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PubMed1994

Similarity landscapes: a way to detect many structural and sequence motifs in both introns and exons.

When investigators undertake searches of DNA databases, they normally discard large numbers of alignments that demonstrate very weak resemblances to each other, retaining only those that show statistically significant levels of resemblance. We show here that a great deal of information can be extracted from these weak alignments by examining them en masse. This is done by building three-dimensional similarity landscapes from the alignments, landscapes that reveal whether an unusual number of individually nonsignificant alignments tend to match up to a particular region of the query sequence being searched. The power of the search is increased by the use of libraries consisting entirely of introns or of exons. We show that (1) similarity landscapes with a variety of features can be generated from both intron and exon libraries, using introns or exons as query sequences; (2) the landscape features are real and not a statistical artifact; (3) well-known protein motifs used as query sequences can generate various landscape features; and (4) there is some evidence for resemblances between short regions of sequence carried by introns and exons. One possible interpretation of these results is that both introns and exons may have been built up during their evolution from short regions of sequence that as a result are now widely distributed throughout eukaryotic genomes. Such an interpretation would imply that these short regions have common ancestry. Alternatively, the wide sharing of short pieces of DNA may reflect regions with particular structural properties that have arisen through convergent evolution. The similarity-landscape approach can be used to detect such widespread structural motifs and sequence motifs in the genome that might be missed by less-global searches. It can also be used in conjunction with algorithms developed for detecting significant multiple alignments by isolating promising subsets of the databases that can be examined in more detail.

Animals↗
PubMed1994

Evolution of the ATP-binding-cassette transmembrane transporters of vertebrates.

The ATP-binding-cassette transmembrane transporters (ABC transporters) known from vertebrates belong to four major subfamilies: (1) the P-glycoproteins (Pgp); (2) the cystic fibrosis transmembrane conductance regulators (CFTR); (3) the Tap proteins encoded with the major histocompatibility complex of mammals; and (4) the peroxisomal membrane proteins. Both Pgp and CFTR have a structure suggesting a past internal gene duplication; a phylogenetic analysis indicated that these duplications occurred independently, while an independent tandem gene duplication occurred in the case of the Tap family. Both the Pgp and Tap proteins show evidence of relationship to bacterial ABC transporters lacking internal duplication, and both are significantly more closely related to the HlyB and MsbA families of transporters from purple bacteria than they are to ABC transporters from nonpurple bacteria. The simplest hypothesis to explain this observation is that eukaryotic Pgp and Tap genes are descended from a mitochondrial gene or genes that were subsequently translocated to the nuclear genome. The Pgp genes of eukaryotes are characterized by a remarkable degree of convergent evolution between the ATP-binding cassettes of their N-terminal and C-terminal halves, whereas no such convergence is seen between the two halves of CFTR genes or between the duplicated Tap genes. Exon 13 of the CFTR gene, which encodes a putative regulatory domain not found in other ABC transporters apart from CFTR, showed high levels of both synonymous and nonsynonymous difference in comparisons among different mammalian species, suggesting that this region is a mutational hot spot.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2006

Adaptive evolution of tetrodotoxin resistance in animals.

Tetrodotoxin (TTX), first isolated from pufferfish (tetraodontids), is a highly potent neurotoxin that selectively binds to voltage-gated sodium channels (Na(v)) in muscle and nerve tissues causing paralysis and death. Saxitoxin (STX) is a TTX-related neurotoxin produced by dinoflagellates. Recent investigations have implicated diverse substitutions in the P-loop regions of skeletal muscle and neuronal Na(v) channels in the convergent evolution of neurotoxin resistance in pufferfish, garter snakes and softshell clams, which has enabled them to feed on TTX- and STX-bearing organisms.

Amino Acid Sequence↗
PubMed2002

Parsimony in protein evolution.

Pohl found the activation enthalpy and entropy for melting of his mesophilic proteins to be linear in the total number of residues and Privalov and colleagues found this same linearity for the standard heat-capacity, enthalpy and entropy changes in the overall melting equilibria. Despite the small samples these results suggest that mesophiles individually, and as a class, are related through a single standard representative. If so, very extensive convergent evolution has provided both great simplification and very sophisticated goals for genome decoding and quantitative description of protein substructures [R. Lumry, The protein primer, http://www.umn.edu.chem. /groupslumry].

Evolution, Molecular↗
PubMed2005

The evolution and function of blue and red light photoreceptors.

Photoreceptors allow living organisms to optimize perception of light in the natural environment and thus to gain information about their external world. In this review, we describe blue and red light photoreceptors in bacteria, plants, and animals in relation to their evolution. Analyses performed in different organisms have revealed wonderful examples of structural modifications of the light-sensing proteins themselves, as well as diversification of the signal transduction pathways they use in relation with their evolutionary history and function. In different organisms, the same photoreceptor may have a very conserved role (convergent evolution of function) or may modulate different responses (acquisition of new function). Multiple photoreceptors of the same family in the same organism indicate gene duplication events during evolution, with a consequent enhanced sensitivity to variations in ambient light. Conversely, two different photoreceptors may be involved in the control of the same physiological response. Genomic analysis in marine diatoms, combined with phylogenetic studies, has also revealed the presence of blue and red light photoreceptors in the marine environment. This discovery has intriguing implications for the understanding of light perception and its evolution in photosynthetic organisms. In addition, the characterization of these photoreceptors likely will add to our understanding of photoreceptor diversity as an adaptation to different habitats.

Animals↗
PubMed2005

The evolution of music in comparative perspective.

In this paper, I briefly review some comparative data that provide an empirical basis for research on the evolution of music making in humans. First, a brief comparison of music and language leads to discussion of design features of music, suggesting a deep connection between the biology of music and language. I then selectively review data on animal "music." Examining sound production in animals, we find examples of repeated convergent evolution or analogy (the evolution of vocal learning of complex songs in birds, whales, and seals). A fascinating but overlooked potential homology to instrumental music is provided by manual percussion in African apes. Such comparative behavioral data, combined with neuroscientific and developmental data, provide an important starting point for any hypothesis about how or why human music evolved. Regarding these functional and phylogenetic questions, I discuss some previously proposed functions of music, including Pinker's "cheesecake" hypothesis; Darwin's and others' sexual selection model; Dunbar's group "grooming" hypothesis; and Trehub's caregiving model. I conclude that only the last hypothesis receives strong support from currently available data. I end with a brief synopsis of Darwin's model of a songlike musical "protolanguage," concluding that Darwin's model is consistent with much of the available evidence concerning the evolution of both music and language. There is a rich future for empirical investigations of the evolution of music, both in investigations of individual differences among humans, and in interspecific investigations of musical abilities in other animals, especially those of our ape cousins, about which we know little.

Animals↗
PubMed2004

Evolution of polydnaviruses as insect immune suppressors.

Polydnaviruses (PDVs) are endogenous particles that are used by some endoparasitic hymenoptera to disrupt host immunity and development. Recent analyses of encapsidated PDV genes have increased the number of known PDV gene families, which are often closely related to insect genes. Several PDV proteins inactivate host haemocytes by damaging their actin cytoskeleton. These proteins share no significant sequence homology and occur in polyphyletic PDV genera, possibly indicating that convergent evolution has produced functionally similar immune-suppressive molecules causing a haemocyte phenotype characterised by damaged cytoskeleton and inactivation. These phenomena provide further insights into the immune-suppressive activity of PDVs and raise interesting questions about PDV evolution, a topic that has puzzled researchers ever since the discovery of PDVs.

Animals↗
PubMed2003

Correlated evolution of life-history with size at maturity in Daphnia pulicaria: patterns within and between populations.

Explaining the repeated evolution of similar sets of traits under similar environmental conditions is an important issue in evolutionary biology. The extreme alternative classes of explanations for correlated suites of traits are optimal adaptation and genetic constraint resulting from pleiotropy. Adaptive explanations presume that individual traits are free to evolve to their local optima and that convergent evolution represents particularly adaptive combinations of traits. Alternatively, if pleiotropy is strong and difficult to break, strong selection on one or a few particularly important characters would be expected to result in consistent correlated evolution of associated traits. If pleiotropy is common, we predict that the pattern of divergence among populations will consistently reflect the within-population genetic architecture. To test the idea that the multivariate life-history phenotype is largely a byproduct of strong selection on body size, we imposed divergent artificial selection on size at maturity upon two populations of the cladoceran Daphnia pulicaria, chosen on the basis of their extreme divergence in body size. Overall, the trajectory of divergence between the two natural populations did not differ from that predicted by the genetic architecture within each population. However, the pattern of correlated responses suggested the presence of strong pleiotropic constraints only for adult body size and not for other life-history traits. One trait, offspring size, appears to have evolved in a way different from that expected from the within-population genetic architecture and may be under stabilizing selection.

Animals↗
PubMed2006

Amplification of DNA from preserved specimens shows blowflies were preadapted for the rapid evolution of insecticide resistance.

Mutations of esterase 3 confer two forms of organophosphate resistance on contemporary Australasian Lucilia cuprina. One form, called diazinon resistance, is slightly more effective against commonly used insecticides and is now more prevalent than the other form, called malathion resistance. We report here that the single amino acid replacement associated with diazinon resistance and two replacements associated with malathion resistance also occur in esterase 3 in the sibling species Lucilia sericata, suggesting convergent evolution around a finite set of resistance options. We also find parallels between the species in the geographic distributions of the polymorphisms: In both cases, the diazinon-resistance change is absent or rare outside Australasia where insecticide pressure is lower, whereas the changes associated with malathion resistance are widespread. Furthermore, PCR analysis of pinned specimens of Australasian L. cuprina collected before the release of organophosphate insecticides reveals no cases of the diazinon-resistance change but several cases of those associated with malathion resistance. Thus, the early outbreak of resistance in this species can be explained by the preexistence of mutant alleles encoding malathion resistance. The pinned specimen analysis also shows much higher genetic diversity at the locus before organophosphate use, suggesting that the subsequent sweep of diazinon resistance in Australasia has compromised the scope for the locus to respond further to the ongoing challenge of the insecticides.

Adaptation, Physiological↗
PubMed2004

Molecules consolidate the placental mammal tree.

Deciphering relationships among the orders of placental mammals remains an important problem in evolutionary biology and has implications for understanding patterns of morphological character evolution, reconstructing the ancestral placental genome, and evaluating the role of plate tectonics and dispersal in the biogeographic history of this group. Until recently, both molecular and morphological studies provided only a limited and questionable resolution of placental relationships. Studies based on larger and more diverse molecular datasets, and using an array of methodological approaches, are now converging on a stable tree topology with four major groups of placental mammals. The emerging tree has revealed numerous instances of convergent evolution and suggests a role for plate tectonics in the early evolutionary history of placental mammals. The reconstruction of mammalian phylogeny illustrates both the pitfalls and the powers of molecular systematics.

Journal Article↗
PubMedDate not supplied

[A case of tongueworms (Pentastomida): a specific problem in context of the modern phylogenetics].

A short essay on anatomy, ultrastructure and larval development, life cycles, classification, palaeontology and phylogenetic relationships of Pentastomida is given. Currently, the Pentastomida are usually placed within Crustacea, as sister group of Branchiura (Crustacea, Maxillopoda). The grounds are striking similarities in ultrastructures of spermatozoa and congruence in the 18S rRNA nucleotide sequence. Both taxa are however sharply disparate in all other characters concerning morphology, embryology, life cycles and geological history. A direct introduction of Pentastomida in the system of Crustacea implies an unjustified inflation of the taxonomic diagnosis of the latter group; hence it is unacceptable. Two alternative hypotheses are suggested as tentative phylogenetic relationships to be tested. Each hypothesis infers however a very complex and unlikely evolutionary scenario. 1) Pentastomida and Branchiura are true sister groups as justified by coincidence in spermatozoan ultrastructure and sequence of ribosomal RNA. Since their divergence, the evolutions of pentastomids and branchiurans ran in different milieus, in different shapes and with different rates. To present time, the pentastomids lost nearly all characters of maxillopods and crustaceans as well as majority of anthropod features. 2) Pentastomida and Branchiura are not close related. The similarity in ultrastructural details of spermatozoa may be occasional or resulted from convergent evolution with unknown factors. Coincidence in nucleotide sequences or ribosomal RNA should be reexamined and tested with other pentastomid species. The second hypothesis seems to be more likely.

Animals↗
PubMed2005

Avian and mammalian "prefrontal cortices": limited degrees of freedom in the evolution of the neural mechanisms of goal-state maintenance.

Is it possible to produce the same cognitive function with different brain organizations? This question is approached for working memory, a cognitive entity that is equally organized in birds and mammals. The critical forebrain structure for working memory is the nidopallium caudolaterale (NCL) in birds and the prefrontal cortex (PFC) in mammals. Although both structures share a large number of neural architectural features, they are probably not homologous but represent a remarkable case of convergent evolution. In reviewing the neuronal mechanisms for working memory in birds and mammals it becomes apparent that the similarities of NCL and PFC extend from the neuronal activation patterns during memory tasks down to the biophysical mechanisms of synaptic currents. Both in mammals and birds, dopamine acts via D1-receptors to tune preactivated neurons into sustained high-frequency patterns with which goal states can be held over time until an appropriate response can be generated. The degrees of freedom to create different neural architectures to solve the problem of 'stimulus maintenance' seem to be very small.

Animals↗
PubMed2005

Microsatellite variation and evolution of human lactase persistence.

The levels of haplotype diversity within the lineages defined by two single-nucleotide polymorphisms (SNPs) (-13910 C/T and -22018 G/A) associated with human lactase persistence were assessed with four fast-evolving microsatellite loci in 794 chromosomes from Portugal, Italy, Fulbe from Cameroon, São Tomé and Mozambique. Age estimates based on the intraallelic microsatellite variation indicate that the -13910*T allele, which is more tightly associated with lactase persistence, originated in Eurasia before the Neolithic and after the emergence of modern humans outside Africa. We detected significant departures from neutrality for the -13910*T variant in geographically and evolutionary distant populations from southern Europe (Portuguese and Italians) and Africa (Fulbe) by using a neutrality test based on the congruence between the frequency of the allele and the levels of intraallelic variability measured by the number of mutations in adjacent microsatellites. This result supports the role of selection in the evolution of lactase persistence, ruling out possible confounding effects from recombination suppression and population history. Reevaluation of the available evidence on variation of the -13910 and -22018 loci indicates that lactase persistence probably originated from different mutations in Europe and most of Africa, even if 13910*T is not the causal allele, suggesting that selective pressure could have promoted the convergent evolution of the trait. Our study shows that a limited number of microsatellite loci may provide sufficient resolution to reconstruct key aspects of the evolutionary history of lactase persistence, providing an alternative to approaches based on large numbers of SNPs.

Africa↗
PubMed1992

Genetic sex determination mechanisms and evolution.

Different animal groups exhibit a surprisingly diversity of sex determination systems. Moreover, even systems that are superficially similar may utilize different underlying mechanisms. This diversity is illustrated by a comparison of sex determination in three well-studied model organisms: the fruitfly Drosophila melanogaster, the nematode Caenorhabditis elegans, and the mouse. All three animals exhibit male heterogamety, extensive sexual dimorphism and sex chromosome dosage compensation, yet the molecular and cellular processes involved are now known to be quite unrelated. The similarities must have arisen by convergent evolution. Studies of sex determination demonstrate that evolution can produce a variety of solutions to the same basic problems in development.

Animals↗
PubMed2001

Neurogenesis in the developing visual system of the branchiopod crustacean Triops longicaudatus (LeConte, 1846): corresponding patterns of compound-eye formation in Crustacea and Insecta?

In the discussion on arthropod phylogeny, the structural evolution of compound eyes and optic ganglia in Crustacea and Insecta is an important topic. On the one hand, many morphological features as well as developmental aspects of the visual system in Insecta and Crustacea correspond in so much detail that eye design in these two groups is likely to have a common euarthropodan ancestor. On the other hand, however, some authors advocate a convergent evolution of the crustacean and insect visual system founding their arguments on differences in the arrangement of the visual neuropils and the fibre connections between Malacostraca and Entomostraca (the "entomostracan enigma"). Therefore, information about cellular aspects of visual system formation in entomostracan Crustacea is likely to enliven this debate, but is not yet available. To fill this gap, we examined the proliferation of neuronal stem cells in the developing visual system of the tadpole shrimp Triops longicaudatus (LeConte, 1846) (Entomostraca, Branchiopoda, Phyllopoda, Calmanostraca, Notostraca) by in vivo incorporation of the proliferation marker bromodeoxyuridine and subsequent immunohistochemical detection. Our results indicate that in the developing visual system of T. longicaudatus, three band-shaped zones containing neuronal stem cells are present corresponding to the proliferation zones found in Malacostraca. We therefore conclude that the ontogenetic mechanisms of visual-system formation are evolutionarily conserved (homologous) in Branchiopoda, Malacostraca, and Insecta.

Animals↗
PubMed2000

Do extraterrestrials have sex (and intelligence)?

This thought experiment addresses the range of possible evolved psychologies likely to be associated with extraterrestrial (ET) intelligence. The analysis rests on: (1) a number of assumptions shared by the SETI project; (2) recent arguments concerning convergent evolution; and (3) current theories of how intelligence evolved in our own species. It concludes that, regardless of how and which cognitive abilities arise initially, extraterrestrially they can develop into intelligence only if an amplification process involving a form of predation and/or sexual selection occurs. Depending on the amplification process, ETs may be xenophobic; however, it is more probable that they will be ethnocentric. Their ideas of reciprocity and fairness are likely to at least overlap with our own. They will definitely be culture-bearing and probably have two sexes, both of which are intelligent. Regardless of the degree of physical similarity of ETs to ourselves, convergence makes it likely that we will at least find their evolved psychology similar enough to our own for comprehension.

Adaptation, Physiological↗
PubMed2004

The DxDxDG motif for calcium binding: multiple structural contexts and implications for evolution.

Calcium ions regulate many cellular processes and have important structural roles in living organisms. Despite the great variety of calcium-binding proteins (CaBPs), many of them contain the same Ca(2+)-binding helix-loop-helix structure, referred to as the EF-hand. In the canonical EF-hand, the loop contains three calcium-binding aspartic acid residues, which form the DxDxDG sequence motif, and is flanked by two alpha-helices. Recently, other CaBPs containing the same motif, but lacking one or both helices, have been described. Here, structural motif searches were used to analyse the full diversity of structural context in the known set of DxDxDG-containing CaBPs, including those where the structural resemblance of a given DxDxDG motif to that of EF-hands had not been noted. The results obtained indicate that the EF-hand represents but one, among many, structural context for the DxDxDG-like Ca(2+)-binding loops. While the structural similarity of the binuclear calcium-binding sites in anthrax protective antigen and human thrombospondin suggests that they are homologous, evolutionary relationships for mononuclear sites are harder to discern. The possible scenarios for the evolution of DxDxDG motif-containing calcium-binding loops in a variety of non-homologous proteins suggested loop transplant as a mechanism perhaps responsible for much of the diversity in structural contexts of present day DxDxDG-type CaBPs. Additionally, while it can be shown that existence of a DxDxDG sequence is not enough to confer a conformation suitable for calcium binding, local convergent evolution may still have a role. The analysis presented here has consequences for the prediction of calcium binding from sequence alone.

Amino Acid Motifs↗
PubMed1992

Evolution of major histocompatibility complex class II allelic diversity: direct descent in mice and humans.

The high degree of polymorphism seen at major histocompatibility complex (MHC) class II loci is a feature unique to the MHC. Most of the beta-chain polymorphism is localized in "hypervariable" regions (HVRs). HVR amino acid sequence similarity between distantly related species has recently been found. We have employed a Monte-Carlo statistic to show that shared HVR polymorphism between beta-chain genes of humans and mice represents direct descent of ancestral sequences rather than convergent evolution. Furthermore, half the sequence polymorphism seen in class II beta-chain genes of mice persists in evolution and is encoded by the same DNA sequence in humans. No evidence for increased mutation rate within the HVR was found. We postulate that the HVR can be considered the genetic unit of recombination, with selection for HVR sequences and combinations of HVRs constrained by functional considerations.

Alleles↗