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PubMed2001

Inferring speciation rates from phylogenies.

It is possible to estimate the rate of diversification of clades from phylogenies with a temporal dimension. First, I present several methods for constructing confidence intervals for the speciation rate under the simple assumption of a pure birth process. I discuss the relationships among these methods in the hope of clarifying some fundamental theory in this area. Their performances are compared in a simulation study and one is recommended for use as a result. A variety of other questions that may, in fact, be the questions of primary interest (e.g., Has the rate of cladogenesis been declining?) are then recast as biological variants of the purely statistical question-Is the birth process model appropriate for my data? Seen in this way, a preexisting arsenal of statistical techniques is opened up for use in this area: in particular, techniques developed for the analysis of Poisson processes and the analysis of survival data. These two approaches start from different representations of the data--the branch lengths in the tree--and I explicitly relate the two. Aiming for a synoptic account of useful theory in this area, I briefly discuss some important results from the analysis of two distinct birth-death processes: the one introduced into this area by Hey (1992) is refitted with some powerful statistical tools.

Animals↗
PubMed2005

Maximum body size in a radiating clade as a function of time.

The behavior of the maximum body size (body length) in an evolving clade is exemplified by the evolutionary histories of Bivalvia, Cetacea, and Camerata (Crinoidea). Changes of the maximum size with time track closely diversification history: when a clade diversifies exponentially, the maximum size also increases exponentially, and when the number of species changes irregularly (at varying rates), the maximum size also changes in that manner. However, within any given clade, the maximum body size changes at lower rates than diversity does. The observed shifts in maximum body size approximate the rate of diversification per unit of time to the power of about 0.5.

Animals↗
PubMedDate not supplied

Molecular evolution of human immunodeficiency virus type 1 subtype A in Senegal: 1988-1997.

OBJECTIVE: Few studies have been able to track the genetic diversity of HIV-1 viruses in human populations over time. We analyzed the molecular evolution of subtype A over a 10-year period, in a cohort of female sex workers with a known time of infection. STUDY DESIGN/METHODS: We amplified and sequenced the C2-V3 region of the surface envelope glycoprotein from 73 HIV-1-infected women, infected between 1987-1997. RESULTS: Fifty-one patients were infected by subtype A viruses. The viruses demonstrated significant diversification (p < 0.001) with mean genetic distance increasing from 8.6% in 1989 to 15.9% in 1997. The slope of the fitted curve suggested a rate of diversification of 0.7% per year. The majority of subtype A viruses clustered with HIV-1 subtype A/G recombinant form (IbNG). CONCLUSION: The genetic diversity of HIV-1 subtype A infections doubled over the first 10 years of this high risk population's epidemic, suggesting that implementation of vaccines early in the epidemic may have a higher likelihood of success based on levels of genetic diversity. The A/G recombinant form (IbNG) has taken epidemic proportions in West Africa. This is of particular importance in understanding the epidemiology of HIV-1 subtypes in Africa and to further dissect the potential phenotypic and biological characteristics of these viruses.

Cohort Studies↗
PubMed2006

Divergent timing and patterns of species accumulation in lowland and highland neotropical birds.

Late Pliocene and Pleistocene climatic instability has been invoked to explain the buildup of Neotropical biodiversity, although other theories date Neotropical diversification to earlier periods. If these climatic fluctuations drove Neotropical diversification, then a large proportion of species should date to this period and faunas should exhibit accelerated rates of speciation. However, the unique role of recent climatic fluctuations in promoting diversification could be rejected if late Pliocene and Pleistocene rates declined. To test these temporal predictions, dateable molecular phylogenies for 27 avian taxa were used to contrast the timing and rates of diversification in lowland and highland Neotropical faunas. Trends in diversification rates were analyzed in two ways. First, rates within taxa were analyzed for increasing or decreasing speciation rates through time. There was a significant trend within lowland taxa towards decreasing speciation rates, but no significant trend was observed within most highland taxa. Second, fauna wide diversification rates through time were estimated during one-million-year intervals by combining rates across taxa. In the lowlands, rates were highest during the late Miocene and then decreased towards the present. The decline in rates observed both within taxa and for the fauna as a whole probably resulted from density dependent cladogenesis. In the highlands, faunawide rates did not vary greatly before the Pleistocene but did increase significantly during the last one million years of the Pleistocene following the onset of severe glacial cycles in the Andes. These contrasting patterns of species accumulation suggest that lowland and highland regions were affected differently by recent climatic fluctuations. Evidently, habitat alterations associated with global climate change were not enough to promote an increase in the rate of diversification in lowland faunas. In contrast, direct fragmentation of habitats by glaciers and severe altitudinal migration of montane vegetation zones during climatic cycles may have resulted in the late Pleistocene increase in highland diversification rates. This increase resulted in a fauna with one third of its species dating to the last one million years.

Animals↗
PubMed2002

New inferences from tree shape: numbers of missing taxa and population growth rates.

The relative positions of branching events in a phylogeny contain information about evolutionary and population dynamic processes. We provide new summary statistics of branching event times and describe how these statistics can be used to infer rates of species diversification from interspecies trees or rates of population growth from intraspecies trees. We also introduce a phylogenetic method for estimating the level of taxon sampling in a clade. Different evolutionary models and different sampling regimes can produce similar patterns of branching events, so it is important to consider explicitly the model assumptions involved when making evolutionary inferences. Results of an analysis of the phylogeny of the mosquito-borne flaviviruses suggest that there could be several thousand currently unidentified viruses in this clade.

Animals↗
PubMed2002

Age at maturity and diversification in woody angiosperms.

Angiosperm diversification has been associated with plant-animal interactions such as seed dispersal and pollination and life-history characters such as rapid growth and fast reproduction. This paper relates a life-history character (age at maturity) to woody angiosperm diversification. Here I present a comparative analysis of data drawn from the literature, indicating that time to first reproduction is shorter in woody angiosperms than in gymnosperms. In addition, age at maturity is negatively correlated with the rate of diversification (measured as the number of species per genus) at all the taxonomic levels analyzed and also when phylogenetically independent contrasts were conducted. This correlation suggests that early reproduction promotes diversification in woody angiosperms. Furthermore, this correlation is not a confounding effect of the association between age at maturity and other ecological factors that promote angiosperm diversification, such as pollination and seed dispersal systems.

Biological Evolution↗
PubMed2004

Ice sheets promote speciation in boreal birds.

The premise that Pleistocene ice ages played an important role in generating present-day species diversity has been challenged by genetic data indicating that most of the youngest terrestrial species on Earth coalesced long before major glacial advances. However, study has been biased towards faunas distributed at low latitudes that were not directly fragmented by advancing ice sheets. Using mitochondrial sequence divergence and a molecular clock, we compared the coalescence times of pairs of avian species belonging to superspecies complexes from the high-latitude boreal forest with those of sub-boreal and tropical avifaunas of the New World. Remarkably, all coalescence events in boreal superspecies date to the Pleistocene, providing direct evidence that speciation was commonly initiated during recent glacial periods. A pattern of endemism in boreal superspecies plausibly links the timing of divergence to the fragmentation of the boreal forest by ice sheets during the Mid- and Late Pleistocene. In contrast to the boreal superspecies, only 56% of sub-boreal and 46% of tropical superspecies members coalesced during the Pleistocene, suggesting that avifaunas directly fragmented by ice sheets experienced rapid rates of diversification, whereas those distributed farther south were affected to a lesser extent. One explanation for the absence of pre-Pleistocene superspecies in boreal avifaunas is that strong selection pressures operated in boreal refugia, causing superspecies members to achieve ecological differentiation at an accelerated rate.

Animals↗
PubMed2006

Anti-Müllerian hormone (AMH/AMH) in the European sea bass: its gene structure, regulatory elements, and the expression of alternatively-spliced isoforms.

In mammals, a multitude of studies have shown that anti-Müllerian hormone (AMH/AMH), apart from inducing Müllerian duct regression during male sexual differentiation, exerts inhibitory effects on male and female gonadal steroidogenesis and differentiation. However, in lower vertebrates like teleost fish, the function of AMH/AMH has been far less explored. As a first step to unravel its potential role in reproduction in teleost fish, we isolated and characterised the AMH gene in the European sea bass (sb), Dicentrachus labrax, determined putative regulatory elements of its 5'-flanking region, and analysed its gene expression and those of alternatively-spliced transcripts. The characterisation of sb-AMH revealed distinct features that distinguishes it from mammalian and bird AMH, suggesting a high rate of diversification of AMH during vertebrate evolution. It contained 7 exons that were divided by 6 introns, of which the last intron (intron vi) was localised only a few nucleotides upstream of the putative peptide cleavage site. The guanine and cytosine content of the open reading frame (ORF) was 52.7% and thus notably lower than that of bird and mammalian AMH. Sb-AMH cDNA was 2045 base pairs (bp) long, containing an ORF of 1599 bp encoding 533 amino acids. Deduced amino acid similarities of the conserved, carboxyterminal domain were highest with AMH in Japanese flounder (84.2%) and lowest with chicken AMH (45.5%). In the proximal promoter sequence of sb-AMH, a steroidogenic factor-1 (SF-1) binding site was present; however other regulatory sequences essential for transcriptional activation of AMH in mammals were absent. Likewise, there was no sequence homology to an SF3A2 sequence within the first 3200 bp upstream of the sb-AMH translation start site. Gene expression of sb-AMH and of alternatively-spliced sb-AMH transcripts were analysed in male and female juvenile and adult gonads as well as in somatic tissues of juvenile males. sb-AMH expression was highest in juvenile testis, but still remarkably high in juvenile ovaries and adult testis, as well as in brain, pituitary, and heart of juvenile male sea bass. Apart from adult ovary, levels of alternatively-spliced sb-AMHexonII/-99 were marginal in comparison with sb-AMH. In contrast, the transcript variant sb-AMHexonVII/+5 was expressed to a similar extent as sb-AMH in all tissues examined. The results of this work have provided the basis for future studies concerning the regulation and function of AMH/AMH in this species.

5' Flanking Region↗
PubMed2001

Defining and interpreting intraspecific molecular variation.

Defining the extent and character of intraspecific genetic variation provides important information about gene function and organismal history. Powerful tests may be applied to sequenced alleles in order to critically examine whether natural selection is responsible for limiting or elevating intraspecific polymorphism in particular genes. Unconventional patterns of sequence variation and unusual allelic frequency distributions can be used to test whether genes encoding parasite antigens are being diversified by immune selection. The strikingly limited genetic variation in the falciparum malaria genome, and in human chromosomes encoding resistance to severe malaria, date the emergence of this disease to within the last few thousand years, illustrating the power of population genetic analysis to elucidate the history of host-parasite interactions. Coupling phylogenetic and geographic information and analyzing the rate of diversification in intraspecific gene trees provides new and rich sources of information on microbial evolution and epidemiology.

Alleles↗
PubMed2005

Species diversity can drive speciation.

A fundamental question in evolutionary ecology and conservation biology is: why do some areas contain greater species diversity than others? Island biogeographic theory has identified the roles of immigration and extinction in relation to area size and proximity to source areas, and the role of speciation is also recognized as an important factor. However, one as yet unexplored possibility is that species diversity itself might help to promote speciation, and indeed the central tenets of island biogeographic theory support such a prediction. Here we use data for plants and arthropods of the volcanic archipelagos of the Canary and Hawaiian Islands to address whether there is a positive relationship between species diversity and rate of diversification. Our index of diversification for each island is the proportion of species that are endemic, and we test our prediction that this increases with increasing species number. We show that even after controlling for several important physical features of islands, diversification is strongly related to species number.

Animals↗
PubMed2001

How many species of cichlid fishes are there in African lakes?

The endemic cichlid fishes of Lakes Malawi, Tanganyika and Victoria are textbook examples of explosive speciation and adaptive radiation, and their study promises to yield important insights into these processes. Accurate estimates of species richness of lineages in these lakes, and elsewhere, will be a necessary prerequisite for a thorough comparative analysis of the intrinsic and extrinsic factors influencing rates of diversification. This review presents recent findings on the discoveries of new species and species flocks and critically appraises the relevant evidence on species richness from recent studies of polymorphism and assortative mating, generally using behavioural and molecular methods. Within the haplochromines, the most species-rich lineage, there are few reported cases of postzygotic isolation, and these are generally among allopatric taxa that are likely to have diverged a relatively long time in the past. However, many taxa, including many which occur sympatrically and do not interbreed in nature, produce viable, fertile hybrids. Prezygotic barriers are more important, and persist in laboratory conditions in which environmental factors have been controlled, indicating the primary importance of direct mate preferences. Studies to date indicate that estimates of alpha (within-site) diversity appear to be robust. Although within-species colour polymorphisms are common, these have been taken into account in previous estimates of species richness. However, overall estimates of species richness in Lakes Malawi and Victoria are heavily dependent on the assignation of species status to allopatric populations differing in male colour. Appropriate methods for testing the specific status of allopatric cichlid taxa are reviewed and preliminary results presented.

Africa↗
PubMed2003

Spatial grain and the causes of regional diversity gradients in ants.

Gradients of species richness (S; the number of species of a given taxon in a given area and time) are ubiquitous. A key goal in ecology is to understand whether and how the many processes that generate these gradients act at different spatial scales. Here we evaluate six hypotheses for diversity gradients with 49 New World ant communities, from tundra to rain forest. We contrast their performance at three spatial grains from S(plot), the average number of ant species nesting in a m2 plot, through Fisher's alpha, an index that treats our 30 1-m2 plots as subsamples of a locality's diversity. At the smallest grain, S(plot), was tightly correlated (r2 = 0.99) with colony abundance in a fashion indistinguishable from the packing of randomly selected individuals into a fixed space. As spatial grain increased, the coaction of two factors linked to high net rates of diversification--warm temperatures and large areas of uniform climate--accounted for 75% of the variation in Fisher's alpha. However, the mechanisms underlying these correlations (i.e., precisely how temperature and area shape the balance of speciation to extinction) remain elusive.

Animals↗
PubMed1994

Clonotypic dominance and variable gene elements of pathogenic anti-DNA autoantibodies from a single patient with lupus.

This study explores the usage and diversity of the variable gene elements expressed by human lupus antibodies to DNA bearing the 0-81 idiotype, a marker of pathogenic anti-DNA autoantibodies. Rather than studying DNA-specific clonotypes from different patients, a panel of idiotype positive anti-DNA autoantibody-secreting clones from a single individual were analysed. By cloning and nucleotide-sequencing the heavy-chain variable gene segments, evidence was found for dominance of clonotypic patterns. Also noted was a high rate of diversification among the variable (VH), diversity (DH) and junctional (JH) gene segments utilized, with a pattern of mutations indicative of antigenic selection. These features suggest that the clones secreting the lupus pathogenic autoantibodies have been selected over multiple generations through an affinity-maturation process that is reminiscent of antigen-driven immune responses.

Adult↗
PubMed2001

Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins.

BACKGROUND: Detection of changes in a protein's evolutionary rate may reveal cases of change in that protein's function. We developed and implemented a simple relative rates test in an attempt to assess the rate constancy of protein evolution and to detect cases of functional diversification between orthologous proteins. The test was performed on clusters of orthologous protein sequences from complete bacterial genomes (Chlamydia trachomatis, C. muridarum and Chlamydophila pneumoniae), complete archaeal genomes (Pyrococcus horikoshii, P. abyssi and P. furiosus) and partially sequenced mammalian genomes (human, mouse and rat). RESULTS: Amino-acid sequence evolution rates are significantly correlated on different branches of phylogenetic trees representing the great majority of analyzed orthologous protein sets from all three domains of life. However, approximately 1% of the proteins from each group of species deviates from this pattern and instead shows variation that is consistent with an acceleration of the rate of amino-acid substitution, which may be due to functional diversification. Most of the putative functionally diversified proteins from all three species groups are predicted to function at the periphery of the cells and mediate their interaction with the environment. CONCLUSIONS: Relative rates of protein evolution are remarkably constant for the three species groups analyzed here. Deviations from this rate constancy are probably due to changes in selective constraints associated with diversification between orthologs. Functional diversification between orthologs is thought to be a relatively rare event. However, the resolution afforded by the test designed specifically for genomic-scale datasets allowed us to identify numerous cases of possible functional diversification between orthologous proteins.

Animals↗
PubMed2005

Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary.

Tertiary macrofossils of the flowering plant family Leguminosae (legumes) were used as time constraints to estimate ages of the earliest branching clades identified in separate plastid matK and rbcL gene phylogenies. Penalized likelihood rate smoothing was performed on sets of Bayesian likelihood trees generated with the AIC-selected GTR+ Gamma +I substitution model. Unequivocal legume fossils dating from the Recent continuously back to about 56 million years ago were used to fix the family stem clade at 60 million years (Ma), and at 1-Ma intervals back to 70 Ma. Specific fossils that showed distinctive combinations of apomorphic traits were used to constrain the minimum age of 12 specific internal nodes. These constraints were placed on stem rather than respective crown clades in order to bias for younger age estimates. Regardless, the mean age of the legume crown clade differs by only 1.0 to 2.5 Ma from the fixed age of the legume stem clade. Additionally, the oldest caesalpinioid, mimosoid, and papilionoid crown clades show approximately the same age range of 39 to 59 Ma. These findings all point to a rapid family-wide diversification, and predict few if any legume fossils prior to the Cenozoic. The range of the matK substitution rate, 2.1-24.6 x 10(-10) substitutions per site per year, is higher than that of rbcL, 1.6- 8.6 x 10(-10), and is accompanied by more uniform rate variation among codon positions. The matK and rbcL substitution rates are highly correlated across the legume family. For example, both loci have the slowest substitution rates among the mimosoids and the fastest rates among the millettioid legumes. This explains why groups such as the millettioids are amenable to species-level phylogenetic analysis with these loci, whereas other legume groups are not.

Bayes Theorem↗
PubMed1984

Generation of phenotypic diversity and progression in metastatic tumor cells.

The emergence of diversified tumor cell subpopulations in malignant neoplasms accounts for their heterogeneous cellular phenotypes and virtually ensures that some tumor cells will ultimately evolve with the most favorable properties for their enhanced abilities to survive, grow, invade and metastasize (tumor progression). The rates of cellular phenotypic diversification appear to vary greatly among different tumors and within the same tumor, and they are probably controlled, at least in part, by cellular instability due to chromosomal defects and random somatic mutational events, the rates of which are known to be higher in more malignant cells, and by epigenetic events, which may vary widely depending on the nature of the tumor cells and their microenvironments. As tumor progression proceeds, the most malignant cell subpopulations appear to lose their responsiveness to changes in tumor microenvironment while maintaining their high rates of phenotypic diversification. Tumor and normal cell-cell and cell-extracellular matrix interactions, as well as tumor cell nutrients, oxygen, hormones, growth factors, inducers and other regulatory molecules provide individual malignant cells with microenvironmental signals that could act through epigenetic cellular modifications, such as DNA methylation, and transcriptional, posttranscriptional, translational and posttranslational controls, or combinations of these. In addition, integration of viral gene sequences or viral modification of host DNA in critical regions could affect phenotypic stability. Finally, manipulation of tumor cells by antitumor therapy can also have profound effects on the rates of phenotypic diversification of the surviving tumor cells. A model for generating cellular phenotypic diversity based on the proposed mechanism for rapid generation of immunoglobulin molecular diversity in B cells may be applicable to malignant cells and to cells in general. In this model the expression and activity of gene products from multigene families are affected by a variety of genetic and epigenetic controlling mechanisms, and alterations in regulatory genes caused by recombination, methylation, mutation, or other changes could lead to differences in gene expression, resulting in widespread quantitative (and perhaps some qualitative) changes in particular gene products or their activities. As they proceed down different pathways of gene expression, each cell would be exposed to continual host selection pressures creating diverse, ever-changing malignant cell-populations.

Animals↗
PubMed2006

Antimutator role of the DNA glycosylase mutY gene in Helicobacter pylori.

Helicobacter pylori has a highly variable genome with ongoing diversification via inter- and intragenomic recombination and spontaneous mutation. DNA repair genes modulating mutation and recombination rates that influence diversification have not been well characterized for H. pylori. To examine the role of putative base excision repair ung and mutY glycosylase and xthA apurinic/apyrimidinic endonuclease genes in H. pylori, mutants of each were constructed in strain JP26 by allelic exchange. Spontaneous mutation frequencies of JP26 mutY mutants, assessed by rifampin resistance, were consistently higher (26-fold) than that of the wild type, whereas the ung and xthA mutants showed smaller increases. In trans complementation of the JP26 mutY mutant restored spontaneous mutation frequencies to wild-type levels. In cross-species studies, H. pylori mutY complemented an Escherichia coli mutY mutant and vice versa. In contrast, the ung and mutY mutants did not show higher frequencies of intergenomic recombination or greater sensitivity to UV-induced DNA damage than the wild type. The H. pylori mutY open reading frame contains an eight-adenine homonucleotide tract; we provide evidence that this is subject to slipped-strand mispairing, leading to frameshifts that eliminate gene function. Our findings indicate that H. pylori possesses phase-variable base excision repair, consistent with a tension between repair and mutation.

Adenine↗
PubMed1998

"Inordinate Fondness" explained: why are there So many beetles?

The phylogeny of the Phytophaga, the largest and oldest radiation of herbivorous beetles, was reconstructed from 115 complete DNA sequences for the 18S nuclear ribosomal subunit and from 212 morphological characters. The results of these analyses were used to interpret the role of angiosperms in beetle diversification. Jurassic fossils represent basal lineages that are still associated with conifers and cycads. Repeated origins of angiosperm-feeding beetle lineages are associated with enhanced rates of beetle diversification, indicating a series of adaptive radiations. Collectively, these radiations represent nearly half of the species in the order Coleoptera and a similar proportion of herbivorous insect species.

Journal Article↗