Strong effects of variation in taxonomic opinion on diversification analyses

Exploring the evolutionary dynamics of myrmecophytism: Perspectives from the Southeast Asian Macaranga ant-plant symbiosis

Myrmecophytic plants utilise defensive services offered by obligate ant partners nesting in their domatia in a novel means of survival in tropical habitats. Although much is known about the ecology of myrmecophytism, there aren't enough empirical examples to demonstrate whether it substantially influences evolutionary patterns in host plant lineages. In this study, we make use of the species-rich Macaranga (Euphorbiaceae) ant-plant symbiosis distributed in the Southeast Asian Sundaland to delve into the evolutionary dynamics of myrmecophytism in host plants. We generated the most comprehensive dated phylogeny of myrmecophytic Macaranga till date using genotyping-by-sequencing (GBS). With this in hand, we traced the evolutionary history of myrmecophytism in Macaranga using parametric biogeography and ancestral state reconstruction. Diversification rate analysis methods were employed to determine if myrmecophytism enhanced diversification rates in the genus. Our results demonstrate that myrmecophytism is labile and easily lost. Ancestral state reconstruction supported a single origin of myrmecophytism in Macaranga ∼18 mya on Borneo followed by multiple losses. Diversification rate analysis methods did not yield sufficient evidence to support the hypothesis that myrmecophytism enhanced diversification rates in Macaranga; we found that topographical features on Borneo may have played a more direct role in the divergence of clades instead. Our study provides evidence that while the acquisition of domatia clearly functions as a key innovation that has enabled host plants to exploit the environment in novel ways, it may not necessarily enhance diversification rates. In fact, we hypothesise that overly specialised cases of myrmecophytism may even be an evolutionary dead end.

Scientific history, biogeography, and biological traits predict presence of cryptic or overlooked species

Genetic data show that many nominal species are composed of more than one biological species, and thus contain cryptic species in the broad sense (including overlooked species). When ignored, cryptic species generate confusion which, beyond biodiversity or vulnerability underestimation, blurs our understanding of ecological and evolutionary processes and may impact the soundness of decisions in conservation or medicine. However, very few hypotheses have been tested about factors that predispose a taxon to contain cryptic or overlooked species. To fill this gap, we surveyed the literature on free-living marine metazoans and built two data sets, one of 187,603 nominal species and another of 83 classes or phyla, to test several hypotheses, correcting for sequence data availability, taxon size and phylogenetic relatedness. We found a strong effect of scientific history: the probability of a taxon containing cryptic species was highest for the earliest described species and varied among time periods potentially consistently with an influence of prevailing scientific theories. The probability of cryptic species being present was also increased for species with large distribution ranges. They were more frequent in the north polar and south polar zones, contradicting previous predictions of more cryptic species in the tropics, and supporting the hypothesis that many cryptic species diverged recently. The number of cryptic species varied among classes, with an excess in hydrozoans and polychaetes, and a deficit in actinopterygians, for example, but precise class ranking was relatively sensitive to the statistical model used. For all models, biological traits, rather than phylum, appeared responsible for the variation among classes: there were fewer cryptic species than expected in classes with hard skeletons (perhaps because they provide good characters for taxonomy) and image-forming vision (in which selection against heterospecific mating may enhance morphological divergence), and more in classes with internal fertilisation. We estimate that among marine free-living metazoans, several thousand additional cryptic species complexes could be identified as more sequence data become available. The factors identified as important for marine animal cryptic species are likely important for other biomes and taxa and should aid many areas in biology that rely on accurate species identification.

Widespread support for a global species list with a formal governance system

Taxonomic data are a scientific common. Unlike nomenclature, which has strong governance institutions, there are currently no generally accepted governance institutions for the compilation of taxonomic data into an accepted global list. This gap results in challenges for conservation, ecological research, policymaking, international trade, and other areas of scientific and societal importance. Consensus on a global list and its management requires effective governance and standards, including agreed mechanisms for choosing among competing taxonomies and partial lists. However, governance frameworks are currently lacking, and a call for governance in 2017 generated critical responses. Any governance system to which compliance is voluntary requires a high level of legitimacy and credibility among those by and for whom it is created. Legitimacy and credibility, in turn, require adequate and credible consultation. Here, we report on the results of a global survey of taxonomists, scientists from other disciplines, and users of taxonomy designed to assess views and test ideas for a new system of taxonomic list governance. We found a surprisingly high degree of agreement on the need for a global list of accepted species and their names, and consistent views on what such a list should provide to users and how it should be governed. The survey suggests that consensus on a mechanism to create, manage, and govern a single widely accepted list of all the world's species is achievable. This finding was unexpected given past controversies about the merits of list governance.

The Major Features of Macroevolution

Evolutionary dynamics operating across deep time leave footprints in the shapes of phylogenetic trees. For the last several decades, researchers have used increasingly large and robust phylogenies to study the evolutionary history of individual clades and to investigate the causes of the glaring disparities in diversity among groups. Whereas typically not the focal point of individual clade-level studies, many researchers have remarked on recurrent patterns that have been observed across many different groups and at many different time scales. Whereas previous studies have documented various such regularities in topology and branch length distributions, they have typically focused on a single pattern and used a disparate collection (oftentimes, of quite variable reliability) of trees to assess it. Here we take advantage of modern megaphylogenies and unify previous disparate observations about the shapes embedded in the Tree of Life to create a catalog of the "major features of macroevolution." By characterizing such a large swath of subtrees in a consistent way, we hope to provide a set of phenomena that process-based macroevolutionary models of diversification ought to seek to explain.

Madagascar’s extraordinary biodiversity: Threats and opportunities

Madagascar’s unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar’s terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation statuses, the most prevalent and relevant threats, ex situ collections and programs, and the coverage and comprehensiveness of protected areas. The existing terrestrial protected area network in Madagascar covers 10.4% of its land area and includes at least part of the range of the majority of described native species of vertebrates with known distributions (97.1% of freshwater fishes, amphibians, reptiles, birds, and mammals combined) and plants (67.7%). The overall figures are higher for threatened species (97.7% of threatened vertebrates and 79.6% of threatened plants occurring within at least one protected area). International Union for Conservation of Nature (IUCN) Red List assessments and Bayesian neural network analyses for plants identify overexploitation of biological resources and unsustainable agriculture as the most prominent threats to biodiversity. We highlight five opportunities for action at multiple levels to ensure that conservation and ecological restoration objectives, programs, and activities take account of complex underlying and interacting factors and produce tangible benefits for the biodiversity and people of Madagascar.

Species as a heuristic: reconciling theory and practice

Species are crucial to most branches of biological research, yet remain controversial in terms of definition, delimitation, and reality. The difficulty of resolving the “species problem” stems from the tension between their theoretical concept as groups of evolving and highly variable organisms and the practical need for a stable and comparable unit of biology. Here, we suggest that treating species as a heuristic can be consistent with a theoretical definition of what species are and with the practical means by which they are identified and delimited. Specifically, we suggest that theoretically species are heuristic since they comprise clusters of closely related individuals responding in a similar manner to comparable sets of evolutionary and ecological forces, whilst they are practically heuristic because they are identifiable by the congruence of contingent properties indicative of those forces. This reconciliation of the theoretical basis of species with their practical applications in biological research allows for a loose but relatively consistent definition of species based on the strategic analysis and integration of genotypic, phenotypic, and ecotypic data. [Cohesion; heuristic; homeostasis; lineage; species problem.]

Mesoamerica is a cradle and the Atlantic Forest is a museum of Neotropical butterfly diversity: insights from the evolution and biogeography of Brassolini (Lepidoptera: Nymphalidae)

Regional species diversity is explained ultimately by speciation, extinction and dispersal. Here, we estimate dispersal and speciation rates of Neotropical butterflies to propose an explanation for the distribution and diversity of extant species. We focused on the tribe Brassolini (owl butterflies and allies), a Neotropical group that comprises 17 genera and 108 species, most of them endemic to rainforest biomes. We inferred a robust species tree using the multispecies coalescent framework and a dataset including molecular and morphological characters. This formed the basis for three changes in Brassolini classification: (1) Naropina syn. nov. is subsumed within Brassolina; (2) Aponarope syn. nov. is subsumed within Narope; and (3) Selenophanes orgetorix comb. nov. is reassigned from Catoblepia to Selenophanes. By applying biogeographical stochastic mapping, we found contrasting species diversification and dispersal dynamics across rainforest biomes, which might be explained, in part, by the geological and environmental history of each bioregion. Our results revealed a mosaic of biome-specific evolutionary histories within the Neotropics, where butterfly species have diversified rapidly (cradles: Mesoamerica), have accumulated gradually (museums: Atlantic Forest) or have diversified and accumulated alternately (Amazonia). Our study contributes evidence from a major butterfly lineage that the Neotropics are a museum and a cradle of species diversity.

High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox

In a context of ongoing biodiversity erosion, obtaining genomic resources from wildlife is essential for conservation. The thousands of yearly mammalian roadkill provide a useful source material for genomic surveys. To illustrate the potential of this underexploited resource, we used roadkill samples to study the genomic diversity of the bat-eared fox (Otocyon megalotis) and the aardwolf (Proteles cristatus), both having subspecies with similar disjunct distributions in Eastern and Southern Africa. First, we obtained reference genomes with high contiguity and gene completeness by combining Nanopore long reads and Illumina short reads. Then, we showed that the two subspecies of aardwolf might warrant species status (P. cristatus and P. septentrionalis) by comparing their genome-wide genetic differentiation to pairs of well-defined species across Carnivora with a new Genetic Differentiation index (GDI) based on only a few resequenced individuals. Finally, we obtained a genome-scale Carnivora phylogeny including the new aardwolf species.

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.

Geo-Climatic Changes and Apomixis as Major Drivers of Diversification in the Mediterranean Sea Lavenders (Limonium Mill.)

The Mediterranean realm, comprising the Mediterranean and Macaronesian regions, has long been recognized as one of the world's biodiversity hotspots, owing to its remarkable species richness and endemism. Several hypotheses on biotic and abiotic drivers of species diversification in the region have been often proposed but rarely tested in an explicit phylogenetic framework. Here, we investigate the impact of both species-intrinsic and -extrinsic factors on diversification in the species-rich, cosmopolitan Limonium, an angiosperm genus with center of diversity in the Mediterranean. First, we infer and time-calibrate the largest Limonium phylogeny to date. We then estimate ancestral ranges and diversification dynamics at both global and regional scales. At the global scale, we test whether the identified shifts in diversification rates are linked to specific geological and/or climatic events in the Mediterranean area and/or asexual reproduction (apomixis). Our results support a late Paleogene origin in the proto-Mediterranean area for Limonium, followed by extensive in situ diversification in the Mediterranean region during the late Miocene, Pliocene, and Pleistocene. We found significant increases of diversification rates in the "Mediterranean lineage" associated with the Messinian Salinity Crisis, onset of Mediterranean climate, Plio-Pleistocene sea-level fluctuations, and apomixis. Additionally, the Euro-Mediterranean area acted as the major source of species dispersals to the surrounding areas. At the regional scale, we infer the biogeographic origins of insular endemics in the oceanic archipelagos of Macaronesia, and test whether woodiness in the Canarian Nobiles clade is a derived trait linked to insular life and a biotic driver of diversification. We find that Limonium species diversity on the Canary Islands and Cape Verde archipelagos is the product of multiple colonization events followed by in situ diversification, and that woodiness of the Canarian endemics is indeed a derived trait but is not associated with a significant shift to higher diversification rates. Our study expands knowledge on how the interaction between abiotic and biotic drivers shape the uneven distribution of species diversity across taxonomic and geographical scales.

Darwin's second 'abominable mystery': trait flexibility as the innovation leading to angiosperm diversity

The fact that angiosperms are so species-rich and ecologically diverse - Darwin's second abominable mystery - could be explained by their ability to 'reinvent' themselves by evolving functional traits repeatedly over time, space and taxonomic clades. These trait innovations may facilitate adaptation and increase diversification rates. In this article, I quantify this 'trait flexibility' by reviewing the literature on trait transition rates and trait-dependent diversification rates in angiosperms and their extant sister clade, acrogymnosperms. I show that angiosperms indeed evolved elevated trait transition and trait-dependent diversification rates compared to gymnosperms, and rates are highest within species-rich angiosperm orders (e.g. Fabales, Lamiales). The (genetic) ability of certain angiosperm lineages to repeatedly evolve adaptive traits may have facilitated sustained high net diversification resulting from numerous episodic radiations.

Principles for creating a single authoritative list of the world's species

Lists of species underpin many fields of human endeavour, but there are currently no universally accepted principles for deciding which biological species should be accepted when there are alternative taxonomic treatments (and, by extension, which scientific names should be applied to those species). As improvements in information technology make it easier to communicate, access, and aggregate biodiversity information, there is a need for a framework that helps taxonomists and the users of taxonomy decide which taxa and names should be used by society whilst continuing to encourage taxonomic research that leads to new species discoveries, new knowledge of species relationships, and the refinement of existing species concepts. Here, we present 10 principles that can underpin such a governance framework, namely (i) the species list must be based on science and free from nontaxonomic considerations and interference, (ii) governance of the species list must aim for community support and use, (iii) all decisions about list composition must be transparent, (iv) the governance of validated lists of species is separate from the governance of the names of taxa, (v) governance of lists of accepted species must not constrain academic freedom, (vi) the set of criteria considered sufficient to recognise species boundaries may appropriately vary between different taxonomic groups but should be consistent when possible, (vii) a global list must balance conflicting needs for currency and stability by having archived versions, (viii) contributors need appropriate recognition, (ix) list content should be traceable, and (x) a global listing process needs both to encompass global diversity and to accommodate local knowledge of that diversity. We conclude by outlining issues that must be resolved if such a system of taxonomic list governance and a unified list of accepted scientific names generated are to be universally adopted.

Currently there are no rules on compiling lists of accepted names of species, meaning that many people use a variety of competing lists, which results in confusion and inefficiencies. This Perspective article provides principles for developing global lists of species that are needed if such lists are to be accepted by both taxonomists and users of taxonomy.

Towards reconciliation of the four world bird lists: hotspots of disagreement in taxonomy of raptors

There are currently four world bird lists referenced by different stakeholders including governments, academic journals, museums and citizen scientists. Consolidation of these lists is a conservation and research priority. In reconciling lists, care must be taken to ensure agreement in taxonomic concepts-the actual groups of individual organisms circumscribed by a given scientific epithet. Here, we compare species-level taxonomic concepts for raptors across the four lists, highlighting areas of disagreement. Of the 665 species-level raptor taxa observed at least once among the four lists, only 453 (68%) were consistent across all four lists. The Howard and Moore Checklist of the Birds of the World contains the fewest raptor species (528), whereas the International Ornithological Community World Bird List contains the most (580) and these two lists are in the most disagreement. Of the disagreements, 67% involved owls, and Indonesia was the country containing the most disagreed upon species (169). Finally, we calculated the amount of species-level agreement across lists for each avian order and found raptor orders spread throughout the rankings of agreement. Our results emphasize the need to reconcile the four world bird lists for all avian orders, highlight broad disagreements across lists and identify hotspots of disagreement for raptors, in particular.

Endemism patterns are scale dependent

Areas of endemism are important in biogeography because they capture facets of biodiversity not represented elsewhere. However, the scales at which they are relevant to research and conservation are poorly analysed. Here, we calculate weighted endemism (WE) and phylogenetic endemism (PE) separately for all birds and amphibians across the globe. We show that scale dependence is widespread for both indices and manifests across grain sizes, spatial extents and taxonomic treatments. Variations in taxonomic opinions-whether species are treated by systematic 'lumping' or 'splitting'-can profoundly affect the allocation of WE hotspots. Global patterns of PE can provide insights into complex evolutionary processes but this congruence is lost at the continental to country extents. These findings are explained by environmental heterogeneity at coarser grains, and to a far lesser extent at finer resolutions. Regardless of scale, we find widespread deficits of protection for endemism hotspots. Our study presents a framework for assessing areas for conservation that are robust to assumptions on taxonomy, spatial grain and extent.

Predicting the Impact of Describing New Species on Phylogenetic Patterns

Although our inventory of Earth’s biodiversity remains incomplete, we still require analyses using the Tree of Life to understand evolutionary and ecological patterns. Because incomplete sampling may bias our inferences, we must evaluate how future additions of newly discovered species might impact analyses performed today. We describe an approach that uses taxonomic history and phylogenetic trees to characterize the impact of past species discoveries on phylogenetic knowledge using patterns of branch-length variation, tree shape, and phylogenetic diversity. This provides a framework for assessing the relative completeness of taxonomic knowledge of lineages within a phylogeny. To demonstrate this approach, we use recent large phylogenies for amphibians, reptiles, flowering plants, and invertebrates. Well-known clades exhibit a decline in the mean and range of branch lengths that are added each year as new species are described. With increased taxonomic knowledge over time, deep lineages of well-known clades become known such that most recently described new species are added close to the tips of the tree, reflecting changing tree shape over the course of taxonomic history. The same analyses reveal other clades to be candidates for future discoveries that could dramatically impact our phylogenetic knowledge. Our work reveals that species are often added non-randomly to the phylogeny over multiyear time-scales in a predictable pattern of taxonomic maturation. Our results suggest that we can make informed predictions about how new species will be added across the phylogeny of a given clade, thus providing a framework for accommodating unsampled undescribed species in evolutionary analyses.

Mammalian species and the twofold nature of taxonomy: a comment on Taylor et al. 2019

In a recently published paper, Taylor and colleagues discussed different approaches and interpretations of mammalian taxonomy and their bearing on more general issues such as conservation and evolutionary biology. We fully endorse the fundamental importance of taxonomy and its being grounded on scientific principles. However, we also deplore a lack of awareness in the literature of the fact that taxonomy is a twofold enterprise that encompasses not only (i) the scientific description and quantitative analysis of biodiversity but also (ii) an executive decision as to how the results of (i) are translated into names. This has serious ramifications for the conservation of our planet’s dwindling biodiversity and when taxonomic names are used as raw data for ecological and evolutionary analyses.

The Origins and Diversification of the Exceptionally Rich Gemsnakes (Colubroidea: Lamprophiidae: Pseudoxyrhophiinae) in Madagascar

Processes leading to spectacular diversity of both form and species on islands have been well-documented under island biogeography theory, where distance from source and island size are key factors determining immigration and extinction resistance. But far less understood are the processes governing in situ diversification on the world’s mega islands, where large and isolated land masses produced morphologically distinct radiations from related taxa on continental regions. Madagascar has long been recognized as a natural laboratory due to its isolation, lack of influence from adjacent continents, and diversification of spectacular vertebrate radiations. However, only a handful of studies have examined rate shifts of in situ diversification for this island. Here, we examine rates of diversification in the Malagasy snakes of the family Pseudoxyrhophiinae (gemsnakes) to understand if rates of speciation were initially high, enhanced by diversification into distinct biomes, and associated with key dentition traits. Using a genomic sequence-capture data set for 366 samples, we determine that all previously described and newly discovered species are delimitable and therefore useful candidates for understanding diversification trajectories through time. Our analysis detected no shifts in diversification rate between clades or changes in biome or dentition type. Remarkably, we demonstrate that rates of diversification of the gemsnake radiation, which originated in Madagascar during the early Miocene, remained steady throughout the Neogene. However, we do detect a significant slowdown in diversification during the Pleistocene. We also comment on the apparent paradox where most living species originated in the Pleistocene, despite diversification rates being substantially higher during the earlier 15 myr.

Macroevolutionary dynamics of nectar spurs, a key evolutionary innovation

Floral nectar spurs are widely considered a key innovation promoting diversification in angiosperms by means of pollinator shifts. We investigated the macroevolutionary dynamics of nectar spurs in the tribe Antirrhineae (Plantaginaceae), which contains 29 genera and 300-400 species (70-80% spurred). The effect of nectar spurs on diversification was tested, with special focus on Linaria, the genus with the highest number of species. We generated the most comprehensive phylogeny of Antirrhineae to date and reconstructed the evolution of nectar spurs. Diversification rate heterogeneity was investigated using trait-dependent and trait-independent methods, and accounting for taxonomic uncertainty. The association between changes in spur length and speciation was examined within Linaria using model testing and ancestral state reconstructions. We inferred four independent acquisitions of nectar spurs. Diversification analyses revealed that nectar spurs are loosely associated with increased diversification rates. Detected rate shifts were delayed by 5-15 Myr with respect to the acquisition of the trait. Active evolution of spur length, fitting a speciational model, was inferred in Linaria, which is consistent with a scenario of pollinator shifts driving diversification. Nectar spurs played a role in diversification of the Antirrhineae, but diversification dynamics can only be fully explained by the complex interaction of multiple biotic and abiotic factors.

Delineating species in the speciation continuum: A proposal

Delineating species is a difficult and seemingly uninteresting issue that is still essential to address. Taxonomic methodology is heterogeneous according to the taxa and scientists involved due to the disparate data quality and quantity and disagreements over the species concept. This has negative impacts on basic and applied research. Genomic data substantially enhance our understanding of the speciation process but do not provide a ubiquitous solution to the species problem. The relevance of comparative approaches in speciation research has nevertheless recently been demonstrated. I suggest moving towards a more unified taxonomic classification through a reference-based decision procedure.

Problems and Questions Posed by Cryptic Species. A Framework to Guide Future Studies

Species are the currency of biology and important units of biodiversity, thus errors in species delimitations potentially have important consequences. During the last decades, owing to the use of genetic markers, many nominal species appeared to consist of several reproductively isolated entities called cryptic species (hereafter CS). In this chapter we explain why CS are important for practical reasons related to community and ecosystem monitoring, and for biological knowledge, particularly for understanding ecological and evolutionary processes. To find solutions to practical problems and to correct biological errors, a thorough analysis of the distinct types of CS reported in the literature is necessary and some general rules have to be identified. Here we explain how to identify CS, and we propose a rational and practical classification of CS (and putative CS), based on the crossing of distinct levels of genetic isolation with distinct levels of morphological differentiation. We also explain how to identify likely explanations for a given CS (either inherent to taxonomic processes or related to taxon biology, ecology and geography) and how to build a comprehensive database aimed at answering these practical and theoretical questions. Our pilot review of the literature in marine animals established that half of the reported cases are not CS sensu stricto (i.e. where morphology cannot distinguish the entities) and just need taxonomic revision. It also revealed significant associations between CS features, such as a higher proportion of diagnostic morphological differences in sympatric than in allopatric CS and more frequent ecological differentiation between sympatric than allopatric CS, both observations supporting the competitive exclusion theory, thus suggesting that ignoring CS causes not only species diversity but also functional diversity underestimation.

Closing the gap between palaeontological and neontological speciation and extinction rate estimates

Measuring the pace at which speciation and extinction occur is fundamental to understanding the origin and evolution of biodiversity. Both the fossil record and molecular phylogenies of living species can provide independent estimates of speciation and extinction rates, but often produce strikingly divergent results. Despite its implications, the theoretical reasons for this discrepancy remain unknown. Here, we reveal a conceptual and methodological basis able to reconcile palaeontological and molecular evidence: discrepancies are driven by different implicit assumptions about the processes of speciation and species evolution in palaeontological and neontological analyses. We present the "birth-death chronospecies" model that clarifies the definition of speciation and extinction processes allowing for a coherent joint analysis of fossil and phylogenetic data. Using simulations and empirical analyses we demonstrate not only that this model explains much of the apparent incongruence between fossils and phylogenies, but that differences in rate estimates are actually informative about the prevalence of different speciation modes.

Conceptual and empirical advances in Neotropical biodiversity research

The unparalleled biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in recent years in our understanding of the origin and diversification of many Neotropical taxa and biotic regions, many questions remain to be answered. Additional biological and geological data are still needed, as well as methodological advances that are capable of bridging these research fields. In this review, aimed primarily at advanced students and early-career scientists, we introduce the concept of "trans-disciplinary biogeography," which refers to the integration of data from multiple areas of research in biology (e.g., community ecology, phylogeography, systematics, historical biogeography) and Earth and the physical sciences (e.g., geology, climatology, palaeontology), as a means to reconstruct the giant puzzle of Neotropical biodiversity and evolution in space and time. We caution against extrapolating results derived from the study of one or a few taxa to convey general scenarios of Neotropical evolution and landscape formation. We urge more coordination and integration of data and ideas among disciplines, transcending their traditional boundaries, as a basis for advancing tomorrow's ground-breaking research. Our review highlights the great opportunities for studying the Neotropical biota to understand the evolution of life.

Comparing spatial diversification and meta-population models in the Indo-Australian Archipelago

Reconstructing the processes that have shaped the emergence of biodiversity gradients is critical to understand the dynamics of diversification of life on Earth. Islands have traditionally been used as model systems to unravel the processes shaping biological diversity. MacArthur and Wilson's island biogeographic model predicts diversity to be based on dynamic interactions between colonization and extinction rates, while treating islands themselves as geologically static entities. The current spatial configuration of islands should influence meta-population dynamics, but long-term geological changes within archipelagos are also expected to have shaped island biodiversity, in part by driving diversification. Here, we compare two mechanistic models providing inferences on species richness at a biogeographic scale: a mechanistic spatial-temporal model of species diversification and a spatial meta-population model. While the meta-population model operates over a static landscape, the diversification model is driven by changes in the size and spatial configuration of islands through time. We compare the inferences of both models to floristic diversity patterns among land patches of the Indo-Australian Archipelago. Simulation results from the diversification model better matched observed diversity than a meta-population model constrained only by the contemporary landscape. The diversification model suggests that the dynamic re-positioning of islands promoting land disconnection and reconnection induced an accumulation of particularly high species diversity on Borneo, which is central within the island network. By contrast, the meta-population model predicts a higher diversity on the mainlands, which is less compatible with empirical data. Our analyses highlight that, by comparing models with contrasting assumptions, we can pinpoint the processes that are most compatible with extant biodiversity patterns.

Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa

Rapidly growing biological data—including molecular sequences and fossils—hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyze these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction. Here we introduce a modular framework termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of evolutionary and biogeographical research. This framework assembles comprehensive data sets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data produced through next-generation sequencing techniques. We exemplify the application of our method by presenting phylogenetic and dating analyses for the mammal order Primates and for the plant family Arecaceae (palms). We believe that this framework will provide a valuable tool for a wide range of hypothesis-driven research questions in systematics, biogeography, and evolution. SUPERSMART will also accelerate the inference of a “Dated Tree of Life” where all node ages are directly comparable.