Model Of Diversification Research Articles

Rise and fall of a continental mesic radiation in Australia: spine evolution, biogeography, and diversification of Cryptandra (Rhamnaceae: Pomaderreae)

Abstract The Australian continent has experienced progressive aridification since the Miocene, spurring recent radiations of arid-adapted lineages and the likely decline of mesic biotic groups. While examples of the former have been relatively well-documented, post-Miocene declines of non-arid sclerophyllous floras are less well understood. Here, we present a well-sampled time-calibrated nuclear phylogeny (140 accessions representing 60/65 species) of an Australian plant genus (Cryptandra Sm.: Rhamnaceae) and using ancestral range reconstructions and diversification analyses, elucidate its evolutionary history through space and time. We used high-throughput sequencing to recover 30 orthologous nuclear loci and BioGeoBEARS to infer ancestral areas. We show that the present-day distribution of Cryptandra can be explained by multiple vicariance events followed by in situ diversification with little exchange between regions. All diversification models show a speciation rate decline in Cryptandra after its radiation in the Miocene (c. 23 Mya). This coincides with aridification episodes across Australia and indicates that diversification of this genus has been negatively affected by the expansion of aridity. We also show that there were no significant differences in diversification rates between spinescent and non-spinescent Cryptandra lineages, suggesting that spinescent lineages may be the legacies of selection from extinct megaherbivores.

Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops).

Can knowledge about genome architecture inform biogeographic and phylogenetic inference? Selection, drift, recombination, and gene flow interact to produce a genomic landscape of divergence wherein patterns of differentiation and genealogy vary nonrandomly across the genomes of diverging populations. For instance, genealogical patterns that arise due to gene flow should be more likely to occur on smaller chromosomes, which experience high recombination, whereas those tracking histories of geographic isolation (reduced gene flow caused by a barrier) and divergence should be more likely to occur on larger and sex chromosomes. In Amazonia, populations of many bird species diverge and introgress across rivers, resulting in reticulated genomic signals. Herein, we used reduced representation genomic data to disentangle the evolutionary history of 4 populations of an Amazonian antbird, Thamnophilus aethiops, whose biogeographic history was associated with the dynamic evolution of the Madeira River Basin. Specifically, we evaluate whether a large river capture event ca. 200 Ka, gave rise to reticulated genealogies in the genome by making spatially explicit predictions about isolation and gene flow based on knowledge about genomic processes. We first estimated chromosome-level phylogenies and recovered 2 primary topologies across the genome. The first topology (T1) was most consistent with predictions about population divergence and was recovered for the Z-chromosome. The second (T2), was consistent with predictions about gene flow upon secondary contact. To evaluate support for these topologies, we trained a convolutional neural network to classify our data into alternative diversification models and estimate demographic parameters. The best-fit model was concordant with T1 and included gene flow between non-sister taxa. Finally, we modeled levels of divergence and introgression as functions of chromosome length and found that smaller chromosomes experienced higher gene flow. Given that (1) genetrees supporting T2 were more likely to occur on smaller chromosomes and (2) we found lower levels of introgression on larger chromosomes (and especially the Z-chromosome), we argue that T1 represents the history of population divergence across rivers and T2 the history of secondary contact due to barrier loss. Our results suggest that a significant portion of genomic heterogeneity arises due to extrinsic biogeographic processes such as river capture interacting with intrinsic processes associated with genome architecture. Future phylogeographic studies would benefit from accounting for genomic processes, as different parts of the genome reveal contrasting, albeit complementary histories, all of which are relevant for disentangling the intricate geogenomic mechanisms of biotic diversification. [Amazonia; biogeography; demographic modeling; gene flow; gene tree; genome architecture; geogenomics; introgression; linked selection; neural network; phylogenomic; phylogeography; reproductive isolation; speciation; species tree.].

Unraveling the complex phylogeographic history of freshwater fishes in Lower Central America: A study of the electric fish Brachyhypopomus occidentalis

Lower Central America (LCA) has a complex biogeographic history shaped by the rise of the Isthmus of Panama and the global climatic oscillations of the Pleistocene. These events have been crucial in structuring biodiversity in LCA, but their consequences for the distribution and partitions of genetic diversity across the region remain to be elucidated. We combined complete mitochondrial genomes and nuclear ultraconserved elements (UCEs) to study the phylogeographic history and population genetic structure of the electric fish Brachyhypopomus occidentalis in LCA. Our results are consistent with the known phylogeographic history of B. occidentalis in LCA, but we update this history in several important ways that help illuminate the phylogeographic history of freshwater fishes in the region. We provide: i) support for three waves of colonization, two of which occurred prior to the final closure of the Panama Isthmus; ii) a more precise understanding of each colonization event, with evidence for a larger footprint of the first event, as well as genetic exchange across the continental divide in subsequent events; and iii) evidence for high levels of previously unrecognized population genetic structure across LCA. This updated model of colonization and diversification of B. occidentalis consists of three waves of dispersal and colonization, which triggered the evolution of geographic breaks in both nuclear and mitochondrial genomes across LCA. These processes are tightly linked to the dynamic uplift of the Isthmus, recent volcanic activity in the region, and the sea-level oscillations of the Pleistocene. These results improve previous phylogeographic inferences regarding the distribution and diversification of freshwater fishes in LCA, and generate testable hypotheses to guide future research exploring the factors shaping biodiversity in the region.

Elevational Goldilocks zone underlies the exceptional diversity of a large lizard radiation (Liolaemus; Liolaemidae).

Mountains are among the most biodiverse regions on the planet, and how these landforms shape diversification through the interaction of biological traits and geo-climatic dynamics is integral to understanding global biodiversity. In this study, we investigate the dual roles of climate change and mountain uplift on the evolution of a hyper-diverse radiation, Liolaemus lizards, with a spatially explicit model of diversification using a reconstruction of uplift and paleotemperature in central and southern South America. The diversification model captures a hotspot for Liolaemus around 40°S in lineages with low-dispersal ability and narrow niche breadths. Under the model, speciation rates are highest in low latitudes (<35°S) and mid elevations (~1,000 m), while extinction rates are highest at higher latitudes (>35°S) and higher elevations (>2,000 m). Temperature change through the Cenozoic explained variation in speciation and extinction rates through time and across different elevational bands. Our results point to the conditions of mid elevations being optimal for diversification (i.e., Goldilocks Zone), driven by the combination of (1) a complex topography that facilitates speciation during periods of climatic change, and (2) a relatively moderate climate that enables the persistence of ectothermic lineages and buffers species from extinction.

Diversification and biogeography of Rhacophoridae – a model testing approach

A central focus of evolutionary biology is to understand species diversity by studying how they arrived at their current geographic distributions. The biogeography of the Old World tree frogs in the family Rhacophoridae has been extensively studied suggesting an early Paleogene origin in Asia (out of Asia hypothesis) with alternative hypotheses in play. However, these alternative hypotheses especially considering adjacency of biogeographical regions and plate tectonics have not been tested empirically. Here using a comprehensive time calibrated phylogeny and constrained dispersal multipliers we studied the biogeographical history and diversification of Rhacophoridae, distributed in five biogeographical regions. Five hypotheses suggesting different centers of origin, and additional hypotheses considering adjacency and plate tectonics were tested to delineate the biogeographical history of Rhacophoridae. In addition, various diversification models that accounted for factors such as lineage isolation time, diversity-dependence, paleotemperatures, speciation and extinction rates were also used to test patterns of diversification. Results confirmed an East/Southeast Asian center of origin (out of Asia), with dispersal likely mediated by plate tectonics and adjacency of biogeographical regions, which could be linked to periodic sea level fluctuations and climate changes. The best-fitting diversification models explained diversification through lineage isolation time and paleotemperature regimes, while diversity-dependent models had low support. Speciation was linearly dependent on time and paleotemperatures, while extinction rates were exponentially dependent on time and linearly dependent on paleotemperature. Our findings demonstrate that variable extinction rates contribute towards maintaining a constant diversification rate for rhacophorids. We discuss that episodic major extinction events on the Indian Plate may have played a major role in shaping the early evolution of Rhacophoridae thus favoring an Out of Asia hypothesis in the empirical models. However, current biogeographic models may not be sufficient to explain the origin of Rhacophoridae, as multiple factors are likely at play.

Rules of teeth development align microevolution with macroevolution in extant and extinct primates.

Macroevolutionary biologists have classically rejected the notion that higher-level patterns of divergence arise through microevolutionary processes acting within populations. For morphology, this consensus partly derives from the inability of quantitative genetics models to correctly predict the behaviour of evolutionary processes at the scale of millions of years. Developmental studies (evo-devo) have been proposed to reconcile micro- and macroevolution. However, there has been little progress in establishing a formal framework to apply evo-devo models of phenotypic diversification. Here we reframe this issue by asking whether using evo-devo models to quantify biological variation can improve the explanatory power of comparative models, thus helping us bridge the gap between micro- and macroevolution. We test this prediction by evaluating the evolution of primate lower molars in a comprehensive dataset densely sampled across living and extinct taxa. Our results suggest that biologically informed morphospaces alongside quantitative genetics models allow a seamless transition between the micro- and macroscales, whereas biologically uninformed spaces do not. We show that the adaptive landscape for primate teeth is corridor like, with changes in morphology within the corridor being nearly neutral. Overall, our framework provides a basis for integrating evo-devo into the modern synthesis, allowing an operational way to evaluate the ultimate causes of macroevolution.

Crop rotation-driven changes in rhizosphere metabolite profiles regulate soil microbial diversity and functional capacity

Plants are increasingly revealed to have the ability to shape microbiome composition and function by triggering rhizosphere metabolites. Rotation, a model of crop diversification, promotes crop production by influencing rhizosphere microbiome. However, the rhizosphere metabolites of different rice rotations are rarely reported and, in particular, the regulation of key metabolites on rhizosphere microbiome is unclear. To address this gap, we collected the bulk and rhizosphere soils of four crop rotations (rice-rice, tobacco-rice, rice-oilseed rape, and rice-rice-oilseed rape) to assess rhizosphere metabolites, soil bacterial and fungal diversity, as well as functional microbial populations from a long-term (more than 20 years) field experiment. Compared with the rice-rice system, rhizosphere metabolites, such as deazaflavin, 10-Deacetylbaccatin III, and paclobutrazol, significantly increased in the rice rotation systems with tobacco and oilseed rape. Metabolite components (e.g., azelaic acid, soyasapogenol B, and canrenone) and microbial taxa (Xanthobacteraceae, Bradyrhizobium, and Mortierella) were the keystones regulating the co-occurring correlations of rhizosphere metabolites and soil microorganisms. Compared with the rice-rice, the bulk and rhizosphere soil of rice rotations with oilseed rape or tobacco showed higher abundance of the microbial populations related to C degradation and fixation, N fixation, nitrification, nitrate reduction, inorganic P (Pi) solubilization, and organic P (Po) mineralization. Metabolites, such as 7-chloro-norlichexanthone, daidzein, and soyasapogenol B, were the keystones regulating the co-occurrence relationships of rhizosphere metabolites and functional microbial populations. Rhizosphere metabolite composition was positively related to the populations associated with C fixation and degradation, nitrification, and P solubilization, and negatively related to those associated with methane metabolism, nitrate reduction, denitrification, and anammox (P ≤ 0.05). Soyasapogenol B, daidzei, and [1,1'-biphenyl]− 2,2'-dicarboxylic acid enriched in rotation systems were negatively correlated with dominant microbial taxa such as phylum Bacteroidetes and Chytridiomycota, and positively correlated with phylum Zoopagomycota and the populations associated with key soil functions such as C degradation, nitrate reduction, and P solubilization (P ≤ 0.05). These results demonstrated the importance of rhizosphere metabolites in regulating soil microbiome composition and functional capacity, which deepens understanding of rotations improving rice production via rhizosphere effect.

Estimating clade‐specific diversification rates and palaeodiversity dynamics from reconstructed phylogenies

Abstract Understanding palaeodiversity dynamics through time and space is a central goal of macroevolution. Estimating palaeodiversity dynamics has been historically addressed with fossil data because it directly reflects the past variations of biodiversity. Unfortunately, some groups or regions lack a good fossil record, and dated phylogenies can be useful to estimate diversification dynamics. Recent methodological developments have unlocked the possibility to investigate palaeodiversity dynamics by using phylogenetic birth‐death models with non‐homogeneous rates through time and across clades. One of them seems particularly promising to detect clades whose diversity has declined through time. However, empirical applications of the method have been hampered by the lack of a robust, accessible implementation of the whole procedure, therefore requiring users to conduct all the steps of the analysis by hand in a time‐consuming and error‐prone way. Here we propose an automation of Morlon et al. (2011) clade‐shift model with additional features accounting for recent developments, and we implement it in the R package RPANDA. We also test the approach with simulations focusing on its ability to detect shifts of diversification and to infer palaeodiversity dynamics. Finally, we illustrate the automation by investigating the palaeodiversity dynamics of Cetacea, Vangidae, Parnassiinae and Cycadales. Simulations showed that we accurately detected shifts of diversification although false shift detections were higher for time‐dependent diversification models with extinction. The median global error of palaeodiversity dynamics estimated with the automated model is low, showing that the method can capture diversity declines. We detected shifts of diversification for three of the four empirical examples considered (Cetacea, Parnassiinae and Cycadales). Our analyses unveil a waxing‐and‐waning pattern due to a phase of negative net diversification rate embedded in the trees after isolating recent radiations. Our work makes it possible to easily apply non‐homogeneous models of diversification in which rates can vary through time and across clades to reconstruct palaeodiversity dynamics. By doing so, we detected palaeodiversity declines among three of the four groups tested, highlighting that such periods of negative net diversification might be common. We discuss the extent to which this approach might provide reliable estimates of extinction rates, and we provide guidelines for users.

Deep Learning from Phylogenies for Diversification Analyses.

Birth-death (BD) models are widely used in combination with species phylogenies to study past diversification dynamics. Current inference approaches typically rely on likelihood-based methods. These methods are not generalizable, as a new likelihood formula must be established each time a new model is proposed; for some models, such a formula is not even tractable. Deep learning can bring solutions in such situations, as deep neural networks can be trained to learn the relation between simulations and parameter values as a regression problem. In this paper, we adapt a recently developed deep learning method from pathogen phylodynamics to the case of diversification inference, and we extend its applicability to the case of the inference of state-dependent diversification models from phylogenies associated with trait data. We demonstrate the accuracy and time efficiency of the approach for the time-constant homogeneous BD model and the Binary-State Speciation and Extinction model. Finally, we illustrate the use of the proposed inference machinery by reanalyzing a phylogeny of primates and their associated ecological role as seed dispersers. Deep learning inference provides at least the same accuracy as likelihood-based inference while being faster by several orders of magnitude, offering a promising new inference approach for the deployment of future models in the field.

Pliocene sigmodontine rodents (Mammalia: Cricetidae) in northernmost South America: test of biogeographic hypotheses and revised evolutionary scenarios.

We document the first occurrence of Sigmodontinae (Mammalia, Rodentia, Cricetidae) from the Pliocene of northern South America, from the San Gregorio Formation of northwestern Venezuela. The recovered isolated molars are identified as Oligoryzomys sp. and Zygodontomys sp., two currently widespread sigmodontines in South America. These records constitute the oldest representatives of these genera, potentially new species, and the first Pliocene occurrence for Oryzomyini and the whole subfamily outside Argentina. Hypotheses on the historical biogeography of sigmodontines have been constructed almost exclusively using genetic data and the fossils we report provide a new kind of evidence. The occurrence of Oligoryzomys sp. and Zygodontomys sp. in Venezuela provides novel information for the diversification models suggested for Oligoryzomys, by supporting a potential eastern corridor of open environments from northern to southern South America. The presence of sigmodontines from the locality home of the new reports, Norte Casa Chiguaje, is consistent with the palaeoenvironmental conditions originally proposed for it based on mammals and botanical records, being characterized as mixed open grassland/forest areas surrounding permanent freshwater systems. The new sigmodontine evidence is used to discuss the putative scenarios of the ancient evolution of the subfamily in South America, favouring a model in which open areas (savannahs) to the east of the Andes played crucial role aiding or obstructing Late Miocene-Pliocene sigmodontine dispersion southwards.

Diversification processes in Gerp's mouse lemur demonstrate the importance of rivers and altitude as biogeographic barriers in Madagascar's humid rainforests.

Madagascar exhibits exceptionally high levels of biodiversity and endemism. Models to explain the diversification and distribution of species in Madagascar stress the importance of historical variability in climate conditions which may have led to the formation of geographic barriers by changing water and habitat availability. The relative importance of these models for the diversification of the various forest-adapted taxa of Madagascar has yet to be understood. Here, we reconstructed the phylogeographic history of Gerp's mouse lemur (Microcebus gerpi) to identify relevant mechanisms and drivers of diversification in Madagascar's humid rainforests. We used restriction site associated DNA (RAD) markers and applied population genomic and coalescent-based techniques to estimate genetic diversity, population structure, gene flow and divergence times among M. gerpi populations and its two sister species M. jollyae and M. marohita. Genomic results were complemented with ecological niche models to better understand the relative barrier function of rivers and altitude. We show that M. gerpi diversified during the late Pleistocene. The inferred ecological niche, patterns of gene flow and genetic differentiation in M. gerpi suggest that the potential for rivers to act as biogeographic barriers depended on both size and elevation of headwaters. Populations on opposite sides of the largest river in the area with headwaters that extend far into the highlands show particularly high genetic differentiation, whereas rivers with lower elevation headwaters have weaker barrier functions, indicated by higher migration rates and admixture. We conclude that M. gerpi likely diversified through repeated cycles of dispersal punctuated by isolation to refugia as a result of paleoclimatic fluctuations during the Pleistocene. We argue that this diversification scenario serves as a model of diversification for other rainforest taxa that are similarly limited by geographic factors. In addition, we highlight conservation implications for this critically endangered species, which faces extreme habitat loss and fragmentation.

A timescale for placental mammal diversification based on Bayesian modeling of the fossil record

The timing of the placental mammal radiation has been the focus of debate over the efficacy of competing methods for establishing evolutionary timescales. Molecular clock analyses estimate that placental mammals originated before the Cretaceous-Paleogene (K-Pg) mass extinction, anywhere from the Late Cretaceous to the Jurassic. However, the absence of definitive fossils of placentals before the K-Pg boundary is compatible with a post-Cretaceous origin. Nevertheless, lineage divergence must occur before it can be manifest phenotypically in descendent lineages. This, combined with the non-uniformity of the rock and fossil records, requires the fossil record to be interpreted rather than read literally. To achieve this, we introduce an extended Bayesian Brownian bridge model that estimates the age of origination and, where applicable, extinction through a probabilistic interpretation of the fossil record. The model estimates the origination of placentals in the Late Cretaceous, with ordinal crown groups originating at or after the K-Pg boundary. The results reduce the plausible interval for placental mammal origination to the younger range of molecular clock estimates. Our findings support both the Long Fuse and Soft Explosive models of placental mammal diversification, indicating that the placentals originated shortly prior to the K-Pg mass extinction. The origination of many modern mammal lineages overlapped with and followed the K-Pg mass extinction.

The ClaDS rate-heterogeneous birth-death prior for full phylogenetic inference in BEAST2.

Bayesian phylogenetic inference requires a tree prior, which models the underlying diversification process that gives rise to the phylogeny. Existing birth-death diversification models include a wide range of features, for instance, lineage-specific variations in speciation and extinction (SSE) rates. While across-lineage variation in SSE rates is widespread in empirical datasets, few heterogeneous rate models have been implemented as tree priors for Bayesian phylogenetic inference. As a consequence, rate heterogeneity is typically ignored when reconstructing phylogenies, and rate heterogeneity is usually investigated on fixed trees. In this paper, we present a new BEAST2 package implementing the cladogenetic diversification rate shift (ClaDS) model as a tree prior. ClaDS is a birth-death diversification model designed to capture small progressive variations in birth and death rates along a phylogeny. Unlike previous implementations of ClaDS, which were designed to be used with fixed, user-chosen phylogenies, our package is implemented in the BEAST2 framework and thus allows full phylogenetic inference, where the phylogeny and model parameters are co-estimated from a molecular alignment. Our package provides all necessary components of the inference, including a new tree object and operators to propose moves to the Monte-Carlo Markov chain. It also includes a graphical interface through BEAUti. We validate our implementation of the package by comparing the produced distributions to simulated data and show an empirical example of the full inference, using a dataset of cetaceans.

The build-up of the present-day tropical diversity of tetrapods

The extraordinary number of species in the tropics when compared to the extra-tropics is probably the most prominent and consistent pattern in biogeography, suggesting that overarching processes regulate this diversity gradient. A major challenge to characterizing which processes are at play relies on quantifying how the frequency and determinants of tropical and extra-tropical speciation, extinction, and dispersal events shaped evolutionary radiations. We address this question by developing and applying spatiotemporal phylogenetic and paleontological models of diversification for tetrapod species incorporating paleoenvironmental variation. Our phylogenetic model results show that area, energy, or species richness did not uniformly affect speciation rates across tetrapods and dispute expectations of a latitudinal gradient in speciation rates. Instead, both neontological and fossil evidence coincide in underscoring the role of extra-tropical extinctions and the outflow of tropical species in shaping biodiversity. These diversification dynamics accurately predict present-day levels of species richness across latitudes and uncover temporal idiosyncrasies but spatial generality across the major tetrapod radiations.

Ornamentation diversified faster than eco-morphology across Nearctic dragonflies

AbstractEco-morphology and ornamentation are two phenotypic dimensions along which co-existing species often diverge, yet theory makes contrasting predictions about how these phenotypes diversify relative to each other. Some theory predicts that intense reproductive demands cause more pronounced divergence in ornamentation than in eco-morphology. Other theory predicts that preferences for condition-dependent ornamentation in species encountering divergent ecological conditions will facilitate rapid divergence in eco-morphology but not ornamentation. We evaluated these conflicting predictions in Nearctic Libelluloidea dragonflies by testing if the diversification of a condition-dependent ornament, male wing melanization, was slower and less pronounced between species than the diversification of two key eco-morphological traits, body size and relative wing size. We found that male wing melanization evolved much faster than either body size or relative wing size. Furthermore, in contrast to the patterns for either eco-morphological trait, the best-supported models of diversification in male wing melanization indicate that the majority of divergence arose between the most closely related species. These results reveal that the primary axis of divergence between closely related Libelluloidea dragonflies is ornamentation rather than eco-morphology. Our study therefore suggests that evolutionary responses to disparate reproductive demands may be fundamental to the persistence and co-existence of closely related species.

Who Owns What? A Factor Model for Direct Stockholding

ABSTRACTWe build a cross‐sectional factor model for investors' direct stockholdings and estimate it using data from almost 10 million retail accounts in the Indian stock market. Our model identifies strong investor clienteles for stock characteristics, most notably firm age and share price, and for particular clusters of stock characteristics. These clienteles are intuitively associated with investor attributes such as account age, size, and diversification. Coheld stocks tend to have higher return covariance, inconsistent with simple models of diversification but suggestive that clientele demands influence stock returns.

Climate-influenced boreotropical survival and rampant introgressionsexplain the thriving of New World grapes in the north temperate zone.

The north temperate region was characterized by a warm climate and a rich thermophilic flora before the Eocene, but early diversifications of the temperate biome under global climate change and biome shift remain uncertain. Moreover, it is becoming clear that hybridization/introgression is an important driving force of speciation in plant diversity. Here, we applied analyses from biogeography and phylogenetic networks to account for both introgression and incomplete lineage sorting based on genomic data from the New World Vitis, a charismatic component of the temperate North American flora with known and suspected gene flow among species. Biogeographic inference and fossil evidence suggest that the grapes were widely distributed from North America to Europe during the Paleocene to the Eocene, followed by widespread extinction and survival of relicts in the tropical New World. During the climate warming in the early Miocene, a Vitis ancestor migrated northward from the refugia with subsequent diversification in the North American region. We found strong evidence for widespread incongruence and reticulate evolution among nuclear genes within both recent and ancient lineages of the New World Vitis. Furthermore, the organellar genomes showed strong conflicts with the inferred species tree from the nuclear genomes. Our phylogenomic analyses provided an important assessment of the wide occurrence of reticulate introgression in the New World Vitis, which potentially represents one of the most important mechanisms for the diversification of Vitis species in temperate North America and even the entire temperate Northern Hemisphere. The scenario we report here may be a common model of temperate diversification of flowering plants adapted to the global climate cooling and fluctuation in the Neogene.

Diversification Models Conflate Likelihood and Prior, and Cannot be Compared Using Conventional Model-Comparison Tools.

Time-calibrated phylogenetic trees are a tremendously powerful tool for studying evolutionary, ecological, and epidemiological phenomena. Such trees are predominantly inferred in a Bayesian framework, with the phylogeny itself treated as a parameter with a prior distribution (a "tree prior"). However, we show that the tree "parameter" consists, in part, of data, in the form of taxon samples. Treating the tree as a parameter fails to account for these data and compromises our ability to compare among models using standard techniques (e.g., marginal likelihoods estimated using path-sampling and stepping-stone sampling algorithms). Since accuracy of the inferred phylogeny strongly depends on how well the tree prior approximates the true diversification process that gave rise to the tree, the inability to accurately compare competing tree priors has broad implications for applications based on time-calibrated trees. We outline potential remedies to this problem, and provide guidance for researchers interested in assessing the fit of tree models. [Bayes factors; Bayesian model comparison; birth-death models; divergence-time estimation; lineage diversification].

Diversification and performance of microfinance institutions: does Islamic microfinance model matter?

Purpose The aim of this study is to investigate the effect of income and geographic diversification on the double bottom line of microfinance institutions (MFIs) in Middle East and North Africa (MENA) countries where conventional and Islamic MFIs coexist. The idea is to explore whether diversification impacts MFIs' financial performance and outreach differ for Islamic microfinance. Design/methodology/approach The authors test the effect of diversification and business models of MFIs on their performance and poverty outreach. The authors’ data set is an unbalanced panel sample of 81 (Islamic and conventional) MFIs in MENA countries covering 1999–2018, comprising 743 MFI-year observations. Findings The authors find that increasing income diversification in microfinance and focusing on rural areas decreases the financial performance of MFIs in MENA countries. Islamic MFIs benefit from income diversification by increasing their financial performance. The results provide evidence of a nonlinear relationship between income diversification and the financial performance of MFIs. Although conventional MFIs improve their depth of outreach by diversifying their income, Islamic MFIs have a lower breadth of outreach because they show a higher degree of income diversification. Practical implications This research contributes to the ongoing debate of whether MFIs should focus on or diversify their services to Islamic microfinance. Therefore, the findings of this study are practically crucial for MFIs' stakeholders to understand the contribution of diversification strategies in improving the Islamic MFIs to achieve both financial and social objectives. Originality/value To the best of the authors’ knowledge, it is the first research that addresses the impact of diversification strategies in Islamic microfinance. Additionally, using a panel data set of conventional and Islamic MFIs in MENA countries spanning 1999–2018, this study provides empirical evidence on the diversification versus focus issue from the microfinance industry and the subset of Islamic microfinance.

Towards a global perspective for Salvia L.: Phylogeny, diversification and floral evolution.

Salvia is the most species-rich genus in Lamiaceae, encompassing approximately 1000 species distributed all over the world. We sought a new evolutionary perspective for Salvia by employing macroevolutionary analyses to address the tempo and mode of diversification. To study the association of floral traits with speciation and extinction, we modelled and explored the evolution of corolla length and the lever-mechanism pollination system across our Salvia phylogeny. We reconstructed a multigene phylogeny for 366 species of Salvia in the broad sense including all major recognized lineages and 50 species from Iran, a region previously overlooked in studies of the genus. Our comprehensive sampling of Iranian species of Salvia provides higher phylogenetic resolution for southwestern Asian species than obtained in previous studies. Our phylogenetic data in combination with divergence time estimates were used to examine the evolution of corolla length, woody versus herbaceous habit, and presence versus absence of a lever mechanism. We investigated the timing and dependence of Salvia diversification related to corolla length evolution through a disparity test and BAMM analysis. A HiSSE model was used to evaluate the dependency of diversification on the lever-mechanism pollination system in Salvia. A medium corolla length (15-18 mm) was reconstructed as the ancestral state for Salvia with multiple shifts to shorter and longer corollas. Macroevolutionary model analyses indicate that corolla length disparity is high throughout Salvia evolution, significantly different from expectations under a Brownian motion model during the last 28 million years of evolution. Our analyses show evidence of a higher diversification rate of corolla length for some Andean species of Salvia compared to other members of the genus. Based on our tests of diversification models, we reject the hypothesis of a direct effect of the lever mechanism on Salvia diversification. Therefore, we suggest caution in considering the lever-mechanism pollination system as one of the main drivers of speciation in Salvia.