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PubMed2000

Competition and the Effect of Spatial Resource Heterogeneity on Evolutionary Diversification.

A model is presented to explore how the form of selection arising from competition for resources is affected by spatial resource heterogeneity. The model consists of a single species occupying two patches connected by migration, where the two patches can differ in the type of resources that they contain. The main goal is to determine the conditions under which competition for resources results in disruptive selection (i.e., selection favoring a polymorphism) since it is this form of selection that will give rise to the evolutionary diversification of resource exploitation strategies. In particular, comparing the conditions giving rise to disruptive selection when the two patches are identical to the conditions when they contain different resources reveals the effect of spatial resource heterogeneity. Results show that when the patches are identical, the conditions giving rise to disruptive selection are identical to those that give rise to character displacement in previous models. When the patches are different, the conditions giving rise to disruptive selection can be either more or less stringent depending upon demographic parameters such as the intrinsic rate of increase and the migration rate. Surprisingly, spatial resource heterogeneity can actually make forms of evolutionary diversification such as character displacement less likely. It is also found that results are dependent on how the resource exploitation strategies and the spatial resource heterogeneity affect the population dynamics. One robust conclusion however, is that spatial resource heterogeneity always has a disruptive effect when the migration rate between patches is low.

Lotka‐Volterra↗
PubMed2000

The Evolutionary Status of SS 433.

We consider possible evolutionary models for SS 433. We assume that common envelope evolution is avoided if radiation pressure is able to expel most of a super-Eddington accretion flow from a region smaller than the accretor's Roche lobe. This condition is satisfied, at least initially, for largely radiative donors with masses in the range 4-12 M middle dot in circle. For donors more massive than about 5 M middle dot in circle, moderate mass ratios q=M2&solm0;M1 greater, similar1 are indicated, thus tending to favor black hole accretors. For lower mass donors, evolutionary considerations do not distinguish between a neutron star or black hole accretor. In all cases the mass transfer (and mass-loss) rates M&d2;tr approximately 7x10-6 to 4x10-4 M middle dot in circle yr-1 are much larger than the likely mass-loss rate M&d2;jet approximately 10-6 M middle dot in circle yr-1 in the precessing jets. Almost all of the transferred mass is expelled at radii considerably larger than the jet acceleration region, producing the "stationary" Halpha line and the infrared luminosity and accounting for the low X-ray luminosity.

Journal Article↗
PubMed2000

Molecular evolutionary analysis of the complete nucleotide sequence of hepatitis B virus (HBV) in a case of HBV infection acquired through a needlestick accident.

To elucidate needlestick transmission of hepatitis B virus (HBV), strains isolated from 1 physician who acquired HBV infection through a needlestick accident and 3 patients with chronic hepatitis B (donor patients A, B, and C) were tested using molecular evolutionary analysis based on full-length HBV genomic sequences. Nucleotide sequences of these isolates were aligned with 55 previously reported full-length genomic sequences. Genetic distances were estimated using the 6-parameter method, and phylogenetic trees were constructed using the neighbor-joining method. Strains isolated from patient A and the recipient pair were clustered within a closer range of evolutionary distances than were strains recovered from the recipient pair and patients B and C. Furthermore, strains from patient A and the recipient were also clustered on the S gene sequences of HBV. These results demonstrated that patient A alone was the source of direct transmission to the recipient. This approach can be used to investigate the transmission route of HBV.

Adult↗
PubMed2003

A populationwide coalescent analysis of Icelandic matrilineal and patrilineal genealogies: evidence for a faster evolutionary rate of mtDNA lineages than Y chromosomes.

Historical inferences from genetic data increasingly depend on assumptions about the genealogical process that shapes the frequencies of alleles over time. Yet little is known about the structure of human genealogies over long periods of time and how they depart from expectations of standard demographic models, such as that attributed to Wright and Fisher. To obtain such information and to examine the recent evolutionary history of mtDNA and Y-chromosome haplotypes in the Icelandic gene pool, we traced the matrilineal and patrilineal ancestry of all 131,060 Icelanders born after 1972 back to two cohorts of ancestors, one born between 1848 and 1892 and the other between 1798 and 1742. This populationwide coalescent analysis of Icelandic genealogies revealed highly positively skewed distributions of descendants to ancestors, with the vast majority of potential ancestors contributing one or no descendants and a minority of ancestors contributing large numbers of descendants. The expansion and loss of matrilines and patrilines has caused considerable fluctuation in the frequencies of mtDNA and Y-chromosome haplotypes, despite a rapid population expansion in Iceland during the past 300 years. Contrary to a widespread assumption, the rate of evolution caused by this lineage-sorting process was markedly faster in matrilines (mtDNA) than in patrilines (Y chromosomes). The primary cause is a 10% shorter matrilineal generation interval. Variance in the number of offspring produced within each generation was not an important differentiating factor. We observed an intergenerational correlation in offspring number and in the length of generation intervals in the matrilineal and patrilineal genealogies, which was stronger in matrilines and thus contributes to their faster evolutionary rate. These findings may have implications for coalescent date estimates based on mtDNA and Y chromosomes.

Alleles↗
PubMed2003

Identification of four highly conserved genes between breakpoint hotspots BP1 and BP2 of the Prader-Willi/Angelman syndromes deletion region that have undergone evolutionary transposition mediated by flanking duplicons.

Prader-Willi and Angelman syndromes (PWS and AS) typically result from an approximately 4-Mb deletion of human chromosome 15q11-q13, with clustered breakpoints (BP) at either of two proximal sites (BP1 and BP2) and one distal site (BP3). HERC2 and other duplicons map to these BP regions, with the 2-Mb PWS/AS imprinted domain just distal of BP2. Previously, the presence of genes and their imprinted status have not been examined between BP1 and BP2. Here, we identify two known (CYFIP1 and GCP5) and two novel (NIPA1 and NIPA2) genes in this region in human and their orthologs in mouse chromosome 7C. These genes are expressed from a broad range of tissues and are nonimprinted, as they are expressed in cells derived from normal individuals, patients with PWS or AS, and the corresponding mouse models. However, replication-timing studies in the mouse reveal that they are located in a genomic domain showing asynchronous replication, a feature typically ascribed to monoallelically expressed loci. The novel genes NIPA1 and NIPA2 each encode putative polypeptides with nine transmembrane domains, suggesting function as receptors or as transporters. Phylogenetic analyses show that NIPA1 and NIPA2 are highly conserved in vertebrate species, with ancestral members in invertebrates and plants. Intriguingly, evolutionary studies show conservation of the four-gene cassette between BP1 and BP2 in human, including NIPA1/2, CYFIP1, and GCP5, and proximity to the Herc2 gene in both mouse and Fugu. These observations support a model in which duplications of the HERC2 gene at BP3 in primates first flanked the four-gene cassette, with subsequent transposition of these four unique genes by a HERC2 duplicon-mediated process to form the BP1-BP2 region. Duplicons therefore appear to mediate genomic fluidity in both disease and evolutionary processes.

Adaptor Proteins, Signal Transducing↗
PubMed2000

Evolutionary origins of human alcoholism in primate frugivory.

Evolutionary origins of alcohol consumption have rarely been considered in studies of ethanol addiction. However, the occurrence of ethanol in ripe and decaying fruit and the substantial heritability of alcoholism in humans suggest an important historical association between primate frugivory and alcohol consumption. Olfactory localization of ripe fruit via volatilized alcohols, the use of ethanol as an appetitive stimulant, and the consumption of fruits with substantial ethanol content potentially characterize all frugivorous primates, including hominoids and the lineage leading to modern humans. Patterns of alcohol use by humans in contemporary environments may thus reflect a maladaptive co-option of ancestral nutritional strategies. Although diverse factors contribute to the expression of alcoholism as a clinical syndrome, historical selection for the consumption of ethanol in the course of frugivory can be viewed as a subtle yet pervasive evolutionary influence on modern humans.

Adaptation, Physiological↗
PubMed2004

Flower color microevolution in wild radish: evolutionary response to pollinator-mediated selection.

Evolutionary ecologists are fundamentally interested in how species interactions affect evolutionary change. We tested the degree to which plant-pollinator interactions affect the frequency of flower color morphs of Raphanus sativus. Petal color in R. sativus is determined by two independently assorting loci, producing four petal colors (yellow, white, pink, and bronze). We assessed the impact of pollinator discrimination on changes in flower color variation by comparing the frequency of colors produced in the presence (open pollination) versus absence (null pollination) of pollinator discrimination. We also assessed the impact of postpollination and developmental effects on progeny colors using equal pollinations with all four color morphs. Our results from open pollinations found an overrepresentation of yellow progeny in the next generation, when compared with both null pollinations and cumulative ratios based on Hardy-Weinberg and linkage equilibria assumptions. When these results were combined with those from equal pollinations, the overrepresentation of yellow could be attributed to selection from pollinators. Yet, surveys in the field the following year found no flower color frequency changes in the next generation. These results illustrate that flower color microevolution can be driven by both pollinator discrimination and other nonpollinator selective forces acting during the seed-to-adult transition, countering selection imposed by pollinators.

Animals↗
PubMed2005

Autosomal recessive primary microcephaly (MCPH): a review of clinical, molecular, and evolutionary findings.

Autosomal recessive primary microcephaly (MCPH) is a neurodevelopmental disorder. It is characterized by two principal features, microcephaly present at birth and nonprogressive mental retardation. The microcephaly is the consequence of a small but architecturally normal brain, and it is the cerebral cortex that shows the greatest size reduction. There are at least seven MCPH loci, and four of the genes have been identified: MCPH1, encoding Microcephalin; MCPH3, encoding CDK5RAP2; MCPH5, encoding ASPM; and MCPH6, encoding CENPJ. These findings are starting to have an impact on the clinical management of families affected with MCPH. Present data suggest that MCPH is the consequence of deficient neurogenesis within the neurogenic epithelium. Evolutionary interest in MCPH has been sparked by the suggestion that changes in the MCPH genes might also be responsible for the increase in brain size during human evolution. Indeed, evolutionary analyses of Microcephalin and ASPM reveal evidence for positive selection during human and great ape evolution. So an understanding of this rare genetic disorder may offer us significant insights into neurogenic mitosis and the evolution of the most striking differences between us and our closest living relatives: brain size and cognitive ability.

Animals↗
PubMed2005

Estimating HIV evolutionary pathways and the genetic barrier to drug resistance.

BACKGROUND: The evolution of drug-resistant viruses challenges the management of human immunodeficiency virus (HIV) infections. Understanding this evolutionary process is important for the design of effective therapeutic strategies. METHODS: We used mutagenetic trees, a family of probabilistic graphical models, to describe the accumulation of resistance-associated mutations in the viral genome. On the basis of these models, we defined the genetic barrier, a quantity that summarizes the difficulty for the virus to escape from the selective pressure of the drug by developing escape mutations. RESULTS: From HIV reverse-transcriptase sequences that had been obtained from treated patients, we derived evolutionary models for zidovudine, zidovudine plus lamivudine, and zidovudine plus didanosine. The genetic barriers to resistance to zidovudine, stavudine, lamivudine, and didanosine, for the above 3 regimens, were computed and analyzed. We found both the mode and the rate of development of resistance to be heterogeneous. The genetic barrier to zidovudine resistance was increased if lamivudine was added to zidovudine but was decreased for didanosine. The barrier to lamivudine resistance was maintained with zidovudine plus didanosine, whereas the barrier to didanosine resistance was reduced most with zidovudine plus lamivudine. CONCLUSION: Mutagenetic trees provide a quantitative picture of the evolution of drug resistance. The genetic barrier is a useful tool for design of effective treatment strategies.

Anti-HIV Agents↗
PubMed2005

Adaptation: "a critique of some current evolutionary thought".

In his classic Adaptation and Natural Selection: A Critique of Some Current Evolutionary Thought (1966), George Williams showed definitively that our understanding of adaptation, a central concept of evolutionary theory, must be gene-centered. The purpose of adaptations is to further the replication of genes. Genes are machines for turning out more genes; and adaptations are the means by which genes pluck resources from the world to promote this self-replication. Thus adaptations transform potential resources from part of the indifferent world-at-large into tailor-made environments, environments brimming with resources for organisms' distinctive adaptive needs. Systematically dif ferent adaptive problems therefore give rise to different environments; and so different species, for example, have different environments. Thus a gene-centered analysis of adaptations implies a gene-centered theory of environments. Without genes to specify what constitutes an environment, environments would not exist. Rather than being separate from biology, an autonomous, independent force, environments are themselves the products of biology. So a gene-centered view, far from depreciating the environment, furnishes a rich and precise understanding of its importance.

Adaptation, Physiological↗
PubMed2005

Evolution of sexual dimorphism and male dimorphism in the expression of beetle horns: phylogenetic evidence for modularity, evolutionary lability, and constraint.

Beetle horns are enlarged outgrowths of the head or thorax that are used as weapons in contests over access to mates. Horn development is typically confined to males (sexual dimorphism) and often only to the largest males (male dimorphism). Both types of dimorphism result from endocrine threshold mechanisms that coordinate cell proliferation near the end of the larval period. Here, we map the presence/absence of each type of dimorphism onto a recent phylogeny for the genus Onthophagus (Coleoptera: Scarabaeidae) to explore how horn development has changed over time. Our results provide empirical support for several recent predictions regarding the evolutionary lability of developmental thresholds, including uncoupled evolution of alternative phenotypes and repeated fixation of phenotypes. We also report striking evidence of a possible developmental constraint. We show that male dimorphism and sexual dimorphism map together on the phylogeny; whenever small males have horns, females also have horns (and vice versa). We raise the possibility that correlated evolution of these two phenomena results from a shared element in their endocrine regulatory mechanisms rather than a history of common selection pressures. These results illustrate the type of insight that can be gained only from the integration of developmental and evolutionary perspectives.

Animals↗
PubMed2005

Evolutionary feedback mediated through population density, illustrated with viruses in chemostats.

A cornerstone of evolutionary ecology is that population density affects adaptation: r and K selection is the obvious example. The reverse is also appreciated: adaptation impacts population density. Yet, empirically demonstrating a direct connection between population density and adaptation is challenging. Here, we address both evolution and ecology of population density in models of viral (bacteriophage) chemostats. Chemostats supply nutrients for host cell growth, and the hosts are prey for viral reproduction. Two different chemostat designs have profoundly different consequences for viral evolution. If host and virus are confined to the same chamber, as in a predator-prey system, viral regulation of hosts feeds back to maintain low viral density (measured as infections per cell). Viral adaptation impacts host density but has a small effect on equilibrium viral density. More interesting are chemostats that supply the viral population with hosts from a virus-free refuge. Here, a type of evolutionary succession operates: adaptation at low viral density leads to higher density, but high density then favors competitive ability. Experiments support these models with both phenotypic and molecular data. Parallels to these designs exist in many natural systems, so these experimental systems may yield insights to the evolution and regulation of natural populations.

Adaptation, Biological↗
PubMed2007

The causes of evolutionary radiations in archipelagoes: passerine birds in the Lesser Antilles.

To investigate why some lineages undergo evolutionary radiation, we compare the passerine avifaunas of the Hawaiian and Galapagos archipelagoes, which have supported well-known radiations of birds, with those of the Lesser Antilles, which have not. We focus on four steps required for the buildup of diversity through allopatric speciation and secondary sympatry: genetic divergence in isolation, persistence of island populations, recolonization of source islands, and ecological compatibility in secondary sympatry. Analysis of genetic divergence among island populations in the Lesser Antilles reveals evidence of both prolonged independent evolution and re-expansion of differentiated island populations through the archipelago but little evidence of secondary sympatry of divergent genetic lineages. Archipelagoes with high rates of colonization from continental or nearby large-island sources might fail to promote evolutionary radiations because colonists fill ecological space and constrain diversification through competition. However, morphological analysis demonstrated similar divergence between allopatric populations in species in Hawaii, Galapagos, and the Lesser Antilles, although the rate of divergence between secondarily sympatric species evidently is more rapid in Hawaii and the Galapagos. Alternatively, endemic buildup of diversity might be facilitated by the relative absence of pathogens in Hawaii and Galapagos that otherwise could prevent the secondary sympatry of populations owing to disease-mediated competition.

Animals↗
PubMed1997

Multilocus genotypes, a tree of individuals, and human evolutionary history.

Our goal is to infer, from human genetic data, general patterns as well as details of human evolutionary history. Here we present the results of an analysis of genetic data at the level of the individual. A tree relating 144 individuals from 12 human groups of Africa, Asia, Europe, and Oceania, inferred from an average of 75 DNA polymorphisms/individual, is remarkable in that most individuals cluster with other members of their regional group. In order to interpret this tree, we consider the factors that influence the tree pattern, including the number of genetic loci examined, the length of population isolation, the sampling process, and the extent of gene flow among groups. Understanding the impact of these factors enables us to infer details of human evolutionary history that might otherwise remain undetected. Our analyses indicate that some recent ancestor(s) of each of a few of the individuals tested may have immigrated. In general, the populations within regional groups appear to have been isolated from one another for <25,000 years. Regional groups may have been isolated for somewhat longer.

Biological Evolution↗
PubMed2004

Inhibition of protein crystallization by evolutionary negative design.

Why are proteins so hard to crystallize? We propose an 'evolutionary negative design' principle to explain this difficulty. Proteins have evolved to avoid crystallization because crystallization compromises the viability of the cell. Evolutionary negative design is supported by much evidence in the literature, including the effect of mutations on the crystallizability of a protein, the correlations found in the properties of crystal contacts in bioinformatics databases, and the positive use of protein crystallization by bacteria and viruses.

Biophysical Phenomena↗
PubMed2002

Novel evolutionary analyses of full-length HIV type 1 subtype C molecular clones from Cape Town, South Africa.

Understanding the origin, distribution, and evolving dominance of HIV-1 subtype C strains is an important component in the design and evaluation of a globally effective AIDS vaccine. To better understand subtype C viruses, we constructed complete molecular clones of primary, CCR-5-using isolates from South Africa and analyzed the molecular phylogenies of these clones using best fitting evolutionary substitution models. Analyses were performed on three full-length sequences, and on the individual genes. All clones were nonrecombinant, and although two of three had open reading frames and intact splice sites, they were not infectious. At the genomic level, the models demonstrated the increasing variability of subtype C in South Africa. At the subgenomic level, they revealed marked differences in the evolutionary patterns of individual genes, a finding that suggests that the genes are under different selective pressures and constraints. These data underscore the dynamic nature of the subtype C epidemic and emphasize the need for continuous monitoring of local strains.

Acquired Immunodeficiency Syndrome↗
PubMed1981

Cloning of bovine prolactin cDNA and evolutionary implications of its sequence.

Prolactin, growth hormone, and chorionic somatomammotropin (placental lactogen) constitute a set of related polypeptides believed to derive from a common evolutionary ancestor protein. We have cloned and sequenced DNA complementary to the mRNA coding for bovine prolactin. This cDNA contains 702 bases corresponding to 10 amino acids in the leader peptide, all 199 amino acids of the hormone, and 75 nucleotides in the 3' untranslated region of the mRNA. Nucleotide sequence analysis of this cDNA permitted the identification of 10 amino acids in the signal peptide, plus the correction or elucidation of amino acid assignments at 16 sites where aspartic and glutamic acids had not been distinguished from their amides by amino acid sequencing. Codon usage in bovine prolactin mRNA is nonrandom, but, similarly to rat and human prolactins, it does not exhibit the strong preference for G or C in codon third positions seen in bovine, rat, and human growth hormone mRNAs. The translational termination signal in bovine prolactin in UAA, also the same as in rat and human prolactins and differing from the UAG "stop" codon used in bovine, rat, and human growth hormones and human chorionic somatomammotropin. The amino acid and mRNA nucleotide sequences of bovine, rat, and human prolactins and growth hormones were compared by several techniques based on various theories of molecular evolution. The comparison of prolactin to growth hormone is consistent in all three species, suggesting that the genes for these two hormones diverged about 350 million years ago. However, comparisons among the three prolactins or among the three growth hormones to determine the times of evolutionary divergence of the three species generated values that were inconsistent with each other and with the fossil record. Analysis of these discrepancies suggests that the genes for prolactin and growth hormone may now be evolving by different mechanisms.

Amino Acid Sequence↗
PubMed1999

Menstrual cycling and breast cancer: an evolutionary perspective.

This article attempts to bridge the disciplinary gap between evolutionary biology and clinical studies of women's health. The resulting dialogue is predicted to have useful implications for research aimed at the prevention of women's reproductive cancers. The specific focus is on the relationship between breast cancer and exposure to ovarian hormones during normal menstrual cycling. The clinician's view of normal cycling is radically different from that uncovered by evolutionary studies of noncontracepting populations. This point is illustrated by data on the Dogon of Mali, a traditional West African population with a mean of 8.6 +/- 0.3 live births per woman. The Dogon data include hormonal profiles (urinary estrone-3-glucuronide and pregnanediol-3-glucuronide) of 93 women (sampled twice weekly for 10 weeks) and a census of women's visits to menstrual huts (n = 736 days). Dogon women menstruated regularly only if they were sterile. Otherwise, women aged 20-34 years had a median of only two menses each over the 2-year study period. The median number of menses per lifetime was approximately 100, about a third as many as experienced by an American woman who had three live births. These results contribute to a growing body of evidence that women's bodies were designed by natural selection to spend most of the time in lactational amenorrhea and add support to the view that contraceptives can be made safer if they forego the hormonal swings associated with menstruation. This conclusion is further reinforced by evidence that menstrual bleeding serves no adaptive purpose.

Adolescent↗