Functional convergence in gastric lysozymes of foregut-fermenting rodents, ruminants, and primates is not attributed to convergent molecular evolution.

Convergent evolution is a widespread phenomenon. While there are many examples of convergent evolution at the phenotypic scale, convergence at the molecular level has been more difficult to identify. A classic example of convergent evolution across scales is that of the digestive lysozyme found in ruminants and Colobine monkeys. These herbivorous species rely on foregut fermentation, which has evolved to function more optimally under acidic conditions. Here, we explored if rodents with similar dietary strategies and digestive morphologies have convergently evolved a lysozyme with digestive functions. At the phenotypic level, we find that rodents with bilocular stomach morphologies exhibited a lysozyme that maintained higher relative activities at low pH values, similar to the lysozymes of ruminants and Colobine monkeys. Additionally, the lysozyme of Peromyscus leucopus shared a similar predicted protonation state as that observed in previously identified digestive lysozymes. However, we found limited evidence of positive selection acting on the lysozyme gene in foregut-fermenting species and did not identify patterns of convergent molecular evolution in this gene. This study emphasizes that phenotypic convergence need not be the result of convergent genetic modifications, and we encourage further exploration into the mechanisms regulating convergence across biological scales.

Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements.

Vocal production learning ("vocal learning") is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical, and neurophysiological data from the Egyptian fruit bat (Rousettus aegyptiacus) with analyses of the genomes of 215 placental mammals. First, we identified a set of proteins evolving more slowly in vocal learners. Then, we discovered a vocal motor cortical region in the Egyptian fruit bat, an emergent vocal learner, and leveraged that knowledge to identify active cis-regulatory elements in the motor cortex of vocal learners. Machine learning methods applied to motor cortex open chromatin revealed 50 enhancers robustly associated with vocal learning whose activity tended to be lower in vocal learners. Our research implicates convergent losses of motor cortex regulatory elements in mammalian vocal learning evolution.

RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution.

Comparative genomics approaches seek to associate evolutionary genetic changes with the evolution of phenotypes across a phylogeny. Many of these methods, including our evolutionary rates based method, RERconverge, lack the capability of analyzing non-ordinal, multicategorical traits. To address this limitation, we introduce an expansion to RERconverge that associates shifts in evolutionary rates with the convergent evolution of multi-categorical traits. The categorical RERconverge expansion includes methods for performing categorical ancestral state reconstruction, statistical tests for associating relative evolutionary rates with categorical variables, and a new method for performing phylogenetic permulations on multi-categorical traits. In addition to demonstrating our new method on a three-category diet phenotype, we compare its performance to naive pairwise binary RERconverge analyses and two existing methods for comparative genomic analyses of categorical traits: phylogenetic simulations and a phylogenetic signal based method. We also present a diagnostic analysis of the new permulations approach demonstrating how the method scales with the number of species and the number of categories included in the analysis. Our results show that our new categorical method outperforms phylogenetic simulations at identifying genes and enriched pathways significantly associated with the diet phenotype and that the new ancestral reconstruction drives an improvement in our ability to capture diet-related enriched pathways. Our categorical permulations were able to account for non-uniform null distributions and correct for non-independence in gene rank during pathway enrichment analysis. The categorical expansion to RERconverge will provide a strong foundation for applying the comparative method to categorical traits on larger data sets with more species and more complex trait evolution.

Reduction of Paraoxonase Expression Followed by Inactivation across Independent Semiaquatic Mammals Suggests Stepwise Path to Pseudogenization.

Convergent adaptation to the same environment by multiple lineages frequently involves rapid evolutionary change at the same genes, implicating these genes as important for environmental adaptation. Such adaptive molecular changes may yield either change or loss of protein function; loss of function can eliminate newly deleterious proteins or reduce energy necessary for protein production. We previously found a striking case of recurrent pseudogenization of the Paraoxonase 1 (Pon1) gene among aquatic mammal lineages-Pon1 became a pseudogene with genetic lesions, such as stop codons and frameshifts, at least four times independently in aquatic and semiaquatic mammals. Here, we assess the landscape and pace of pseudogenization by studying Pon1 sequences, expression levels, and enzymatic activity across four aquatic and semiaquatic mammal lineages: pinnipeds, cetaceans, otters, and beavers. We observe in beavers and pinnipeds an unexpected reduction in expression of Pon3, a paralog with similar expression patterns but different substrate preferences. Ultimately, in all lineages with aquatic/semiaquatic members, we find that preceding any coding-level pseudogenization events in Pon1, there is a drastic decrease in expression, followed by relaxed selection, thus allowing accumulation of disrupting mutations. The recurrent loss of Pon1 function in aquatic/semiaquatic lineages is consistent with a benefit to Pon1 functional loss in aquatic environments. Accordingly, we examine diving and dietary traits across pinniped species as potential driving forces of Pon1 functional loss. We find that loss is best associated with diving activity and likely results from changes in selective pressures associated with hypoxia and hypoxia-induced inflammation.

The contribution of historical processes to contemporary extinction risk in placental mammals.

Species persistence can be influenced by the amount, type, and distribution of diversity across the genome, suggesting a potential relationship between historical demography and resilience. In this study, we surveyed genetic variation across single genomes of 240 mammals that compose the Zoonomia alignment to evaluate how historical effective population size (Ne) affects heterozygosity and deleterious genetic load and how these factors may contribute to extinction risk. We find that species with smaller historical Ne carry a proportionally larger burden of deleterious alleles owing to long-term accumulation and fixation of genetic load and have a higher risk of extinction. This suggests that historical demography can inform contemporary resilience. Models that included genomic data were predictive of species' conservation status, suggesting that, in the absence of adequate census or ecological data, genomic information may provide an initial risk assessment.

Relating enhancer genetic variation across mammals to complex phenotypes using machine learning.

Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.

NCBI's Virus Discovery Codeathon: Building "FIVE" -The Federated Index of Viral Experiments API Index.

Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. However, some consequences of previously decentralized (unfederated) data are lack of consensus or comparisons between feature annotations. Unifying or displaying alternative annotations should be a priority both for communities with robust entry representation and for nascent communities with burgeoning data sources. To this end, during this three-day continuation of the Virus Hunting Toolkit codeathon series (VHT-2), a new integrated and federated viral index was elaborated. This Federated Index of Viral Experiments (FIVE) integrates pre-existing and novel functional and taxonomy annotations and virus-host pairings. Variability in the context of viral genomic diversity is often overlooked in virus databases. As a proof-of-concept, FIVE was the first attempt to include viral genome variation for HIV, the most well-studied human pathogen, through viral genome diversity graphs. As per the publication of this manuscript, FIVE is the first implementation of a virus-specific federated index of such scope. FIVE is coded in BigQuery for optimal access of large quantities of data and is publicly accessible. Many projects of database or index federation fail to provide easier alternatives to access or query information. To this end, a Python API query system was developed to enhance the accessibility of FIVE.

RERconverge: an R package for associating evolutionary rates with convergent traits.

MOTIVATION: When different lineages of organisms independently adapt to similar environments, selection often acts repeatedly upon the same genes, leading to signatures of convergent evolutionary rate shifts at these genes. With the increasing availability of genome sequences for organisms displaying a variety of convergent traits, the ability to identify genes with such convergent rate signatures would enable new insights into the molecular basis of these traits. RESULTS: Here we present the R package RERconverge, which tests for association between relative evolutionary rates of genes and the evolution of traits across a phylogeny. RERconverge can perform associations with binary and continuous traits, and it contains tools for visualization and enrichment analyses of association results. AVAILABILITY AND IMPLEMENTATION: RERconverge source code, documentation and a detailed usage walk-through are freely available at https://github.com/nclark-lab/RERconverge. Datasets for mammals, Drosophila and yeast are available at https://bit.ly/2J2QBnj. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Ancient convergent losses of Paraoxonase 1 yield potential risks for modern marine mammals.

Mammals diversified by colonizing drastically different environments, with each transition yielding numerous molecular changes, including losses of protein function. Though not initially deleterious, these losses could subsequently carry deleterious pleiotropic consequences. We have used phylogenetic methods to identify convergent functional losses across independent marine mammal lineages. In one extreme case, Paraoxonase 1 (PON1) accrued lesions in all marine lineages, while remaining intact in all terrestrial mammals. These lesions coincide with PON1 enzymatic activity loss in marine species' blood plasma. This convergent loss is likely explained by parallel shifts in marine ancestors' lipid metabolism and/or bloodstream oxidative environment affecting PON1's role in fatty acid oxidation. PON1 loss also eliminates marine mammals' main defense against neurotoxicity from specific man-made organophosphorus compounds, implying potential risks in modern environments.

Evolutionary history inferred from the de novo assembly of a nonmodel organism, the blue-eyed black lemur.

Lemurs, the living primates most distantly related to humans, demonstrate incredible diversity in behaviour, life history patterns and adaptive traits. Although many lemur species are endangered within their native Madagascar, there is no high-quality genome assembly from this taxon, limiting population and conservation genetic studies. One critically endangered lemur is the blue-eyed black lemur Eulemur flavifrons. This species is fixed for blue irises, a convergent trait that evolved at least four times in primates and was subject to positive selection in humans, where 5' regulatory variation of OCA2 explains most of the brown/blue eye colour differences. We built a de novo genome assembly for E. flavifrons, providing the most complete lemur genome to date, and a high confidence consensus sequence for close sister species E. macaco, the (brown-eyed) black lemur. From diversity and divergence patterns across the genomes, we estimated a recent split time of the two species (160 Kya) and temporal fluctuations in effective population sizes that accord with known environmental changes. By looking for regions of unusually low diversity, we identified potential signals of directional selection in E. flavifrons at MITF, a melanocyte development gene that regulates OCA2 and has previously been associated with variation in human iris colour, as well as at several other genes involved in melanin biosynthesis in mammals. Our study thus illustrates how whole-genome sequencing of a few individuals can illuminate the demographic and selection history of nonmodel species.

Relationship between dual-energy X-ray absorptiometry volumetric assessment and X-ray computed tomography-derived single-slice measurement of visceral fat.

To reduce radiation exposure and cost, visceral adipose tissue (VAT) measurement on X-ray computed tomography (CT) has been limited to a single slice. Recently, the US Food and Drug Administration has approved a dual-energy X-ray absorptiometry (DXA) application validated against CT to measure VAT volume. The purpose of this study was to develop an algorithm to compute single-slice area values on DXA at 2 common landmarks, L2/3 and L4/5, from an automated volumetrically derived measurement of VAT. Volumetric CT and total body DXA were measured in 55 males (age: 21-77 yr; body mass index [BMI]: 21.1-37.9) and 60 females (age: 21-85 yr; BMI: 20.0-39.7). Equations were developed by applying the relationship of CT single-slice area and volume measurements of VAT to the DXA VAT volume measure as well as validating these against the CT single-slice measurements. Correlation coefficients between DXA estimate of single-slice area and CT were 0.94 for L2/3 and 0.96 for L4/5. The mean difference between DXA estimate of single-slice area and CT was 5 cm(2) at L2/3 and 3.8 cm(2) at L4/5. Bland-Altman analysis showed a fairly constant difference across the single-slice range in this study, and the 95% limits of agreement for the 2 methods were -44.6 to +54.6 cm(2) for L2/3 and -47.3 to +54.9 cm(2) for L4/5. In conclusion, a volumetric measurement of VAT by DXA can be used to estimate single-slice measurements at the L2/3 and the L4/5 landmarks.

The convergent evolution of blue iris pigmentation in primates took distinct molecular paths.

How many distinct molecular paths lead to the same phenotype? One approach to this question has been to examine the genetic basis of convergent traits, which likely evolved repeatedly under a shared selective pressure. We investigated the convergent phenotype of blue iris pigmentation, which has arisen independently in four primate lineages: humans, blue-eyed black lemurs, Japanese macaques, and spider monkeys. Characterizing the phenotype across these species, we found that the variation within the blue-eyed subsets of each species occupies strongly overlapping regions of CIE L*a*b* color space. Yet whereas Japanese macaques and humans display continuous variation, the phenotypes of blue-eyed black lemurs and their sister species (whose irises are brown) occupy more clustered subspaces. Variation in an enhancer of OCA2 is primarily responsible for the phenotypic difference between humans with blue and brown irises. In the orthologous region, we found no variant that distinguishes the two lemur species or associates with quantitative phenotypic variation in Japanese macaques. Given the high similarity between the blue iris phenotypes in these species and that in humans, this finding implies that evolution has used different molecular paths to reach the same end.

Abdominal visceral fat measurement using dual-energy X-ray: association with cardiometabolic risk factors.

OBJECTIVE: To examine the association between cardiometabolic risk factors and visceral adipose tissue (VAT) measurements using a dual-energy X-ray absorptiometry (DXA) based approach. DESIGN AND METHODS: An analysis of cross-sectional relationships between DXA VAT measured using CoreScan (GE Healthcare) and cardiometabolic indicators was conducted on a sample of 939 subjects (541 females and 398 males; average age, 56 years; average BMI, 26 kg/m2) who had previously undergone a total body DXA scan as well as measurements of key cardiometabolic risk factors. RESULTS: Sex-specific, age-adjusted multivariable regression analysis showed that for both men and women, DXA VAT was significantly associated with increased odds of hypertension, impaired fasting glucose, metabolic syndrome, and type 2 diabetes (P < 0.001). After additional model adjustment for BMI and waist circumference, the odds ratio (per SD change in VAT) for type 2 diabetes was 2.07 for women and 2.25 for men. Similarly, the odds ratio for metabolic syndrome for women was 3.46 and for men was 1.75. CONCLUSIONS: VAT measured using DXA showed a significant association with cardiometabolic risk factors and disease. These relationships persist after statistical adjustment for age, BMI, and waist circumference. DXA VAT may provide a new accessible option for quantifying VAT-related cardiometabolic risk.

Precision of a new tool to measure visceral adipose tissue (VAT) using dual-energy X-Ray absorptiometry (DXA).

OBJECTIVE: A new tool to quantify visceral adipose tissue (VAT) over the android region of a total body dual-energy x-ray absorptiometry (DXA) scan has recently been reported. The measurement, CoreScan, is currently available on Lunar iDXA densitometers. The purpose of the study was to determine the precision of the CoreScan VAT measurement, which is critical for understanding the utility of this measure in longitudinal trials. DESIGN AND METHODS: VAT precision was characterized in both an anthropomorphic imaging phantom (measured on 10 Lunar iDXA systems) and a clinical population consisting of obese women (n = 32). RESULTS: The intrascanner precision for the VAT phantom across 9 quantities of VAT mass (0-1,800 g) ranged from 28.4 to 38.0 g. The interscanner precision ranged from 24.7 to 38.4 g. There was no statistical dependence on the quantity of VAT for either the inter- or intrascanner precision result (p = 0.670). Combining inter- and intrascanner precision yielded a total phantom precision estimate of 47.6 g for VAT mass, which corresponds to a 4.8% coefficient of variance (CV) for a 1 kg VAT mass. Our clinical population, who completed replicate total body scans with repositioning between scans, showed a precision of 56.8 g on an average VAT mass of 1110.4 g. This corresponds to a 5.1% CV. Hence, the in vivo precision result was similar to the phantom precision result. CONCLUSIONS: The study suggests that CoreScan has a relatively low precision error in both phantoms and obese women and therefore may be a useful addition to clinical trials where interventions are targeted towards changes in visceral adiposity.

Quantification of visceral adipose tissue using lunar dual-energy X-ray absorptiometry in Asian Chinese.

OBJECTIVE: To evaluate the new DXA VAT method on an Asian Chinese population by comparing to a reference method, computed tomography (CT). DESIGN AND METHODS: In total, 145 adult men and women volunteers, representing a wide range of ages (19-83 years) and BMI values (18.5-39.3 kg/m(2) ) were studied with both DXA and CT. RESULTS: The coefficient of determination (r(2) ) for regression of CT on DXA values was 0.947 for females, 0.891 for males and 0.915 combined. The 95% confidence interval for r was 0.940-0.969 for the combined data. The Bland-Altman test showed a VAT bias (CT as standard method) of 143 cm(3) for females and 379 cm(3) for males. Combined, the bias was 262 cm(3) with 95% limits of agreement of -232 to 755 cm(3) . While the current DXA method moderately overestimates the VAT volume for the study subjects, a further analysis suggested that the overestimation could be largely contributed to VAT movement due to breath-holding status. CONCLUSIONS: For Asian Chinese, VAT measured with DXA is highly correlated to VAT measured with CT. Validation of the DXA VAT tool using a reference method (e.g., CT) needs to carefully control the breath-holding protocol.

Visceral adipose tissue quantification using Lunar Prodigy.

A dual-energy X-ray absorptiometry (DXA) application to measure visceral adipose tissue (VAT) in the android region of a total body DXA scan has recently been developed. This new application, CoreScan, has been validated on the Lunar iDXA (GE Healthcare, Madison, WI) densitometer against volumetric computed tomography. The geometric assumptions underlying the CoreScan model are the same on the Prodigy (GE Healthcare, Madison, WI) densitometer. However, differences between the peak X-ray voltage and detector array configurations may lead to differences in VAT quantification. The purpose of this study was to evaluate the agreement of Prodigy and iDXA CoreScan values and to characterize differences in VAT precision between the instruments. Data from volunteers with paired Prodigy and iDXA measurements were used to define empirical adjustments to the VAT algorithm parameters (n=59) and validate performance on Prodigy (n=62). Prodigy VAT measurements were highly correlated to iDXA (r=0.984). The mean of the Prodigy-iDXA VAT volume differences was -13.8cm³ with a 95% confidence interval of -45 to +17cm³. The Bland-Altman 95% limits of agreement for the 2 methods were -252 to +224cm³. Measurement of short-term precision showed that measurement error variance on iDXA was smaller (p<0.01) than Prodigy (coefficient of variance: 7.3% vs 9.8%). Precision results are in agreement with previous reports on the differences between Prodigy and iDXA for body composition measures. Prodigy and iDXA measures of VAT are similar, but the lower precision of the Prodigy may require investigators to target larger changes in VAT.

Revisiting an old riddle: what determines genetic diversity levels within species?

Understanding why some species have more genetic diversity than others is central to the study of ecology and evolution, and carries potentially important implications for conservation biology. Yet not only does this question remain unresolved, it has largely fallen into disregard. With the rapid decrease in sequencing costs, we argue that it is time to revive it.

A multinational study to develop universal standardization of whole-body bone density and composition using GE Healthcare Lunar and Hologic DXA systems.

Dual-energy x-ray absorptiometry (DXA) is used to assess bone mineral density (BMD) and body composition, but measurements vary among instruments from different manufacturers. We sought to develop cross-calibration equations for whole-body bone density and composition derived using GE Healthcare Lunar and Hologic DXA systems. This multinational study recruited 199 adult and pediatric participants from a site in the US (n = 40, ages 6 through 16 years) and one in China (n = 159, ages 5 through 81 years). The mean age of the participants was 44.2 years. Each participant was scanned on both GE Healthcare Lunar and Hologic Discovery or Delphi DXA systems on the same day (US) or within 1 week (China) and all scans were centrally analyzed by a single technologist using GE Healthcare Lunar Encore version 14.0 and Hologic Apex version 3.0. Paired t-tests were used to test the results differences between the systems. Multiple regression and Deming regressions were used to derive the cross-conversion equations between the GE Healthcare Lunar and Hologic whole-body scans. Bone and soft tissue measures were highly correlated between the GE Healthcare Lunar and Hologic and systems, with r ranging from 0.96 percent fat [PFAT] to 0.98 (BMC). Significant differences were found between the two systems, with average absolute differences for PFAT, BMC, and BMD of 1.4%, 176.8 g and 0.013 g/cm(2) , respectively. After cross-calibration, no significant differences remained between GE Healthcare Lunar measured results and the results converted from Hologic. The equations we derived reduce differences between BMD and body composition as determined by GE Healthcare Lunar and Hologic systems and will facilitate combining study results in clinical or epidemiological studies.

Evaluating the evidence for transmission distortion in human pedigrees.

Children of a heterozygous parent are expected to carry either allele with equal probability. Exceptions can occur, however, due to meiotic drive, competition among gametes, or viability selection, which we collectively term "transmission distortion" (TD). Although there are several well-characterized examples of these phenomena, their existence in humans remains unknown. We therefore performed a genome-wide scan for TD by applying the transmission disequilibrium test (TDT) genome-wide to three large sets of human pedigrees of European descent: the Framingham Heart Study (FHS), a founder population of European origin (HUTT), and a subset of the Autism Genetic Resource Exchange (AGRE). Genotyping error is an important confounder in this type of analysis. In FHS and HUTT, despite extensive quality control, we did not find sufficient evidence to exclude genotyping error in the strongest signals. In AGRE, however, many signals extended across multiple SNPs, a pattern highly unlikely to arise from genotyping error. We identified several candidate regions in this data set, notably a locus in 10q26.13 displaying a genome-wide significant TDT in combined female and male transmissions and a signature of recent positive selection, as well as a paternal TD signal in 6p21.1, the same region in which a significant TD signal was previously observed in 30 European males. Neither region replicated in FHS, however, and the paternal signal was not visible in sperm competition assays or as allelic imbalance in sperm. In maternal transmissions, we detected no strong signals near centromeres or telomeres, the regions predicted to be most susceptible to female-specific meiotic drive, but we found a significant enrichment of top signals among genes involved in cell junctions. These results illustrate both the potential benefits and the challenges of using the TDT to study transmission distortion and provide candidates for investigation in future studies.