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PubMed2005

Evaluating social influences on food-processing behavior in white-faced capuchins (Cebus capucinus).

Interpopulation variability in patterns of food processing, similar to what is described as "traditional" or "cultural" variation in chimpanzees (Pan troglodytes) and orangutans (Pongo pygmaeus), was identified in white-faced capuchins (Cebus capucinus). However, recent comparisons of food processing in capuchins were conducted only at the population level, with relatively little attention given to variability among groups, age/sex classes, or individuals. This paper examines variability in the processing of specific food types within the context of various social networks (i.e., patterns of association, rank, and kinship) among free-ranging Cebus capucinus at Santa Rosa National Park in Costa Rica. We collected data on two groups of white-faced capuchins in 2001, identifying rates of "food interest" for each individual, as well as forms of processing for specific food types. Juveniles exhibited the most interest in the food-processing behavior of other group members, and food interest was directed most frequently toward adult females. We identified distinctive processing techniques for several food items (Luehea candida pods, Sloanea terniflora fruits, and caterpillars) that facilitated comparisons among individuals within groups. Food-processing techniques for Sloanea fruit and caterpillars appeared to vary independently of the social networks examined in this study. However, we found evidence that variation in Luehea candida processing is to some degree linked to both patterns of association and social rank. The potential influence of these variables on observed food processing patterns warrants further scrutiny.

Animals↗
PubMed2025

Molecular mechanisms and breeding strategies for heat tolerance in vegetable crops under global warming.

Extreme heat driven by climate change poses a catastrophic threat to global vegetable production, undermining nutritional security because of the heightened physiological sensitivity and succulent tissues of these crops. This review synthesizes the multistage impacts of heat stress across critical developmental phases-from germination to reproduction-emphasizing morphological impairments (such as leaf wilting and floral abortion) and physiological disruptions (including photosynthetic inhibition and oxidative damage). We systematically dissect thermotolerance mechanisms in vegetables, highlighting transcriptional reprogramming by HSFs, WRKY, and NAC transcription factors; chaperone-mediated proteostasis via HSPs; epigenetic remodeling; Ca2+-ROS signaling pathways; and the role of phase separation dynamics. Importantly, we propose six strategic pathways to develop heat-resilient vegetables: harnessing natural variation through pan-genome-driven allele mining; employing biotechnological interventions such as CRISPR-mediated editing and synthetic promoters; engineering multistress tolerance by targeting conserved 'core response' pathways; exploiting epigenetic memory to achieve transgenerational resilience; optimizing source-sink dynamics with ''Climate-Responsive Carbon Optimization; and applying plant growth regulators and nanotechnology to enhance thermotolerance. Together, these strategies chart a clear roadmap for climate-smart vegetable breeding and call for interdisciplinary collaboration to translate molecular discoveries into practical breeding approaches for sustainable food systems under escalating thermal extremes.

Journal Article↗
PubMed2001

The salience of pan-national Hispanic and Asian identities in U.S. marriage markets.

In this paper I test whether "Hispanic" and "Asian" identities are salient in the U.S. marriage market. That is, I determine whether the different Asian and Hispanic national groups intermarry often enough to suggest that Asian and Hispanic pan-national identities are important. Analysis of census data from 1980 and 1990 suggests that both Hispanic and Asian pan-national identities are significant forces. Variations in the strength of pan-national Hispanic and Asian associations by region, education, and nativity are discussed.

Asian↗
PubMed2025

PlantPan: A comprehensive multi-species plant pan-genome database.

The pan-genome represents the complete genomic diversity of specific species, serving as a valuable resource for studying species evolution, crop domestication, and guiding crop breeding and improvement. While there are several single-species-specific plant pan-genome databases, the availability of multi-species pan-genome databases is limited. Additionally, variations in methods and data types used for plant pan-genome analysis across different databases hinder the comparison and integration of pan-genome information from various projects at multi-species or single-species levels. To tackle this challenge, we introduce PlantPan, a comprehensive database housing the results of pan-genome analysis for 195 genomes from 11 plant species. PlantPan aims to provide extensive information, including gene-centric and sequence-centric pan-genome information, graph-based pan-genome, pan-genome openness profiles, gene functions and its variation characteristics, homologous genes, and gene clusters across different species. Statistically, PlantPan incorporates 9 163 011 genes, 694 191 gene clusters, 526 973 370 genome variations, and 1 616 089 non-redundant genome variation groups at the species level, 33 455,098 genome synteny, and 177 827 non-redundant genome synteny groups at the species level. Regarding functional genes, PlantPan contains 5 222 720 genes related to transcription factors, 395 247 literature-reported resistance genes, 455 748 predicted microbial/disease resistance genes, and 1 612 112 genes related to molecular pathways. In summary, PlantPan is a vital platform for advancing the application of pan-genomes in molecular breeding for crops and evolutionary research for plants.

Genome, Plant↗
PubMed1980

[Electrophoretic polymorphism of seric and erythrocytes proteins and enzymes in the chimpanzee (Pan troglodytes) (author's transl)].

The electrophoretic mobilities of serum enzymes and other proteins were investigated at 35 loci in 25 unrelated individuals of the chimpanzee Pan troglodytes. In this population the mean average of individual polymorphism is P = 0.181, and the average level of heterozygoty H = 0.022. The same pattern of individual variability is found in Pan troglodytes and Homo sapiens.

Animals↗
PubMed2026

Pan-genomics and multi-omics for deciphering genetic variation and accelerating genetic improvement in ruminant livestock.

Livestock reference genomes have transformed the discovery of variants associated with production, reproduction, health, and environmental adaptation. Nevertheless, a single linear reference represents only one mosaic haplotype and incompletely captures sequence diversity within a species, particularly structural variants, copy-number changes, repeat-rich regions, and breed-specific sequences. Pangenomes address this limitation by integrating multiple high-quality assemblies or population-scale variants into a unified sequence or graph representation. Concurrently, multi-omics approaches connect genomic variation with transcriptomic, epigenomic, manuscriptproteomic, metabolomic, and microbiome responses, thereby improving biological interpretation of genotype-phenotype relationships. This review synthesizes recent progress in livestock pangenomics and multi-omics, with emphasis on cattle, goats, sheep, water buffalo, and chickens. It describes advances in long-read and haplotype-resolved sequencing, graph construction, structural-variant discovery and genotyping, functional annotation, and integrative analysis. Recent pangenome studies have uncovered substantial non-reference sequence, reduced reference bias, identified breed- and population-specific structural variants, and resolved candidate variants underlying pigmentation, body size, tail morphology, cashmere production, altitude adaptation, and other economically relevant traits. However, translation into routine breeding remains constrained by uneven population representation, inconsistent structural-variant definitions, limited functional annotation, computational demands, and insufficient validation across environments. Future progress will depend on diverse near-complete assemblies, graph-aware imputation and genomic prediction, long-read transcriptomics, single-cell and spatial omics, rigorous causal validation, and open, interoperable resources. Together, these developments can support more accurate, resilient, and biologically informed livestock improvement. Importantly, current dairy-cattle evidence indicates that pangenome-derived structural variants can substantially improve variant discovery and functional interpretation while yielding only marginal average gains in routine genomic prediction, favoring targeted augmentation rather than wholesale replacement of established SNP-based evaluations.

Animals↗
PubMed2004

Evidence for a complex demographic history of chimpanzees.

To characterize patterns of genomic variation in central chimpanzees (Pan troglodytes troglodytes) and gain insight into their evolution, we sequenced nine unlinked, intergenic regions, representing a total of 19,000 base pairs, in 14 individuals. When these DNA sequences are compared with homologous sequences previously collected in humans and in western chimpanzees (Pan troglodytes verus), nucleotide diversity is higher in central chimpanzees than in western chimpanzees or in humans. Consistent with a larger effective population size of central chimpanzees, levels of linkage disequilibrium are lower than in humans. Patterns of linkage disequilibrium further suggest that homologous gene conversion may be an important contributor to genetic exchange at short distances, in agreement with a previous study of the same DNA sequences in humans. In central chimpanzees, but not in western chimpanzees, the allele frequency spectrum is significantly skewed towards rare alleles, pointing to population size changes or fine-scale population structure. Strikingly, the extent of genetic differentiation between western and central chimpanzees is much stronger than what is seen between human populations. This suggests that careful attention should be paid to geographic sampling in studies of chimpanzee genetic variation.

Alleles↗
PubMed2004

Interobserver error involved in independent attempts to measure cusp base areas of Pan M1s.

Cusp base areas measured from digitized images increase the amount of detailed quantitative information one can collect from post-canine crown morphology. Although this method is gaining wide usage for taxonomic analyses of extant and extinct hominoids, the techniques for digitizing images and taking measurements differ between researchers. The aim of this study was to investigate interobserver error in order to help assess the reliability of cusp base area measurement within extant and extinct hominoid taxa. Two of the authors measured individual cusp base areas and total cusp base area of 23 maxillary first molars (M(1)) of Pan. From these, relative cusp base areas were calculated. No statistically significant interobserver differences were found for either absolute or relative cusp base areas. On average the hypocone and paracone showed the least interobserver error (< 1%) whereas the protocone and metacone showed the most (2.6-4.5%). We suggest that the larger measurement error in the metacone/protocone is due primarily to either weakly defined fissure patterns and/or the presence of accessory occlusal features. Overall, levels of interobserver error are similar to those found for intraobserver error. The results of our study suggest that if certain prescribed standards are employed then cusp and crown base areas measured by different individuals can be pooled into a single database.

Animals↗
PubMed1999

Distribution of corticotropin-releasing hormone promoter polymorphism in different ethnic groups: evidence for natural selection in human populations.

The regulatory region of the corticotropin-releasing hormone (CRH) is highly conserved across species and plays a crucial role in the response of the organism to stress. Release of CRH initiates a cascade of events leading to the release of cortisol and the regulation of inflammatory and immune events. In this report we describe polymorphisms in the 5' regulatory region of the CRH gene in humans. We studied the distribution of CRH alleles in three different African populations, in white UK Caucasoids, and in a Chinese population. In the African and UK populations we found three new polymorphisms which cosegregated, resulting in two alleles, A1 and A2. Gene frequencies for A1 and A2 were extremely divergent between the African and the UK populations. The African A1 frequency ranged from 0.27-0.3, while the UK Caucasoid frequency was 0.9. Compound alleles could be assigned by taking into account the previously described biallelic polymorphism at position 225 in the CRH promoter. The A2B1 compound allele is the commonest in contemporary African human populations (allele frequency range 0. 44-0.61) and was the only allele observed in a population of chimpanzees from Sierra Leone. Wright's F(ST )for the A2B1 allele over the four sampled populations was 0.612, a value exceeded in human populations only by loci which have apparently been subject to natural selection. Taken together, these findings support A2B1 as the ancestral allele and suggest that the CRH genomic region may have been subject to strong disruptive selection throughout human evolution.

Alleles↗
PubMed2001

On the direction and magnitude of radical substituent effects: the role of polar interaction on thermodynamic stabilities of benzylic C-H bonds and related carbon radicals.

The C-H bond dissociation enthalpies (BDEs) of polarized benzylic molecules, i.e., para-substituted phenylacetonitriles (PANs), and the spin variations of the radicals of the general type p-GC6H4CH*-Y were investigated using density functional theory (DFT) calculations. In contrast to the commonly observed S-type substituent effect (see text), the present work shows that there should be three (rather than one) primary patterns (i.e., S, O, and counter-O) for remote G to affect spin and radical stability, depending upon the polarity of the alpha-Y group. Correlation analyses reveal that both the direction and magnitude of spin/radical effects are quantitatively related to the intensity of polar interaction in radical system, as registered by either the calculated group charges of the phenyl ring (C(Ph)) or by the polar constant sigma(+)s (Figures 1-4). A unified platform (Scheme 1) to rationalize the apparent differences of radical substituent effect is proposed.

Journal Article↗
PubMed1990

A simple method for estimating average number of nucleotide substitutions within and between populations from restriction data.

A simple method is proposed for estimating the average number of nucleotide substitutions per site within and between populations for the case where a large number of individuals are examined for many restriction enzymes. This method gives essentially the same results as those obtained by Nei and Li's method but saves a large amount of computer time. The variances of the quantities estimated can be obtained by the jackknife method, and these variances are very similar to those obtained by Nei and Jin's more sophisticated method. A similar method can also be applied to DNA sequence data.

Analysis of Variance↗
PubMed2001

Nitrogen fertilizer rate and crop management effects on nitrate leaching from an agricultural field in central Pennsylvania.

Eighteen pan lysimeters were installed at a depth of 1.2 m in a Hagerstown silt loam soil in a corn field in central Pennsylvania in 1988. In 1995, wick lysimeters were also installed at 1.2 m depth in the same access pits. Treatments have included N fertilizer rates, use of manure, crop rotation (continuous corn, corn-soybean, alfalfa-corn), and tillage (chisel plow-disk, no-till). The leachate data were used to evaluate a number of nitrate leaching models. Some of the highlights of the 11 years of results include the following: 1) growing corn without organic N inputs at the economic optimum N rate (EON) resulted in NO3--N concentrations of 15 to 20 mg l(-1) in leachate; 2) use of manure or previous alfalfa crop as partial source of N also resulted in 15 to 20 mg l(-1) of NO3--N in leachate below corn at EON; 3) NO3--N concentration in leachate below alfalfa was approximately 4 mg l(-1); 4) NO3--N concentration in leachate below soybeans following corn was influenced by fertilizer N rate applied to corn; 5) the mass of NO3--N leached below corn at the EON rate averaged 90 kg N ha(-1) (approx. 40% of fertilizer N applied at EON); 6) wick lysimeters collected approximately 100% of leachate vs. 40-50% collected by pan lysimeters. Coefficients of variation of the collected leachate volumes for both lysimeter types were similar; 7) tillage did not markedly affect nitrate leaching losses; 8) tested leaching models could accurately predict leachate volumes and could be calibrated to match nitrate leaching losses in calibration years, but only one model (SOILN) accurately predicted nitrate leaching losses in the majority of validation treatment years. Apparent problems with tested models: there was difficulty estimating sizes of organic N pools and their transformation rates, and the models either did not include a macropore flow component or did not handle macropore flow well.

Agriculture↗
PubMed2025

An allelic resolution gene atlas for tetraploid potato provides insights into tuberization and stress resilience.

Tubers are modified underground stems that enable asexual, clonal reproduction and serve as a mechanism for overwintering and avoidance of herbivory. Tubers are wide-spread across angiosperms with some species such as Solanum tuberosum L. (potato) serving as a vital crop for human consumption. Genes responsible for tuber initiation and disease resistance have been characterized in potato including StSP6A, a homolog of Flowering Time, that functions as tuberigen, the equivalent of florigen. To elucidate additional molecular and genetic mechanisms underlying potato biology including tuber initiation, tuber development, and stress responses, we generated a developmental and abiotic/biotic-stress gene expression atlas from 34 tissues and treatments of Atlantic, a tetraploid cultivar. Using the haplotype-phased tetraploid Atlantic genome assembly and expression abundances of 129,218 genes, we constructed gene coexpression modules that represent networks associated with distinct developmental stages as well as stress responses. Functional annotations were given to modules and used to identify genes involved in tuberization and stress resilience. Structural variation from a pan-genomic analysis across four cultivated potato genome assemblies as well as domestication and wild introgression data allowed for deeper insights into the modules to identify key genes involved in tuberization and stress responses. This study underscores the importance of transcriptional regulation in tuberization and provides a comprehensive framework for future research on potato development and improvement.

Journal Article↗
PubMed2025

An allelic resolution gene atlas for tetraploid potato provides insights into tuberization and stress resilience.

Tubers are modified underground stems that enable asexual, clonal reproduction and serve as a mechanism for overwintering and avoidance of herbivory. Potato (Solanum tuberosum L.) is cultivated for its tubers, which serve as a major crop. Genes responsible for tuber initiation and disease resistance have been characterized in potato including StSP6A, a homolog of flowering time, that functions as a tuberigen, the equivalent of a florigen. To elucidate additional molecular and genetic mechanisms underlying potato biology including tuber initiation, tuber development, and stress responses, we generated a developmental and abiotic/biotic-stress gene expression atlas from 34 tissues and treatments of the tetraploid potato cultivar, Atlantic. Using the haplotype-phased tetraploid Atlantic genome assembly and expression abundances of 129&#x2009;218 genes, we constructed gene coexpression modules that represent networks associated with distinct developmental stages as well as stress responses. Functional annotations were given to modules and used to identify genes involved in tuberization and stress resilience. Structural variation from a pan-genomic analysis across four cultivated potato genome assemblies as well as domestication and wild introgression data allowed for deeper insights into the modules to identify key genes involved in tuberization and stress responses. This study underscores the importance of transcriptional regulation in tuberization and provides a comprehensive framework for future research on potato development and improvement.

Solanum tuberosum↗
PubMed2006

Gene losses during human origins.

Pseudogenization is a widespread phenomenon in genome evolution, and it has been proposed to serve as an engine of evolutionary change, especially during human origins (the "less-is-more" hypothesis). However, there has been no comprehensive analysis of human-specific pseudogenes. Furthermore, it is unclear whether pseudogenization itself can be selectively favored and thus play an active role in human evolution. Here we conduct a comparative genomic analysis and a literature survey to identify 80 nonprocessed pseudogenes that were inactivated in the human lineage after its separation from the chimpanzee lineage. Many functions are involved among these genes, with chemoreception and immune response being outstandingly overrepresented, suggesting potential species-specific features in these aspects of human physiology. To explore the possibility of adaptive pseudogenization, we focus on CASPASE12, a cysteinyl aspartate proteinase participating in inflammatory and innate immune response to endotoxins. We provide population genetic evidence that the nearly complete fixation of a null allele at CASPASE12 has been driven by positive selection, probably because the null allele confers protection from severe sepsis. We estimate that the selective advantage of the null allele is about 0.9% and the pseudogenization started shortly before the out-of-Africa migration of modern humans. Interestingly, two other genes related to sepsis were also pseudogenized in humans, possibly by selection. These adaptive gene losses might have occurred because of changes in our environment or genetic background that altered the threat from or response to sepsis. The identification and analysis of human-specific pseudogenes open the door for understanding the roles of gene losses in human origins, and the demonstration that gene loss itself can be adaptive supports and extends the "less-is-more" hypothesis.

Animals↗
PubMed1977

[Anatomical variations and taxonomic relatedness in Hominoidea].

31 anatomical variations were examined in 125 Pan paniscus and 96 Gorilla gorilla beringei skulls. Comparisons with published data of Hominoidea show that differences in their frequencies are proportional and parallel to taxonomic relationships on the subspecific, specific and generic level.

Animals↗