[Autoregulated mechanisms, demographic evolution, and intraregional diversification. The example of the population of Galicia at the end of the eighteenth century].
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Age Distribution↗
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Molecular phylogenetic dating of asterid flowering plants shows early Cretaceous diversification.
We present a phylogenetic dating of asterids, based on a 111-taxon tree representing all major groups and orders and 83 of the 102 families of asterids, with an underlying data set comprising six chloroplast DNA markers totaling 9914 positions. Phylogenetic dating was done with semiparametric rate smoothing by penalized likelihood. Confidence intervals were calculated by bootstrapping. Six reference fossils were used for calibration. To explore the effects of various sources of error, we repeated the analyses with alternative dating methods (nonparametric rate smoothing and the Langley-Fitch clock-based method), alternative tree topologies, reduced taxon sampling (22 of the 111 taxa deleted), partitioning the data into three genes and three noncoding regions, and calibrating with single reference fossils. The analyses with alternative topologies, reduced taxon sampling, and coding versus noncoding sequences all yielded small or in some cases no deviations. The choice of method influenced the age estimates of a few nodes considerably. Calibration with reference fossils is a critical issue, and use of single reference fossils yielded different results depending on the fossil. The bootstrap confidence intervals were generally small. Our results show that asterids and their major subgroups euasterids, campanulids, and lamiids diversified during the Early Cretaceous. Cornales, Ericales, and Aquifoliales also have crown node ages from the Early Cretaceous. Dipsacales and Solanales are from the Mid-Cretaceous, the other orders of core campanulids and core lamiids from the Late Cretaceous. The considerable diversity exhibited by asterids almost from their first appearance in the fossil record also supports an origin and first phase of diversification in the Early Cretaceous.
DNA, Chloroplast↗
Multiple phenotypic divergence of mammary adenocarcinoma cell clones. II. Sensitivity to radiation, hyperthermia and FUdR.
We have shown that, with in vitro passage, subclones derived from clonal cell populations of 13762NF mammary adenocarcinoma undergo phenotypic drift and diversification in their cellular properties. Here we examine whether phenotypic divergence of 13762NF cell clones extends to therapeutic treatments used in eliminating mammary tumors and whether the apparent rates of phenotypic divergence vary for different treatments. Six subclones isolated from low passage clone MTF7 (T11; tissue culture passage 11) cells were compared to a similar number of subclones isolated from high passage clone MTF7 (T35; tissue culture passage 35) cells. Subclones derived from clone MTF7 (T11) were relatively homogeneous (not significantly different) in their inherent sensitivities to ionizing radiation, extrapolation coefficients and quasithreshold dose values (Do = 1.61-1.99 Gy; n = 0.89-3.42; Dq = 0-2.34). When the MTF7 (T11) subclones were examined for their sensitivities to 45 degrees C hyperthermic treatment, the inherent sensitivities and dose-response curve parameters (Do = 5.24-10.05 min; n = 1.08-10.47; Dq = 0.78-12.31) were heterogeneous (significantly different). In addition, the MTF7 (T11) subclones were heterogeneous (significantly different) in their sensitivities and dose-response curve parameters to 5-fluoro-2'-deoxyuridine (FUdR) treatment (slope = -0.70 to -1.59; y-intercept = 1.31 X 10(2) to 47.80 X 10(2]. The LD50 values for FUdR ranged from 14-150 nM for the MTF7 (T11) subclones. At high passage MTF7 (T35) subclones were heterogeneous in their dose-response parameters to ionizing radiation (Do = 1.17-2.05 Gy; n = 0.80-41.18; Dq = 1.79-4.94), hyperthermia (Do = 3.57-6.32 min; n = 2.08-13.54; Dq = 3.68-9.30) and FUdR (slope = -0.77 to -0.93; y-intercept = 4.64 X 10(2) to 8.83 X 10(2); LD50 = 50-160 nM). The results indicate that clonal cells diverge for distinct phenotypic properties at differing rates to form heterogeneous cell populations with unique sensitivities to various therapeutic treatments.
Adenocarcinoma↗
Leaves of Salicaceae (Salix and Populus) from Oligocene Sediments Near Tepexi de Rodríguez, Puebla, Mexico.
Eleven new salicaceous taxa based on fossil leaves, seven Salix and four Populus species, are described from the Oligocene Los Ahuehuetes locality, Pie de Vaca Formation, near Tepexi de Rodríguez in Puebla, Mexico. They are characterized by the presence of typical salicoid teeth, camptodromous secondary venation, and elliptic or lanceolate shape. Morphological differences between these new fossil plants and those reported previously from the United States and elsewhere indicate that diversification among these taxa occurred early during their differentiation. Furthermore, the limited morphological similarities of the fossil and extant plants growing naturally in Mexico also indicate a high rate of evolution. Documenting the expansion of high-latitude North American taxa into lower latitudes at the time of deposition of the Pie de Vaca Formation confirms that at least some of the typical boreal taxa were part of dry tropical communities in low-latitude North America and underscores the need to reevaluate the origin of this southern vegetation.
Journal Article↗
Transporter associated with antigen-processing-1 (TAP1) alleles in Gorilla gorilla: diversification of the locus postspeciation.
The transporter associated with antigen-processing (TAP) proteins are required for the transport of cytosolic peptides into the endoplasmic reticulum for assembly with class I major histocompatibility molecules. In the rat, allelic variants of the TAP genes impart specificity to the process of peptide transport. However, differential transport has yet to be demonstrated with the human molecules. TAP genes from humans and rodents have been studied thus far; analysis of another species more closely related to humans is necessary for a clearer understanding of the evolution of TAP genes. Three TAP1 alleles from four gorilla cell lines were characterized in this study. There is limited genetic distance at the locus, either within the gorilla (0.2%) or between the two hominoid species (0.8%). Nucleotide substitution analysis demonstrates that TAP1 and TAP2 are evolving at comparable rates under similar selection pressures. This pattern is in marked contrast to that observed for MHC class I genes of hominoids or rodents. Although there is limited evidence for trans-species evolution of the gorilla locus, the bulk of the diversification occurred after speciation as evidenced by a lack of shared amino acid polymorphism with human homologues. An evolutionary scheme predicts that the ancestral hominoid TAP1 molecule most closely resembled the human TAP1*02011.
ATP Binding Cassette Transporter, Subfamily B, Mem↗
Molecular phylogeny of Banza (Orthoptera: Tettigoniidae), the endemic katydids of the Hawaiian Archipelago.
The extant endemic katydids (Orthoptera: Tettigoniidae) of the Hawaiian Archipelago include one to three species per high island and a single species on Nihoa, all currently placed in the genus Banza. These acoustic insects provide an excellent opportunity for investigating the evolution of reproductive isolation and speciation, but such studies require an understanding of phylogenetic relationships within the group. We use maximum parsimony, likelihood-based Bayesian inference, and maximum likelihood to infer phylogenetic relationships among these taxa, based on approximately 2kb of mitochondrial cytochrome oxidase I and cytochrome b. Our results strongly support two distinct high island clades: one clade ("Clade I") composed of species from Kauai, Oahu, Molokai, and Lanai and another clade ("Clade II") composed of species from Maui and Hawaii (Banza unica, from Oahu, may be basal to both these clades, but its placement is not well resolved). Within these clades, some inferred relationships are strongly supported, such as the sister status of B. kauaiensis (Kauai) and B. parvula (Oahu) within Clade I, but other relationships remain more ambiguous, such as the relative position of B. brunnea (Maui) within Clade II. Although a detailed reconstruction of the historical biogeography of the Hawaiian katydids is difficult, we use our genetic data combined with the known geological history of the Hawaiian Islands to set limits on plausible historical scenarios for diversification of this group. Beyond these historical biogeographic inferences, our results indicate possible cryptic speciation on both Oahu and Hawaii, as well as what may be unusually high average rates of nucleotide substitution. The present work sets the stage for future genetic and experimental investigations of this group.
Animals↗
ErbB receptors and EGF-like ligands: cell lineage determination and oncogenesis through combinatorial signaling.
The ErbB/HER family of transmembrane receptor tyrosine kinases includes four members that bind more than two dozens ligands sharing an epidermal growth factor- (EGF)3 like motif. This family plays a pivotal role in cell lineage determination in a variety of tissues, including mesenchyme-epithelial inductive processes and the interactions between neurons and muscle, glia and Schwann cells. Certain ligands and receptors of the family, especially the ErbB-2 receptor tyrosine kinase, contribute to a relatively virulent phenotype of some human tumors; most notable are carcinomas of secretory epithelia. This large variety of biological signals is generated through a combinatorial network of signal transduction in which different ErbB ligands are apparently capable of stabilizing discrete homo- and heterodimeric receptor complexes, each coupled to a specific set of cytoplasmic signaling proteins. Because each receptor is unique in terms of catalytic activity, cellular routing and transmodulation, the resulting network allows not only an enormous potential for signal diversification but also fine tuning and stringent control of cellular functions. ErbB-2 emerges as a master coordinator of the network, prolonging and amplifying signaling by decelerating the dissociation rates of its heterologous ligands. Thus, the tumorigenic action of ErbB-2 may be attributed to its ability to act as a shared signaling subunit, rather than by functioning as a bone fide receptor.
Animals↗
Correlated evolution of morphology and vocal signal structure in Darwin's finches.
Speciation in many animal taxa is catalysed by the evolutionary diversification of mating signals. According to classical theories of speciation, mating signals diversify, in part, as an incidental byproduct of adaptation by natural selection to divergent ecologies, although empirical evidence in support of this hypothesis has been limited. Here I show, in Darwin's finches of the Galápagos Islands, that diversification of beak morphology and body size has shaped patterns of vocal signal evolution, such that birds with large beaks and body sizes have evolved songs with comparatively low rates of syllable repetition and narrow frequency bandwidths. The converse is true for small birds. Patterns of correlated evolution among morphology and song are consistent with the hypothesis that beak morphology constrains vocal evolution, with different beak morphologies differentially limiting a bird's ability to modulate vocal tract configurations during song production. These data illustrate how morphological adaptation may drive signal evolution and reproductive isolation, and furthermore identify a possible cause for rapid speciation in Darwin's finches.
Adaptation, Physiological↗
The evolution of genes for pigmentation in African cichlid fishes.
The cichlid fishes in the East African Great Lakes exhibit a great diversity of color patterns, presumably as adaptations to species-specific habitats and/or due to the action of sexual selection on color for species discrimination or female mate choice. To elucidate the mechanisms underlying such pigment pattern diversity, we cloned the cichlid homologs of tyrosinase, endothelin receptor b1, mitf, and Aim1 that previously had been cloned and characterized from pigmentation mutants of zebrafish and medaka fish. Gene sequence analysis among five cichlid species from the Great Lakes shows that the evolutionary rate of amino acid replacement in mitf is the highest of these four genes. We then compared the mitf amino acid replacement rates between species from the lacustrine and tilapiine/steatocranus lineages, and between Lake Malawi- and Victoria-haplochromine cichlids and Lake Tanganyika Lamprologini. We show that the evolutionary rate within the lacustrine lineage is twice that of the tilapiine/steatocranus lineage, but that rates for the Malawi-Victoria haplochromine and Lamprologini lineages are almost the same. These results suggest that the accelerated evolution of mitf might have occurred concomitantly with pigment pattern diversification in Great Lakes species, but not necessarily correlated with species under intense sexual selection on male mating color via female mate choice. Finally, we characterized a novel alternatively spliced variant of cichlid mitf that is similar to a mammalian mitf splice variant generated using alternate splice sites. We suggest that this new variant in cichlids, like that in mammals, encodes an MITF transcriptional factor having higher relative DNA binding affinity. These data provide a novel example of functional convergence in which a particular splice variant is independently generated via alternative splicing of a specific gene in different lineages.
Alternative Splicing↗
Spatial scaling of microbial eukaryote diversity.
Patterns in the spatial distribution of organisms provide important information about mechanisms that regulate the diversity of life and the complexity of ecosystems. Although microorganisms may comprise much of the Earth's biodiversity and have critical roles in biogeochemistry and ecosystem functioning, little is known about their spatial diversification. Here we present quantitative estimates of microbial community turnover at local and regional scales using the largest spatially explicit microbial diversity data set available (> 10(6) sample pairs). Turnover rates were small across large geographical distances, of similar magnitude when measured within distinct habitats, and did not increase going from one vegetation type to another. The taxa-area relationship of these terrestrial microbial eukaryotes was relatively flat (slope z = 0.074) and consistent with those reported in aquatic habitats. This suggests that despite high local diversity, microorganisms may have only moderate regional diversity. We show how turnover patterns can be used to project taxa-area relationships up to whole continents. Taxa dissimilarities across continents and between them would strengthen these projections. Such data do not yet exist, but would be feasible to collect.
Ascomycota↗
Inference of a radiation in Mastus (Gastropoda, Pulmonata, Enidae) on the island of Crete.
The Mediterranean land snail genus Mastus (Beck, 1837) is highly divergent. Thirty-two Mastus species have been recorded throughout the genus range, and 23 of them are endemic to the islands of the Aegean Sea and mainland Greece. Of these, all 16 Mastus species reported from Crete are endemic to this island. A robust molecular phylogenetic framework based on mitochondrial and nuclear genes (1623 bp) allowed us to explore the temporal diversification pattern of lineages, using molecular clock approaches. Our results showed an initial radiation in the evolutionary history of the Cretan lineage, followed by a subsequent slowdown of lineage splitting rate. Using a dated major vicariant event of the Aegean area, we estimated the absolute time of the radiation event and proposed a biogeographic scenario accounting for the observed pattern. Additionally, we tried to infer the processes that led to the divergence of the Cretan Mastus species, by applying comparative methods in phylogenetically informated context. Overall, our results favoured a nonecological radiation scenario in the Cretan Mastus species due to an allopatric divergence of secondary sexual characters.
Animals↗
Immunoglobulin gene hyperconversion ongoing in chicken splenic germinal centers.
It has been believed that the peripheral lymphocytes in chickens proliferate by self-renewing amplification of the preimmune repertoire generated in bursa. We amplified rearranged immunoglobulin variable (V) region genes from the single germinal centers induced by immunization. The sequence analysis of these genes revealed that most were derived from distinct B-cell clones which expanded locally, generating somatic antibody mutants at a high rate. Somatic hypermutations included unlinked base changes and the linked base modifications interpreted as unidirectional transfer of sequences from V region pseudogenes. This finding demonstrates the ongoing post-bursal diversification of B-cells in splenic germinal centers by templated gene conversion as well as untemplated point mutations.
Amino Acid Sequence↗
Dynamics of HIV-1 recombination in its natural target cells.
Genetic recombination is believed to assist HIV-1 diversification and escape from host immunity and antiviral therapies, yet this process remains largely unexamined within the natural target-cell populations. We developed a method for measuring HIV-1 recombination directly that employs reporter viruses bearing functional enhanced yellow fluorescent protein (YFP) and enhanced cyan fluorescent protein (CFP) genes in which recombination produces a modified GFP gene and GFP fluorescence in the infected cells. These reporter viruses allow simultaneous quantification of the dynamics of HIV-1 infection, coinfection, and recombination in cell culture and in animal models by flow-cytometric analysis. Multiround infection assays revealed that productive cellular coinfection was subject to little functional inhibition. As a result, generation of recombinants proceeded according to the square of the infection rate during HIV-1 replication in T lymphocytes and within human thymic grafts in severe combined immunodeficient (SCID)-hu (Thy/Liv) mice. These results suggest that increases in viral load may confer a compounding risk of virus escape by means of recombinational diversification. A single round of replication in T lymphocytes in culture generated an average of nine recombination events per virus, and infection of macrophages led to approximately 30 crossover events, making HIV-1 up to an order of magnitude more recombinogenic than recognized previously and demonstrating that the infected cell exerts a profound influence on the frequency of recombination.
Animals↗
Quaternary diversification in European alpine plants: pattern and process.
Molecular clock approaches applied previously to European alpine plants suggest that Primula sect. Auricula, Gentiana sect. Ciminalis and Soldanella diversified at the beginning of the Quaternary or well within this period, whereas Globularia had already started diversifying in the (Late-)Tertiary. In the first part of this paper we present evidence that, in contrast to Globularia and Soldanella, the branching patterns of the molecular internal transcribed spacer phylogenies of both Primula and Gentiana are incompatible with a constant-rates birth-death model. In both of these last two taxa, speciation probably decreased through Quaternary times, perhaps because of some niche-filling process and/or a decrease in specific range size. In the second part, we apply nonlinear regression analyses to the lineage-through-time plots of P. sect. Auricula to test a range of capacity-dependent models of diversification, and the effect of Quaternary climatic oscillations on diversification and extinction. At least for one major clade of sect. Auricula there is firm evidence that both diversification and extinction are a function of temperature. Intriguingly, temperature appears to be correlated positively with extinction, but negatively with diversification. This suggests that diversification did not take place, as previously assumed, in geographical isolation in high-altitude interglacial refugia, but rather at low altitudes in geographically isolated glacial refugia.
Europe↗
Functional diversification of B MADS-box homeotic regulators of flower development: Adaptive evolution in protein-protein interaction domains after major gene duplication events.
B-class MADS-box genes have been shown to be the key regulators of petal and stamen specification in several eudicot model species such as Arabidopsis thaliana, Antirrhinum majus, and Petunia hybrida. Orthologs of these genes have been found across angiosperms and gymnosperms, and it is thought that the basic regulatory function of B proteins is conserved in seed plant lineages. The evolution of B genes is characterized by numerous duplications that might represent key elements fostering the functional diversification of duplicates with a deep impact on their role in the evolution of the floral developmental program. To evaluate this, we performed a rigorous statistical analysis with B gene sequences. Using maximum likelihood and Bayesian methods, we estimated molecular substitution rates and determined the selective regimes operating at each residue of B proteins. We implemented tests that rely on phylogenetic hypotheses and codon substitution models to detect significant differences in substitution rates (DSRs) and sites under positive adaptive selection (PS) in specific lineages before and after duplication events. With these methods, we identified several protein residues fixed by PS shortly after the origin of PISTILLATA-like and APETALA3-like lineages in angiosperms and shortly after the origin of the euAP3-like lineage in core eudicots, the 2 main B gene duplications. The residues inferred to have been fixed by positive selection lie mostly within the K domain of the protein, which is key to promote heterodimerization. Additionally, we used a likelihood method that accommodates DSRs among lineages to estimate duplication dates for AP3-PI and euAP3-TM6, calibrating with data from the fossil record. The dates obtained are consistent with angiosperm origins and diversification of core eudicots. Our results strongly suggest that novel multimer formation with other MADS proteins could have been crucial for the functional divergence of B MADS-box genes. We thus propose a mechanism of functional diversification and persistence of gene duplicates by the appearance of novel multimerization capabilities after duplications. Multimer formation in different combinations of regulatory proteins can be a mechanistic basis for the origin of novel regulatory functions and a gene regulatory mechanism for the appearance of morphological innovations.
Amino Acid Sequence↗
Nipah virus in the era of global connectivity: molecular evolution, transmission risk, and preparedness strategies.
Nipah virus (NiV) is a highly pathogenic zoonotic RNA virus belonging to the genus Henipavirus within the family Paramyxoviridae, representing a continuing global health concern due to its high case fatality rate and potential for epidemic expansion in the era of increasing international connectivity. The virus demonstrates strong evolutionary adaptability driven by the absence of proofreading mechanisms during RNA replication, enabling genetic diversification that may influence host range, virulence, and transmission dynamics. Molecular pathogenesis of NiV is primarily mediated through interaction of viral glycoproteins with ephrin-B2 and ephrin-B3 receptors, facilitating host cell entry, endothelial damage, and neuroinvasion. Immune evasion facilitated by the action of accessory proteins encoded by the P gene (P, V, W, and C) acts to suppress innate antiviral immunity through the inhibition of interferon induction and JAK/STAT signaling. Human-to-human transmission of Nipah virus remains limited, with epidemiological evidence indicating basic reproduction numbers generally below unity; however, respiratory involvement and healthcare-associated exposure may enhance cluster outbreaks. Global travel, ecological disruption, and fragmented surveillance systems contribute to spillover risk, particularly in South and Southeast Asia where fruit bats of the genus Pteropus serve as natural reservoirs. Despite advances in vaccine technology, including subunit, viral vector, mRNA-based platforms, and monoclonal antibody therapies, no licensed prophylactic or therapeutic agent is currently available for human use. Global preparedness remains challenged by the scarcity of high-containment biosafety facilities, limited research funding, and absence of integrated One Health surveillance networks. Ethical considerations surrounding wildlife population control further complicate disease mitigation strategies. Emerging genomic surveillance, artificial intelligence-assisted predictive modeling, and regional data-sharing frameworks are essential for early detection and response. Strengthening molecular research on viral-host interactions and transmission determinants will be critical for preventing future Nipah virus outbreaks in an increasingly interconnected world.
Genomic surveillance↗
Eukaryotic domain evolution inferred from genome comparisons.
Comparative analyses of eukaryotic genomes are providing insights into the mode and tempo of domain family evolution. Gene duplication, the source of family expansion, far exceeds the rate of emergence of domains from non-coding sequence, and the rate of recruitment of domains into novel architectures. Domain families that appear to be restricted to certain lineages are likely to be the result of gene duplication, coupled with rapid sequence diversification. If such families are evidence of past adaptation, then their functions must relate to the underlying mechanism of selection: competition among organisms.
Animals↗
Reconstructing the diversification of subtilisins in the pathogenic fungus Metarhizium anisopliae.
Fungi secrete subtilisin proteinases to acquire nutrients and breach host barriers. Here we sought a global characterization of the diversity of subtilisins in the insect pathogen Metarhizium anisopliae. Expressed sequence tag (EST) analyses showed that a broad host range strain of M. anisopliae sf. anisopliae (strain 2575) expressed 11 subtilisins during growth on insect cuticle, the largest number of subtilisins reported from any fungus. Polymerase chain reaction amplified 10 of their orthologs from a second strain with multiple hosts (strain 820) and seven from the locust specialist M. anisopliae sf. acridum (strain 324). Analyses based on sequence similarities and exon-intron structure grouped M. anisopliae subtilisins into four clusters-a class I ("bacterial") subtilisin (Pr1C), and three clusters of proteinase K-like class II subtilisins: extracellular subfamily 1 (Pr1A, Pr1B, Pr1G, Pr1I and Pr1K), extracellular subfamily 2 (Pr1D, Pr1E, Pr1F and Pr1J) and an endocellular subtilisin (Pr1H). Phylogenetic analysis of homologous sequences from other genera revealed that this subdivision of proteinase K-like subtilisins into three subfamilies preceded speciation of major fungal lineages. However, diversification has continued during the evolution of Metarhizium subtilisins with evidence of gene duplication events after divergence of M. anisopliae sf. anisopliae and M. anisopliae sf. acridum. Comparing alignments and nonsynonymous/synonymous rates for Pr1 isoenzymes within a lineage and between lineages showed that while overall divergence of subtilisins followed neutral expectations, amino acids involved in catalysis were under strong selective constraint. This suggests that each Pr1 paralog contributes to the pathogens fitness. Furthermore, homology modeling predicted differences between the Pr1's in their secondary substrate specificities, adsorption properties to cuticle and alkaline stability, indicative of functional differences.
Amino Acid Sequence↗