Taenioides sp. is a small temperate fish originally known to inhabit muddy bottoms of brackish waters in coastal areas of China. However, it began to invade multiple inland freshwaters and caused severe damage to Chinese aquatic ecosystems in recent years. To investigate the sources and invasive history of this species, we examined the population structure of 141 individuals collected from seven locations based on partial mitochondrial D-loop regions. The results revealed that the genetic diversity gradually decreased from south to north, with the Yangtze River Estuary and Taihu Lake populations possessing the highest haplotype diversity (Hd), average number of differences (k), and nucleotide diversity (π) values, suggesting that they may be the sources of Taenioides sp. invasions. Isolation-by-distance analysis revealed a non-significant correlation (p = 0.166) between genetic and geographic distances among seven populations, indicating that dispersal mediated through the regional hydraulic projects may have played an essential role in Taenioides sp. invasions. The population genetic structure analysis revealed two diverged clades among seven populations, with clade 2 only detected in source populations, suggesting a possible difference in the invasion ability of the two clades. Our results provide insights into how native estuary fish become invasive through hydraulic projects and may provide critical information for the future control of this invasive species.

Ethiopia has about 52 million indigenous goats with marked phenotypic variability, which is the outcome of natural and artificial selection. Here, we obtained whole-genome sequence data of three Ethiopian indigenous goat populations (Arab, Fellata, and Oromo) from northwestern Ethiopia and analyzed their genome-wide genetic diversity, population structure, and signatures of selection. We included genotype data from four other Ethiopian goat populations (Abergelle, Keffa, Gumuz, and Woyto-Guji) and goats from Asia; Europe; and eastern, southern, western, and northern Africa to investigate the genetic predisposition of the three Ethiopian populations and performed comparative genomic analysis. Genetic diversity analysis showed that Fellata goats exhibited the lowest heterozygosity values (Ho = 0.288 ± 0.005 and He = 0.334 ± 0.0001). The highest values were observed in Arab goats (Ho = 0.310 ± 0.010 and He = 0.347 ± 4.35e-05). A higher inbreeding coefficient (FROH = 0.137 ± 0.016) was recorded for Fellata goats than the 0.105 ± 0.030 recorded for Arab and the 0.112 ± 0.034 recorded for Oromo goats. This indicates that the Fellata goat population should be prioritized in future conservation activities. The three goat populations showed the majority (∼63%) of runs of homozygosity in the shorter (100-150 Kb) length category, illustrating ancient inbreeding and/or small founder effects. Population relationship and structure analysis separated the Ethiopian indigenous goats into two distinct genetic clusters lacking phylogeographic structure. Arab, Fellata, Oromo, Abergelle, and Keffa represented one genetic cluster. Gumuz and Woyto-Guji formed a separate cluster and shared a common genetic background with the Kenyan Boran goat. Genome-wide selection signature analysis identified nine strongest regions spanning 163 genes influencing adaptation to arid and semi-arid environments (HOXC12, HOXC13, HOXC4, HOXC6, and HOXC9, MAPK8IP2), immune response (IL18, TYK2, ICAM3, ADGRG1, and ADGRG3), and production and reproduction (RARG and DNMT1). Our results provide insights into a thorough understanding of genetic architecture underlying selection signatures in Ethiopian indigenous goats in a semi-arid tropical environment and deliver valuable information for goat genetic improvement, conservation strategy, genome-wide association study, and marker-assisted breeding.

Bryophytes, known as poikilohydric plants, possess vegetative desiccation-tolerant (DT) ability to withstand water deficit stress. Consequently, they offer valuable genetic resources for enhancing resistance to water scarcity stress. In this research, we examined the physiological, phytohormonal, and transcriptomic changes in DT mosses Calohypnum plumiforme from two populations, with and without desiccation treatment. Comparative analysis revealed population differentiation at physiological, gene sequence, and expression levels. Under desiccation stress, the activities of superoxide dismutase (SOD) and peroxidase (POD) showed significant increases, along with elevation of soluble sugars and proteins, consistent with the transcriptome changes. Notable activation of the bypass pathway of JA biosynthesis suggested their roles in compensating for JA accumulation. Furthermore, our analysis revealed significant correlations among phytohormones and DEGs in their respective signaling pathway, indicating potential complex interplays of hormones in C plumiforme. Protein phosphatase 2C (PP2C) in the abscisic acid signaling pathway emerged as the pivotal hub in the phytohormone crosstalk regulation network. Overall, this study was one of the first comprehensive transcriptome analyses of moss C. plumiforme under slow desiccation rates, expanding our knowledge of bryophyte transcriptomes and shedding light on the gene regulatory network involved in response to desiccation, as well as the evolutionary processes of local adaptation across moss populations.

Eucalyptus pellita has the characteristics of rapid growth and high resistance. However, there is little research on molecular breeding of E. pellita, which is essential to shortening breeding life and selecting quality varieties. Therefore, a crucial step before selective breeding can be carried out to increase the wood quality of E. pellita is identifying genetic diversity and population structure using single nucleotide polymorphism (SNP) markers. In this study, the genetic diversity of 1st generation 196 E. pellita families from 23 geographically defined was assessed using 1,677,732 SNP markers identified by whole genome resequencing. SNP annotation showed that the ratio of non-synonymous to synonymous coding mutations was 0.83. Principal component analysis (PCA), phylogenetic tree, and population structure analysis permitted the families to be categorized into three groups, one of which (G2) contains most of the Indonesian (IDN) and Papua New Guinea (PNG) families. Genetic relationship analysis showed that IDN was closely related to PNG. Genetic diversity analysis showed that He, PIC, I, and H mean values were 0.2502, 0.2027, 0.3815, and 0.2680, respectively. PCA analysis classified various provenances in QLD into two categories (G1 and G3). The genetic diversity of G3 was higher than that of G2. The results of genetic differentiation (Fst) showed that PNG region was divided into two groups (PNG1 and PNG2), the Fst (0.172) between QLD and PNG2 region was higher than QLD and PNG1, and the Fst (0.024) between IDN and PNG1 is smaller than IDN and PNG2. A Mantel test revealed a positive correlation between the genetic and geographic distance of E. pellita. This study has a certain reference value for genetic identification, germplasm preservation, and breeding of E. pellita. Also, it provides a basis for subsequent association analysis to explore excellent alleles and introduction.

The major histocompatibility complex (MHC) plays a key role in the adaptive immune response to pathogens due to its extraordinary polymorphism. However, the spatial patterns of MHC variation in the striped hamster remain unclear, particularly regarding the relative contribution of the balancing selection in shaping MHC spatial variation and diversity compared to neutral forces.
In this study, we investigated the immunogenic variation of the striped hamster in four wild populations in Inner Mongolia which experience a heterogeneous parasitic burden. Our goal was to identify local adaptation by comparing the genetic structure at the MHC with that at seven microsatellite loci, taking into account neutral processes.
We observed significant variation in parasite pressure among sites, with parasite burden showing a correlation with temperature and precipitation. Molecular analysis revealed a similar co-structure between MHC and microsatellite loci. We observed lower genetic differentiation at MHC loci compared to microsatellite loci, and no correlation was found between the two.
Overall, these results suggest a complex interplay between neutral evolutionary forces and balancing selection in shaping the spatial patterns of MHC variation. Local adaptation was not detected on a small scale but may be applicable on a larger scale.

Saussurea medusa Maxim. is a typical \"sky island\" species and one with the highest altitude distributions among flowering plants. The present study aimed at analyzing the genetic diversity and population structure of 300 S. medusa accessions collected from 20 populations in the Qilian Mountains in the northeastern Qinghai-Tibet Plateau (QTP), using sequence-related amplified polymorphism (SRAP) markers. A total of 14 SRAP primer combinations were employed to analyze genetic diversity and population structure across all accessions. Out of 511 amplified bands, 496 (97.06%) were polymorphic. The populations in the eastern Qilian Mountains had significantly higher genetic diversity than those in the central and western groups. Population structure analysis revealed greater genetic differentiation among populations with a Gst of 0.4926. UPGMA-based clustering classified the 300 S. medusa accessions into 3 major clusters, while the Bayesian STRUCTURE analysis categorized them into 2 groups. Correlation analyses showed that the genetic affinity of the populations was based on differences in geographical distance, moisture conditions, and photothermal conditions between the habitats. This study represents the first comprehensive genetic assessment of S. medusa and provides important genetic baseline data for the conservation of the species.

Rapid adaptive evolution and phenotypic plasticity are two mechanisms that often underlie invasiveness of alien plant species, but whether they can co-occur within invasive plant populations under altered environmental conditions such as nitrogen (N) enrichment has seldom been explored. Latitudinal clines in plant trait responses to variation in environmental factors may provide evidence of local adaptation. Here, we inferred the relative contributions of phenotypic plasticity and local adaptation to the performance of the invasive plant Ambrosia artemisiifolia under different soil N levels, using a common garden approach. We grew A. artemisiifolia individuals raised from seeds that were sampled from six invasive populations along a wide latitudinal cline in China (23°42\' N to 45°43\' N) under three N (0, 5, and 10 g N m-2 ) levels in a common garden. Results show significant interpopulation genetic differentiation in plant height, number of branches, total biomass, and transpiration rate of the invader A. artemisiifolia across the N treatments. The populations also expressed genetic differentiation in basal diameter, growth rate, leaf area, seed width, root biomass, aboveground biomass, stomatal conductance, and intercellular CO2 concentration regardless of N treatments. Moreover, plants from different populations of the invader displayed plastic responses in time to first flower, hundred-grain weight, net photosynthetic rate, and relative biomass allocation to roots and shoots and seed length under different N treatments. Additionally, individuals of A. artemisiifolia from higher latitudes grew shorter and allocated less biomass to the roots regardless of N treatment, while latitudinal cline (or lack thereof) in other traits depended on the level of N in which the plants were grown. Overall, these results suggest that rapid adaptive evolution and phenotypic plasticity in the various traits that we quantified may jointly contribute to invasiveness of A. artemisiifolia under different levels of N availability. More broadly, the results support the idea that phenotypic plasticity and rapid adaptive evolution can jointly enable invasive plants to colonize a wide range of environmental conditions.
快速适应进化和表型可塑性是阐释外来植物入侵的两个机制，但是它们是否可以在变化的环境条件下(比如氮富集)同时作用于入侵种群，这方面的研究还不多。植物性状对环境因子变化响应的纬度趋势可能提供了局域适应的证据。本文采用同质园实验的方法，探究表现可塑性和局域适应对入侵植物豚草(Ambrosia artemisiifolia)在不同土壤氮水平下表现的相对贡献。我们沿中国纬度梯度(23°42′ N-45°43′ N)收集六个豚草入侵种群的种子，分别设置三个氮水平(0，5以及10 g N m−2 )种植在同质园中。结果表明，在不同的氮水平下，入侵豚草的株高、分枝数、总生物量和蒸腾速率存在显著的种群间遗传差异。在三种氮处理水平下，基径、生长速率、叶面积、种子宽度、根生物量、地上生物量、气孔导度和胞间二氧化碳浓度在种群间也存在遗传分化。在不同的氮处理下，来自不同种群的豚草植株在开花时间、百粒重、净光合速率、根冠比以及种子长度上表现出可塑性响应。此外，在所有氮处理水平下，来自更高纬度种群的豚草个体株高较小，分配到根部的生物量较少，而其他性状的纬度差异取决于氮处理水平。总之，研究结果表明，我们测量的各种性状中的快速适应性进化和表型可塑性可能联合作用，共同促进豚草在不同的氮水平下的入侵。广而言之，研究结果支持表型可塑性和快速适应性进化可以共同促进入侵植物在不同环境条件下定殖。.

Investigating the genetic mechanisms of local adaptation is critical to understanding how species adapt to heterogeneous environments. In the present study, we analyzed restriction site-associated DNA sequencing (RADseq) data in order to explore genetic diversity, genetic structure, genetic differentiation, and local adaptation of Stipa breviflora. In total, 135 individual plants were sequenced and 25,786 polymorphic loci were obtained. We found low genetic diversity (He = 0.1284) within populations of S. breviflora. Four genetic clusters were identified along its distribution range. The Mantel test, partial Mantel test, and multiple matrix regression with randomization (MMRR) indicate that population differentiation was caused by both geographic distance and environmental factors. Through the FST outlier test and environmental association analysis (EAA), 113 candidate loci were identified as putatively adaptive loci. RPK2 and CPRF1, which are associated with meristem maintenance and light responsiveness, respectively, were annotated. To explore the effects of climatic factors on genetic differentiation and local adaptation of S. breviflora, gradient forest (GF) analysis was applied to 25,786 single nucleotide polymorphisms (SNPs) and 113 candidate loci, respectively. The results showed that both temperature and precipitation affected the genetic differentiation of S. breviflora, and precipitation was strongly related to local adaptation. Our study provides a theoretical basis for understanding the local adaptation of S. breviflora.

BACKGROUND: As an important source of genetic variation, copy number variation (CNV) can alter the dosage of DNA segments, which in turn may affect gene expression level and phenotype. However, our knowledge of CNV in apple is still limited. Here, we obtained high-confidence CNVs and investigated their functional impact based on genome resequencing data of two apple populations, cultivars and wild relatives.
RESULTS: In this study, we identified 914,610 CNVs comprising 14,839 CNV regions (CNVRs) from 346 apple accessions, including 289 cultivars and 57 wild relatives. CNVRs summed to 71.19 Mb, accounting for 10.03% of the apple genome. Under the low linkage disequilibrium (LD) with nearby SNPs, they could also accurately reflect the population structure of apple independent of SNPs. Furthermore, A total of 3,621 genes were covered by CNVRs and functionally involved in biological processes such as defense response, reproduction and metabolic processes. In addition, the population differentiation index ([Formula: see text]) analysis between cultivars and wild relatives revealed 127 CN-differentiated genes, which may contribute to trait differences in these two populations.
CONCLUSIONS: This study was based on identification of CNVs from 346 diverse apple accessions, which to our knowledge was the largest dataset for CNV analysis in apple. Our work presented the first comprehensive CNV map and provided valuable resources for understanding genomic variations in apple.

Antarctic krill (Euphausia superba) is Earth\'s most abundant wild animal, and its enormous biomass is vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome-level Antarctic krill genome, whose large genome size appears to have resulted from inter-genic transposable element expansions. Our assembly reveals the molecular architecture of the Antarctic krill circadian clock and uncovers expanded gene families associated with molting and energy metabolism, providing insights into adaptations to the cold and highly seasonal Antarctic environment. Population-level genome re-sequencing from four geographical sites around the Antarctic continent reveals no clear population structure but highlights natural selection associated with environmental variables. An apparent drastic reduction in krill population size 10 mya and a subsequent rebound 100 thousand years ago coincides with climate change events. Our findings uncover the genomic basis of Antarctic krill adaptations to the Southern Ocean and provide valuable resources for future Antarctic research.