversity. Latitudes and depths with both high species and phylogenetic diversity would be a priority for conservation. We compared latitudinal and depth gradients of species richness, and three measures of phylogenetic diversity, namely average phylogenetic diversity (AvPD), the sum of the higher taxonomic levels (STL) and the sum of the higher taxonomic levels divided by the number of species (STL/spp) for modelled ranges of 5,619 marine fish species. We distinguished all, bony and cartilaginous fish groups and four depth zones namely: whole water column; 0 -200 m; 201-1,000 m; and 1,001-6,000 m; at 5°  latitudinal intervals from 75°S to 75°N, and at 100 m depth intervals from 0 m to 3,500 m. Species richness and higher taxonomic richness (STL) were higher in the tropics and subtropics with a small dip at the equator, and were significantly correlated among fish groups and depth zones. Species assemblages had closer phylogenetic relationships (lower AvPD and STL/spp) in warmer (low latitudes and shallow water) than colder environments (high latitudes and deep sea). This supports the hypothesis that warmer shallow latitudes and depths have had higher rates of evolution across a range of higher taxa. We also found distinct assemblages of species in different depth zones such that deeper sea species are not simply a subset of shallow assemblages. Thus, conservation needs to be representative of all latitudes and depth zones to encompass global biodiversity.

The hierarchy of factors predicting the latitudinal diversity gradient

The numerous explanations for why Earth's biodiversity is concentrated at low latitudes fail to explain variation in the strength and even direction of the gradient through deep time. Consequently, we do not know if today's gradient is representative of what might be expected on other planets or is merely an idiosyncrasy of Earth's history. We propose a hierarchy of factors driving the latitudinal distribution of diversity: (i) over geologically long time spans, diversity is largely predicted by climate; (ii) when climatic gradients are shallow, diversity tracks habitat area; and (iii) historical contingencies linked to niche conservatism have geologically short-term, transient influence at most. Thus, latitudinal diversity gradients, although variable in strength and direction, are largely predictable on our planet and possibly others.

Alternating regimes of shallow and deep-sea diversification explain a species-richness paradox in marine fishes

The deep sea contains a surprising diversity of life, including iconic fish groups such as anglerfishes and lanternfishes. Still, >65% of marine teleost fish species are restricted to the photic zone <200 m, which comprises less than 10% of the ocean's total volume. From a macroevolutionary perspective, this paradox may be explained by three hypotheses: 1) shallow water lineages have had more time to diversify than deep-sea lineages, 2) shallow water lineages have faster rates of speciation than deep-sea lineages, or 3) shallow-to-deep sea transition rates limit deep-sea richness. Here we use phylogenetic comparative methods to test among these three non-mutually exclusive hypotheses. While we found support for all hypotheses, the disparity in species richness is better described as the uneven outcome of alternating phases that favored shallow or deep diversification over the past 200 million y. Shallow marine teleosts became incredibly diverse 100 million y ago during a period of warm temperatures and high sea level, suggesting the importance of reefs and epicontinental settings. Conversely, deep-sea colonization and speciation was favored during brief episodes when cooling temperatures increased the efficiency of the ocean's carbon pump. Finally, time-variable ecological filters limited shallow-to-deep colonization for much of teleost history, which helped maintain higher shallow richness. A pelagic lifestyle and large jaws were associated with early deep-sea colonists, while a demersal lifestyle and a tapered body plan were typical of later colonists. Therefore, we also suggest that some hallmark characteristics of deep-sea fishes evolved prior to colonizing the deep sea.

Temperature-dependent evolutionary speed shapes the evolution of biodiversity patterns across tetrapod radiations

Biodiversity varies predictably with environmental energy around the globe, but the underlaying mechanisms remain incompletely understood. The evolutionary speed hypothesis predicts that environmental kinetic energy shapes variation in speciation rates through temperature- or life history-dependent rates of evolution. To test whether variation in evolutionary speed can explain the relationship between energy and biodiversity in birds, mammals, amphibians, and reptiles, we simulated diversification over 65 million years of geological and climatic change with a spatially explicit eco-evolutionary simulation model. We modelled four distinct evolutionary scenarios in which speciation-completion rates were dependent on temperature (M1), life history (M2), temperature and life history (M3), or were independent of temperature and life-history (M0). To assess the agreement between simulated and empirical data, we performed model selection by fitting supervised machine learning models to multidimensional biodiversity patterns. We show that a model with temperature-dependent rates of speciation (M1) consistently had the strongest support. In contrast to statistical inferences, which showed no general relationships between temperature and speciation rates in tetrapods, we demonstrate how process-based modelling can disentangle the causes behind empirical biodiversity patterns. Our study highlights how environmental energy has played a fundamental role in the evolution of biodiversity over deep time.

Analysing diversification dynamics using barcoding data: The case of an obligate mycorrhizal symbiont

Analysing diversification dynamics is key to understanding the past evolutionary history of clades that led to present-day biodiversity patterns. While such analyses are widespread in well-characterized groups of species, they are much more challenging in groups for which diversity is mostly known through molecular techniques. Here, we use the largest global database on the small subunit (SSU) rRNA gene of Glomeromycotina, a subphylum of microscopic arbuscular mycorrhizal fungi that provide mineral nutrients to most land plants by forming one of the oldest terrestrial symbioses, to analyse the diversification dynamics of this clade in the past 500 million years. We perform a range of sensitivity analyses and simulations to control for potential biases linked to the nature of the data. We find that Glomeromycotina tend to have low speciation rates compared to other eukaryotes. After a peak of speciations between 200 and 100 million years ago, they experienced an important decline in speciation rates toward the present. Such a decline could be at least partially related to a shrinking of their mycorrhizal niches and to their limited ability to colonize new niches. Our analyses identify patterns of diversification in a group of obligate symbionts of major ecological and evolutionary importance and illustrate that short molecular markers combined with intensive sensitivity analyses can be useful for studying diversification dynamics in microbial groups.

Learning from the past: opportunities for advancing ecological research and practice using palaeoecological data

Palaeoecology involves analysis of fossil and sub-fossil evidence preserved within sediments to understand past species distributions, habitats and ecosystems. However, while palaeoecological research is sometimes made relevant to contemporary ecology, especially to advance understanding of biogeographical theory or inform habitat-based conservation at specific sites, most ecologists do not routinely incorporate palaeoecological evidence into their work. Thus most cross-discipline links are palaeoecology → ecology rather than ecology → palaeoecology. This is likely due to lack of awareness and/or the misnomer that palaeoecology invariably relates to the "distant past" (thousands of years) rather than being applicable to the "recent past" (last ~ 100-200 years). Here, we highlight opportunities for greater integration of palaeoecology within contemporary ecological research, policy, and practice. We identify situations where palaeoecology has been, or could be, used to (1) quantify recent temporal change (e.g. population dynamics; predator-prey cycles); (2) "rewind" to a particular point in ecological time (e.g. setting restoration/rewilding targets; classifying cryptogenic species); (3) understand current ecological processes that are hard to study real-time (e.g. identifying keystone species; detecting ecological tipping points); (4) complement primary data and historical records to bridge knowledge gaps (e.g. informing reintroductions and bioindicator frameworks); (5) disentangle natural and anthropogenic processes (e.g. climate change); and (6) draw palaeoecological analogues (e.g. impacts of pests). We conclude that the possibilities for better uniting ecology and palaeoecology to form an emerging cross-boundary paradigm are as extensive as they are exciting: we urge ecologists to learn from the past and seek opportunities to extend, improve, and strengthen their work using palaeoecological data.

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 criticized 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 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 modeling, but they in no way suggest we should abandon diversification modeling 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. [Birth–death models; extinction; phylogenetics; speciation.]

Evolution of Dispersal, Habit, and Pollination in Africa Pushed Apocynaceae Diversification After the Eocene-Oligocene Climate Transition

Apocynaceae (the dogbane and milkweed family) is one of the ten largest flowering plant families, with approximately 5,350 species and diverse morphology and ecology, ranging from large trees and lianas that are emblematic of tropical rainforests, to herbs in temperate grasslands, to succulents in dry, open landscapes, and to vines in a wide variety of habitats. Despite a specialized and conservative basic floral architecture, Apocynaceae are hyperdiverse in flower size, corolla shape, and especially derived floral morphological features. These are mainly associated with the development of corolline and/or staminal coronas and a spectrum of integration of floral structures culminating with the formation of a gynostegium and pollinaria—specialized pollen dispersal units. To date, no detailed analysis has been conducted to estimate the origin and diversification of this lineage in space and time. Here, we use the most comprehensive time-calibrated phylogeny of Apocynaceae, which includes approximately 20% of the species covering all major lineages, and information on species number and distributions obtained from the most up-to-date monograph of the family to investigate the biogeographical history of the lineage and its diversification dynamics. South America, Africa, and Southeast Asia (potentially including Oceania), were recovered as the most likely ancestral area of extant Apocynaceae diversity; this tropical climatic belt in the equatorial region retained the oldest extant lineages and these three tropical regions likely represent museums of the family. Africa was confirmed as the cradle of pollinia-bearing lineages and the main source of Apocynaceae intercontinental dispersals. We detected 12 shifts toward accelerated species diversification, of which 11 were in the APSA clade (apocynoids, Periplocoideae, Secamonoideae, and Asclepiadoideae), eight of these in the pollinia-bearing lineages and six within Asclepiadoideae. Wind-dispersed comose seeds, climbing growth form, and pollinia appeared sequentially within the APSA clade and probably work synergistically in the occupation of drier and cooler habitats. Overall, we hypothesize that temporal patterns in diversification of Apocynaceae was mainly shaped by a sequence of morphological innovations that conferred higher capacity to disperse and establish in seasonal, unstable, and open habitats, which have expanded since the Eocene-Oligocene climate transition.

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.

Comparing diversification rates in lakes, rivers, and the sea

The diversity of species inhabiting freshwater relative to marine habitats is striking, given that freshwater habitats encompass <1% of Earth's water. The most commonly proposed explanation for this pattern is that freshwater habitats are more fragmented than marine habitats, allowing more opportunities for allopatric speciation and thus increased diversification rates in freshwater. However, speciation may be generally faster in sympatry than in allopatry, as illustrated by lacustrine radiations such as African cichlids. Such differences between rivers and lakes may be important to consider when comparing diversification broadly among freshwater and marine groups. Here I compared diversification rates of teleost fishes in marine, riverine and lacustrine habitats. I found that lakes had faster speciation and net diversification rates than other aquatic habitats. However, most freshwater diversity arose in rivers. Surprisingly, riverine and marine habitats had similar rates of net diversification on average. Biogeographic models suggest that lacustrine habitats are evolutionarily unstable, explaining the dearth of lacustrine species in spite of their rapid diversification. Collectively, these results suggest that strong diversification rate differences are unlikely to explain the freshwater paradox. Instead, this pattern may be attributable to the comparable amount of time spent in riverine and marine habitats over the 200-million-year history of teleosts.

Evolutionary drivers, morphological evolution and diversity dynamics of a surviving mammal clade: cainotherioids at the Eocene-Oligocene transition

The Eocene-Oligocene transition (EOT) represents a period of global environmental changes particularly marked in Europe and coincides with a dramatic biotic turnover. Here, using an exceptional fossil preservation, we document and analyse the diversity dynamics of a mammal clade, Cainotherioidea (Artiodactyla), that survived the EOT and radiated rapidly immediately after. We infer their diversification history from Quercy Konzentrat-Lagerstätte (south-west France) at the species level using Bayesian birth-death models. We show that cainotherioid diversity fluctuated through time, with extinction events at the EOT and in the late Oligocene, and a major speciation burst in the early Oligocene. The latter is in line with our finding that cainotherioids had a high morphological adaptability following environmental changes throughout the EOT, which probably played a key role in the survival and evolutionary success of this clade in the aftermath. Speciation is positively associated with temperature and continental fragmentation in a time-continuous way, while extinction seems to synchronize with environmental change in a punctuated way. Within-clade interactions negatively affected the cainotherioid diversification, while inter-clade competition might explain their final decline during the late Oligocene. Our results provide a detailed dynamic picture of the evolutionary history of a mammal clade in a context of global change.

Phytogeographic history of the Tea family inferred through high-resolution phylogeny and fossils

The tea family (Theaceae) has a highly unusual amphi-Pacific disjunct distribution: most extant species in the family are restricted to subtropical evergreen broadleaf forests in East Asia, while a handful of species occur exclusively in the subtropical and tropical Americas. Here we used an approach that integrates the rich fossil evidence of this group with phylogenies in biogeographic analysis to study the processes behind this distribution pattern. We first combined genome-skimming sequencing with existing molecular data to build a robust species-level phylogeny for c.140 Theaceae species, resolving most important unclarified relationships. We then developed an empirical Bayesian method to incorporate distribution evidence from fossil specimens into historical biogeographic analyses and used this method to account for the spatiotemporal history of Theaceae fossils. We compared our method with an alternative Bayesian approach and show that it provides consistent results while significantly reduces computational demands which allows analyses of much larger datasets. Our analyses revealed a circumboreal distribution of the family from the early Cenozoic to the Miocene and inferred repeated expansions and retractions of the modelled distribution in the Northern Hemisphere, suggesting that the current Theaceae distribution could be the remnant of a larger continuous distribution associated with the boreotropical forest that has been hypothesized to occupy most of the northern latitudes in the early Cenozoic. These results contradict with studies that only considered current species distributions and showcase the necessity of integrating fossil and molecular data in phylogeny-based parametric biogeographic models to improve the reliability of inferred biogeographical events.

Out of the extratropics: the evolution of the latitudinal diversity gradient of Cenozoic marine plankton

Many ecological and evolutionary hypotheses have been proposed to explain the latitudinal diversity gradient, i.e. the increase in species richness from the poles to the tropics. Among the evolutionary hypotheses, the 'out of the tropics' (OTT) hypothesis has received considerable attention. The OTT posits that the tropics are both a cradle and source of biodiversity for extratropical regions. To test the generality of the OTT hypothesis, we explored the spatial biodiversity dynamics of unicellular marine plankton over the Cenozoic era (the last 66 Myr). We find large-scale climatic changes during the Cenozoic shaped the diversification and dispersal of marine plankton. Origination was generally more likely in the extratropics and net dispersal was towards the tropics rather than in the opposite direction, especially during the warmer climates of the early Cenozoic. Although migration proportions varied among major plankton groups and climate phases, we provide evidence that the extratropics were a source of tropical microplankton biodiversity over the last 66 Myr.

Truncated bimodal latitudinal diversity gradient in early Paleozoic phytoplankton

The latitudinal diversity gradient (LDG)-the decline in species richness from the equator to the poles-is classically considered as the most pervasive macroecological pattern on Earth, but the timing of its establishment, its ubiquity in the geological past, and explanatory mechanisms remain uncertain. By combining empirical and modeling approaches, we show that the first representatives of marine phytoplankton exhibited an LDG from the beginning of the Cambrian, when most major phyla appeared. However, this LDG showed a single peak of diversity centered on the Southern Hemisphere, in contrast to the equatorial peak classically observed for most modern taxa. We find that this LDG most likely corresponds to a truncated bimodal gradient, which probably results from an uneven sediment preservation, smaller sampling effort, and/or lower initial diversity in the Northern Hemisphere. Variation of the documented LDG through time resulted primarily from fluctuations in annual sea-surface temperature and long-term climate changes.

Spatial sampling heterogeneity limits the detectability of deep time latitudinal biodiversity gradients

The latitudinal biodiversity gradient (LBG), in which species richness decreases from tropical to polar regions, is a pervasive pattern of the modern biosphere. Although the distribution of fossil occurrences suggests this pattern has varied through deep time, the recognition of palaeobiogeographic patterns is hampered by geological and anthropogenic biases. In particular, spatial sampling heterogeneity has the capacity to impact upon the reconstruction of deep time LBGs. Here we use a simulation framework to test the detectability of three different types of LBG (flat, unimodal and bimodal) over the last 300 Myr. We show that heterogeneity in spatial sampling significantly impacts upon the detectability of genuine LBGs, with known biodiversity patterns regularly obscured after applying the spatial sampling window of fossil collections. Sampling-standardization aids the reconstruction of relative biodiversity gradients, but cannot account for artefactual absences introduced by geological and anthropogenic biases. Therefore, we argue that some previous studies might have failed to recover the ‘true’ LBG type owing to incomplete and heterogeneous sampling, particularly between 200 and 20 Ma. Furthermore, these issues also have the potential to bias global estimates of past biodiversity, as well as inhibit the recognition of extinction and radiation events.

The evolution of a tropical biodiversity hotspot

The tropics are the source of most biodiversity yet inadequate sampling obscures answers to fundamental questions about how this diversity evolves. We leveraged samples assembled over decades of fieldwork to study diversification of the largest tropical bird radiation, the suboscine passerines. Our phylogeny, estimated using data from 2389 genomic regions in 1940 individuals of 1283 species, reveals that peak suboscine species diversity in the Neotropics is not associated with high recent speciation rates but rather with the gradual accumulation of species over time. Paradoxically, the highest speciation rates are in lineages from regions with low species diversity, which are generally cold, dry, unstable environments. Our results reveal a model in which species are forming faster in environmental extremes but have accumulated in moderate environments to form tropical biodiversity hotspots.

Unraveling the Spiraling Radiation: A Phylogenomic Analysis of Neotropical Costus L

The family of pantropical spiral gingers (Costaceae Nakai; c. 125 spp.) can be used as a model to enhance our understanding of the mechanisms underlying Neotropical diversity. Costaceae has higher taxonomic diversity in South and Central America (c. 72 Neotropical species, c. 30 African, c. 23 Southeast Asian), particularly due to a radiation of Neotropical species of the genus Costus L. (c. 57 spp.). However, a well-supported phylogeny of the Neotropical spiral gingers including thorough sampling of proposed species encompassing their full morphologic and geographic variation is lacking, partly due to poor resolution recovered in previous analyses using a small sampling of loci. Here we use a phylogenomic approach to estimate the phylogeny of a sample of Neotropical Costus species using a targeted enrichment approach. Baits were designed to capture conserved elements' variable at the species level using available genomic sequences of Costus species and relatives. We obtained 832 loci (generating 791,954 aligned base pairs and 31,142 parsimony informative sites) for samples that encompassed the geographical and/or morphological diversity of some recognized species. Higher support values that improve the results of previous studies were obtained when including all the available loci, even those producing unresolved gene trees and having a low proportion of variable sites. Concatenation and coalescent-based species trees methods converge in almost the same topology suggesting a robust estimation of the relationships, even under the high levels of gene tree conflict presented here. The bait set design here presented made inferring a robust phylogeny to test taxonomic hypotheses possible and will improve our understanding of the origins of the charismatic diversity of the Neotropical spiral gingers.

Digest: The contribution of historical climate events in shaping the modern latitudinal diversity gradient of ancient reptiles

It is recognized that biodiversity changes across the planet latitudinally; however, the timing of and reasons for diversity loss at higher latitudes are not well understood. Meseguer and Condamine investigate phylogenies and fossil evidence of reptilian species and determine that global warming and cooling events allowed asymmetric extinction and dispersion across latitudes, suggesting a hypothesis where climate profoundly shapes the latitudinal diversity gradient in certain taxa.

The latitudinal diversity gradient of tetrapods across the Permo-Triassic mass extinction and recovery interval

The decline in species richness from the equator to the poles is referred to as the latitudinal diversity gradient (LDG). Higher equatorial diversity has been recognized for over 200 years, but the consistency of this pattern in deep time remains uncertain. Examination of spatial biodiversity patterns in the past across different global climate regimes and continental configurations can reveal how LDGs have varied over Earth history and potentially differentiate between suggested causal mechanisms. The Late Permian-Middle Triassic represents an ideal time interval for study, because it is characterized by large-scale volcanic episodes, extreme greenhouse temperatures and the most severe mass extinction event in Earth history. We examined terrestrial and marine tetrapod spatial biodiversity patterns using a database of global tetrapod occurrences. Terrestrial tetrapods exhibit a bimodal richness distribution throughout the Late Permian-Middle Triassic, with peaks in the northern low latitudes and southern mid-latitudes around 20-40° N and 60° S, respectively. Marine reptile fossils are known almost exclusively from the Northern Hemisphere in the Early and Middle Triassic, with highest diversity around 20° N. Reconstructed terrestrial LDGs contrast strongly with the generally unimodal gradients of today, potentially reflecting high global temperatures and prevailing Pangaean super-monsoonal climate system during the Permo-Triassic.