High-resolution species trees without concatenation

The vast majority of phylogenetic models focus on resolution of gene trees, despite the fact that phylogenies of species in which gene trees are embedded are of primary interest. We analyze a Bayesian model for estimating species trees that accounts for the stochastic variation expected for gene trees from multiple unlinked loci sampled from a single species history after a coalescent process. Application of the model to a 106-gene data set from yeast shows that the set of gene trees recovered by statistically acknowledging the shared but unknown species tree from which gene trees are sampled is much reduced compared with treating the history of each locus independently of an overarching species tree. The analysis also yields a concentrated posterior distribution of the yeast species tree whose mode is congruent with the concatenated gene tree but can do so with less than half the loci required by the concatenation method. Using simulations, we show that, with large numbers of loci, highly resolved species trees can be estimated under conditions in which concatenation of sequence data will positively mislead phylogeny, and when the proportion of gene trees matching the species tree is <10%. However, when gene tree/species tree congruence is high, species trees can be resolved with just two or three loci. These results make accessible an alternative paradigm for combining data in phylogenomics that focuses attention on the singularity of species histories and away from the idiosyncrasies and multiplicities of individual gene histories.     

Semipermeable species boundaries between Anopheles gambiae and Anopheles arabiensis: evidence from multilocus DNA sequence variation

Attempts to reconstruct the phylogenetic history of the Anopheles gambiae cryptic species complex have yielded strongly conflicting results. In particular, An. gambiae, the primary African malaria vector, is variously placed as a sister taxon to either Anopheles arabiensis or Anopheles merus. The recent divergence times for members of this complex complicate phylogenetic analysis, making it difficult to unambiguously implicate interspecific gene flow, versus retained ancestral polymorphism, as the source of conflict. Using sequences at four unlinked loci, which were determined from multiple specimens within each of five species in the complex, we found contrasting patterns of sequence divergence between the X chromosome and the autosomes. The isolation model of speciation assumes a lack of gene flow between species since their separation. This model could not be rejected for An. gambiae and An. arabiensis, although the data fit the model poorly. On the other hand, evidence from gene trees supports genetic introgression of chromosome 2 inversions between An. gambiae and An. arabiensis, and also points to more broad scale genetic exchange of autosomal sequences between this species pair. That such exchange has been relatively recent is suggested not only by the lack of fixed differences at three autosomal loci but also by the sharing of full haplotypes at two of the three loci, which is in contrast to several fixed differences and considerably deeper divergence on the X. The proposed acquisition by An. gambiae of sequences from the more arid-adapted An. arabiensis may have contributed to the spread and ecological dominance of this malaria vector.     

INAUGURAL ARTICLE by a Recently Elected Academy Member:Constructing primate phylogenies from ancient retrovirus sequences

The genomes of modern humans are riddled with thousands of endogenous retroviruses (HERVs), the proviral remnants of ancient viral infections of the primate lineage. Most HERVs are nonfunctional, selectively neutral loci. This fact, coupled with their sheer abundance in primate genomes, makes HERVs ideal for exploitation as phylogenetic markers. Endogenous retroviruses (ERVs) provide phylogenetic information in two ways: (i) by comparison of integration site polymorphism and (ii) by orthologous comparison of evolving, proviral, nucleotide sequence. In this study, trees are constructed with the noncoding long terminal repeats (LTRs) of several ERV loci. Because the two LTRs of an ERV are identical at the time of integration but evolve independently, each ERV locus can provide two estimates of species phylogeny based on molecular evolution of the same ancestral sequence. Moreover, tree topology is highly sensitive to conversion events, allowing for easy detection of sequences involved in recombination as well as correction for such events. Although other animal species are rich in ERV sequences, the specific use of HERVs in this study allows comparison of trees to a well established phylogenetic standard, that of the Old World primates. HERVs, and by extension the ERVs of other species, constitute a unique and plentiful resource for studying the evolutionary history of the Retroviridae and their animal hosts.     

Evolution of alcohol dehydrogenase genes in the palm and grass families.

The alcohol dehydrogenase (Adh; alcohol:NAD+ oxidoreductase, EC 1.1.1.1) gene family has two or three loci in a broad array of angiosperm species. The relative stability in the number of Adh loci led Gottlieb [Gottlieb, L. D. (1982) Science 216, 373-380] to propose that the Adh gene family arose from an ancient gene duplication. In this study, the isolation of three loci from the California fan palm (Washingtonia robusta) is reported. The three loci from palm are highly diverged. One palm Adh gene, referred to here as adhB, has been completely sequenced, including 950 nucleotides of the upstream regulatory region. For the second locus, adhA, 81% of the exon sequence is complete. Both show the same basic structure as grass Adh genes in terms of intron number and intron location. The third locus, adhC, for which only a small amount of sequence is available (12% of exon sequence) appears to be more highly diverged. Comparison of the Adh gene families from palms and grasses shows that the adh1 and adh2 genes of grasses, and the adhA and adhB genes of palms, arose by duplication following the divergence of the two families. This finding suggests that the multiple Adh loci in different monocot lineages are not the result of a single ancestral duplication but, rather, of multiple duplication events.     

Calculation of evolutionary trees from sequence data.

Evolutionary trees are usually calculated from comparisons of protein or nucleic acid sequences from present-day organisms by use of algorithms that use only the difference matrix, where the difference matrix is constructed from the sequence differences between pairs of sequences from the organisms. The difference matrix alone cannot define uniquely the correct position of the ancestor of the present-day organisms (root of the tree). Furthermore, methods using the difference matrix alone often fail to give the correct pattern of tree branching (topology) when the different sequences evolve at different rates. Only for equal rates of evolution can the difference matrix (when used with the so-called matrix method) yield exactly the correct topology and root. In this paper we present a method for calculating evolutionary trees from sequence data that uses, along with the difference matrix, the rate of evolution of the various sequences from their common ancestor. It is proven analytically that this method uniquely determines both the correct topology and root in theory for unequal rates of sequence evolution. How one would estimate an ancestral sequence to be used in the method is discussed in particular for the 5S RNA sequences from prokaryotes and eukaryotes and for ferredoxin sequences.     

Isolation of a shark immunoglobulin light chain cDNA clone encoding a protein resembling mammalian kappa light chains: implications for the evolution of light chains.

The time of emergence of immunoglobulin kappa and lambda light (L) chains in evolution is unknown. An L chain cDNA clone was isolated from the nurse shark (Ginglymostoma cirratum), a cartilaginous fish, whose predicted variable (V) region amino acid sequence has up to 60% sequence identity to mammalian V kappa domains. Genomic analyses suggest a cluster-type gene organization for this L chain locus, similar to the shark lambda-like immunoglobulin L chain loci rather than mammalian kappa loci. We propose that divergence of the ancestral L chain into isotypes likely occurred before the emergence of elasmobranchs 400-450 million years ago. Similarities in gene organization between the two isotypes in sharks may reflect the gene organization utilized by the ancestral L chain.     

Allopatric genetic origins for sympatric host-plant shifts and race formation in Rhagoletis

Tephritid fruit flies belonging to the Rhagoletis pomonella sibling species complex are controversial because they have been proposed to diverge in sympatry (in the absence of geographic isolation) by shifting and adapting to new host plants. Here, we report evidence suggesting a surprising source of genetic variation contributing to sympatric host shifts for these flies. From DNA sequence data for three nuclear loci and mtDNA, we infer that an ancestral, hawthorn-infesting R. pomonella population became geographically subdivided into Mexican and North American isolates approximately 1.57 million years ago. Episodes of gene flow from Mexico subsequently infused the North American population with inversion polymorphism affecting key diapause traits, forming adaptive clines. Sometime later (perhaps +/-1 million years), diapause variation in the latitudinal clines appears to have aided North American flies in adapting to a variety of plants with differing fruiting times, helping to spawn several new taxa. Thus, important raw genetic material facilitating the adaptive radiation of R. pomonella originated in a different time and place than the proximate ecological host shifts triggering sympatric divergence.     

African origin of human-specific polymorphic Alu insertions.

Alu elements are a family of interspersed repeats that have mobilized throughout primate genomes by retroposition from a few "master" genes. Among the 500,000 Alu elements in the human genome are members of the human-specific subfamily that are not fixed in the human species; that is, not all chromosomes carry an Alu element at a particular locus. Four such polymorphic human-specific Alu insertions were analyzed by a rapid, PCR-based assay that uses primers that flank the insertion point to determine genotypes based on the presence or absence of the Alu element. These four polymorphic Alu insertions were shown to be absent from the genomes of a number of nonhuman primates, consistent with their arising as human genetic polymorphisms sometime after the human/African ape divergence. Analysis of 664 unrelated individuals from 16 population groups from around the world revealed substantial levels of variation within population groups and significant genetic differentiation among groups. No significant associations were found among the four loci, consistent with their location on different chromosomes. A maximum-likelihood tree of population relationships showed four major groupings consisting of Africa, Europe, Asia/Americas, and Australia/New Guinea, which is concordant with similar trees based on other loci. A particularly useful feature of the polymorphic Alu insertions is that the ancestral state is known to be the absence of the Alu element, and the presence of the Alu element at a particular chromosomal site reflects a single, unique event in human evolution. A hypothetical ancestral group can then be included in the tree analysis, with the frequency of each insertion set to zero. The ancestral group connected to the maximum-likelihood tree within the African branch, which suggests an African origin of these polymorphic Alu insertions. These data are concordant with other diverse data sets, which lends further support to the recent African origin hypothesis for modern humans. Polymorphic Alu insertions represent a source of genetic variation for studying human population structure and evolution.     

Multilocus genetic structure of ancestral Spanish and colonial Californian populations of Avena barbata.

We have applied a multivariate log-linear technique to the analysis of interlocus allelic associations among 14 allozyme loci in a sample of 4011 plants from 42 Spanish populations of Avena barbata. The loci fell into three natural groups of five, five, and four loci. The five loci of the first group are invariant, or nearly so, throughout the range of the species. The genetic organization of the loci of this set is defined by a single five-locus genotype; each allele of this predominant genotype is a "wild-type" allele that contributes favorably to adaptedness in all single-locus and multilocus configurations regardless of environment. Although allelic diversity is high in Spain for the nine loci of the second and third sets, log-linear analyses showed that these loci are tied together in Spanish populations through complex networks of overlapping lower-order interlocus interactions. The ancestral Spanish and colonial Californian gene pools are closely similar in allelic composition on a locus-by-locus basis; however, Spanish allelic configurations at two-locus and higher-order levels are usually different from and much less tightly organized than in Californian populations. We conclude that the major force involved in the evolution of the colonial populations was selection that led to reorganization, at the interlocus level, of the ancestral Spanish allelic ingredients into different multilocus genotypes adapted to Californian habitats.     

Differential loss of embryonic globin genes during the radiation of placental mammals

The differential gain and loss of genes from homologous gene families represents an important source of functional variation among the genomes of different species. Differences in gene content between species are primarily attributable to lineage-specific gene gains via duplication and lineage-specific losses via deletion or inactivation. Here, we use a comparative genomic approach to investigate this process of gene turnover in the β-globin gene family of placental mammals. By analyzing genomic sequence data from representatives of each of the main superordinal clades of placental mammals, we were able to reconstruct pathways of gene family evolution during the basal radiation of this physiologically and morphologically diverse vertebrate group. Our analysis revealed that an initial expansion of the nonadult portion of the β-globin gene cluster in the ancestor of placental mammals was followed by the differential loss and retention of ancestral gene lineages, thereby generating variation in the complement of embryonic globin genes among contemporary species. The sorting of ε-, γ-, and η-globin gene lineages among the basal clades of placental mammals has produced species differences in the functional types of hemoglobin isoforms that can be synthesized during the course of embryonic development.     

On the origin of Lake Malawi cichlid species: a population genetic analysis of divergence

The cichlid fishes of Lake Malawi are famously diverse. However, phylogenetic and population genetic studies of their history have been difficult because of the great amount of genetic variation that is shared between species. We apply a recently developed method for fitting the "isolation with migration" divergence model to a data set of specially designed compound loci to develop portraits of cichlid species divergence. Outgroup sequences from a cichlid from Lake Tanganyika permit model parameter estimates in units of years and effective population sizes. Estimated speciation times range from 1,000 to 17,000 years for species in the genus Tropheops. These exceptionally recent dates suggest that Malawi cichlids as a group experience a very active and dynamic diversification process. Current effective population size estimates range form 2,000 to near 40,000, and to >120,000 for estimates of ancestral population sizes. It appears that very recent speciation and gene flow are among the reasons why it has been difficult to discern the phylogenetic history of Malawi cichlids.     

Phylogenetic incongruence arising from fragmented speciation in enteric bacteria

Evolutionary relationships among species are often assumed to be fundamentally unambiguous, where genes within a genome are thought to evolve in concert and phylogenetic incongruence between individual orthologs is attributed to idiosyncrasies in their evolution. We have identified substantial incongruence between the phylogenies of orthologous genes in Escherichia, Salmonella, and Citrobacter, or E. coli, E. fergusonii, and E. albertii. The source of incongruence was inferred to be recombination, because individual genes support conflicting topology more robustly than expected from stochastic sequence homoplasies. Clustering of phylogenetically informative sites on the genome indicated that the regions of recombination extended over several kilobases. Analysis of phylogenetically distant taxa resulted in consensus among individual gene phylogenies, suggesting that recombination is not ongoing; instead, conflicting relationships among genes in descendent taxa reflect recombination among their ancestors. Incongruence could have resulted from random assortment of ancestral polymorphisms if species were instantly created from the division of a recombining population. However, the estimated branch lengths in alternative phylogenies would require ancestral populations with far more diversity than is found in extant populations. Rather, these and previous data collectively suggest that genome-wide recombination rates decreased gradually, with variation in rate among loci, leading to pluralistic relationships among their descendent taxa.     

基于凝集素基因对部分隐孢子虫种类的分子鉴定

目的 为了解隐孢子虫凝集素基因在不同分离株的序列差异及其遗传进化关系,以SSU rRNA基因作参照,评价Lectin基因位点作为隐孢子虫基因分型和进化关系分析的可行性。方法 采用巢式PCR,分别在Lectin和SSU rRNA位点处对本实验室分离保存的多个隐孢子虫分离株进行PCR的扩增。用Clustalx对扩增序列与参考序列进行比对,用MEGA5中的邻近法(Neighbor joining method NJ),进行进化树的构建。结果 基于Lectin基因位点,在C. parvum、C. hominis、C. cuniculus及其在SSU rRNA 处与人源C. hominis极为相近的horse genotype、驴源C. hominis均成功扩增出了大小在450 bp左右的目的 条带,并进行了进化树的分析,不同种类和同种不同动物来源的隐孢子虫分布在不同的分支上。结论 Lectin基因位点可很好的区分SSU rRNA序列极为相似的几种隐孢子虫,有望为人兽共患隐孢子虫分类和遗传研究提供新的基因靶标。     

Evolution of the insulin superfamily: cloning of a hybrid insulin/insulin-like growth factor cDNA from amphioxus.

Although insulin and the insulin-like growth factors (IGFs) share marked similarities in amino acid sequence and biological activity, their evolutionary origins have not been resolved. To investigate this issue, we recently cloned a cDNA encoding an insulin-like peptide (ILP) from a primitive chordate species, amphioxus (Branchiostoma californiensis). The deduced sequence of amphioxus preproILP indicates that it is a hybrid molecule containing features characteristic of both insulin and IGF. Like proinsulin, amphioxus proILP contains a C-peptide, which is flanked by paired basic residues and is probably removed by proteolysis. However, proILP also contains an extended carboxyl-terminal peptide region that can be divided into D and E domains similar to those of proIGF. Sequence comparisons show that the amphioxus ILP A and B domains are equally homologous to those of human insulin and IGF-I and -II. Based on these results and the exon-intron organization of the amphioxus ILP gene, we propose that IGF emerged at a very early stage in vertebrate evolution from an ancestral insulin-type gene.     

Patterns of Genetic Differentiation in the Slender Wild Oat Species Avena barbata

Allozyme frequencies at five enzyme loci were determined for 14 California populations of Avena barbata, a species introduced to California from the Mediterranean Basin during the colonization of North America. Allelic frequencies at these loci were also determined in Mediterranean collections of this species. The pattern of divergence of the California populations from the ancestral gene pool was not random and was strongly correlated with environment; thus, the pattern is not in accord with the hypothesis that most electrophoretically detectable variants are adaptively neutral. Rates of gene substitution in California were also not in accord with the neutrality hypothesis. The observations are, however, compatible with predictions of Neo-Darwinian evolutionary theory. We interpret these observations to indicate that natural selection plays a major role in determining the unique patterns of distribution of genetic variability in the slender wild oat in California.     

Evolution of Neurophysin Proteins: The Partial Sequence of Bovine Neurophysin-I

The sequence of the first 50 amino-acid residues of bovine neurophysin-I was determined. A comparison of this sequence with that of the 97-residue bovine neurophysin-II and the 92-residue porcine neurophysin-I molecules reveals a high degree of homology among these proteins. It is suggested that the binding site of neurophysin proteins for neurohypophyseal hormones is located in the middle portion of these molecules, where their sequences are virtually identical. The sequence data, as well as the occurrence of at least two neurophysins in both the pig and the cow, suggest that each species inherited at least two structural genes controlling the synthesis of these proteins. The most striking finding in the study was the observation of internal sequence homologies within the neurophysins. This result implies that these molecules arose by way of a series of partial gene duplications of a primitive gene that coded for a smaller ancestral protein.     

Recent common ancestry of human Y chromosomes: evidence from DNA sequence data

We consider a data set of DNA sequence variation at three Y chromosome genes (SMCY, DBY, and DFFRY) in a worldwide sample of human Y chromosomes. Between 53 and 70 chromosomes were fully screened for sequence variation at each locus by using the method of denaturing high-performance liquid chromatography. The sum of the lengths of the three genes is 64,120 bp. We have used these data to study the ancestral genealogy of human Y chromosomes. In particular, we focused on estimating the expected time to the most recent common ancestor and the expected ages of certain mutations with interesting geographic distributions. Although the geographic structure of the inferred haplotype tree is reminiscent of that obtained for other loci (the root is in Africa, and most of the oldest non-African lineages are Asian), the expected time to the most recent common ancestor is remarkably short, on the order of 50,000 years. Thus, although previous studies have noted that Y chromosome variation shows extreme geographic structure, we estimate that the spread of Y chromosomes out of Africa is much more recent than previously was thought. We also show that our data indicate substantial population growth in the effective number of human Y chromosomes.     

Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution

The amount of lateral gene transfer (LGT) that has occurred in microbial evolution is heavily debated. Efforts to quantify LGT through gene-tree comparisons have delivered estimates that between 2% and 60% of all prokaryotic genes have been affected by LGT, the 30-fold discrepancy reflecting differences among gene samples studied and uncertainties inherent in phylogenetic reconstruction. Here we present a simple method that is independent of gene-tree comparisons to estimate the LGT rate among sequenced prokaryotic genomes. If little or no LGT has occurred during evolution, ancestral genome sizes would become unrealistically large, whereas too much LGT would render them far too small. We determine the amount of LGT that is necessary and sufficient to bring the distribution of inferred ancestral genome sizes into agreement with that observed among modern microbes. Rather than testing for phylogenetic congruence or lack thereof across genes, we assume that all gene trees are compatible; hence, our method delivers very conservative lower-bound estimates of the average LGT rate. The results indicate that among 57,670 gene families distributed across 190 sequenced genomes, at least two-thirds and probably all, have been affected by LGT at some time in their evolutionary past. A component of common ancestry nonetheless remains detectable in gene distribution patterns. We estimate the minimum lower bound for the average LGT rate across all genes as 1.1 LGT events per gene family and gene family lifespan and this minimum rate increases sharply when genes present in only a few genomes are excluded from the analysis.     

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.     

Major histocompatibility complex class I genes of the coelacanth Latimeria chalumnae.

The coelacanth fish Latimeria chalumnae is the sole surviving species of a phylogenetic lineage that was founded more than 400 million years ago and that has changed morphologically very little since that time. Little is known about the molecular evolution of this "living fossil," considered by some taxonomists to be the closest living relative of tetrapods. Here we describe the isolation and characterization of L. chalumnae major histocompatibility complex (MHC) class I genes. The exon-intron organization of these genes is the same as that of their mammalian counterparts. The genes fall into four families, which we designate Lach-UA through Lach-UD. There are multiple loci in all of the families. Genes of the first two families are transcribed. The Lach-UA family bears the characteristics of functional, polymorphic class I genes; the other three families may be represented by nonclassical genes. All the Lach loci arose by duplication from an ancestral gene after the foundation of the coelacanth lineage. Intergenic variation is highest at positions corresponding to the mammalian peptide-binding region. The closest relatives of the Lach genes among the MHC genes sequenced thus far are those of the amphibian Xenopus.