bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel phylogenetic comparative method for evaluating the strength of branch-specific directional selection
Authors: Ohkubo Yusaku , Kutsukake Nobuyuki , Koizumi Itsuro 
Published: March 2023

AbstractPhylogenetic comparative methods (PCMs) have played a central role in studying the evolution of phenotypic traits. However, when a trait experienced directional selection, previous PCMs have faced a dilemma between mathematically tractable but restrictive models (i.e., simple Gaussian process models) and flexible but intractable approaches (i.e., a simulation-based process model of phenotype evolution built on population genetics frameworks). This paper proposes a novel Gaussian process macroevolutionary model, called the “branch-specific directional selection (BSDS),” for evaluating the strength of directional selection to reconcile these two approaches. This model is based on a second-order approximation of a previous simulation-based process model but has a closed-form likelihood function. This can also be extended to incorporate intraspecies variations and to linear mixed models, which are necessary for meta-analysis. We conduct numerical experiments to validate the proposed method and apply it to the brain volume of Hominidae species. The results show that the proposed methods yield statistically more reliable inferences and computational time is about hundred thousand times faster than the previous simulation-based methods. Further extensions of the BSDS model are expected to provide a clearer picture of the connection of microevolutionary processes and macroevolutionary patterns.
Diet versatility and functional trade-offs shape tooth morphology in squirrels
Authors: Menéndez Iris , Swiderski Donald L , Gómez Cano Ana R , Hernández Fernández Manuel , Álvarez-Sierra María A , Zelditch Miriam L 
Published: March 2023

AbstractIdentifying the drivers of adaptation is key to understanding the origin and evolution of diversity. Here we study the morphological evolution of tooth morphology, a classic example of a conserved structure, to gain insights into the conditions that can overcome resistance to evolutionary change. We use geometric morphometrics of the occlusal surface outline of the fourth lower premolar (p4) of squirrels, a paradigm of a stable tooth morphology, to explore morphological adaptations to diet. Although a versatile generalist dental morphology favors the retention of the ancestral shape, the acquisition of diets that require strong mechanical processing drives morphological change. In particular, species that eat both grass and dry fruits evolved disparate tooth shape morphologies, related to trade-offs between feeding performance that lead to a more or less pronounced change depending on the proportion of those items in their diet. Also, some folivores develop relatively large p4s, and most bark gleaners have relatively small p4s. Ultimately, despite the role of diet shaping these patterns, we showed that diet is not the only factor driving the evolution of tooth morphology.
The phenotypic determinants of diet variation between divergent lineages of threespine stickleback
Authors: Moosmann Marvin , Hudson Cameron M , Seehausen Ole , Matthews Blake 
Published: March 2023

AbstractLineages with independent evolutionary histories often differ in both their morphology and diet. Experimental work has improved our understanding of the links between the biomechanics of morphological traits and foraging performance (trait utility). However, because the expression of foraging-relevant traits and their utility can be highly context-specific, it is often unclear how dietary divergence arises from evolved phenotypic differences. Here, we explore the phenotypic causes of dietary divergence between two genetically and phenotypically divergent lineages of threespine stickleback (Gasterosteus aculeatus) with independent evolutionary histories of freshwater colonization and adaptation. First, using individuals from a line-cross breeding design, we conducted 150 common-garden foraging trials with a community of multiple prey species and performed morphological and behavioral analyses to test for prey-specific trait utility. Second, we tested if the traits that explain variation in foraging performance among all individuals could also explain the dietary divergence between the lineages. Overall, we found evidence for the utility of several foraging traits, but these traits did not explain the observed dietary divergence between the lineages in a common garden. This work suggests that evolved dietary divergence results not only from differences in morphology but also from divergence in behaviors that underlie prey capture success in species-rich prey communities.
Strongly exclusive distribution with putative character displacement in two flying stag beetles
Authors: Zhang Sheng-Nan , Kubota Kôhei 
Published: March 2023

AbstractCharacter displacement is considered a key driver of evolutionary divergence and adaptation. Few examples of reproductive character displacement with a narrow contact zone have been identified. We examined the genetic structure, body length variation, and genital morphology in the contact and allopatric areas of Platycerus takakuwai and P. viridicuprus to investigate character displacement and gene flow. In the contact area, the species identifications based on endophallic morphology and nuclear genes were identical, whereas mitochondrial gene did not exhibit a perfect match. This incongruence suggests that interspecific hybridization followed by the mitochondrial introgression has likely occurred during historical secondary contact. The species are essentially parapatric in contact area, co-occurring at only one of 28 adjacent sampling sites despite being flying species, and no hybrids based on morphology have been found, which indicates a strongly exclusive distribution. The results showed that the body length variation was consistent with character displacement after controlling for variation along geographic and environmental gradients. Interspecific body size differentiation may have evolved to reduce incorrect mating between the species. Moreover, selective pressure caused by reproductive interference between the two species may act on body size that have likely resulted in strongly exclusive distribution at the edge of their ranges.
The distribution of the Lansing Effect across animal species
Authors: Ivimey-Cook Edward R , Shorr Sarema , Moorad Jacob A 
Published: March 2023

AbstractMaternal senescence is the reduction in individual performance associated with increased maternal age at conception. When manifested on adult lifespan, this phenomenon is known as the “Lansing Effect.” Single-species studies report both maternal age-related increases and decreases in adult lifespan, but no comprehensive review of the literature has yet been undertaken to determine if the Lansing Effect is a widespread phenomenon. To address this knowledge gap, we performed a meta-analysis of maternal aging rates taken from all available published studies. We recovered 78 estimates from 22 studies representing 15 species. All studies taken together suggest a propensity for a Lansing Effect, with an estimated average effect of maternal age on offspring’s adult lifespan of between -17% and -22%, depending upon our specific choice of model. We failed to find a significant effect of animal class or insect order but given the oversampling of insect species in the published literature and the paucity of vertebrate studies, we infer that only rotifers and insects yet demonstrate a tendency toward expressing the phenomenon.
Population bottleneck associated with but likely preceded the recent evolution of self-fertilization in a coastal dune plant
Authors: Greer Stephanie U , Wright Stephen I , Eckert Christopher G 
Published: March 2023

AbstractEvolution of self-fertilization may be initiated by a historical population bottleneck, which should diagnostically reduce lineage-wide genetic variation. However, selfing can also strongly reduce genetic variation after it evolves. Distinguishing process from pattern is less problematic if mating system divergence is recent and geographically simple. Dramatically reduced diversity is associated with the transition from outcrossing to selfing in the Pacific coastal endemic Abronia umbellata that includes large-flowered, self-incompatible populations (var. umbellata) south of San Francisco Bay and small-flowered, autogamous populations (var. breviflora) to the north. Compared to umbellata, synonymous nucleotide diversity across 10 single-copy nuclear genes was reduced by 94% within individual populations and 90% across the whole selfing breviflora lineage, which contained no unique polymorphisms. The geographic pattern of genetic variation is consistent with a single origin of selfing that occurred recently (7–28 kya). These results are best explained by a historical bottleneck, but the two most northerly umbellata populations also contained little variation and clustered with selfing populations, suggesting that substantial diversity loss preceded the origin of selfing. A bottleneck may have set the stage for the eventual evolution of selfing by purging genetic load that prevents the spread of selfing.
Life history and chemical defense interact to drive patterns of adaptation in an annual monkeyflower
Authors: Scharnagl Anna , Genung Mark A , Holeski Liza M , Kooyers Nicholas J 
Published: March 2023

Abstract
Although chemical defenses and herbivore pressure are widely established as key targets and agents of selection, their roles in local adaptation and determining potential evolutionary responses to changing climates are often neglected. Here, we explore fitness differences between 11 rangewide M. guttatus populations in a field common garden experiment and assess the agents and targets of selection driving relative fitness patterns. We use piecewise structural equation models to disentangle associations between chemical defenses, (phenylpropanoid glycosides; PPGs), and life history traits with herbivory and fitness. While the historical environment of populations is not predictive of fitness differences between populations, &gt;90% of variation in fitness can be predicted by the flowering time and foliar PPG defense arsenal of a population. Piecewise structural equation models indicate that life history traits, particularly earlier flowering time, are strongly and directly linked to fitness. However, herbivory, particularly fruit predation, is also an important agent of selection that creates indirect links between fitness and both chemical defenses and life history traits. Our results emphasize the multivariate nature of the agents and targets of selections in producing adaptation and suggest that future responses to selection must navigate a complex fitness landscape.
Digest: environmental variability as a constraint on cognitive evolution in lizards
Authors: Ashton Benjamin J , Baeckens Simon 
Published: March 2023

AbstractHow does ecology influence cognitive evolution in lizards? Taking a comparative approach, De Meester et al. (2022) discovered that species living in temporally fluctuating environments tend to perform relatively poorly on cognitive tasks associated with behavioral flexibility compared to species living in more climatically stable environments. The negative association between environmental variability and cognitive performance suggests that stochastic environments can hamper, rather than stimulate, the evolution of cognitive ability.
The genetic basis of plumage coloration and elevation adaptation in a clade of recently diverged alpine and arctic songbirds
Authors: Funk Erik R , Spellman Garth M , Winker Kevin , Withrow Jack J , Ruegg Kristen C , Taylor Scott A 
Published: March 2023

AbstractTrait genetic architecture plays an important role in the probability that variation in that trait leads to divergence and speciation. In some cases, speciation may be driven by the generation of novel phenotypes through the recombination of genes associated with traits that are important for local adaptation or sexual selection. Here, we investigate the genetic basis of three plumage color traits, and one ecological trait, breeding elevation, in a recent avian radiation, the North American rosy-finches (Leucosticte spp.). We identify unique genomic regions associated with each trait and highlight 11 candidate genes. Among these are well-characterized melanogenesis genes, including Mitf and Tyrp1, and previously reported hypoxia-related genes including Egln1. Additionally, we use mitochondrial data to date the divergence of rosy-finch clades which appear to have diverged within the past 250 ky. Given the low levels of genome-wide differentiation among rosy-finch taxa, and evidence for extensive introgression in North America, plumage coloration and adaptation to high elevations have likely played large roles in generating the observed patterns of lineage divergence. The relative independence of these candidate regions across the genome suggests that recombination might have led to multiple phenotypes, and subsequent rosy-finch speciation, over short periods of time.
Balancing selection and the crossing of fitness valleys in structured populations: diversification in the gametophytic self-incompatibility system
Authors: Stetsenko Roman , Brom Thomas , Castric Vincent , Billiard Sylvain 
Published: March 2023

AbstractThe self-incompatibility locus (S-locus) of flowering plants displays a striking allelic diversity. How such a diversity has emerged remains unclear. In this article, we performed numerical simulations in a finite island population genetics model to investigate how population subdivision affects the diversification process at a S-locus, given that the two-gene architecture typical of S-loci involves the crossing of a fitness valley. We show that population structure slightly reduces the parameter range allowing for the diversification of self-incompatibility haplotypes (S-haplotypes), but at the same time also increases the number of these haplotypes maintained in the whole metapopulation. This increase is partly due to a higher rate of diversification and replacement of S-haplotypes within and among demes. We also show that the two-gene architecture leads to a higher diversity in structured populations compared with a simpler genetic architecture, where new S-haplotypes appear in a single mutation step. Overall, our results suggest that population subdivision can act in two opposite directions: it renders S-haplotypes diversification easier, although it also increases the risk that the self-incompatibility system is lost.
Simultaneous integration and modularity underlie the exceptional body shape diversification of characiform fishes
Authors: Burns Michael D , Collyer Michael L , Sidlauskas Brian L 
Published: March 2023

AbstractEvolutionary biology has long striven to understand why some lineages diversify exceptionally while others do not. Most studies have focused on how extrinsic factors can promote differences in diversification dynamics, but a clade’s intrinsic modularity and integration can also catalyze or restrict its evolution. Here, we integrate geometric morphometrics, phylogenetic comparative methods and visualizations of covariance to infer the presence of distinct modules in the body plan of Characiformes, an ecomorphologically diverse fish radiation. Strong covariances reveal a cranial module, and more subtle patterns support a statistically significant subdivision of the postcranium into anterior (precaudal) and posterior (caudal) modules. We uncover substantial covariation among cranial and postcranial landmarks, indicating body-wide evolutionary integration as lineages transition between compressiform and fusiform body shapes. A novel method of matrix subdivision reveals that within- and among-module covariation contributes substantially to the overall eigenstructure of characiform morphospace, and that both phenomena led to biologically important divergence among characiform lineages. Functional integration between the cranium and post-cranial skeleton appears to have allowed lineages to optimize the aspect ratio of their bodies for locomotion, while the capacity for independent change in the head, body and tail likely eased adaptation to diverse dietary and hydrological regimes. These results reinforce a growing consensus that modularity and integration synergize to promote diversification.
Impacts of agroecological practices on soil microbial communities in experimental open-field vegetable cropping systems
Authors: Moulin Coraline , Pruneau Ludovic , Vaillant Victor , Loranger-Merciris Gladys 
Published: March 2023

AbstractThis study aimed to determine the impact of different agroecological practices on the composition and diversity of edaphic bacterial and fungal communities. We designed two experimental agroecological vegetable cropping systems and analyzed their effects on soil microbial communities by pyrosequencing the 16S and 18S ribosomal RNA genes. Our results highlighted modifications to the Operational Taxonomic Units in both experimental systems compared with bare soil, particularly for the phyla Actinobacteria, Ascomycota, Bacteroidetes, and Mucoromycota. Multidimensional scaling plots based on beta diversity showed a clear distinction between the two experimental systems for fungi, whereas differences were observed between bare soil and the two experimental systems for bacteria. Overall, the agroecological systems enhanced soil microbial diversity. We showed a distinction between the two experimental systems and bare soil, correlated with the high total N and total P contents in the agroecological systems. Both experimental systems promoted soil enrichment with certain essential minerals. The agroecological systems had a positive impact on soil microbial communities, particularly by promoting the development of beneficial soil bacteria like Actinobacteria. In the two experimental systems, changes in the quality and quantity of organic matter (i.e. mulch, vermicompost, plant diversity) could have modified the abundance and diversity of microbial communities.
Long-read-based Genome Assembly ofDrosophila gunungcolaReveals Fewer Chemosensory Genes in Flower-breeding Species
Authors: Negi Ateesha , Liao Ben-Yang , Yeh Shu-Dan 
Published: March 2023

AbstractDrosophila gunungcola exhibits reproductive activities on the fresh flowers of several plant species and is an emerging model to study the co-option of morphological and behavioral traits in male courtship display. Here, we report a near-chromosome-level genome assembly that was constructed based on long-read PacBio sequencing data (with ∼66× coverage) and annotated with the assistant from RNA-seq transcriptome data of whole organisms at various developmental stages. A nuclear genome of 189 Mb with 13,950 protein-coding genes and a mitogenome of 17.5 kb were acquired. Few interchromosomal rearrangements were found in the comparisons of synteny with Drosophila elegans, its sister species, and Drosophila melanogaster, suggesting that the gene compositions on each Muller element are evolutionarily conserved. Loss events of several OR and IR genes in D. gunungcola and D. elegans were revealed when orthologous genomic regions were compared across species in the D. melanogaster species group. This high-quality reference genome will facilitate further comparative studies on traits related to the evolution of sexual behavior and diet specialization.
2022 updates to the Rat Genome Database: a Findable, Accessible, Interoperable, and Reusable (FAIR) resource
Authors: Vedi Mahima , Smith Jennifer R , Thomas Hayman G , Tutaj Monika , Brodie Kent C , De Pons Jeffrey L , Demos Wendy M , Gibson Adam C , Kaldunski Mary L , Lamers Logan , Laulederkind Stanley J F , Thota Jyothi , Thorat Ketaki , Tutaj Marek A , Wang Shur-Jen , Zacher Stacy , Dwinell Melinda R , Kwitek Anne E 
Published: March 2023

Abstract
The Rat Genome Database (RGD, https://rgd.mcw.edu) has evolved from simply a resource for rat genetic markers, maps, and genes, by adding multiple genomic data types and extensive disease and phenotype annotations and developing tools to effectively mine, analyze, and visualize the available data, to empower investigators in their hypothesis-driven research. Leveraging its robust and flexible infrastructure, RGD has added data for human and eight other model organisms (mouse, 13-lined ground squirrel, chinchilla, naked mole-rat, dog, pig, African green monkey/vervet, and bonobo) besides rat to enhance its translational aspect. This article presents an overview of the database with the most recent additions to RGD’s genome, variant, and quantitative phenotype data. We also briefly introduce Virtual Comparative Map (VCMap), an updated tool that explores synteny between species as an improvement to RGD’s suite of tools, followed by a discussion regarding the refinements to the existing PhenoMiner tool that assists researchers in finding and comparing quantitative data across rat strains. Collectively, RGD focuses on providing a continuously improving, consistent, and high-quality data resource for researchers while advancing data reproducibility and fulfilling Findable, Accessible, Interoperable, and Reusable (FAIR) data principles.
Population structure and connectivity in the genusMolvain the Northeast Atlantic
Authors: McGill L , McDevitt A D , Hellemans B , Neat F , Knutsen H , Mariani S , Christiansen H , Johansen T , Volckaert F A M , Coscia I 
Published: March 2023

AbstractIn fisheries, operational management units and biological data often do not coincide. In many cases, this is not even known due to the lack of information about a species’ population structure or behaviour. This study focuses on two such species, the common ling Molva molva and the blue ling M. dypterygia, two Northeast Atlantic gadoids with overlapping geographical distribution, but different depth habitats. Heavily exploited throughout their ranges, with declining catches, little is known about their population structure. Genotyping-by-sequencing at thousands of genetic markers indicated that both species are separated into two major groups, one represented by samples from the coasts of western Scotland, Greenland, and the Bay of Biscay and the other off the coast of Norway. This signal is stronger for the deeper dwelling blue ling, even though adult dispersal was also identified for this species. Despite small sample sizes, fine-scale patterns of genetic structure were identified along Norway for common ling. Signatures of adaptation in blue ling consisted in signs of selections in genes involved in vision, growth, and adaptation to cold temperatures.
The Evolution of Assessing Central Nervous System Complications in Human Immunodeficiency Virus: Where Do We Go From Here?
Authors: McIntosh Roger C , Clark Uraina S , Cherner Mariana , Cysique Lucette A , Heaton Robert K , Levin Jules , Remien Robert H , Thames April , Moore David J , Rubin Leah H 
Published: March 2023

AbstractIn this fifth decade of the human immunodeficiency virus (HIV) epidemic, central nervous system (CNS) complications including cognitive impairment and mental health remain a burden for people with HIV (PWH) on antiretroviral therapy. Despite the persistence of these complications, which often co-occur, the underlying pathophysiology remains elusive and consequently treatments remain limited. To continue to grow our understanding of the underlying mechanisms of CNS complications among PWH, there is a need to reexamine our current approaches, which are now more than 2 decades old. At the 2021 National Institutes of Health–sponsored meeting on Biotypes of CNS Complications in PWH, the Neurobehavioral Working Group addressed the following: (1) challenges inherent to determining CNS complications; (2) heterogeneity in CNS complications; and (3) problems and solutions for examining integrated biotypes. The review below provides a summary of the main points presented and discussed by the Neurobehavioral Working Group at the meeting.