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A comparison of phenotypic variation and covariation patterns and the role of phylogeny, ecology, and ontogeny during cranial evolution of new world monkeys.

Similarity of genetic and phenotypic variation patterns among populations is important for making quantitative inferences about past evolutionary forces acting to differentiate populations and for evaluating the evolution of relationships among traits in response to new functional and developmental relationships. Here, phenotypic co variance and correlation structure is compared among Platyrrhine Neotropical primates. Comparisons range from among species within a genus to the superfamily level. Matrix correlation followed by Mantel's test and vector correlation among responses to random natural selection vectors (random skewers) were used to compare correlation and variance/covariance matrices of 39 skull traits. Sampling errors involved in matrix estimates were taken into account in comparisons using matrix repeatability to set upper limits for each pairwise comparison. Results indicate that covariance structure is not strictly constant but that the amount of variance pattern divergence observed among taxa is generally low and not associated with taxonomic distance. Specific instances of divergence are identified. There is no correlation between the amount of divergence in covariance patterns among the 16 genera and their phylogenetic distance derived from a conjoint analysis of four already published nuclear gene datasets. In contrast, there is a significant correlation between phylogenetic distance and morphological distance (Mahalanobis distance among genus centroids). This result indicates that while the phenotypic means were evolving during the last 30 millions years of New World monkey evolution, phenotypic covariance structures of Neotropical primate skulls have remained relatively consistent. Neotropical primates can be divided into four major groups based on their feeding habits (fruit-leaves, seed-fruits, insect-fruits, and gum-insect-fruits). Differences in phenotypic covariance structure are correlated with differences in feeding habits, indicating that to some extent changes in interrelationships among skull traits are associated with changes in feeding habits. Finally, common patterns and levels of morphological integration are found among Platyrrhine primates, suggesting that functional/developmental integration could be one major factor keeping covariance structure relatively stable during evolutionary diversification of South American monkeys.

Animals↗

The rate and pattern of cladogenesis in microbes.

Theories of macroevolution rarely have been extended to include microbes; however, because microbes represent the most ancient and diverse assemblage of organismal diversity, such oversight limits our understanding of evolutionary history. Our analysis of phylogenetic trees for microbes suggests that macroevolution may differ between prokaryotes and both micro- and macroeukaryotes (mainly plants and animals). Phylogenetic trees inferred for prokaryotes and some microbial eukaryotes conformed to expectations assuming a constant rate of cladogenesis over time and among lineages: nevertheless, microbial eukaryote trees exhibited more variation in rates of cladogenesis than prokaryote trees. We hypothesize that the contrast of macroevolutionary dynamics between prokaryotes and many eukaryotes is due, at least in part, to differences in the prevalence of lateral gene transfer (LGT) between the two groups. Inheritance is predominantly, if not wholly, vertical within eukaryotes, a feature that allows for the emergence and maintenance of heritable variation among lineages. By contrast, frequent LGT in prokaryotes may ameliorate heritable variation in rate of cladogenesis resulting from the emergence of key innovations; thus, the inferred difference in macroevolution might reflect exclusivity of key innovations in eukaryotes and their promiscuous nature in prokaryotes.

Archaea↗

Matching genomic evidence to claims about Mycobacterium avium subsp. paratuberculosis: Host association, host adaptation, mechanism, and virulence.

Whole-genome sequencing (WGS) permits high-resolution comparison of Mycobacterium avium subsp. paratuberculosis (MAP) isolates and pangenome analysis. Combined with animal-movement data, WGS can support transmission inference, but resolution alone does not establish the biological meaning of genomic variation. This focused narrative review applies a two-dimensional framework to purposively selected MAP studies, separating claim targets from support profiles. Claim targets include lineage identity, host-source or lineage characterization, host association, transmission, candidate genomic features, measured bacterial or host-cell phenotypes, natural-host infection fitness, disease or damage, shedding, and control outcomes. Depending on the claim, evidence operations may include characterization, context-aware comparative inference, direct endpoint ascertainment, and controlled feature perturbation; these are non-ordinal and may co-occur. On-target attribution, independent replication, and transportability are reported separately. The claim, not the study, is the unit of assessment. Typing markers support isolate or lineage discrimination, whereas phylogenomics supports evolutionary inference; neither alone establishes host adaptation. Pangenome comparisons and microbial genome-wide association studies nominate candidate features rather than establish adaptation. Cell-envelope and iron-associated studies support specified biochemical, transcriptional, or physiological phenotypes under defined conditions, while macrophage and calf models support only the endpoints measured. Annotated sequence variation alone nominates pathogenicity hypotheses. Across the illustrative studies selected here, MAP genomics most directly supported lineage classification, candidate discovery, measured bacterial phenotypes, bounded transmission inference, and natural-host infection-fitness claims. Claims about adaptation, mechanism, virulence, or control require endpoints and comparisons matched to the stated claim and model; feature-specific causal claims additionally require evidence linking the bacterial feature to the measured endpoint.

Claim boundaries↗

Variability of cost-effectiveness estimates for pharmaceuticals in Western Europe: lessons for inferring generalizability.

OBJECTIVES: It has long been suggested that, whereas the results of clinical studies of pharmaceuticals are generalizable from one jurisdiction to another, the results of economic evaluations are location dependent. There has been, however, little study of the causes of variation, whether differences in study results among countries are systematic, or whether they are important for decision making. METHODS: A literature search was conducted to identify economic evaluations of pharmaceuticals conducted in two or more European countries. The studies identified were then classified by methodological type and analyzed to assess their level of variability and to identify the main causes of variation. Assessments were also made of the extent to which differences in study results among countries were systematic and whether they would lead to a different decision, assuming a range of values of the threshold willingness-to-pay for a life-year or quality-adjusted life-year (QALY). RESULTS: In total 46 intercountry drug comparisons were identified, 29 in multicountry studies and 17 in comparable single country studies that were considered to be sufficiently similar in terms of methodology. The type of study (i.e., trial-based or modeling study) had some impact on variability, but the most important factor was the extent of variation across countries in effectiveness, resource use or unit costs, allowed by the researcher's chosen methodology. There were few systematic differences in study results among countries, so a decision maker in country B, on seeing a recent economic evaluation of a new drug in country A, would have little basis on which to predict whether the drug, if evaluated, would be more or less cost-effective in his or her country. Given the extent of variation in cost-effectiveness estimates among countries, the importance of this for decision making depends on decision makers' thresholds in willingness-to-pay for a QALY or life-year. If a cost-effectiveness threshold (i.e., willingness-to-pay) for a life-year or QALY of dollar 50,000 were assumed, the same conclusion regarding cost-effectiveness would be reached in most cases. CONCLUSION: This review shows that cost-effectiveness results for pharmaceuticals vary from country to country in Western Europe and that these variations are not systematic. In addition, constraints imposed by analysts may reduce apparent variability in the estimates. The lessons for inferring generalizability are not straightforward, although the implications of variation for decision making depend critically on the cost-effectiveness thresholds applying in Western Europe.

Clinical Trials as Topic↗

Analysis of infraspecific variation among five strains of Eimeria maxima from North America.

Two laboratory strains from the eastern shore of Maryland 15 years ago and from an Ontario broiler house 23 years ago and three recent field strains of Eimeria maxima (isolated in Maryland, North Carolina and Florida) were examined for phenotypic and genotypic variation using protein profiles, random amplified polymorphic DNA-PCR analysis and DNA sequences obtained from the internal transcribed spacer regions of the rRNA genes. Staining profiles obtained by one-dimensional SDS-PAGE of sporozoite proteins were identical in all five strains. Using random amplified polymorphic DNA-PCR analysis with high %G-C content decamers as primers, we were able to confirm that the five strains are all E. maxima, but were unable to discern any relationships among them because of the limited number of shared polymorphisms identified. In contrast, cloning and sequencing of the internal transcribed spacer-1, 5.8S rDNA and internal transcribed spacer-2 regions of the rRNA genes provided sufficient sequence information to infer phylogenetic relationships among the strains. Almost all of the infraspecific variation was located in the internal transcribed spacer regions. Only two base changes were identified within the 5.8S rRNA gene. Evolutionary relationships among the strains inferred using parsimony analysis of the aligned internal transcribed spacer sequences were well supported, but the hypothesised relationships did not correlate well with the demonstrated immunological cross-reactivities of these strains.

Animals↗

Patterns of nucleotide variation in homoeologous regulatory genes in the allotetraploid Hawaiian silversword alliance (Asteraceae).

Genome-wide duplication (polyploidization) is prevalent in a large number of eukaryotic organisms and is particularly widespread in flowering plants. Polyploid species appear to vary from their diploid progenitors in a variety of ecologically important traits, suggesting that genome duplications provide a mechanism for ecological diversification. Studies of nucleotide variation at duplicate genes that arise via polyploidization allow us to infer the evolutionary forces that act on these polyploid loci. In an effort to examine the evolutionary dynamics of homoeologous loci, molecular population genetic analyses were undertaken for duplicate regulatory genes in the allopolyploid Hawaiian silversword alliance, a premier example of adaptive radiation. The levels and patterns of nucleotide variation for the floral homeotic genes ASAPETALA1 (ASAP1) and ASAPETALA3/TM6 (ASAP3/TM6) were studied in two species representing different lineages within the Hawaiian silversword alliance: Argyroxiphium sandwicense ssp. macrocephalum and Dubautia ciliolata ssp. glutinosa. Homoeologueous copies of ASAP1 and ASAP3/TM6 show differing levels and patterns of nucleotide polymorphism. Duplicate ASAP1 copies have similar levels of nucleotide diversity and haplotype structure in both species; by contrast, duplicate ASAP3/TM6 genes display different levels and patterns of variation in D. ciliolata ssp. glutinosa. Additionally, D. ciliolata ssp. glutinosa appears to be segregating for a moderate frequency null allele in one ASAP3/TM6 homoeologue. These results suggest that differing evolutionary forces can affect duplicate loci arising from allopolyploidization.

Asteraceae↗

Effect of mobility on femur midshaft external shape and robusticity.

This study investigates differences in femur midshaft shape, robusticity, and sexual dimorphism derived from external measurements between a broad range of prehistoric and historic North American populations with different subsistence strategies and inferred levels of mobility. The sample was divided into six groups to test whether observed femur midshaft variables follow the patterns predicted based on archaeologically and historically determined subsistence and mobility data. The results suggest significant variation in femur midshaft shape and robusticity in all populations, and that inferred mobility levels do not correspond consistently with femur midshaft structure in either males or females. Results do, however, support the prediction that sexual dimorphism is generally greater in more mobile populations.

Anthropology, Cultural↗

Trends in leptospirosis epidemiology in France. Sixty-six years of passive serological surveillance from 1920 to 2003.

OBJECTIVES: The incidence of leptospirosis, a worldwide zoonosis, has significantly decreased in Western Europe during the last decades. Our aim was to analyse all reliable data collected at the Institut Pasteur from 1920 to 2003 to evaluate more precisely the evolution of the incidence of leptospirosis in France. METHODS: The passive surveillance system used as early as 1920 allows the evaluation of leptospirosis incidence. Serological results inferred from the microagglutination procedure were used to evaluate variation in the incidence of the disease and the evolution of the Leptospira serogroups involved in the human disease. RESULTS: No significant variation either in the number of leptospirosis cases or in the incidence of the disease was observed. However, the period of the 1970s was characterized by a rather low incidence. The weather plays a major role by modifying fresh water abundance, rodent populations and human behaviour. However the weather's influence is not the sole factor involved in the incidence rate. No cyclic variation was evident. CONCLUSION: Although France has the highest incidence of leptospirosis in Europe, the analysis of serological data collected over 66 years has allowed us to conclude that in France, the incidence is slowly decreasing.

Agglutination Tests↗

Transcriptome identification of putative genes involved in protein catabolism and innate immune response in human body louse (Pediculicidae: Pediculus humanus).

Genomics information relating to human body lice is surprisingly scarce, and this has constrained studies of their physiology, immunology and vector biology. To identify novel body louse genes, we used engorged adult lice to generate a cDNA library. Initially, 1152 clones were screened for inserts, edited for removal of vector sequences and base pairs of poor quality, and viewed for splicing variations, gene families and polymorphism. Computational methods identified 506 inferred open reading frames including the first predicted louse defensin. The inferred defensin aligns well with other insect defensins and has highly conserved cysteine residues, as are known for other defensin sequences. Two cysteine and five serine proteinases were categorized according to their inferred catalytic sites. We also discovered seven putative ubiquitin-pathway genes and four iron metabolizing deduced enzymes. Finally, glutathione-S-transferases and cytochrome P450 genes were among the detoxification enzymes found. Results from this first systematic effort to discover human body louse genes should promote further studies in Phthiraptera and lice.

Amino Acid Sequence↗

Diversity, genetic structure and evidence of outcrossing in British populations of the rock fern Adiantum capillus-veneris using microsatellites.

Microsatellites were isolated and a marker system was developed in the fern Adiantum capillus-veneris. Polymorphic markers were then used to study the genetic diversity and structure of populations within the UK and Ireland where this species grows at the northern edge of its range, requiring a specific rock habitat and limited to a few scattered populations. Three dinucleotide loci detected a high level of diversity (23 alleles and 28 multilocus genotypes) across the UK and Ireland, with nearly all variation partitioned among rather than within populations. Of 17 populations represented by multiple samples, all except four were monomorphic. Heterozygosity was detected in three populations, all within Glamorgan, Wales (UK), showing evidence of outcrossing. We make inferences on the factors determining the observed levels and patterns of genetic variation and the possible evolutionary history of the populations.

Alleles↗

Phylogenetic network for European mtDNA.

The sequence in the first hypervariable segment (HVS-I) of the control region has been used as a source of evolutionary information in most phylogenetic analyses of mtDNA. Population genetic inference would benefit from a better understanding of the variation in the mtDNA coding region, but, thus far, complete mtDNA sequences have been rare. We determined the nucleotide sequence in the coding region of mtDNA from 121 Finns, by conformation-sensitive gel electrophoresis and subsequent sequencing and by direct sequencing of the D loop. Furthermore, 71 sequences from our previous reports were included, so that the samples represented all the mtDNA haplogroups present in the Finnish population. We found a total of 297 variable sites in the coding region, which allowed the compilation of unambiguous phylogenetic networks. The D loop harbored 104 variable sites, and, in most cases, these could be localized within the coding-region networks, without discrepancies. Interestingly, many homoplasies were detected in the coding region. Nucleotide variation in the rRNA and tRNA genes was 6%, and that in the third nucleotide positions of structural genes amounted to 22% of that in the HVS-I. The complete networks enabled the relationships between the mtDNA haplogroups to be analyzed. Phylogenetic networks based on the entire coding-region sequence in mtDNA provide a rich source for further population genetic studies, and complete sequences make it easier to differentiate between disease-causing mutations and rare polymorphisms.

Codon↗

HAPLOT: a graphical comparison of haplotype blocks, tagSNP sets and SNP variation for multiple populations.

UNLABELLED: Understanding of human variation relevant to association studies can benefit from population comparison, especially comparing populations in the same geographical region. Variations in linkage disequilibrium patterns, in tagSNP sets, and in SNP heterozygosities among populations can be used to infer the evolutionary pattern. We present here a win32 system based Perl/Tk application for visual comparisons of these variations in different populations. AVAILABILITY: The application package is available at http://info.med.yale.edu/genetics/kkidd/programs.html CONTACT: sheng.gu@yale.edu.

Chromosome Mapping↗

Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophila.

In Escherichia coli, Saccharomyces cerevisiae, and Drosophila melanogaster, codon bias may be maintained by a balance among mutation pressure, genetic drift, and natural selection favoring translationally superior codons. Under such an evolutionary model, silent mutations fall into two fitness categories: preferred mutations that increase codon bias and unpreferred changes in the opposite direction. This prediction can be tested by comparing the frequency spectra of synonymous changes segregating within populations; natural selection will elevate the frequencies of advantageous mutations relative to that of deleterious changes. The frequency distributions of preferred and unpreferred mutations differ in the predicted direction among 99 alleles of two D. pseudoobscura genes and five alleles of eight D. simulans genes. This result confirms the existence of fitness classes of silent mutations. Maximum likelihood estimates suggest that selection intensity at silent sites is, on average, very weak in both D. pseudoobscura and D. simulans (magnitude of NS approximately 1). Inference of evolutionary processes from within-species sequence variation is often hindered by the assumption of a stationary frequency distribution. This assumption can be avoided when identifying the action of selection and tested when estimating selection intensity.

Animals↗

Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies.

Recent studies have revealed that linkage disequilibrium (LD) patterns vary across the human genome with some regions of high LD interspersed by regions of low LD. A small fraction of SNPs (tag SNPs) is sufficient to capture most of the haplotype structure of the human genome. In this paper, we develop a method to partition haplotypes into blocks and to identify tag SNPs based on genotype data by combining a dynamic programming algorithm for haplotype block partitioning and tag SNP selection based on haplotype data with a variation of the expectation maximization (EM) algorithm for haplotype inference. We assess the effects of using either haplotype or genotype data in haplotype block identification and tag SNP selection as a function of several factors, including sample size, density or number of SNPs studied, allele frequencies, fraction of missing data, and genotyping error rate, using extensive simulations. We find that a modest number of haplotype or genotype samples will result in consistent block partitions and tag SNP selection. The power of association studies based on tag SNPs using genotype data is similar to that using haplotype data.

Algorithms↗

A Deep Model Framework for Morphological Trait Imputation Across Taxonomic Groups.

Incomplete morphological trait data pose major hurdles for trait-based analyses, particularly when missing values, multicollinearity, and sparse sampling constrain inference. These issues limit our ability to quantify trait variation and explore broad patterns of functional differentiation across taxa. Here, we introduce FS-DeepRBFNet, which overcomes these pitfalls through integrating correlation-based feature selection with a dual-layer adaptive radial basis function (RBF) network. This end-to-end approach effectively reduces noise and captures both linear allometric trends and nonlinear morphological relationships. We tested the framework on a large species-level morphological trait dataset of Chinese birds and further validated its cross-taxon transferability using the Amphibian Database (Caudata). FS-DeepRBFNet consistently outperformed conventional methods such as KNN, Random Forest, and XGBoost, demonstrating superior predictive accuracy across multiple traits. Beyond improvements, the model revealed biologically interpretable trait associations and stable cross-taxon generalization. These results demonstrate that FS-DeepRBFNet provides a robust and biologically grounded solution for morphological trait prediction, enabling reliable imputation for comparative phylogenetics, functional ecology, and biodiversity forecasting in data-limited situations.

cross‐taxon transferability↗

Historic cycles of fragmentation and expansion in Parnassius smintheus (papilionidae) inferred using mitochondrial DNA.

Climate oscillations of the Quaternary drove the repeated expansion and contraction of ecosystems. Alpine organisms were probably isolated in sky island refugia during warm interglacials, such as now, and expanded their range by migrating down-slope during glacial periods. We used population genetic and phylogenetic approaches to infer how paleoclimatic events influenced the distribution of genetic variation in the predominantly alpine butterfly Parnassius smintheus. We sequenced a 789 bp region of cytochrome oxidase I for 385 individuals from 20 locations throughout the Rocky Mountains, ranging from southern Colorado to northern Montana. Analyses revealed at lease two centers of diversity in the northern and southern Rocky Mountains and strong population structure. Nested clade analysis suggested that the species experienced repeated cycles of population expansion and fragmentation. The estimated ages of these events, assuming a molecular clock, corresponded with paleoclimatic data on habitat expansion and contraction over the past 400,000 years. We propose that alpine butterflies persisted in an archipelago of isolated sky islands during interglacials and that populations expanded and became more connected during cold glacial periods. An archipelago model implies that the effects of genetic drift and selection varied among populations, depending on their latitude, area, and local environment. Alpine organisms are sensitive indicators of climate change and their history can be used to predict how high-elevation ecosystems might respond to further climate warming.

Animals↗

Pathophysiological topography of acute ischemia by combined diffusion-weighted and perfusion MRI.

BACKGROUND AND PURPOSE: Combined echoplanar MRI diffusion-weighted imaging (DWI), perfusion imaging (PI), and magnetic resonance angiography (MRA) can be used to visualize acute brain ischemia and predict lesion evolution and functional outcome. The appearance of a larger lesion by PI than by DWI quantitatively defines a mismatch of potential clinical importance. Qualitative lesion variations exist in the topographic concordance of this mismatch. We examined both the topographic heterogeneity and relative frequency of mismatched patterns in acute stroke using these MRI techniques. METHODS: Acute DWI, PI, and MRA studies of 34 prospectively recruited patients with supratentorial ischemic lesions scanned within 24 hours of stroke onset (range 2.5 to 23.3 hours, 12 patients <6 hours) were analyzed. RESULTS: Ischemic lesions were predominantly in the middle cerebral artery (MCA) territory (94%), with DWI lesions most commonly affecting the insular region. Mismatched patterns with PI lesion larger than DWI lesion occurred in 21 patients (62% overall), in all 4 patients imaged within 3 hours, and in 44% of patients imaged after 18 hours. A patient with a large PI but no DWI lesion and severe clinical deficit at 2.5 hours after stroke onset recovered completely. Regional variations in DWI and PI lesion loci were found, inferring site of proximal MCA occlusion, embolic pathogenesis, and regional arterial reperfusion. CONCLUSIONS: Analysis of the topographic concordance of PI and DWI lesions in acute stroke reveals regional PI lesions without concomitant DWI lesions, which do not necessarily progress to infarction but may suggest stroke pathogenesis and site of current arterial occlusion. Location of DWI lesions may suggest an earlier site of arterial occlusion and regions of maximal perfusion deficit.

Aged↗

The absence of mitochondrial DNA diversity among common laboratory inbred mouse strains.

Mitochondrial DNA (mtDNA), which exhibits a maternal inheritance and a high rate of evolution, has been widely used as a genetic marker when analyzing maternal lineage and inferring phylogenetic relationships among species. In this study, mtDNA variations among four classical (BALB/c, C3H, C57BL/6J and DBA/2) and three Chinese (TA2, 615 and T739) inbred strains of laboratory mice were analyzed by PCR-RFLP (polymerase chain reaction coupled with restriction fragment length polymorphism) and PCR-SSCP (polymerase chain reaction coupled with single-stranded conformational polymorphism) techniques. PCR-RFLP analyses on 46 restriction sites revealed no variations in mtDNA D-loop (displacement loop), tRNA(Met+Glu+Ile) and ND3 (NADH dehydrogenase subunit 3) gene fragments in these strains. Furthermore, PCR-SSCP analyses demonstrated no variations in D-loop 5' and 3' end fragments in them. In view of enormous polymorphisms in mtDNA among mice and dramatic differences in nuclear genomes of these seven strains, our findings were surprising. However, in light of the maternal inheritance of mtDNA, the results indicate that the three Chinese strains, including TA2, T739 and 615, and the four classical strains, share a common maternal lineage.

Animals↗