Population Bottlenecks Research Articles

Genetic polymorphism of merozoite surface protein 1 and merozoite surface protein 2 in the Vietnam Plasmodium falciparum population

BackgroundPlasmodium falciparum merozoite surface proteins 1 (PfMSP1) and 2 (PfMSP2) are potential candidates for malaria vaccine development. However, the genetic diversity of these genes in the global P. falciparum population presents a significant challenge in developing an effective vaccine. Hence, understanding the genetic diversity and evolutionary trends in the global P. falciparum population is crucial.MethodsThis study analyzed the genetic variations and evolutionary changes of pfmsp1 and pfmsp2 in P. falciparum isolates from the Central Highland and South-Central regions of Vietnam. DNASTAR and MEGA7 programs were utilized for analyses. The polymorphic nature of global pfmsp1 and pfmsp2 was also investigated.ResultsA total of 337 sequences of pfmsp1 and 289 sequences of pfmsp2 were obtained. The pfmsp1 and pfmsp2 from Vietnam revealed a higher degree of genetic homogeneity compared to those from other malaria-endemic countries. Remarkably, the allele diversity patterns of Vietnam pfmsp1 and pfmsp2 differed significantly from those of neighboring countries in the Greater Mekong Subregion. Declines in allele diversity and polymorphic patterns of Vietnam pfmsp1 and pfmsp2 were observed.ConclusionsThe Vietnam P. falciparum population might be genetically isolated from the parasite populations in other neighboring GMS countries, likely due to geographical barriers and distinct evolutionary pressures. Furthermore, bottleneck effects or selective sweeps may have contributed to the genetic homogeneity of Vietnam pfmsp1 and pfmsp2.

Antibonding valence states induce low lattice thermal conductivity in metal halide semiconductors

Reduction of phonon mediated thermal transport properties, i.e., lattice thermal conductivity (κL), of semiconductors can strongly affect the performance of thermoelectrics and optoelectronics. Although extrinsic routes to reduce κL have been achieved through selective scattering of phonons via doping, alloying, and hierarchical nano-structuring, semiconductors with intrinsically low κL have recently gained widespread attention due to their ability to decouple electronic and phonon transports. While innate low κL in crystalline semiconductors is a desired requirement to achieve high performance thermoelectrics, the solar upconversion efficiency of photovoltaics based on metal halide perovskites (MHPs) have been shown to increase due to their ultralow κL through the hot-phonon bottleneck effect. Therefore, understanding the microscopic mechanisms underlying ultralow κL in crystalline semiconductors is extremely important. Several structural factors that are intrinsic to a material have been shown to strongly influence the reduction of κL. Among them, the presence of rattling atoms, lone-pair electrons, and large lattice anharmonicity have been widely studied. Here, we bring out yet another largely unexplored intrinsic characteristic of materials related to the filled antibonding valence states (AVS) near the Fermi level, which are shown to induce low κL in crystalline compounds. We focus our review on an emerging class of compounds–metal halide semiconductors including MHPs and investigate the interplay between structures, chemical bonding and κL, carefully curating from literature a list of 33 compounds having different structure dimensionality with known κL. We established a universal connection between the elastic moduli, speeds of sound, and κL with the presence of AVS just below the Fermi level. We found that large peak in the AVS correlates positively with lower values of elastic moduli, speeds of sound, and κL, providing antibonding states based design criteria of low-κL compounds. Furthermore, we discuss different synthesis strategies, which are crucial for experimental realization of ultralow κL through structure manipulation. Additionally, we outline how chemical bonding data can be utilized in machine learning models for predictive modeling of κL. We hope that our approach of understanding low-κL through the viewpoint of chemical bonding theory would encourage exploration of phonon transport properties in other families of materials having filled AVS that can provide further insights on the structure-bonding-property relationships aiding novel materials design approaches.

Repeated horizontal acquisition of lagriamide-producing symbionts in Lagriinae beetles.

Microbial symbionts associate with multicellular organisms on a continuum from facultative associations to mutual codependency. In the oldest intracellular symbioses there is exclusive vertical symbiont transmission, and co-diversification of symbiotic partners over millions of years. Such symbionts often undergo genome reduction due to low effective population sizes, frequent population bottlenecks, and reduced purifying selection. Here, we describe multiple independent acquisition events of closely related defensive symbionts followed by genome erosion in a group of Lagriinae beetles. Previous work in Lagria villosa revealed the dominant genome-eroded symbiont of the genus Burkholderia produces the antifungal compound lagriamide, protecting the beetle's eggs and larvae from antagonistic fungi. Here, we use metagenomics to assemble 11 additional genomes of lagriamide-producing symbionts from seven different host species within Lagriinae from five countries, to unravel the evolutionary history of this symbiotic relationship. In each host, we detected one dominant genome-eroded Burkholderia symbiont encoding the lagriamide biosynthetic gene cluster. However, we did not find evidence for host-symbiont co-diversification, or for monophyly of the lagriamide-producing symbionts. Instead, our analyses support a single ancestral acquisition of the gene cluster followed by at least four independent symbiont acquisitions and subsequent genome erosion in each lineage. By contrast, a clade of plant-associated relatives retained large genomes but secondarily lost the lagriamide gene cluster. Our results, therefore, reveal a dynamic evolutionary history with multiple independent symbiont acquisitions characterized by a high degree of specificity, and highlight the importance of the specialized metabolite lagriamide for the establishment and maintenance of this defensive symbiosis.

Population Genetic Investigation of Hypophthalmichthys nobilis in the Yangtze River Basin Based on RAD Sequencing Data.

The Bighead carp (Hypophthalmichthys nobilis), a primary freshwater aquaculture species in China, faces challenges due to over-exploitation and environmental changes. We leveraged RAD-seq to perform a comprehensive population genetic analysis on 14 H. nobilis populations sampled from the Yangtze River (13 populations) and the Marseilles Reach of the Illinois River (one population). Analysis of genetic diversity showed that different parameters demonstrated varied inferences, and notably, Zhongxian (ZX2), Wanhzou (WZ2), Yangzhou hatchery (YZYZ), Yangzhou (YZ), and Taihu (TH) populations showed apparent heterozygote deficiency. Linkage disequilibrium (LD) analysis exhibited a trend of higher linkage disequilibrium in populations from the upper reaches of the Yangtze River, followed by those from the middle reaches and then those from the lower reaches. Additionally, the reconstructed polygenetic tree and PCA plot clustered all populations into 2 major subgroups, while the results of structure analysis indicated 4 ancestors. The pairwise FST values ranged from 0 to 0.5530. Among these, high FST values (0.1931-0.5530) were only observed between populations WZ2, YZ, YZYZ, and the remaining 11 populations. Furthermore, genetic bottlenecks were observed in all populations 20-30 thousand years ago. Overall, the research offers insights essential for genetic management practices for sustainable aquaculture and biodiversity conservation of bighead carp.

Bottleneck Effect Analysis in Indigenous Poonchi Chicken Located Near International Border of India and Pakistan

Background: Poonch is the remotest district of Jammu, India located near to line of control with Pakistan. Poonchi chicken is the first native poultry breed of Jammu region which is being characterized and registered with National Bureau of Animal Genetic Resources. Present study is the first study on genetic bottleneck assessment in Poonchi chicken population using recommended microsatellite markers. This study in Poonchi chicken would be of immense use in tracing evolutionary origin and formulating effective conservation strategies for genetic diversity within breeds. Methods: Blood samples were collected randomly from Poonch and Rajouri districts of Jammu for DNA extraction and analysis. Microsatellite markers selected for the analysis were ADL0268, MCW0206, MCW0081, ADL0278, MCW0069, MCW0248, MCW0111, MCW0222, MCW0016 and LEI0094. To evaluate the Poonchi chicken for mutation drift equilibrium, Bottleneck software was used. Infinite allele model (IAM), two phase model of mutation (TPM) and stepwise mutation model (SMM) tests were done. Mode shift test was also used as another method of qualitative test for allele frequency. Result: Total number of alleles observed were 72, with the total number alleles ranged from 6 to 9. The results of all three models (IAM, TPM, SMM) in Sign test depicted the heterozygosity was more in the expected number of loci in Poonchi chicken as 5.97 (P less than 0.05), 5.93 (P less than 0.05), 5.90 (P less than 0.05) respectively. Whereas for Wilcoxon rank test the IAM, TPM and SMM revealed significant values of (P less than 0.05) deviation indicating that all the loci deviate from mutation-drift equilibrium. Mode shift test graph obtained depicted a slight shift from normal L-shaped curve indicating recent bottleneck effect in Poonchi chicken. This might have resulted in the loss of number of effective alleles which suggests a need of planning and implementing an effective breeding policy in order to preserve and promote this native breed.

Increasing temperature threatens post‐fire auto‐successional dynamics of a Mediterranean obligate seeder

Abstract Reproductive traits influence plant auto‐successional dynamics in post‐fire regeneration. Obligate seeding species rely on their seedbank and on the climatic conditions following the fire to ensure a successful recovery, defining the window of opportunity for seedling emergence. In the Mediterranean basin, emergence opportunities generally begin with autumnal rains. However, climate change‐induced increases in temperature and drought could jeopardise the regeneration capacity of seeding species by causing temporal shifts in emergence opportunities or by modifying wildfire seasonality. This study aimed to explore the impact of experimentally induced climate change on regeneration dynamics of Aleppo pine (Pinus halepensis), a serotinous Mediterranean obligate seeder. In March 2021, we set up an 18‐month climate change simulation experiment with 15 open‐top chambers (OTC), each paired with a control subplot (CON) on top of Aleppo pines that were naturally regenerating after a stand‐replacing wildfire in SW Catalonia (June 2019). We tagged 178 young Aleppo pine recruits in OTC and CON subplots (98 and 81 respectively), classified according to their initial size, to periodically measure height growth and survival throughout the experiment duration. Furthermore, Aleppo pine seeds were seasonally sown (7900 total seeds) in 10 subplot pairs between May 2021 and April 2022, to monthly monitor temporal patterns of seedling emergence and survival. We found that OTCs reduced overall emergence rates and caused the loss of the autumnal window of opportunity for the emergence of Aleppo pine seedlings. Furthermore, seedlings which emerged within OTCs faced higher mortality rates in all seasons, with only 1% of seedlings surviving compared with 21.1% of seedlings in control plots. The OTC‐induced conditions were also detrimental to the survival of recruited seedlings, especially those with a smaller initial size, although no significant effects of temperature increase were found on growth. Synthesis. Climate change is likely to interfere with the post‐fire regeneration dynamics of obligate seeders by shortening the temporal window of opportunities for emergence and by enhancing the bottleneck effects throughout the recruitment process in the early phases of pine demographic recovery. Altogether, it could threaten post‐fire regeneration by increasing the hazard of a demographic collapse of Aleppo pine.

The effect of building bottlenecks on crowd dynamics involving individuals with simulated disabilities

With the development of urbanization and the growth of population, there is a growing demand for safety in public building facilities. As one of the essential building components of urban architecture, bottlenecks have a significant impact on the evacuation efficiency of crowds. Furthermore, the heterogeneity of crowds also contributes to the complexity of crowd movement through bottlenecks, while aggravating the magnitude of congestion induced by bottlenecks. The objective of this paper is to explore the movement characteristics of heterogeneous crowds passing through a corridor with a bottleneck by conducting a controlled experiment. There were three variables in this experiment, namely the individual categories (i.e., able-bodied individuals, simulated individuals on crutches and simulated wheelchair users), bottleneck width (i.e., 1.2, 1.6 and 2.0 m) and proportion of simulated disabilities in crowds (i.e., 0 %, 5 % and 10 %). Then offset angle, passing efficiency, fundamental diagram, etc., were analyzed. In trials involving simulated individuals on crutches, a higher detouring degree is observed compared to trials involving simulated wheelchair users or mixed groups of two types of simulated disabilities. There is an increase in flow rate induced by increasing the bottleneck width and decreasing the proportion of simulated disabilities. The passing efficiency at the upstream of the bottleneck in all tests is primarily influenced by the bottleneck width, while by the type and proportion of simulated disabilities at the downstream or inside the bottleneck. The findings are intended to complement the dynamic theory of heterogeneous crowds at building bottlenecks, while providing a reference for congestion control of crowds at bottlenecks.

The evolving three-dimensional landscape of human adaptation.

Over the past 3 million years, humans have expanded their ecological niche and adapted to more diverse environments. The temporal evolution and underlying drivers behind this niche expansion remain largely unknown. By combining archeological findings with landscape topographic data and model simulations of the climate and biomes, we show that human sites clustered in areas with increased terrain roughness, corresponding to higher levels of biodiversity. We find a gradual increase in human habitat preferences toward rough terrains until about 1.1 million years ago (Ma), followed by a 300 thousand-year-long contraction of the ecological niche. This period coincided with the Mid-Pleistocene Transition and previously hypothesized ancestral population bottlenecks. Our statistical analysis further reveals that from 0.8 Ma onward, the human niche expanded again, with human species (e.g., H. heidelbergensis, H. neanderthalensis, and H. sapiens) adapting to rougher terrain, colder and drier conditions, and toward regions of higher ecological diversity.

Harnessing Flex Point Symmetry to Estimate Logistic Tumor Population Growth.

The observed time evolution of a population is well approximated by a logistic growth function in many research fields, including oncology, ecology, chemistry, demography, economy, linguistics, and artificial neural networks. Initial growth is exponential, then decelerates as the population approaches its limit size, i.e., the carrying capacity. In mathematical oncology, the tumor carrying capacity has been postulated to be dynamically evolving as the tumor overcomes several evolutionary bottlenecks and, thus, to be patient specific. As the relative tumor-over-carrying capacity ratio may be predictive and prognostic for tumor growth and treatment response dynamics, it is paramount to estimate it from limited clinical data. We show that exploiting the logistic function's rotation symmetry can help estimate the population's growth rate and carry capacity from fewer data points than conventional regression approaches. We test this novel approach against published pan-cancer animal and human breast cancer data, achieving a 30% to 40% reduction in the time at which subsequent data collection is necessary to estimate the logistic growth rate and carrying capacity correctly. These results could improve tumor dynamics forecasting and augment the clinical decision-making process.

Ancient mitochondrial DNA extraction from Bison bison long bones from Head-Smashed-In Buffalo Jump, UNESCO World Heritage site

Head-Smashed-In Buffalo Jump (HSIBJ) is a UNESCO World Heritage Site located on the southern end of the Porcupine Hills, near Fort Macleod, Alberta, Canada. Using a system of drive lanes, Indigenous groups drove herds of bison over the cliff edge for thousands of years. The well-stratified deposits at the base of the cliff offer a unique opportunity to investigate the genetic diversity of the American bison before European contact and their genetic bottleneck in the 19th century. We extracted ancient DNA from twenty-one bison long bones, amplified and sequenced the mitochondrial DNA control region. Comparisons between ancient and modern bison populations revealed novel haplotypes in the HSIBJ population, suggesting a loss of genetic diversity due to the bottleneck. Furthermore, we discovered a shared haplotype between the bison hunted at the site and modern populations, which may help elucidate the complex history of living herds.

Genome-wide identification of m6A-related gene family and the involvement of TdFIP37 in salt stress in wild emmer wheat.

The genomic organization, phylogenetic relationship, expression patterns, and genetic variations of m6A-related genes were systematically investigated in wild emmer wheat and the function of TdFIP37 regulating salt tolerance was preliminarily determined. m6A modification is one of the most abundant and crucial RNA modifications in eukaryotics, playing the indispensable role in growth and development as well as stress response in plants. However, its significance in wild emmer wheat remains elusive. Here, a genome-wide search of m6A-related genes was conducted in wild emmer wheat to obtain 64 candidates, including 21 writers, 17 erasers, and 26 readers. Phylogenetic and collinearity analysis demonstrated that segmental duplication and polyploidization contributed mainly to the expansion of m6A-related genes in wild emmer. A number of cis-acting elements involving in stress and hormonal regulation were found in the promoter regions of them, such as MBS, LTR, and ABRE. Genetic variation of them was also investigated using resequencing data and obvious genetic bottleneck was occurred on them during wild emmer wheat domestication process. Furthermore, the salt-responsive candidates were investigated through RNA-seq data and qRT-PCR validation using the salt-tolerant and -sensitive genotypes and the co-expression analysis showed that they played the hub role in regulating salt stress response. Finally, the loss-function mutant of Tdfip37 displayed the significantly higher salt-sensitive compared to WT and then RNA-seq analysis demonstrated that FIP37 mediated the MAPK pathway, hormone signal transduction, as well as transcription factor to regulate salt tolerance. This study provided the potential m6A genes for functional analysis, which will contribute to better understand the regulatory roles of m6A modification and also improve the salt tolerance from the perspective of epigenetic approach in emmer wheat and other crops.

Identification of potential auxin response candidate genes for soybean rapid canopy coverage through comparative evolution and expression analysis.

Throughout domestication, crop plants have gone through strong genetic bottlenecks, dramatically reducing the genetic diversity in today's available germplasm. This has also reduced the diversity in traits necessary for breeders to develop improved varieties. Many strategies have been developed to improve both genetic and trait diversity in crops, from backcrossing with wild relatives, to chemical/radiation mutagenesis, to genetic engineering. However, even with recent advances in genetic engineering we still face the rate limiting step of identifying which genes and mutations we should target to generate diversity in specific traits. Here, we apply a comparative evolutionary approach, pairing phylogenetic and expression analyses to identify potential candidate genes for diversifying soybean (Glycine max) canopy cover development via the nuclear auxin signaling gene families, while minimizing pleiotropic effects in other tissues. In soybean, rapid canopy cover development is correlated with yield and also suppresses weeds in organic cultivation. We identified genes most specifically expressed during early canopy development from the TIR1/AFB auxin receptor, Aux/IAA auxin co-receptor, and ARF auxin response factor gene families in soybean, using principal component analysis. We defined Arabidopsis thaliana and model legume species orthologs for each soybean gene in these families allowing us to speculate potential soybean phenotypes based on well-characterized mutants in these model species. In future work, we aim to connect genetic and functional diversity in these candidate genes with phenotypic diversity in planta allowing for improvements in soybean rapid canopy cover, yield, and weed suppression. Further development of this and similar algorithms for defining and quantifying tissue- and phenotype-specificity in gene expression may allow expansion of diversity in valuable phenotypes in important crops.

Evaluation of Aedes aegypti control intervention with pyriproxyfen by lcWGS in Manacapuru, Amazonas, Brazil.

Ae. aegypti mosquitoes are considered a global threat to public health due to its ability to transmit arboviruses such as yellow fever, dengue, Zika and Chikungunya to humans. The lack of effective arboviral vaccines and etiological treatments make vector control strategies fundamental in interrupting the transmission cycle of these pathogens. This study evaluated Ae. aegypti mosquito populations pre- and post-intervention period with disseminating stations of the larvicide pyriproxyfen to understand its potential influence on the genetic structure and population diversity of these vectors. This study was conducted in Manacapuru city, Amazonas, Brazil, where 1,000 pyriproxyfen dissemination stations were deployed and monitored from FEB/2014 to FEB/2015 (pre-intervention) and AUG/2015 to JAN/2016 (post-intervention). Low-coverage whole genome sequencing of 36 individuals was performed, revealing significant stratification between pre- and post-intervention groups (pairwise FST estimate of 0.1126; p-value < 0.033). Tajima's D estimates were -3.25 and -3.07 (both p-value < 0.01) for pre- and post-intervention groups, respectively. Molecular diversity estimates (Theta(S) and Theta(Pi)) also showed divergences between pre- and post-intervention groups. PCA and K-means analysis showed clustering for SNP frequency matrix and SNP genotype matrix, respectively, being both mainly represented by the first principal component. PCA and K-means clustering also showed significant results that corroborate the impact of pyriproxyfen intervention on genetic structure populations of Ae. aegypti mosquitoes. The results revealed a bottleneck effect and reduced mosquito populations during intervention, followed by reintroduction from adjacent and unaffected populations by this vector. We highlighted that low-coverage whole genome sequencing can contribute to genetic and structure population data, and also generate important information to aid in genomic and epidemiological surveillance.

Slowing down the hot electron cooling to activate near-infrared photocatalytic activity in potassium/carbon co-doped polymeric carbon nitride

The research on hot electron cooling in photocatalysis has been neglected. Here, taking polymeric carbon nitride as an example, a potassium/carbon (K/C) co-doping strategy is proposed to slow down hot electron cooling. The K/C co-doping reduces the specific arrangement and overlap of electronic band structures, and decreases the degeneracy of conduction band energy levels, thus exciting phonon bottleneck effect to effectively suppress the relaxation of hot electrons by reducing the interaction between hot electrons and phonons. Our work benefits to improve the efficiency of photocatalytic energy conversion.

Archaeogenomic analysis of Chesapeake Atlantic sturgeon illustrates shaping of its populations in recovery from severe overexploitation.

Atlantic sturgeon (Acipenser oxyrinchus ssp. oxyrinchus) has been a food resource in North America for millennia. However, industrial-scale fishing activities following the establishment of European colonies led to multiple collapses of sturgeon stocks, driving populations such as those in the Chesapeake area close to extinction. While recent conservation efforts have been successful in restoring census numbers, little is known regarding genomic consequences of the population bottleneck. Here, we characterize its effect on present-day population structuring and genomic diversity in James River populations. To establish a pre-collapse baseline, we collected genomic data from archaeological remains from Middle Woodland Maycock's Point (c. 200-900 CE), as well as Jamestown and Williamsburg colonial sites. Demographic analysis of recovered mitogenomes reveals a historical collapse in effective population size, also reflected in diminished present-day mitogenomic diversity and structure. We infer that James River fall- and spring-spawning populations likely took shape in recent years of population recovery, where genetic drift enhanced the degree of population structure. The mismatch of mitogenomic lineages to geographical-seasonal groupings implies that despite their homing instinct and differential adaptation manifested as season-specific behaviour, colonization of new rivers has been a key ecological strategy for Atlantic sturgeon over evolutionary timescales.

The genetic consequences of historic climate change on the contemporary population structure of a widespread temperate North American songbird

Studies of widely distributed species can inform our understanding of how past demographic events tied to historic glaciation and ongoing population genetic processes interact to shape contemporaneous patterns of biodiversity at a continental scale. In this study, we used whole-genome resequencing to investigate the current population structure and genetic signatures of past demographic events in the widespread migratory American goldfinch (Spinus tristis). Phylogenetic relationships inferred from whole mitochondrial genomes were poorly resolved. In contrast, a genome-wide panel of > 4.5 million single nucleotide polymorphisms (SNPs) strongly supported the existence of eastern and western populations separated by western mountain ranges and additional population structuring within the western clade. Demographic modeling estimated that the eastern and western populations diverged approximately one million years ago, and both populations experienced subsequent population bottlenecks during the last glacial period. Species distribution models showed a severe contraction of suitable habitat for the American goldfinch during this period, with predicted discontinuities that are consistent with multiple, isolated glacial refugia that coincide with present-day population structure. Low overall genetic differentiation between the eastern and western populations (FST ∼ 0.01) suggests ongoing gene flow accompanied divergence, and individuals with admixed genomic signatures were sampled along a potential contact zone. Nevertheless, outlier SNPs were identified near genes associated with feather color, song, and migratory behavior and provide strong candidates for further study of the mechanisms underlying reproductive isolation and speciation in birds.

Chemical Vapor Deposited Thin Palladium Sulfide Crystals for Highly Photoresponsive Photodetector

AbstractNonlayered palladium sulfide (PdS) is of interest due to its rich physical properties and promising applications in optoelectronic devices. However, the growth of thin nonlayered PdS remains challenging because of its intrinsic 3D lattice structure. Here, the first demonstration of the direct synthesis of thin rectangular PdS ribbons/flakes on SiO2/Si substrates by a facile chemical vapor deposition (CVD) approach is presented. The atomic structure and high crystalline quality of CVD‐derived PdS crystals are shown by scanning transmission electron microscopy. The nonlinear saturable absorption and absorption enhancement are revealed by using ultrafast optical pump‐probe spectroscopy, and the photocarrier dynamics present the hot phonon bottleneck and Auger recombination effects. Additionally, the Raman vibration modes display the polarization‐dependent properties verified by angle‐resolved polarized Raman spectroscopy. Importantly, the photodetector based on PdS ribbon demonstrates a decent photoresponsivity of ≈7.7 × 103 A W−1. This results provide an effective way to form thin nonlayered PdS with potential applications in the field of photodetection.

Variation in the Local Grey Mullet Populations (Mugil cephalus) on the Western Pacific Fringe

Background: Understanding population genetic structures is crucial for planning and implementing conservation programmes to preserve species’ adaptive and evolutionary potential and thus ensure their long-term persistence. The grey mullet (Mugil cephalus) is a globally distributed coastal fish. Its populations in waters surrounding Taiwan on the western Pacific fringe are divided into at least two stocks (migratory and residential), but questions remain regarding their genetic divergence and gene flow. Methods and Results: To cast more light on this, allozyme variations at 21 presumptive gene loci of 1217 adult grey mullets from 15 localities in Japan, Taiwan and mainland China, and four gene loci from 1470 juveniles from three localities in Taiwan were used to investigate patterns of genetic variation. The mean expected heterozygosity (He) was 0.128—ranging from 0.031 (Matsu) to 0.442 (Kaoping)—and the mean observed heterozygosity (Ho) was 0.086—ranging from 0.017 (Kaohsiung) to 0.215 (Kaoping). Both AMOVA and the high overall mean FST of 0.252 indicated enormous genetic differentiation among populations and the positive mean value of FIS was 0.328, indicating a deficiency of heterozygotes. PCoA indicated that the samples of M. cephalus could be split into three groups and STRUCTURE analysis showed that all individuals were grouped into three genetic clusters. The results of mutation-drift equilibrium tests did not suggest that the populations experienced any recent genetic bottleneck. The results from all localities in the present investigation showed significant change in the GPI-A genotype frequencies with latitudes—e.g., increases in GPI-A*135/135 homozygote frequencies and GPI-A*100/100 frequencies were highly correlated with latitudinal cline. All migratory populations with the GPI-A genotype were almost exclusively the GPI-A*100/100 homozygote. During the life history of M. cephalus, the GPI-A*100/135 heterozygote frequency significantly decreases with age. Conclusions: Based on these data, we suggest that each GPI-A genotype represents trait combinations of higher fitness in some portions of the environment. Furthermore, the genotypic frequencies change in accordance with life stages, suggesting that selection occurs throughout the life span.

Exploring the wild almond, Prunus arabica (Olivier), as a genetic source for almond breeding

During the process of almond (Prunus dulcis) domestication, essential traits, which gave plants the plasticity for facing unstable environmental conditions, were lost. In general, the domestication process often narrows the natural genetic diversity. Modern selections (i.e., breeding programs) dramatically accelerated this genetic bottleneck trend to a few successful almond cultivars, which are presently the founders of most commercial cultivars worldwide. The concept of utilizing wild species as a source for important traits and for the enrichment of the gene pool was deeply discussed in previous studies. However, in almonds and other Prunus species, deliberate utilization of wild species as a genetic resource for breeding programs is quite rare. To address these significant challenges, we generated an interspecific F1 population between the Israeli almond cultivar Um el Fahem (UEF) and a specimen of a local wild almond species, Prunus arabica (P. arabica), originating from the Judea desert. This interspecific F1 population possesses high phenotypic variability, and sixteen segregating traits were phenotyped. Among the segregating traits, we were able to genetically associate six agriculturally important traits, such as leaf chlorophyll content (LCC), flower size, and fruit size. The alleles for Self-Compatibility (SC) and kernel bitterness were previously mapped in almond and were reexamined on the background of the distinctive wild genetic material of P. arabica. Finally, phenotypic interactions between traits were suggested, such as rootstock perimeter and canopy area that were positively correlated with total yield in the F1 population. This study is a first step towards developing a well-characterized almond interspecies genetic population. The availability of such a genetic tool with detailed phenotypic analysis is crucial to address and explore the profound influence of almond wild species in Prunus genetic research and breeding. By using the interspecific population as the infrastructure, we show the advantages and importance of utilizing wild relatives.

Pedigree-Based Description of Danubia Alba Rabbit Breed Lines.

The diversity of livestock animal breeds is an integral part of global biodiversity and requires careful management for sustainability and future availability. Avoiding inbreeding is a crucial aspect of mating of breeding animals. Our aims were to describe the quality of the pedigree, generation interval, gene origin, inbreeding, and effective population size of Danubia Alba rabbit lines. Line "D" is the maternal, whereas lines "C" and "X" are used as the paternal lines. The pedigree information was followed back from the actual breeding rabbits up to the founder animals. The rabbits having offspring in 2023 were chosen as reference populations for each line. The complete generation equivalent (GenCom) was 17.68 for line "C", 18.32 for line "D", and 17.49 for line "X", respectively. The maximum number of generations (GenMax) was above 30 for each line. The estimated bottleneck effect is mostly the result of selection and not a real genetic loss. The Wright inbreeding coefficient (F_Wright) was the highest for the "X" line rabbits, whereas it was the lowest for the line "D". Kalinowski's decomposition of inbreeding showed that it originated mostly from the past; the current fixation of alleles was quite similar for the line "C" and "D". Based on the predicted effective population sizes, it seems that there is no problem in maintaining of Danubia Alba lines.