Nevin Manimala

JAMA Health Forum. 2025 Sep 5;6(9):e253020. doi: 10.1001/jamahealthforum.2025.3020.

ABSTRACT

IMPORTANCE: The concentration of poverty and multidimensional disadvantage has been shown to limit access to health care in these communities. There is a growing interest in using area-level socioeconomic indexes to address the unequal geographic distribution of health care resources. However, the association of area-level socioeconomic indexes with access to primary care-a key area in health policy-has not been determined.

OBJECTIVE: To investigate the association of Medicaid primary care utilization with the concentration of poverty and multidimensional disadvantage at the zip code level.

DESIGN, SETTINGS, AND PARTICIPANTS: This cross-sectional study used the 2019 Transformed-Medicaid Statistical Information System to identify variations in primary care utilization among Medicaid and the Children’s Health Insurance Program beneficiaries (age <65 years) by poverty and multidimensional disadvantage levels of their area of residence. Included beneficiaries were enrolled in Medicaid from January 1 to December 31, 2019, and were not dually eligible for Medicare. The zip code-level Social Vulnerability Index (SVI) was used to assess the likelihood of a beneficiary having an annual primary care visit, while controlling for individual beneficiary demographic and health characteristics. An activity-based approach was adopted to classify clinicians billing Medicaid for primary care and to identify primary care visits at federally qualified health centers (FQHCs). SVI results were compared with results using income-based poverty rates alone. Data analysis was performed from May 1, 2023, through February 28, 2025.

EXPOSURE: Zip code-level deciles of the SVI and poverty rates.

MAIN OUTCOMES AND MEASURES: Regression analysis was performed at the beneficiary level, using a binary indicator for having a primary care visit on a set of dummy variables for SVI deciles, controlling for age and sex interactions, disability status, and indicators for having been diagnosed with behavioral health or chronic physical health conditions.

RESULTS: The total population analyzed comprised 34 890 932 Medicaid beneficiaries (<65 years old; 54.2% female and 45.8% male), more than half of whom resided in the top 20% of socially vulnerable zip codes; approximately 33%, in the top 10%; and another 20%, in the ninth decile. Of the total, 68.1% had at least 1 primary care visit in 2019, at either a non-FQHC practice (61.1%) or a FQHC (12.7%). The probability of having a primary care visit was highest for children (age <18 years) but varied substantially by age. Compared to those residing in the first decile of the SVI (least socially vulnerable), beneficiaries in the tenth decile (most socially vulnerable) were 8.9 (95% CI, -9.9 to -7.9) percentage points (pp) less likely to have a primary care visit when not counting FQHC visits, but this increased to 4.7 (95% CI, -5.5 to -3.8) pp less likely when including FQHC visits. Beneficiaries in the tenth decile were 5.9 (95% CI, 4.9 to 6.8) pp more likely to have a FQHC visit than beneficiaries in the first decile. The SVI results identified more beneficiaries with disparities compared to the area-level poverty rate alone.

CONCLUSIONS AND RELEVANCE: The findings of this cross-sectional study suggest that Medicaid policy should focus on addressing geography-based disparities in access to care using new measures to target resources. The multidimensional SVI is likely a useful tool to identify small geographic areas with barriers to accessing adequate health care. The FQHC findings suggest that substantially increasing investments and support for FQHCs would address geographic inequities in access to health care.

PMID:40911326 | DOI:10.1001/jamahealthforum.2025.3020

JAMA Health Forum. 2025 Sep 5;6(9):e253035. doi: 10.1001/jamahealthforum.2025.3035.

ABSTRACT

IMPORTANCE: Access to and quality of care vary substantially by area socioeconomic status. Expanding hospital health information technology (HIT) adoption may help reduce these disparities, given hospitals’ central role in serving underserved populations.

OBJECTIVE: To examine variations in US hospital adoption of telehealth and health information exchange (HIE) functionalities by hospital service area (HSA) socioeconomic deprivation.

DESIGN, SETTING, AND PARTICIPANTS: This cross-sectional study links data from the 2018-2023 American Hospital Association Annual Survey and Information Technology Survey with HSA-level area deprivation index. Nonfederal acute care hospitals with complete data on HIT outcomes, comprising 16 646 observations for the telehealth outcomes and 9218 observations for the HIE outcomes across 6 years, were included. Data were analyzed from February 2024 to February 2025.

EXPOSURES: HSA-level area deprivation index in quartiles.

MAIN OUTCOMES AND MEASURES: Hospital adoption of treatment-stage telehealth and postdischarge telehealth services and HIE infrastructure supporting electronic data query and availability. Descriptive, regression, and Blinder-Oaxaca decomposition analyses and visualized time trends in hospital HIT adoption were used in analyses.

RESULTS: This study included 16 646 hospital-level observations and 9218 observations for health information exchange functionalities. Hospitals in the most socioeconomically deprived HSAs were significantly less likely to adopt HIT compared with those in the least deprived areas (treatment-stage telehealth: marginal effect [ME], -0.03; 95% CI, -0.06 to -0.01; postdischarge telehealth: ME, -0.03; 95% CI, -0.07 to 0.01; electronic data query capability: ME, -0.03; 95% CI, -0.06 to -0.01; electronic data availability: ME, -0.06; 95% CI, -0.11 to -0.01). Year fixed effects indicated significant increases in HIT adoption from 2018 to 2023, regardless of HSA deprivation level. Decomposition analyses showed that differences in hospital bed size, urban/rural location, and accountable care organization participation explained a substantial portion of the disparities by HSA deprivation.

CONCLUSIONS AND RELEVANCE: In this study, hospitals in more socioeconomically disadvantaged HSAs remained likely to adopt telehealth and HIE functionalities. Nevertheless, HIT adoption has grown steadily over time. Accountable care organization participation may support HIT infrastructure and help reduce geographic disparities in adoption and access to care.

PMID:40911325 | DOI:10.1001/jamahealthforum.2025.3035

JAMA Netw Open. 2025 Sep 2;8(9):e2527431. doi: 10.1001/jamanetworkopen.2025.27431.

ABSTRACT

IMPORTANCE: Preterm children face a higher risk of cardiovascular conditions, including hypertension. However, studies have not isolated the associations of prematurity with cardiovascular conditions from the associations of subsequent complications with cardiovascular conditions, especially among those admitted to a neonatal intensive care unit (NICU).

OBJECTIVE: To investigate prospective associations of prematurity and NICU complications with childhood hypertension while accounting for prenatal and perinatal factors.

DESIGN, SETTING, AND PARTICIPANTS: This cohort study analyzed longitudinal data from the Boston Birth Cohort on 2459 infants (695 preterm, 468 with NICU admission) born between January 1, 1999, and December 31, 2014. Statistical analysis was performed from January 1, 1999, to December 31, 2020.

MAIN OUTCOMES AND MEASURES: Children were categorized into 5 subgroups based on preterm birth status, NICU admission, and major complications (sepsis, chronic lung disease, necrotizing enterocolitis, and intraventricular hemorrhage). The primary end point was hypertension (episodic and persistent) per American Academy of Pediatrics guidelines, with elevated blood pressure (BP) and BP percentiles as secondary end points. Modified Poisson and proportional hazards regression were used to determine crude and adjusted relative risks (RRs) and hazard ratios (HRs). Secondary analyses used linear generalized estimating equations to assess repeated BP measurements over time, standardized to population-based BP percentiles.

RESULTS: Of the 2459 infants (695 preterm: mean [SD] gestational age, 33.2 [3.5] weeks; 358 boys [51.5%]; and 1764 full term: mean [SD] gestational age, 39.4 [1.3] weeks; 879 boys [49.7%]) in this study, 468 (19.0%) were admitted to the NICU. The incidence of persistent hypertension was higher among children born preterm compared with those born at full term (25.2% [175 of 695] vs 15.8% [278 of 1764]). Preterm infants and infants admitted to the NICU had a greater risk of developing persistent hypertension compared with full term-born children without NICU admission or neonatal complications, independent of pertinent maternal and infant characteristics. Preterm infants with an NICU stay, both with (adjusted RR, 1.87 [95% CI, 1.19-2.94]) and without (adjusted RR, 1.62 [95% CI, 1.27-2.07]) a neonatal complication, had the greatest risk for persistent hypertension. Cox proportional hazards regression analysis identified preterm infants with an NICU stay, particularly those with a complication, as having the highest risk of developing persistent hypertension (adjusted HR, 2.37 [95% CI, 1.44-3.89]). On average, infants born prematurely without an NICU admission or complication (β, 2.74 percentile points [95% CI, 0.38-5.10 percentile points]) and those born prematurely with an NICU admission but no complications (β, 4.06 percentile points [95% CI, 2.11-6.02 percentile points]) had higher systolic BP percentiles and those born prematurely with an NICU admission but no complications had higher diastolic BP percentiles (β, 4.01 percentile points [95% CI, 2.52-5.49 percentile points]) during follow-up up to 18 years of age.

CONCLUSIONS AND RELEVANCE: This prospective cohort study found incrementally stronger associations for NICU admission, prematurity, and prematurity-related complications with the risk of developing persistent hypertension in childhood. These findings support the need for hypertension screening, coordinated primary and specialist care, and cardiovascular health promotion among children born preterm.

PMID:40911310 | DOI:10.1001/jamanetworkopen.2025.27431

JAMA Netw Open. 2025 Sep 2;8(9):e2530624. doi: 10.1001/jamanetworkopen.2025.30624.

ABSTRACT

IMPORTANCE: Among men with favorable-risk (ie, low-risk or favorable intermediate-risk) prostate cancer, confirmatory testing substantially improves the detection of aggressive cancers that may merit treatment instead of conservative management. Despite guideline recommendations, confirmatory testing is inconsistently used, and more than half of men do not receive it. Value-based interventions and payment incentives may improve care quality by motivating adherence to guideline-concordant care.

OBJECTIVE: To examine the use of confirmatory testing among men with low-risk prostate cancer, after the application of a multifaceted intervention, which included physician education and a payment incentive, sponsored by a commercial payer to support its use.

DESIGN, SETTING, AND PARTICIPANTS: This cohort study used data from the Michigan Urological Surgery Improvement Collaborative on men who received a diagnosis of low-risk prostate cancer between January 1, 2017, and July 1, 2022, with a minimum 6 months of follow-up. Statistical analysis was performed from October 2024 to June 2025.

EXPOSURE: Multifaceted intervention with a payment incentive, applied specifically to men who received a diagnosis of low-risk prostate cancer between April 1, 2018, and May 30, 2019. On meeting the payment incentive’s benchmark (ie, ≥45% of men with low-risk prostate cancer complete confirmatory testing within 6 months of diagnosis), the insurer would distribute enhanced reimbursement on claims covered by commercial preferred provider organization plans.

MAIN OUTCOMES AND MEASURES: Confirmatory testing completion (ie, magnetic resonance imaging before or after diagnostic biopsy, repeat prostate biopsy, or genomics test) relative to the preincentive period among men with low-risk prostate cancer. Secondary analyses examined practices by baseline confirmatory testing completion and proportion of patients with insurance plans covered by the insurer sponsoring the payment incentive.

RESULTS: The study included 6609 patients (median age, 65 years [IQR, 60-70 years]), of whom 72.9% (n = 4818) elected for active surveillance. Confirmatory testing increased between 2017 (44.6% [725 of 1625]) and 2022 (64.3% [774 of 1203]) (P < .001). During the payment incentive period, patients had a 7.5% (95% CI, 0.0%-15.4%; P = .06) increase in the predicted probability of confirmatory testing completion relative to the preincentive period, although this change was not statistically significant (odds ratio, 1.43 [95% CI, 0.99-2.09]; P = .06).

CONCLUSIONS AND RELEVANCE: In this cohort study of men with prostate cancer, confirmatory testing completion improved over the study period. However, the payment incentive was not associated with a robust increase in its use. The results suggest collaboration between payers and physicians has the potential to improve measures of prostate cancer care quality, but also highlight the challenges associated with payment incentives and alternative payment model implementation.

PMID:40911309 | DOI:10.1001/jamanetworkopen.2025.30624

JAMA Netw Open. 2025 Sep 2;8(9):e2530677. doi: 10.1001/jamanetworkopen.2025.30677.

ABSTRACT

IMPORTANCE: The association of cardiopulmonary point-of-care ultrasonography (POCUS) with length of stay (LOS) and hospitalization costs for patients admitted to internal medicine wards remains uncertain.

OBJECTIVE: To evaluate a collaborative implementation model involving hospitalists, sonographers, and a remote cardiologist for integrating cardiopulmonary POCUS into the assessment of adult patients (≥18 years) hospitalized with undifferentiated dyspnea, and to assess its association with LOS and hospitalization costs.

DESIGN, SETTING, AND PARTICIPANTS: This quality improvement study employed a type 1 effectiveness-implementation hybrid design using a 6-month stepped-wedge cluster randomized approach, conducted at a tertiary care hospital in the US between December 7, 2023, and July 2, 2024, to compare the standard-of-care (control) with the intervention group. Patients were eligible for inclusion if they were older than 18 years, admitted to 1 of the 5 internal medicine teaching hospitalist teams, and presented with undifferentiated dyspnea.

EXPOSURE: Structured cardiopulmonary POCUS examinations performed by hospitalists and/or sonographers, integrated into routine assessment of dyspnea.

MAIN OUTCOMES AND MEASURES: Study outcomes (LOS and hospitalization costs) were presented using the reach, effectiveness, adoption, and implementation (RE-AIM) framework.

RESULTS: The study reached 208 patients (median [IQR] age, 71 [59-80] years; 121 female [58%]), including 107 in the control group and 101 in the POCUS group. The implementation of cardiopulmonary POCUS was associated with a 30.3% (95% CI, 5.5%-48.9%) reduction in expected LOS (mean [SD] LOS, 8.3 [5.2] days for the POCUS group vs 11.9 [7.5] days in the control group). Based on cumulative assessments, POCUS use was associated with a total reduction of 246 hospital bed-days and direct cost savings of $751 537, with an incremental cost-effectiveness ratio of $3055 per hospital bed-day saved. POCUS altered medical decisions in 30 patients (35%). Adoption and implementation of POCUS by hospitalists remained limited despite comprehensive training, with only 20% of POCUS evaluations (17 patients) being performed independently, while the majority relied on sonographers.

CONCLUSIONS AND RELEVANCE: In this quality improvement study, cardiopulmonary POCUS implementation was associated with a significant reduction in LOS and hospitalization costs, highlighting its clinical utility and potential for improved hospital efficiency; however, limited adoption by hospitalists underscores the need for ongoing training, support, and professional incentives to strengthen competency and motivation. Multicenter studies are needed to evaluate tailored educational models and sustainable support systems to optimize long-term integration of POCUS into routine practice.

PMID:40911308 | DOI:10.1001/jamanetworkopen.2025.30677

JAMA Netw Open. 2025 Sep 2;8(9):e2530691. doi: 10.1001/jamanetworkopen.2025.30691.

ABSTRACT

IMPORTANCE: In the US, children in food-insecure households are at risk for adverse psychological outcomes despite being shielded from hunger and malnutrition by their caregivers and school- and community-based programs. Parenting stress may be an important mechanism through which food insecurity is associated with negative outcomes for child mental health.

OBJECTIVE: To investigate associations of household food insecurity with child mental health, parenting stress, and family functioning.

DESIGN, SETTING, AND PARTICIPANTS: This cross-sectional study used a daily-diary design in a community-based sample to examine associations between daily fluctuations in food insecurity and child and family functioning. The study was conducted remotely during the COVID-19 pandemic in the rural (defined by the Health Resource Services Administration) Northeastern US. Caregivers of school-aged children were enrolled during the 2021 school year and completed a baseline visit followed by mobile surveys for 30 days. Participants were adult, legal caregivers of children ages 6 to 12 years who experienced food insecurity within the past month. Participants were required to have English proficiency and access to a device with internet and texting capabilities. Prospective participants completed an online questionnaire to determine eligibility. A total of 553 respondents were screened, of which 327 respondents (59.1%) met all inclusion criteria. The most common reason for ineligibility was not having a child in the study age range. Data analyses were performed between May 2022 and April 2023.

EXPOSURE: Household food insecurity.

MAIN OUTCOMES AND MEASURES: The primary outcomes were caregiver hunger, negative affect, executive functioning, and parent-child interactions (measured via a daily self-report survey) and child mental health problems (measured via the Child Behavior Checklist [CBCL]).

RESULTS: Among 61 caregivers (mean [SD] age, 36.1 [5.9] years; 51 women [83.6%]; 2 American Indian or Alaska Native [3.3%], 1 Black [1.6%], and 55 non-Hispanic White [90.2%]), greater day-to-day fluctuations in household and child food insecurity were associated with more severe child internalizing problems (CBCL Internalizing Problems scale: β = 0.40; P = .003 for household and β = 0.49; P < .001 for child food insecurity) and total mental health problems (CBCL Total Problems scale: β = 0.34; P = .01 for household and β = 0.35; P = .01 for child food insecurity). Additionally, the daily association between food insecurity and parent-child conflict was fully mediated via 2 sequential pathways of caregiver hunger and negative affect (b = .02; P = .001) and caregiver hunger and attention and impulse control (b = 0.01; P = .04). This model explained 17% of variability in daily parent-child conflict (R2 = 0.17).

CONCLUSIONS AND RELEVANCE: This study’s findings suggest that caregiver stress and household instability may be key mechanisms by which food insecurity is negatively associated with child mental health.

PMID:40911307 | DOI:10.1001/jamanetworkopen.2025.30691

JAMA Netw Open. 2025 Sep 2;8(9):e2530972. doi: 10.1001/jamanetworkopen.2025.30972.

ABSTRACT

IMPORTANCE: Predialysis nephrology care is associated with the likelihood of having a mature, usable arteriovenous access for starting hemodialysis (ie, incident vascular access), a key care quality metric for patients with kidney failure. However, the magnitude of this association has not been quantified to date.

OBJECTIVE: To quantify the attributable association between lack of access to predialysis nephrology care and incident vascular access outcomes among Hispanic patients.

DESIGN, SETTING, AND PARTICIPANTS: This cohort study is a retrospective analysis of the 2021 US Renal Database System. Participants were all adult Medicare recipients initiating hemodialysis between 2010 and 2019; primary analysis was restricted to those with at least 6 months of predialysis Medicare status. Data analysis was performed from June 2022 to November 2024.

EXPOSURE: Self-reported race and ethnicity, with the non-Hispanic White category serving as the reference and Hispanic ethnicity as the primary comparator. Any predialysis nephrology care was the primary mediator, and at least 6 months of nephrology care and predialysis kidney disease education were the mediators for sensitivity analyses.

MAIN OUTCOMES AND MEASURES: The attributable association between predialysis nephrology care and incident vascular access (ie, the composite of arteriovenous fistula [AVF] or arteriovenous graft [AVG]) disparity was the primary outcome, and its attributable association between remaining incident access types, including central venous catheter (CVC) with maturing in-situ AVF or AVG, and CVC without any other access (CVC only) disparity, were the secondary outcomes. Causal mediation analysis with logistic regression was used to determine the unadjusted and adjusted associations.

RESULTS: Among 427 340 eligible patients undergoing incident hemodialysis (mean [SD] age, 72.65 [10.68] years; 241 420 male [56.5%]), 92 887 (21.7%) were Black, 46 146 (10.8%) were Hispanic, 269 697 (63.1%) were White, and 18 610 (4.35%) were other races and ethnicities. AVF was used in 62 075 patients (14.5%), AVG in 13 163 patients (3.1%), and CVC in 351 315 patients (82.2%). Compared with White patients, Hispanic patients had adjusted odds ratios (aORs) of 0.70 (95% CI, 0.68-0.72) for receiving predialysis nephrology care and 0.77 (95% CI, 0.75-0.80) for receiving incident vascular access, for a 23% lower rate. A lack of nephrology care accounted for 32.59% of incident vascular access and 62.00% of maturing vascular access underuse. Sensitivity analyses enhancing the predialysis care disparities strengthened incident vascular access disparity and the attributable association. Secondary analyses revealed that compared with White patients, Hispanic individuals with CVC and a maturing AVF or AVG had 38% (aOR, 1.38; 95% CI, 1.23-1.53) higher odds and those with CVC only had 30% (aOR, 1.30; 95% CI, 1.25-1.35) higher odds of conversion to a functional AVF or AVG within the first year of dialysis, with predialysis care negatively mediating these outcomes.

CONCLUSIONS AND RELEVANCE: This retrospective cohort study of incident hemodialysis patients found that system-based disparities in predialysis access to nephrology care contribute to approximately one-third of incident vascular access disparities among Hispanic individuals. Targeted system-based remedies and policies are needed to improve timely identification and nephrology referrals among Hispanic individuals, for equitable improvements in incident kidney failure outcomes.

PMID:40911306 | DOI:10.1001/jamanetworkopen.2025.30972

JAMA Netw Open. 2025 Sep 2;8(9):e2531038. doi: 10.1001/jamanetworkopen.2025.31038.

ABSTRACT

IMPORTANCE: Subjective cognitive decline (SCD) may be an early indicator of Alzheimer disease and related dementias (ADRD), yet its association with plasma biomarkers remains unclear among middle-aged and older adults (aged 50-86 years).

OBJECTIVE: To examine associations between plasma biomarkers of amyloid, tau, neuroaxonal damage, and glial activation with SCD in a heterogeneous cohort of Hispanic and/or Latino adults.

DESIGN, SETTING, AND PARTICIPANTS: This cross-sectional study used survey-weighted data from the Study of Latinos-Investigation of Neurocognitive Aging, an ancillary study of the Hispanic Community Health Study/Study of Latinos. Participants were aged 50 to 86 years and resided in 4 major US cities. Data were collected from 2016 to 2018 and analyzed between December 2024 and June 2025.

EXPOSURE: Plasma biomarkers included amyloid-beta (Aβ42/40), phosphorylated tau-181 (ptau-181), neurofilament light chain (NfL), and glial fibrillary acidic protein (GFAP), quantified using Simoa (Quanterix HD-X) and log-transformed (ln) to reduce skewness.

MAIN OUTCOMES AND MEASURES: SCD was assessed using the short-form Everyday Cognition Scale (ECog-12), evaluating global-, executive-, and memory-related SCD, and a single-item cognitive concerns question. Survey-weighted linear and logistic regression models tested associations between biomarkers and SCD, adjusting for demographic, cardiovascular, kidney, and APOE genotype covariates.

RESULTS: Among 5712 adults (mean [SD] age, 63.47 (8.15) years; unweighted 3663 [53.92%] female), higher ln(ptau-181) was associated with ECog-12 memory (unstandardized β = 0.088; 95% CI, 0.005-0.170). Higher ln(NfL) levels were associated with greater ECog-12 global (unstandardized β = 0.169; 95% CI, 0.074-0.265), executive (unstandardized β = 0.182; 95% CI, 0.087-0.277), and memory (unstandardized β = 0.156; 95% CI, 0.065-0.248) domains. Higher ln(GFAP) levels were associated with greater ECog-12 global (unstandardized β = 0.109; 95% CI, 0.019-0.198) and executive (unstandardized β = 0.121; 95% CI, 0.031-0.211) domains. Ln(Aβ42/40) was not associated with SCD domains. Cognitive concerns significantly modified the associations between ln(NfL) and ECog-12 domains, with more pronounced associations among those reporting cognitive concerns. No biomarkers were associated with the single-item cognitive concerns score.

CONCLUSIONS AND RELEVANCE: In this study of middle-aged and older Hispanic and/or Latino adults, plasma biomarkers of p-tau181, NfL, and GFAP, but not Aβ42/40, were associated with greater SCD. These findings underscore their potential utility in early ADRD detection strategies.

PMID:40911305 | DOI:10.1001/jamanetworkopen.2025.31038

Evolution. 2025 Sep 5:qpaf177. doi: 10.1093/evolut/qpaf177. Online ahead of print.

ABSTRACT

Intraspecific phenotypic variation provides the basic substrate upon which the evolutionary processes that give rise to morphological innovation, such as adaptation, operate. Work in living clades has shown standing population-level variation fuels ecological speciation and gives rise to adaptive radiations. Despite its importance in evolutionary biology, the role of intraspecific variation in shaping phylogenetic and macroevolutionary patterns and processes has remained underexplored. I introduce a model of morphological evolution that accommodates polymorphism. The model describes the stochastic gain and loss of phenotypic character states within taxa, i.e., anagenesis, and the sorting of ancestral polymorphic variation during speciation, i.e., cladogenesis. I explore the behaviour of the model using simulations, then deploy it to reconstruct evolutionary relationships between the highly variable species belonging to the Cretaceous echinoid genus Micraster. The analysis revealed strong statistical support for several contentious relationships. The clade depicts a pattern where morphological variation accumulates within a small number of ancestral lineages and then is sorted into descendants without being fully replenished by anagenetic gains. This disproportionate maintenance of variation within early taxa and loss among later taxa could provide a link between the population processes that maintain intraspecific variation and the radiation and decline of clades.

PMID:40911295 | DOI:10.1093/evolut/qpaf177

Syst Biol. 2025 Sep 5:syaf061. doi: 10.1093/sysbio/syaf061. Online ahead of print.

ABSTRACT

For many questions in ecology and evolution, the most relevant data to consider are attributes of lineage pairs. Comparative tests for causal relationships among traits like ‘diet niche overlap’, ‘divergence time’, and ‘strength of reproductive isolation (RI)’ – measured for pairwise combinations of related species or populations – have led to several groundbreaking insights, but the correct statistical approach for these analyses has never been clear. Lineage-pair traits are non-independent, but unlike the expected covariance among species’ traits, which is captured by a phylogenetic covariance matrix arising from a given model, the expected covariance among lineage-pair traits has not been explicitly formulated. Analyses of pairwise-defined data have thus employed untested workarounds for non-independence rather than direct models of lineage-pair covariance, with consequences that are unexplored. Here, we consider how evolutionary relatedness among taxa translates into non-independence among taxonomic pairs. We develop models by which phylogenetic signal in an underlying character generates covariance among pairs in a lineage-pair trait. We incorporate the resulting lineage-pair covariance matrices into modified versions of phylogenetic generalized least squares and a new phylogenetic beta regression for bounded response variables. Both outperform previous approaches in simulation tests. We find that a common heuristic method, node averaging, imparts a greater cost to model performance than does the non-independence it was designed to correct. We re-analyze two empirical datasets to find dramatic improvements in model fit and, in the case of avian hybridization data, an even stronger relationship between pair age and RI than is revealed from uncorrected analysis. We finally present a new tool, the R package phylopairs, that allows empiricists to test relationships among pairwise-defined variables in a way that is statistically robust and more straightforward to implement.

PMID:40911284 | DOI:10.1093/sysbio/syaf061