Search Results (27)

Fish year-class strength (YCS) has been estimated via longitudinal analysis of catch-at-age data and via catch-curve regression, but no study has compared the two approaches. The objective of this study was to compare YCS estimates between the two approaches with application to the lake trout (Salvelinus namaycush) population in the main basin of Lake Huron, one of the Laurentian Great Lakes of North America. YCSs were reconstructed for both hatchery-stocked and wild lake trout. Akaike information criterion (AIC) and Bayesian information criterion (BIC) were used to compare 14 linear mixed-effects models for longitudinal analysis of catch-at-age data, and three linear mixed-effects models for catch-curve regression. From the best models based on AIC or BIC comparisons, YCS estimates with year-class as a fixed effect were consistent with those estimated with year-class as a random effect. Estimated YCS patterns and trends were the same or similar between the longitudinal analysis and the catch-curve regression, indicating that both approaches provide robust estimates of YCS. Potential bias in using the approach of catch-curve regression could be caused by abrupt changes in adult mortality. It is also critical to recognize multiple recruitment origins for using the approach of longitudinal analysis of catch-at-age data. Full article

The breeding of large animals in the family Cervidae in China contributes to achieving two tasks: restoring the provenance of wild populations and providing raw materials for traditional Chinese medicine. Currently, red deer (Cervus elaphus), sika deer (C. nippon), and white-lipped deer (C. albirostris) maintain a large number of breeding populations. Some studies on the relationship between the intestinal microbiota and the feed of these deer have been conducted; however, owing to differences in feeding conditions between studies, it has been impossible to compare the intestinal microecology and related adaptability between species. Therefore, the present study is aiming to investigate whether the differences in intestinal microbiota of the three deer species are related to the distance of phylogenetic relationships under the same feeding environment. On this basis, we discuss whether there are differences in the adaptability of the intestinal microbiota of the three deer species to feed nutrients, deepen the understanding of the relationship between the three deer intestinal microbiota and feed nutrition, and provide basic data for improving the scientific feeding of the three deer species. In this study, 16S rRNA high-throughput sequencing technology was utilized to analyze the intestinal microbiota in feces of the abovementioned healthy deer species. The results of this study indicated that the intestinal microbiota diversity and relative abundance in female white-lipped deer (FWLD) were significantly lower than those in female sika deer (FSD) and female red deer (FRD; p < 0.05); however, there was no significant difference between the latter two groups (p > 0.05). The community compositions of the intestinal microbiota in FSD and FRD were more similar, whereas that of FWLD was significantly different from those of the first two groups. Firmicutes and Bacteroidetes were the most abundant phyla in the intestinal microbiota of all three deer species, and Ruminococcceae_UCG-005 was the most abundant genus. No known obligatory pathogenic bacteria were observed in any sample. The relative abundance of the operational taxonomic units Christensenellaceae_R-7_group, Treponema_2, and Akkermansia exhibited significant differences among FSD, FRD, and FWLD, respectively. Therefore, the phylogenetic relatedness of the three deer species appears to play a major role in their intestinal microecology under the same feeding conditions—the greater the phylogenetic relatedness between hosts, the more similar is their intestinal microbiota. In addition, the PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) function prediction results indicated that FSD were less capable than FRD and FWLD in the functional category of nutrient metabolism, and FWLD were less capable than FSD and FRD in the functional category of intestinal absorption. These results indicated that there may be differences in the nutritional adaptation abilities of the three deer species under different feeding conditions. In summary, these results revealed the differences in intestinal microbiota among the three deer species under the same food conditions, indicating that the intestinal microbiota of the three deer species had significant differences in food adaptation. Based on this, the nutritional supply of feed for the three deer should consider the species differences. Full article

DNA sequence from a new alloherpesvirus named acipenserid herpesvirus 3 (AciHV-3) was found in sturgeon species that are vulnerable to decline globally. A study was undertaken to develop a better understanding of the virus genome and to develop diagnostic tools to support an epidemiological investigation. A 184,426 bp genome was assembled from PacBio HiFi sequences generated with DNA from a Lake Sturgeon Acipenser fulvescens gonad cell line. The AciHV-3 genome was contiguous with host chromosomal DNA and was structured with telomere-like terminal direct repeat regions, five internal direct repeat regions and a U region that included intact open reading frames encoding alloherpesvirus core proteins. Diagnostic testing conducted with a newly developed and analytically validated qPCR assay established the ubiquitous presence and high titer of AciHV-3 DNA in somatic and germline tissues from wild Lake Sturgeon in the Hudson Bay drainage basin. Phylogenetic reconstructions confirm that the monophyletic AciHV-3 lineage shares a common ancestor with AciHV-1 and that AciHV-3 taxa cluster according to their sturgeon host. The same genotype of AciHV-3 is found in disjunctive Lake Sturgeon populations within and among drainage basins. The results support the hypotheses that AciHV-3 has established latency through germline chromosomal integration, is vertically transmitted via a Mendelian pattern of inheritance, is evolving in a manner consistent with a replication competent virus and has co-evolved with its host reaching genetic fixation in Lake Sturgeon populations in central Canada. Full article

Species of the family Prosthogonimidae are considered the most pathogenic trematodes of poultry and wild birds worldwide, causing heavy economic losses in many countries. Prosthogonimosis was a common parasitic disease of Grus japonensis (Müller, 1776) which caused inflammation of the cloaca and bursa of Fabricius and even death. Morphological identifications of Prosthogonimus species are easily confusing; therefore, molecular characterization is used for discrimination. The present study was conducted to identify Prosthogonimus species at Zhalong National Nature Reserve, northeast of China. Considering the morphological variability and wide host range of individual Prosthogonimus species, a combination of both morphological and molecular analyses is indispensable for the valid identification of this parasite and the internal transcribed spacer (ITS) region was amplified for the sequence analysis and phylogenetic analysis. The results of molecular analysis together with phylogenetic reconstruction indicated that the Prosthogonimus pellucidus (von Linstow, 1873) in this study form a single cluster with P. pellucidus, revealing potentially high diversity within the genus Prosthogonimus. Classification of Prosthogonimus species seems to be unrelated to the host and may be related to geographical location. These data provide a significant resource of molecular markers for studying the taxonomy, population genetics, and systematics of Prosthogonimidae. Full article

Pleurotus tuoliensis is a unique species discovered in Xinjiang, China, which is recognized for its significant edible, medicinal, and economic value. It has been successfully incorporated into industrial production. Controversy has emerged concerning the evolution and environmental adaptability of this species due to inadequate interspecific ecology and molecular data. This study examines the germplasm resources of P. tuoliensis in the Xinjiang region. A total of 225 wild and cultivated strains of P. tuoliensis were gathered from seven representative regions. Phylogenetic analysis revealed that seven populations were notably segregated into three distinct groups, primarily attributed to environmental factors as the underlying cause for this differentiation. Population historical size data indicate that P. tuoliensis underwent two expansion events, one between 2 and 0.9 Mya (Miocene) and the other between 15 and 4 Mya (Early Pleistocene). The ancient climate fluctuations in the Xinjiang region might have contributed to the comparatively modest population size during the Pliocene epoch. Moreover, through the integration of biogeography and ancestral state reconstruction, it was determined that group C of P. tuoliensis emerged initially and subsequently dispersed to groups D and B, in that order. Subsequently, group D underwent independent evolution, whereas group B continued to diversify into groups A and EFG. The primary factor influencing this mode of transmission route is related to the geographical conditions and prevailing wind direction of each group. Subsequent research endeavors focused on assessing the domestication adaptability of P. tuoliensis to different substrates. It was found that the metabolic processes adapted during the domestication process were mainly related to energy metabolism, DNA repair, and environmental adaptability. Processes adapted to the host adaptability include responses to the host (meiosis, cell cycle, etc.) and stress in the growth environment (cysteine and methionine metabolism, sulfur metabolism, etc.). This study analyzed the systematic evolution and genetic differentiation of P. tuoliensis in Xinjiang. The identified loci and genes provide a theoretical basis for the subsequent improvement of germplasm resources and conducting molecular breeding. Full article

Viral diseases pose a significant threat to tomato crops (Solanum lycopersicum L.), one of the world’s most economically important vegetable crops. The limited genetic diversity of cultivated tomatoes contributes to their high susceptibility to viral infections. To address this challenge, tomato breeding programs must harness the genetic resources found in native populations and wild relatives. Breeding efforts may aim to develop broad-spectrum resistance against the virome. To identify the viruses naturally infecting 19 advanced lines, derived from native tomatoes, high-throughput sequencing (HTS) of small RNAs and confirmation with PCR and RT-PCR were used. Single and mixed infections with tomato mosaic virus (ToMV), tomato golden mosaic virus (ToGMoV), and pepper huasteco yellow vein virus (PHYVV) were detected. The complete consensus genomes of three variants of Mexican ToMV isolates were reconstructed, potentially forming a new ToMV clade with a distinct 3’ UTR. The absence of reported mutations associated with resistance-breaking to ToMV suggests that the Tm-1, Tm-2, and Tm-2² genes could theoretically be used to confer resistance. However, the high mutation rates and a 63 nucleotide insertion in the 3’ UTR, as well as amino acid mutations in the ORFs encoding 126 KDa, 183 KDa, and MP of Mexican ToMV isolates, suggest that it is necessary to evaluate the capacity of these variants to overcome Tm-1, Tm-2, and Tm-2² resistance genes. This evaluation, along with the characterization of advanced lines using molecular markers linked to these resistant genes, will be addressed in future studies as part of the breeding strategy. This study emphasizes the importance of using HTS for accurate identification and characterization of plant viruses that naturally infect tomato germplasm based on the consensus genome sequences. This study provides crucial insights to select appropriate disease management strategies and resistance genes and guide breeding efforts toward the development of virus-resistant tomato varieties. Full article

The human pathogen Yersinia pestis is responsible for bubonic, septicemic, and pneumonic plague. A deeply comprehensive overview of its historical context, bacteriological characteristics, genomic analysis based on ancient DNA (aDNA) and modern strains, and its impact on historical and actual human populations, is explored. The results from multiple studies have been synthesized to investigate the origins of plague, its transmission, and effects on different populations. Additionally, molecular interactions of Y. pestis, from its evolutionary origins to its adaptation to flea-born transmission, and its impact on human and wild populations are considered. The characteristic combinations of aDNA patterns, which plays a decisive role in the reconstruction and analysis of ancient genomes, are reviewed. Bioinformatics is fundamental in identifying specific Y. pestis lineages, and automated pipelines are among the valuable tools in implementing such studies. Plague, which remains among human history’s most lethal infectious diseases, but also other zoonotic diseases, requires the continuous investigation of plague topics. This can be achieved by improving molecular and genetic screening of animal populations, identifying ecological and social determinants of outbreaks, increasing interdisciplinary collaborations among scientists and public healthcare providers, and continued research into the characterization, diagnosis, and treatment of these diseases. Full article

Single-cell DNA sequencing can address the sequence of somatic genetic events during myeloid transformation in relapsed acute myeloid leukemia (AML). We present an NPM1-mutated AML patient with an initial low ratio of FLT3-ITD (low-risk ELN-2017), treated with midostaurin combined with standard chemotherapy as front-line treatment, and with salvage therapy plus gilteritinib following allogenic stem cell transplantation after relapse. Simultaneous single-cell DNA sequencing and cell-surface immunophenotyping was used in diagnostic and relapse samples to understand the clinical scenario of this patient and to reconstruct the clonal composition of both tumors. Four independent clones were present before treatment: DNMT3A/DNMT3A/NPM1 (63.9%), DNMT3A/DNMT3A (13.9%), DNMT3A/DNMT3A/NPM1/FLT3 (13.8%), as well as a wild-type clone (8.3%), but only the minor clone with FLT3-ITD survived and expanded after therapy, being the most represented one (58.6%) at relapse. FLT3-ITD was subclonal and was found only in the myeloid blast population (CD38/CD117/CD123). Our study shows the usefulness of this approach to reveal the clonal architecture of the leukemia and the identification of small subclones at diagnosis and relapse that may explain how the neoplastic cells can escape from the activity of different treatments in a stepwise process that impedes the disease cure despite different stages of complete remission. Full article

Climate change and anthropogenic habitat destruction have led to the extinction of many species. Ostrya rehderiana (Betulaceae) is a typical rare and endangered species, and only five wild individuals have survived. In the 1980s, the offspring of the five wild trees were planted for ex situ conservation and have grown into stable cultivated populations. To protect O. rehderiana resources, the genetic diversity and genetic structure of this species were analysed using SSR markers. A total of 167 alleles were detected among 116 individuals from the only wild population and five cultivated populations at 12 SSR loci. The genetic diversity level of O. rehderiana was He = 0.88. Genetic differentiations occurred among populations (Fst = 0.17), which was also validated via an analysis of molecular variance (AMOVA). The cultivated populations TM1, TM2 and WC showed considerable genetic differences from the wild population WP based on Bayesian clustering analysis, phylogenetic tree reconstruction and principal coordinate analysis (PCoA). The cultivated populations had more genetic diversity than the wild one. It is speculated that novel alleles may have emerged out of natural processes of evolution and adaptation. The cultivated population QY with the most unique alleles has begun to propagate seedlings naturally, and the small population size and geographical isolation may negatively influence the founding of this population. To weaken the effects of bottlenecks and genetic drift, anthropogenic gene flow among populations is necessary. In addition to the wild population, the cultivated population QY and six individuals from populations QY and WC were also found to be important for the conservation of O. rehderiana. The results of this study may guide the development of conservation policies for endangered O. rehderiana. Full article

Our understanding of the gene regulatory network that constitutes the circadian clock has greatly increased in recent decades, notably due to the use of Drosophila as a model system. In contrast, the analysis of natural genetic variation that enables the robust function of the clock under a broad range of environments has developed more slowly. In the current study, we analyzed comprehensive genome sequencing data from wild European populations of Drosophila, which were densely sampled through time and space. We identified hundreds of single nucleotide polymorphisms (SNPs) in nine genes associated with the clock, 276 of which exhibited a latitudinal cline in their allele frequencies. While the effect sizes of these clinal patterns were small, indicating subtle adaptations driven by natural selection, they provided important insights into the genetic dynamics of circadian rhythms in natural populations. We selected nine SNPs in different genes and assessed their impact on circadian and seasonal phenotypes by reconstructing outbred populations fixed for either of the SNP alleles, from inbred DGRP strains. The circadian free-running period of the locomotor activity rhythm was affected by an SNP in doubletime (dbt) and eyes absent (Eya). The SNPs in Clock (Clk), Shaggy (Sgg), period (per), and timeless (tim) affected the acrophase. The alleles of the SNP in Eya conferred different levels of diapause and the chill coma recovery response. Full article

Disentangling phylogenetic and phylogeographic patterns is fundamental to reconstruct the evolutionary histories of taxa and assess their actual conservation status. Therefore, in this study, for the first time, the most exhaustive biogeographic history of European wildcat (Felis silvestris) populations was reconstructed by typing 430 European wildcats, 213 domestic cats, and 72 putative admixed individuals, collected across the entire species’ distribution range, at a highly diagnostic portion of the mitochondrial ND5 gene. Phylogenetic and phylogeographic analyses identified two main ND5 lineages (D and W) roughly associated with domestic and wild polymorphisms. Lineage D included all domestic cats, 83.3% of putative admixed individuals, and also 41.4% of wildcats; these latter mostly showed haplotypes belonging to sub-clade Ia, that diverged about 37,700 years ago, long pre-dating any evidence for cat domestication. Lineage W included all the remaining wildcats and putative admixed individuals, spatially clustered into four main geographic groups, which started to diverge about 64,200 years ago, corresponding to (i) the isolated Scottish population, (ii) the Iberian population, (iii) a South-Eastern European cluster, and (iv) a Central European cluster. Our results suggest that the last Pleistocene glacial isolation and subsequent re-expansion from Mediterranean and extra-Mediterranean glacial refugia were pivotal drivers in shaping the extant European wildcat phylogenetic and phylogeographic patterns, which were further modeled by both historical natural gene flow among wild lineages and more recent wild x domestic anthropogenic hybridization, as confirmed by the finding of F. catus/lybica shared haplotypes. The reconstructed evolutionary histories and the wild ancestry contents detected in this study could be used to identify adequate Conservation Units within European wildcat populations and help to design appropriate long-term management actions. Full article

The local populations of relict plant taxa living near the limits of their geographical range are particularly vulnerable to extinction. For example, Salix lapponum is one of the rarest and most endangered glacial relicts in Western and Central Europe. In Poland, the number of its sites has dramatically decreased over the past few decades, prompting us to take conservation measures focused on saving endangered populations. During a field experiment aimed at the reconstruction of the downy willow population in the Knyszyn Forest (NE Poland), 730 individuals of the species were planted in four different natural sites. The seedlings were obtained by micropropagation from parts of vegetative individuals taken from the most abundant population of this species in eastern Poland (Lake Bikcze). The success of the reintroduction, measured by the number of individuals that survived 2–3 years in the wild and took up growth, was about 67%, however, with low flowering efficiency (7.5%). Additionally, monitoring showed significant differences in plant survival and growth rates under different habitat conditions prevailing at the site and with different cover from competing species, especially tall grasses. However, the restoration projects for relict shrub species should include periodic removal of competing plants and protection of plants from trampling and browsing by herbivorous mammals to increase reintroduction success. Full article

Peru is an important center of diversity for maize; its different cultivars have been adapted to distinct altitudes and water availability and possess an array of kernel colors (red, blue, and purple), which are highly appreciated by local populations. Specifically, Peruvian purple maize is a collection of native landraces selected and maintained by indigenous cultures due to its intense purple color in the seed, bract, and cob. This color is produced by anthocyanin pigments, which have gained interest due to their potential use in the food, agriculture, and pharmaceutical industry. It is generally accepted that the Peruvian purple maize originated from a single ancestral landrace ‘Kculli’, but it is not well understood. To study the origin of the Peruvian purple maize, we assembled the plastid genomes of the new cultivar ‘INIA 601’ with a high concentration of anthocyanins, comparing them with 27 cultivars/landraces of South America, 9 Z. mays subsp. parviglumis, and 5 partial genomes of Z. mays subsp. mexicana. Using these genomes, plus four other maize genomes and two outgroups from the NCBI database, we reconstructed the phylogenetic relationship of Z. mays. Our results suggest a polyphyletic origin of purple maize in South America and agree with a complex scenario of domestication with recurrent gene flow from wild relatives. Additionally, we identify 18 plastid positions that can be used as high-confidence genetic markers for further studies. Altogether, these plastid genomes constitute a valuable resource to study the evolution and domestication of Z. mays in South America. Full article

(1) The accuracy of patient-derived xenografts (PDXs) in predicting ADP-ribose polymerase inhibitor (PARPi) efficacy in ovarian cancer was tested, novel biomarkers were investigated, and whether PARPis could replace platinum-based chemotherapy as a first-line therapy was explored. (2) PDXs were reconstructed for 40 patients with ovarian cancer, and niraparib, olaparib and paclitaxel, and carboplatin (TC) sensitivity tests were conducted. Whole exon sequencing and homologous recombination deficiency (HRD) scores were performed, and patient clinical information was collected. The molecular biomarkers were identified by reverse-transcription quantitative PCR and immunoblotting. (3) Niraparib and olaparib sensitivity were tested in 26 patients and showed high consistency. Approximately half of BRCA wild-type, HRD-negative, and platinum-resistant patients may benefit from PARPis. AKT1 enrichment indicated PARPi resistance; high KRAS expression indicated PARPi sensitivity. CA125 below 10 U/mL during chemotherapy has a sensitivity and specificity similar to platinum sensitivity in predicting PARPi efficacy. Niraparib and TC sensitivity tests were performed on 23 patients, and TC showed a better response in this preclinical trial. (4) PDX can indicate individualized PARPi efficacy. Decreased CA125 levels and KRAS and ATK1 expression levels may be novel biomarkers. The preclinical evidence does not support the implementation of PARPis as the first-line treatment in an unselected population. Full article

Wild Foeniculum vulgare populations from the region of Istria have been subjected to a genetic and chemical study. Headspace-gas chromatography analysis of volatile secondary metabolites and PCR-RFLP analysis of the ribosomal DNA internal transcribed spacer region has been chosen to analyze the chemical and genetic traits of single plants, respectively. Large intrapopulation and interpopulation differences have been observed in both chemical profiles and restriction patterns of PCR products. The data from chemical and genetic analyses were pooled and used to assess allele frequencies of three putative genetic loci on individual populations. The pooled allele frequencies were used to determine interpopulation distances for phenogram reconstruction. The combined use of chemical and genetic datasets for genetic variation analysis proved to be a more comprehensive approach for such a study, compared to the use of single datasets, even using such relatively simple analytical tools. Full article