Model Of Diversification Research Articles

Does Clade Density Constrain Geographical Range Evolution?

The role of biotic interactions, such as interspecific competition, in driving geographical range evolution is still poorly understood. For instance, lineages distributed across regions with a large number of potential competitors might experience some level of geographical packing of their range limits, so that changes in their geographical distributions are hampered. Conversely, a large number of competitors could instead lead to accelerated rates of geographical range evolution, with lineages shifting their ranges to avoid competition. We recently introduced the concept of clade density (CD; the sum of the areas of overlap between a species and other members of its higher taxon, weighted by their phylogenetic distance) as a proxy of the potential for interspecific competition across the geographical distribution of a given species. In this study, we used a large dataset with 5936 terrestrial vertebrate species to test whether CD is significantly associated with variation in the rate of geographical range evolution using two alternative approaches. First, we tested if there is a significant relationship between CD and the geographical distance between sister species. In addition, we estimated tip rates of geographical range evolution and tested if they were consistently associated with variation in CD. We found no evidence for an effect of CD on geographical range evolution in either of the tested approaches, even after accounting for phylogenetic uncertainty. These results are inconsistent with equilibrial models of species diversification and suggest that interspecific competition might not play a pervasive role in geographical range evolution of terrestrial vertebrates.

Opening the species box: What parsimonious microscopic models of speciation have to say about macroevolution.

In the last two decades, lineage-based models of diversification, where species are viewed as particles that can divide (speciate) or die (become extinct) at rates depending on some evolving trait, have been very popular tools to study macroevolutionary processes. Here, we argue that this approach cannot be used to break down the inner workings of species diversification and that "opening the species box" is necessary to understand the causes of macroevolution, but that too detailed speciation models also fail to make robust macroevolutionary predictions. We set up a general framework for parsimonious models of speciation that rely on a minimal number of mechanistic principles: (i) reproductive isolation is caused by excessive dissimilarity between genotypes; (ii) dissimilarity results from a balance between differentiation processes and homogenizing processes; and (iii) dissimilarity can feed back on these processes by decelerating homogenization. We classify such models according to the main homogenizing process : (1) clonal evolution models (ecological drift), (2) models of genetic isolation (gene flow) and (3) models of isolation by distance (spatial drift). We review these models and their specific predictions on macroscopic variables such as species abundances, speciation rates, interfertility relationships or phylogenetic tree structure. We propose new avenues of research by displaying conceptual questions remaining to be solved and new models to address them: the failure of speciation at secondary contact, the feedback of dissimilarity on homogenization, the emergence in space of breeding barriers.

What happens when tourism is turned off: Exploring the outcomes of the COVID-19 pandemic travel restrictions for Indigenous people in Rarotonga, The Cook Islands

The sea, sand, and sun allure of the Cook Islands has seen tourism become the most significant driver of the country's economic development. However, the increasing reliance on the tourism sector since the 1980's has created a mono-economy at the expense of diversification and alternative economic models. The COVID-19 pandemic emphasized the risks and consequences associated with an over- reliance on international tourism as the lockdown measures and international travel restrictions caused the sudden shutdown of international tourism, resulting in serious negative economic consequences for tourism-dependent communities. However, the pandemic also offered an opportunity for small island societies to reflect on pre-existing challenges associated with the tourism industry. Through qualitative semi-structured interviews with Indigenous Cook Islanders in Rarotonga, this study aimed to develop a deeper understanding of how the lived experiences of participants responding to the sudden collapse of tourism may have influenced how Indigenous Cook Islands peoples perceive the role of tourism in supporting the wellbeing of their small island nation. The presented study is the result of a collaborative research partnership between an Indigenous Pacific scholar and non-Indigenous European scholar. While the research adopted a western methodology, the relationships developed between the researchers and participants were guided by the cultural values of reciprocity and respect, which are key principles underpinning Indigenous research in the Pacific. The findings revealed that participants adapted to the adverse impacts of COVID-19 through the revitalization of their traditional socio-economies, the resurgence of customary practices, a strengthened connection to nature, and a renewed sense of community spirit and pride in cultural identity—all of which were perceived to positively impact their spiritual, social, cultural, environmental, physical, and mental wellbeing. By demonstrating the positive adaptive responses of participants, this article aims to emphasize the non-economic dimensions of wellbeing that are critical to supporting the cultural values, social priorities, and the Indigenous ways of life that preceded the development of tourism. These findings can be used to inform and guide international development policy makers and tourism stakeholders who seek to reduce the adverse impacts of tourism on the wellbeing of Indigenous communities in the Pacific.

Identifying the multiple drivers of cactus diversification

Our understanding of the complexity of forces at play in the rise of major angiosperm lineages remains incomplete. The diversity and heterogeneous distribution of most angiosperm lineages is so extraordinary that it confounds our ability to identify simple drivers of diversification. Using machine learning in combination with phylogenetic modelling, we show that five separate abiotic and biotic variables significantly contribute to the diversification of Cactaceae. We reconstruct a comprehensive phylogeny, build a dataset of 39 abiotic and biotic variables, and predict the variables of central importance, while accounting for potential interactions between those variables. We use state-dependent diversification models to confirm that five abiotic and biotic variables shape diversification in the cactus family. Of highest importance are diurnal air temperature range, soil sand content and plant size, with lesser importance identified in isothermality and geographic range size. Interestingly, each of the estimated optimal conditions for abiotic variables were intermediate, indicating that cactus diversification is promoted by moderate, not extreme, climates. Our results reveal the potential primary drivers of cactus diversification, and the need to account for the complexity underlying the evolution of angiosperm lineages.

PhyloJunction: a computational framework for simulating, developing, and teaching evolutionary models.

We introduce PhyloJunction, a computational framework designed to facilitate the prototyping, test- ing, and characterization of evolutionary models. PhyloJunction is distributed as an open-source Python library that can be used to implement a variety of models, thanks to its flexible graphical modeling architecture and dedicated model specification language. Model design and use are exposed to users via command-line and graphical interfaces, which integrate the steps of simulating, summarizing, and visualizing data. This paper describes the features of PhyloJunction - which include, but are not limited to, a general implementation of a popular family of phylogenetic diversification models - and, moving forward, how it may be expanded to not only include new models, but to also become a platform for conducting and teaching statistical learning.

Retraction: GerardDeepak, ArumugamSanthanavijayan. QGMS: A query growth model for personalization and diversification of semantic search based on differential ontology semantics using artificial intelligence. Comput Intell40: e12514, 2024 (10.1111/coin.12514)

The above article, published online on 08 March 2022 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the Editor‐in‐Chief, Diana Inkpen, and Wiley Periodicals LLC. The article was published as part of a guest‐edited special issue. Following publication, it came to our attention that two of those named as Guest Editors of this issue were being impersonated and/or misrepresented by a fraudulent entity. An investigation by the publisher found that all of the articles, including this one, experienced compromised editorial handling and peer review which was not in line with the journal's ethical standards. Therefore, a decision has been made to retract this article. The authors have been informed of the decision to retract.

International Portfolio Diversification Benefits: An Empirical Investigation of the 28 European Stock Markets During the Period 2014–2024

Abstract This study investigates the benefits of international diversification in the stock markets of the 28 European countries (the EU and the UK) over two five-year periods: a stable period from 2014 to 2019 and a turbulent period from 2019 to 2024. The analysis draws on the Markowitz mean-variance, Sharpe reward-to-variability, and naive diversification models, based on which different investment strategies were developed and implemented. We find that actively managed portfolios perform significantly better than naively diversified portfolios. The analyzed markets exhibit positive short-term associations, with an average correlation coefficient of 0.29 in the first period and 0.46 in the second period. However, these markets do not show long-term cointegration. Recent crises have reduced diversification benefits, yet significant opportunities for diversification remain. Diversification benefits are almost halved in the second period: average single-market standard deviation can be reduced by 60.5% with investments in 20-indices portfolios in the stable period, and only by 33.7% with the same portfolio size in the turbulent period.

Sequential trait evolution did not drive deep-time diversification in sharks.

Estimating how traits evolved and impacted diversification across the tree of life represents a critical topic in ecology and evolution. Although there has been considerable research in comparative biology, large parts of the tree of life remain underexplored. Sharks are an iconic clade of marine vertebrates, and key components of marine ecosystems since the early Mesozoic. However, few studies have addressed how traits evolved or whether they impacted their extant diversity patterns. Our study aimed to fill this gap by reconstructing the largest time-calibrated species-level phylogeny of sharks and compiling an exhaustive database for ecological (diet, habitat) and biological (reproduction, maximum body length) traits. Using state-of-the-art models of evolution and diversification, we outlined the major character shifts and modes of trait evolution across shark species. We found support for sequential models of trait evolution and estimated a small to medium-sized lecithotrophic and coastal-dwelling most recent common ancestor for extant sharks. However, our exhaustive hidden traits analyses do not support trait-dependent diversification for any examined traits, challenging previous works. This suggests that the role of traits in shaping sharks' diversification dynamics might have been previously overestimated and should motivate future macroevolutionary studies to investigate other drivers of diversification in this clade.

Macroevolutionary Dynamics in Micro-organisms: Generalists Give Rise to Specialists Across Biomes in the Ubiquitous Bacterial Phylum Myxococcota.

Prokaryotes dominate the Tree of Life, but our understanding of the macroevolutionary processes generating this diversity is still limited. Habitat transitions are thought to be a key driver of prokaryote diversity. However, relatively little is known about how prokaryotes successfully transition and persist across environments, and how these processes might vary between biomes and lineages. Here, we investigate biome transitions and specialization in natural populations of a focal bacterial phylum, the Myxococcota, sampled across a range of replicated soils and freshwater and marine sediments in Cornwall (UK). By targeted deep sequencing of the protein-coding gene rpoB, we found >2,000 unique Myxococcota lineages, with the majority (77%) classified as biome specialists and with only <5% of lineages distributed across the salt barrier. Discrete character evolution models revealed that specialists in one biome rarely transitioned into specialists in another biome. Instead, evolved generalism mediated transitions between biome specialists. State-dependent diversification models found variation in speciation rates across the tree, but this variation was independent of biome association or specialization. Our findings were robust to phylogenetic uncertainty, different levels of species delineation, and different assumed amounts of unsampled diversity resulting in an incomplete phylogeny. Overall, our results are consistent with a "jack-of-all-trades" tradeoff where generalists suffer a cost in any individual environment, resulting in rapid evolution of niche specialists and shed light on how bacteria could transition between biomes.

The Competitive Challenges in China's Prepared Dishes Industry: A Focus on Anjoy Foods

This research investigated Anjoy Foods Co., Ltd.'s strategies in China's prepared dish market amidst the COVID-19 pandemic, focusing on the period 20202023. The pandemic led to a surge in demand for prepared dishes due to changing consumer behaviors, such as reduced outings and a scarcity of fresh food. Despite Anjoy Foods' revenue growth (from 673 million RMB in 2020 to over 3 billion RMB by 2022), its gross profit margin declined from 29.72% in 2018 to 11.42% in 2022. This paper employed the marketing mix theory (product, price, promotion, and place) to analyze Anjoy Foods' market strategies and identify key areas for improvement. The research highlighted that Anjoy Foods' product line fails to align with the growing consumer interest in health-focused and convenient food options. It also notes the company's premium pricing strategy as a disadvantage in a price-sensitive market. Additionally, the study pointed out a reduction in promotional activities, particularly in digital advertising, which affects engagement with key demographics. The paper suggested strategic innovations in product diversification, adopting tiered and value-based pricing models, and enhancing digital marketing efforts. These strategies aim to realign Anjoy Foods with evolving market demands and consumer preferences. The conclusion emphasized the importance of continuous adaptation and innovation for market competitiveness, recommending further research on practical strategy applications and broader market trends.

Differential Stage-Specific Mortality as a Mechanism for Diversification.

AbstractIndividual variability in mortality is widespread in nature. The general rule is that larger organisms have a greater chance of survival than smaller conspecifics. There is growing evidence that differential mortality between developmental stages has important consequences for the ecology and evolution of populations and communities. However, we know little about how it can influence diversification. Using an eco-evolutionary model of diversification that considers individual variability in mortality, I show that commonly observed differences in mortality between juveniles and adults can facilitate adaptive diversification. In particular, diversification is expected to be less restricted when mortality is more biased toward juveniles. Additionally, I find stage-specific differences in metabolic cost and foraging capacity to further facilitate diversification when adults are slightly superior competitors, due to either a lower metabolic cost or a higher foraging capacity, than juveniles. This is because by altering the population composition, differential stage-specific mortality and competitive ability can modulate the strength of intraspecific competition, which in turn determines the outcome of diversification. These results demonstrate the strong influence that ecological differences between developmental stages have on diversification and highlight the need for integrating developmental processes into diversification theory.

Enhancing Portfolio Performance through Financial Time-Series Decomposition-Based Variational Encoder-Decoder Data Augmentation

The objective of portfolio diversification is to reduce risk and potentially enhance returns by spreading investments across different asset classes. Existing portfolio diversification models have traditionally been trained on historical financial time series data. However, several issues arise with historical financial time series data, making it challenging to train models effectively to achieve the portfolio diversification objective: an insufficient amount of training data and the uncertainty deficiency problem, wherein the uncertainty that existed in the past is not visible in the present. Insufficient datasets, characterized by small data size, result in information asymmetry and compromise portfolio performance. This limitation underscores the importance of adopting a pattern-centric data augmentation approach, capable of unveiling hidden patterns and structures within the financial time series data. To address these challenges, this paper introduces the financial time series decomposition-based variational encoder-decoder (FED) method to augment financial time series data, overcoming the limitations of insufficient training data and providing a more realistic and dynamic simulation of the financial market environment. By decomposing the data into distinct components, such as trend, dispersion, and residual, FED leverages pattern-centric data augmentation within the financial time series data. In the environment generated using the FED method, this paper proposes a two-class portfolio diversification, called FED2Port. It integrates stochastic elements into the reward function, enabling a reinforcement learning algorithm to learn from a comprehensive spectrum of financial market uncertainties. The experimental results demonstrate that the proposed model significantly enhances portfolio performance.

Palaearctic origin and repeated dispersal over the world shaped the biogeographic history of the saprophytic genus Coprinopsis (Psathyrellaceae, Basidiomycota)

AbstractAimThe biogeographic history of most fungi is still poorly known, as well as the patterns and processes responsible for their diversification. Recent studies uncovered that most fungi have originated and present higher diversification rates in the temperate zone. The distributional pattern known for fungi is also different from many plants, animals and microbes. Using the most comprehensive phylogeny of the saprotrophic genus Coprinopsis, we aim to infer the biogeographic history and test evolutionary hypotheses in the genus.LocationWorldwide.TaxonFungi, Basidiomycota, Psathyrellaceae, Coprinopsis.MethodsWe used a four‐gene alignment with 100 species to estimate divergence times using two fossil calibrations within Agaricales. The chronograms were used to estimate diversification rates and geographic state‐dependent models were applied. We further reconstructed the ancestral range history of the genus.ResultsMolecular dating estimated that the genus has diverged ca. 41 Ma (Eocene) and was originated in the Palaearctic region. Diversification rates showed a decreasing pattern towards the present across Coprinopsis, especially after the Miocene (ca. 14 Ma). The diversification models dependent on distribution showed cosmopolitan lineages with a higher net‐diversification rates. When we compared temperate and tropical regions, we found that temperate lineages have higher net‐diversification rates. The biogeographic history of Coprinopsis estimated different routes of dispersal. The most common dispersal route was from Palaearctic to the Nearctic (15 times), followed by Palaearctic to the Neotropics (14 times).Main ConclusionsThe study is the first to estimate the diversification rates and the historical biogeography of the coprinoid genus Coprinopsis. The diversification dynamics estimates in Coprinopsis are in agreement with the ‘generalized diversification rates model’, where we found higher diversification rates in temperate regions compared with tropical regions. In general, the ancestral area and major dispersals routes recovered in the genus are similar to findings in other groups of fungi.

Management of the diversification of a trading company’s activities

The strategy of overcoming the crisis is still relevant for Ukraine’s economy: diversification, entering new areas of business and trade, and searching for risks and alternatives have become important tasks after the full-scale invasion in 2022 and the declaration of martial law. The purpose of this study was to investigate the features of diversification of trading activities in crisis conditions on the example of Ukraine. Using the method of statistical analysis, the most effective and popular methods of risk distribution and features of Ukrainian crisis management were identified. The study proved the effectiveness of such diversification measures as the transition of sales to online formats, the use of postal and courier delivery services, duplication of export routes in the process of developing supply chains during martial law, and the expansion of the range of private label products by retailers. Separately, statistics on the dynamics of sales of dietary supplements in Ukrainian pharmacy chains were analysed and it was proved that sales of this group of products increased during the crisis. Based on the data obtained and the conclusions, the need to tackle corruption and immediately reform the judiciary and tax systems was proved, as these are the actions expected by the Ukrainian business community. Using the modelling, a model of enterprise diversification was created. The practical significance of the study lies in the publication of systematic information on ways of diversification, which can be useful for representatives of business and the economic block of power

Limited ecological opportunity influences the tempo of morphological evolution in birds

According to classic models of lineage diversification and adaptive radiation, phenotypic evolution should accelerate in the context of ecological opportunity and slow down when niches become saturated.1,2 However, only weak support for these ideas has been found in nature, perhaps because most analyses make the biologically unrealistic assumption that clade members contribute equally to reducing ecological opportunity, even when they occur in different continents or specialize on different habitats and diets. To view this problem through a different lens, we adapted a new phylogenetic modeling approach that accounts for the fact that competition for ecological opportunity only occurs between species that coexist and share similar habitats and diets. Applying this method to trait data for nearly all extant species of landbirds,3 we find a widespread signature of decelerating trait evolution in lineages adapted to similar habitats or diets. The strength of this pattern was consistent across latitudes when comparing tropical and temperate assemblages. Our results provide little support for the idea that increased diversity and tighter packing of niches accentuates evolutionary slowdowns in the tropics and instead suggest that limited ecological opportunity can be an important factor determining the rate of morphological diversification at a global scale.

Analysis of the criteria selection problem in diversification models

The digitalization of the economy reduces the cost of doing business by automating the relevant processes, but any transformation creates new risks and economic instability. Economic instability leads to a drop in the standard of living and, as a result, negatively affects the activities of trade enterprises. Small and medium businesses are especially sensitive to any changes. The decrease in demand for most everyday goods has a painful effect on the activities of small and medium-sized businesses and leads to the emergence of new risks. These risks have a significant impact on reducing the profitability of enterprises. Therefore, it is important for each enterprise to diversify the activities of the enterprise, which includes the expansion of the product range, the reorientation of sales markets and the optimal distribution of goods between divisions of one enterprise. The subject of the article is multi-criteria models of a diversified portfolio that minimize the risks that arise in the era of the digital economy when managing retail chains. To formalize the problem, five models are proposed that differ in vector objective functions, both in the quantity and quality of the selected criteria. The aim of the work is to analyze the problem of choosing criteria in the corresponding multicriteria or vector diversification problems. The article examines the advantages of introducing an additional criterion of entropy maximization into the criteria of the classical two-criteria model of portfolio theory, which characterizes the degree of diversity of the portfolio composition. A complex combination of methods of classical portfolio theory and multicriteria optimization is applied. The results include a comparison of three methods for solving the following problems: criteria convolution, successive concessions, and computer simulation of the Pareto set. Conclusions: the results obtained will be useful for automating the risk management of retail chains. The practical value is that the obtained results of real data for the network have demonstrated the possibility of using the developed tool for automatic allocation of resources in the form of pareto-optimal portfolios in order to minimize risks.

Hidden shifts in allometry scaling between sound production and perception in anurans.

Animal communication consists of signal production and perception, which are crucial for social interactions. The main form used by anurans is auditory communication, in most cases produced as advertisement calls. Furthermore, sound perception happens mainly through an external tympanic membrane, and plays an important role in social behavior. In this study, we evaluated the influence of body and tympanic membrane sizes on call frequency across the phylogeny of anurans. We use data on snout-vent length, tympanic membrane diameter, and dominant frequency of the advertisement call from the literature and from natural history museum collections. We mapped these traits across the anuran phylogeny and tested different models of diversification. Our final dataset includes data on body size, tympanic membrane size, and call dominant frequency of 735 anuran species. The best explanatory model includes body and tympanum size with no interaction term. Although our results show that call frequency is strongly constrained by body and tympanum size, we identify five evolutionary shifts in allometry from that ancestral constraint. We relate these evolutionary shifts to the background noise experienced by populations. Body size is important for myriad ecological interactions and tympanum size is strongly associated with female call frequency preferences. Thus, allometric escape in frog calls might arise through environmental selection such as breeding in fast flowing or soundscape competition, as well as sexual selection linked to tympanum size.

All about being old and shooting hairs: clade age and urticating hair explain the patterns of diversification in tarantulas.

The extreme asymmetry of species richness distribution across the tree of life has always intrigued evolutionary biologists. Two competing explanations have been proposed to explain this pattern-the clade age hypothesis and diversification rate variation. While these two scenarios may not be mutually exclusive, to what extent time and diversification rates interact to explain species richness patterns remains understudied. Here, we investigate the relative influence of these two scenarios using tarantulas (Family: Theraphosidae) as a model. Tarantulas represent a speciose group of spiders found worldwide but exceptionally diverse in South America. These spiders show two distinct patterns of microhabitat use (ground-dwelling or arboreal) and defense strategies (presence or absence of urticating hairs). Using various trait-independent and dependent diversification models, we test the clade age hypothesis, the role of microhabitat, antipredator defense strategy, and geography in influencing diversification rates. Our results suggest that clade age is the primary predictor of species richness distribution across the tarantula subfamilies. However, the presence of urticating hair probably disrupted this pattern in some clades by increasing the net diversification rates, not by increasing the speciation rate but by reducing the extinction rate.

Exploring congruent diversification histories with flexibility and parsimony

Abstract Using phylogenies of present‐day species to estimate diversification rate trajectories—speciation and extinction rates over time—is a challenging task due to non‐identifiability issues. Given a phylogeny, there exists an infinite set of trajectories that result in the same likelihood; this set has been coined a congruence class. Previous work has developed approaches for sampling trajectories within a given congruence class, with the aim to assess the extent to which congruent scenarios can vary from one another. Based on this sampling approach, it has been suggested that rapid changes in speciation or extinction rates are conserved across the class. Reaching such conclusions requires to sample the broadest possible set of distinct trajectories. We introduce a new method for exploring congruence classes that we implement in the R package CRABS. Whereas existing methods constrain either the speciation rate or the extinction rate trajectory, ours provides more flexibility by sampling congruent speciation and extinction rate trajectories simultaneously. This allows covering a more representative set of distinct diversification rate trajectories. We also implement a filtering step that allows selecting the most parsimonious trajectories within a class. We demonstrate the utility of our new sampling strategy using a simulated scenario. Next, we apply our approach to the study of mammalian diversification history. We show that rapid changes in speciation and extinction rates need not be conserved across a congruence class, but that selecting the most parsimonious trajectories shrinks the class to concordant scenarios. Our approach opens new avenues both to truly explore the myriad of potential diversification histories consistent with a given phylogeny, embracing the uncertainty inherent to phylogenetic diversification models, and to select among these different histories. This should help refining our inference of diversification trajectories from extant data.

Implications of headwater contact zones for the riverine barrier hypothesis: a case study of the Blue-capped Manakin (Lepidothrix coronata).

Rivers frequently delimit the geographic ranges of species in the Amazon Basin. These rivers also define the boundaries between genetic clusters within many species, yet river boundaries have been documented to break down in headwater regions where rivers are narrower. To explore the evolutionary implications of headwater contact zones in Amazonia, we examined genetic variation in the Blue-capped Manakin (Lepidothrix coronata), a species previously shown to contain several genetically and phenotypically distinct populations across the western Amazon Basin. We collected restriction site-associated DNA sequence data (RADcap) for 706 individuals and found that spatial patterns of genetic structure indicate several rivers, particularly the Amazon and Ucayali, are dispersal barriers for L. coronata. We also found evidence that genetic connectivity is elevated across several headwater regions, highlighting the importance of headwater gene flow for models of Amazonian diversification. The headwater region of the Ucayali River provided a notable exception to findings of headwater gene flow by harboring non-admixed populations of L. coronata on opposite sides of a < 1-km-wide river channel with a known dynamic history, suggesting that additional prezygotic barriers may be limiting gene flow in this region.