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PubMed1991

What is resource partitioning?

The concept of resource partitioning, as originally developed, relates to evolutionary change in species in response to selection pressures generated by interspecific competition. More recently it has taken on another meaning, one that is not defined in terms of evolutionary function, and which refers simply to differences in resource use between species regardless of the origins of the differences. Such a shift in usage has several drawbacks for ecological theory, which are discussed. Of most practical significance to ecologists is the inappropriate justification conferred on the continued use of a category that contains characters that are not equivalents. Ecologists are therefore frequently in the position of explaining the presence of species in an area by reference to the by-products of their adaptive evolution.

Animals↗

PubMed1989

The inheritance of acquired epigenetic variations.

There is evidence that the functional history of a gene in one generation can influence its expression in the next. In somatic cells, changes in gene activity are frequently associated with changes in the pattern of methylation of the cytosines in DNA; these methylation patterns are stably inherited. Recent work suggests that information about patterns of methylation and other epigenetic states can also be transmitted from parents to offspring. This evidence is the basis of a model for the inheritance of acquired epigenetic variations. According to the model, an environmental stimulus can induce heritable chromatin modifications which are very specific and predictable, and might result in an adaptive response to the stimulus. This type of response probably has most significance for adaptive evolution in organisms such as fungi and plants, which lack distinct segregation of the soma and germ line. However, in all organisms, the accumulation of specific and random chromatin modifications in the germ line may be important in speciation, because these modifications could lead to reproductive isolation between populations. Heritable chromatin variations may also alter the frequency and distribution of classical mutations and meiotic recombination. Therefore, inherited epigenetic changes in the structure of chromatin can influence neo-Darwinian evolution as well as cause a type of "Lamarckian" inheritance.

Base Sequence↗

PubMed1990

Molecular and phenotypic variation in the achaete-scute region of Drosophila melanogaster.

Variation in quantitative characters underlies much adaptive evolution and provides the basis for selective improvement of domestic species, yet the genetic nature of quantitative variation is poorly understood. Many loci affecting quantitative traits have been identified by the segregation of mutant alleles with major qualitative effects. These alleles may represent an extreme of a continuum of allelic effects, and most quantitative variation could result from the segregation of alleles with subtle effects at loci identified by alleles with major effects. The achaete-scute complex in Drosophila melanogaster plays a central part in bristle development and has been characterized at the molecular level. The hypothesis that naturally occurring quantitative variation in bristle number could be associated with wild-type alleles of achaete-scute was tested by correlating phenotypic variation in bristle number with molecular variation in restriction maps in this region among chromosomes extracted from natural populations. DNA insertion variation in the achaete-scute region was found to be strongly associated with variation in bristle number.

Alleles↗

PubMed1975

Genetic differences between the Chinese and European races of the common carp.I. Analysis of genotype-environment interactions for growth rate.

Growth rate of 12 groups of common carp was measured at five experimental environments. Three of the 12 tested groups were strains of the domesticated European race of the common carp, one group was a representative of the Big-Belly Chinese race, and the remaining eight groups were F1 crossbreds among the European strains and between the European and the Chinese races. The average growth rate over the five environments of the Chinese Big-Belly was considerably poorer than that of the European carp. All the inter-race crossbreds and the crossbreds among the European strains showed heterosis. When the genotype-environment interaction was presented as a linear function of the quality of the environment, the regression coefficient (the overall responsiveness parameter) assumed relatively low values in the Big-Belly and two to two-and-a-half fold higher values in the European carp. The overall responsiveness of crossbreds was, on the average, intermediate between the two parents. When, however, it was partitioned into a scale function of the average genotype and specific independent responsiveness, the two components showed a high degree of heterosis but in opposite directions. An explanation of this genetic system in terms of adaptive evolution to the diverse modes of carp domestication in Europe and China was given.

Animals↗

PubMed2025

Lineage-specific targets of positive selection in three leaf beetles correspond with defence capacity against their shared parasitoid wasp.

Parasitoid wasps are major causes of mortality of many species, making host immune defences a common target of adaptive evolution, though such targets outside model species are poorly understood. In this study, we used two tests of positive selection to compare across three closely related Galerucella leaf beetles that show substantial differences in their phenotypic response to the shared parasitoid wasp Asecodes parviclava, their main natural enemy. Using a codon-based test, which detects excess amino acid fixations per locus along each species' lineage, we found more evidence of positive selection on parasitoid-relevant immune genes in the species with the strongest immunocompetence (G. pusilla) compared with the species having weaker immunocompetence (G. tenella and G. calmariensis). Moreover, genes coding for the early phases in the immune response cascade were predominantly among the positively selected immune genes, providing targets for future functional genomic study to pin-point connections between genotypic and phenotypic differences in defences towards a parasitoid wasp. In contrast, genome-wide analyses of the haplotype frequency spectrum, which quantify selection over recent evolutionary time scales, revealed similar signatures of positive selection on immune genes across species. These results advance the field of host-parasitoid dynamics by providing novel insights into the tempo and mode of insect host evolutionary dynamics, and offering a framework for making genotype to phenotype connections for immunocompetence phenotypes.

Animals↗

PubMed2025

A high-quality chromosome-level genome assembly and annotation of the giant freshwater prawn (Macrobrachium rosenbergii).

The giant freshwater prawn, Macrobrachium rosenbergii, is native to Southeast Asia and is used in aquacultural practices worldwide. It is considered advantageous because of its rapid growth, high nutritional value, and economic benefits. As one of the three major freshwater aquaculture shrimp sources in China, a high-quality genome resource is of great significance for promoting the germplasm improvement of varieties. This study presents a high-quality chromosome-level genome assembly of M. rosenbergii that was generated by combining PacBio, MGI, and Hi-C reads. The assembled genome was 2.96 Gb in size, with a contig N50 of 0.64 Mb and a scaffold N50 of 55.76 Mb, which was positioned on 59 pseudo-chromosomes. The Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis for genome assembly reached 94.37%. In total, 27,111 protein-coding genes were identified, of which 25,470 were functionally annotated. These results provide a foundation for future research into adaptive evolution, genomics, and molecular breeding in M. rosenbergii.

Animals↗

PubMed2025

Chromosome-level genome assembly of Sinocyclocheilus jii based on PacBio HiFi and Hi-C sequencing.

Sinocyclocheilus jii, a cavefish species endemic to China, belongs to the genus Sinocyclocheilus within the family Cyprinidae. Species within this genus exhibit significant morphological differentiation, making it not only the most species-rich genus within Cyprinidae in China but also the most diverse group of cavefishes worldwide. However, the limited availability of genomic resources has limited investigations into the genetic basis of trait variations, phylogenetic relationships, and adaptive evolution in this genus. In this study, we assembled a chromosome-level reference genome for S. jii by integrating PacBio HiFi long reads, Illumina short reads, and Hi-C sequencing data. Flow cytometry was used to estimate the genome size prior to assembly, providing a key step in technical validation. The final genome assembly spans 1.75 Gb with a contig N50 of 35.0 Mb. Using Hi-C sequencing data, the assembled scaffolds were successfully anchored to 50 chromosomes. The completeness of the chromosome-level assembly was estimated at 98.9% by BUSCO analysis. Genome annotation identified 855.5 Mb of repetitive sequences and predicted a total of 52,867 protein-coding genes, of which 51,932 genes were functionally annotated. This study presents a high-quality chromosome-level genome assembly and annotation of S. jii, providing a fundamental genomic resource for future phylogenetic and evolutionary studies.

Animals↗

PubMed2026

Chromosome-level genome assembly of Manglietia pachyphylla.

Manglietia pachyphylla, an endangered evergreen tree within the Magnoliaceae family, is renowned for its exceptional ornamental value in landscape horticulture. Despite its classification as a Category II nationally protected plant species in China, the genetic basis of its adaptive traits and conservation priorities remains poorly understood. To address this, we present the first chromosome-scale genome assembly of M. pachyphylla utilizing an integrated approach combining PacBio HiFi long-read and Hi-C chromosome conformation capture sequencing technologies. The assembled genome spans 2.15 Gb (contig N50 = 43.57 Mb), exhibiting a heterozygosity rate of 0.78% and repeat content of 78.64%, predominantly comprising long terminal repeat (LTR) retrotransposons (52.86%). Hi-C scaffolding anchored 99.57% of the assembly to 19 pseudochromosomes, achieving a BUSCO completeness score of 96.4%. Annotation revealed 42,505 putative protein-coding genes, with 84.46% of predicted genes were functionally annotated. Phylogenomic analysis positioned M. pachyphylla and Oyama sieboldii clustered together in a well-supported group. This high-contiguity genome assembly enables future investigations into adaptive evolution, functional genomics, and evidence-based conservation strategies for this endangered species.

Chromosomes, Plant↗

PubMed2026

High-Resolution Chromosome-Level Genome Assembly and Annotation of Triplophysa stewarti, an Endemic Plateau Loach from the Qinghai-Tibet Plateau.

The bottom-dwelling fish Triplophysa stewarti, endemic to the Qinghai-Tibet Plateau, is a valuable model for studying high-altitude adaptation in aquatic ecosystems. However, the lack of a high-quality reference genome has hindered comparative genomic and evolutionary studies within this genus. Here, we present a chromosome-level genome assembly for T. stewarti, generated using PacBio HiFi long-read sequencing and Hi-C scaffolding. The 697.9 Mb assembly is highly continuous (scaffold N50 of 253.58 Mb) and encompasses 25 chromosomes, representing 92.65% of the genome. BUSCO analysis indicated a 98.4% completeness, supporting the high quality of the assembly. We annotated 28,009 protein-coding genes, with 97.04% being functionally assigned across multiple databases (NR, UniProt, KEGG, GO, Pfam and InterPro). Additionally, repetitive elements constituted 42.47% of the genome, and we identified 52,709 non-coding RNAs. This high-quality reference genome provides a fundamental resource for exploring the adaptive evolution, population structure, and conservation genetics of T. stewarti and related species on the Qinghai-Tibet Plateau.

Animals↗

PubMed2026

Chromosome-level genome assembly of the small-sized Taihang donkey (Equus asinus).

China harbors a rich diversity of donkey breeds, with small-sized donkeys (<110 cm) representing a largely underexplored group. Here, we present the first high-quality, chromosome-level genome assembly of a small-sized donkey, generated using PacBio HiFi sequencing (286.7 Gb), Hi-C scaffolding (240.47 Gb), and annotated with RNA-seq data. The final assembly has a total length of 2.7 Gb and comprises 32 chromosomes (including both X and Y chromosomes), in which five chromosomes were fully assembled without gaps. It possesses a scaffold N50 of 106.70 Mb and 84 contigs (contig N50 = 63.60 Mb), and captures 99.2% of BUSCO genes. The assembly achieved a consensus quality value (QV) of 77.44, corresponding to an extremely low base-level error rate, indicating exceptional nucleotide accuracy. This high-quality genome provides a valuable resource for investigating genetic variation, adaptive evolution, and domestication processes in small-sized donkeys, and will facilitate the conservation and sustainable utilization of rich donkey genetic resources in China.

Animals↗

PubMed1990

Genotypic variation within asexual lineages of Taraxacum officinale.

Restriction site variation in DNA that encodes rRNA (rDNA) was surveyed among 714 offspring within 31 lineages (26 genotypes) of obligate asexually reproducing Taraxacum officinale (dandelions). Although clonal offspring are expected, plants with nonparental rDNA were produced from two parents that were themselves siblings (same genotype). The variation is best characterized by the loss of an EcoRI restriction site that maps to the spacer region in the parental rDNA and is most likely involved in amplification of rare or unique rDNA repeats. In one family, 41 surveyed offspring lacked the EcoRI site. In the other family, only 1 of 26 offspring lost the EcoRI site. Other classes of DNA surveyed, chloroplast DNA and the alcohol dehydrogenase 2 gene (Adh2), showed no variation. However, offspring with nonparental rDNA also had nonparental alcohol dehydrogenase 1 (Adh1) restriction fragments. Because somatic mutations in plants can be incorporated into reproductive tissue, we propose that somatic events affecting at least both multicopy rDNA and DNA homologous to the maize Adh1 gene occurred at different developmental times in the two families. An event early in development would result in all variant offspring; an event late in development would result in a single variant offspring. These results support the view that mutation (in the broad sense) influences the level of genotypic variation in asexual organisms, which may facilitate adaptive evolution of asexual species.

Alcohol Dehydrogenase↗

PubMed1991

Excess nonsynonymous substitution of shared polymorphic sites among self-incompatibility alleles of Solanaceae.

The function of the self-incompatibility locus (S locus) of many plant species dictates that natural selection will favor high levels of protein diversity. Pairwise sequence comparisons between S alleles from four species of Solanaceae reveal remarkably high sequence diversity and evidence for shared polymorphism. The level of amino acid constraint was found to be significantly heterogeneous among different regions of the gene, with some regions being highly constrained and others appearing to be virtually unconstrained. In some regions of the protein, there was an excess of nonsynonymous over synonymous substitution, consistent with the strong diversifying selection that must operate on this locus. These hypervariable regions are candidates for the sites that determine functional allelic identity. Simple contingency table tests show that sites that have polymorphism shared between species have more nonsynonymous substitution than polymorphic sites that do not exhibit shared polymorphism. This is consistent with the idea that adaptive evolution favoring amino acid replacement is occurring at sites with shared polymorphism. Tests of clustered polymorphism reveal that an unusually low rate of recombination must be occurring in this locus, allowing very ancient alleles to preserve their identity.

Alleles↗

PubMed1991

Color vision in Lycaena butterflies: spectral tuning of receptor arrays in relation to behavioral ecology.

Males of two closely related, co-occurring species of Lycaena butterflies have dorsally blue (Lycaena heteronea) or red-orange plus ultraviolet (Lycaena rubidus) wings. Males are selectively territorial against conspecific males. Virgin females accept only conspecific males, probably chosen by wing color. Females are nonterritorial and spend most of their adult activity ovipositing on the correct larval food plants. Eyes of both species contain four spectral types of visual pigments (P360, P437, P500, and P568) but the distribution of these pigments within the receptor mosaic is quite different between both species and sexes. The ventral eye region of L. heteronea is tetrachromatic but that of L. rubidus is trichromatic, lacking the blue-sensitive visual pigment P437. The dorsal eye region of males of both species is dichromatic (P360 and P437). Visual-pigment spectra and wing-reflectance spectra are well matched for effective discrimination of wings of conspecific males from those of other species. The dorsal region of female eyes is trichromatic, containing P360, P437, and P568. The third visual pigment, P568, is important for long-range detection by ovipositing females of red coloration on Eriogonum and Rumex food plants. P568 has the same absorbance spectrum as the human red-cone and is considerably red-shifted compared to the P530 possessed by most insects. That the sexes and closely related species can have such major differences in distribution of visual pigments indicates that the visual system is as readily altered as wing coloration in the course of adaptive evolution.

Animals↗

PubMed2026

Pervasive positive selection on X-linked ampliconic genes in primates.

Mammalian sex chromosomes harbour ampliconic gene families, which are multi-copy genes with ≥97% sequence identity, predominantly expressed in testis tissue and essential for male fertility. The amplification of testis-specific genes is conserved across mammals, yet the specific gene families that expand show striking lineage-specific variation. Previous studies suggest a dynamic turnover with adaptive evolution for several of these families, but their analysis has been limited by the quality of reference genomes of repetitive regions. To characterise the molecular evolutionary processes of ampliconic gene families on both sex chromosomes, we analysed telomere-to-telomere genome assemblies from eight primate species spanning 25 million years of evolution. We identified 53 X-linked and 19 Y-linked ampliconic gene families with dynamic copy number variation. Gene conversion through palindromic pairing and tandem arrays maintained high sequence similarity despite accumulating mutations. X-linked families maintained conserved chromosomal positions despite copy number changes, whereas Y-linked families showed frequent positional turnover. Strikingly, multiple X-linked families (GAGE, SSX, CSAG, and VCX) showed pervasive positive selection across the primate phylogeny and multiple (MAGEB, CT45, HSFX) showed lineage specific positive selection. Y-linked families predominantly evolve under purifying selection. Examining intraspecific copy number variation of the X-linked ampliconic families in chimpanzees, humans, and gorillas, we found variation among individuals but clear differences between species, with the largest families varying the most. These patterns could suggest that sperm competition, meiotic drive, or dosage-dependent selection drive the rapid, lineage-specific evolution of testis-expressed ampliconic genes in primates.

Journal Article↗

PubMed1983

Population genetics of Drosophila amylase. IV. Selection in laboratory populations maintained on different carbohydrates.

Two polymorphic systems impinging on alpha-amylase in Drosophila pseudoobscura have been studied in laboratory populations maintained on medium in which the only carbohydrate source was starch (the substrate of amylase) and replicas maintained on medium in which the only carbohydrate source was maltose (the product of amylase). The two polymorphic systems were alleles at the structural gene (Amy) coding for the enzyme (allozymes) and variation in the tissue-specific expression along the adult midgut controlled by several genes. In the seven populations on maltose medium little consistent change was noted in either system. In the seven populations on starch medium, both polymorphisms exhibited selective changes. A midgut pattern of very limited expression of amylase rose in frequency in all starch populations, as did the frequency of the "fast" (1.00) Amy allele. The overall specific amylase activity did not differ between starch-adapted and maltose-adapted flies.--The results, along with previous studies, indicate that when a gene-enzyme system is specifically stressed in laboratory populations, allozymes often exhibit selective differences. Such results make the selectionist hypothesis at least tenable. Furthermore, the fact that both types of polymorphisms responded to selection indicates the role of structural gene vs. gene regulation changes in adaptive evolution is not an either/or question but one of relative roles and interactions.

Alleles↗

PubMed1988

A fourth Escherichia coli gene system with the potential to evolve beta-glucoside utilization.

Escherichia coli K12 is being used to study the potential for adaptive evolution that is present in the genome of a single organism. Wild-type E. coli K12 do not utilize any of the beta-glucoside sugars arbutin, salicin or cellobiose. It has been shown that mutations at three cryptic loci allow utilization of these sugars. Mutations in the bgl operon allow inducible growth on arbutin and salicin while cel mutations allow constitutive utilization of cellobiose as well as arbutin and salicin. Mutations in a third cryptic locus, arbT, allow the transport of arbutin. A salicin+ arbutin+ cellobiose+ mutant has been isolated from a strain which is deleted for the both the bgl and cel operons. Because the mutant utilized salicin and cellobiose as well as arbutin, it is unlikely it is the result of a mutation in arbT. A second step mutant exhibited enhanced growth on salicin and a third step mutant showed better growth on cellobiose. A fourfold level of induction in response to arbutin and a twofold level of induction in response to salicin was observed when these mutants were assayed on the artificial substrate p-nitrophenyl-beta-D-glucoside. Although growth on cellobiose minimal medium can be detected after prolonged periods of time, these strains are severely inhibited by cellobiose in liquid medium. This system has been cloned and does not hybridize to either bgl or cel specific probes. We have designated this gene system the sac locus. The sac locus is a fourth set of genes with the potential for evolving to provide beta-glucoside utilization.

Cellobiose↗

PubMed2026

Population and landscape genomics provide insights into the adaptive genetic variation and future climate-induced vulnerability of the endangered tree species Phoebe bournei.

Elucidating the genomic underpinnings of adaptive variation is highly important for the conservation, landscape application, and management of ornamental trees against the backdrop of global climate change. However, research on the genetic mechanisms underlying climate adaptation in Phoebe bournei-a near-threatened subtropical tree species endemic to China, which is endowed with exceptionally high ornamental and ecological value-remains scarce. Whole-genome resequencing was conducted on 362 individuals from 27 natural populations across the geographical range of the species. Genome-environment association analyses were employed to identify 1556 climate-associated variants and 167 candidate genes associated with temperature and precipitation variables. Through functional annotation and expression profiling, pivotal genes, including TRX-M4 and FBD1, were identified as integral to drought and heat stress responses, with adaptive alleles displaying distinct geographic frequency distributions and significant phenotypic differentiation. Divergent evolutionary trajectories were deduced among populations, with southeastern populations distinguished by elevated genetic diversity and strong signatures of local adaptation. Nevertheless, projections derived from the Risk of Non-Adaptedness and gradient forest models suggest that these southeastern populations will face substantial genomic offset under future climate scenarios, signaling heightened vulnerability and the need for prioritized conservation and management. This study provides the first genome-wide perspective into the adaptive evolution of P. bournei and offers a robust foundation for its conservation and climate-resilient management.

Journal Article↗

PubMed1990

Protein structure and function at low temperatures.

Proteins represent the major components in the living cell that provide the whole repertoire of constituents of cellular organization and metabolism. In the process of evolution, adaptation to extreme conditions mainly referred to temperature, pH and low water activity. With respect to life at low temperatures, effects on protein structure, protein stability and protein folding need consideration. The sequences and topologies of proteins from psychrophilic, mesophilic and thermophilic organisms are found to be highly homologous. Commonly, adaptive changes refer to multiple alterations of the amino acid sequence, which presently cannot be correlated with specific changes of structure and stability; so far it has not been possible to attribute specific increments in the free energy of stabilization to well-defined amino-acid exchanges in an unambiguous way. The stability of proteins is limited at high and low temperatures. Their expression and self-organization may be accomplished under conditions strongly deviating from optimum growth conditions. Molecular adaptation to extremes of temperature seems to be accompanied by a flattening of the temperature profile of the free energy of stabilization. In principle, the free energy of stabilization of proteins is small compared to the total molecular energy. As a consequence, molecular adaptation to extremes of physical conditions only requires marginal alterations of the intermolecular interactions and packing density. Careful statistical and structural analyses indicate that altering the number of ion pairs and hydrophobic interactions allows the flexibility of proteins to be adjusted so that full catalytic function is maintained at varying temperatures.

Drug Stability↗