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PubMed1994

Craniometric variation, genetic theory, and modern human origins.

Recent controversies surrounding models of modern human origins have focused on among-group variation, particularly the reconstruction of phylogenetic trees from mitochondrial DNA (mtDNA) and the dating of population divergence. Problems in tree estimation have been seen as weakening the case for a replacement model and favoring a multiregional evolution model. There has been less discussion of patterns of within-group variation, although the mtDNA evidence has consistently shown the greatest diversity within African populations. Problems of interpretation abound given the numerous factors that can influence within-group variation, including the possibility of earlier divergence, differences in population size, patterns of population expansion, and variation in migration rates. We present a model of within-group phenotypic variation and apply it to a large set of craniometric data representing major Old World geographic regions (57 measurements for 1,159 cases in four regions: Europe, Sub-Saharan Africa, Australasia, and the Far East). The model predicts a linear relationship between variation within populations (the average within-group variance) and variation between populations (the genetic distance of populations to pooled phenotypic means). On a global level this relationship should hold if the long-term effective population sizes of each region are correctly specified. Other potential effects on within-group variation are accounted for by the model. Comparison of observed and expected variances under the assumption of equal effective sizes for four regions indicates significantly greater within-group variation in Africa and significantly less within-group variation in Europe. These results suggest that the long-term effective population size was greatest in Africa. Closer examination of the model suggests that the long-term African effective size was roughly three times that of any other geographic region. Using these estimates of relative population size, we present a method for analyzing ancient population structure, which provides estimates of ancient migration. This method allows us to reconstruct migration history between geographic regions after adjustment for the effect of genetic drift on interpopulational distances. Our results show a clear isolation of Africa from other regions. We then present a method that allows direct estimation of the ancient migration matrix, thus providing us with information on the actual extent of interregional migration. These methods also provide estimates of time frames necessary to reach genetic equilibrium. The ultimate goal is extracting as much information from present-day patterns of human variation relevant to issues of human origins.(ABSTRACT TRUNCATED AT 400 WORDS)

Africa↗

PubMed1990

Compartmentalized isozyme genes and the origin of introns.

Both the mouse cytosolic malate dehydrogenase gene and its mitochondrial counterpart contain eight introns, of which two are present at identical positions between the isozyme genes. The probability that the two intron positions coincide by chance between the two genes has been shown to be significantly small (= 1.3 x 10(-3), suggesting that the conservation of the intron positions has a biological significance. On the basis of a rooted phylogenetic tree inferred from a comparison of these isozymes and lactate dehydrogenases, we have shown that the origins of the conserved introns are very old, possibly going back to a date before the divergence of eubacteria, archaebacteria, and eukaryotes. In the aspartate aminotransferase isozyme genes, five of the introns are at identical places. The origins of the five conserved introns, however, are not obvious at present. It remains possible that some or all of the conserved introns have evolved after the divergence of eubacteria and eukaryotes.

Amino Acid Sequence↗

PubMed2004

The resurrection of oceanic dispersal in historical biogeography.

Geographical distributions of terrestrial or freshwater taxa that are broken up by oceans can be explained by either oceanic dispersal or vicariance in the form of fragmentation of a previously contiguous landmass. The validation of plate-tectonics theory provided a global vicariance mechanism and, along with cladistic arguments for the primacy of vicariance, helped create a view of oceanic dispersal as a rare phenomenon and an explanation of last resort. Here, I describe recent work that suggests that the importance of oceanic dispersal has been strongly underestimated. In particular, molecular dating of lineage divergences favors oceanic dispersal over tectonic vicariance as an explanation for disjunct distributions in a wide variety of taxa, from frogs to beetles to baobab trees. Other evidence, such as substantial gene flow among island populations of Anolis lizards, also indicates unexpectedly high frequencies of oceanic dispersal. The resurrection of oceanic dispersal is the most striking aspect of a major shift in historical biogeography toward a more even balance between vicariance and dispersal explanations. This new view implies that biotas are more dynamic and have more recent origins than had been thought previously. A high frequency of dispersal also suggests that a fundamental methodological assumption of many biogeographical studies--that vicariance is a priori a more probable explanation than dispersal--needs to be re-evaluated and perhaps discarded.

Journal Article↗

PubMed1992

Autosomal localization of the amelogenin gene in monotremes and marsupials: implications for mammalian sex chromosome evolution.

We have determined by Southern blot analysis that DNA sequences homologous to the AMG gene probe are present in the genomes of both marsupial and monotreme mammals, although adult monotremes lack teeth. In situ hybridization and Southern analysis of cell hybrids demonstrate that AMG homologues are located on autosomes. In the Tammar Wallaby, AMG homologues are located on chromosomes 5q and 1q and in the Platypus, on chromosomes 1 and 2. The autosomal location of the AMG homologues provides additional support for the hypothesis that an autosomal region equivalent to the human Xp was translocated to the X chromosome in the Eutheria after the divergence of the marsupials 150 million years ago. The region containing the AMG gene is therefore likely to have been added 80-150 million years ago to a pseudoautosomal region shared by the ancestral eutherian X and Y chromosome; the X and Y alleles must have begun diverging after this date.

Amelogenin↗

PubMed2001

Origin of alternative splicing by tandem exon duplication.

Genes with new functions often evolve by gene duplication. Alternative splicing is another means of evolutionary innovation in eukaryotes, which allows a single gene to encode functionally diverse proteins. We investigate a connection between these two evolutionary phenomena. For approximately 10% of the described cases of substitution alternative splicing, such that either one or another amino acid sequence is included into the protein, evidence of origin by tandem exon duplication was found. This is a conservative estimate because alternative exons are typically short and, on many occasions, duplicates may have diverged beyond recognition. Dating exon duplications through a combination of the available experimental data on alternative splicing in orthologous genes from different species and computational analysis indicates that most of the duplications antedate at least the radiation of mammalian orders or even the radiation of vertebrate classes. At present, tandem exon duplication is the only mechanism of evolution of substitution alternative splicing that can be specifically demonstrated. Along with gene duplication, this could be a major route for generating functional diversity during evolution of multicellular eukaryotes.

Alternative Splicing↗

PubMedDate not supplied

Modern African ape populations as genetic and demographic models of the last common ancestor of humans, chimpanzees, and gorillas.

In order to fully understand human evolutionary history through the use of molecular data, it is essential to include our closest relatives as a comparison. We provide here estimates of nucleotide diversity and effective population size of modern African ape species using data from several independent noncoding nuclear loci, and use these estimates to make predictions about the nature of the ancestral population that eventually gave rise to the living species of African apes, including humans. Chimpanzees, bonobos, and gorillas possess two to three times more nucleotide diversity than modern humans. We hypothesize that the last common ancestor (LCA) of these species had an effective population size more similar to modern apes than modern humans. In addition, estimated dates for the divergence of the Homo, Pan, and Gorilla lineages suggest that the LCA may have had stronger geographic structuring to its mtDNA than its nuclear DNA, perhaps indicative of strong female philopatry or a dispersal system analogous to gorillas, where females disperse only short distances from their natal group. Synthesizing different classes of data, and the inferences drawn from them, allows us to predict some of the genetic and demographic properties of the LCA of humans, chimpanzees, and gorillas.

Africa↗

PubMed1998

Tracing the origins of louping ill virus by molecular phylogenetic analysis.

The nucleotide and deduced amino acid sequences of louping ill (LI) virus isolates, collected from representative regions of the British Isles and Norway, were determined for either the entire envelope gene (20 isolates) or for a portion of the envelope gene that spans a hypervariable region and includes an LI virus specific marker sequence (53 isolates). Phylogenetic analysis reveals the presence of three major geographical populations of LI virus in the British Isles, viz. Irish, Welsh and British LI viruses, which all cause encephalomyelitis in animals, predominantly sheep, and co-habit the same tick population. British LI virus occurs throughout Scotland, England, Ireland and Norway. Irish and Welsh LI viruses occur only in Ireland and Wales, respectively. Phylogenetic analysis also predicts that LI virus initially emerged in Ireland and that a descendant was introduced into Great Britain via Wales and was subsequently transported to the borders of Scotland, from where it was dispersed throughout Scotland, northern England and Norway. More recently, the British LI virus was reintroduced into Ireland and also into south-west England. Dates of lineage divergence, calculated from the synonymous substitution rate, indicate that LI virus emerged in the British Isles less than 800 years ago and most LI virus dispersal occurred during the last 300 years. By combining these data with historical records it appears that livestock movement can be implicated in the dispersal of LI virus.

Animals↗

PubMed2006

Gis-based niche models reveal unifying climatic mechanisms that maintain the location of avian hybrid zones in a North American suture zone.

The existence of suture zones in North America has recently been verified, yet the environmental factors responsible for the maintenance of their structure and position have remained undetermined. The Great Plains suture zone in the US is perhaps the most significant and broadly studied in North America. Numerous avian hybrid zones that cluster in this region have been extensively studied over the last half-century. A primary result of this work is that exogenous factors present in this region have promoted and maintained avian species divergence. Yet, to date the variables most important in the generation and the clustered positioning of these hybrid zones in relation to one another have not been determined. The present study aims to advance our understanding of this North American suture zone by using niche modelling to quantify which environmental variables are most important in its formation and maintenance. Through the generation of fundamental niches for four hybrids and their parental species, similarities linking the hybrid zones were uncovered. The results show that temperature holds this suture zone in position and also suggest that temperature played a primary role in promoting niche differentiation among these sister species pairs during Pleistocene glacial cycles.

Animals↗

PubMedDate not supplied

Terminal addition, the Cambrian radiation and the Phanerozoic evolution of bilaterian form.

We examine terminal addition, the process of addition of serial elements in a posterior subterminal growth zone during animal development, across modern taxa and fossil material. We argue that terminal addition was the basal condition in Bilateria, and that modification of terminal addition was an important component of the rapid Cambrian evolution of novel bilaterian morphology. We categorize the often-convergent modifications of terminal addition from the presumed ancestral condition. Our focus on terminal addition and its modification highlights trends in the history of animal evolution evident in the fossil record. These trends appear to be the product of departure from the initial terminal addition state, as is evident in evolutionary patterns within-fossil groups such as trilobites, but is also more generally related to shifts in types of morphologic change through the early Phanerozoic. Our argument is contingent on dates of metazoan divergence that are roughly convergent with the first appearance of metazoan fossils in the latest Proterozoic and Cambrian, as well as on an inference of homology of terminal addition across bilaterian Metazoa.

Animals↗

PubMed1995

In vivo restriction by LlaI is encoded by three genes, arranged in an operon with llaIM, on the conjugative Lactococcus plasmid pTR2030.

The LlaI restriction and modification (R/M) system is encoded on pTR2030, a 46.2-kb conjugative plasmid from Lactococcus lactis. The llaI methylase gene, sequenced previously, encodes a functional type IIS methylase and is located approximately 5 kb upstream from the abiA gene, encoding abortive phage resistance. In this study, the sequence of the region between llaIM and abiA was determined and revealed four consecutive open reading frames (ORFs). Northern (RNA) analysis showed that the four ORFs were part of a 7-kb operon with llaIM and the downstream abiA gene on a separate transcriptional unit. The deduced protein sequence of ORF2 revealed a P-loop consensus motif for ATP/GTP-binding sites and a three-part consensus motif for GTP-binding proteins. Data bank searches with the deduced protein sequences for all four ORFs revealed no homology except for ORF2 with MerB, in three regions that coincided with the GTP-binding motifs in both proteins. To phenotypically analyze the llaI operon, a 9.0-kb fragment was cloned into a high-copy-number lactococcal shuttle vector, pTRKH2. The resulting construct, pTRK370, exhibited a significantly higher level of in vivo restriction and modification in L. lactis NCK203 than the low-copy-number parental plasmid, pTR2030. A combination of deletion constructions and frameshift mutations indicated that the first three ORFs were involved in LlaI restriction, and they were therefore designated llaI.1, llaI.2, and llaI.3. Mutating llaI.1 completely abolished restriction, while disrupting llaI.2 or llaI.3 allowed an inefficient restriction of phage DNA to occur, manifested primarily by a variable plaque phenotype. ORF4 had no discernible effect on in vivo restriction. A frameshift mutation in llaIM proved lethal to L. lactis NCK203, implying that the restriction component was active without the modification subunit. These results suggested that the LlaI R/M system is unlike any other R/M system studied to date and has diverged from the type IIS class of restriction enzymes by acquiring some characteristics reminiscent of type I enzymes.

Amino Acid Sequence↗

PubMed2004

The planetary biology of cytochrome P450 aromatases.

BACKGROUND: Joining a model for the molecular evolution of a protein family to the paleontological and geological records (geobiology), and then to the chemical structures of substrates, products, and protein folds, is emerging as a broad strategy for generating hypotheses concerning function in a post-genomic world. This strategy expands systems biology to a planetary context, necessary for a notion of fitness to underlie (as it must) any discussion of function within a biomolecular system. RESULTS: Here, we report an example of such an expansion, where tools from planetary biology were used to analyze three genes from the pig Sus scrofa that encode cytochrome P450 aromatases-enzymes that convert androgens into estrogens. The evolutionary history of the vertebrate aromatase gene family was reconstructed. Transition redundant exchange silent substitution metrics were used to interpolate dates for the divergence of family members, the paleontological record was consulted to identify changes in physiology that correlated in time with the change in molecular behavior, and new aromatase sequences from peccary were obtained. Metrics that detect changing function in proteins were then applied, including KA/KS values and those that exploit structural biology. These identified specific amino acid replacements that were associated with changing substrate and product specificity during the time of presumed adaptive change. The combined analysis suggests that aromatase paralogs arose in pigs as a result of selection for Suoidea with larger litters than their ancestors, and permitted the Suoidea to survive the global climatic trauma that began in the Eocene. CONCLUSIONS: This combination of bioinformatics analysis, molecular evolution, paleontology, cladistics, global climatology, structural biology, and organic chemistry serves as a paradigm in planetary biology. As the geological, paleontological, and genomic records improve, this approach should become widely useful to make systems biology statements about high-level function for biomolecular systems.

Amino Acid Sequence↗

PubMed2006

Multilocus analysis of nucleotide variation and speciation in Oryza officinalis and its close relatives.

Nucleotide variation in 10 unlinked nuclear genes was investigated in species-wide samples of Oryza officinalis and its close relatives (Oryza eichingeri and Oryza rhizomatis). Average estimates of nucleotide diversity were the lowest in O. rhizomatis ((sil) = 0.0038) and the highest in O. eichingeri ((sil) = 0.0057) that is disjunctly distributed in Africa and Sri Lanka. These wild rice species appeared to harbor relatively low levels of nucleotide variation relative to other plant species because the diversity level of O. eichingeri is only 23-46% of those in Zea species and 35% of that in Arabidopsis thaliana. The lower nucleotide diversity in these Oryza species could be best explained by their smaller historic effective population sizes. The speciation model test indicated that O. officinalis and its close relatives might have undergone a process of population contraction since divergence from their ancestor. Incongruent topologies among 10 gene trees, particularly regarding the positions of O. eichingeri and O. rhizomatis accessions might be attributed to lineage sorting arising from ancient polymorphism and hybridization/introgression between the Sri Lankan O. eichingeri and O. rhizomatis. However, the null hypothesis of the isolation model was not rejected for any contrast between taxa, which suggested that no subsequent gene flow shaped the present patterns of nucleotide variation since their divergence and that introgression was not pervasive in this group of species. Our molecular dating provides an approximate divergence time of 0.37 Myr between 2 geographical races of O. eichingeri, much more recent compared with the times of other speciation events in this group (0.63-0.68 Myr). A long-distance dispersal from West Africa to Sri Lanka was more likely to play a role in the disjunct distribution of O. eichingeri.

Africa↗

PubMed2000

Rooting a phylogeny with homologous genes on opposite sex chromosomes (gametologs): a case study using avian CHD.

We describe a previously unrecognized form of gene homology using the term "gametology," which we define as homology arising through lack of recombination and subsequent differentiation of sex chromosomes. We demonstrate use of gametologous genes to root each other in phylogenetic analyses of sex-specific avian Chromo-helicase-DNA binding gene (CHD) sequences. Phylogenetic analyses of a set of neognath bird sequences yield monophyletic groups for CHD-W and CHD-Z gametologs, as well as congruent relationships between these two clades and between them and current views of avian taxonomy. Phylogenetic analyses including paleognath bird CHD sequences and rooting with crocodilian CHD sequences, suggest an early divergence for paleognath CHD within the avian CHD clade. Based on our CHD analyses calibrated with avian fossil dates, we estimate the divergence between CHD-W and CHD-Z at 123 MYA, suggesting an early differentiation of sex chromosomes that predates most extant avian orders. In agreement with the notion of male-driven evolution, we find a faster rate of change in male-linked CHD-Z sequences.

Animals↗

PubMed1995

Evolutionary origin of human and primate malarias: evidence from the circumsporozoite protein gene.

We have analyzed the conserved regions of the gene coding for the circumsporozoite protein (CSP) in 12 species of Plasmodium, the malaria parasite. The closest evolutionary relative of P. falciparum, the agent of malignant human malaria, is P. reichenowi, a chimpanzee parasite. This is consistent with the hypothesis that P. falciparum is an ancient human parasite, associated with humans since the divergence of the hominids from their closest hominoid relatives. Three other human Plasmodium species are each genetically indistinguishable from species parasitic to nonhuman primates; that is, for the DNA sequences included in our analysis, the differences between species are not greater than the differences between strains of the human species. The human P. malariae is indistinguishable from P. brasilianum, and P. vivax is indistinguishable from P. simium; P. brasilianum and P. simium are parasitic to New World monkeys. The human P. vivax-like is indistinguishable from P. simiovale, a parasite of Old World macaques. We conjecture that P. malariae, P. vivax, and P. vivax-like are evolutionarily recent human parasites, the first two at least acquired only within the last several thousand years, and perhaps within the last few hundred years, after the expansion of human populations in South America following the European colonizations. We estimate the rate of evolution of the conserved regions of the CSP gene as 2.46 x 10(-9) per site per year. The divergence between the P. falciparum and P. reichenowi lineages is accordingly dated 8.9 Myr ago. The divergence between the three lineages leading to the human parasites is very ancient, about 100 Myr old between P. malariae and P. vivax (and P. vivax-like) and about 165 Myr old between P. falciparum and the other two.

Animals↗

PubMed2004

Host-associated genetic differentiation in Thrips tabaci (Insecta; Thysanoptera), as determined from mtDNA sequence data.

We tested for host-associated genetic differentiation in 22 populations of Thrips tabaci collected from tobacco and leek, respectively. Clustering analyses and haplotype networks based on sequence variation at a fragment of the mitochondrial cytochrome oxidase I gene yielded three major evolutionary lineages; two were clearly associated with leek and the third with tobacco. These genetic findings corroborated recent experimental observations on the heterogeneity of T. tabaci populations with regard to host-plant preference and their capacity to be vectors for tomato spotted wilt virus. Estimated divergence times suggested an ancient divergence of these lineages dating back to the Miocene 28-21 million years ago. F(ST) values between these lineages ranged between 0.824 and 0.954 (P<0.001 for all comparisons), and sequence divergences ranged between 4 and 11%. Given these findings and by the standards of genetic and ecological differentiation in other published species groups, T. tabaci must be considered a complex of cryptic (sub)species.

Animals↗

PubMed2000

Ancestral chloroplast genome in Mesostigma viride reveals an early branch of green plant evolution.

Sequence comparisons suggest that all living green plants belong to one of two major phyla: Streptophyta (land plants and their closest green algal relatives, the charophytes); and Chlorophyta (the rest of green algae). Because no green algae are known that pre-date the Streptophyta/Chlorophyta split, and also because the earliest diverging green algae show considerable morphological variation, the nature of the unicellular flagellate ancestor of the two green plant phyla is unknown. Here we report that the flagellate Mesostigma viride belongs to the earliest diverging green plant lineage discovered to date. We have sequenced the entire chloroplast DNA (118,360 base pairs) of this green alga and have conducted phylogenetic analyses of sequences derived from this genome. Mesostigma represents a lineage that emerged before the divergence of the Streptophyta and Chlorophyta, a position that is supported by several features of its chloroplast DNA. The structure and gene organization of this genome indicate that chloroplast DNA architecture has been extremely well conserved in the line leading to land plants.

Chlorophyta↗

PubMed2005

Time dependency of molecular rate estimates and systematic overestimation of recent divergence times.

Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various genes and taxa. Recent studies based on population-level and pedigree data have produced remarkably high estimates of mutation rate, which strongly contrast with substitution rates inferred in phylogenetic (species-level) studies. Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (< 1-2 Myr) mutation rate and the low, long-term substitution rate. The relationship between the age of the calibration and the rate of change can be described by a vertically translated exponential decay curve, which may be used for correcting molecular date estimates. The phylogenetic substitution rates in mitochondria are approximately 0.5% per million years for avian protein-coding sequences and 1.5% per million years for primate protein-coding and d-loop sequences. Further analyses showed that purifying selection offers the most convincing explanation for the observed relationship between the estimated rate and the depth of the calibration. We rule out the possibility that it is a spurious result arising from sequence errors, and find it unlikely that the apparent decline in rates over time is caused by mutational saturation. Using a rate curve estimated from the d-loop data, several dates for last common ancestors were calculated: modern humans and Neandertals (354 ka; 222-705 ka), Neandertals (108 ka; 70-156 ka), and modern humans (76 ka; 47-110 ka). If the rate curve for a particular taxonomic group can be accurately estimated, it can be a useful tool for correcting divergence date estimates by taking the rate decay into account. Our results show that it is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution.

Animals↗

PubMed1996

The presence of a divergent T-lymphotropic virus in a wild-caught pygmy chimpanzee (Pan paniscus) supports an African origin for the human T-lymphotropic/simian T-lymphotropic group of viruses.

We isolated a divergent simian T-lymphotropic virus (STLV) (strain PP1664) from a wild-caught African bonobo (pygmy chimpanzee, Pan paniscus). Molecular and phylogenetic characterization of this virus show that it reliably separates from the two well-established primate T-lymphotropic virus types, HTLV-I/STLV-I (PTLV-I) and PTLV-II, and from a third type isolated from an African-born Papio hamadryas and designated by us as PTLV-L. Four of eight bonobos kept at the Antwerp Zoo, Belgium, showed an aberrant PTLV serology. We amplified and sequenced a 709 bp PTLV proviral tax/rex fragment from one of the reactive bonobos. It differs by about 25 % from the homologous nucleotide sequences of PTLV-I and PTLV-L and by about 17 % from PTLV-II. This is comparable to the differences among the three known types. Including the most divergent STLV-I strains sequenced to date, for example, strain PHSu1 sequenced here, the divergence in this region within PTLV-I is less than 11 % and within PTLV-II less than 4%. Although very divergent, this new bonobo STLV is the closest well-characterized simian relative of HTLV-II, raising the possibility of very divergent new HTLV strains. Our results show that the number of PTLV types should be considered open and that the variety of indigenous viruses in the PTLV group is greatest in Africa. Thus, as for the other primate retroviruses HIV and SIV, PTLV most probably has its origins in Africa.

Africa↗