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Condamine, F. L.

Publications and source records attributed to Condamine, F. L..

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Bayesian inference of global land plant diversification dynamics across the Phanerozoic

Underlying diversification patterns and potential drivers of land plants remain puzzling, particularly at deep-time and global scales. Here, we reconstruct the diversification dynamics of land plants using an updated time-calibrated phylogeny comprising approximately 30,000 extant species, and nearly 40,000 fossil occurrences within the Bayesian birth-death frameworks. Our analyses indicate that angiosperms exhibit the highest diversification rates, whereas ferns underwent a marked diversification increase during the Cretaceous, coincident with the rapid radiation of angiosperms. Among the major Phanerozoic mass extinctions, the Cretaceous-Paleogene event has the most significant impact on land plant diversity, with estimated genus-level losses of 13%, 14%, and 4% in bryophytes, pteridophytes, and gymnosperms. We identify a pattern consistent with competitive displacement scenario, in which pteridophytes origination rates declined as gymnosperm diversity increased, accompanying the transition from pteridophyte- to gymnosperm-dominated floras. We find that plant-insect interactions have originated as early as the emergence of pteridophytes, potentially promoting the diversification of pteridophytes and gymnosperms. During the Cretaceous, these associations shifted toward angiosperms, as indicated by a positive relationship between insect diversity and angiosperm origination rates. Finally, continental fragmentation, fluctuations in aridity, atmospheric carbon and sedimentary dynamics, showed stronger associations with the successive rise and decline of major land plant groups.

evolutionary biology↗

Macroevolutionary dynamics of beetles reveal long-term coupling with vascular plant diversification

Beetles (Coleoptera) represent the most species-rich group of organisms, yet the macroevolutionary processes underlying their exceptional diversification remain unresolved. Here, we estimated their origination and extinction dynamics as well as the potential drivers shaping these patterns, using Bayesian birth-death models applied to a comprehensive fossil occurrence dataset. We find that beetles have experienced low extinction rates and exhibited high resilience through major extinction events. Vascular plant diversities emerge as a key driver of beetle diversification, with origination rates positively correlated with angiosperms, and extinction rates negatively correlated, especially for Polyphaga, the most diverse beetle clade. Together, our results provide quantitative evidence that the angiosperm radiation not only promoted beetle origination, but also buffered them against extinction, illustrating how ecological interactions can shape macroevolution.

evolutionary biology↗

Fossil-based analyses of clades' diversification patterns require taxonomic expertise and appropriate methodology

SummaryEstimating deep-time diversification patterns and the establishment of extant biodiversity represent major challenges in macroevolution. Fossil record data provide essential information to address these topics, but their heterogeneous temporal and geographical distributions require using analytical approaches to process these data. Gardiner et al.1 (hereafter GEA) used a deep-learning model2 and a fossil-occurrences dataset3 to estimate neoselachian richness over the last 145 myr. Results and DiscussionGEA1 found that neoselachian diversity increased throughout the Cretaceous, was little impacted by the Cretaceous-Paleogene (K/Pg) mass extinction ([~]10% species loss), and peaked in the mid-Eocene but declined until the Present. While the Cretaceous increase in neoselachian richness is well known4, the other findings of GEA1 are at odds with current knowledge. With the exception of lamniform sharks, the perceived decrease in species richness in the recent past is most likely due to a drop in available fossil record data combined with difficulties in identifying extant species in the fossil record5. Similarly, all previous analyses of the impact of the K/Pg mass extinction on elasmobranch diversification have reported high extinction rates, a marked diversity drop, and delayed recovery6-7, despite heterogeneity across clades, ecology, and geographical distribution7. Taking the K/Pg as an example, we demonstrate that the discrepancies between GEA1s results and current consensus is most likely due to a combination of incomplete, unverified, and incorrect fossil-occurrence data with inappropriate methodology.

paleontology↗

Termites became the dominant decomposers of the tropics after two diversification pulses

Insects have the highest species richness among animals, but the extent of their diversity and the timing of their diversification remain unclear. Insect diversification is difficult to infer due to the incompleteness of the fossil record. Phylogenetic trees of extant species reconstructed from an exhaustive sampling can be useful to address major evolutionary questions. Here, we investigated the diversification of termites, which comprise 2,995 described species, using estimates of speciation, extinction, and net diversification rates inferred from molecular phylogenies including 2,800 samples representing 1,377 putative species. Termites originated in the Early Cretaceous [~]132 million years ago. Estimated extinction rates were close to zero despite fossil evidence of extinction; therefore, we focused our interpretations on the net diversification rates. Our analyses detected two significant rate shifts. The first shift occurred at the end of the Cretaceous, initially in the Kalotermitidae, then in the Neoisoptera as they started outcompeting Kalotermitidae. The second shift involved multiple lineages of Neoisoptera, especially Termitidae, which diversified as they colonized the world after the global cooling initiated at the Eocene-Oligocene transition. Our results indicate that termites became the dominant insect decomposers of tropical ecosystems as global climate change impacted ecosystems.

evolutionary biology↗

Phylogenomics of Messor harvester ants (Hymenoptera: Formicidae: Stenammini) unravels their biogeographical origin and diversification patterns

As a major abiotic factor, climate change is expected to profoundly alter biological communities. On this basis, identifying how past temperature variations affected species diversification and distribution can help to predict the effects of the ongoing climate change. In this study, we focused on the harvester ant genus Messor which is mostly adapted to dry environments dominated by seed-producing plants. The phylogenetic analysis of 2,524 markers obtained from 58 Messor species/subspecies, supports their emergence in the Irano-Indian area approximately 20 Mya. Phylogenetic relationships uncovered in this study enabled us to redefine historical taxonomic groups, providing a solid basis for future revisions that encompass the entire genus diversity. Their diversification appears to be affected by temperature, with a higher speciation rate during warmer periods. This confirms that the ecological specialization of Messor makes them strongly dependent on thermal conditions. Our results highlight the importance of abiotic factors on diversification processes, especially for highly specialized species that may exhibit predictable evolutionary responses to climate changes.

evolutionary biology↗

Early Cretaceous Origin and Evolutionary History of Palms (Arecaceae) inferred from 1,033 Nuclear Genes and a New Synthesis of Fossil Evidence

AO_SCPLOWBSTRACTC_SCPLOWTropical rainforests are home to almost half of all known plant diversity, yet a shortfall in tropical plant phylogenetic hypotheses is hindering our understanding of how rainforests have formed and adapted to past global changes. Phylogenetic and historical biogeographic evidence from key rainforest lineages, including palms (Arecaceae), are required to illuminate the history of these ecosystems. However, our current understanding of the palm tree of life is based on uneven sampling of data from the plastid and nuclear genome, and numerous palm genera and palm fossils have been described or revised over the past decade, casting doubt on many palm relationships, ages and ancestral ranges inferred in previous studies. Here, we infer the phylogenetic relationships of all palm genera based on data from 1,033 nuclear genes generated using target sequence capture. Our palm tree of life is highly resolved and supported. Remaining areas of ambiguity reflect the complex dynamics of palm evolution, including many rapid diversification events in subfamily Arecoideae and putative cases of ancient reticulation throughout the family. We review the phylogenetic placement and age of hundreds of palm fossils and use a vetted selection to estimate divergence times and ancestral ranges for all palm genera. We show that the family is older than previously thought, likely first diversifying in the Early Cretaceous in Laurasia, and that three quarters of the genera had originated by the Oligocene. The early spread of palms across the world involved at least 40 long-distance dispersals across oceanic gaps. Dispersals away from northern latitudes vastly outnumber dispersals into these latitudes, consistent with the ancient affinity of palms for megathermal climates, and suggesting that global cooling during the Oligocene was a major constraint on early palm distribution. Our dated phylogenomic tree and curated fossil dataset provide a new foundation for evolutionary studies on palms, opening the door to deeper research on the rainforest biome in which they thrive.

evolutionary biology↗

The Origin And Speciation Of Orchids

Orchids constitute one of the most spectacular radiations of flowering plants. However, their geographical origin, historical spread across the globe, and hotspots of speciation remain uncertain due to the lack of a broad phylogenomic framework. We present a new Orchidaceae phylogeny based on high-throughput and Sanger sequencing datasets, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and [~]7% (1,921) of the currently 29,524 accepted species. We then use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distribution data through the World Checklist of Vascular Plants. Orchids most recent common ancestor is traced back to the Late Cretaceous in Laurasia. The modern Southeast Asian range of subfamily Apostasioideae is interpreted as relictual, matching the history of numerous clades that went extinct at higher latitudes following the global climate cooled during the Oligocene. Despite their ancient origins, modern orchid species diversity mainly originated over the last 5 Ma, with the fastest speciation rates found in south-eastern Central America. Our results substantially alter our understanding of the geographic origin of orchids, previously proposed as Australian, and further pinpoint the role of Central American as a region of recent and explosive speciation.

evolutionary biology↗

Convergence in sympatric swallowtail butterflies reveals ecological interactions as a key driver of worldwide trait diversification.

Ecological interactions may fuel phenotypic diversification in sympatric species. While competition can enhance trait divergence, other ecological interactions may promote convergence in sympatric species. Within butterflies, evolutionary convergences in wing color patterns have been reported between distantly-related species, especially in females from palatable species, where mimetic color patterns are promoted by predator communities shared with defended species living in sympatry. Wing color patterns are also often involved in species recognition in butterflies, and divergence in this trait has been reported in closely-related species living in sympatry as a result of reproductive character displacement. Here we investigate the effect of sympatry between species on the convergence vs. divergence of their wing color patterns in relation to phylogenetic distance, focusing on the iconic swallowtail butterflies (family Papilionidae). We developed a new unsupervised machine-learning-based method to estimate phenotypic distances among wing color patterns from 337 species allowing to finely quantify morphological diversity at global scale within and among species, allowing to compute pairwise phenotypic distances between sympatric and allopatric species pairs. We found that sympatry promoted strong convergence, while divergence in sympatry was less frequent and weaker. The effect of sympatry on convergence was stronger on females than males, suggesting that differential selective pressures acting on the two sexes drove sexual dimorphism. Our results highlight the significant effect of ecological interactions driven by predation pressures on trait diversification in Papilionidae and evidence the interaction between phylogenetic proximity and ecological interactions in sympatry acting on macroevolutionary patterns of phenotypic diversification.

evolutionary biology↗

The dual role of the angiosperm radiation on insect diversification

Most of the animal pollination is realized by insects, interactions between them and flowering plants have been hypothesized to be important drivers of diversification. Yet, there is weak support for coevolutionary diversification in plant-pollinator interactions. Macroevolutionary studies on insect and plant diversities support the hypothesis that angiosperms evolved after an insect diversity peak in the Early Cretaceous, suggesting that gymnosperm pollinators may have been accessible for angiosperms when they evolved. We examined fossil and phylogenetic evidence documenting this hypothesis and provide new clues on the impact of angiosperm radiation on insect diversification. Using the family-level fossil record of insects and a Bayesian process-based approach, we estimated diversification rates and the role of six different variables on insect macroevolutionary history. We found that, among the six tested variables, angiosperms had a dual role that has changed through time with an attenuation of insect extinction in the Cretaceous and a driver of insect origination in the Cenozoic. However, increasing insect diversity, spore plants and global temperature also showed strong positive correlation with both origination and extinction rates of insects, suggesting that different drivers had important effect on insect evolution, not just angiosperms, which would deserve further studies.

paleontology↗

Phylogenomics Illuminates the Evolutionary History of Wild Silkmoths in Space and Time (Lepidoptera: Saturniidae)

AO_SCPLOWBSTRACTC_SCPLOWWild silkmoths (Saturniidae) are one of the most emblematic and most studied families of moths. Yet, the absence of a robust phylogenetic framework based on a comprehensive taxonomic sampling impedes our understanding of their evolutionary history. We analyzed 1,024 ultraconserved elements (UCEs) and their flanking regions to infer the relationships among 338 species of Saturniidae representing all described subfamilies, tribes, and genera. We investigated systematic biases in genomic data and performed dating and historical biogeographic analyses to reconstruct the evolutionary history of wild silkmoths in space and time. Using Gene Genealogy Interrogation, we showed that saturation of nucleotide sequence data blurred our understanding of early divergences and first biogeographic events. Our analyses support a Neotropical origin of saturniids, shortly after the Cretaceous-Paleogene extinction event (ca 64.0 [stem] - 52.0 [crown] Ma), and two independent colonization events of the Old World during the Eocene, presumably through the Bering Land Bridge. Early divergences strongly shaped the distribution of extant subfamilies as they showed very limited mobility across biogeographical regions, except for Saturniinae, a subfamily now present on all continents but Antarctica. Overall, our results provide a framework for in-depth investigations into the spatial and temporal dynamics of all saturniid lineages and for the integration of their evolutionary history into further global studies of biodiversity and conservation. Rather unexpectedly for a taxonomically well-known family such as Saturniidae, the proper alignment of taxonomic divisions and ranks with our phylogenetic results leads us to propose substantial rearrangements of the family classification, including the description of one new subfamily and two new tribes.

evolutionary biology↗

Mountain radiations are not only rapid and recent: ancient diversification of South American frog and lizard families related to Paleogene Andean orogeny and Cenozoic climate variations

Mountainous areas host a disproportionately large fraction of Earths biodiversity, suggesting a causal relationship between mountain building and biological diversification. Mountain clade radiations are generally associated with changes in environment, climate, and the increase in heterogeneity therein during mountain building. However, examining the causal relationship between mountain building and diversification is a complex challenge, because isolating the effects of surface uplift from other abiotic (climate) or biotic variables is not straightforward. In this study, we investigate the relative contributions of abiotic climate-driven (temperature) and geology-driven (elevation) drivers on evolutionary rates of ancient groups of organisms in the South American Andes. We present regional curves of Andean elevation based on a recent compilation of paleo-elevational data back to the Late Cretaceous, and analyse the diversification history of six Andean frog and lizard families that originated equally far back in time. For two clades (Aromobatidae and Leptodactylidae), we find that they diversified most rapidly during the early phase of mountain building (Late Cretaceous - Paleogene), when the first high-elevation habitats emerged in South America. The diversification of one clade (Centrolenidae) is correlated with Cenozoic temperature variations, with higher speciation rates during warm periods. The last three clades (Dendrobatidae, Hemiphractidae and Liolaemidae) are best explained by environment-independent diversification, although for Liolaemidae, an almost equally strong positive correlation was found between speciation and Andean elevation since the late Eocene. Our findings imply that throughout the long-lived history of surface uplift in the Andes, mountain building drove the diversification of different clades at different times, while not directly affecting other clades. Our study illustrates the importance of paleogeographic reconstructions that capture the complexity and heterogeneity of mountain building in our understanding of the effects that a changing environment plays in shaping biodiversity patterns observed today. HighlightsO_LIWe provide novel regional paleoelevation curves for the Andes back to the Late Cretaceous C_LIO_LIThe diversification history of six Andean-centered clades is studied C_LIO_LIWe find clade-specific responses to environmental changes C_LIO_LIThe impact of Andean uplift could reach further back in time than previously thought C_LI

evolutionary biology↗

Punctual ecological changes rather than global factors drive species diversification and the evolution of wing phenotypes in Morpho butterflies.

Assessing the relative importance of geographical and ecological drivers of evolution is paramount to understand the diversification of species and traits at the macroevolutionary scale. Here, we use an integrative approach, combining phylogenetics, biogeography, ecology, and quantified phenotypes to investigate the drivers of both species and phenotypic diversification of the iconic Neotropical butterfly genus Morpho. We generated a time-calibrated phylogeny for all known species and inferred historical biogeography. We fitted models of time-dependent (accounting for rate heterogeneity across the phylogeny) and paleoenvironment-dependent diversification (accounting for global effect on the phylogeny). We used geometric morphometrics to assess variation of wing size and shape across the tree, and investigated their dynamics of evolution. We found that the diversification of Morpho is best explained when considering multiple independent diversification dynamics across the tree, possibly associated with lineages occupying different microhabitat conditions. First, a shift from understory to canopy was characterized by an increased speciation rate partially coupled with an increasing rate of wing shape evolution. Second, the occupation of dense bamboo thickets accompanying a major host-plant shift from dicotyledons towards monocotyledons was associated with a simultaneous diversification rate shift and an evolutionary "jump" of wing size. Our study points to a diversification pattern driven by punctual ecological changes instead of a global driver or biogeographic history.

evolutionary biology↗

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

AO_SCPLOWBSTRACTC_SCPLOWEstimating 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 lead 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 demonstrate 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 methodological shortcomings, but by acknowledging them we can better target our joint efforts as a scientific community.

evolutionary biology↗

Ancient tropical extinctions contributed to the latitudinal diversity gradient

Biodiversity currently peaks at the equator, decreasing toward the poles. Growing fossil evidence suggest that this hump-shaped latitudinal diversity gradient (LDG) has not been persistent through time, with similar species diversity across latitudes flattening out the LDG during past greenhouse periods. This provides a new starting point for LDG research. Most studies assume the processes shaping the LDG have acted constantly through time and seek to understand why diversity accumulated in the Holarctic at lower levels than at the equator, e.g. as the result of limited dispersal, or higher turnover in Holarctic regions. However, fossil investigations suggest that we need to explain when and why diversity was lost at high latitudes to generate the LDG. Unfortunately, diversity lost scenarios in the Holarctic have been repeatedly proposed but not yet clearly demonstrated. Here, we use diversification approaches for both phylogenies and fossils to study the LDG of Testudines, Crocodilia and Lepidosauria. We show the LDG of these groups has varied over time, with high latitudes serving as a source of tropical diversity but suffering disproportionate extinction during transitional periods to cold climate. We outline the asymmetric gradient of extinction and dispersal (AGED) framework, which contextualizes previous ideas behind the LDG under a time-variable scenario. We suggest the current steep LDG may be explained by the extinction of clades adapted to warmer conditions from the new temperate regions formed in the Neogene, together with the equator-ward dispersal of organisms tracking their own climatic preferences, when tropical biomes became restricted to the equator. Conversely, high rates of speciation and pole-ward dispersals can account for the formation of an ancient flat LDG during the Cretaceous-Paleogene greenhouse period. Our results demonstrate that the inclusion of fossils in macroevolutionary studies allows detecting extinction events less detectable in analyses restricted to present-day data only.

evolutionary biology↗

Testing the role of the Red Queen and Court Jester as drivers of the macroevolution of Apollo butterflies

In macroevolution, the Red Queen (RQ) model posits that biodiversity dynamics depend mainly on species-intrinsic biotic factors such as interactions among species or life-history traits, while the Court Jester (CJ) model states that extrinsic environmental abiotic factors have a stronger role. Until recently, a lack of relevant methodological approaches has prevented the unraveling of contributions from these two types of factors to the evolutionary history of a lineage. Here we take advantage of the rapid development of new macroevolution models that tie diversification rates to changes in paleoenvironmental (extrinsic) and/or biotic (intrinsic) factors. We inferred a robust and fully-sampled species-level phylogeny, as well as divergence times and ancestral geographic ranges, and related these to the radiation of Apollo butterflies (Parnassiinae) using both extant (molecular) and extinct (fossil/morphological) evidence. We tested whether their diversification dynamics are better explained by a RQ or CJ hypothesis, by assessing whether speciation and extinction were mediated by diversity-dependence (niche filling) and clade-dependent host-plant association (RQ) or by large-scale continuous changes in extrinsic factors such as climate or geology (CJ). For the RQ hypothesis, we found significant differences in speciation rates associated with different host-plants but detected no sign of diversity-dependence. For CJ, the role of Himalayan-Tibetan building was substantial for biogeography but not a driver of high speciation, while positive dependence between warm climate and speciation/extinction was supported by continuously varying maximum-likelihood models. We find that rather than a single factor, the joint effect of multiple factors (biogeography, species traits, environmental drivers, and mass extinction) is responsible for current diversity patterns, and that the same factor might act differently across clades, emphasizing the notion of opportunity. This study confirms the importance of the confluence of several factors rather than single explanations in modeling diversification within lineages.

evolutionary biology↗

Multiple Geographical Origins of Environmental Sex Determination enhanced the diversification of Darwins Favourite Orchids

Environmental sex determination (ESD) - a change in sexual function during an individual life span driven by environmental cues - is an exceedingly rare sexual system among angiosperms. Because ESD can directly affect reproduction success, it could influence diversification rate as compared with lineages that have alternative mating systems. Here we test this hypothesis using a solid phylogenetic framework of Neotropical Catasetinae, the angiosperm lineage richest in taxa with ESD. We assess whether gains of ESD are associated with higher diversification rates compared to lineages with alternative systems while considering additional traits known to positively affect diversification rates in orchids. We found that ESD has evolved asynchronously three times during the last ~5 Myr. Lineages with ESD have consistently higher diversification rates than related lineages with other sexual systems. Habitat fragmentation due to mega-wetlands extinction, and climate instability are suggested as the driving forces for ESD evolution.

evolutionary biology↗

Recent origin of Neotropical orchids in the world’s richest plant biodiversity hotspot

* The Andean mountains of South America are the most species-rich biodiversity hotspot worldwide with about 15% of the worlds plant species, in only 1% of the worlds land surface. Orchids are a key element of the Andean flora, and one of the most prominent components of the Neotropical epiphyte diversity, yet very little is known about their origin and diversification.\n\n* We address this knowledge gap by inferring the biogeographical history and evolutionary dynamics of the two largest Neotropical orchid groups (Cymbidieae and Pleurothallidinae), using two unparalleled, densely-sampled orchid phylogenies (including 400+ newly generated DNA sequences), comparative phylogenetic methods, geological and biological datasets.\n\n* We find that the majority of Andean orchid lineages only originated in the last 15 million years. Most Andean lineages are derived from lowland Amazonian ancestors, with additional contributions from Central America and the Antilles. Species diversification is correlated with Andean orogeny, and multiple migrations and re-colonizations across the Andes indicate that mountains do not constrain orchid dispersal over long timescales.\n\n* Our study sheds new light on the timing and geography of a major Neotropical radiation, and suggests that mountain uplift promotes species diversification across all elevational zones.

evolutionary biology↗

The improbable journeys of epiphytic plants across the Andes: Historical biogeography of Cycnoches (Catasetinae, Orchidaceae)

The Andean uplift is one of the major orographic events in the New World and has impacted considerably the diversification of numerous Neotropical organisms. Despite its importance for biogeography, the specific role of mountain ranges as a dispersal barrier between South and Central American lowland plant lineages is still poorly understood. The swan orchids (Cycnoches) comprise ca 34 epiphytic species distributed in lowland and pre-montane forests of Central and South America. Here, we study the historical biogeography of Cycnoches to better understand the impact of the Andean uplift on the diversification of Neotropical lowland plant lineages. Using novel molecular sequences (five nuclear and plastid regions) and twelve biogeographic models with and without founder-event speciation, we infer that the most recent common ancestor of Cycnoches may have originated in Amazonia ca 5 Mya. The first colonization of Central America occurred from a direct migration event from Amazonia, and multiple bidirectional trans-Andean migrations between Amazonia and Central America took place subsequently. Notably, such biological exchange occurred well after major mountain building periods. The Andes have not acted as an impassable barrier for epiphytic lowland lineages such as orchids having a great potential for effortless dispersal because of the very light, anemochorous seeds.

evolutionary biology↗