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PubMed2006

Optimal gene trees from sequences and species trees using a soft interpretation of parsimony.

Gene duplication and gene loss as well as other biological events can result in multiple copies of genes in a given species. Because of these gene duplication and loss dynamics, in addition to variation in sequence evolution and other sources of uncertainty, different gene trees ultimately present different evolutionary histories. All of this together results in gene trees that give different topologies from each other, making consensus species trees ambiguous in places. Other sources of data to generate species trees are also unable to provide completely resolved binary species trees. However, in addition to gene duplication events, speciation events have provided some underlying phylogenetic signal, enabling development of algorithms to characterize these processes. Therefore, a soft parsimony algorithm has been developed that enables the mapping of gene trees onto species trees and modification of uncertain or weakly supported branches based on minimizing the number of gene duplication and loss events implied by the tree. The algorithm also allows for rooting of unrooted trees and for removal of in-paralogues (lineage-specific duplicates and redundant sequences masquerading as such). The algorithm has also been made available for download as a software package, Softparsmap.

Algorithms↗
PubMed1996

Complex dynamics of multilocus systems subjected to cyclical selection.

Earlier we have shown that oscillations with a long period ("supercycles") may arise in two-locus systems experiencing cyclical selection with a short period. However, this mode of complex limiting behavior appeared to be possible for narrow ranges of parameters. Here we demonstrate that a multilocus system subjected to stabilizing selection with cyclically moving optimum can generate ubiquitous complex limiting behavior including supercycles, T-cycles, and chaotic-like phenomena. This mode of multilocus dynamics far exceeds the potential attainable under ordinary selection models resulting in simple behavior. It may represent a novel evolutionary mechanism increasing genetic diversity over long-term time periods.

Biological Evolution↗
PubMedDate not supplied

Seasonal changes in the physiology of male Virginia opossums (Didelphis virginiana): signs of the Dasyurid semelparity syndrome?

Semelparity, which is multiplying once in a lifetime, is a rare reproductive strategy among mammals. Several species of the marsupial family Dasyuridae experience 100% male mortality following an intense mating period. We investigated seasonal physiological changes that may be associated with early mortality in the male Virginia opossum (Didelphis virginiana; Didelphidae) and compared these changes with those of semelparous, male dasyurids. Free-ranging male Virginia opossums (n=36) were collected during 2001 at the Oklahoma State University Cross Timbers Experimental Range. Seasonal data were collected on hematological, morphological, and helminth parameters of these individuals. We used one-way ANOVA to determine whether there were seasonal differences among means for each parameter. It appeared that male Virginia opossums experienced some physiological changes similar to those of male dasyurids exhibiting semelparity. All males collected in summer (August) were juveniles of the year. Lack of adult males in August suggests high mortality of this cohort during the breeding season. Opossum characteristics exhibiting the dasyurid semelparity syndrome included packed cell volume, adrenal mass, and helminth numbers. Minor lymphocytopenia, neutrophilia, and testosterone concentrations also were similar to semelparous dasyurids. However, a lack of change in serum cortisol concentration and body mass and dynamics in immunoglobulin protein, serum protein, and testes mass were not consistent with previous reports of semelparous dasyurid physiology. Evolutionary divergence and differences in breeding behavior between dasyurids and didelphids may be responsible for the lack of consistency between the taxa.

Animals↗
PubMed2002

The evolution of self-fertilization in density-regulated populations.

The evolution of selfing in hermaphrodites has been studied to reveal the demographic conditions that lead to intermediate selfing rates. Using a demographic model based on Ricker-type density regulation, we assume first that, independent of population density, inbred individuals survive less well than outbred individuals and second, that inbred and outbred individuals differ in their competitive abilities in density-regulated populations. The evolution of selfing, driven by inbreeding depression and the cost of outcrossing, is then analysed for three fundamentally different demographic scenarios: stable population densities, deterministically varying population densities (resulting from cyclical or chaotic population dynamics) and stochastic fluctuations of carrying capacities (resulting from environmental noise). We show that even under stable demographic conditions evolutionary outcomes are not confined to either complete selfing or full outcrossing. Instead, intermediate selfing rates arise under a wide range of conditions, depending on the nature of competitive interactions between inbred and outbred individuals. We also explore the evolution of selfing under deterministic and stochastic density fluctuations to demonstrate that such environmental conditions can evolutionarily stabilize intermediate selfing rates. This is the first study, to our knowledge, to consider in detail the effect of density regulation on the evolution of selfing rates.

Adaptation, Physiological↗
PubMed2005

The structures of mouse and human L1 elements reflect their insertion mechanism.

L1 is an abundant, interspersed repeated DNA element of mammalian genomes. It has achieved its high copy number via retrotransposition. Like other non-LTR retrotransposons, L1 insertion into chromosomal DNA apparently occurs by target-site primed reverse transcription, or TPRT. L1 retrotransposition often generates elements with 5' truncations that are flanked by a duplication of the genomic target site (TSD). It is typically assumed that the 5' truncated elements are the consequence of poor processivity of the L1 reverse transcriptase. However, we find that the majority of young L1 elements from both the human and mouse genomes are truncated at sequences that can basepair with the target site. Thus, to whatever extent truncation is a consequence of poor processivity, we suggest that truncation is likely to occur when target site sequence can basepair with L1 sequence. This finding supports a model for insertion that occurs by two sequential TPRT reactions, the second of which relies upon the homology between the target site and L1. Because perfect heteroduplex formation is not required for all insertions, a dynamic relationship between the primer, template and enzyme during reverse transcription is inferred. 5' truncation may be a successful evolutionary strategy that is exploited by L1 as a means to escape host suppression of transposition.

Animals↗
PubMed2000

Comparative genomics of chalcone synthase and Myb genes in the grass family.

Most plant genes occur as members of multigene families where new copies arise through duplication. Duplicate genes that do not confer an adaptive advantage to the plant are expected to rapidly erode into pseudogenes owing to the accumulation of transpositions, insertion/deletion mutations and nucleotide changes. Nonfunctional copies will drift to fixation within a few million years and ultimately erode beyond recognition. Duplicate genes that are retained over longer periods of evolutionary time must be positively selected based on some adaptive advantage conferred on the plant species. We explore the dynamics of the recruitment of new duplicate genes for chalcone synthase, the enzyme that catalyzes the first committed step of flavonoid biosynthesis, and for the myb family of transcriptional activators. Our analyses show that new chs genes are recruited into the genome of grasses at a rate of one new copy every 15 to 25 million years. In contrast, the myb gene family is much older and many duplicate copies appear to predate the separation of the angiosperm lineage from other seed plants. The general pattern suggests a rapid adaptive proliferation of new chs genes but a more ancient elaboration of regulatory gene functions. Our analyses also reveal accelerated rates of protein evolution following gene duplication and evidence is presented for interlocus exchange among duplicate gene loci.

Acyltransferases↗
PubMed2005

Fibroblast growth factor signalling and regional specification of the pharyngeal ectoderm.

Branchial arch development involves dynamic interactions between neural crest cells as well as ectodermal, endodermal and mesodermal cell populations. Despite their importance and evolutionary conservation, the intercellular interactions guiding the early development of the branchial arches are still poorly understood. We have here studied fibroblast growth factor (FGF) signalling in early pharyngeal development. In mice homozygous for a hypomorphic allele of Fgfr1, neural crest cells migrating from the hindbrain mostly fail to enter the second branchial arch. This defect is non-cell-autonomous suggesting that Fgfr1 provides a permissive environment for neural crest cell migration. Here we demonstrate localized down-regulation of the expression of the FGF responsive gene, Sprouty1 in the epithelium covering the presumptive second branchial arch of hypomorphic Fgfr1 mutants. This appears to result in a failure to establish an ectodermal signalling center expressing Fgf3 and Fgf15. We also studied differentiation of the ectoderm in the second branchial arch region. Development of the geniculate placode as well as the VIIth cranial ganglion is affected in Fgfr1 hypomorphs. Our results suggest that Fgfr1 is important for localized signalling in the pharyngeal ectoderm and consequently for normal tissue interactions in the developing second branchial arch.

Adaptor Proteins, Signal Transducing↗
PubMed1993

[Lumbar spinal stenosis. An overview 50 years following initial description].

About 50 years after the first descriptions of lumbar stenosis and its most frequent symptom, neurogenic intermittent claudication, this update gives an overview of present-day concepts of the disease and of new experience in this area. Stenosis of the central and lateral lumbar spine is chiefly held to be one of the results of segmental degenerative instability throughout the several stages of spondylosis. The degenerative process of the spine has its starting point in regressive changes of the disc. This leads to instability of the motion segment, which explains the pathophysiological dynamics of the stenosis and its symptoms, including intermittent neurogenic claudication. Segmental instability is the crucial lesion causing all the changes in the degenerative process, which are not to be considered as separate entities but as part of the dynamics of the same disease. The spine's congenital anatomic individual patterns, which confirm the population thinking of the evolutionary biology (since they are different from one motion segment to the other) help to determine the outline of single cases. The disparity between radiological and clinical patterns is pointed out: severe stenosis may be asymptomatic or cause just modest monoradicular trouble as well as serious multiradicular deficit. The reason for the discrepancy is unknown. One must be careful to avoid surgery on a silent, purely radiological stenosis. Experience of more than 15 years confirms the uselessness of performing a complete laminectomy to achieve sufficient decompression. The author's method of selective decompression is described briefly. The English term "undercutting decompression" runs the risk of being misunderstood, since it is also used for rather destroying procedures. Finally, we point out that surgery for spinal stenosis must resolve both root compression and degenerative instability in the majority of cases. In most cases of lumbar stenosis, if decompression alone is performed, only the consequence, and not the cause of the disease, segmental degenerative instability, is treated. Osteophyte formation is an attempt by nature to stabilize the motion segments by stiffening its components. Spinal fusion tries to achieve the same effect. For most cases of spinal stenosis, we suggest our own technique, which combines safe and preserving ("selective") decompression according to Benini [1,7] with the translaminar screw fixation of Magerl [7]. In cases of degenerative spondylolisthesis, however, transpeduncular fusion is mandatory.

Aged↗
PubMed2004

Molecular evidence links cryptic diversification in polar planktonic protists to Quaternary climate dynamics.

It is unknown how pelagic marine protists undergo diversification and speciation. Superficially, the open ocean appears homogeneous, with few clear barriers to gene flow, allowing extensive, even global, dispersal. Yet, despite the apparent lack of opportunity for genetic isolation, diversity is prevalent within marine taxa. A lack of candidate isolating mechanisms would seem to favor sympatric over allopatric speciation models to explain the diversity and biogeographic patterns observed in the oceans today. However, the ocean is a dynamic system, and both current and past circulation patterns must be considered in concert to gain a true perspective of gene flow through time. We have derived a comprehensive picture of the mechanisms potentially at play in the high latitudes by combining molecular, biogeographic, fossil, and paleoceanographic data to reconstruct the evolutionary history of the polar planktonic foraminifer Neogloboquadrina pachyderma sinistral. We have discovered extensive genetic diversity within this morphospecies and that its current "extreme" polar affinity did not appear until late in its evolutionary history. The molecular data demonstrate a stepwise progression of diversification starting with the allopatric isolation of Atlantic Arctic and Antarctic populations after the onset of the Northern Hemisphere glaciation. Further diversification occurred only in the Southern Hemisphere and seems to have been linked to glacial-interglacial climate dynamics. Our findings demonstrate the role of Quaternary climate instability in shaping the modern high-latitude plankton. The divergent evolutionary history of N. pachyderma sinistral genotypes implies that paleoceanographic proxies based on this taxon should be calibrated independently.

Animals↗
PubMed1999

Studies on karyotype evolution in higher primates in relation to human chromosome 14 and 9 by comparative mapping of immunoglobulin C epsilon genes with fluorescence in situ hybridization.

Karyotypic homologies in relation to human chromosome 14 and 9 were studied through comparative mapping of the immunoglobulin C epsilon genes in higher primates by fluorescence in situ hybridization (FISH) technique. The C epsilon genes will be suitable probes for the analysis of evolutionary rearrangements due to that the multiple recombinational events such as gene duplications and deletions have occurred repeatedly in the immunoglobulin CH gene family (IGH@) during the course of primate evolution. IGH@ locating on the terminal region of human chromosome 14 (HSA14), at band HSA14q32.33, has generated multiple pseudogenes and among subclasses of IGH@ the C epsilon genes have shown most dynamic changes with generating both truncated type (C epsilon 2) and processed type (C epsilon 3) pseudogenes. In this study, chromosomal homologies and rearrangements on HSA14 (C epsilon 1) and HSA9 (C epsilon 3) in relation to the evolutionary genesis of their primate homologous chromosomes in speciation were investigated by comparative mapping with FISH and chromosome painting (ZOO-FISH) techniques. Comparative mapping of the C epsilon 1 gene at HSA14q32.33 was carried out in seven species of nonhuman primates: common chimpanzee (PTR), pygmy chimpanzee (PPA), gorilla (GGO), orangutan (PPY), white-handed gibbon (HLA), agile gibbon (HAG), and Japanese macaque (MFU). The C epsilon 1 gene was assigned to the telomeric region of HSA14 homologues in each species, namely, PTR15q32, PPA15q32, GGO18q16, PPY15q32, HLA17qter, HAG17qter, and MFU7q29, respectively. These results suggested that HSA14 has high degree of syntenic organization with its primate homologues confirmed by ZOO-FISH. Concerning HSA9, comparative mapping of the C epsilon 3 gene at HSA9p24.2-->p24.1 was performed. The mapped positions indicated the HSA9 homologous regions detected by ZOO-FISH in each species, namely, PTR11q34, PPA11q34, GGO13q22, PPY13q16, HLA8qter, HAG8qter, and MFU14q22, respectively, suggesting that several dynamic chromosomal rearrangements including at least twice pericentric inversions have occurred during the course of hominoid evolution. The comparison of syntenic groups and painting results has provided a hypothesis of the evolutionary genesis of HSA9 and its homologues with defined breakpoints on the present chromosomes. Likewise, studies on karyotype evolution will be promoted by combining comparative mapping with ZOO-FISH that can more clearly define the chromosomal rearrangements among species.

Animals↗
PubMed2001

Long-term studies of vegetation dynamics.

By integrating a wide range of experimental, comparative, and theoretical approaches, ecologists are starting to gain a detailed understanding of the long-term dynamics of vegetation. We explore how patterns of variation in demographic traits among species have provided insight into the processes that structure plant communities. We find a common set of mechanisms, derived from ecological and evolutionary principles, that underlie the main forces shaping systems as diverse as annual plant communities and tropical forests. Trait variation between species maintains diversity and has important implications for ecosystem processes. Hence, greater understanding of how Earth's vegetation functions will likely require integration of ecosystem science with ideas from plant evolutionary, population, and community ecology.

Animals↗
PubMed1997

High coordination lattice models of protein structure, dynamics and thermodynamics.

A high coordination lattice discretization of protein conformational space is described. The model allows discrete representation of polypeptide chains of globular proteins and small macromolecular assemblies with an accuracy comparable to the accuracy of crystallographic structures. Knowledge based force field, that consists of sequence specific short range interactions, cooperative model of hydrogen bond network and tertiary one body, two body and multibody interactions, is outlined and discussed. A model of stochastic dynamics for these protein models is also described. The proposed method enables moderate resolution tertiary structure prediction of simple and small globular proteins. Its applicability in structure prediction increases significantly when evolutionary information is exploited or/and when sparse experimental data are available. The model responds correctly to sequence mutations and could be used at early stages of a computer aided protein design and protein redesign. Computational speed, associated with the discrete structure of the model, enables studies of the long time dynamics of polypeptides and proteins and quite detailed theoretical studies of thermodynamics of nontrivial protein models.

Amino Acid Sequence↗
PubMed2002

Application of information theory and extreme physical information to carcinogenesis.

Cellular information dynamics during somatic evolution of the malignant phenotypes are complex and poorly understood. Accumulating, random genetic mutations and, therefore, loss of genomic information appears necessary for carcinogenesis. However, additional control parameters can be inferred because unconstrained mutagenesis would ultimately produce cellular information degradation incompatible with life. Similarly, the stability of some genomic segments, such as those controlling proliferation and metabolism, indicates the presence of selective mutational constraints. By applying Information Theory and Extreme Physical Information (EPI) analysis, we demonstrate that the phenotypic characteristics and growth pattern of cancer populations are emergent properties resulting from the nonlinear dynamics of accumulating, random genetic mutations and tissue selection factors. Maximum quantitative loss of transgenerational information is demonstrated in genomic segments encoding negative or neutral evolutionary properties. This is most evident in the progressive dedifferentiation observed during carcinogenesis and may terminate in a differentiation "information catastrophe" producing decoherent cellular morphology and function. In contrast, microenvironmental selection pressures preserve genomic information controlling properties that confer selective growth advantages even in the presence of a high background mutation rate. Thus, phenotypic traits characteristically retained by tumor populations can be identified as critical selection parameters favoring clonal proliferation. The information model of carcinogenesis is tested by applying EPI analysis to predict tumor growth dynamics. We found that cellular proliferation attributable to information degradation will produce power law tumor growth with an exponent of 1.62. Data from six published studies that use sequential mammograms to measure the volume of small, untreated human breast cancers demonstrate power law tumor growth with a mean exponent value of 1.73 +/- 0.23. Other predictions including exponential growth of tumor cells in vitro are also supported by experimental observations. The nonlinear dynamics of stochastic information loss constrained by somatic evolution indicate that carcinogenesis will not be associated with any predictable, fixed sequence of genomic alterations. Rather, sporadic clinical cancers are emergent structures produced by multiple, fundamentally nondeterministic genetic pathways.

Animals↗
PubMed2001

From arctic lemmings to adaptive dynamics: Charles Elton's legacy in population ecology.

We shall examine the impact of Charles S. Elton's 1924 article on periodic fluctuations in animal populations on the development of modern population ecology. We argue that his impact has been substantial and that during the past 75 years of research on multi-annual periodic fluctuations in numbers of voles, lemmings, hares, lynx and game animals he has contributed much to the contemporary understanding of the causes and consequences of population regulation. Elton was convinced that the cause of the regular fluctuations was climatic variation. To support this conclusion, he examined long-term population data then available. Despite his firm belief in a climatic cause of the self-repeating periodic dynamics which many species display, Elton was insightful and far-sighted enough to outline many of the other hypotheses since put forward as an explanation for the enigmatic long-term dynamics of some animal populations. An interesting, but largely neglected aspect in Elton's paper is that it ends with speculation regarding the evolutionary consequences of periodic population fluctuations. The modern understanding of these issues will also be scrutinised here. In population ecology, Elton's 1924 paper has spawned a whole industry of research on populations displaying multi-annual periodicity. Despite the efforts of numerous research teams and individuals focusing on the origins of multi-annual population cycles, and despite the early availability of different explanatory hypotheses, we are still lacking rigorous tests of some of these hypotheses and, consequently, a consensus of the causes of periodic fluctuations in animal populations. Although Elton would have been happy to see so much effort spent on cyclic populations, we also argue that it is unfortunate if this focus on a special case of population dynamics should distract our attention from more general problems in population and community dynamics.

Adaptation, Physiological↗
PubMed2025

Habitat Specialisation Impacts Clownfish Demographic Resilience to Pleistocene Sea-Level Fluctuations.

Habitat fragmentation and loss are key threats to biodiversity, yet their impacts on marine species remain poorly understood. Clownfishes, which rely on sea anemones for shelter and reproduction, provide an interesting model to explore how ecological specialisation mediates species responses to habitat perturbations. We used whole-genome data from 382 individuals across 10 species with varying host specialisations to reconstruct demographic histories and infer spatial genetic structure to assess the impact of Pleistocene sea-level fluctuations. Generalist species, associated with multiple hosts, maintained stable effective population sizes () and population connectivity during habitat fragmentation, reflecting resilience to environmental instability. In contrast, specialists experienced severedeclines and genetic structuring, driven by their dependence on specific hosts, without signs of population recovery following habitat reconnection. Spatial genomic analyses identified the Indonesian Through-Flow as a key dispersal corridor and the Coral Triangle as a critical hub of genetic diversity, while continental shelves and extensive open ocean regions appeared as barriers to gene flow. Our findings reveal how host specialisation shapes clownfish population dynamics, emphasising the importance of incorporating ecological dependencies into conservation assessments and deepening our understanding of species responses to ecological constraints and environmental changes over evolutionary timescales.

Animals↗
PubMed2003

PROSPECT II: protein structure prediction program for genome-scale applications.

A new method for fold recognition is developed and added to the general protein structure prediction package PROSPECT (http://compbio.ornl.gov/PROSPECT/). The new method (PROSPECT II) has four key features. (i) We have developed an efficient way to utilize the evolutionary information for evaluating the threading potentials including singleton and pairwise energies. (ii) We have developed a two-stage threading strategy: (a) threading using dynamic programming without considering the pairwise energy and (b) fold recognition considering all the energy terms, including the pairwise energy calculated from the dynamic programming threading alignments. (iii) We have developed a combined z-score scheme for fold recognition, which takes into consideration the z-scores of each energy term. (iv) Based on the z-scores, we have developed a confidence index, which measures the reliability of a prediction and a possible structure-function relationship based on a statistical analysis of a large data set consisting of threadings of 600 query proteins against the entire FSSP templates. Tests on several benchmark sets indicate that the evolutionary information and other new features of PROSPECT II greatly improve the alignment accuracy. We also demonstrate that the performance of PROSPECT II on fold recognition is significantly better than any other method available at all levels of similarity. Improvement in the sensitivity of the fold recognition, especially at the superfamily and fold levels, makes PROSPECT II a reliable and fully automated protein structure and function prediction program for genome-scale applications.

Algorithms↗
PubMed2006

Niche breadth, competitive strength and range size of tree species: a trade-off based framework to understand species distribution.

Understanding the mechanisms causing latitudinal gradients in species richness and species range size is a central issue in ecology, particularly in the current context of global climate change. Different hypotheses have been put forward to explain these patterns, emphasizing climatic variability, energy availability and competition. Here we show, using a comparative analysis controlling for phylogeny on 234 temperate/boreal tree species, that these hypotheses can be included into a single framework in an attempt to explain latitudinal gradients in species range size. We find that species tend to have larger ranges when (i) closer to the poles, (ii) successionally seral, (iii) having small and light seeds, and (iv) having short generations. The patterns can simply be explained by energy constraints associated with different life-history strategies. Overall, these findings shed a new light on our understanding of species distribution and biodiversity patterns, bringing new insights into underlying large-scale evolutionary processes.

Ecosystem↗