Speciation Rates Research Articles

Bacterial generalists in earthworm gut had stronger environmental adaptation potential and higher network vulnerability under antimony stress

Deciphering how communities assemble in gut bacteria in response to antimony (Sb) stress is beneficial to better understand the detoxification mechanism of earthworms to Sb, which is crucial for comprehensive understanding in situ remediation of Sb contaminated soil. However, little is known about the assembly processes of generalists and specialists in earthworm gut, particularly with their environmental adaptation potential. Herein, we conducted a 4-week exposure experiment, and analyzed the evolutionary characteristics, community assembly processes and network stability of generalists and specialists in earthworm (Eisenia fetida) gut and soil taxa. The results demonstrated that the taxonomic distance and phylogenetic distance of generalists were significantly lower than those of specialists (P < 0.001) both in earthworm gut and in soil. The environmental thresholds of generalists in earthworm gut were generally higher than those in soil, while the environmental thresholds of specialists in earthworm gut were lower. Generalists had stronger phylogenetic signals than specialists did both in earthworm gut and in soil. The binary-state speciation and extinction model revealed that the speciation rates of generalists and specialists in earthworm gut were 7.67 and 0.96, which increased by 7.42 and decreased by 1.72 compared with the corresponding rates in soil, respectively. Generalists and specialists had higher evolutionary efficiency in earthworm gut than in soil. The null model analysis exhibited that the stochastic processes of generalists and specialists in earthworm gut were mainly determined by undominated part (98.48% and 86.36%, respectively), while those in soil were primarily determined by homogenizing dispersal (80.30%) and dispersal limitation (78.79%), respectively. The network analysis displayed that the nodes and edges of the global network and the specialist sub-networks in soil were more than those in earthworm gut, while the nodes and edges of the generalist sub-networks in soil were less than those in earthworm gut. The sub-networks of generalists and specialists had stronger robustness at low Sb concentration, and generalist sub-network was more vulnerable than specialist sub-network. These results make up for the knowledge gaps of the speciation, evolution and maintenance mechanism of bacterial communities in earthworm gut under Sb stress, and provide new evidence for formulating bioremediation strategies of Sb contaminated soil.

The robustness of a simple dynamic model of island biodiversity to geological and sea‐level change

AbstractAimBiodiversity on islands is influenced by geophysical processes and sea‐level fluctuations. Oceanic islands (never connected to a landmass) are initially vacant with diversity accumulating via colonisation and speciation, and then declining as islands shrink. Continental islands have species upon disconnection from the mainland and may have transient land‐bridge connections. Theoretical predictions for the effects of these geophysical processes on rates of colonisation, speciation, and extinction have been proposed. However, paleogeographic reconstructions are currently unavailable for most islands, and phylogenetic models overlook island ontogeny, sea‐level changes, or past landmass connections. We analyse to what extent ignoring geodynamics in the inference model affects model predictions when confronted with data simulated with geodynamics.LocationSimulations of oceanic and continental islands.TaxaSimulated lineages.MethodsWe extend the island biogeography simulation model DAISIE to include: (i) area‐dependent rates of colonisation and diversification associated with island ontogeny and sea‐level fluctuations, (ii) continental islands with biota present upon separation from the mainland, and (iii) shifts in colonisation to mimic temporary land‐bridges. We quantify the error of ignoring geodynamic processes by applying DAISIE's inference method to geodynamic simulations.ResultsRobustness of the model to dynamic island area is generally high for oceanic islands and for continental islands that have been separated for a long time, suggesting that it is possible to obtain reliable results when ignoring geodynamics. However, for continental islands that have been recently or frequently connected, robustness of the model is low.Main conclusionsUnder many island biogeographic geodynamic scenarios (oceanic islands and ancient continental fragments) a simple phylogenetic model ignoring geodynamics is empirically applicable and informative. However, recent connection to the continent cannot be ignored, requiring new model development. Our results show that for oceanic islands, reliable insights can be obtained from phylogenetic data in the absence of paleogeographic reconstructions of island area.

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

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

CRABS: Congruent rate analyses in birth–death scenarios

Abstract Diversification rates inferred from phylogenies are not identifiable if the rates are allowed to vary freely over time. There are infinitely many combinations of speciation and extinction rate functions that have the exact same likelihood score for a given phylogeny, building a congruence class. The specific shape and characteristics of such congruence classes have not yet been studied. Whether speciation and extinction rate functions within a congruence class share common features is also not known. Prior hypotheses typically render diversification rates identifiable, but the results then depend on these a priori hypotheses and assumptions. To test the robustness of diversification results to these a priori hypotheses, we use two different approaches to explore congruence classes: (i) constructing congruent models under alternative hypotheses and (ii) sampling alternative rate function within the congruence class. Our methods are implemented in the open‐source R package CRABS (https://github.com/afmagee/CRABS). CRABS provides a flexible approach to explore the congruence class and provides summaries of rate functions within a congruence class. The summaries can highlight common trends, that is, increasing, flat or decreasing rates. Although there are infinitely many equally likely diversification rate functions, these can share common features. CRABS can be used to assess if diversification rate patterns are robust despite the non‐identifiability of the birth–death model. In our example, we clearly identify three phases of diversification rate changes that are common among all models which we sampled from the congruence class. Thus, congruence classes are not necessarily a problem for studying historical patterns of biodiversity from phylogenies.

Population divergence associated with spatial asynchrony in precipitation in Neotropical frogs

AbstractAimThe role that geography plays in promoting speciation by spatially isolating populations has been studied extensively, but less attention has been devoted to assessing the role of isolation by time mediated by spatial variation in climate as a mechanism promoting population divergence. Gene flow between populations differing in their reproductive schedules might be reduced relative to that between populations with overlapping breeding seasons, potentially leading to genetic divergence. Assuming that precipitation influences reproductive schedules, we explored the effect of asynchronous precipitation regimes on intraspecific genetic divergence. In addition, we examined whether microevolutionary processes are reflected in macroevolutionary patterns by assessing whether regions with more asynchronous precipitation across space have higher frog species richness and have experienced greater speciation rates than regions with more spatially synchronous precipitation regimes.LocationCentral and South America.TaxonAnurans: across 38 species of Neotropical frogs.MethodsFor microevolutionary analyses, we assessed the relationship between spatial asynchrony in precipitation and mitochondrial DNA genetic divergence accounting for ecological connectivity using multiple regression and phylogenetic meta‐analyses. For macroevolutionary analyses, we assessed the relationship between species richness, speciation rates estimated from a comprehensive molecular phylogeny, and the degree of spatial asynchrony in precipitation using generalized linear models.ResultsWe found that spatial asynchrony in precipitation is positively associated with genetic differentiation in 39% of the species tested, resulting in a weak cross‐species effect. However, the effect of asynchrony in precipitation on population divergence seems not to scale to macroevolutionary patterns because spatial asynchrony in precipitation was not associated with geographical patterns of species richness nor speciation rates.Main ConclusionsOur results indicate that asynchronous breeding may promote genetic divergence even in the absence of geographical barriers in species where breeding is associated with water availability, but such effects may not be stable enough through time to influence macroevolutionary patterns.

Mito-nuclear selection induces a trade-off between species ecological dominance and evolutionary lifespan.

Mitochondrial and nuclear genomes must be co-adapted to ensure proper cellular respiration and energy production. Mito-nuclear incompatibility reduces individual fitness and induces hybrid infertility, which can drive reproductive barriers and speciation. Here, we develop a birth-death model for evolution in spatially extended populations under selection for mito-nuclear co-adaptation. Mating is constrained by physical and genetic proximity, and offspring inherit nuclear genomes from both parents, with recombination. The model predicts macroscopic patterns including a community's species diversity, species abundance distribution, speciation and extinction rates, as well as intraspecific and interspecific genetic variation. We explore how these long-term outcomes depend upon the parameters of reproduction: individual fitness governed by mito-nuclear compatibility, constraints on mating compatibility and ecological carrying capacity. We find that strong selection for mito-nuclear compatibility reduces the equilibrium number of species after a radiation, increasing species' abundances and simultaneously increasing both speciation and extinction rates. The negative correlation between species diversity and diversification rates in our model agrees with the broad empirical pattern of lower diversity and higher speciation/extinction rates in temperate regions, compared to the tropics. We conclude that these empirical patterns may be caused in part by latitudinal variation in metabolic demands and corresponding variation in selection for mito-nuclear function.

Multigene phylogeny of the Indo–West Pacific genus Enosteoides (Crustacea, Decapoda, Porcellanidae) with description of a new species from Australia

The porcellanid genus Enosteoides Johnson, 1970, currently containing six species, was raised in the 1970s to contain aberrant Indo–West Pacific forms of the diverse and cosmopolitan genus Porcellana Lamarck, 1801. Here, we describe the most aberrant form as Enosteoides spinosussp. nov., from the northeast and northwest coasts of Australia and present results on phylogenetic reconstructions of the genus, based on an 1,870 bp alignment of concatenated DNA sequences of three mitochondrial and one nuclear gene. The new species is peculiarly spiny and has a higher morphological affinity to the type species of the genus, E. ornatus (Stimpson, 1858), than to the other congeneric species. Our molecular results indicate that Enosteoides is not monophyletic. The new species and E. ornatus are encompassed in a clade, which does not share immediate common ancestry with the clade containing the other species of Enosteoides. This clade is more closely related to species of Porcellana and Pisidia. Relatively large interspecific genetic distances between and within the two clades, as compared to distances estimated in American pairs of species on each side of the Panama Isthmus, suggest ancient divergence, probably followed by extinction events or low speciation rate. Relatively large intraspecific distances between Australian populations of the new species of Enosteoides from geographically distant locations suggest some level of phylogeographic structure.

Mapping species diversification metrics in macroecology: Prospects and challenges

The intersection of macroecology and macroevolution is one of today’s most active research in biology. In the last decade, we have witnessed a steady increment of macroecological studies that use metrics attempting to capture macroevolutionary processes to explain present-day biodiversity patterns. Evolutionary explanations of current species richness gradients are fundamental for understanding how diversity accumulates in a region. Although multiple hypotheses have been proposed to explain the patterns we observe in nature, it is well-known that the present-day diversity patterns result from speciation, extinction, colonization from nearby areas, or a combination of these macroevolutionary processes. Whether these metrics capture macroevolutionary processes across space is unknown. Some tip-rate metrics calculated directly from a phylogenetic tree (e.g., mean root distance -MRD-; mean diversification rate -mDR-) seem to return very similar geographical patterns regardless of how they are estimated (e.g., using branch lengths explicitly or not). Model-based tip-rate metrics —those estimated using macroevolutionary mixtures, e.g., the BAMM approach— seem to provide better net diversification estimates than only speciation rates. We argue that the lack of appropriate estimates of extinction and dispersal rates in phylogenetic trees may strongly limit our inferences about how species richness gradients have emerged at spatial and temporal scales. Here, we present a literature review about this topic and empirical comparisons between select taxa with several of these metrics. We implemented a simple null model approach to evaluate whether mapping of these metrics deviates from a random sampling process. We show that phylogenetic metrics by themselves are relatively poor at capturing speciation, extinction, and dispersal processes across geographical gradients. Furthermore, we provide evidence of how parametric biogeographic methods can improve our inference of past events and, therefore, our conclusions about the evolutionary processes driving biodiversity patterns. We recommend that further studies include several approaches simultaneously (e.g., spatial diversification modeling, parametric biogeographic methods, simulations) to disentangle the relative role of speciation, extinction, and dispersal in the generation and maintenance of species richness gradients at regional and global scales.

Genomic novelty within a "great speciator" revealed by a high-quality reference genome of the collared kingfisher (Todiramphus chloris collaris).

Islands are natural laboratories for studying patterns and processes of evolution. Research on island endemic birds has revealed elevated speciation rates and rapid phenotypic evolution in several groups (e.g. white-eyes, Darwin's finches). However, understanding the evolutionary processes behind these patterns requires an understanding of how genotypes map to novel phenotypes. To date, there are few high-quality reference genomes for species found on islands. Here, we sequence the genome of one of Ernst Mayr's "great speciators," the collared kingfisher (Todiramphus chloris collaris). Utilizing high molecular weight DNA and linked-read sequencing technology, we assembled a draft high-quality genome with highly contiguous scaffolds (scaffold N50 = 19 Mb). Based on universal single-copy orthologs, we estimated a gene space completeness of 96.6% for the draft genome assembly. The population demographic history analyses reveal a distinct pattern of contraction and expansion in population size throughout the Pleistocene. Comparative genomic analysis of gene family evolution revealed that species-specific and rapidly expanding gene families in the collared kingfisher (relative to other Coraciiformes) are mainly involved in the ErbB signaling pathway and focal adhesion. Todiramphus kingfishers are a species-rich group that has become a focus of speciation research. This draft genome will be a platform for future taxonomic, phylogeographic, and speciation research in the group. For example, target genes will enable testing of changes in sensory structures associated with changes in vision and taste genes across kingfishers.

Variation in macroevolutionary dynamics among extant primates

AbstractObjectivesThis study examines how speciation and extinction rates vary across primates, with a focus on the recent macroevolutionary dynamics that have shaped extant primate biodiversity.Materials and methodsLineage‐specific macroevolutionary rates were estimated for each tip in a tree containing 307 species using a hidden‐state likelihood model. Differences in tip rates among major clades were evaluated using phylogenetic ANOVA. Differences among diurnal, nocturnal, and cathemeral lineages were also evaluated, based on previous work indicating that activity pattern influences primate diversification.ResultsRate variation in extant primates is low within clades and high between clades. As in previous studies, cercopithecoids stand out in having high net diversification rates, driven by high speciation rates and very low extinction rates. Platyrrhines combine high speciation and high extinction rates, giving them high rates of lineage turnover. Strepsirrhines and tarsiids have low rates of speciation, extinction, turnover, and net diversification. Hominoids are intermediate between platyrrhines and the strepsirrhine‐tarsiid group, and there is evidence for differentiation between hominids and hylobatids. Diurnal lineages have significantly higher speciation rates than nocturnal lineages.ConclusionsRecent anthropoid macroevolution has been characterized by marked variation in diversification dynamics among clades. Strepsirrhines and tarsiids are more uniform, despite divergent evolutionary and biogeographic histories. Higher speciation rates in diurnal lineages may be driven by greater ecological opportunity or reliance on visual signals for mate recognition. However, the differences among anthropoids indicate that factors other than activity pattern (e.g., clade competition, historical contingency) have had a more influential role in shaping recent primate diversification.

Bio Ecology of Aquatic and Semi-Aquatic Insects Of Order Coleoptera In The World

Background: Aquatic Coleoptera plays a major role in freshwater ecosystems and is regarded as an effective bioindicator. At least 23 beetle families, from three of the four extant suborders, are predominantly aquatic as adults, larvae, or both. They play important role in ecosystem functioning, nutrient cycling primary production , decomposition and materials translocation. Methods: In this study, various databases including PubMed, Web of Knowledge, Scopus, Google Scholar and sciencedirect were used. Results: Aquatic Coleoptera known as water beetles, with more than 13,000 described species, is one of the most abundant aquatic insects. Out of 4 suborders of Coleoptera, the suborder Myxophaga is truly aquatic whereas 8 of the 11 extant families of Adephaga are regarded as truly. As far as Polyphaga is concerned, the largest suborder of Coleoptera, only 13 of the 150 families are regarded as truly aquatic. Discussion and Conclusion: Water beetles, although defined by their affinity for aquatic ways of life, occupy a broad array of habitats, and have shifted secondarily back to their terrestrial roots (either as adults, larvae or both) on multiple occasions. This ecological variability coupled with repeated, parallel transitions has positioned water beetles as a premier study group for questions related to dispersal, ecological speciation, and diversification rates. The characteristics of a bioindicator are: richness and diversity species, easy handling, ecological faithfulness, fragility to small environmental changes and good organism responses, and water beetles are very integral parts of any biotic component of any water bodies or wetlands. They are indicators of ecological diversity and habitat characteristics

Insights on biodiversity drivers to predict species richness in tropical forests at the local scale

Disentangling the relative importance of different biodiversity drivers (i.e., climate, edaphic, historical factors, or human impact) to predict plant species richness at the local scale is one of the most important challenges in ecology. Biodiversity modelling is a key tool for the integration of these drivers and the predictions generated are essential, for example, for climate change forecast and conservation planning. However, the reliability of biodiversity models at the local scale remains poorly understood, especially in tropical species-rich areas, where they are required. We inventoried all woody plants with stems ≥ 2.5 cm in 397 plots across the Andes-Amazon gradient. We generated and mapped 19 uncorrelated biodiversity drivers at 90 m resolution, grouped into four categories: microclimatic, microtopographic, anthropic, and edaphic. In order to evaluate the importance of the different categories, we grouped biodiversity drivers into four different clusters by categories. For each of the four clusters of biodiversity drivers, we modelled the observed species richness using two statistical techniques (random forest and Bayesian inference) and two modelling procedures (including or excluding a spatial component). All the biodiversity models produced were evaluated by cross-validation. Species richness was accurately predicted by random forest (Spearman correlation up to 0.85 and explained variance up to 67%). The results suggest that precipitation and temperature are important driving forces of species richness in the region. Nonetheless, a spatial component should be considered to properly predict biodiversity. This could reflect macroevolutionary underlying forces not considered here, such as colonization time, dispersal capacities, or speciation rates. However, the proposed biodiversity modelling approach can predict accurately species richness at the local scale and detailed resolution (90 m) in tropical areas, something that previous works had found extremely challenging. The innovative methodology presented here could be employed in other areas with conservation needs.

The missing link in biogeographic reconstruction: Accounting for lineage extinction rewrites history

AbstractAimIn the most widely used family of methods for ancestral range estimation (ARE), dispersal, speciation and extirpation events are estimated from information on extant lineages. However, this approach fails to consider the geographic distribution of extinct species and their position on the phylogenetic tree, an omission that could compromise reconstruction. Here, we present a method that models the geographic distribution of extinct species and we quantify the potential inaccuracy in ancestral range estimation when extinction rates are above zero.LocationGlobal applications, with an example from the Americas.TaxonAll taxa, with an example from hummingbirds (Amazilia).MethodsMethods capable of explicitly modelling extinct branches along with their reconstructed geographic information (GeoSSE) have been overlooked in ARE analysis, perhaps due to the inherent complexity of implementation. We develop a user‐friendly platform, which we term LEMAD (Lineage Extinction Model of Ancestral Distribution) that generalizes the likelihood described in GeoSSE for any number of areas and under several sets of geographic assumptions. We compare LEMAD and extinction‐free approaches using extensive simulations under different macroevolutionary scenarios. We apply our method to revisit the historical biogeography of Amazilia hummingbirds.ResultsWe find that accounting for the lineages removed from a tree by extinction improves reconstructions of ancestral distributions, especially when rates of vicariant speciation are higher than rates of in situ speciation, and when rates of extinction and range evolution are high. Rates of in situ and vicariant speciation are accurately estimated by LEMAD in all scenarios. North America as the most likely region for the common ancestor of hummingbirds.Main conclusionsMethods that neglect lineage extinction are less likely to accurately reconstruct true biogeographic histories of extant clades. Our findings on an empirical dataset reconcile the Eurasian origin of Amazilia with biogeographic reconstructions when lineage extinction is considered.

Short-term paleogeographic reorganizations and climate events shaped diversification of North American freshwater gastropods over deep time

What controls species diversity and diversification is one of the major questions in evolutionary biology and paleontology. Previous studies have addressed this issue based on various plant and animal groups, geographic regions, and time intervals. However, as most previous research focused on terrestrial or marine ecosystems, our understanding of the controls on diversification of biota (and particularly invertebrates) in freshwater environments in deep time is still limited. Here, we infer diversification rates of North American freshwater gastropods from the Late Triassic to the Pleistocene and explore potential links between shifts in speciation and extinction and major changes in paleogeography, climate, and biotic interactions. We found that variation in the speciation rate is best explained by changes in continental fragmentation, with rate shifts coinciding with major paleogeographic reorganizations in the Mesozoic, in particular the retreat of the Sundance Sea and subsequent development of the Bighorn wetland and the advance of the Western Interior Seaway. Climatic events in the Cenozoic (Middle Eocene Climate Optimum, Miocene Climate Optimum) variably coincide with shifts in speciation and extinction as well, but no significant long-term association could be detected. Similarly, no influence of diversity dependence was found across the entire time frame of ~ 214 Myr. Our results indicate that short-term climatic events and paleogeographic changes are relevant to the diversification of continental freshwater biota, while long-term trends have limited effect.

Corrigendum

Corrigendum

Sexual Signals Persist over Deep Time: Ancient Co-option of Bioluminescence for Courtship Displays in Cypridinid Ostracods.

Although the diversity, beauty, and intricacy of sexually selected courtship displays command the attention of evolutionists, the longevity of these traits in deep time is poorly understood. Population-based theory suggests sexual selection could either lower or raise extinction risk, resulting in high or low persistence of lineages with sexually selected traits. Furthermore, empirical studies that directly estimate the longevity of sexually selected traits are uncommon. Sexually selected signals-including bioluminescent courtship-originated multiple times during evolution, allowing the empirical study of their longevity after careful phylogenetic and divergence time analyses. Here, we estimate the first transcriptome-based molecular phylogeny and divergence times of Cypridinidae. We report extreme longevity of bioluminescent courtship, a trait important in mate choice and probably under sexual selection. Our relaxed-clock estimates of divergence times coupled with stochastic character mapping show luminous courtship evolved only once in Cypridinidae-in a Sub-Tribe, we name Luxorina-at least 151 millions of years ago from cypridinid ancestors that used bioluminescence only in antipredator displays, defining a Tribe we name Luminini. This time-calibrated molecular phylogeny of cypridinids will serve as a foundation for integrative and comparative studies on the biochemistry, molecular evolution, courtship, diversification, and ecology of cypridinid bioluminescence. The persistence of luminous courtship for hundreds of millions of years suggests that sexual selection did not cause a rapid loss of associated traits, and that rates of speciation within the group exceeded extinction risk, which may contribute to the persistence of a diverse clade of signaling species. [Ancestral state reconstruction; Biodiversity; co-option; divergence time estimates; macroevolution; Ostracoda; phylogenomics; sexual selection.].

Which is the richest of them all? Comparing area-adjusted plant diversities of Mediterranean- and tropical-climate regions

Mediterranean- and tropical-climate regions harbour the richest regional-scale floras globally. Until recently, however, comparisons of their diversities have been hindered by a lack of comprehensive inventories of tropical floras. Using taxonomically verified floras, we analyse area-adjusted plant diversities of five Mediterranean- and 35 tropical-climate regions to determine which are the most species-rich regions on Earth. On average, the Neotropics and tropical Southeast Asia support the most diverse floras globally. However, the area-adjusted diversities of the richest floras in these tropical regions are matched by those of two Mediterranean-climate floras, namely the Cape (second richest) and Mediterranean Basin (sixth richest). Except for Madagascar and Burundi, the Afrotropical regions were substantially less diverse than other tropical floras and half of the Afrotropical floras were poorer than the least diverse Mediterranean-climate region, namely Central Chile. We evaluate the likely ecological and evolutionary drivers of these plant diversity patterns in terms of three hypotheses that are apposite for global scale comparisons, namely water-energy dynamics, biome stability, and ecological heterogeneity. Water-energy dynamics appear to have little influence in explaining these diversity patterns: nodes of high global plant diversity are associated with climates that support year-round plant production (tropical climates) and those where the growing season is constrained by a winter rainfall regime (Mediterranean-type climates). Moreover, while the Afrotropics have higher primary production than the Neotropics and Southeast Asian tropics, they have markedly lower plant diversity. Instead, these patterns appear to be consistent with the hypothesis that the synergy of historical biome stability (reducing extinction rates) and high ecological heterogeneity (promoting speciation rates) better explain global patterns of regional-scale plant diversity.

Phylogenomics and body shape morphometrics reveal recent diversification in the goatfishes (Syngnatharia: Mullidae)

Clades of marine fishes exhibit many patterns of diversification, ranging from relatively constant throughout time to rapid changes in the rates of speciation and extinction. The goatfishes (Syngnatharia: Mullidae) are a family of marine, reef associated fishes with a relatively recent origin, distributed globally in tropical and temperate waters. Despite their abundance and economic importance, the goatfishes remain one of the few coral reef families for which the species level relationships have not been examined using genomic techniques. Here we use phylogenomic analysis of ultra-conserved elements (UCE) and exon data to resolve a well-supported, time-calibrated phylogeny for 72 species of goatfishes, supporting a recent crown age of the goatfishes at 21.9 million years ago. We used this framework to test hypotheses about the associations among body shape morphometrics, taxonomy, and phylogeny, as well as to explore relative diversification rates across the phylogeny. Body shape was strongly associated with generic-level taxonomy of goatfishes, with morphometric analyses showing evidence for high phylogenetic signal across all morphotypes. Rates of diversification in this clade reveal a recent sharp increase in lineage accumulation, with 92% of the goatfish species sampled across all clades and major body plans having originated in just the past 5 million years. We suggest that habitat diversity in the early Pliocene oceans and the generalist ecology of goatfishes are key factors in the unusual evolutionary tempo of the family Mullidae.

Taxonomy of Cryptic Isoëtes Species from the Brazilian Semi-Arid Region, with a Note about the Putative Maternal Origin of Polyploids

Revealing the unrecognized diversity within cryptic species has profound implications in the taxonomy, systematics, evolutionary studies, and species protections throughout plant groups. Isoëtes is prone to a high rate of cryptic speciation because of its morphological simplicity, stasis, and convergence. Phylogenetic studies revealed cryptic species in the genus from the Brazilian semi-arid region (the Caatinga), which comprises the least studied and most endangered flora in Brazil. Here we conducted morphological analyses and chromosome counts, and took advantage of phylogenetic analyses already published for the genus to provide a taxonomic revision of Isoëtes from the Caatinga. Isoëtes anamariae and I. harleyi are two new species, which were revealed by molecular data and subtle morphological characters. This study provides descriptions, chromosome counts, illustrations of the most important morpho-taxonomic characters of species from the Caatinga, and a key to identify them. All species from this region are diploid and we show the importance of diploids in detangling the origin of polyploids in Brazil.

COMPARATIVE TRANSCRIPTOME ANALYSIS OF TWO CLOSELY RELATED BEGONIA SPECIES REVEALS DIVERGENT PATTERNS IN KEY LIGHT-REGULATED PATHWAYS

Begonia is one of the most diverse angiosperm genera, comprising more than 2000 described species. The wide morphological and ecological range represented in the genus makes it a good model for studying the generation and maintenance of diversity. Previous research has shown that strong population structure, poor seed dispersal, and high levels of drift contribute to high rates of speciation and morphological variation. In the present study, we used transcriptomics to compare two closely related but morphologically and ecologically divergent species, Begonia conchifolia A.Dietr. and B. plebeja Liebm., to identify genes putatively involved in ecological divergence. Using publicly available multitissue RNA-seq data, we asked what genetic pathways show species-specific patterns of divergence between our two study species. The results of differential expression and gene ontology enrichment analyses showed species-specific enrichment of light-regulated functions in Begonia plebeja. Concomitant enrichment of ethylene and jasmonate pathways in Begonia plebeja indicate an increased shade avoidance response, suggesting that light availability may be a key factor in the divergent adaptation of B. conchifolia and B. plebeja.