Structural Divergence Research Articles

Complex cycles of divergence and migration shape lineage structure in the common kingsnake species complex.

The Nearctic is a complex patchwork of habitats and geologic features that form barriers to gene flow resulting in phylogeographic structure and speciation in many lineages. Habitats are rarely stable over geologic time, and the Nearctic has undergone major climatic changes in the past few million years. We use the common kingsnake species complex to study how climate, geography, and history influence lineage formation over a large, complex landscape. Nearctic/North America. Common kingsnake, Lampropeltis getula, species complex. We analyzed genome-wide sequence data from 51 snakes spanning the majority of the species complex's range. We used population clustering, generalized dissimilarity modeling, and coalescent methods to identify the number of genetic clusters within the L. getula complex, infer the environmental correlates of genetic differentiation, and estimate models of divergence and gene flow among lineages. We identified three major lineages within the L. getula complex and further continuous spatial structure within lineages. The most important ecological correlates of genetic distance in the complex are related to aridity and precipitation, consistent with lineage breaks at the Great Plains/Desert ecotone and the Cochise Filter Barrier. Lineages are estimated to have undergone multiple rounds of isolation and secondary contact, with highly asymmetric migration occurring at present. Changing climates combined with a large and geologically complex landscape have resulted in a mosaic of discrete and spatially continuous genetic structure. Multiple rounds of isolation and secondary contact as climate fluctuated over the past ~4.4 My have likely driven the evolution of discrete lineages that maintain high levels of gene flow. Continuous structure is strongly shaped by aridity and precipitation, suggesting roles for major precipitation gradients in helping to maintain lineage identity in the face of gene flow when lineages are in geographic contact.

Poly(rC)-binding proteins as pleiotropic regulators in hematopoiesis and hematological malignancy.

Poly(rC)-binding proteins (PCBPs), a defined subfamily of RNA binding proteins, are characterized by their high affinity and sequence-specific interaction with poly-cytosine (poly-C). The PCBP family comprises five members, including hnRNP K and PCBP1-4. These proteins share a relatively similar structure motif, with triple hnRNP K homology (KH) domains responsible for recognizing and combining C-rich regions of mRNA and single- and double-stranded DNA. Numerous studies have indicated that PCBPs play a prominent role in hematopoietic cell growth, differentiation, and tumorigenesis at multiple levels of regulation. Herein, we summarized the currently available literature regarding the structural and functional divergence of various PCBP family members. Furthermore, we focused on their roles in normal hematopoiesis, particularly in erythropoiesis. More importantly, we also discussed and highlighted their involvement in carcinogenesis, including leukemia and lymphoma, aiming to clarify the pleiotropic roles and molecular mechanisms in the hematopoietic compartment.

Highly-ordered arrangement of Co(OH)F filaments: Planting flower-like Co(OH)F in conductive membrane substrate accelerating Li+ transfer and redox reaction in Li–S batteries

Here, the conventionally disordered Co(OH)F filaments are rearranged to form highly-ordered flower-like Co(OH)F architectures in a conductive membrane substrate. The important findings contribute to designing delicate nanostructures and improving the catalytic activity of advanced materials for energy applications. The hierarchically porous CNT@NC membrane with CNT as the core and N-doped carbon as the crosslinking shell is scalably designed firstly for strengthening the transport of Li+ and electrons in the electrode, providing an ultrahigh porosity for growing flower-like Co(OH)F on both surfaces and interior of the membrane, as well as offering electrons for the redox reactions through the roots of the Co(OH)F flowers. Furthermore, the ordered Co(OH)F bundles with divergent and open-ended structures provide the catalyst with the broad reaction interface and active sites for polysulfides (LiPSs) anchoring and catalytic conversion at a low energy barrier, significantly facilitating the diffusion of ions and electrolyte in the catalyst, and thus effectively alleviating the shuttle effect. Owing to the synergistic effect between the conductive membrane substrate and the grown Co(OH)F catalyst, the Co(OH)F-CNT@NC cathode generates a high reversible capacity and excellent long-term cycling performance (622 mAh·g−1 at 1C after 600 cycles). Conclusively, the proposed facile strategy provides insights regarding the design of novel cathode materials for high-areal-capacity Li–S batteries.

Metagenomic Insights into Microbial Community Structure, Function, and Salt Adaptation in Saline Soils of Arid Land, China.

Soil salinization is spread in the dryland of NW China due to the dry or extreme dry climate. Increased salinization damages the health and function of soil systems and influences the microbial community structure and function. Some studies have been conducted to reveal the microbial community structure and isolate the microorganisms of saline soil or salt-lake sediments in this region. However, the functions of microorganisms and their response to salinization, i.e., their adaptation strategy to a wide salinization range in arid environments, are less understood. Here, we applied metagenomics technology to investigate the microbial community structure, function, and their relationship with salinization, and discussed the adaptative strategy of microorganisms to different saline environments. A total of 42 samples were sequenced on the Illumina PE500 platform. The archaea and bacteria constituted the dominant kingdoms; Actinobacteria, Proteobacteria, Bacteroidetes, and Firmicutes were the dominant bacterial phyla; and Euryarchaeota were the dominant archaeal phylum. The microbial communities showed significant structure divergence according to the salt concentration (saline (mean EC 22 mS/cm) and hypersaline (mean EC 70 mS/cm)), wherein the communities were dominated by bacteria in saline soils and archaea in hypersaline soils. Most of the dominant bacterial representation decreased with salinity, while the archaea increased with salinity. KEGG functional annotation showed that at level 2, the cell motility, environmental adaptation, signal transduction, signaling molecules and interaction, glycan biosynthesis and metabolism, and metabolism of other amino acids were reduced from saline to hypersaline, whereas the metabolism of cofactors and vitamins, folding sorting and degradation, replication and repair, transcription and translation, amino acid biosynthesis, glycolysis/gluconeogenesis, and carbon fixation increased with salinity. The increased salt content decreased the carbohydrate activities of microorganisms. The osmolyte regulation substance synthesis and absorption-related genes were more abundant in saline soils than in hypersaline soils, whereas the Na+/H+ antiporter genes (mnhB-E) and H+/Na+-transporting ATPase genes (atpA-F, I, K) were significantly higher in hypersaline soils. This indicated that in saline soils, microorganisms primarily synthesize and/or uptake compatible solutes to cope with osmotic stress, whereas in the hypersaline habitat, the high-salt-in strategy was predicated to be adopted by the halophilic/extremely halophilic microorganisms, coupled with a high abundance of replication and repair, cofactors and vitamin metabolism, nucleotide metabolism, and carbon fixation to provide energy and ensure cell regeneration. In conclusion, increases in salinity influence the microbial communities' structure and function, as well as the adaptation of microorganisms.

Holographic complexity of LST and single trace Toverline{T} , Joverline{T} and Toverline{J} deformations

This work is an extension of our previous work [1] where we exploited holography to compute the complexity characteristics of Little String Theory (LST), a nonlocal, nongravitational field theory which flows to a local 2d CFT in the IR under RG via an integrable irrelevant left(Toverline{T}right) deformation. Here we look at the more general LST obtained by UV deforming the 2d CFT by incorporating Lorentz violating irrelevant Joverline{T} and Toverline{J} deformations on top of Toverline{T} deformation, in an effort to capture the novel signatures of Lorentz violation (on top of nonlocality) on quantum complexity. In anticipation of the fact that the dual field theory is Lorentz violating, we compute the volume complexity in two different Lorentz frames and the comparison is drawn between the results. It turns out that for this system the nonlocality and Lorentz violation effects are inextricably intertwined in the UV divergence structure of the quantum complexity. The coefficients of the divergences carry the signature of Lorentz boost violation. We also compute the subregion complexity which displays a (Hagedorn) phase transition with the transition point being the same as that for the phase transition of entanglement entropy [2]. These new results are consistent with our previous work [1]. Null warped AdS3 is treated as special case of interest.

Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements

Mitoribosomes of green algae display a great structural divergence from their tracheophyte relatives, with fragmentation of both rRNA and proteins as a defining feature. Here, we report a 2.9 Å resolution structure of the mitoribosome from the alga Polytomella magna harbouring a reduced rRNA split into 13 fragments. We found that the rRNA contains a non-canonical reduced form of the 5S, as well as a permutation of the LSU domain I. The mt-5S rRNA is stabilised by mL40 that is also found in mitoribosomes lacking the 5S, which suggests an evolutionary pathway. Through comparison to other ribosomes with fragmented rRNAs, we observe that the pattern is shared across large evolutionary distances, and between cellular compartments, indicating an evolutionary convergence and supporting the concept of a primordial fragmented ribosome. On the protein level, eleven peripherally associated HEAT-repeat proteins are involved in the binding of 3′ rRNA termini, and the structure features a prominent pseudo-trimer of one of them (mL116). Finally, in the exit tunnel, mL128 constricts the tunnel width of the vestibular area, and mL105, a homolog of a membrane targeting component mediates contacts with an inner membrane bound insertase. Together, the structural analysis provides insight into the evolution of the ribosomal machinery in mitochondria.

Genetic diversity and population structure of bighead carp (Hypophthalmichthys nobilis) from the middle and lower reaches of the Yangtze River revealed using microsatellite markers

The bighead carp, Hypophthalmichthys nobilis, is one of the most economically important freshwater fish species native to China. In recent decades, fishery resources of the bighead carp in the Yangtze River have been severely depleted, and there is limited information on the genetic features of the bighead carp in the Yangtze River. In this study, we analyzed the genetic divergence and population structure of bighead carps from 8 populations in the middle and lower reaches of the Yangtze River by using 15 microsatellite DNA markers. A relatively high genetic diversity was detected in the populations, with similar Ho and He (0.694–0.769 and 0.706–0.734, respectively). Weak genetic differentiation was found among the populations (Fst = 0.02, p < 0.01); and admixture of genetic clusters was generally present at the individual level. The Mantel test demonstrated a low correlation between genetic and geographic distances (r = 0.442, p < 0.01), implying admixture was partly due to dispersal between contiguous populations. Different relative directional migration rates (0.23–1.00) were inferred between population pairs, indicating the presence of both directional gene flows (dispersals). In addition, no significant heterozygosity excess was found in any of the populations (p > 0.05), and normal distribution of allele frequency indicated that no recent genetic bottleneck had occurred in any population. In summary, we found high diversity and weak genetic structuring within bighead carp populations in the middle and lower reaches of the Yangtze River, suggesting that genetic connectivity exists across these sections and the decline in fishery resource in the recent decades has not resulted in a bottleneck effect in this fish species. These findings provide vital genetic information on the bighead carp as well as a baseline for future conservation and breeding programs.

Comparative and evolutionary analysis of RIP kinases in immune responses.

The group of receptor-interacting protein (RIP) kinases has seven members (RIPK1–7), with one homologous kinase domain but distinct non-kinase regions. Although RIPK1–3 have emerged as key modulators of inflammation and cell death, few studies have connected RIPK4–7 to immune responses. The divergence in domain structures and paralogue information in the Ensembl database have raised question about the phylogeny of RIPK1–7. In this study, phylogenetic trees of RIPK1–7 and paralogues constructed using full-length amino acid sequences or Kinase domain demonstrate that RIPK6 and RIPK7 are distinct from RIPK1–5 and paralogues shown in the Ensembl database are inaccurate. Comparative and evolutionary analyses were subsequently performed to gain new clues about the potential functions of RIPK3–7. RIPK3 gene loss in birds and animals that undergo torpor, a common physiological phenomenon in cold environments, implies that RIPK3 may be involved in ischemia-reperfusion injury and/or high metabolic rate. The negligible expression of RIPK4 and RIPK5 in immune cells is likely responsible for the lack of studies on the direct role of these members in immunity; RIPK6 and RIPK7 are conserved among plants, invertebrates and vertebrates, and dominantly expressed in innate immune cells, indicating their roles in innate immunity. Overall, our results provide insights into the multifaceted and conserved biochemical functions of RIP kinases.

Grazing season regulates plant community structure and production by altering plant litter mass in a typical steppe

AbstractAimsGrazing different grasslands with seasonal changes is the tradition in pastoral systems in natural grassland regions worldwide. The effects and mechanisms of different grazing seasons on semi‐arid steppe vegetation are less explored on the Mongolian Plateau. Therefore, we assessed the impact and underlying mechanisms of grazing seasons on grassland community structure and production.LocationXilingol, Inner Mongolia, China.MethodsWe conducted a three‐year experiment to investigate the effects of grazing in four different seasons under the same grazing intensities on plant community structure and production in a typical steppe rangeland. The experiment was a random‐block design, with 20 grassland paddocks of 50 m × 50 m, representing five treatments (i.e., early spring, summer, autumn, mid‐winter, and no grazing), replicated by four blocks. We monitored the changes in soil properties, plant litter mass (i.e., standing dead biomass and dead plant material on the soil surface) and plant species composition and production across grazing treatments.ResultsPlant community height and above‐ground biomass were higher under early spring and winter grazing than autumn and summer grazing and no grazing. This divergence in plant community structure was mainly mediated by the seasonal patterns of plant litter mass across the grazing regimes. A high plant litter mass enhanced soil moisture by accumulating snow in winter and reducing soil evaporation during the growing season, which benefit plant growth. The removal of plant litter before the growing season increased the reception of solar radiation, thus improving soil temperature and plant production. The changes in community microenvironment and selective grazing led to the changes in plant species composition especially under summer and autumn grazing.ConclusionsOur results imply that grazing in winter or in early spring before plants start to turn green is more efficient than the complete animal exclusion for the natural recovery of degraded grassland in Inner Mongolia. It is suitable to incorporate cold‐season grazing in the development of sustainable grassland management systems.

High-density genomic data reveal fine-scale population structure and pronounced islands of adaptive divergence in lake whitefish (Coregonus clupeaformis) from Lake Michigan.

Understanding patterns of genetic structure and adaptive variation in natural populations is crucial for informing conservation and management. Past genetic research using 11 microsatellite loci identified six genetic stocks of lake whitefish (Coregonus clupeaformis) within Lake Michigan, USA. However, ambiguity in genetic stock assignments suggested those neutral microsatellite markers did not provide adequate power for delineating lake whitefish stocks in this system, prompting calls for a genomics approach to investigate stock structure. Here, we generated a dense genomic dataset to characterize population structure and investigate patterns of neutral and adaptive genetic diversity among lake whitefish populations in Lake Michigan. Using Rapture sequencing, we genotyped 829 individuals collected from 17 baseline populations at 197,588 SNP markers after quality filtering. Although the overall pattern of genetic structure was similar to the previous microsatellite study, our genomic data provided several novel insights. Our results indicated a large genetic break between the northwestern and eastern sides of Lake Michigan, and we found a much greater level of population structure on the eastern side compared to the northwestern side. Collectively, we observed five genomic islands of adaptive divergence on five different chromosomes. Each island displayed a different pattern of population structure, suggesting that combinations of genotypes at these adaptive regions are facilitating local adaptation to spatially heterogenous selection pressures. Additionally, we identified a large linkage disequilibrium block of ~8.5Mb on chromosome 20 that is suggestive of a putative inversion but with a low frequency of the minor haplotype. Our study provides a comprehensive assessment of population structure and adaptive variation that can help inform the management of Lake Michigan's lake whitefish fishery and highlights the utility of incorporating adaptive loci into fisheries management.

Contrasting drought legacy effects on gross primary productivity in a mixed versus pure beech forest

Abstract. Droughts affect terrestrial ecosystems directly and concurrently and can additionally induce lagged effects in subsequent seasons and years. Such legacy effects of drought on vegetation growth and state have been widely studied in tree ring records and satellite-based vegetation greenness, while legacies on ecosystem carbon fluxes are still poorly quantified and understood. Here, we focus on two ecosystem monitoring sites in central Germany with a similar climate but characterised by different species and age structures. Using eddy covariance measurements, we detect legacies on gross primary productivity (GPP) by calculating the difference between random forest model estimates of potential GPP and observed GPP. Our results showed that, at both sites, droughts caused significant legacy effects on GPP at seasonal and annual timescales, which were partly explained by reduced leaf development. The GPP reduction due to drought legacy effects is of comparable magnitude to the concurrent drought effects but differed between two neighbouring forests with divergent species and age structures. The methodology proposed here allows the quantification of the temporal dynamics of legacy effects at the sub-seasonal scale and the separation of legacy effects from model uncertainties. The application of the methodology at a larger range of sites will help us to quantify whether the identified lag effects are general and on which factors they may depend.

Plastome structure, phylogenomics, and divergence times of tribe Cinnamomeae (Lauraceae)

BackgroundTribe Cinnamomeae is a species-rich and ecologically important group in tropical and subtropical forests. Previous studies explored its phylogenetic relationships and historical biogeography using limited loci, which might result in biased molecular dating due to insufficient parsimony-informative sites. Thus, 15 plastomes were newly sequenced and combined with published plastomes to study plastome structural variations, gene evolution, phylogenetic relationships, and divergence times of this tribe.ResultsAmong the 15 newly generated plastomes, 14 ranged from 152,551 bp to 152,847 bp, and the remaining one (Cinnamomum chartophyllum XTBGLQM0164) was 158,657 bp. The inverted repeat (IR) regions of XTBGLQM0164 contained complete ycf2, trnICAU, rpl32, and rpl2. Four hypervariable plastid loci (ycf1, ycf2, ndhF-rpl32-trnLUAG, and petA-psbJ) were identified as candidate DNA barcodes. Divergence times based on a few loci were primarily determined by prior age constraints rather than by DNA data. In contrast, molecular dating using complete plastid protein-coding genes (PCGs) was determined by DNA data rather than by prior age constraints. Dating analyses using PCGs showed that Cinnamomum sect. Camphora diverged from C. sect. Cinnamomum in the late Oligocene (27.47 Ma).ConclusionsThis study reports the first case of drastic IR expansion in tribe Cinnamomeae, and indicates that plastomes have sufficient parsimony-informative sites for molecular dating. Besides, the dating analyses provide preliminary insights into the divergence time within tribe Cinnamomeae and can facilitate future studies on its historical biogeography.

Single-Ion Behavior in New 2-D and 3-D Gadolinium 4f7 Materials: CsGd(SO4)2 and Cs[Gd(H2O)3(SO4)2]·H2O.

The recent creation of 4f7 gadolinium materials has enabled vital studies of the free-ion properties of the Gd(III) cations. While the 8 S ground state in a trivalent Gd compound is, in principle, isotropic, it has been demonstrated that there is a residual orbital angular momentum affected by the crystal field and structural distortion in certain systems. By exploiting the atomistic control innate to material growth, we address a fundamental question of how the isotropic nature of Gd(III) is preserved in different dimensionalities of crystal structures. To achieve this, we designed two new trivalent Gd materials possessing two structurally distinct features, a 2-D CsGd(SO4)2 and a 3-D Cs[Gd(H2O)3(SO4)2]·H2O. The tunability of the structural dimension is facilitated by O-H---O hydrogen bonds. The structural divergence between the two compounds allows us to investigate each material individually and make a comparison between them regarding their physical properties as a function of lattice dimension. Our results demonstrate that structural dimensions have a negligible effect on the single-ion behavior of the materials. Magnetization measurements for the Gd(III) complexes yielded paramagnetic states with the isotropic spin-only nature. Specific heat data suggest that there is a lack of magnetic phase transition down to T = 1.8 K, and coupled lattice vibrations in the materials are attributable to strong covalent bonding characters of the (SO4)2- and H2O ligands. This work offers a pathway for retaining the single-ion property of Gd(III) while constructing the large spin magnetic moment S = 7/2 in large-scale extended frameworks.

Autopolyploid inheritance and a heterozygous reciprocal translocation shape chromosome genetic behavior in tetraploid blueberry (Vaccinium corymbosum).

Understanding chromosome recombination behavior in polyploidy species is key to advancing genetic discoveries. In blueberry, a tetraploid species, the line of evidences about its genetic behavior still remain poorly understood, owing to the inter-specific, and inter-ploidy admixture of its genome and lack of in depth genome-wide inheritance and comparative structural studies. Here we describe a new high-quality, phased, chromosome-scale genome of a diploid blueberry, clone W85. The genome was integrated with cytogenetics and high-density, genetic maps representing six tetraploid blueberry cultivars, harboring different levels of wild genome admixture, to uncover recombination behavior and structural genome divergence across tetraploid and wild diploid species. Analysis of chromosome inheritance and pairing demonstrated that tetraploid blueberry behaves as an autotetraploid with tetrasomic inheritance. Comparative analysis demonstrated the presence of a reciprocal, heterozygous, translocation spanning one homolog of chr-6 and one of chr-10 in the cultivar Draper. The translocation affects pairing and recombination of chromosomes 6 and 10. Besides the translocation detected in Draper, no other structural genomic divergences were detected across tetraploid cultivars and highly inter-crossable wild diploid species. These findings and resources will facilitate new genetic and comparative genomic studies in Vaccinium and the development of genomic assisted selection strategy for this crop.

Mitochondrial DNA cytochrome-b assisted DNA barcoding for the exploration of spatio-genetic variation among the population of Labeo rohita from different parts of India

Labeo rohita, of the Cyprinidae family, is one of the most important fish species in any aquaculture system, with immense potential in terms of both commercial production and biodiversity maintenance. Accordingly, in order to find out the spatio-genetic variation and uncover any divergence in the population structure among the Labeo rohita population, partial sequencing of the 425 bp cytochrome b (mt Cytb ) gene was carried out. The study revealed the presence of eleven haplotypes with nine polymorphic sites, of which 2 are singleton sites and six parsimony informative sites. It was observed that the haplotypes obtained from the same water system clustered separately, which suggests the variability due to the spatial distribution of the population in different environmental conditions. These detected high phenotypic differences between the rivers lead us to think and investigate that the divergent populations may have evolved over time and have been undergoing mutation. They may undergo micro-evolutionary processes and differentiate into genetically distinct sub-populations or stocks over time if reproductively and geographically isolated. Thus, the study signifies the presence of the huge biodiversity of Labeo rohita in the Indian River systems, which helps the species to adapt to the environmental changes and will also prove helpful for the breeding of new and better adaptable strains suitable for the climate change scenario.

BESFA: bioinformatics based evolutionary, structural & functional analysis of Prostate, Placenta, Ovary, Testis, and Embryo (POTE) paralogs

The POTE family comprises 14 paralogues and is primarily expressed in Prostate, Placenta, Ovary, Testis, Embryo (POTE), and cancerous cells. The prospective function of the POTE protein family under physiological conditions is less understood. We systematically analyzed their cellular localization and molecular docking analysis to elucidate POTE proteins' structure, function, and Adaptive Divergence. Our results suggest that group three POTE paralogs (POTEE, POTEF, POTEI, POTEJ, and POTEKP (a pseudogene)) exhibits significant variation among other members could be because of their Adaptive Divergence. Furthermore, our molecular docking studies on POTE protein revealed the highest binding affinity with NCI-approved anticancer compounds. Additionally, POTEE, POTEF, POTEI, and POTEJ were subject to an explicit molecular dynamic simulation for 50ns. MM-GBSA and other essential electrostatics were calculated that showcased that only POTEE and POTEF have absolute binding affinities with minimum energy exploitation. Thus, this study’s outcomes are expected to drive cancer research to successful utilization of POTE genes family as a new biomarker, which could pave the way for the discovery of new therapies.

The kingdom of the prolyl-isomerase Pin1: The structural and functional convergence and divergence of Pin1

More than 20 years since its discovery, our understanding of Pin1 function in various diseases continues to improve. Pin1 plays a crucial role in pathogenesis and has been implicated in metabolic disorders, cardiovascular diseases, inflammatory diseases, viral infection, cancer and neurodegenerative diseases such as Alzheimer’s, Parkinson’s and Huntington’s disease. In particular, the role of Pin1 in neurodegenerative diseases and cancer has been extensively studied. Our understanding of Pin1 in cancer also led to the development of cancer therapeutic drugs targeting Pin1, with some currently in clinical trial phases. However, identifying a Pin1-specific drug with good cancer therapeutic effect remains elusive, thus leading to the continued efforts in Pin1 research. The importance of Pin1 is highlighted by the presence of Pin1 orthologs across various species: from vertebrates to invertebrates and Kingdom Animalia to Plantae. Among these Pin1 orthologs, their sequence and structural similarity demonstrate the presence of conservation. Moreover, their similar functionality between species further highlights the conservancy of Pin1. As researchers continue to unlock the mysteries of Pin1 in various diseases, using different Pin1 models might shed light on how to better target Pin1 for disease therapeutics. This review aims to highlight the various Pin1 orthologs in numerous species and their divergent functional roles. We will examine their sequence and structural similarities and discuss their functional similarities and uniqueness to demonstrate the interconnectivity of Pin1 orthologs in multiple diseases.

Vertical characterisation of phylogenetic divergence of microbial community structures, interaction, and sustainability in estuary and marine ecosystems

The changes in the aquatic environmental conditions often influence the microbial community assemblages and genome repertoire. Studies investigating the aquatic diversity and ecosystem services were primarily conducted in horizontal environments while neglecting the microbial phylogenetic divergences, biotrophic interactions, and eco-sustainability at water vertical layers. We investigated the mechanisms of microbial transitions, and the ecological significance of water depth layers in the estuary and marine ecosystems. The results demonstrated that the salinity and turbidity increased with increasing water depth (0–50 m), while temperature and pH decreased significantly. The bacterial and eukaryotic diversity and composition significantly increased with an elevating water depth. Bacterial phyla such as Desulfobacterota, Acidobacteriota, Myxococcota, Gemmatimonadota, Campilobacterota, and Latescibacterota were increased significantly. However, niche preference occurred, and some microbes showed differential nestedness at water vertical layers. In the eukaryotic community, Eustigmatales group were the only clades predominantly phylogenetically nested at the surface water depth. c_Conoidasida, o_Gregarinasina, f_Eugregarinorida, and g_Lankesteria were the most predominant at the middle depth. While Mediophyceae clades, p_SAR, and the Animalia clades were the most predominant groups nested at the bottom depths. The microbial interaction, structure, and stability were increased with increasing depth. The vertical phylogenetic turnover of the microbial community was related to the feeding mechanisms. Phototrophic organisms were particularly adapted at the surface, and middle depth by parasitic and pathogenic organisms, while the bottom was inhabited by diatoms, decomposers, and detritus protists. This study demonstrated that the bottom depth was the most ecologically stable area with more profound ecosystem services.

Population genomics reveal deep divergence and strong geographical structure in gentians in the Hengduan Mountains.

Understanding the evolutionary and ecological processes driving population differentiation and speciation can provide critical insights into the formation of biodiversity. Here, we examine the link between population genetic processes and biogeographic history underlying the generation of diversity in the Hengduan Mountains (HM), a region harboring a rich and dynamic flora. We used restriction site-associated DNA sequencing to generate 1,907 single-nucleotide polymorphisms (SNPs) and four-kb of plastid sequence in species of the Gentiana hexaphylla complex (Gentianaceae). We performed genetic clustering with spatial and non-spatial models, phylogenetic reconstructions, and ancestral range estimation, with the aim of addressing the processes influencing diversification of G. hexaphylla in the HM. We find the G. hexaphylla complex is characterized by geographic genetic structure with clusters corresponding to the South, North and the central HM. Phylogenetic reconstruction and pairwise FST analyses showed deep differentiation between Southern and Northern populations in the HM. The population in Mount Taibai exhibited the highest genetic similarity to the North HM. Ancestral range estimation indicated that the G. hexaphylla complex originated in the central HM and then diverged in the Pliocene and the Early Pleistocene, before dispersing widely, resulting in the current distinct lineages. Overall, we found deep genomic differentiation in the G. hexaphylla complex corresponds to geographic barriers to dispersal in the HM and highlights a critical role of the uplift of the Daxue Mountains and subsequent climatic fluctuations underlying diversification. The colonization of G. hexaphylla in the Mount Taibai region suggests directional dispersal between the alpine flora of the Qinling Mountains and the HM.

Historical Westward Migration Phases of Ovis aries Inferred from the Population Structure and the Phylogeography of Occidental Mediterranean Native Sheep Breeds.

In this study, the genetic relationship and the population structure of western Mediterranean basin native sheep breeds are investigated, analyzing Maghrebian, Central Italian, and Venetian sheep with a highly informative microsatellite markers panel. The phylogeographical analysis, between breeds’ differentiation level (Wright’s fixation index), gene flow, ancestral relatedness measured by molecular coancestry, genetic distances, divergence times estimates and structure analyses, were revealed based on the assessment of 975 genotyped animals. The results unveiled the past introduction and migration history of sheep in the occidental Mediterranean basin since the early Neolithic. Our findings provided a scenario of three westward sheep migration phases fitting properly to the westward Neolithic expansion argued by zooarcheological, historical and human genetic studies.