bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toward the integration of speciation research
Authors: Stankowski Sean , Cutter Asher D , Satokangas Ina , Lerch Brian A , Rolland Jonathan , Smadja Carole M , Segami Marzal J Carolina , Cooney Christopher R , Feulner Philine G D , Domingos Fabricius Maia Chaves Bicalho , North Henry L , Yamaguchi Ryo , Butlin Roger K , Wolf Jochen B W , Coughlan Jenn , Heidbreder Patrick , Hernández-Gutiérrez Rebeca , Barnard-Kubow Karen B , Peede David , Rancilhac Loïs , Salvador Rodrigo Brincalepe , Thompson Ken A , Stacy Elizabeth A , Moyle Leonie C , Garlovsky Martin D , Maulana Arif , Kantelinen Annina , Cacho N Ivalú , Schneemann Hilde , Domínguez Marisol , Dopman Erik B , Lohse Konrad , Rometsch Sina J , Comeault Aaron A , Merrill Richard M , Scordato Elizabeth S C , Singhal Sonal , Pärssinen Varpu , Lackey Alycia C R , Kumar Sanghamitra , Meier Joana I , Barton Nicholas , Fraïsse Christelle , Ravinet Mark , Kulmuni Jonna 
Published: February 2024

Abstract
Speciation research—the scientific field focused on understanding the origin and diversity of species—has a long and complex history. While relevant to one another, the specific goals and activities of speciation researchers are highly diverse, and scattered across a collection of different perspectives. Thus, our understanding of speciation will benefit from efforts to bridge scientific findings and the diverse people who do the work. In this paper, we outline two ways of integrating speciation research: (i) scientific integration, through the bringing together of ideas, data, and approaches; and (ii) social integration, by creating ways for a diversity of researchers to participate in the scientific process. We then discuss five challenges to integration: (i) the multidisciplinary nature of speciation research, (ii) the complex language of speciation; (iii) a bias toward certain study systems; (iv) the challenges of working across scales; and (v) inconsistent measures and reporting standards. We provide practical steps that individuals and groups can take to help overcome these challenges, and argue that integration is a team effort in which we all have a role to play.
Influence of host phylogeny and water physicochemistry on microbial assemblages of the fish skin microbiome
Authors: Bell Ashley G , McMurtrie Jamie , Bolaños Luis M , Cable Jo , Temperton Ben , Tyler Charles R 
Published: February 2024

Abstract
The skin of fish contains a diverse microbiota that has symbiotic functions with the host, facilitating pathogen exclusion, immune system priming, and nutrient degradation. The composition of fish skin microbiomes varies across species and in response to a variety of stressors, however, there has been no systematic analysis across these studies to evaluate how these factors shape fish skin microbiomes. Here, we examined 1922 fish skin microbiomes from 36 studies that included 98 species and nine rearing conditions to investigate associations between fish skin microbiome, fish species, and water physiochemical factors. Proteobacteria, particularly the class Gammaproteobacteria, were present in all marine and freshwater fish skin microbiomes. Acinetobacter, Aeromonas, Ralstonia, Sphingomonas and Flavobacterium were the most abundant genera within freshwater fish skin microbiomes, and Alteromonas, Photobacterium, Pseudoalteromonas, Psychrobacter and Vibrio were the most abundant in saltwater fish. Our results show that different culturing (rearing) environments have a small but significant effect on the skin bacterial community compositions. Water temperature, pH, dissolved oxygen concentration, and salinity significantly correlated with differences in beta-diversity but not necessarily alpha-diversity. To improve study comparability on fish skin microbiomes, we provide recommendations for approaches to the analyses of sequencing data and improve study reproducibility.
Metric analysis of the patella for sex estimation in a Portuguese sample
Authors: Maio Cláudia , Cunha Eugénia , Navega David 
Published: February 2024

Abstract
The biological profile estimation is the first step toward positive identification. However, it is not always possible to access a complete and well-preserved skeleton due to postmortem damage and taphonomic changes. As such, there is a need to develop new alternatives to analyze different bones of the human skeleton. The present study aims to analyze the patellar osteometry, with attention to its degree of sexual dimorphism, to establish a simple method for estimating sex in Portuguese adults. Six measurements were taken from 222 patella pairs, including 117 females and 105 males from the XXI Century Identified Skeleton Collection of the University of Coimbra. Subsequently, this method was validated in a different sample of 50 individuals equally representing both sexes. Maximum height stands out with a 77.0% of correct sex estimation, reaching 98.0% when applied to the new sample. The linear discriminant function analysis containing all the six variables showed the best results, with 80.2% of correct classification after cross-validation and 96.0% when applied to the independent sample.
An efficient and robust ABC approach to infer the rate and strength of adaptation
Authors: Murga-Moreno Jesús , Casillas Sònia , Barbadilla Antonio , Uricchio Lawrence , Enard David 
Published: February 2024

Abstract
Inferring the effects of positive selection on genomes remains a critical step in characterizing the ultimate and proximate causes of adaptation across species, and quantifying positive selection remains a challenge due to the confounding effects of many other evolutionary processes. Robust and efficient approaches for adaptation inference could help characterize the rate and strength of adaptation in nonmodel species for which demographic history, mutational processes, and recombination patterns are not currently well-described. Here, we introduce an efficient and user-friendly extension of the McDonald–Kreitman test (ABC-MK) for quantifying long-term protein adaptation in specific lineages of interest. We characterize the performance of our approach with forward simulations and find that it is robust to many demographic perturbations and positive selection configurations, demonstrating its suitability for applications to nonmodel genomes. We apply ABC-MK to the human proteome and a set of known virus interacting proteins (VIPs) to test the long-term adaptation in genes interacting with viruses. We find substantially stronger signatures of positive selection on RNA-VIPs than DNA-VIPs, suggesting that RNA viruses may be an important driver of human adaptation over deep evolutionary time scales.
Embryonic spatiotemporal expression pattern of Folded gastrulation suggests roles in multiple morphogenetic events and regulation by AbdA
Authors: Katagade Vrushali , Kandroo Manisha , Ratnaparkhi Anuradha 
Published: February 2024

Abstract
In Drosophila, the signaling pathway activated by the ligand Folded gastrulation (Fog) is among the few known G protein–coupled receptor (GPCR) pathways to regulate cell shape change with a well-characterized role in gastrulation. However, an understanding of the spectrum of morphogenetic events regulated by Fog signaling is still lacking. Here, we present an analysis of the expression pattern and regulation of fog using a genome-engineered Fog::sfGFP line. We show that Fog expression is widespread and in tissues previously not associated with the signaling pathway including germ cells, trachea, and amnioserosa. In the central nervous system (CNS), we find that the ligand is expressed in multiple types of glia indicating a prominent role in the development of these cells. Consistent with this, we have identified 3 intronic enhancers whose expression in the CNS overlaps with Fog::sfGFP. Further, we show that enhancer-1, (fogintenh-1) located proximal to the coding exon is responsive to AbdA. Supporting this, we find that fog expression is downregulated in abdA mutants. Together, our study highlights the broad scope of Fog-GPCR signaling during embryogenesis and identifies Hox gene AbdA as a novel regulator of fog expression.
Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae
Authors: Armstrong Ellie E , Bissell Ky L , Fatima H Sophia , Heikkinen Maya A , Jessup Anika , Junaid Maryam O , Lee Dong H , Lieb Emily C , Liem Josef T , Martin Estelle M , Moreno Mauricio , Otgonbayar Khuslen , Romans Betsy W , Royar Kim , Adler Mary Beth , Needle David B , Harkess Alex , Kelley Joanna L , Mooney Jazlyn A , Mychajliw Alexis M 
Published: February 2024

Abstract
Reference genome assemblies have been created from multiple lineages within the Canidae family; however, despite its phylogenetic relevance as a basal genus within the clade, there is currently no reference genome for the gray fox (Urocyon cinereoargenteus). Here, we present a chromosome-level assembly for the gray fox (U. cinereoargenteus), which represents the most contiguous, non-domestic canid reference genome available to date, with 90% of the genome contained in just 34 scaffolds and a contig N50 and scaffold N50 of 59.4 and 72.9 Megabases, respectively. Repeat analyses identified an increased number of simple repeats relative to other canids. Based on mitochondrial DNA, our Vermont sample clusters with other gray fox samples from the northeastern United States and contains slightly lower levels of heterozygosity than gray foxes on the west coast of California. This new assembly lays the groundwork for future studies to describe past and present population dynamics, including the delineation of evolutionarily significant units of management relevance. Importantly, the phylogenetic position of Urocyon allows us to verify the loss of PRDM9 functionality in the basal canid lineage, confirming that pseudogenization occurred at least 10 million years ago.
The Biofilm Lifestyle Shapes the Evolution of β-Lactamases
Authors: Lorentzen Øyvind M , Haukefer Anne Sofie B , Johnsen Pål J , Frøhlich Christopher 
Published: February 2024

Abstract
The evolutionary relationship between the biofilm lifestyle and antibiotic resistance enzymes remains a subject of limited understanding. Here, we investigate how β-lactamases affect biofilm formation in Vibrio cholerae and how selection for a biofilm lifestyle impacts the evolution of these enzymes. Genetically diverse β-lactamases expressed in V. cholerae displayed a strong inhibitory effect on biofilm production. To understand how natural evolution affects this antagonistic pleiotropy, we randomly mutagenized a β-lactamase and selected for elevated biofilm formation. Our results revealed that biofilm evolution selects for β-lactamase variants able to hydrolyze β-lactams without inhibiting biofilms. Mutational analysis of evolved variants demonstrated that restoration of biofilm development was achieved either independently of enzymatic function or by actively leveraging enzymatic activity. Taken together, the biofilm lifestyle can impose a profound selective pressure on antimicrobial resistance enzymes. Shedding light on such evolutionary interplays is of importance to understand the factors driving antimicrobial resistance.
Intestinal Permeability, Gut Inflammation, and Gut Immune System Response Are Linked to Aging-Related Changes in Gut Microbiota Composition: A Study in Female Mice
Authors: Gámez-Macías Paola Elizabeth , Félix-Soriano Elisa , Samblas Mirian , Sáinz Neira , Moreno-Aliaga María Jesús , González-Muniesa Pedro 
Published: February 2024

Abstract
Aging entails changes at the cellular level that increase the risk of various pathologies. An association between gut microbiota and age-related diseases has also been attributed. This study aims to analyze changes in fecal microbiota composition and their association with genes related to immune response, gut inflammation, and intestinal barrier impairment. Fecal samples of female mice at different ages (2 months, 6 months, 12 months, and 18 months) and gene expression in colon tissue were analyzed. Results showed that the older mice group had a more diverse microbiota than the younger group. Additionally, the abundance of Cyanobacteria, Proteobacteria, Flavobacteriaceae, Bacteroides, Parabacteroides, Prevotellaceae_UCG-001, Akkermansia, and Parabacteroides goldsteinii increased with age. In contrast, there was a notable decline in Clostridiaceae, Lactobacillaceae, Monoglobaceae, Ligilactobacillus, Limosilactobacillus, Mucispirillum, and Bacteroides faecichinchillae. These bacteria imbalances were positively correlated with increased inflammation markers in the colon, including Tnf-α, Ccl2, and Ccl12, and negatively with the expression of tight junction genes (Jam2, Tjp1, and Tjp2), as well as immune response genes (Cd4, Cd72, Tlr7, Tlr12, and Lbp). In conclusion, high levels of diversity did not result in improved health in older mice; however, the imbalance in bacteria abundance that occurs with aging might contribute to immune senescence, inflammation, and leaky gut disease.
Metabolome-Wide Mendelian Randomization Assessing the Causal Relationship Between Blood Metabolites and Sarcopenia-Related Traits
Authors: Chen Simin , Dong Yiran , Aiheti Nuerbiyamu , Wang Jie , Yan Shikang , Kuribanjiang Kaidiriyan , Li Huilong , Peng Xing , Wupuer Abudunaibi , Li Yihan , Yang Lei , Zhao Jianping 
Published: February 2024

Abstract
Sarcopenia is among the most common musculoskeletal illnesses, yet its underlying biochemical mechanisms remain incompletely understood. In this study, we used Mendelian randomization (MR) to investigate the causal relationship between the genetically determined blood metabolites and sarcopenia, with the overall objective of identifying likely molecular pathways for sarcopenia. We used 2-sample MR to investigate the effects of blood metabolites on sarcopenia-related traits. 452 metabolites were exposure, and 3 sarcopenia-related traits as the outcomes: handgrip strength, appendicular lean mass, and walking pace. The inverse-variance weighted (IVW) causal estimates were determined. For sensitivity analysis, methods such as MR-Egger regression, the weighted median, the weighted mode, and the heterogeneity test were used. Additionally, for complementation, we performed replication, meta-analysis, and metabolic pathway analyses. Candidate biomarkers were defined by meeting one of the following criteria: (1) significant metabolites are defined as pIVW &lt; pBonferroni [1.11 × 10−4 (.05/452)]; (2) strong metabolites are defined as 4 MR methods p &lt; .05; and (3) suggestive metabolites are defined as passing sensitivity analysis. Three metabolites (creatine, 1-arachidonoylglycerophosphocholine, and pentadecanoate [15:0]) with significant causality, 3 metabolites (glycine, 1-arachidonoylglycerophosphocholine, and epiandrosterone sulfate) with strong causality, and 25 metabolites (including leucylleucin, pyruvic acid, etc.) with suggestive causality were associated with sarcopenia-related traits. After further replication analyses and meta-analysis, these metabolites maintained substantial effects on sarcopenia-related traits. We additionally identified 14 important sarcopenia-related trait metabolic pathways. By combining metabolomics with genomics, these candidate metabolites and metabolic pathways identified in our study may provide new clues regarding the mechanisms underlying sarcopenia.
Associations Between D3Cr Muscle Mass and Magnetic Resonance Thigh Muscle Volume With Strength, Power, Physical Performance, Fitness, and Limitations in Older Adults in the SOMMA Study
Authors: Cawthon Peggy M , Blackwell Terri L , Kritchevsky Stephen B , Newman Anne B , Hepple Russell T , Coen Paul M , Goodpaster Bret H , Duchowny Kate , Hetherington-Rauth Megan , Mau Theresa , Shankaran Mahalakshmi , Hellerstein Marc , Evans William J , Cummings Steven R 
Published: February 2024

Abstract

Background
How magnetic resonance (MR) derived thigh muscle volume and deuterated creatine dilution derived muscle mass (D3Cr muscle mass) differentially relate to strength, fitness, and other functions in older adults—and whether associations vary by sex—is not known.

Methods
Men (N = 345) and women (N = 482) aged ≥70 years from the Study of Muscle, Mobility, and Aging completed leg extension strength (1-repetition max) and cardiopulmonary exercise testing to assess fitness (VO2peak). Correlations and adjusted regression models stratified by sex were used to assess the association between muscle size measures, study outcomes, and sex interactions.

Results
D3Cr muscle mass and MR thigh muscle volume were correlated (men: r = 0.62, women: r = 0.51, p &lt; .001). Each standard deviation (SD) decrement in D3Cr muscle mass was associated with lower 1-repetition max strength (−14 kg men, −4 kg women, p &lt; .001 for both; p-interaction = .003) and lower VO2peak (−79 mL/min men, −30 mL/min women, p &lt; .001 for both, p-interaction: .016). Each SD decrement in MR thigh muscle volume was also associated with lower strength (−32 kg men, −20 kg women, p &lt; .001 for both; p-interaction = .139) and lower VO2peak (−217 mL/min men, −111 mL/min women, p &lt; .001 for both, p-interaction = .010). There were associations, though less consistent, between muscle size or mass with physical performance and function; associations varied by sex.

Conclusions
Less muscle—measured by either D3Cr muscle mass or MR thigh muscle volume—was associated with lower strength and fitness. Varied associations by sex and assessment method suggest consideration be given to which measurement to use in future studies.
Identity Development and Disruption in Older Adults During COVID-19: A Longitudinal, Mixed-Methods Study
Authors: Mitchell Lauren L , Burns Mary K , Impellizzeri Daniel Koch , Falso Victoria R , Famularo Maeve , Finlay Jessica M 
Published: February 2024

Abstract

Objectives
Disruptive life events, such as the coronavirus disease 2019 (COVID-19) pandemic, may trigger adjustment and revision of older adults’ identities. This mixed-methods study explored how older adults perceived their identities changing as a result of the pandemic, and how such identity dynamics related to pandemic-related events and well-being.

Methods
Participants included 2,248 older adults who participated in the longitudinal COVID-19 Coping Study spanning from April/May 2020 to April/May 2021. Mean age was 67.8 years, 70% were women, and 93% were White. We used qualitative thematic analysis to identify the ways the pandemic affected participants’ identities. We then investigated the association between identity themes and testing positive for COVID-19, having a friend or family member hospitalized or dying due to COVID-19, or being vaccinated. Finally, we tested whether identity disruption was associated with 12-month trajectories of well-being (including life satisfaction, loneliness, depressive symptoms, anxiety, and self-rated health) using latent growth curve models.

Results
Some participants reported positive identity themes, such as rethinking and revising priorities and realization of strength and resilience. Others indicated harmful effects, including identity disruption. Individuals reporting identity disruption had worse well-being at baseline and remained consistently worse over time.

Discussion
Findings highlight that identity remains malleable in later life and that stressful events like the COVID-19 pandemic may trigger positive adaptive identity processes, but can also cause identity disruption that is associated with persistently worse well-being over time.
Association of Childhood Friendship Experience and Depressive Symptoms Among Older Adults: A Causal Mediation Approach
Authors: Zhou Zi 
Published: February 2024

Abstract

Objectives
Few studies to date have investigated the potential mechanisms linking childhood friendship experiences to late-life depressive symptoms. This study examines the association of childhood friendship experiences with depressive symptoms among older adults and the mediating effects of social disconnectedness and cognitive function.

Methods
A retrospective cohort analysis was performed using longitudinal data from a sample of 8,745 participants aged 60 years and above in the China Health and Retirement Longitudinal Study from 2013 to 2018. The causal association of childhood friendship experiences with depressive symptoms and the mediating roles of social disconnectedness and cognitive function were estimated using marginal structural models and the inverse odds ratio weighting method. Mediation proportions and confidence intervals (CIs) were calculated using a bootstrap resampling method.

Results
Respondents with greater childhood friendship deficits were more likely to have depressive symptoms (odds ratio: 1.19, 95% CI: 1.11, 1.26) than those with more favorable friendship experiences during childhood. The causal mediation analysis revealed that social disconnectedness, cognitive function, and their combination partially mediated the association of childhood friendship experiences with depressive symptoms by 15.70% (95% CI: 8.66%–24.17%), 17.18 % (95% CI: 7.61%–30.00%), 28.35% (95% CI: 17.75%–42.56%), respectively.

Discussion
Friendship experiences during childhood were related to the risk of depressive symptoms in older Chinese adults; more importantly, social disconnectedness and cognitive function partially mediated this association. Thus, improving social engagement and cognitive function in older adults could alleviate the accumulated disadvantages due to childhood friendship deficits and help to improve their psychological well-being.
A Greater Variety of Social Activities Is Associated With Lower Mortality Risk
Authors: Jeon Sangha , Turiano Nicholas A , Charles Susan T 
Published: February 2024

Abstract

Objectives
More frequent engagement in social activity is often associated with better physical health outcomes. Yet, less is known about whether engagement in a greater variety of social activities such as a mix of volunteering and attending club meetings (social activity variety) is important for health. The current study assessed whether social activity variety relates to mortality risk after adjusting for social activity frequency, nonsocial activity frequency and variety, and sociodemographic covariates, and how this relationship varies depending on age.

Methods
Using data from the Health and Retirement Study, we included 5,017 adults aged 51 and older who completed questions about social activity participation in 2008 and whose mortality status was recorded up to 2019. We also examined whether age moderated the relationship between social activity variety and mortality risk.

Results
Cox proportional hazard model analyses revealed that those with higher activity variety in social activities were more likely to survive over the following 11 years than those with low social activity variety. Moreover, age moderation indicated that the association between social activity variety with mortality risk was stronger among the oldest adults.

Discussion
Findings suggest that a greater variety of social activities is linked to mortality risk even after adjusting for social activity frequency, nonsocial activities, and health status across adulthood.