bluuebunny/crossref_metadata_2025 huggingface dataset:
Variability in Sleep Duration and Biomarkers of Cardiovascular Disease Across the Menstrual Cycle
Authors: Dunietz Galit Levi , Shedden Kerby , Michels Kara A , Chervin Ronald D , Lyu Xiru , Freeman Joshua R , Baylin Ana , O’Brien Louise M , Wactawski-Wende Jean , Schisterman Enrique F , Mumford Sunni L
Published: March 2023

Variability in sleep duration and cardiovascular health have been infrequently investigated, particularly among reproductive-age women. We examined these associations across the menstrual cycle among a cohort of 250 healthy premenopausal women, aged 18-44 years. The BioCycle study (New York, 2005–2007) collected cardiovascular biomarkers (serum high- and low-density lipoprotein (HDL, LDL), total cholesterol, triglycerides, and C-reactive protein (CRP)) at key time points along the menstrual cycle (follicular, ovulatory, and luteal phases). Women also recorded sleep duration in daily diaries. From these data, we computed L-moments, robust versions of location, dispersion, skewness, and kurtosis. We fitted linear mixed models with random intercepts and inverse probability weighting to estimate associations between sleep variability and cardiovascular biomarkers, accounting for demographic, lifestyle, health, and reproductive factors. Sleep dispersion (any deviation from mean duration) was associated with lower mean LDL for nonshift workers and non-White women. Skewed sleep duration was associated with higher mean CRP and lower mean total cholesterol. Sleep durations with extreme short and long bouts (kurtosis) were associated with a lower mean HDL, but not mean CRP, LDL, or triglycerides. Sleep duration modified associations between sleep dispersion and LDL, HDL, and total cholesterol. Even in young and healthy women, sleep duration variability could influence cardiovascular health.
Invited Commentary: Improving Instruments to Counter the Bias in Their Construction
Authors: Caqueo-Urízar Alejandra , Irarrázaval Matías
Published: March 2023

In this issue of the Journal, Villalonga-Olives et al. (Am J Epidemiol. 2023;192(8):1264-1273) examined the psychometric properties of social capital indicators, comparing responses from Black and White people to identify whether there was differential item functioning (DIF) in social capital by race, and also when stratified by educational attainment, as a measure of socioeconomic status. The authors tested whether there is DIF in social capital items between Black and White people and found that DIF across these items was significant although not large, but they were still indicative of measurement error, which they suspected was related to the way these items were developed—that is, based on cultural assumptions tested in mainstream White America. However, some gaps remain to be fleshed out.
sBGC-hm: an atlas of secondary metabolite biosynthetic gene clusters from the human gut microbiome
Authors: Zou Huixi , Sun Tianli , Jin Bangqun , Wang Shengqin
Published: March 2023

Microbial secondary metabolites exhibit potential medicinal value. A large number of secondary metabolite biosynthetic gene clusters (BGCs) in the human gut microbiome, which exhibit essential biological activity in microbe–microbe and microbe–host interactions, have not been adequately characterized, making it difficult to prioritize these BGCs for experimental characterization. Here, we present the sBGC-hm, an atlas of secondary metabolite BGCs allows researchers to explore the potential therapeutic benefits of these natural products. One of its key features is the ability to assist in optimizing the BGC structure by utilizing the gene co-occurrence matrix obtained from Human Microbiome Project data. Results are viewable online and can be downloaded as spreadsheets.

Availability and implementation

The database is openly available at https://www.wzubio.com/sbgc. The website is powered by Apache 2 server with PHP and MariaDB.
Hormonal profile prior to luteolysis modulates the uterine luminal transcriptome in the subsequent cycle in beef cross-bred cows
Authors: Silva Felipe A C C , Martins Thiago , Sponchiado Mariana , Rocha Cecilia C , Pohler Ky G , Peñagaricano Francisco , Binelli Mario
Published: March 2023

Sex steroid concentrations modulate endometrial function and fertility in cattle. Our objective was to compare the post-estrus luminal transcriptome of cows that were exposed to contrasting concentrations of progesterone (P4) before luteolysis that displayed estrus and ovulated spontaneously. Cross-bred beef cows received either (1) a new CIDR and GnRH (day −9; high progesterone treatment; HP4; n = 16) or (2) a previously used CIDR, PGF2α, and GnRH (low progesterone treatment; LP4; n = 24). All cows received PGF2α at CIDR removal (day −2). Ovarian ultrasonography and blood collections were performed on days −9, −2, −0.5, and 0 (day of observed estrus), and days 4, 7, and 14 for measurement of ovarian structures, P4, and estradiol (E2). Luminal epithelial cells were collected using a cytology brush on days 4, 7, and 14 for RNAseq. On day −2, CL area and concentrations of P4 were greater, while on day −0.5, concentrations of E2 were decreased in HP4. Ovarian structures and hormonal concentrations were similar on days 4, 7, or 14 (P > 0.05). There were enriched pathways in HP4 related to activation and signaling of the innate immune system at day 4, downregulation in the network involved in the extracellular matrix remodeling at day 7, and exacerbated inflammatory response as well as differentiation and activation of macrophages at day 14 (Benjamini–Hochberg P-value ≤ 0.05). In conclusion, manipulation of pre-luteolysis sex steroid concentrations altered the post-estrus luminal transcriptome even though all cows showed estrus and ovulated spontaneously.
A Transdisciplinary Framework to Unlock the Potential Benefits of Green Spaces for Urban Communities Under Changing Contexts
Authors: Lin Brenda B , Andersson Erik
Published: March 2023

New urban models increasingly seek to create more sustainable, livable, and healthier cities by reinvigorating green space. In this article, we highlight and briefly review several main but disconnected areas of study in which the factors that frame human–environment interactions and therefore also influence the potential well-being outcomes of those interactions are studied. We then use the intersection of affordance theory and socio-institutional programming to provide a conceptual framework that ties together these spheres of research, and we discuss some critical keys for enabling different positive green space experiences. Urban communities are not homogeneous, and accounting for the intersection between individual differences and landscape programming opens up more diverse pathways for affording positive human–environment interactions and different well-being outcomes.
Characteristics and outcomes for participants with congenital ichthyosis who responded to treatment with the topical isotretinoin formulation TMB-001: results from the Phase IIb CONTROL study
Authors: Bunick Christopher G , Teng Joyce M C , Guenthner Scott , Marathe Kalyani , Kempers Steven , Eads Kimmie , Castelo-Soccio Leslie , Mendelsohn Alan M , Raiz Jessica , Murrell Dédée F
Published: March 2023

Background

Emollients and keratolytics are frequently used to manage symptoms of congenital ichthyosis (CI). Systemic retinoid treatment is complicated by teratogenicity and dose-limiting adverse effects.

Objectives

This analysis from the randomized Phase IIb CONTROL study investigated the characteristics of participants who responded to treatment with TMB-001, a novel topical isotretinoin ointment formulation.

Methods

Participants ≥ 9 years of age with genetically confirmed CI and ≥ 2 (out of 4) Visual Index for Ichthyosis Severity (VIIS) assessment areas with ≥ 3 scaling score were randomized 1 : 1 : 1 to TMB-001 0.05%, TMB-001 0.1% or vehicle, twice daily for 12 weeks. Efficacy endpoints included the proportion of participants with ≥ 50% reduction in VIIS-scaling (VIIS-50) compared with baseline and ≥ 2-grade reduction in Investigator's Global Assessment (IGA)-scaling score compared with baseline. Changes in body surface area (BSA) involvement, Dermatology Life Quality Index (DLQI) scores and Itch-Numeric Rating Scale (I-NRS) scores were assessed.

Results

Among the 33 participants (11 randomized to TMB-001 0.05%, 10 to TMB-001 0.1% and 12 to vehicle), median age was 29 years (range 9–80), and most were male (64%) and White (79%). Baseline demographics were generally similar among participants who did or did not achieve TMB-001 treatment success. Participants who had lower mean BSA involvement and higher DLQI and I-NRS scores at baseline were more likely to achieve VIIS-50. Similarly, higher baseline DLQI and I-NRS scores were associated with IGA response; BSA involvement was similar for IGA responders vs. nonresponders.

Conclusions

Higher DLQI and I-NRS scores at baseline were associated with participants achieving treatment success by VIIS-50 and IGA response. Lower BSA involvement was associated with VIIS-50 success.
Hierarchical brain structural–functional coupling associated with cognitive impairments in mild traumatic brain injury
Authors: Pan Yizhen , Li Xuan , Liu Yuling , Jia Xiaoyan , Wang Shan , Ji Qiuyu , Zhao Wenpu , Yin Bo , Bai Guanghui , Zhang Jie , Bai Lijun
Published: March 2023

Mild traumatic brain injury (mTBI) disrupts the integrity of white matter microstructure, which affects brain functional connectivity supporting cognitive function. Although the relationship between structural and functional connectivity (SC and FC), here called SC–FC coupling, has been studied on global level in brain disorders, the long-term disruption of SC–FC coupling in mTBI at regional scale was still unclear. The current study investigated the alteration pattern of regional SC–FC coupling in 104 acute mTBI patients (41 with 6–12 months of follow-up) and 56 healthy controls (HCs). SC and FC networks were constructed to measure regional, intra-network, and inter-network SC–FC coupling. Compared with HCs, acute mTBI exhibited altered SC–FC coupling of the sensorimotor network (SMN). The coupling laterality indicators of the SMN can identify mTBI from controls. The persistent SC–FC decoupling of the SMN and the additional decoupling of the default mode network (DMN) were observed in chronic mTBI. Crucially, decoupling of the SMN and DMN predicted better cognitive outcomes. The findings revealed the SC–FC coupling alternations exhibited hierarchical trend originating from the sensorimotor cortex to high-order cognitive regions with the progression of mTBI. The regional and hierarchical SC–FC coupling may be a prognostic biomarker to provide insights into the pathophysiology mechanism of mTBI.
Mapping cross-species connectome atlas of human and macaque striatum
Authors: Xia Xiaoluan , Zeng Xinglin , Gao Fei , Yuan Zhen
Published: March 2023

Cross-species connectome atlas (CCA) that can provide connectionally homogeneous and homologous brain nodes is essential and customized for cross-species neuroscience. However, existing CCAs were flawed in design and coarse-grained in results. In this study, a normative mapping framework of CCA was proposed and applied on human and macaque striatum. Specifically, all striatal voxels in the 2 species were mixed together and classified based on their represented and characterized feature of within-striatum resting-state functional connectivity, which was shared between the species. Six pairs of striatal parcels in these species were delineated in both hemispheres. Furthermore, this striatal parcellation was demonstrated by the best-matched whole-brain functional and structural connectivity between interspecies corresponding subregions. Besides, detailed interspecies differences in whole-brain multimodal connectivities and involved brain functions of these subregions were described to flesh out this CCA of striatum. In particular, this flexible and scalable mapping framework enables reliable construction of CCA of the whole brain, which would enable reliable findings in future cross-species research and advance our understandings into how the human brain works.
Altered structural connectome of children with auditory processing disorder: a diffusion MRI study
Authors: Alvand Ashkan , Kuruvilla-Mathew Abin , Roberts Reece P , Pedersen Mangor , Kirk Ian J , Purdy Suzanne C
Published: March 2023

Auditory processing disorder (APD) is a listening impairment that some school-aged children may experience despite having normal peripheral hearing. Recent resting-state functional magnetic resonance imaging (MRI) has revealed an alteration in regional functional brain topology in children with APD. However, little is known about the structural organization in APD. We used diffusion MRI data to investigate the structural connectome of 58 children from 8 to 14 years old diagnosed with APD (n = 29) and children without hearing complaints (healthy controls, HC; n = 29). We investigated the rich-club organization and structural connection differences between groups. The APD group showed similar rich-club organization and edge-wise connection compared with the HC group. However, at the regional level, we observed increased average path length (APL) and betweenness centrality in the right inferior parietal lobule and inferior precentral gyrus, respectively, in the APD group. Only HCs demonstrated a positive association between APL and the listening-in-spatialized-noise-sentences task in the left orbital gyrus. In line with previous findings, the current results provide evidence for altered structural networks at the regional level in the APD group, suggesting the involvement of multimodal deficits and a role for structure-function alteration in the listening difficulties of children with APD.
Aperiodic neural activity reflects metacontrol
Authors: Zhang Chenyan , Stock Ann-Kathrin , Mückschel Moritz , Hommel Bernhard , Beste Christian
Published: March 2023

Higher-level cognitive functions are mediated via complex oscillatory activity patterns and its analysis is dominating cognitive neuroscience research. However, besides oscillatory (period) activity, also aperiodic activity constitutes neural dynamics, but its relevance for higher-level cognitive functions is only beginning to be understood. The present study examined whether the broadband EEG aperiodic activity reflects principles of metacontrol. Metacontrol conceptualizes whether it is more useful to engage in more flexible processing of incoming information or to shield cognitive processes from incoming information (persistence-heavy processing). We examined EEG and behavioral data from a sample of n = 191 healthy participants performing a Simon Go/NoGo task that can be assumed to induce different metacontrol states (persistence-biased vs. flexibility-biased). Aperiodic activity was estimated using the FOOOF toolbox in the EEG power spectrum. There was a higher aperiodic exponent and offset in NoGo trials compared with Go trials, in incongruent (Go) trials compared with congruent (Go) trials. Thus, aperiodic activity increases during persistence-heavy processing, but decreases during flexibility-heavy processing. These findings link aperiodic features of the EEG signal and concepts describing the dynamics of how cognitive control modes are applied. Therefore, the study substantially extends the importance of aperiodic activity in understanding cognitive functions.
Hypertension in young adults with autosomal dominant polycystic kidney disease: a case for early screening?
Authors: Cadnapaphornchai Melissa A , Ong Albert C M
Published: March 2023

ADPKD is the most common hereditary kidney disease and a major cause of kidney failure world-wide. Significant kidney enlargement occurs decades preceding loss of kidney function. However, the earliest clinical manifestations of disease have been less well characterized in young adults, a typically healthy population who do not often seek routine medical care. In this study, Martinez and colleagues report a high prevalence of hypertension among young adults (18–30 years) enrolled in the Spanish ADPKD registry REPQRAD. Their findings confirm previous studies in children and young adults with ADPKD and make a strong case for earlier screening and intervention within this age group.
Oxygen stress on age-stage, two-sex life tables and transcriptomic response of diamondback moth (Plutella xylostella)
Authors: Liu Tian-sheng , Zhu Xiang-yu , He Di , You Min-sheng , You Shi-jun
Published: March 2023

Elucidating the genetic basis of local adaption is one of the important tasks in evolutionary biology. The Qinghai-Tibet Plateau has the highest biodiversity for an extreme environment worldwide, and provides an ideal natural laboratory to study adaptive evolution. The diamondback moth (DBM), Plutella xylostella, is one of the most devastating pests of the global Brassica industry. A highly heterozygous genome of this pest has facilitated its adaptation to a variety of complex environments, and so provides an ideal model to study fast adaptation. We conducted a pilot study combining RNA-seq with an age-stage, two-sex life table to study the effects of oxygen deprivation on DBM. The developmental periods of all instars were significantly shorter in the hypoxic environment. We compared the transcriptomes of DBM from Fuzhou, Fujian (low-altitude) and Lhasa, Tibet (high-altitude) under hypoxia treatment in a hypoxic chamber. Some DEGs are enriched in pathways associated with DNA replication, such as DNA repair, nucleotide excision repair, base excision repair, mismatch repair and homologous recombination. The pathways with significant changes were associated with metabolism process and cell development. Thus, we assumed that insects could adapt to different environments by regulating their metabolism. Our findings indicated that although adaptive mechanisms to hypoxia in different DBM strains could be similar, DBM individuals from Tibet had superior tolerance to hypoxia compared with those of Fuzhou. Local adaptation of the Tibetan colony was assumed to be responsible for this difference. Our research suggests novel mechanisms of insect responses to hypoxia stress.
Cardio-cutaneous fistulae—beware the late sternal wound lesion
Authors: Ratnaraj Vignesh , Ivanov Asen , Buratto Edward , Skillington Peter
Published: March 2023

Cardio-cutaneous fistula is a very rare complication of cardiac surgery, and the optimal management strategy is unclear. We present a case of a right ventricle-to-pulmonary artery conduit (RV–PA) forming a cutaneous fistulate that was successfully surgically repaired. A 43-year-old male presented for an elective RV–PA conduit replacement with a cutaneous skin lesion and associated sub-sternal collection. The patient underwent redo-sternotomy for the previous surgical replacement RV–PA conduit, of pulmonary atresia, ventricular septal defect, and ligation of main aorto-pulmonary collateral arteries in childhood, with the subsequent upgrade of the RV–PA conduit using pulmonary homograft. Upon entry into the thoracic cavity, it was clear that there was a direct fistula formed from the RV–PA conduit that was responsible for the skin lesion and hence a direct communication to the PA. We discuss the surgical method and surrounding discussions regarding Cardio-cutaneous fistula in a successful surgical repair when the pathology is difficult to truly identify preoperatively.
Twenty-year trends in the prevalence of modifiable cardiovascular risk factors in young acute coronary syndrome patients hospitalized in Switzerland
Authors: Mahendiran Thabo , Hoepli André , Foster-Witassek Fabienne , Rickli Hans , Roffi Marco , Eberli Franz , Pedrazzini Giovanni , Jeger Raban , Radovanovic Dragana , Fournier Stephane ,   the AMIS Plus Investigators, Lessing P , Hess F , Simon R , Hangartner P J , Hufschmid U , Jeger R , Altwegg L , Schönfelder A , Windecker S , Pilgrim T , Loretan P , Roethlisberger C , Evéquoz D , Mang G , Ryser D , Niedermaier G , Kistler W , Droll A , Hongler T , Stäuble S , Freiwald G , Schmid H P , Stauffer J C , Cook S , Bietenhard K , Roffi M , Oertli B , Schönenberger R , Schmidli M , Federspital B , Weiss E M , Weber K , Zender H , Steffen C , Poepping I , Hugi A , Frei J , Koltai E , Muller O , Pedrazzini G , Erne P , Cuculi F , Heimes T , Pagnamenta A , Urban P , Stettler C , Repond F , Widmer F , Heimgartner C , Polikar R , Bassetti S , Ernst S , Iselin H U , Giger M , Egger P , Kaeslin T , Frey R , Fischer A , Herren T , Flury G , Neumeier C , Girod G , Vogel R , Niggli B , Rickli H , Nossen J , Stoller U , Bächli E , Eriksson U , Fischer T , Peter M , Gasser S , Fatio R , Wyss C , Bertel O , Maggiorini M , Stähli B , Eberli F , Christen S
Published: March 2023

Aims

Modifiable cardiovascular risk factors (RFs) play a key role in the development of coronary artery disease. We evaluated 20-year trends in RF prevalence among young adults hospitalized with acute coronary syndromes (ACS) in Switzerland.

Methods and results

Data were analysed from the Acute Myocardial Infarction in Switzerland (AMIS) Plus registry from 2000 to 2019. Young patients were defined as those aged <50 years. Among 58 028 ACS admissions, 7073 (14.1%) were young (median 45.6 years, IQR 42.0–48.0), of which 91.6% had at least one modifiable RF and 59.0% had at least two RFs. Smoking was the most prevalent RF (71.4%), followed by dyslipidaemia (57.3%), hypertension (35.9%), obesity (21.7%), and diabetes (10.1%). Compared with older patients, young patients were more likely to be obese (21.7% vs. 17.4%, P < 0.001) and active smokers (71.4% vs. 33.9%, P < 0.001). Among young patients, between 2000 and 2019, there was a significant increase in the prevalence of hypertension from 29.0% to 51.3% and obesity from 21.2% to 27.1% (both Ptrend < 0.001) but a significant decrease in active smoking from 72.5% to 62.5% (Ptrend = 0.02). There were no significant changes in the prevalence of diabetes (Ptrend = 0.32) or dyslipidaemia (Ptrend = 0.067).

Conclusion

Young ACS patients in Switzerland exhibit a high prevalence of RFs and are more likely than older patients to be obese and smokers. Between 2000 and 2019, RF prevalence either increased or remained stable, except for smoking which decreased but still affected approximately two-thirds of young patients in 2019. Public health initiatives targeting RFs in young adults in Switzerland are warranted.
Trends in cardiovascular risk factors control among US adults by glycemic statuses, 2007–2018
Authors: Yuan Sheng , Song Chenxi , He Jining , Zhang Rui , Bian Xiaohui , Song Weihua , Dou Kefei
Published: March 2023

Aims

Understanding the national trends in cardiovascular risk factors control of individuals with prediabetes and diabetes is critical for diabetes prevention and management. Our study aims to estimate how cardiovascular risk factors changed in US adults with different glycemic statuses between 2007–2008 and 2017–2018.

Methods and results

This was a serial cross-sectional study based on the National Health and Nutrition Examination Surveys (between 2007–2008 and 2017–2018 cycle). Non-pregnant American participants aged 20 years or older were included. Cardiovascular risk factors including weight, blood pressure, plasma cholesterol, and smoking by glycemic statuses were estimated. A total of 33 040 American adults were included. From 2007–2008 to 2017–2018, the age-adjusted proportions of individuals who reached weight control (body mass index <30 kg/m2) of both normoglycemia group and prediabetes group had a significant decrease over the study period, while the trend in participants with diabetes was not significant (mean difference: -5.34%, 95% confidence interval: -15.28%, 4.59%; P for trend = 0.298). The age-adjusted means of total cholesterol of all three groups decreased during the study decade (P for trend < 0.010), with participants with diabetes maintaining the lowest level. Individuals with high total cholesterol were more likely to receive statin therapy in the diabetes group. Notably, prediabetes participants had the highest level of total cholesterol and low-density lipoprotein cholesterol and were less likely to achieve lipid control with statin therapy. Sensitivity analysis with the second definition of prediabetes and diabetes resulted in a consistent trend.

Conclusions

In this nationally representative cross-sectional study, we systematically estimated the cardiovascular risk factors control in American adults and found poor weight control in the normoglycemia and prediabetes group. Despite the significant decrease trend of plasma total cholesterol in all groups, the high cholesterol level in the prediabetes group deserves special concern.
Ecologically diverse island-associated lizard radiation shows idiosyncratic trait diversification shifts and homogenous speciation dynamics
Authors: Skipwith Phillip L , Oliver Paul M
Published: March 2023

A key area of interest in evolutionary biology has been understanding the role of ecological opportunity in the formation of adaptive radiations, lineages where speciation and phenotypic diversification are driven by open ecological opportunity. Evolutionary theory posits that adaptive radiations should show initial bursts of ecomorphological diversification and rapid speciation, and that these two processes are correlated. Here, we investigate and contrast these predictions across ecomorphologically diverse continental (Australia) and insular (New Caledonia and New Zealand) radiations of diplodactyloid geckos. We test two key hypotheses: (a) that island colonization and the transition to novel niche-space has resulted in increased rates of speciation and trait diversification and (b) that rates of morphological diversification are correlated across multiple trait axes. Surprisingly, we find that speciation rate is homogenous and morphological diversification rates are idiosyncratic and uncorrelated with speciation rates. Tests of morphological integration suggests that while all traits coevolve, constraint may act differentially on individual axes. This accords with a growing number of studies indicating that ecologically diverse and species-rich radiations can show limited or no evidence of exceptional regime shifts in speciation dynamics or morphological diversification, especially in continental contexts.
Ice Age effects on genetic divergence of the American crocodile (Crocodylus acutus) in Panama: reconstructing limits of gene flow and environmental ranges: a reply to O’Dea et al.
Authors: Avila-Cervantes Jose , Larsson Hans C E
Published: March 2023

O’Dea et al. (2022) (Pleistocene sea level changes and crocodile population histories on the isthmus of panama: a comment on Avila-Cervantes et al. (2020). Evolution, 76(11), 2778–2783. https://doi.org/10.1111/evo.14610) question our hypothesis that sea-level changes during the past glaciation played a role in restricting gene flow between Pacific and Caribbean Crocodylus acutus in Panama. They argue that an error in sea-level high-stand reconstruction during the last interglacial period (118–130 ka) does not support our hypothesis. Although they are correct in our high-stand reconstruction error, overlooked the point in that we were presenting a model of restricted gene flow across the Panamanian Isthmus during low sea levels. We review the assumptions of gene demographic methods, emphasizing that we were focusing on times of genetic divergence. We expand here why gene flow between these coastal populations could have been restricted during the last glacial maximum (19–26.5 ka) and the 50,000 years preceding it when sea levels were lower than today. O’Dea et al. suggest local climates may have played larger roles than sea levels. We demonstrate that paleoclimate estimates for the past 3.3 Ma in Panama are within the bounds of extant C. acutus. The importance of Ice Age Sea-level dynamics on Neotropical species was likely profound and should be incorporated into evolutionary studies of these taxa.
Polygamy and purifying selection in birds
Authors: Wanders Kees , Chen Guangji , Feng Shaohong , Zhang Guojie , Székely Tamás , Bruford Mike , Végvári Zsolt , Eichhorn Götz , Urrutia Araxi
Published: March 2023

Good genes theories of sexual selection predict that polygamy will be associated with more efficient removal of deleterious alleles (purifying selection), due to the alignment of sexual selection with natural selection. On the other hand, runaway selection theories expect no such alignment of natural and sexual selection, and may instead predict less efficient purifying selection in polygamous species due to higher reproductive variance. In an analysis of polymorphism data extracted from 150-bird genome assemblies, we show that polygamous species carry significantly fewer nonsynonymous polymorphisms, relative to synonymous polymorphisms, than monogamous bird species (p = .0005). We also show that this effect is independent of effective population size, consistent with the alignment of natural selection with sexual selection and “good genes” theories of sexual selection. Further analyses found no impact of polygamy on genetic diversity, while polygamy in females (polyandry) had a marginally significant impact (p = .045). We also recapitulate previous findings that smaller body mass and greater geographic range size are associated with more efficient purifying selection, more intense GC-biased gene conversion, and greater genetic diversity.
Local adaptation in shell shape traits of a brooding chiton with strong population genomic differentiation
Authors: M Salloum Priscila , D Lavery Shane , de Villemereuil Pierre , W Santure Anna
Published: March 2023

Comparing divergence in quantitative traits and neutral molecular markers, such as QST–FST comparisons, provides a means to distinguish between natural selection and genetic drift as causes of population differentiation in complex polygenic traits. Onithochiton neglectus (Rochebrune, 1881) is a morphologically variable chiton endemic to New Zealand, with populations distributed over a broad latitudinal environmental gradient. In this species, the morphological variants cluster into 2 geographically separated shell shape groups, and the phenotypic variation in shell shape has been hypothesized to be adaptive. Here, we assessed this hypothesis by comparing neutral genomic differentiation between populations (FST) with an index of phenotypic differentiation (PST). We used 7,562 putatively neutral single-nucleotide polymorphisms (SNPs) across 15 populations and 3 clades of O. neglectus throughout New Zealand to infer FST. PST was calculated from 18 shell shape traits and gave highly variable estimates across populations, clades, and shape groups. By systematically comparing PST with FST, we identified evidence of local adaptation in a number of the O. neglectus shell shape traits. This supports the hypothesis that shell shape could be an adaptive trait, potentially correlated with the ability to live and raft in kelp holdfasts.
Multilevel selection on social network traits differs between sexes in experimental populations of forked fungus beetles
Authors: Costello Robin A , Cook Phoebe A , Brodie Edmund D , Formica Vincent A
Published: March 2023

Both individual and group behavior can influence individual fitness, but multilevel selection is rarely quantified on social behaviors. Social networks provide a unique opportunity to study multilevel selection on social behaviors, as they describe complex social traits and patterns of interaction at both the individual and group levels. In this study, we used contextual analysis to measure the consequences of both individual network position and group network structure on individual fitness in experimental populations of forked fungus beetles (Bolitotherus cornutus) with two different resource distributions. We found that males with high individual connectivity (strength) and centrality (betweenness) had higher mating success. However, group network structure did not influence their mating success. Conversely, we found that individual network position had no effect on female reproductive success but that females in populations with many social interactions experienced lower reproductive success. The strength of individual-level selection in males and group-level selection in females intensified when resources were clumped together, showing that habitat structure influences multilevel selection. Individual and emergent group social behavior both influence variation in components of individual fitness, but impact the male mating success and female reproductive success differently, setting up intersexual conflicts over patterns of social interactions at multiple levels.
Introduction history and hybridization determine the hydric balance of an invasive lizard facing a recent climate niche shift
Authors: Baeckens Simon , Losos Jonathan B , Irschick Duncan J , Kolbe Jason J , Bock Dan G
Published: March 2023

As anthropogenic activities are increasing the frequency and severity of droughts, understanding whether and how fast populations can adapt to sudden changes in their hydric environment is critically important. Here, we capitalize on the introduction of the Cuban brown anole lizard (Anolis sagrei) in North America to assess the contemporary evolution of a widespread terrestrial vertebrate to an abrupt climatic niche shift. We characterized hydric balance in 30 populations along a large climatic gradient. We found that while evaporative and cutaneous water loss varied widely, there was no climatic cline, as would be expected under adaptation. Furthermore, the skin of lizards from more arid environments was covered with smaller scales, a condition thought to limit water conservation and thus be maladaptive. In contrast to environmental conditions, genome-averaged ancestry was a significant predictor of water loss. This was reinforced by our genome-wide association analyses, which indicated a significant ancestry-specific effect for water loss at one locus. Thus, our study indicates that the water balance of invasive brown anoles is dictated by an environment-independent introduction and hybridization history and highlights genetic interactions or genetic correlations as factors that might forestall adaptation. Alternative water conservation strategies, including behavioral mitigation, may influence the brown anole invasion success and require future examination.
Testing the predictability of morphological evolution in contrasting thermal environments
Authors: Pilakouta Natalie , Humble Joseph L , Hill Iain D C , Arthur Jessica , Costa Ana P B , Smith Bethany A , Kristjánsson Bjarni K , Skúlason Skúli , Killen Shaun S , Lindström Jan , Metcalfe Neil B , Parsons Kevin J
Published: March 2023

Gaining the ability to predict population responses to climate change is a pressing concern. Using a “natural experiment,” we show that testing for divergent evolution in wild populations from contrasting thermal environments provides a powerful approach, and likely an enhanced predictive power for responses to climate change. Specifically, we used a unique study system in Iceland, where freshwater populations of threespine sticklebacks (Gasterosteus aculeatus) are found in waters warmed by geothermal activity, adjacent to populations in ambient-temperature water. We focused on morphological traits across six pairs from warm and cold habitats. We found that fish from warm habitats tended to have a deeper mid-body, a subterminally orientated jaw, steeper craniofacial profile, and deeper caudal region relative to fish from cold habitats. Our common garden experiment showed that most of these differences were heritable. Population age did not appear to influence the magnitude or type of thermal divergence, but similar types of divergence between thermal habitats were more prevalent across allopatric than sympatric population pairs. These findings suggest that morphological divergence in response to thermal habitat, despite being relatively complex and multivariate, are predictable to a degree. Our data also suggest that the potential for migration of individuals between different thermal habitats may enhance nonparallel evolution and reduce our ability to predict responses to climate change.
Did early shifts to bird pollination impose constraints onSalviaflower evolution?
Authors: Sazatornil Federico , Fornoni Juan , Fragoso-Martínez Itzi , Pérez-Ishiwara Rubén , Benitez-Vieyra Santiago
Published: March 2023

A recent article by Kriebel et al. (2020) examines the relationship between floral shape evolution and pollination shifts in Salvia, a plant genus almost worldwide distributed, but particularly diverse in the New World. Kriebel et al. (2020) argue that a major shift to bird pollination at the origin of the subg. Calosphace (~20 million years ago [Mya]) imposed a legacy of constraints, resulting in significant differences in flower morphology between New World and Old World Salvia. However, reanalyses of the data using hidden states to account for the heterogeneity in evolutionary rates do not support an early origin of bird pollination in this group. Instead, bird pollination may have appeared after the arrival of modern hummingbirds to North America (15.5–12 Mya), as in other North American plant clades. The use of more complex models of ancestral state reconstruction into comparative analyses provides a different perspective to explain morphological differences within Salvia. Our results indicate that bird pollination did not impose constraints on corolla shape evolution. Evolutionary constraints in anther connective and style shapes may have arisen at the origin of Calosphace but they were not associated with shifts to hummingbird pollination, being more likely the product of contingent evolution.
Model selection, hummingbird natural history, and biological hypotheses: a response to Sazatornil et al.
Authors: Kriebel Ricardo , Rose Jeffrey P , Drew Bryan T , González-Gallegos Jesús G , Celep Ferhat , Heeg Luciann , Mahdjoub Mohamed M , Sytsma Kenneth J
Published: March 2023

We have previously suggested that a shift from bee to hummingbird pollination, in concert with floral architecture modifications, occurred at the crown of Salvia subgenus Calosphace in North America ca. 20 mya (Kriebel et al. 2020 and references therein). Sazatornil et al. (2022), using a hidden states model, challenged these assertions, arguing that bees were the ancestral pollinator of subg. Calosphace and claiming that hummingbirds could not have been the ancestral pollinator of subg. Calosphace because hummingbirds were not contemporaneous with crown subg. Calosphace in North America. Here, using a variety of models, we demonstrate that most analyses support hummingbirds as ancestral pollinators of subg. Calosphace and show that Sazatornil et al. (2022) erroneously concluded that hummingbirds were absent from North America ca. 20 mya. We contend that “biological realism” – based on timing and placement of hummingbirds in Mexico ca. 20 mya and the correlative evolution of hummingbird associated floral traits – must be considered when comparing models based on fit and complexity, including hidden states models.
Age-specific effects of deletions: implications for aging theories
Authors: Brengdahl Martin I , Kimber Christopher M , Shenoi Vinesh Naresh , Dumea Miruna , Mital Avani , Friberg Urban
Published: March 2023

The evolution of aging requires mutations with late-life deleterious effects. Classic theories assume these mutations either have neutral (mutation accumulation) or beneficial (antagonistic pleiotropy) effects early in life, but it is also possible that they start out as mildly harmful and gradually become more deleterious with age. Despite a wealth of studies on the genetics of aging, we still have a poor understanding of how common mutations with age-specific effects are and what aging theory they support. To advance our knowledge on this topic, we measure a set of genomic deletions for their heterozygous effects on juvenile performance, fecundity at 3 ages, and adult survival. Most deletions have age-specific effects, and these are commonly harmful late in life. Many of the deletions assayed here would thus contribute to aging if present in a population. Taking only age-specific fecundity into account, some deletions support antagonistic pleiotropy, but the majority of them better fit a scenario where their negative effects on fecundity become progressively worse with age. Most deletions have a negative effect on juvenile performance, a fact that strengthens the conclusion that deletions primarily contribute to aging through negative effects that amplify with age.
Fitness landscapes reveal context-dependent benefits of oviposition behavior
Authors: Ravi Kumar Vrinda , Agavekar Gaurav , Agashe Deepa
Published: March 2023

Resource choice behavior has enormous fitness consequences and can drive niche expansion. However, individual behavioral choices are often mediated by context, determined by past experience. Do such context-dependent behaviors reflect maladaptive variation or are they locally adaptive? Using Tribolium castaneum (the red flour beetle), we demonstrate that context-dependent oviposition behavior reflects distinct, context-specific local fitness peaks. We measured offspring fitness to generate fitness landscapes as a function of all possible oviposition behaviors (i.e., combinations of fecundity and resource preference) in a habitat containing optimal and suboptimal resource patches. We did this by experimentally manipulating egg allocation across patches, which allowed us to assess behaviors not typically observed in the laboratory. We found that females from different age and competition contexts exhibit distinct behaviors which optimize different fitness components, linked in a tradeoff. With prior exposure to strong competition and increasing age, females produce few but fast-developing offspring that are advantageous under high resource competition. In contrast, young naïve females produce significantly more (but slower developing) offspring, which is beneficial under weak competition. Systematically mapping complete context-dependent fitness landscapes is thus critical to infer behavioral optimality and offers predictive power in novel contexts.
Whole-genome sequencing distinguishes the two most common giant kelp ecomorphs
Authors: Gonzalez Sara T , Alberto Filipe , Molano Gary
Published: March 2023

Giant kelp, Macrocystis pyrifera, exists as distinct morphological variants—or “ecomorphs”—in different populations, yet the mechanism for this variation is uncertain, and environmental drivers for either adaptive or plastic phenotypes have not been identified. The ecomorphs Macrocystis “pyrifera” and M. “integrifolia” are distributed throughout temperate waters of North and South America with almost no geographic overlap and exhibit an incongruous, non-mirrored, distribution across the equator. This study evaluates the degree of genetic divergence between M. “pyrifera” and M. “integrifolia” across 18 populations in Chile and California using whole-genome sequencing and single-nucleotide polymorphism markers. Our results based on a principal component analysis, admixture clustering by genetic similarity, and phylogenetic inference demonstrate that M. “pyrifera” and M. “integrifolia” are genetically distinguishable. Analyses reveal separation by Northern and Southern Hemispheres and between morphs within hemispheres, suggesting that the convergent “integrifolia” morphology arose separately in each hemisphere. This is the first study to use whole-genome sequencing to understand genetic divergence in giant kelp ecomorphs, identifying 83 potential genes under selection and providing novel insights about Macrocystis evolution that were not evident with previous genetic techniques. Future studies are needed to uncover the environmental forces driving local adaptation and presumed convergent evolution of these morphs.
The human RAP1 and GFAPɛ proteins increase γ-secretase activity in a yeast model system
Authors: Swanson Mark J , Lewis Kelsey N , Carpenter Robert , Whetzel Alexis , Bae Nancy S
Published: March 2023

Alzheimer's disease (AD) is an age-related disorder that results in progressive cognitive impairment and memory loss. Deposition of amyloid β (Aβ) peptides in senile plaques is a hallmark of AD. γ-secretase produces Aβ peptides, mostly as the soluble Aβ40 with fewer insoluble Aβ42 peptides. Rare, early-onset AD (EOAD) occurs in individuals under 60 years of age. Most EOAD cases are due to unknown genetic causes, but a subset is due to mutations in the genes encoding the amyloid precursor protein that is processed into Aβ peptides or the presenilins (PS1 and PS2) that process APP. PS1 interacts with the epsilon isoform of glial fibrillary acidic protein (GFAPɛ), a protein found in the subventricular zone of the brain. We have found that GFAPɛ interacts with the telomere protection factor RAP1 (TERF2IP). RAP1 can also interact with PS1 alone or with GFAPɛ in vitro. Our data show that the nuclear protein RAP1 has an extratelomeric role in the cytoplasm through its interactions with GFAPɛ and PS1. GFAPɛ coprecipitated with RAP1 from human cell extracts. RAP1, GFAPɛ, and PS1 all colocalized in human SH-SY5Y cells. Using a genetic model of the γ-secretase complex in Saccharomyces cerevisiae, RAP1 increased γ-secretase activity, and this was potentiated by GFAPɛ. Our studies are the first to connect RAP1 with an age-related disorder.
Divergent Evolution of Early Terrestrial Fungi Reveals the Evolution of Mucormycosis Pathogenicity Factors
Authors: Wang Yan , Chang Ying , Ortañez Jericho , Peña Jesús F , Carter-House Derreck , Reynolds Nicole K , Smith Matthew E , Benny Gerald , Mondo Stephen J , Salamov Asaf , Lipzen Anna , Pangilinan Jasmyn , Guo Jie , LaButti Kurt , Andreopolous William , Tritt Andrew , Keymanesh Keykhosrow , Yan Mi , Barry Kerrie , Grigoriev Igor V , Spatafora Joseph W , Stajich Jason E
Published: March 2023

Fungi have evolved over millions of years and their species diversity is predicted to be the second largest on the earth. Fungi have cross-kingdom interactions with many organisms that have mutually shaped their evolutionary trajectories. Zygomycete fungi hold a pivotal position in the fungal tree of life and provide important perspectives on the early evolution of fungi from aquatic to terrestrial environments. Phylogenomic analyses have found that zygomycete fungi diversified into two separate clades, the Mucoromycota which are frequently associated with plants and Zoopagomycota that are commonly animal-associated fungi. Genetic elements that contributed to the fitness and divergence of these lineages may have been shaped by the varied interactions these fungi have had with plants, animals, bacteria, and other microbes. To investigate this, we performed comparative genomic analyses of the two clades of zygomycetes in the context of Kingdom Fungi, benefiting from our generation of a new collection of zygomycete genomes, including nine produced for this study. We identified lineage-specific genomic content that may contribute to the disparate biology observed in these zygomycetes. Our findings include the discovery of undescribed diversity in CotH, a Mucormycosis pathogenicity factor, which was found in a broad set of zygomycetes. Reconciliation analysis identified multiple duplication events and an expansion of CotH copies throughout the Mucoromycotina, Mortierellomycotina, Neocallimastigomycota, and Basidiobolus lineages. A kingdom-level phylogenomic analysis also identified new evolutionary relationships within the subphyla of Mucoromycota and Zoopagomycota, including supporting the sister-clade relationship between Glomeromycotina and Mortierellomycotina and the placement of Basidiobolus as sister to other Zoopagomycota lineages.