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PubMed2026

Disruption of mitonuclear coadaptation and compensatory evolution after an extreme dietary shift in carnivorous butterflies.

Mitochondrial function depends on tight coordination between mitochondrial and nuclear genomes, which requires long-term coevolution to maintain mitonuclear coadaptation. While mitonuclear incompatibility is typically studied in the context of hybridization, other evolutionary scenarios that may disrupt coadaptation between the two genomes remain less explored. Here, we propose that extreme ecological niche shifts may disrupt mitonuclear coadaptation, which we test in carnivorous Miletinae butterflies with an extreme dietary transition. By generating high-quality genome assemblies, we found that Miletinae exhibit extensive chromosomal rearrangements. Comparative phylogenomic analyses revealed a striking asymmetric mitonuclear evolutionary response: Miletinae exhibit elevated mitochondrial nucleotide substitution rates compared to phytophagous relatives, whereas nuclear rates remain stable. This shift reverses the typical lepidopteran pattern where nuclear rates exceed mitochondrial rates. Interestingly, this mitochondrial acceleration is driven primarily by relaxed purifying selection rather than positive selection. To sustain mitochondrial function, the nuclear genome of Miletinae underwent pervasive, multilayered compensatory evolution. We detected strong signatures of positive selection and accelerated evolution in nuclear genes directly interacting with mitochondrial components across oxidative phosphorylation (OXPHOS) complexes, the mitochondrial translation, and replication and transcription machinery. Furthermore, this nuclear compensatory response extends to systems governing mitochondrial homeostasis, including protein quality control and RNA degradation and stabilization. Our results support a model in which extreme ecological transitions can disrupt ancestral mitonuclear coadaptation and promote the emergence of a new coadapted state through systemic nuclear compensation. This study broadens the conceptual framework of mitonuclear coevolution and highlights its role in facilitating evolutionary persistence after major ecological shifts.

Animals↗

PubMed2025

Comparative Phylogenetics Reveal Clade-specific Drivers of Recombination Rate Evolution Across Vertebrates.

Meiotic recombination is an integral cellular process, required for the production of viable gametes. Recombination rate is a fundamental genomic parameter, modulating genomic responses to selection. Our increasingly detailed understanding of its molecular underpinnings raises the prospect that we can gain insight into trait divergence by examining the molecular evolution of recombination genes from a pathway perspective, as in mammals, where protein-coding changes in later stages of the recombination pathway are connected to divergence in intra-clade recombination rate. Here, we leverage increased availability of avian and teleost genomes to reconstruct the evolution of the recombination pathway across two additional vertebrate clades: birds, which have higher and more variable rates of recombination and similar divergence times to mammals, and teleost fish, which have much deeper divergence times. Rates of molecular evolution of recombination genes are highly correlated between vertebrate clades and significantly elevated compared to control panels, suggesting that they experience similar selective pressures. Avian recombination genes are significantly more likely to exhibit signatures of positive selection than other clades, unrestricted to later stages of the pathway. Signatures of positive selection in genes linked to recombination rate variation in mammalian populations and those with signatures of positive selection across the avian phylogeny are highly correlated. In contrast, teleost fish recombination genes have significantly less evidence of positive selection despite high intra-clade recombination rate variability. Gaining clade-specific understanding of patterns of variation in recombination genes can elucidate drivers of recombination rate and thus, factors influencing genetic diversity, selection efficacy, and species divergence.

Animals↗

PubMed1975

Pre-emption of human cell-mediated lympholysis by a suppressive mechanism activated in mixed lymphocyte cultures.

The regulation of B-cell and T-cell immune responses has been extensively examined and in the experimental animal appears to involve regulatory or "suppressor" T cells (1-4). The limitations of in vitro experimentation have made comparable study of nonpathological human suppression quite difficult (5). We report here an in vitro method that generates and quantitates suppressor activity in man after antigen-specific activation in mixed leukocyte culture (MLC). The one-way MLC induces both a proliferative response (6) and the generation of cytotoxic T lymphocytes (CTLs) (7). Both of these responses are mediated by antigen-specific T-cell subpopulations (8,9) and have been correlated with recognitive and destructive phases of allograft rejection. Recent reports have examined the antigen reactivity of mouse (10,11), rat (12), or human (13,14) lymphocytes obtained after proliferation in MLC. In all cases, after the primary MLC proliferative peak, the recovered lymphocytes rapidly differentiate upon re-exposure to the initial stimulating population, but do so only weakly when exposed to a presumably noncross-reactive third-party stimulating population. Velocity sedimentation separation studies have shown that the blast cells produced in a primary MLC revert to small lymphocytes that rapidly differentiate into proliferating and/or cytotoxic T lymphocytes upon restimulation with the initial antigen (15). These findings demonstrate that positive selection for the responding population in primary MLC does exist and may account for at least part of the specificity of the secondary response. However, this positive selection does not preclude possible involvement of a suppressor mechanism. In fact we have detected suppressor activity in primary MLC sensitization cultures at a time when the proliferation responsible for positive selection does not preclude possible involvement of a suppressor mechanism. In fact we have detected suppressor activity in primary MLC sensitization cultures at a time when the proliferation responsible for positive selection in not yet significant, suggesting that suppression may be overriding importance in the specificity of MLC-activated secondary responses.

Antigen-Antibody Reactions↗

PubMed2025

Molecular evolution of the members of the Snq2/Pdr18 subfamily of Pdr transporters in the Hemiascomycete yeasts.

The transporters of the ATP-Binding Cassette (ABC) Superfamily involved in the Multidrug Resistance (MDR) phenomena are also known as ABC-Pleiotropic Drug Resistance (PDR) proteins. The homologs of the Saccharomyces cerevisiae SNQ2 and PDR18 genes were identified in 171 yeast genomes, representing 68 different hemiascomycetous species. All early-divergent yeast species analyzed in this work lack Snq2/Pdr18 homologs, suggesting that the origin of these ABC-PDR genes in hemiascomycete yeasts resulted from a horizontal transfer event. The evolutionary pathway of the Snq2/Pdr18 protein subfamily in pathogenic Candida species was also reconstructed, revealing a main gene lineage leading to the Candida albicans SNQ2 gene. The results indicate that, after the gene duplication event at the origin of the SNQ2/PDR18 paralogs, the PDR18 ortholog has been under strong diversifying selection and suggest that a small portion of the sequence of the SNQ2 ancestral ortholog might have been under mild positive selection. The results also showed that strong positive selection was exerted over one of the two paralogs generated by the Whole Genome Duplication (WGD) event, corresponding to the duplicate at the origin of a "short-lived" WGD sublineage.

Evolution, Molecular↗

PubMed2026

Contrasting signals of selection at the EDAR gene in global and Latin American populations.

The EDAR gene is a classic target of positive selection in humans, mainly through the nonsynonymous variant rs3827760 (EDARV370A) associated with ectodermal traits. Using high-resolution data from the 1000 Genomes Project, we combined sliding-window F_ST, BayeScan, and extended haplotype homozygosity (EHH) analyses to examine global and Latin American patterns of differentiation. Globally, a strong signal of positive selection was confirmed at EDAR, dominated by the rs3827760 haplotype background and its extended linkage disequilibrium structure. In contrast, within Latin America, differentiation reflected admixture-driven haplotype persistence rather than contemporary selection. A genome-wide FST scan comparing individuals from the upper and lower quartiles of Native American ancestry showed that EDAR lies among the most highly differentiated regions in this contrast, consistent with ancestry-driven haplotype structure rather than post-admixture adaptive evolution. These results indicate that EDAR retains its evolutionary signature globally but not within recently admixed populations, where demographic history rather than selection shapes its genetic landscape.

Humans↗

PubMed1979

Hypothesis on the origin of the strong alloreactivity.

The high proportion of alloreactive T lymphocytes and many of the available data on T cell receptors can be explained by one single hypothesis with four basic assumptions: A) The functional induction of T lineage cells in the thymus inherently causes a selection for V-regions that bind to major histocompatibility antigens (MHA). The type of MHA determines the functional pathway of the T cell. B) This process selects with the highest probability for binding sites with high affinity for the self-MHA, yet binding sites with high affinity for non-self-MHA and low affinity for self-MHA will also be selected with a low but finite probability. C) This positive selection for self-MHA binding V-regions is followed by a rigorous selection against self-reactive T cells during the subsequent thymic or post-thymic phase of tolerance induction. D) Most crucial for the hypothesis is, finally, the assumption that the second (negative) selection operates with a higher affinity threshold than the first (positive) selection. The negative selection thus spares T cell clones with low affinity for self-antigens. This provides a strong selective advantage for two major groups of cells, namely alloreactive cells most of which recognize nonself-MHA in complex with nonpolymorphic non-MHA determinants, and cells that recognize nonself-determinants in complex with self-MHA with different degrees of restriction. One of the predictions of this hypothesis is that the proportion of alloreactive cells is relatively small among the T lineage cells that leave the thymus but increases largely during the post-thymic development of the peripheral T cell pool. The hypothesis is not biased in respect to the underlying germ line repertoire of V genes, and is in fact compatible with the simple assumption that T and B cells use the same sets of V genes.

Animals↗

PubMed2025

Multiomic Analyses Reveal the Molecular Mechanisms of Arid Adaptation in a Desert Rodent Species.

Organisms living in desert habitats face multiple simultaneous pressures, such as high temperatures and arid, and the population dynamics and community diversity of small rodents are strongly affected by climate extremes. However, the potential mechanisms by which desert rodents adapt to arid remain largely unexplored. Here, we assembled a 3.18 Gb genome, including 25,812 protein-encoding genes, for Orientallactaga sibirica, which is widely distributed across both arid and semihumid environments in Eurasia. Orientallactaga sibirica has longer ears and hind limbs to enhance heat dissipation, which may be related to the positively selected genes, such as Fgf10, Fgf11, Hoxc4, Hoxd1, and Bmp4. The renal transcriptome revealed increased fat and carbohydrate metabolism for metabolic water production in O. sibirica residing in arid habitats. Pathways such as material metabolism, oxidative stress response, osmoregulation, and water and salt reabsorption were enriched in candidate genes, such as Avp, Ang, and Ace, under positive selection in O. sibirica. Moreover, amino acid replacement was observed in the protein sequences of seven candidate genes, including Aldh7a1, Lnpep, Wnk4, C1qc, and Awat2, and these specific amino acid replacements of genes such as Umod and Scnn1a were related to unique osmoregulation, osmotic protection, and water retention compensation mechanisms. Water deprivation under laboratory conditions induced the upregulation of Umod and Aldh7a1 expression, further supporting the results observed in the wild population. These findings demonstrate that the positively selected genes related to limb development and specific amino acid replacements in the genes Umod and Scnn1a for unique osmoregulation in the renal vascular system may contribute to arid adaptation in the desert rodent species O. sibirica. This study provides novel insights into the adaptive evolution of desert small mammals and can serve as a reference for future research on renal damage-related diseases, such as human kidney stones and salt-sensitive hypertension.

Animals↗

PubMed2025

Primulina pan-genome reveals differential gene retention following whole-genome duplications and provides insights into edaphic specialization.

Primulina, a genus of >200 species specialized to extreme soils, provides a model for edaphic adaptation. We assemble seven genomes and construct a pan-genome spanning nine species from karst, Danxia, and acidic soils. Comparative analyses reveal that karst-adapted species have smaller genomes. Two lineage-specific whole-genome duplications (WGDs) exhibit biased duplicate loss in large gene families but preferential retention of transcription factors, indicating combined adaptive and nonadaptive forces. Pan-genome analyses identify ion channel and transporter genes enriched in variant hotspots and under positive selection in karst lineages. Candidate genes for drought and salt stress tolerance include ABC transporters and ion channels. Notably, an ABC transporter shows positive selection in karst species and unique structural variation in non-karst species. Together, our findings show that genome downsizing, biased post-WGD retention, and evolution of ion-transport pathways shape adaptation to extreme soils. The Primulina pan-genome provides a resource for dissecting mechanisms underlying edaphic specialization.

Gene Duplication↗

PubMed2025

The Demographic History of Populations and Genomic Imprinting have Shaped the Transposon Patterns in Arabidopsis lyrata.

Purifying selection is expected to prevent the accumulation of transposable elements (TEs) within their host, especially when located in and around genes and if affected by epigenetic silencing. However, positive selection may favor the spread of TEs, causing genomic imprinting under parental conflict, as genomic imprinting allows parent-specific influence over resource accumulation to the progeny. Concomitantly, the number and frequency of TE insertions in natural populations are conditioned by demographic events. In this study, we aimed to test how demography and selective forces interact to affect the accumulation of TEs around genes, depending on their epigenetic silencing, with a particular focus on imprinted genes. To this aim, we compared the frequency and distribution of TEs in Arabidopsis lyrata from Europe and North America. Generally, we found that TE insertions showed a lower frequency when they were inserted in or near genes, especially TEs targeted by epigenetic silencing, suggesting purifying selection at work. We also found that many TEs were lost or got fixed in North American populations during the colonization and the postglacial range expansion from refugia of the species in North America, as well as during the transition to selfing, suggesting a potential "TE load." Finally, we found that silenced TEs increased in frequency and even tended to reach fixation when they were linked to imprinted genes. We conclude that in A. lyrata, genomic imprinting has spread in natural populations through demographic events and positive selection acting on silenced TEs, potentially under a parental conflict scenario.

DNA Transposable Elements↗

PubMed1978

Role of the H-2 complex in induction of T helper cells in vivo. I. Antigen-specific selection of donor T cells to sheep erythrocytes in irradiated mice dependent upon sharing of H-2 determinants between donor and host.

When purified CBA lymph node T cells were mixed with sheep erythrocytes (SRC) and filtered from blood to lymph through irradiated syngeneic mice for 1-2 days, the donor cells lost their capacity to stimulate anti-SRC responses by CBA B cells; the response to a third-party antigen (horse erythrocytes) was unaffected and active suppression was not involved. This process of specific negative selection to SRC also occurred when semiallogeneic mice were used as filtration hosts. By contrast, when allogeneic hosts were used the helper function of the donor cells was not reduced; this applied to both primed and unprimed T cells. Studied with congeneic resistant strains indicated that negative selection to SRC occurred only when the donor and host shared H-2 determinants. Studies with T cells depleted of alloreactive lymphocytes showed that negative selection to SRC in irradiated F1 hybrid mice was followed by a stage of positive selection where the donor cells gave greatly increased responses to the injected antigen. Positive selection did not occur in H-2-different mice, however, and the helper function of the donor cells remained unchanged. By these parameters it was concluded that homozygous T helper cells have no detectable capacity to recognize antigen in an H-2-different environment.

Animals↗

PubMed1978

Counterimmunoelectrophoretic detection of a high incidence of precipitin reactions in normal human sera against staphylococcal teichoic acids and protein A.

The use of counterimmunoelectrophoresis (CIE) for detection of serum antibodies to staphylococcal teichoic acids was evaluated against teichoic acids prepared by sonic treatment or lysostaphin extraction of Staphylococcus aureus (Lafferty strain). Of 54 patient sera from suspected cases of staphylococcal endocarditis, osteomyelitis, or septicemia, 33 (61.1%) were positive by CIE analysis; however, 128 of 291 sera (44.0%) from normal adult donors were also positive. Selected CIE-positive sera from patient and control groups were titered by Ouchterlony gel diffusion. In the control group of normal sera, 65% were also positive by gel diffusion, but only 15% had titers of >/=1:2. Of the patient sera, 44.4% had gel diffusion titers of >/=1:2. In addition to the specific teichoic acid band, a second precipitation band could be demonstrated with both patient or normal sera by CIE or gel diffusion. This second precipitin band was shown to involve interactions of test sera with staphylococcal protein A present in the teichoic acid extracts. The protein A precipitins were detected at high concentrations of the antigen extracts, whereas the anti-teichoic acid precipitins were optimally detected at lower antigen concentrations. The formation of protein A precipitin bands did not correlate with the presence of anti-teichoic acid antibodies, as most sera tested were positive for protein A regardless of anti-teichoic acid activity. This study suggests that a high incidence of normal people have levels of antibodies to teichoic acids which are detectable by the highly sensitive, but nonspecific, technique of CIE.

Adult↗

PubMed2026

Evolutionary Reorganization of Transcriptomic Architecture Across a UVB Tolerance Gradient in Fish.

Environmental stressors such as ultraviolet radiation impose strong selective pressures on organisms, yet how adaptation to such stressors shapes transcriptomic responses at the network level remains poorly understood. Although stratospheric ozone is recovering globally, substantial regional variation in UV exposure persists, particularly in high-altitude environments where extreme UV levels can occur. Here, we compared three fish models representing distinct biological responses to UVB exposure: wild-type zebrafish (Danio rerio), a melanin-deficient zebrafish mutant (nacre) lacking a major protective mechanism against UVB damage, and the high-altitude Andean killifish Orestias ascotanensis, a species naturally exposed to extreme UVB radiation. Together, these models define a gradient spanning physiological protection, impaired protection, and evolutionary adaptation to UVB stress. Using RNA-seq and protein-protein interaction networks, we show that transcriptomic responses differ markedly across this gradient. Wild-type and nacre zebrafish exhibited relatively limited transcriptomic changes (∼2%-2.4% of genes changing), whereas O. ascotanensis displayed a large-scale and highly coordinated response (∼21.6% of genes changing) characterized by functionally specialized networks enriched in DNA repair pathways. These differences involved not only transcriptomic magnitude but also marked reorganization of transcriptomic architecture. Integration with positive selection analyses revealed that positively selected genes were concentrated within highly interconnected regions of transcriptomic networks, consistent with adaptation involving network reorganization. Furthermore, ortholog-based analyses suggest that adaptive responses involve differential reorganization of a conserved functional background. Together, our results support a model in which adaptation to environmental stress is associated with the reorganization of conserved transcriptomic networks across physiological and evolutionary contexts, providing a systems-level perspective on the molecular basis of adaptation.

UVB radiation↗

PubMed1976

SPECIFIC positive and negative selection of rat lymphocytes reactive to strong histocompatibility antigens: activation with alloantigens in vitro and in vivo.

This study compares the functional properties of rat thoracic duct lymphocytes (TDL) after stimulation with strong alloantigens of the major histocompatibility complex (MHC) either in vitro in preparative mixed lymphocyte interactions (MLI) or in vivo in systemic graft-vs-host (GVH) reactions. Comparisons were made of PHA responses and reactivity to the specific priming haplotypes or to third party haplotypes in analytical MLI and in GVH reactions either before or after the activated populations were "parked" in syngenetic T cell-deprived (B) rats. These comparisons can be summarized as follows: 1) TDL populations primed in bulk MLI cultures (MLI-TDL) slowed some evidence of specific positive selection when tested immediately; MLI responses to specific alloantigens were both relatively large and accelerated in tempo, whereas responses to third party alloantigens were diminished but also accelerated in tempo. Specific GVH responses were more marked than in third party recipients but they were also decreased relative to normal, and displayed an abberant dose/response slope. MLI-TDL populations tested after they had been stored in syngeneic B rats showed clear evidence of stable-specific positive selection; specific MLI and GVH responses were enriched relative to third party responses and also in comparison to normal, unselected TDL populations. This finding indicates that GVH and MLI reactivity are probably both functional capacities of the same lymphocyte subpopulation since positive selection by one function (MLI) also enriched for a second (GVH). 2) Parental strain TDL activated in vivo in the systemic GVH reaction in irradiated F1 animals and recovered from the thoracic duct 3 to 4 days later (late GVH-TDL) consisted mainly of blast cells, however, in contrast to MLI-TDL these populations showed no evidence of positive selection when tested before or after parking in B rats. MLI responses to specific alloantigens were minimal, and greatly reduced in magnitude compared to normal. GVH responses to specific haplotypes could be detected, but these were not enriched compared to normal, despite the content in the late GVH-TDL populations of a significant proportion of blast cells presumably activated by host alloantigens. 3) Early collections (less than 40 hr) of parental strain GVH-TDL collected from F1 recipients contained no blast cells and showed impressive degrees of negative selection; they were markedly depleted of both GVH and MLI activity to specific alloantigens but displayed normal reactivity to third party alloantigens. Moreover, specific negative selection was persistent in these populations parked for several weeks in B rats, and indication that a specific subpopulation of reactive cells had been physically eliminated. 4) PHA responses of both MLI- and GVH-activated TDL populations tested either before or after parking in B rats were approximately normal on a per T cell basis...

Animals↗

PubMed1978

Lymphocyte cytotoxicity to cultured rat liver cells in patients with chronic liver diseases.

Microcytotoxicity assay revealed that peripheral bloof lymphocytes from patients with chronic active hepatitis were cytotoxic against cultured rat liver cells established by Coon in 1968. Non E-rosette forming cells were cytotoxic in 26 of 28 patients (93%) with chronic active hepatitis, whereas E-rosette forming cells were cytotoxic in only 1 of them. Either an addition of 10 microgram/well of aggregated IgG to non E-rosette forming cell culture or a preincubation of non E-rosette forming cells with 100 microgram/ml of aggregated IgG significantly reduced the cytotoxicity from 62.9 +/- 12.8% to 32.8 +/- 11.6% or to 25.6 +/- 11.3% (p less than 0.001). An addition of antihuman IgG/Fc also reduced the cytotoxicity to 37.4 +/- 17.2%. Significant cytotoxicity of positively selected EA-rosette forming cells was observed in 4 of 10 patients with chronic active hepatitis and that of positively selected EAC-rosette forming cells was demonstrated in 3, whereas in any of these patients neither non EA-rosette forming cells nor non EAC-rosette forming cells were cytotoxic. Cultured liver cells used in this study were seen to possess insoluble liver specific antigen on their surface membranes, but not soluble liver specific lipoprotein of Meyer zum Büschenfelde, by using an indirect immunofluorescence technique. These results suggested that effector cells are Fc-receptor-bearing cells and that the mechanism of the reaction may be mediated in an antibody-dependent cell-mediated reaction directed against insoluble liver specific membrane antigen(s) rather than soluble one.

Animals↗

PubMed2026

Adaptive Evolution of the PFK Gene Family in Chinese Longsnout Catfish, Leiocassis longirostris.

The Chinese longsnout catfish is a typical carnivorous fish with a relatively weak ability to utilize glucose. However, the genomic basis for its glucose metabolic adaptation remains unclear. In this study, we used comparative genomics methods to systematically analyze the evolutionary characteristics of glucose metabolism-related genes in the Chinese longsnout catfish, focusing on gene family evolution, patterns of expansion and contraction, and selective pressures. The results indicate that glucose metabolism-related genes have undergone significant reshaping during evolution. Genes involved in glucose digestion, absorption, and insulin signaling pathways demonstrate a tendency toward contraction, while those associated with protein and lipid metabolism exhibit expansion. This pattern is consistent with the species' long-term adaptation to a high-protein, high-fat diet. Comparative analysis further revealed that, compared to fish with different dietary habits, certain key genes involved in glycolysis in the Chinese longsnout catfish exhibit a reduction in copy number. Molecular evolutionary analysis showed that key genes involved in glycolysis and gluconeogenesis (including hexokinase 2 (hk2), phosphofructokinase, muscle/platelet (pfkm/p)) exhibit signs of accelerated evolution or positive selection. Notably, the PFK gene family exhibits complex evolutionary characteristics resulting from the combined effects of gene contraction, rapid evolution, and positive selection. In summary, this study reveals the genomic evolutionary basis for the glucose metabolic adaptation of the Chinese longsnout catfish and identifies the PFK gene family as a key candidate for elucidating its unique glucose metabolic characteristics.

Leiocassis longirostris↗

PubMed2014

Jarid2 is induced by TCR signalling and controls iNKT cell maturation.

Jarid2 is a reported component of three lysine methyltransferase complexes, polycomb repressive complex 2 (PRC2) that methylates histone 3 lysine 27 (H3K27), and GLP-G9a and SETDB1 complexes that methylate H3K9. Here we show that Jarid2 is upregulated upon TCR stimulation and during positive selection in the thymus. Mice lacking Jarid2 in T cells display an increase in the frequency of IL-4-producing promyelocytic leukemia zinc finger (PLZF)(hi) immature invariant natural killer T (iNKT) cells and innate-like CD8(+) cells; Itk-deficient mice, which have a similar increase of innate-like CD8(+) cells, show blunted upregulation of Jarid2 during positive selection. Jarid2 binds to the Zbtb16 locus, which encodes PLZF, and thymocytes lacking Jarid2 show increased PLZF and decreased H3K9me3 levels. Jarid2-deficient iNKT cells perturb Th17 differentiation, leading to reduced Th17-driven autoimmune pathology. Our results establish Jarid2 as a novel player in iNKT cell maturation that regulates PLZF expression by modulating H3K9 methylation.

Animals↗

PubMed2026

Comparative chloroplast genomics of six Bupleurum (Apiaceae) accessions: candidate barcodes, phylogeny based on available plastomes, and candidate RNA-editing sites.

INTRODUCTION: Bupleurum L. (Apiaceae), a taxonomically intricate genus of about 190 species and a source of Radix Bupleuri (Chai Hu), is difficult to discriminate because of convergent morphology, infraspecific variation, and limited genomic sampling. This study aimed to characterize plastome variation, identify and validate candidate molecular markers, reconstruct plastid phylogenetic relationships, and assess candidate plastid RNA-editing sites in Bupleurum. METHODS: We assembled six plastomes from subgenus Bupleurum, screened 51 Bupleurum plastomes for diagnostic loci, reconstructed whole-plastome and partitioned protein-coding-sequence phylogenies, and predicted plastid C-to-U RNA-editing candidates across the six newly assembled plastomes using a PREP-Cp-compatible workflow. Candidate barcode performance was evaluated against the reference plastome phylogenies, and codon-based models were used to test for positive selection. RESULTS: The plastomes were 154,496-155,778 bp with the canonical quadripartite structure and GC contents of 37.67-37.73%. Gene content was stable (131-132 genes; 86-87 protein-coding genes); B. falcatum subsp. cernuum lacked ycf15 but contained an additional inverted-repeat-associated ycf1 annotation. A/U-ending synonymous codons were favoured. Finite pairwise Ka/Ks estimates were below 1 for most genes, and site-specific codon models detected no positive selection. Each plastome contained 55-61 pure microsatellites, dominated by A/T mononucleotide motifs. MarkerSeek ranked 265 features and identified atpF-atpH, petA-psbJ, rpl32-trnL-UAG, and ycf1 as leading candidate barcodes. ycf1 recovered 38 of 41 nodes strongly supported by both reference trees, whereas a partitioned four-locus analysis recovered 40 of 41 and distinguished all 51 accession sequences. However, only one of seven multi-accession operational binomial groups was monophyletic, and only one showed a positive local barcode gap. The whole-plastome phylogeny recovered Bupleurum as monophyletic relative to Chamaesium. The two sampled Penninervia accessions occupied early-diverging positions without forming an exclusive clade. B. falcatum subsp. cernuum was sister to B. ranunculoides, with B. ranunculoides subsp. telonense sister to that pair. A partitioned 74-CDS analysis recovered the same key relationships and 45 of 50 internal bipartitions. Across the six newly assembled plastomes, 57-63 nonsynonymous C-to-U candidates were predicted per accession (367 total) in 21-22 genes; 269 affected the second codon position and 98 the first. DISCUSSION: Bupleurum plastomes are structurally conservative but retain localised divergence useful for marker development. Concordant whole-plastome and CDS genealogies support genus monophyly, whereas sparse Penninervia sampling and maternal plastid inheritance preclude rejecting traditional subgeneric classification. The predicted RNA-editing sites represent candidates for future experimental validation rather than an established Bupleurum editome. These genomic resources support authentication, conservation, and evolutionary research in Bupleurum.

Apiaceae↗

PubMed2026

Comparative Genomics Reveals Convergent Evolution Between Avivorous Bats (Ia io and Nyctalus aviator).

Investigating the genetic basis of dietary specialization can provide insights into the evolution of niche breadth. In this study, we employed comparative genomics to investigate the adaptive mechanisms enabling two bat species (Nyctalus aviator and Ia io) to shift from insectivory to seasonal bird consumption (avivorous bats). Our findings revealed adaptation related to immune response and lipid metabolism in avivorous bat species. Avivorous bats exhibit strong positive selection and convergent evolution in immune-related genes, which are under heightened selective pressure compared to those of non-avivorous bats. These species also display significantly fewer endogenous retroviral elements. These findings emphasized the significance of immune-driven adaptive evolution in avivory. Additionally, our results showed that the dietary evolution of avivorous bats is accompanied by convergent evolution associated with the lipid metabolism. Notably, CEPT1, the upstream gene required for the activation of the PPAR pathway, underwent positive selection and convergence, which may have affected lipid metabolism. These adaptations may enable avivorous bat species to face the challenge of immune response and nutrition during dietary niche expansion. These findings not only provide comprehensive insights into the adaptive evolution driving the unique diet of avivorous bats but also offered novel perspectives on the molecular mechanisms underlying ecological niche evolution in a dietary context.

Animals↗