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PubMed2006

Amphioxus and tunicates as evolutionary model systems.

One important question in evolutionary biology concerns the origin of vertebrates from invertebrates. The current consensus is that the proximate ancestor of vertebrates was an invertebrate chordate. Today, the invertebrate chordates comprise cephalochordates (amphioxus) and tunicates (each a subphylum in the phylum Chordata, which also includes the vertebrate subphylum). It was widely accepted that, within the chordates, tunicates represent the sister group of a clade of cephalochordates plus vertebrates. However, recent studies suggest that the evolutionary positions of tunicates and cephalochordates should be reversed, the implications of which are considered here. We also review the two major groups of invertebrate chordates and compare relative advantages (and disadvantages) of each as model systems for elucidating the origin of the vertebrates.

Animals↗

PubMed2006

Beyond the evolutionary theory of ageing, from functional genomics to evo-gero.

By the mid 1970s, the mechanisms by which ageing can evolve had a secure theoretical basis in population genetics. Here, we discuss how subsequent evolutionary work has focussed on testing and extending this theory, and on attempting to integrate it with other emerging facets of the biology of ageing, such as genetic studies of long-lived mutants and of phenotypic plasticity in ageing, such as in response to nutritional status. We also describe how functional genomic studies are providing new insights into the evolutionary forces shaping genome evolution and lifespan control. Future challenges include understanding the biochemistry of longevity and how its failure generates ageing and associated diseases, and the determination of the genetic basis of lifespan evolution and the great plasticity that it displays.

Aging↗

PubMed2003

New insights into the evolutionary relationships between arenaviruses provided by comparative analysis of small and large segment sequences.

Arenaviruses are rodent-borne negative-stranded bisegmented RNA viruses. Five arenaviruses are etiologic agents of hemorrhagic fever in humans and are potential agents of bioterrorism. They are classified as Biosafety level 4 agents and listed in the category A of the Pathogen Agents edited by the Center for Disease Control and Prevention. To date, evolution and phylogeny of arenaviruses have been based on the analysis of sequences derived from structural genes (small RNA segment) exclusively, due to the lack of sequences available for the large RNA segment. In this study, partial sequences of the polymerase gene were determined for 18 species of arenaviruses and used to investigate phylogenetic relationships. Comparative analysis of topologies obtained from polymerase and structural gene analyses permitted us to determine the evolutionary origin of the major parent of the North American recombinant arenaviruses, and to investigate the role of genetic exchange (reassortment and recombination) in the evolutionary mechanisms driving the evolution of the genus Arenavirus.

Arenaviruses, New World↗

PubMed2004

Effect of gene location on the evolutionary rate of amino acid substitutions in herpes simplex virus proteins.

In an effort to understand the organization of genes in the herpes simplex virus (HSV-1) genome, I tested the idea that the location of a gene may be related to the evolutionary rate of amino acid sequence variation in the encoded protein. A measure of protein sequence divergence was calculated for homologous proteins in the UL region of six alphaherpesviruses including HSV-1, and this parameter was plotted against position in the HSV-1 genome. The results revealed a cluster of highly conserved proteins (UL27-UL33) encoded near the middle of UL. A similar analysis was restricted to HSV-1 and HSV-2 permitting an examination of U(S) proteins and proteins encoded in repeated regions at the segment ends. This analysis showed that U(S) proteins as a group are more highly divergent than those encoded in UL. A high degree of divergence was also observed in proteins coded at the segment ends including RL1 (gamma(1)34.5), RL2 (alpha0), UL1 (glycoprotein L), UL56, U(S)1, and U(S)12. It is suggested that conserved proteins UL27-UL33 are encoded near the middle of UL to take advantage of a low local mutation rate. Highly divergent proteins are suggested to be encoded selectively in U(S) because of a comparatively rapid evolutionary rate with which genes can be introduced and removed from S in response to environmental variation.

Amino Acid Substitution↗

PubMed2004

Evolutionary aspects of GnRHs, GnRH neuronal systems and GnRH receptors in teleost fish.

Gonadotrophin-releasing hormone (GnRH) was originally believed to be released by a unique set of hypophysiotrophic neurons to stimulate the release of gonadotrophins from the pituitary, therefore acting as a major initiator of the hormonal cascade controlling the reproductive axis. However, it now appears that each vertebrate species expresses two or three GnRH forms in multiple tissues and that GnRHs exert pleiotropic actions via several classes of receptors. This new vision of the GnRH systems arose progressively from numerous comparative studies in all vertebrate classes, but fish in general, and teleosts in particular, have often plaid a leading part in changing established concepts. To date fish still appear as attractive models to decipher the evolutionary mechanisms that led to the diversification of GnRH functions. Not only do teleosts exhibit the highest variety of GnRH variants, but recent data and whole genome analyses indicate that they may also possess multiple GnRH receptors. This paper intends to summarize the current situation with special emphasis on interspecies comparisons which provide insights into the possible evolutionary mechanisms leading to the diversification of GnRH functions.

Animals↗

PubMed2006

Evolutionary movement of centromeres in horse, donkey, and zebra.

Centromere repositioning (CR) is a recently discovered biological phenomenon consisting of the emergence of a new centromere along a chromosome and the inactivation of the old one. After a CR, the primary constriction and the centromeric function are localized in a new position while the order of physical markers on the chromosome remains unchanged. These events profoundly affect chromosomal architecture. Since horses, asses, and zebras, whose evolutionary divergence is relatively recent, show remarkable morphological similarity and capacity to interbreed despite their chromosomes differing considerably, we investigated the role of CR in the karyotype evolution of the genus Equus. Using appropriate panels of BAC clones in FISH experiments, we compared the centromere position and marker order arrangement among orthologous chromosomes of Burchelli's zebra (Equus burchelli), donkey (Equus asinus), and horse (Equus caballus). Surprisingly, at least eight CRs took place during the evolution of this genus. Even more surprisingly, five cases of CR have occurred in the donkey after its divergence from zebra, that is, in a very short evolutionary time (approximately 1 million years). These findings suggest that in some species the CR phenomenon could have played an important role in karyotype shaping, with potential consequences on population dynamics and speciation.

Animals↗

PubMed2005

Environmentally caused dwarfism or a valid species--is Testudo weissingeri Bour, 1996 a distinct evolutionary lineage? New evidence from mitochondrial and nuclear genomic markers.

We examine the evolutionary relationships of the five traditionally recognized species of the western Palearctic tortoise genus Testudo (T. graeca, T. hermanni, T. horsfieldii, T. kleinmanni, and T. marginata) and the newly described dwarfed species T. weissingeri by using sequence data of the mitochondrial cytochrome b gene and nuclear genomic fingerprints with inter-simple sequence repeats (ISSR). Testudo weissingeri differs from T. marginata mainly by its smaller size and some color-pattern characteristics. T. weissingeri lives in the driest, poorest and hottest part of the distributional range of T. marginata. While both data sets demonstrated phylogenetic distinctness of the five traditionally recognized species of Testudo, some subspecies and even some local populations, we detected no differentiation between T. marginata and T. weissingeri. We conclude that T. weissingeri is not a distinct evolutionary unit. We suggest that its small size is the result of suboptimal environmental conditions with limited resources and synonymize it with T. marginata. T. marginata and T. kleinmanni form a clade that is supported both by our mtDNA and nuclear genomic data sets. According to mtDNA data, this clade is the sister taxon to the T. graeca complex. A sister group relationship of T. hermanni and ((T. marginata+T. kleinmanni)+T. graeca) is moderately to weakly supported by mtDNA data; T. horsfieldii is the sister taxon to a clade comprising all other Testudo species.

Animals↗

PubMed2005

Evolutionary history of the greater white-toothed shrew (Crocidura russula) inferred from analysis of mtDNA, Y, and X chromosome markers.

We investigate the evolutionary history of the greater white-toothed shrew across its distribution in northern Africa and mainland Europe using sex-specific (mtDNA and Y chromosome) and biparental (X chromosome) markers. All three loci confirm a large divergence between eastern (Tunisia and Sardinia) and western (Morocco and mainland Europe) lineages, and application of a molecular clock to mtDNA divergence estimates indicates a more ancient separation (2.25 M yr ago) than described by some previous studies, supporting claims for taxonomic revision. Moroccan ancestry for the mainland European population is inconclusive from phylogenetic trees, but is supported by greater nucleotide diversity and a more ancient population expansion in Morocco than in Europe. Signatures of rapid population expansion in mtDNA, combined with low X and Y chromosome diversity, suggest a single colonization of mainland Europe by a small number of Moroccan shrews >38 K yr ago. This study illustrates that multilocus genetic analyses can facilitate the interpretation of species' evolutionary history but that phylogeographic inference using X and Y chromosomes is restricted by low levels of observed polymorphism.

Africa, Northern↗

PubMed2006

The evolutionary origins of nematodes within the order Strongylida are related to predilection sites within hosts.

The evolutionary relationships of the different groups of nematodes within the order Strongylida based on morphological data have been speculative and the subject of conjecture. In this paper, we present a multigene phylogenetic analysis, using sequence data of the 18S and 28S ribosomal RNA genes from representatives of all four suborders and seven superfamilies of the Strongylida, to test existing hypotheses proposed for the relationships of the suborders based on morphological data sets. The results obtained demonstrated that the Strongylida is a monophyletic assemblage, with only the Metastrongylina (but not the other suborders) forming a distinct monophyletic clade. We show that, in contrast to all previous hypotheses, one major lineage comprises taxa which occur exclusively in the pulmonary, circulatory or nervous systems of marsupial and eutherian mammals, whereas a second lineage comprises species occurring in the gastrointestinal tracts or perirenal tissues of vertebrates, or in the lungs of birds. The findings suggest that the predilection site of adult nematodes and host type reflect the evolutionary origin of the different taxonomic groups within the Strongylida.

Animals↗

PubMed2006

Dispersal and vicariance: the complex evolutionary history of boid snakes.

Since the early 1970s, boine snakes (Boidae: Boinae) have served as a prime example of a group whose current distribution was shaped by vicariant events associated with the fragmentation of the supercontinent Gondwana. Early phylogenetic treatments of this group, and what were thought to be closely related groups (Erycinae and Pythoninae) based on morphological features, produced a relatively stable view of relationships that has strongly influenced subsequent molecular-based work. We examined 4307 base pairs (bp) of nucleotide sequence data obtained from five nuclear loci (c-mos, NT3, BDNF, RAG1, and ODC) and one mitochondrial locus (cyt b) for all genera of erycines and boines, plus representatives of other groups, including those previously thought to be closely allied with boines (Ungaliophiidae, Loxocemidae, Xenopeltidae, and Pythoninae). Our results suggest that the Boidae is not monophyletic, and its current division into three subfamilies (Erycinae, Boinae, and Pythoninae) does not accurately reflect evolutionary history. We find that the evolutionary relationships are better reflected by current geographic distributions and tectonic history than by the morphological characters that have long served as the foundation of boid phylogeny. Divergence time estimates suggest that this strong congruence between geography and phylogeny is the result of several vicariant and dispersal events in the Late Cretaceous and Paleocene associated with the fragmentation of the Gondwanan supercontinent. Our results demonstrate the importance of both vicariance and dispersal in shaping the global distributions of terrestrial organisms.

Animals↗

PubMed2006

Balaenoptera omurai is a newly discovered baleen whale that represents an ancient evolutionary lineage.

Balaenoptera omurai, formerly classified as a small form of Bryde's whale, was recently reclassified as a new baleen whale species of the family Balaenopteridae. Although researchers have investigated the evolutionary history of Balaenopteridae and their relatives using molecular phylogenetic methods, the taxonomy of the ordinary Bryde's whale (Balaenoptera brydei) and small-form Bryde's whales (Balaenoptera edeni and B. omurai) remains unclear. We have used complete mtDNA sequences and short interspersed repetitive element (SINE) insertion patterns to construct the evolutionary history of both B. omurai and the taxonomically redefined species, B. edeni. The combined results demonstrate that B. omurai forms a monophyletic lineage with B. musculus, B. brydei, B. edeni and B. borealis and that B. omurai and B. musculus successively diverged from their common ancestor. In addition, we also showed that B. edeni constitutes a sister taxon to B. brydei. Our data suggest that B. omurai evolved as an ancient independent lineage that diverged much earlier than B. borealis, B. brydei and B. edeni, which were previously believed to be closely related to B. omurai.

Animals↗

PubMed2026

Complex evolutionary history of Rosales mediated by extensive incomplete lineage sorting and hybridization.

The angiosperm order Rosales still represents a major challenge for phylogenetic reconstruction. Although its circumscription is now well-defined, phylogenetic relationships among families are still uncertain. Here, we used nuclear, plastid, and mitochondrial genomic data from 33 species representing all nine families to further clarify interfamilial relationships and the group's evolutionary history. We detected significant phylogenetic conflict among the three datasets. Further analyses at the nuclear level identified incomplete lineage sorting (ILS) as the main cause of unstable phylogenetic positions among families. The discordant placements of Rhamnaceae and Elaeagnaceae based on plastid and mitochondrial data are caused by ancient hybridization events, potentially involving differences in organellar inheritance. Our molecular dating confirms earlier suggestions that the ancient rapid diversification of the three Rosaceae subfamilies could be the main reason for the difficulties in resolving their phylogenetic relationships. Our findings provide new insights into the interfamilial relationships of Rosales and demonstrate that the evolutionary history of this order was shaped by ancient and rapid radiation as well as extensive ILS and reticulate evolution. They also suggest that previous attempts to clarify interfamilial relationships in this order were hampered by combining nuclear and organellar sequence data, leading to inconsistent topologies observed across earlier studies.

Phylogeny↗

PubMed2026

Genome-wide insights into the evolutionary and demographic history of the red alga Mazzaella laminarioides: Evidence for speciation with ancient migration along the southeast Pacific coast.

The mechanisms driving lineage divergence in red algae remain unexplored, despite the group's remarkable diversity and ancient evolutionary history. The red alga Mazzaella laminarioides, a Chilean intertidal species complex composed of three parapatric cryptic lineages (North, Center, South), offers a valuable system to evaluate these processes, as its life history combines severe dispersal limitation with a haploid-diploid cycle that may influence the emergence of reproductive barriers. We reconstructed its evolutionary history using whole-genome sequencing and nuclear genome assembly of representative individuals from each lineage. Phylogenomic analyses based on 1,507 single-copy orthologs recovered three deeply divergent lineages with limited nuclear discordance consistent with incomplete lineage sorting. For both splits, demographic modelling was most consistent with an Ancient Migration scenario, although support over strict isolation was moderate, suggesting that divergence may have begun with low asymmetric ancestral gene flow followed by subsequent loss of connectivity, demographic bottlenecks, and later population expansion. Coding sequence analyses revealed lineage-specific dN/dS heterogeneity; only one South-lineage locus passed FDR correction (metaxin-1, mitochondrial protein import), with two further South-lineage candidates in chlorophyll and heme biosynthesis falling below the FDR threshold. Together, these signals suggest that divergent selective pressures on energy acquisition may have contributed to divergence at the southern end of the distribution. These results add to the small but growing body of whole-genome data for red algae and, alongside recent macroalgal studies, suggest that ancestral connectivity could be a recurrent feature of lineage divergence even in marine organisms with extremely restricted dispersal.

Rhodophyta↗

PubMed2006

Natural hybridization in primates: one evolutionary mechanism.

The role and importance of natural hybridization in the evolutionary histories of animal taxa is still debated. This results largely from a history of zoological investigations that assumed, rather than documented, a limited evolutionary role for this process. However, it is now becoming apparent that, just as for plants, the creative effects of reticulate evolution are widespread in animal taxa as well. This conclusion is supported by the documentation of numerous instances of the formation of new taxa and the genetic enrichment through introgressive hybridization. In the present review, we use primates as a paradigm for how natural hybridization can affect the evolution of species complexes and remains a footprint on genomes. Findings for a number of groups, including basal (e.g. lemurs) and derived (e.g. Old World apes) lineages, demonstrate that introgression and hybrid speciation have caused a reticulate pattern that is still detectable in the, often mosaic, genomes of primates. For example, results from genetic analyses of our own species demonstrate the process of past introgressive hybridization with the progenitors of our sister taxa (i.e. chimpanzees and gorillas) and most likely also our extinct, close relatives in the hominid lineage.

Animals↗

PubMed1999

The taxonomic position and evolutionary relationships of Trypanosoma rangeli.

This paper presents a re-evaluation of the taxonomic position and evolutionary relationships of Trypanosoma (Herpetosoma) rangeli based on the phylogenetic analysis of ssrRNA sequences of 64 Trypanosoma species and comparison of mini-exon sequences. All five isolates of T. rangeli grouped together in a clade containing Trypanosoma (Schizotrypanum) cruzi and a range of closely related trypanosome species from bats [Trypanosoma (Schizotrypanum) dionisii, Trypanosoma (Schizotrypanum) vespertilionis] and other South American mammals [Trypanosoma (Herpetosoma) leeuwenhoeki, Trypanosoma (Megatrypanum) minasense, Trypanosoma (Megatrypanum) conorhini] and an as yet unidentified species of trypanosome from an Australian kangaroo. Significantly T. rangeli failed to group with (a) species of subgenus Herpetosoma, other than those which are probably synonyms of T. rangeli, or (b) species transmitted via the salivarian route, although either of these outcomes would have been more consistent with the current taxonomic and biological status of T. rangeli. We propose that use of the names Herpetosoma and Megatrypanum should be discontinued, since these subgenera are clearly polyphyletic and lack evolutionary and taxonomic relevance. We hypothesise that T. rangeli and T. cruzi represent a group of mammalian trypanosomes which completed their early evolution and diversification in South America.

Animals↗

PubMed2002

Elucidation of primary (alpha(3)N) and vestigial (alpha(5)) heavy metal-binding sites in Staphylococcus aureus pI258 CadC: evolutionary implications for metal ion selectivity of ArsR/SmtB metal sensor proteins.

Despite a common evolutionary origin, individual members of the ArsR/SmtB family of bacterial metal-responsive transcriptional repressors sense a wide range of heavy-metal ions. The molecular basis for this metal ion selectivity is unclear. Here, we establish that Staphylococcus aureus plasmid pI258 CadC, a Cd(II)/Pb(II)/Bi(III)/Zn(II) sensor, contains two distinct metal-binding sites: a thiolate-rich alpha(3)N site comprised exclusively of cysteine ligands that preferentially binds larger, softer metal ions such as Cd(II), Pb(II) and Bi(III); and a second C-terminal alpha(5) site, found at the dimer interface, that is devoid of cysteine ligands and preferentially binds smaller, harder metal ions [Co(II) and Zn(II)] concurrently with metal binding to the alpha(3)N site. Optical absorption and X-ray spectroscopies reveal that the alpha(3)N site can adopt distinct coordination geometries in order to accommodate different metal ions, i.e. Cd(II), Bi(III), Co(II) and Zn(II) form distorted tetrahedral S(4) complexes, while Pb(II) adopts a trigonal S(3) complex. Characterization of mutant CadCs reveals that the alpha(3)N site is composed of Cys58 and Cys60 from the alpha(3) helix of the helix-turn-helix DNA-binding domain and Cys7 and/or Cys11 from the N-terminal "arm" of CadC; Cys11 is excluded from the Pb(II) coordination sphere. Only the thiolate-rich alpha(3)N site is metalloregulatory for repressor binding to a fluorescein-labeled cad O/P oligonucleotide upon coordination to Cd(II), Pb(II), Bi(III), Zn(II), and weakly for Co(II). Substitution of Cys60 and Cys7 with non-ligating residues specifically abrogates metal-dependent negative regulation of cad O/P binding, despite the fact that C60G and C7G CadCs maintain high affinity for metals in altered coordination complexes. These findings reveal that formation of metal coordination bonds to Cys7 and Cys60 play primary roles in transducing the allosteric response in CadC. The evolutionary implications for metal ion selectivity of ArsR/SmtB metal sensor proteins are discussed.

Allosteric Regulation↗

PubMed2002

Evaluation of structural and evolutionary contributions to deleterious mutation prediction.

Methods for automated prediction of deleterious protein mutations have utilized both structural and evolutionary information but the relative contribution of these two factors remains unclear. To address this, we have used a variety of structural and evolutionary features to create simple deleterious mutation models that have been tested on both experimental mutagenesis and human allele data. We find that the most accurate predictions are obtained using a solvent-accessibility term, the C(beta) density, and a score derived from homologous sequences, SIFT. A classification tree using these two features has a cross-validated prediction error of 20.5% on an experimental mutagenesis test set when the prior probability for deleterious and neutral cases is equal, whereas this prediction error is 28.8% and 22.2% using either the C(beta) density or SIFT alone. The improvement imparted by structure increases when fewer homologs are available: when restricted to three homologs the prediction error improves from 26.9% using SIFT alone to 22.4% using SIFT and the C(beta) density, or 24.8% using SIFT and a noisy C(beta) density term approximating the inaccuracy of ab initio structures modeled by the Rosetta method. We conclude that methods for deleterious mutation prediction should include structural information when fewer than five to ten homologs are available, and that ab initio predicted structures may soon be useful in such cases when high-resolution structures are unavailable.

Bacterial Proteins↗

PubMed2003

Evolutionary stability in Lotka-Volterra systems.

The Lotka-Volterra model of population ecology, which assumes all individuals in each species behave identically, is combined with the behavioral evolution model of evolutionary game theory. In the resultant monomorphic situation, conditions for the stability of the resident Lotka-Volterra system, when perturbed by a mutant phenotype in each species, are analysed. We develop an evolutionary ecology stability concept, called a monomorphic evolutionarily stable ecological equilibrium, which contains as a special case the original definition by Maynard Smith of an evolutionarily stable strategy for a single species. Heuristically, the concept asserts that the resident ecological system must be stable as well as the phenotypic evolution on the "stationary density surface". The conditions are also shown to be central to analyse stability issues in the polymorphic model that allows arbitrarily many phenotypes in each species, especially when the number of species is small. The mathematical techniques are from the theory of dynamical systems, including linearization, centre manifolds and Molchanov's Theorem.

Animals↗