Clade Age Research Articles

Macroevolutionary trends and diversification dynamics in Atripliceae (Amaranthaceae s.l., Chenopodioideae): a first approach.

Atripliceae evolved and diversified by dispersals and radiations across continents in both hemispheres, colonizing similar semi-arid, saline-alkaline environments throughout the world. Meanwhile, its species developed different life forms, photosynthetic pathways, mono- or dioecy, and different morphological features in flowers, fruiting bracteoles and seeds. In this study, we introduce a first approach to the macroevolutionary patterns and diversification dynamics of the Atripliceae to understand how time, traits, speciation, extinction and new habitats influenced the evolution of this lineage. We performed molecular phylogenetic analyses and clade age estimation of Atripliceae to apply time-, trait- and geographic-dependent diversification analyses and ancestral state reconstructions to explore diversification patterns within the tribe. Opposite diversification dynamics within the two major clades of Atripliceae, the Archiatriplex and Atriplex clades, could explain the unbalanced species richness between them; we found low mean speciation rates in the Archiatriplex clade and one shift to higher speciation rates placed in the branch of the Atriplex core. This acceleration in diversification seems to have started before the transition between C3 and C4 metabolism and before the arrival of Atriplex in the Americas, and matches the Mid-Miocene Climatic Optimum. Besides, the American species of Atriplex exhibit slightly higher net diversification rates than the Australian and Eurasian ones. While time seems not to be associated with diversification, traits such as life form, photosynthetic pathway and plant sex may have played roles as diversification drivers. Traits more than time played a key role in Atripliceae diversification, and we could speculate that climate changes could have triggered speciation. The extreme arid or saline environments where Atripliceae species prevail may explain its particular evolutionary trends and trait correlations compared with other angiosperms and highlight the importance of conservation efforts needed to preserve them as genetic resources to deal with climatic changes.

Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the history of diversification and adaptations in the Araceae.

The Araceae are one of the most diverse monocot families with numerous morphological and ecological novelties. Plastid and mitochondrial genes have been used to investigate the phylogeny and to interpret shifts in the pollination biology and biogeography of the Araceae. In contrast, the role of whole-genome duplication (WGD) in the evolution of eight subfamilies remains unclear. New transcriptomes or low-depth whole-genome sequences of 65 species were generated through Illumina sequencing. We reconstructed the phylogenetic relationships of Araceae using concatenated and species tree methods, and then estimated the age of major clades using TreePL. We inferred the WGD events by Ks and gene tree methods. We investigated the diversification patterns applying time-dependent and trait-dependent models. The expansions of gene families and functional enrichments were analysed using CAFE and InterProScan. Gymnostachydoideae was the earliest diverging lineage followed successively by Orontioideae, Lemnoideae and Lasioideae. In turn, they were followed by the clade of 'bisexual climbers' comprised of Pothoideae and Monsteroideae, which was resolved as the sister to the unisexual flowers clade of Zamioculcadoideae and Aroideae. A special WGD event ψ (psi) shared by the True-Araceae clade occurred in the Early Cretaceous. Net diversification rates first declined and then increased through time in the Araceae. The best diversification rate shift along the stem lineage of the True-Araceae clade was detected, and net diversification rates were enhanced following the ψ-WGD. Functional enrichment analyses revealed that some genes, such as those encoding heat shock proteins, glycosyl hydrolase and cytochrome P450, expanded within the True-Araceae clade. Our results improve our understanding of aroid phylogeny using the large number of single-/low-copy nuclear genes. In contrast to the Proto-Araceae group and the lemnoid clade adaption to aquatic environments, our analyses of WGD, diversification and functional enrichment indicated that WGD may play a more important role in the evolution of adaptations to tropical, terrestrial environments in the True-Araceae clade. These insights provide us with new resources to interpret the evolution of the Araceae.

The scaling of diversification rates with age is likely explained by sampling bias.

Numerous phylogenetic studies reported the existence of a pervasive scaling relationship between the ages of extant eukaryotic clades and their estimated diversification rates. The causes of this age-rate-scaling (ARS), whether biological and/or artifactual, remain unresolved. Here we fit diversification models to thousands of eukaryotic time-calibrated phylogenies to explore multiple potential causes of the ARS including parameter non-identifiability, model inadequacy, biases in taxonomic practice, and an important and ubiquitous form of sampling bias-preferentially analyzing larger extant clades. We distinguish between two mechanism by which such sampling biases can cause an ARS: First, by favoring clades that happen to be unusually large merely by chance (i.e., due to the stochastic nature of the cladogenic process), thus leading to rate overestimation, and second, by favoring clades that have truly higher diversification rates. We find that, of the proposed explanations, only sampling biases are likely to contribute to the observed ARS. We develop methods for fully correcting for sampling bias mechanism 1, and find that despite these corrections a substantial ARS remains. We then confirm using simulations that preferring trees with truly higher rates (mechanism 2) likely explains this residual ARS. Since we do not have a completely unbiased sample of clades, including extinct ones, for phylogenetic analyses, it is difficult to demonstrate unambiguously that sampling biases are the sole cause of the ARS. Sampling biases are, however, a parsimonious and plausible explanation for this widely observed macroevolutionary pattern, and this has implications for how we interpret the distribution of diversification rate estimates in extantclades.

Localized Phylogenetic Discordance Among Nuclear Loci Due to Incomplete Lineage Sorting and Introgression in the Family of Cotton and Cacao (Malvaceae).

The economically important cotton and cacao family (Malvaceae sensu lato) have long been recognized as a monophyletic group. However, the relationships among some subfamilies are still unclear as discordant phylogenetic hypotheses keep arising when different sources of molecular data are analyzed. Phylogenetic discordance has previously been hypothesized to be the result of both introgression and incomplete lineage sorting (ILS), but the extent and source of discordance have not yet been evaluated in the context of loci derived from massive sequencing strategies and for a wide representation of the family. Furthermore, no formal methods have been applied to evaluate if the detected phylogenetic discordance among phylogenomic datasets influences phylogenetic dating estimates of the concordant relationships. The objective of this research was to generate a phylogenetic hypothesis of Malvaceae from nuclear genes, specifically we aimed to (1) investigate the presence of major discordance among hundreds of nuclear gene histories of Malvaceae; (2) evaluate the potential source of discordance; and (3) examine whether discordance and loci heterogeneity influence on time estimates of the origin and diversification of subfamilies. Our study is based on a comprehensive dataset representing 96 genera of the nine subfamilies and 268 nuclear loci. Both concatenated and coalescence-based approaches were followed for phylogenetic inference. Using branch lengths and topology, we located the placement of introgression events to directly evaluate whether discordance is due to introgression rather than ILS. To estimate divergence times, concordance and molecular rate were considered. We filtered loci based on congruence with the species tree and then obtained the molecular rate of each locus to distribute them into three different sets corresponding to shared molecular rate ranges. Bayesian dating was performed for each of the different sets of loci with the same parameters and calibrations. Phylogenomic discordance was detected between methods, as well as gene histories. At deep coalescent times, we found discordance in the position of five subclades probably due to ILS and a relatively small proportion of introgression. Divergence time estimation with each set of loci generated overlapping clade ages, indicating that, even with different molecular rate and gene histories, calibrations generally provide a strong prior.

The Ediacaran origin of Ecdysozoa: integrating fossil and phylogenomic data

Ecdysozoans (Phyla Arthropoda, Kinorhyncha, Loricifera, Nematoda, Nematomorpha, Onychophora, Priapulida, Tardigrada) are invertebrates bearing a tough, periodically moulted cuticle that predisposes them to exceptional preservation. Ecdysozoans dominate the oldest exceptionally preserved bilaterian animal biotas in the early to mid-Cambrian ( c. 520–508 Ma), with possible trace fossils in the latest Ediacaran (<556 Ma). The fossil record of Ecdysozoa is among the best understood of major animal clades and is believed to document their origins and evolutionary history well. Strikingly, however, molecular clock analyses have implied a considerably deeper Precambrian origin for Ecdysozoa, much older than their earliest fossils. Here, using an improved set of fossil calibrations, we performed Bayesian analyses to estimate an evolutionary time-tree for Ecdysozoa, sampling all eight phyla for the first time. Our results recover Scalidophora as the sister group to Nematoida + Panarthropoda (= Cryptovermes nov.) and suggest that the Ediacaran divergence of Ecdysozoa occurred at least 23 myr before the first potential ecdysozoan trace fossils. This finding is impervious to the use of all plausible phylogenies, fossil prior distributions, evolutionary rate models and matrix partitioning strategies. Arthropods exhibit more precision and less incongruence between fossil- and clock-based estimates of clade ages than other ecdysozoan phyla. Supplementary material: Full methodologies used and an appendix of fossil calibration points are available at https://doi.org/10.6084/m9.figshare.c.5811381 Thematic collection: This article is part of the Advances in the Cambrian Explosion collection available at: https://www.lyellcollection.org/cc/advances-cambrian-explosion

How to date a crocodile: estimation of neosuchian clade ages and a comparison of four time‐scaling methods

AbstractClade ages within the crocodylomorph clade Neosuchia have long been debated. Molecular and morphological studies have yielded remarkably divergent results. Despite recent advances, there has been no comprehensive relative comparison of the major time calibration methods available to estimate clade ages based on morphological data. We used four methods (cal3, extended Hedman, smoothed ghost lineage analysis (sGLA) and the fossilized birth–death model (FBD)) to date clade ages derived from a published crocodylomorph supertree and a new neosuchian phylogeny. All time‐scaling methods applied here agree on the origination of Neosuchia during the Late Triassic or Early Jurassic, and the presence of the major extant eusuchian groups (Crocodyloidea, Gavialoidea, Alligatoroidea and Caimaininae) by the end of the Late Cretaceous. The number of distinct lineages present before the K/Pg boundary is less certain, with support for two competing scenarios in which Crocodylinae, Tomistominae and Diplocynodontinae either: (1) diverged from other eusuchian lineages before the K/Pg boundary; or (2) evolved during a ‘burst’ of diversification after the K/Pg event. Cal3 and FBD proved to be the most suitable methods for time‐scaling phylogenetic trees dominated by fossil taxa. Extended Hedman estimates are substantially older than the others, with larger standard deviations and a strong sensitivity to taxon sampling and topological changes; sGLA has similar problems. We conclude that a detailed understanding of phylogenetic relationships, tree reconstruction methods, and good taxonomic coverage (in particular the inclusion of the oldest taxon in each clade) is essential when evaluating the results of such dating analyses.

Predominantly Eastward Long-Distance Dispersal in Pantropical Ochnaceae Inferred From Ancestral Range Estimation and Phylogenomics

Ochnaceae is a pantropical family with multiple transoceanic disjunctions at deep and shallow levels. Earlier attempts to unravel the processes that led to such biogeographic patterns suffered from insufficient phylogenetic resolution and unclear delimitation of some of the genera. In the present study, we estimated divergence time and ancestral ranges based on a phylogenomic framework with a well-resolved phylogenetic backbone to tackle issues of the timing and direction of dispersal that may explain the modern global distribution of Ochnaceae. The nuclear data provided the more robust framework for divergence time estimation compared to the plastome-scale data, although differences in the inferred clade ages were mostly small. While Ochnaceae most likely originated in West Gondwana during the Late Cretaceous, all crown-group disjunctions are inferred as dispersal-based, most of them as transoceanic long-distance dispersal (LDD) during the Cenozoic. All LDDs occurred in an eastward direction except for the SE Asian clade of Sauvagesieae, which was founded by trans-Pacific dispersal from South America. The most species-rich clade by far, Ochninae, originated from either a widespread neotropical-African ancestor or a solely neotropical ancestor which then dispersed to Africa. The ancestors of this clade then diversified in Africa, followed by subsequent dispersal to the Malagasy region and tropical Asia on multiple instances in three genera during the Miocene-Pliocene. In particular, Ochna might have used the South Arabian land corridor to reach South Asia. Thus, the pantropical distribution of Ochnaceae is the result of LDD either transoceanic or via land bridges/corridors, whereas vicariance might have played a role only along the stem of the family.

Linking high diversification rates of rapidly growing Amazonian plants to geophysical landscape transformations promoted by Andean uplift

AbstractAmazonia is extremely biodiverse, but the mechanisms for the origin of this diversity are still under debate. We propose a diversification model for Amazonia based on the interplay of intrinsic clade functional traits, habitat associations and past geological events, using as a model group the species-rich Neotropical family Marantaceae. Our results show that the species richness of the lineage is predicted by functional strategy, rather than clade age, and thus the fast vs. slow growth functional trade-off is a major determinant of clade diversification in Marantaceae. Rapidly growing clades were mostly associated with highly productive habitats, and their origin and diversification dynamics matched the expansion of fertile soils mediated by Andean uplift c. 23 Mya. Fast-growth strategies probably led to fast molecular evolution, speeding up speciation rates and species accumulation, resulting in higher numbers of extant species. Our results indicate that pure allopatric-dispersal models disconnected from past geological and ecological forces may be inadequate for explaining the evolutionary and diversity patterns in Amazonian lowlands. We suggest that a coupling of the functional trait-niche framework with diversification dynamics provides insights into the evolutionary history of tropical forests and helps elucidate the mechanisms underlying the origin and evolution of its spectacular biodiversity.

A species-level timeline of mammal evolution integrating phylogenomic data.

High-throughput sequencing projects generate genome-scale sequence data for species-level phylogenies1-3. However, state-of-the-art Bayesian methods for inferring timetrees are computationally limited to small datasets and cannot exploit the growing number of available genomes4. In the case of mammals, molecular-clock analyses of limited datasets have produced conflicting estimates of clade ages with large uncertainties5,6, and thus the timescale of placental mammal evolution remains contentious7-10. Here we develop a Bayesian molecular-clock dating approach to estimate a timetree of 4,705 mammal species integrating information from 72 mammal genomes. We show that increasingly larger phylogenomic datasets produce diversification time estimates with progressively smaller uncertainties, facilitating precise tests of macroevolutionary hypotheses. For example, we confidently reject an explosive model of placental mammal origination in the Palaeogene8 and show that crown Placentalia originated in the Late Cretaceous with unambiguous ordinal diversification in the Palaeocene/Eocene. Our Bayesian methodology facilitates analysis of complete genomes and thousands of species within an integrated framework, making it possible to address hitherto intractable research questions on species diversifications. This approach can be used to address other contentious cases of animal and plant diversifications that require analysis of species-level phylogenomic datasets.

Insect Radiations on Islands: Biogeographic Pattern and Evolutionary Process in Hawaiian Insects

The spectacular adaptive radiations on the Hawaiian Islands offer the tantalizing possibility of ascertaining the predictability of evolution, especially with regard to how the archipelago’s dynamic geology suggests a priori hypotheses for evolutionary pattern and process. In the past two decades advances in sequencing and phylogenetics have shed new light on the evolution of this model fauna. Here, we provide an overview of recent research on major endemic Hawaiian insect radiations. We find that, in contrast to earlier views, a substantial fraction of Hawaiian insect clades colonized the archipelago prior to the formation of the current high islands (5.1 Ma) and have persisted through one or more rounds of island formation and subsidence prior to the emergence of the current archipelago. Many Hawaiian insect radiations show elements of the progression rule, a null expectation where biogeographic patterns on the phylogeny mirror the chronological sequence of island formation, but few match its predictions exactly. Diversity in most radiations is shaped by a complicated interplay of among-island dispersal and within-island diversification. Finally, we find a positive relationship between clade age and species richness in Hawaiian insects, but with a great deal of variance that is likely explained by aspects of ecology and clade-specific factors.

Basal phylogenetic asymmetry in species-rich natural taxa of plants: a multivariate study

Sister groups at the root of large plant clades (with ≥1000 extant species) are described in terms of variables expressing species richness, geographical distribution, age, diversification rate and speed of molecular evolution. Standard statistical tools and principal component analysis are used to determine and visualize their relationships. In the majority of the 167 groups examined, one clade (the minor) has many fewer species than its sister (the major clade). A striking phenomenon is that many minor clades (17%) contain four or fewer species only. Asymmetry is largely, but not generally reflected by proportions in geographical range and relative speed of molecular evolution: species in the minor clade are more widely distributed than the major clade in 8 groups and – based on available information – we detected longer maximum branch lengths on the minor lineage in 14 cases. The basal lineages considerably differ in diversification rate; the differences are of the same magnitude in many groups as the diversification rate itself calculated for families and orders by other authors. For the major clade, we found a positive relationship between the species richness of clades and geographical range, and negative correlation between the logarithm of species richness and clade age.

Effects of climate and topography on the diversity anomaly of plants disjunctly distributed in eastern Asia and eastern North America

AbstractAimDifferences in physiography have been proposed to explain the diversity anomaly for vascular plants between environmentally similar regions of eastern Asia (EAS) and eastern North America (ENA). Here, we use plant species within disjunct genera to examine whether differences in topography contribute to the diversity anomaly and whether the richness–environment relationships differ between regions. Disjunct plants are used to ensure that the diversity anomaly relates to post‐disjunction evolution and diversification rather than regional differences in clade ages or immigration.LocationEAS and ENA.Time periodCurrent.Major taxa studiedPlant taxa disjunctly distributed in EAS and ENA.MethodsWe compiled county‐level plant distribution data, and calculated species richness and variables of topography and climate within unit grid cells. We compared estimated coefficients of region effects among models, where richness was fitted with or without topography and climate. Topography and climate were also used to separately model within‐region spatial diversity patterns using spatial simultaneous autoregressive error models.ResultsThe coefficients of region effects varied from −.776 for the model only including region to −.309 when topography was controlled for, but remained significant. Climate dominated the spatial diversity patterns in ENA. In contrast, the influence of climate (14.2%) on species richness was weaker than that of topography (18.3%) in the warm area of EAS. Relations to elevation and temperature varied between regions, shifting between positive and negative relationships in several cases.Main conclusionsOur results demonstrate that variability in local topography contributes to the strong regional anomaly in plant species richness between EAS and ENA. Nevertheless, the diversity anomaly persists after controlling for local topography and climate. EAS and ENA also exhibit contrasting richness–environment relationships, providing another divergent aspect between the EAS–ENA disjunct floras. Our findings highlight that regional differences in topography or other environmental factors may underlie the diversity anomaly.

Fossilization processes have little impact on tip‐calibrated divergence time analyses

AbstractThe importance of palaeontological data in divergence time estimation has increased with the introduction of Bayesian total‐evidence dating methods, which use fossil taxa directly for calibration, facilitated by the joint analysis of morphological and molecular data. Fossil taxa are invariably incompletely known as a consequence of taphonomic processes, resulting in the decidedly non‐random distribution of missing data. The impact of non‐random missing data on the accuracy and precision of clade age estimation is unknown. In an attempt to constrain the impact of taphonomy on tip‐calibrated dating analyses, we compared clade ages estimated from a very complete morphological matrix to ages estimated from the same matrix permuted to simulate the progressive loss of anatomical information resulting from taphonomic processes. We demonstrate that systematically distributed missing data negatively influence clade age estimates, but that successive stages within the taphonomic process introduce greater differences in age estimates, when compared to estimates obtained from untreated data. Despite these effects, the general influence of missing data is weak, presumably due to the compensatory effect of extensive morphological data from extant taxa. We suggest that, in the absence of models that can explicitly account for taphonomic processes, morphological datasets should be constructed to minimize the impact of taphonomy on divergence time estimation.

Phylogeny based on ultra-conserved elements clarifies the evolution of rails and allies (Ralloidea) and is the basis for a revised classification

AbstractThe rails (Family Rallidae) are the most diverse and widespread group in the Gruiformes. Their extensive fossil history, global geographic distribution, and tendency to rapidly evolve flightless species on islands make them an attractive subject of evolutionary studies, but the rarity of modern museum specimens of so many rail species has, until recently, limited the scope of molecular phylogenetics studies. As a result, the classification of rails remains one of the most unsettled among major bird radiations. We extracted DNA from museum specimens of 82 species, including 27 from study skins collected as long ago as 1875, and generated nucleotide sequences from thousands of homologous ultra-conserved elements (UCEs). Our phylogenetic analyses, using both concatenation and multispecies coalescent approaches, resulted in well-supported and highly congruent phylogenies that resolve the major lineages of rails and reveal several currently recognized genera to be polyphyletic. A fossil-calibrated time tree is well-resolved and supports the hypothesis that rails split into 2 major lineages (subfamilies Himantornithinae and Rallinae) ~34 mya, but clade age estimates have wide confidence intervals. Our results, combined with results of other recently published phylogenomics studies of rails and other Gruiformes, form the basis for a proposed classification of the Rallidae that recognizes 40 genera in 9 tribes.

Patterns and drivers of phylogenetic structure of pteridophytes in China

AbstractAimPrevious studies have found strikingly different geographical patterns of phylogenetic diversity of gymnosperms and angiosperms, which have been suggested to result, in part, from the greater age of the former. To assess the effects of clade age on phylogenetic structure, we assessed phylodiversity patterns of pteridophytes (lycophytes and ferns), which combine ancient and modern lineages, across China.LocationChina.Time periodPresent day.TaxonPteridophytes.MethodsWe divided China into 66 regions and collated species lists of pteridophytes for each region. We then related taxonomic and phylogenetic diversity, and their related metrics, to six climatic variables for pteridophytes as a whole and for different evolutionary clades. We examined the effect of spatial autocorrelation among regional floras on the results.ResultsWe found that when all pteridophytes or ferns were considered, the patterns resembled those of gymnosperms, presumably reflecting the effects of several ancient global mass extinctions and the relict distribution of old families. In contrast, when we considered only the modern Polypodiales radiation, which accounts for three‐quarters of current fern diversity and is about as old as the angiosperm radiation, we found a pattern similar to that of angiosperms. This pattern is consistent with the tropical niche conservatism hypothesis and suggests that both major groups of land plants have a broadly similar evolutionary trajectory, with most families originating in tropical conditions and few families adapting to cold and arid conditions.Main conclusionsOur study shows that the phylogenetic structures of more recently evolved and diversified clades of pteridophytes are fairly consistent with the tropical niche conservatism hypothesis, suggesting that the age of the taxon, its physiological adaptations and the global climatic changes that it experienced during its evolutionary history are reflected in the composition of current plant assemblages.

Phylogenetic conservatism of fruit development time in Chinese angiosperms and the phylogenetic and climatic correlates

QuestionsDocumenting the patterns and drivers of functional trait distributions at large spatial scales is key to our fundamental understanding of the composition of plant assemblages. However, phylogeographic patterns of fruit development time (FDT, the difference between flowering and fruiting dates) have remained unstudied. Here we compiled reproductive phenology (flowering and fruiting time) and species distribution data for 6838 angiosperm species in China to explore whether FDT is more phylogenetically conserved as latitude and elevation increase, whether the phylogenetic signal of FDT correlates with phylogenetic structure and potential climatic drivers across China, and whether the environmental determinants of phylogenetic signal of FDT differ between herbaceous and woody species. LocationChina MethodsWe divided China into 268 200 × 200 km grid cells and calculated the phylogenetic signals of FDT in each grid cell using pagel’s λ. We then regressed the phylogenetic signals of FDT as a function of either latitude or elevation, individually. We examined the relationship between phylogenetic signals of FDT and climate variables using both ordinary and spatial linear regressions. We also examined the relationship between the phylogenetic signal of FDT and either net relatedness index (NRI) or clade age of each grid-cell. ResultsWe found that phylogenetic signals in FDT increased as elevation and latitude increased. The Pagel’s λ of FDT was negatively correlated with clade age but positively correlated with NRI. Precipitation in the wettest quarter was the primary variable affecting the phylogenetic signal for herbaceous species, while minimum temperature of the coldest month and temperature seasonality were the two most important climatic factors for woody species. ConclusionsStrength of phylogenetic conservatism of FDT is greater at higher latitudes and elevations. The latitudinal and elevational patterns, where mean clade age of species lowers as temperature decreases, and angiosperm assemblages tend to be more phylogenetically clustered at higher elevations and higher latitudes, could be explained by the Tropical Niche Conservatism hypothesis. The phylogenetic signals of herbs and of woody plants are triggered by different climatic drivers. Our findings have important implications for the study of large-scale geographical gradients in plant species richness, phylogenetic diversity and community assembly.

Seeing the forest through many trees: Multi‐taxon patterns of phylogenetic diversity in the Atlantic Forest hotspot

AbstractAimWe combine phylogenetic and point locality data from selected lineages of the Atlantic Forest flora and fauna to compare spatial patterns of biodiversity sustained by the current configuration of forest remnants to a scenario of complete forest preservation. We then ask the question "how much biodiversity is likely lost, already"? Specifically, we assess how habitat loss likely impacted the climatic spaces occupied by the local species, the inferred composition of local communities and the spatial distribution of phylogenetic diversity and endemism.LocationAtlantic Forest, Brazil.MethodsUsing carefully curated point localities, phylogenetic data and parameterized models of species distributions, we generate maps of phylogenetic diversity, phylogenetic endemism and phylogenetic turnover for the entire Atlantic Forest. We map patterns of clade‐specific diversity under complete preservation of forest and then incorporate present‐day deforestation patterns to provide a more realistic scenario.ResultsInstead of a singular pattern, three different reoccurring syndromes described the flora and fauna of the Atlantic Forest. These patterns emerged irrespectively of clade age and life history traits. General turnover patterns were highly consistent with previous analyses of species composition and panbiogeographical studies. Deforestation has altered the availability of climatic spaces in the Atlantic Forest, its biological communities and the distribution of evolutionary lineages in space. However, approximately 60% of the pre‐Columbian climatic space persists in forest remnants, and today's biological communities are estimated to be 45% similar to pre‐deforestation times.Main conclusionsThe Atlantic Forest has been reduced to 8% of its once largely continuous range. However, the disproportionately large amounts of climate, community and lineage diversity that persist in remnants provide hope and support for conservation efforts that combine species occurrence and phylogenetic data. Inclusion of evolutionary thinking into strategic approaches to restoring Brazilian ecosystems could further conservation effectiveness by incorporating the adaptive potential of local assemblages in the face of further environmental shifts.

Character evolution of modern fly‐speck fungi and implications for interpreting thyriothecial fossils

PremiseFossils show that fly‐speck fungi have been reproducing with small, black thyriothecia on leaf surfaces for ~250 million years. We analyzed morphological characters of extant thyriothecial fungi to develop a phylogenetic framework for interpreting fossil taxa.MethodsWe placed 59 extant fly‐speck fungi in a phylogeny of 320 Ascomycota using nuclear ribosomal large and small subunit sequences, including newly determined sequences from nine taxa. We reconstructed ancestral character states using BayesTraits and maximum likelihood after coding 11 morphological characters based on original observations and literature. We analyzed the relationships of three previously published Mesozoic fossils using parsimony and our morphological character matrix, constrained by the molecular phylogeny.ResultsThyriothecia evolved convergently in multiple lineages of superficial, leaf‐inhabiting ascomycetes. The radiate and ostiolate scutellum organization is restricted to Dothideomycetes. Scutellum initiation by intercalary septation of a single hypha characterizes Asterinales and Asterotexiales, and initiation by coordinated growth of two or more adjacent hyphae characterizes Aulographaceae. Scutella in Microthyriales are initiated apically on a lateral hyphal branch. Patterns of hyphal branching in scutella contribute to distinguishing among orders. Parsimony resolves three fossil taxa as Dothideomycetes; one is further resolved as a member of a Microthyriales‐Zeloasperisporiales clade within Dothideomycetes.ConclusionsThis is the most comprehensive systematic study of thyriothecial fungi and their relatives to date. Parsimony analysis of the matrix of character states of modern taxa provides an objective basis for interpreting fossils, leading to insights into morphological evolution and geological ages of Dothideomycetes clades.

A bi‐organellar phylogenomic study of Pandanales: inference of higher‐order relationships and unusual rate‐variation patterns

We used a bi-organellar phylogenomic approach to address higher-order relationships in Pandanales, including the first molecular phylogenetic study of the panama-hat family, Cyclanthaceae. Our genus-level study of plastid and mitochondrial gene sets includes a comprehensive sampling of photosynthetic lineages across the order, and provides a framework for investigating clade ages, biogeographic hypotheses and organellar molecular evolution. Using multiple inference methods and both organellargenomes, we recovered mostly congruent and strongly supported relationships within and between families, including the placement of fully mycoheterotrophic Triuridaceae. Cyclanthaceae and Pandanaceae plastomes have slow substitution rates, contributing to weakly supported plastid-based relationships in Cyclanthaceae. While generally slowly evolving, mitochondrial genomes exhibit sporadic rate elevation across the order. However, we infer well-supported relationships even for slower evolving mitochondrial lineages in Cyclanthaceae. Clade age estimates across photosynthetic lineages are largely consistent with previous studies, are well correlated between the two organellar genomes (with slightly younger inferences from mitochondrial data), and support several biogeographic hypotheses. We show that rapidly evolving non-photosynthetic lineages may bias age estimates upwards at neighbouring photosynthetic nodes, even using a relaxed clock model. Finally, we uncovered new genome structural variants in photosynthetic taxa at plastid inverted repeat boundaries that show promise as interfamilial phylogenetic markers.

Survival and selection biases in early animal evolution and a source of systematic overestimation in molecular clocks.

Important evolutionary events such as the Cambrian Explosion have inspired many attempts at explanation: why do they happen when they do? What shapes them, and why do they eventually come to an end? However, much less attention has been paid to the idea of a ‘null hypothesis’—that certain features of such diversifications arise simply through their statistical structure. Such statistical features also appear to influence our perception of the timing of these events. Here, we show in particular that study of unusually large clades leads to systematic overestimates of clade ages from some types of molecular clocks, and that the size of this effect may be enough to account for the puzzling mismatches seen between these molecular clocks and the fossil record. Our analysis of the fossil record of the late Ediacaran to Cambrian suggests that it is likely to be recording a true evolutionary radiation of the bilaterians at this time, and that explanations involving various sorts of cryptic origins for the bilaterians do not seem to be necessary.