Revision of Madagascar's Dwarf Lemurs (Cheirogaleidae:Cheirogaleus): Designation of Species, Candidate Species Status and Geographic Boundaries Based on Molecular and Morphological Data

The genus Cheirogaleus, the dwarf lemurs, is a radiation of strepsirrhine primates endemic to the island of Madagascar. The dwarf lemurs are taxonomically grouped in the family Cheirogaleidae (Infraorder: Lemuriformes) along with the genera Microcebus, Mirza, Allocebus, and Phaner. The taxonomic history of the genus Cheirogaleus has been controversial since its inception due to a paucity of evidence in support of some proposed species. In this study, we addressed this issue by expanding the geographic breadth of samples by 91 individuals and built upon existing mitochondrial (cytb and COII) and nuclear (FIBA and vWF) DNA datasets to better resolve the phylogeny of Cheirogaleus. The mitochondrial gene fragments D-loop and PAST as well as the CFTR-PAIRB nuclear loci were also sequenced. In agreement with previous genetic studies, numerous deep divergences were resolved in the C. major, C. minor and C. medius lineages. Four of these lineages were segregated as new species, seven were identified as confirmed candidate species, and four were designated as unconfirmed candidate species based on comparative mitochondrial DNA sequence data gleaned from the literature or this study. Additionally, C. thomasi was resurrected. Given the widespread distribution of the genus Cheirogaleus throughout Madagascar, the methodology employed in this study combined all available lines of evidence to standardize investigative procedures in a genus with limited access to type material and a lack of comprehensive sampling across its total distribution. Our results highlighted lineages that likely represent new species and identified localities that may harbor an as-yet undescribed cryptic species diversity pending further field and laboratory work.We are most grateful to the Ahmanson Foundation, the Theodore F. and Claire M. Hubbard Family Foundation, the Primate Action Fund / Conservation International, the Margot Marsh Biodiversity Foundation, and the National Geographic Society, for financial assistance

The relative importance of ecological drivers of arbuscularmycorrhizal fungal distribution varies with taxon phylogeneticresolution

The phylogenetic depth at which arbuscular mycorrhizal (AM) fungi harbor a coherent eco-logical niche is unknown, which has consequences for operational taxonomic unit (OTU)delineation from sequence data and the study of their biogeography. We tested how changes in AM fungi community composition across habitats (beta diver-sity) vary with OTU phylogenetic resolution. We inferred exact sequence variants (ESVs) toresolve phylotypes at resolutions finer than provided by traditional sequence clustering andanalyzed beta diversity profiles up to order-level sequence clusters. At the ESV level, we detected the environmental predictors revealed with traditional OTUsor at higher genetic distances. However, the correlation between environmental predictorsand community turnover steeply increased at a genetic distance ofc. 0.03 substitutions persite. Furthermore, we observed a turnover of either closely or distantly related taxa (respec-tively at or above 0.03 substitutions per site) along different environmental gradients. This study suggests that different axes of AM fungal ecological niche are conserved at dif-ferent phylogenetic depths. Delineating AM fungal phylotypes using DNA sequences shouldscreen different phylogenetic resolutions to better elucidate the factors that shape communi-ties and predict the fate of AM symbioses in a changing environment

The Dfam community resource of transposable element families, sequence models, and genome annotations.

Dfam is an open access database of repetitive DNA families, sequence models, and genome annotations. The 3.0-3.3 releases of Dfam ( https://dfam.org ) represent an evolution from a proof-of-principle collection of transposable element families in model organisms into a community resource for a broad range of species, and for both curated and uncurated datasets. In addition, releases since Dfam 3.0 provide auxiliary consensus sequence models, transposable element protein alignments, and a formalized classification system to support the growing diversity of organisms represented in the resource. The latest release includes 266,740 new de novo generated transposable element families from 336 species contributed by the EBI. This expansion demonstrates the utility of many of Dfam\u27s new features and provides insight into the long term challenges ahead for improving de novo generated transposable element datasets

Folk Classification and Factor Rotations:Whales, Sharks, and the Problems With the Hierarchical Taxonomy of Psychopathology (HiTOP)

The Hierarchical Taxonomy of Psychopathology (HiTOP) uses factor analysis to group self-reported symptoms of mental illness (i.e., like goes with like). It is hailed as a significant improvement over other diagnostic taxonomies. However, the purported advantages and fundamental assumptions of HiTOP have received little, if any, scientific scrutiny. We critically evaluated five fundamental claims about HiTOP. We conclude that HiTOP does not demonstrate a high degree of verisimilitude and has the potential to hinder progress on understanding the etiology of psychopathology. It does not lend itself to theory building or taxonomic evolution, and it cannot account for multifinality, equifinality, or developmental and etiological processes. In its current form, HiTOP is not ready to use in clinical settings and may result in algorithmic bias against underrepresented groups. We recommend a bifurcation strategy moving forward in which the Diagnostic and Statistical Manual of Mental Disorders is used in clinical settings while researchers focus on developing a falsifiable theory-based classification system

Disruptive Innovation & Chance for Latecomer Firms in E-Commerce: The Cases of the YES and PINDUODUO

The e-commerce market is considered one of the potential but fully competitive markets. However, it is also clear that gap-filling or market-dominating is a never-ending process in the e-commerce market. For this reason, this is one of the amazing playgrounds attracting many participants. The question is How and by which latecomer firms can enter and succeed in the existing e-commerce market. Therefore, this paper analyses the chances for latecomer enterprises to enter the competitive e-commerce market. To pursue this goal, the paper will analyze the role of the disruptive innovation theory and its e-commerce applications. The results reveal that applying disruptive business-model innovation is a better way for fledgling e-commerce brands to enter the existing market and succeed in competing with incumbents. Furthermore, the case of THE YES – a women’s fashion e-commerce platform, and Pinduoduo – a Chinese largest agriculture-focused technology platform, are also analyzed as practical cases to join the research’s results

On the floral rewards and flower-visitor assemblages of annual urban flower meadow seed mixes

Flower seed mixes are increasingly used to enhance the biodiversity and amenity values of urban green spaces. Urban or “pictorial” flower seed mixes are often used because they are designed using cultivars and non-native species to provide more colourful and longer-lasting flower displays. Although these seed mixes are effective in providing a high density of large colourful flowers, over an extended season, their value for biodiversity, and in particular the floral rewards they provide for flower-visitors, is largely unknown. The overall aim of my thesis was to assess and improve the value of these new urban habitats as forage resources for flower-visiting insects. My approach was to quantify and compare floral reward provision and insect visitation between meadows grown from three exemplar commercial pictorial flower meadow seed mixes (called Marmalade Annual, Short Annual and Cornfield Annual). I also compared these standard commercial mixes with corresponding ‘nectar-enriched’ formulations, which were designed by increasing the proportional seed weight contribution of selected species predicted to produce high quantities of nectar within each mix. To compare floral rewards and visitation between meadows grown from these seed mixes, I set up a field experiment in Sheffield, UK, using a complete randomised block design with six replicate blocks, each with six 25 m2 plots sown with one of the six seed mix treatments. My first objective was to quantify the floral nectar and pollen rewards provided by each flowering species recorded in the meadows (on the scale of a single flower or inflorescence). My second objective was to use these data to quantify the floral rewards provided per unit area by replicate meadows of different seed mix treatments, testing whether enrichment of seed mixes is an effective method of increasing floral nectar sugar rewards. My third objective was to corroborate/correct my morphology-based flower-visitor identifications using DNA barcoding to screen for misidentifications and morphologically cryptic species. I then used these DNA barcode-based identifications to assess whether there are systematic biases in the structure of flower-visitor networks constructed using molecular taxon identifications compared to traditional morphology-based taxon identifications. My fourth objective was to quantify patterns of insect visitation to meadows, testing whether meadows of different seed mix types attract different flower-visitor assemblages. Meadow floral composition surveys revealed that contamination by unintended horticultural species was widespread across replicate seed mix treatments, with contaminants likely germinating from a seed bank laid down during a failed attempt at this experiment the previous year. Contamination particularly affected Marmalade mixes, mainly because the common contaminant species were often also components of the Short and Cornfield mixes. For example, contaminants contributed on average about a third of nectar sugar mass or pollen volume per unit area in Marmalade mix meadows. Hence, contamination fundamentally undermined the internal validity of seed mix treatments, reducing the ability to directly attribute meadow level patterns in floral rewards or flower-visitors to seed mixes. As result, examination of patterns of floral resource provision and insect visitation were more informative at a species scale. In terms of patterns of insect visitation, Centaurea cyanus received 91% of bumblebee visits, 88% of honeybee visits and 29% of hoverfly visits, whilst T. inodorum received 27% of hoverfly visits. Patterns of bumblebee and honeybee visitation indicated preferential visitation to floral units of Centaurea cyanus. Although this species produced high quantities of nectar sugar mass and pollen volume, this did not differentiate it from other Asteraceae, such as Glebionis segetum, Rudbeckia hirta and Coreopsis tinctoria, which all produced high quantities of both floral rewards. Hence, it is likely that floral traits not measured in this study, such as nectar accessibility (‘nectar-holder depth’) or concentration/volume characteristics (which can affect accessibility due to constraints imposed by feeding morphology), drove patterns of preferential visitation in bumblebees and honeybees to C. cyanus. Given that in the absence of contamination there would have been very few bumblebee or honeybee visitors to Marmalade mix meadows, aesthetically designed pictorial meadows can fail to jointly provide benefits for people and some important flower-visiting insect taxa. DNA barcoding did not change specimen identifications for most morphotaxa. However, splitting and/or lumping processes affected almost one third of morphotaxa, with lumping of morphotaxa the most common type of change. This was in part because males and females from sexually dimorphic species were often separated by morphological identification. These DNA barcode-based changes to visitor taxonomy resulted in consistent minor changes in network size and structure across replicate networks. Lumping of morphotaxa decreased taxon richness, reducing the number of unique links and interaction diversity (the effective number of links). Lumping also increased flower-visitor generality, reducing plant vulnerability and increasing overall network connectance. However, taxonomic changes had no effect on interaction evenness or network specialisation. Thus, for this well-studied fauna, DNA barcode-based flower-visitor networks were systematically biased toward fewer taxa and links, with more generalist visitors and specialist plants. Given that many tropical faunas have more species and are less described than in Britain this pattern may not be replicated in other studies. Further studies in contrasting plant-pollinator communities are required before generalisations can be made about systematic biases between networks constructed using morphological versus molecular data. Overall, meadows grown from annual pictorial flower meadow seed mixes provide abundant floral units per unit area of meadow and are a valuable alternative to traditional horticultural flower beds or amenity grasslands in high profile urban contexts. Nevertheless, care must be taken during design of seed mixes and selection of mixes for planting to ensure that species in the mix provide suitable floral resources for an array of flower-visitors, including bees. This would be aided by the integration of informative measures for candidate species of floral rewards or visitor types and visitation rates during seed mix design

An overview of clustering methods with guidelines for application in mental health research

Cluster analyzes have been widely used in mental health research to decompose inter-individual heterogeneity by identifying more homogeneous subgroups of individuals. However, despite advances in new algorithms and increasing popularity, there is little guidance on model choice, analytical framework and reporting requirements. In this paper, we aimed to address this gap by introducing the philosophy, design, advantages/disadvantages and implementation of major algorithms that are particularly relevant in mental health research. Extensions of basic models, such as kernel methods, deep learning, semi-supervised clustering, and clustering ensembles are subsequently introduced. How to choose algorithms to address common issues as well as methods for pre-clustering data processing, clustering evaluation and validation are then discussed. Importantly, we also provide general guidance on clustering workflow and reporting requirements. To facilitate the implementation of different algorithms, we provide information on R functions and librarie

Mental Function and Cerebral Cartography: Functional Localization in fMRI Research

This dissertation advances a novel philosophical account of the relationship between brain mapping and cognitive theorizing in functional magnetic resonance imaging (fMRI) research. I argue that testing hypotheses about human cognition and behavior with fMRI critically depends on bridging assumptions about how cognitive functions map onto the brain. I demonstrate that in light of recent theoretical (e.g., network thinking) and methodological (e.g., resting state fMRI) advancements, these bridging assumptions are often problematic. I conclude that at this stage of scientific development, fMRI research should focus on articulating and testing new bridging assumptions rather than testing psychological theories