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PubMed1999

(R)evolutionary considerations in hematopoietic development.

Evolutionary aspects of three characteristics of the mammalian hematopoietic system are considered in the context of both established and recent data. First, the lineage relationships among early members of the hematopoietic hierarchy are reconsidered in a tripartite model proposing lineage segregation based on vascular function, innate immunity, and acquired immunity on an evolutionary time scale. Second, the observation of two stem cell populations that differ in cell cycle status is considered as an evolved mechanism to enhance survival of the species in response to exposure to environmental toxins. Finally, the mobilization of hematopoietic stem cells into the peripheral circulation is proposed to be a mechanism for rapid dissemination of myeloid function during acute bacterial infections. These revolutionary hypotheses challenge some conventional concepts of stem cell biology, and provide an evolutionary context for considering mammalian hematopoiesis.

Animals↗

PubMed2000

Evolutionary psychology: counting babies or studying information-processing mechanisms.

Evolutionary psychology focuses on the study of adaptations. Its practitioners put little credence in the study of reproductive success in recent and current environments, and argue for an information-processing, cost-benefit conception of adaptation. Because ancestral and current environments differ, it is necessary to distinguish between innate and operational adaptations and between concurrently contingent and developmentally contingent behaviors. These distinctions lead to an evolutionary classification of behaviors into true pathologies, pseudopathologies, quasinormal behaviors, and adaptive-culturally-variable behaviors. I argue that a complete study of the functioning of a behavioral adaptation involves modeling ancestral selection pressures, cross-cultural research, experimental studies of mental processes, and studies of the proximate biological correlates of information-processing adaptations. Finally, I claim that evolutionary psychology can help us avoid making both naturalistic and moralistic fallacies.

Adaptation, Psychological↗

PubMed2000

Mental traits as fitness indicators. Expanding evolutionary psychology's adaptationism.

According to most evolutionary psychologists, human psychological adaptations can be recognized by criteria such as high efficiency, high complexity, high modularity, low phenotypic variance, low genotypic variance, low heritability, universality across cultures, and universality across individuals. These criteria are appropriate for adaptations that have been shaped through stabilizing selection for survival utility. However, they are often inappropriate for adaptations that have been shaped by sexual selection through mate choice as reliable signals of heritable fitness. If some psychological adaptations evolved as sexually selected fitness indicators of this type, we should expect them to violate many standard criteria used by evolutionary psychology to distinguish adaptations from non-adaptations. This paper addresses the problems raised by new developments in sexual selection theory and animal signaling theory for evolutionary psychology's adaptationism. It suggests that our adaptationist criteria must recognize two typical kinds of psychological adaptations: naturally selected survival mechanisms and sexually selected fitness indicators.

Adaptation, Psychological↗

PubMed2003

Evolutionary genetics of the melanocortin-1 receptor in vertebrates.

The molecular genetic basis of adaptive change in phenotype is a major outstanding issue in evolutionary biology. Evolutionary change in coat and plumage color is a promising system for making progress in this field. Most notably, recent work on the molecular genetic basis of hair and feather color has identified several genes which are candidates for involvement in evolutionary color change in mammals and birds. We have investigated the evolution of one of these candidate genes, the melanocortin-1 receptor (MC1R) gene, in relation to changes in melanin distribution among a wide variety of primate species, and in bananaquits (Coereba flaveola), which are a classic case of melanic plumage polymorphism in birds. In primates, a role of the MC1R coding region in coat color evolution can be ruled out in several cases in which closely related species have drastically different distributions of eumelanin and/or pheomelanin. However, reconstruction of MC1R sequences over primate evolution shows the presence of mutations at important functional sites in several lineages. Most notably, the lion tamarins (Leontopithecus) show a striking pattern of MC1R evolution, including deletions and several nonconservative amino acid changes. In the bananaquit, an E92K substitution in the MC1R is strongly associated with melanism, and this is likely to be the causative mutation. Reconstruction of the evolution of bananaquit MC1R alleles shows that melanism is a derived trait in this species. These results confirm the utility of a candidate gene approach to color evolution in vertebrates and open the way for extensive future research.

Animals↗

PubMed2025

Unraveling evolutionary pathways: allopolyploidization and introgression in polyploid Prunus (Rosaceae).

Allopolyploidization, resulting from hybridization and subsequent whole-genome duplication (WGD), is a fundamental mechanism driving evolutionary diversification across various lineages within the Tree of Life. The polyploid Prunus (Rosaceae), significant for its economic and agricultural value, provides an ideal model for investigating the evolutionary dynamics associated with allopolyploidy. In this study, we utilized deep genome skimming (DGS) data to demonstrate a comprehensive analytical framework for elucidating the underlying allopolyploidy that includes a newly adapted tool (DGS-Tree2GD) tailored explicitly for accurately detecting WGD events. Additionally, we introduced two methods to evaluate the contribution of incomplete lineage sorting (ILS) to lineage diversification. Phylogenomic discordance analyses revealed that allopolyploidization, rather than ILS, played a dominant role in the origin and dynamics of polyploid Prunus. Moreover, we inferred that the uplift of the Himalayas from the Middle to Late Miocene was a key driver in the rapid diversification of the Maddenia clade, an endemic group in East Asia. This geological event facilitated extensive hybridization and allopolyploidization, particularly the introgression between the Himalayas-Hengduan and Central-Eastern China clades. This case study demonstrates the robustness and efficacy of our analytical approach in precisely identifying WGD events and elucidating the evolutionary mechanisms underlying allopolyploidization in polyploid Prunus.

Polyploidy↗

PubMed2004

Penalized likelihood fluence optimization with evolutionary components for intensity modulated radiation therapy treatment planning.

A novel iterative penalized likelihood algorithm with evolutionary components for the optimization of beamlet fluences for intensity modulated radiation therapy (IMRT) is presented. This algorithm is designed to be flexible in terms of the objective function and automatically escalates dose, as long as the objective function increases and all constraints are met. For this study, the objective function employed was the product of target equivalent uniform dose (EUD) and fraction of target tissue within set homogeneity constraints. The likelihood component of the algorithm iteratively attempts to minimize the mean squared error between a homogeneous dose prescription and the actual target dose distribution. The updated beamlet fluences are then adjusted via a quadratic penalty function that is based on the dose-volume histogram (DVH) constraints of the organs at risk. The evolutionary components were included to prevent the algorithm from converging to a local maximum. The algorithm was applied to a prostate cancer dataset, with especially difficult DVH constraints on bladder, rectum, and femoral heads. Dose distributions were generated for manually selected sets of three-, four-, five-, and seven-field treatment plans. Additionally, a global search was performed to find the optimal orientations for an axial three-beam plan. The results from this optimal orientation set were compared to results for manually selected orientation (gantry angle) sets of 3- (0 degrees, 90 degrees, 270 degrees), 4- (0 degrees, 90 degrees, 180 degrees, 270 degrees), 5- (0 degrees, 50 degrees, 130 degrees, 230 degrees, 310 degrees), and 7- (0 degrees, 40 degrees, 90 degrees, 140 degrees, 230 degrees, 270 degrees, 320 degrees) field axial treatment plans. For all the plans generated, all DVH constraints were met and average optimization computation time was approximately 30 seconds. For the manually selected orientations, the algorithm was successful in providing a relatively homogeneous target dose distribution, while simultaneously satisfying dose-volume limits by diverting dose away from proximal critical structures. The global search for an optimal three-beam orientation set yielded gantry angles of 70 degrees, 170 degrees, and 320 degrees. The EUD for this orientation set was 58 Gy, with 96% of the target within the set upper and lower limits. In comparison, optimized EUDs for the manually selected orientation sets of three, four, five and seven beams were 52.3, 52.6, 56.9, and 61.3 Gy, respectively. The orientation optimized three-beam plan yielded higher EUDs than the manually selected three-, four-, and five-beam plans, but lower EUDs than the seven-beam plan. In conclusion, a novel penalized likelihood algorithm with evolutionary components has successfully been implemented to optimize beamlet fluences for IMRT. Initial results are promising for dose conformity and uniformity of dose to target. When combined with optimal beam orientation selection for prostate cancer treatment planning, the results indicate that plans with a small number of optimized beam orientations achieve results comparable to those with a larger number of conventionally oriented beams.

Bone and Bones↗

PubMed2003

Tempo and mode of evolutionary radiation in iguanian lizards.

Identification of general properties of evolutionary radiations has been hindered by the lack of a general statistical and phylogenetic approach applicable across diverse taxa. We present a comparative analytical framework for examining phylogenetic patterns of diversification and morphological disparity with data from four iguanian-lizard taxa that exhibit substantially different patterns of evolution. Taxa whose diversification occurred disproportionately early in their evolutionary history partition more of their morphological disparity among, rather than within, subclades. This inverse relationship between timing of diversification and morphological disparity within subclades may be a general feature that transcends the historically contingent properties of different evolutionary radiations.

Adaptation, Biological↗

PubMed1997

Phylogenetic methods come of age: testing hypotheses in an evolutionary context.

The use of molecular phylogenies to examine evolutionary questions has become commonplace with the automation of DNA sequencing and the availability of efficient computer programs to perform phylogenetic analyses. The application of computer simulation and likelihood ratio tests to evolutionary hypotheses represents a recent methodological development in this field. Likelihood ratio tests have enabled biologists to address many questions in evolutionary biology that have been difficult to resolve in the past, such as whether host-parasite systems are cospeciating and whether models of DNA substitution adequately explain observed sequences.

Animals↗

PubMed1997

Extinction and the loss of evolutionary history.

Extinction episodes, such as the anthropogenic one currently under way, result in a pruned tree of life. But what fraction of the underlying evolutionary history survives when k of n species in a taxon are lost? This is relevant both to how species loss has translated into a loss of evolutionary history and to assigning conservation priorities. Here it is shown that approximately 80 percent of the underlying tree of life can survive even when approximately 95 percent of species are lost, and that algorithms that maximize the amount of evolutionary history preserved are not much better than choosing the survivors at random. Given the political, economic, and social realities constraining conservation biology, these findings may be helpful.

Animals↗

PubMed2001

Humans as the world's greatest evolutionary force.

In addition to altering global ecology, technology and human population growth also affect evolutionary trajectories, dramatically accelerating evolutionary change in other species, especially in commercially important, pest, and disease organisms. Such changes are apparent in antibiotic and human immunodeficiency virus (HIV) resistance to drugs, plant and insect resistance to pesticides, rapid changes in invasive species, life-history change in commercial fisheries, and pest adaptation to biological engineering products. This accelerated evolution costs at least $33 billion to $50 billion a year in the United States. Slowing and controlling arms races in disease and pest management have been successful in diverse ecological and economic systems, illustrating how applied evolutionary principles can help reduce the impact of humankind on evolution.

Adaptation, Physiological↗

PubMed2007

Evolutionary relationships of "Candidatus Riesia spp.," endosymbiotic enterobacteriaceae living within hematophagous primate lice.

The primary endosymbiotic bacteria from three species of parasitic primate lice were characterized molecularly. We have confirmed the characterization of the primary endosymbiont (P-endosymbiont) of the human head/body louse Pediculus humanus and provide new characterizations of the P-endosymbionts from Pediculus schaeffi from chimpanzees and Pthirus pubis, the pubic louse of humans. The endosymbionts show an average percent sequence divergence of 11 to 15% from the most closely related known bacterium "Candidatus Arsenophonus insecticola." We propose that two additional species be added to the genus "Candidatus Riesia." The new species proposed within "Candidatus Riesia" have sequence divergences of 3.4% and 10 to 12% based on uncorrected pairwise differences. Our Bayesian analysis shows that the branching pattern for the primary endosymbionts was the same as that for their louse hosts, suggesting a long coevolutionary history between primate lice and their primary endosymbionts. We used a calibration of 5.6 million years to date the divergence between endosymbionts from human and chimpanzee lice and estimated an evolutionary rate of nucleotide substitution of 0.67% per million years, which is 15 to 30 times faster than previous estimates calculated for Buchnera, the primary endosymbiont in aphids. Given the evidence for cospeciation with primate lice and the evidence for fast evolutionary rates, this lineage of endosymbiotic bacteria can be evaluated as a fast-evolving marker of both louse and primate evolutionary histories.

Animals↗

PubMed2004

Transferable antibiotic resistance elements in Haemophilus influenzae share a common evolutionary origin with a diverse family of syntenic genomic islands.

Transferable antibiotic resistance in Haemophilus influenzae was first detected in the early 1970s. After this, resistance spread rapidly worldwide and was shown to be transferred by a large 40- to 60-kb conjugative element. Bioinformatics analysis of the complete sequence of a typical H. influenzae conjugative resistance element, ICEHin1056, revealed the shared evolutionary origin of this element. ICEHin1056 has homology to 20 contiguous sequences in the National Center for Biotechnology Information database. Systematic comparison of these homologous sequences resulted in identification of a conserved syntenic genomic island consisting of up to 33 core genes in 16 beta- and gamma-Proteobacteria. These diverse genomic islands shared a common evolutionary origin, insert into tRNA genes, and have diverged widely, with G+C contents ranging from 40 to 70% and amino acid homologies as low as 20 to 25% for shared core genes. These core genes are likely to account for the conjugative transfer of the genomic islands and may even encode autonomous replication. Accessory gene clusters were nestled among the core genes and encode the following diverse major attributes: antibiotic, metal, and antiseptic resistance; degradation of chemicals; type IV secretion systems; two-component signaling systems; Vi antigen capsule synthesis; toxin production; and a wide range of metabolic functions. These related genomic islands include the following well-characterized structures: SPI-7, found in Salmonella enterica serovar Typhi; PAP1 or pKLC102, found in Pseudomonas aeruginosa; and the clc element, found in Pseudomonas sp. strain B13. This is the first report of a diverse family of related syntenic genomic islands with a deep evolutionary origin, and our findings challenge the view that genomic islands consist only of independently evolving modules.

Base Sequence↗

PubMed2004

eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data.

The introduction of multilocus sequence typing (MLST) for the precise characterization of isolates of bacterial pathogens has had a marked impact on both routine epidemiological surveillance and microbial population biology. In both fields, a key prerequisite for exploiting this resource is the ability to discern the relatedness and patterns of evolutionary descent among isolates with similar genotypes. Traditional clustering techniques, such as dendrograms, provide a very poor representation of recent evolutionary events, as they attempt to reconstruct relationships in the absence of a realistic model of the way in which bacterial clones emerge and diversify to form clonal complexes. An increasingly popular approach, called BURST, has been used as an alternative, but present implementations are unable to cope with very large data sets and offer crude graphical outputs. Here we present a new implementation of this algorithm, eBURST, which divides an MLST data set of any size into groups of related isolates and clonal complexes, predicts the founding (ancestral) genotype of each clonal complex, and computes the bootstrap support for the assignment. The most parsimonious patterns of descent of all isolates in each clonal complex from the predicted founder(s) are then displayed. The advantages of eBURST for exploring patterns of evolutionary descent are demonstrated with a number of examples, including the simple Spain(23F)-1 clonal complex of Streptococcus pneumoniae, "population snapshots" of the entire S. pneumoniae and Staphylococcus aureus MLST databases, and the more complicated clonal complexes observed for Campylobacter jejuni and Neisseria meningitidis.

Algorithms↗

PubMed2025

Hidden diversity in Enterococcus faecalis revealed by CRISPR2 screening: eco-evolutionary insights into a novel subspecies.

Enterococcus faecalis is a commensal bacterium that colonizes the gut of humans and animals and is a major opportunistic pathogen, known for causing multidrug-resistant healthcare-associated infections (HAIs). Its ability to thrive in diverse environments and disseminate antimicrobial resistance genes (ARGs) across ecological niches highlights the importance of understanding its ecological, evolutionary, and epidemiological dynamics. The CRISPR2 locus has been used as a valuable marker for assessing clonality and phylogenetic relationships in E. faecalis. In this study, we identified a group of E. faecalis strains lacking CRISPR2, forming a distinct, well-supported clade. We demonstrate that this clade meets the genomic criteria for classification as a novel subspecies, here referred to as "subspecies B." Through a comprehensive pangenome analysis and comparative genomics, we explored the adaptive ecological traits underlying this diversification process, identifying clade-specific features and their predicted functional roles. Our findings suggest that the frequent isolation of subspecies B from meat products and processing facilities may reflect dissemination routes involving environmental contamination (e.g., water, plants, soil) from avian species. The absence of key virulence traits required for pathogenicity in mammals, particularly humans, and the lack of clinically relevant resistance determinants indicate that subspecies B currently poses minimal threat to public health compared with the broadly disseminated "subspecies A." Nevertheless, the unclear potential for genetic exchange between these subspecies and the frequent association of subspecies B with food sources calls for continued genomic surveillance of E. faecalis from a One Health perspective to detect and mitigate the emergence of high-risk variants in advance.IMPORTANCEExploring intraspecific genetic variability in generalist bacteria with pathogenic potential, such as Enterococcus faecalis, is a key to uncovering stable evolutionary trends. By screening the CRISPR2 locus across a representative set of genomes from diverse sources, this study reveals a previously unrecognized lineage within the population structure of E. faecalis, associated with underexplored nonhuman and nonhospital reservoirs. These findings broaden our knowledge of the species' genetic landscape and shed light on its adaptive strategies and patterns of ecological dissemination. By bridging phylogenetic patterns with variation in genetic defense systems and accessory traits, the study generates testable hypotheses about the genomic determinants and corresponding selective pressures that shape the species' behavior and long-term dissemination. This work offers new perspectives on the eco-evolutionary dynamics of E. faecalis and highlights the value of genomic surveillance beyond clinical settings, in alignment with One Health principles.

Enterococcus faecalis↗

PubMed2025

Evolutionary adaptations of a pediatric pathogen: low-inflammatory and high-resistance phenotypes in the emerging Salmonella typhimurium monophasic variant 1,4,[5],12:i:

Salmonella enterica serovar 1,4,[5],12:i:- (S.1,4,[5],12:i:-), a monophasic variant of Salmonella typhimurium (S. typhimurium), is an emerging multidrug-resistant pathogen posing a significant threat to pediatric health. Research on this variant remains limited, and due to challenges associated with traditional identification methods, S.1,4,[5],12:i:- has often been misclassified as S. typhimurium. This study collected clinical data from 122 children infected with S.1,4,[5],12:i:- and 42 with traditional S. typhimurium in Fujian Province, China, between 2014 and 2023. Whole-genome sequencing was used for strain analysis. Our findings revealed that 77.87% of children with S.1,4,[5],12:i:- infection were aged between 1 month and 2 years. Compared with traditional S. typhimurium, children with S.1,4,[5],12:i:- exhibited milder clinical symptoms, as evidenced by lower levels of the inflammatory marker C-reactive protein (16.53 mg/L vs. 33.94 mg/L, P < 0.05) and a lower hospitalization rate (26.23% vs. 42.86%, P < 0.05). These differences may be attributed to the high carriage rate of the anti-inflammatory gene gogB in S.1,4,[5],12:i:- (95.08% vs. 16.67%, P < 0.0001). Additionally, S.1,4,[5],12:i:- exhibited a higher resistance rate to multiple antibiotics, particularly ceftriaxone, than traditional S. typhimurium (32.79% vs. 7.14%, P < 0.001). This increased resistance may be associated with the carriage of the IncHI2/IncHI2A plasmid. The S.1,4,[5],12:i:- ST34 clone prevalent in this region aligns with the global epidemic trend but exhibits greater genetic diversity. Overall, the stealthy evolutionary adaptation of low-inflammation and high-resistance provides novel insights into this variant's global dominance. These findings underscore the importance of heightened clinical awareness and targeted interventions, particularly for vulnerable pediatric populations. IMPORTANCE S.1,4,[5],12:i:- poses a growing global health threat, particularly endangering infants and young children. Characterized by increasing prevalence, multidrug resistance, and diagnostic challenges, this variant demonstrates milder inflammatory responses yet stronger antibiotic resistance than traditional S. typhimurium in pediatric infections. Crucially, we identified its unique "low-inflammation, high-resistance" evolutionary strategy associated with anti-inflammatory gene gogB and resistance plasmid IncHI2/IncHI2A. The stealthy evolutionary adaptation provides novel insights into this variant's global dominance, while offering critical guidance for improving clinical management and formulating targeted public health measures to protect vulnerable pediatric populations against this cunning pathogen.

Humans↗

PubMed1988

Somatic immunoglobulin sequence divergence and its implications for studies of evolutionary divergence.

The divergence of immunoglobulin genes due to somatic mutation provides a natural example of DNA sequence divergence. This divergence was examined to gain insight into the processes of evolution and the determinants of the variance-to-mean ratio of sequence divergence. Normally, this ratio is found to be larger than expected (1.0 under Poisson assumptions) for the evolutionary divergence or most genes. Although not significantly less than one, all seven groups of immunoglobulin amino acid sequences have ratios smaller than expected, contrary to the evolutionary pattern generally observed. The substitutions in the immunoglobulin genes appear to be highly nonrandom and an excess of parallel changes (the major nonrandom feature of these mutations) is shown to cause smaller ratios. Because convergent or parallel mutations are often observed in the evolutionary divergence of genes, this suggests that forces causing the large observed ratios may actually have to be more powerful than previously expected. Further, since selection is one of the likely causes of parallel mutations, it should be noted that selection could significantly decrease the variance-to-mean ratio. The high frequency of parallel mutations and their resulting effects, as observed in the immunoglobulin genes, suggest that only poor inferences of sequence divergence can be made without actual knowledge of the ancestral sequence.

Amino Acid Sequence↗

PubMed1996

Evolutionary rate variation within Mus APRT.

Rodents are thought to have relatively high rates of evolution, twice as fast as the rates for mammals in other orders. However, the uniformly high rates of evolution inferred for the order Rodentia from Mus musculus and Rattus norvegicus are not consistently found for other rodent species. Using a maximum likelihood phylogenetic algorithm (DNAML), we show here that Mus spicilegus has a fivefold different rate of evolution in 1100 bp around the adenine phosphoribosyltransferase gene (APRT) since its divergence from a common ancestor with Mus musculus. A greater than threefold difference in rates is also found in a comparison of the number of evolutionary events directly detected from the APRT sequences of these two closely related Mus species. The evolutionary events can be directly detected, since M. spicilegus, M. musculus, and the four rodent outgroup species used to determine the ancestral sequence are so closely related. One of the major differences between M. spicilegus and M. musculus that might affect evolutionary rate is the degree of commensalism with man. The Mus species therefore provide a useful model for testing various hypotheses for the causes of rate variations between genes, and possibly, between lineages.

Adenine Phosphoribosyltransferase↗

PubMed2004

Phylogenetic motif detection by expectation-maximization on evolutionary mixtures.

The preferential conservation of transcription factor binding sites implies that non-coding sequence data from related species will prove a powerful asset to motif discovery. We present a unified probabilistic framework for motif discovery that incorporates evolutionary information. We treat aligned DNA sequence as a mixture of evolutionary models, for motif and background, and, following the example of the MEME program, provide an algorithm to estimate the parameters by Expectation-Maximization. We examine a variety of evolutionary models and show that our approach can take advantage of phylogenic information to avoid false positives and discover motifs upstream of groups of characterized target genes. We compare our method to traditional motif finding on only conserved regions. An implementation will be made available at http://rana.lbl.gov.

Algorithms↗