Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Lineage tree”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 703 records · Page 39Linked to original sources
PubMed2005

Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees.

Multilocus genealogical approaches are still uncommon in phylogeography and historical demography, fields which have been dominated by microsatellite markers and mitochondrial DNA, particularly for vertebrates. Using 30 newly developed anonymous nuclear loci, we estimated population divergence times and ancestral population sizes of three closely related species of Australian grass finches (Poephila) distributed across two barriers in northern Australia. We verified that substitution rates were generally constant both among lineages and among loci, and that intralocus recombination was uncommon in our dataset, thereby satisfying two assumptions of our multilocus analysis. The reconstructed gene trees exhibited all three possible tree topologies and displayed considerable variation in coalescent times, yet this information provided the raw data for maximum likelihood and Bayesian estimation of population divergence times and ancestral population sizes. Estimates of these parameters were in close agreement with each other regardless of statistical approach and our Bayesian estimates were robust to prior assumptions. Our results suggest that black-throated finches (Poephila cincta) diverged from long-tailed finches (P. acuticauda and P. hecki) across the Carpentarian Barrier in northeastern Australia around 0.6 million years ago (mya), and that P. acuticauda diverged from P. hecki across the Kimberley Plateau-Arnhem Land Barrier in northwestern Australia approximately 0.3 mya. Bayesian 95% credibility intervals around these estimates strongly support Pleistocene timing for both speciation events, despite the fact that many gene divergences across the Carpentarian region clearly predated the Pleistocene. Estimates of ancestral effective population sizes for the basal ancestor and long-tailed finch ancestor were large (about 521,000 and about 384,000, respectively). Although the errors around the population size parameter estimates are considerable, they are the first for birds taking into account multiple sources of variance.

Animals↗
PubMed2005

Human mtDNA hypervariable regions, HVR I and II, hint at deep common maternal founder and subsequent maternal gene flow in Indian population groups.

We have analysed the hypervariable regions (HVR I and II) of human mitochondrial DNA (mtDNA) in individuals from Uttar Pradesh (UP), Bihar (BI) and Punjab (PUNJ), belonging to the Indo-European linguistic group, and from South India (SI), that have their linguistic roots in Dravidian language. Our analysis revealed the presence of known and novel mutations in both hypervariable regions in the studied population groups. Median joining network analyses based on mtDNA showed extensive overlap in mtDNA lineages despite the extensive cultural and linguistic diversity. MDS plot analysis based on Fst distances suggested increased maternal genetic proximity for the studied population groups compared with other world populations. Mismatch distribution curves, respective neighbour joining trees and other statistical analyses showed that there were significant expansions. The study revealed an ancient common ancestry for the studied population groups, most probably through common founder female lineage(s), and also indicated that human migrations occurred (maybe across and within the Indian subcontinent) even after the initial phase of female migration to India.

DNA, Mitochondrial↗
PubMed2005

Forty million years of independent evolution: a mitochondrial gene and its corresponding nuclear pseudogene in primates.

Sequences from nuclear mitochondrial pseudogenes (numts) that originated by transfer of genetic information from mitochondria to the nucleus offer a unique opportunity to compare different regimes of molecular evolution. Analyzing a 1621-nt-long numt of the rRNA specifying mitochondrial DNA residing on human chromosome 3 and its corresponding mitochondrial gene in 18 anthropoid primates, we were able to retrace about 40 MY of primate rDNA evolutionary history. The results illustrate strengths and weaknesses of mtDNA data sets in reconstructing and dating the phylogenetic history of primates. We were able to show the following. In contrast to numt-DNA, (1) the nucleotide composition of mtDNA changed dramatically in the different primate lineages. This is assumed to lead to significant misinterpretations of the mitochondrial evolutionary history. (2) Due to the nucleotide compositional plasticity of primate mtDNA, the phylogenetic reconstruction combining mitochondrial and nuclear sequences is unlikely to yield reliable information for either tree topologies or branch lengths. This is because a major part of the underlying sequence evolution model--the nucleotide composition--is undergoing dramatic change in different mitochondrial lineages. We propose that this problem is also expressed in the occasional unexpected long branches leading to the "common ancestor" of orthologous numt sequences of different primate taxa. (3) The heterogeneous and lineage-specific evolution of mitochondrial sequences in primates renders molecular dating based on primate mtDNA problematic, whereas the numt sequences provide a much more reliable base for dating.

Animals↗
PubMed1996

Population structure of Streptococcus agalactiae reveals an association between specific evolutionary lineages and putative virulence factors but not disease.

To evaluate the genetic diversity and relationships in a collection of 85 Danish strains of Streptococcus agalactiae (group B streptococcus) we have performed restriction fragment length polymorphism analysis on EcoRI- and MspI-digested whole-cell DNA using as probes rRNA, DNA fragments representing the genes encoding hyaluronidase, C5a-peptidase, alpha-antigen, and beta-antigen as well as two randomly selected genomic DNA fragments for which the coding potential is unknown. In addition, we have assayed for expression of hyaluronidase activity and beta-antigen. Combined analyses of our data and those previously obtained by multilocus enzyme electrophoresis and serotyping revealed a population separating into six major lineages that correlate with individual serotypes. The significant linkage disequilibrium of alleles indicates that the S. agalactiae population examined is predominantly clonal. Notably, strains expressing the serotype III capsule divide into two distant evolutionary lineages, of which one lacks expression of hyaluronidase activity. Six North American isolates of serotype III clustered together with multiple Danish serotype III strains, showing that the combinations of characters on which the phylogenetic tree was based are conserved worldwide. Occurrence of beta-antigen correlated with a specific version of the alpha-antigen gene and was exclusively associated with a single major phylogenetic lineage. Comparisons with the clinical history of the strains revealed no evidence of differences in pathogenic potential among the six major genetic divisions.

Adhesins, Bacterial↗
PubMed2005

Explosive radiation of Malpighiales supports a mid-cretaceous origin of modern tropical rain forests.

Fossil data have been interpreted as indicating that Late Cretaceous tropical forests were open and dry adapted and that modern closed-canopy rain forest did not originate until after the Cretaceous-Tertiary (K/T) boundary. However, some mid-Cretaceous leaf floras have been interpreted as rain forest. Molecular divergence-time estimates within the clade Malpighiales, which constitute a large percentage of species in the shaded, shrub, and small tree layer in tropical rain forests worldwide, provide new tests of these hypotheses. We estimate that all 28 major lineages (i.e., traditionally recognized families) within this clade originated in tropical rain forest well before the Tertiary, mostly during the Albian and Cenomanian (112-94 Ma). Their rapid rise in the mid-Cretaceous may have resulted from the origin of adaptations to survive and reproduce under a closed forest canopy. This pattern may also be paralleled by other similarly diverse lineages and supports fossil indications that closed-canopy tropical rain forests existed well before the K/T boundary. This case illustrates that dated phylogenies can provide an important new source of evidence bearing on the timing of major environmental changes, which may be especially useful when fossil evidence is limited or controversial.

Biological Evolution↗
PubMed2006

Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages.

Hemiascomycete yeasts cover an evolutionary span comparable to that of the entire phylum of chordates. Since this group currently contains the largest number of complete genome sequences it presents unique opportunities to understand the evolution of genome organization in eukaryotes. We inferred rates of genome instability on all branches of a phylogenetic tree for 11 species and calculated species-specific rates of genome rearrangements. We characterized all inversion events that occurred within synteny blocks between six representatives of the different lineages. We show that the rates of macro- and microrearrangements of gene order are correlated within individual lineages but are highly variable across different lineages. The most unstable genomes correspond to the pathogenic yeasts Candida albicans and Candida glabrata. Chromosomal maps have been intensively shuffled by numerous interchromosomal rearrangements, even between species that have retained a very high physical fraction of their genomes within small synteny blocks. Despite this intensive reshuffling of gene positions, essential genes, which cluster in low recombination regions in the genome of Saccharomyces cerevisiae, tend to remain syntenic during evolution. This work reveals that the high plasticity of eukaryotic genomes results from rearrangement rates that vary between lineages but also at different evolutionary times of a given lineage.

Candida albicans↗
PubMed2004

Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer.

Comparative analysis of the domain architectures of the beta, beta', and sigma(70) subunits of bacterial DNA-dependent RNA polymerases (DdRp), combined with sequence-based phylogenetic analysis, revealed a fundamental split among bacteria. DNA-dependent RNA polymerase subunits of Group I, which includes Proteobacteria, Aquifex, Chlamydia, Spirochaetes, Cytophaga-Chlorobium, and Planctomycetes, are characterized by three distinct inserts, namely a Sandwich Barrel Hybrid Motif domain in the beta subunit, a beta-beta' module (BBM) 1 domain in the beta' subunit, and a distinct helical module in the sigma subunit. The DdRp subunits of remaining bacteria, which comprise Group II, lack these inserts, although some additional inserted domains are present in individual lineages. The separation of bacteria into Group I and Group II is generally compatible with the topologies of phylogenetic trees of the conserved regions of DdRp subunits and concatenated ribosomal proteins and might represent the primary bifurcation in bacterial evolution. A striking deviation from this evolutionary pattern is Aquifex whose DdRp subunits cluster within Group I, whereas phylogenetic analysis of ribosomal proteins identifies Aquifex as grouping with Thermotoga another bacterial hyperthemophile belonging to Group II. The inferred evolutionary scenario for the DdRp subunits includes domain accretion and rearrangement, with some likely horizontal transfer events. Although evolution of bacterial DdRp appeared to be generally dominated by vertical inheritance, horizontal transfer of complete genes for all or some of the subunits, resulting in displacement of the ancestral genes, might have played a role in several lineages, such as Aquifex, Thermotoga, and Fusobacterium.

Amino Acid Sequence↗
PubMed2006

Evolution of a protein-folding machine: genomic and evolutionary analyses reveal three lineages of the archaeal hsp70(dnaK) gene.

The stress chaperone protein Hsp70 (DnaK) (abbreviated DnaK) and its co-chaperones Hsp40(DnaJ) (or DnaJ) and GrpE are universal in bacteria and eukaryotes but occur only in some archaea clustered in the order 5'-grpE-dnaK-dnaJ-3' in a locus termed Locus I. Three structural varieties of Locus I, termed Types I, II, and III, were identified, respectively, in Methanosarcinales, in Thermoplasmatales and Methanothermobacter thermoautotrophicus, and in Halobacteriales. These Locus I types corresponded to three groups identified by phylogenetic trees of archaeal DnaK proteins including the same archaeal subdivisions. These archaeal DnaK groups were not significantly interrelated, clustering instead with DnaKs from three bacterial lineages, Methanosarcinales with Firmicutes, Thermoplasmatales and M. thermoautotrophicus with Thermotoga, and Halobacteriales with Actinobacteria, suggesting that the three archaeal types of Locus I were acquired by independent events of lateral gene transfer. These associations, however, lacked strong bootstrap support and were sensitive to dataset choice and tree-reconstruction method. Structural features of dnaK loci in bacteria revealed that Methanosarcinales and Firmicutes shared a similar structure, also common to most other bacterial groups. Structural differences were observed instead in Thermotoga compared to Thermoplasmatales and M. thermoautotrophicus, and in Actinobacteria compared to Halobacteriales. It was also found that the association between the DnaK sequences from Halobacteriales and Actinobacteria likely reflects common biases in their amino acid compositions. Although the loci structural features and the DnaK trees suggested the possibility of lateral gene transfer between Firmicutes and Methanosarcinales, the similarity between the archaeal and the ancestral bacterial loci favors the more parsimonious hypothesis that all archaeal sequences originated from a unique prokaryotic ancestor.

Amino Acid Sequence↗
PubMed1997

Analysis of the cluster of ribosomal protein genes in the plastid genome of a unicellular red alga Cyanidioschyzon merolae: translocation of the str cluster as an early event in the rhodophyte-chromophyte lineage of plastid evolution.

The nucleotide sequence of a cluster of ribosomal protein genes in the plastid genome of a unicellular red alga, Cyanidioschyzon merolae, which has been supposed to be the most primitive alga, was determined. The phylogenetic tree inferred from the amino acid sequence of ribosomal proteins of two rhodophytes, a chromophyte, a glaucophyte, two chlorophytes (land plants), a cyanobacterium, and three eubacteria suggested a close relationship between the cyanobacterium Synechocystis PCC6803 and the plastids of various species in the kingdom Plantae, which is consistent with the hypothesis of the endosymbiotic origin of plastids. In this tree, the two species of rhodophytes were grouped with the chromophyte, and the glaucophyte was grouped with the chlorophytes. Analysis of the organization of the genes encoding the ribosomal proteins suggested that the translocation of the str cluster occurred early in the lineage of rhodophytes and chromophytes after these groups had been separated from chlorophytes and glaucophytes.

Cyanobacteria↗
PubMed2005

Epithelial progenitors in the normal human mammary gland.

The human mammary gland is organized developmentally as a hierarchy of progenitor cells that become progressively restricted in their proliferative abilities and lineage options. Three types of human mammary epithelial cell progenitors are now identified. The first is thought to be a luminal-restricted progenitor; in vitro under conditions that support both luminal and myoepithelial cell differentiation, this cell produces clones of differentiating daughter cells that are exclusively positive for markers characteristic of luminal cells produced in vivo (i.e., keratins 8/18 and 19, epithelial cell adhesion molecule [EpCAM] and MUC1). The second type is a bipotent progenitor. It is identified by its ability to produce "mixed" colonies in single cell assays. These colonies contain a central core of cells expressing luminal markers surrounded by cells with a morphology and markers (e.g., keratin 14(+)) characteristic of myoepithelial cells. Serial passage in vitro of an enriched population of bipotent progenitors promotes the expansion of a third type of progenitor that is thought to be myoepithelial-restricted because it only produces cells with myoepithelial features. Luminal-restricted and bipotent progenitors can prospectively be isolated as distinct subpopulations from freshly dissociated suspensions of normal human mammary cells. Both are distinguished from many other cell types in mammary tissue by their expression of EpCAM and CD49f (alpha6 integrin). They are distinguished from each other by their differential expression of MUC1, which is expressed at much higher levels on the luminal progenitors. To relate the role of these progenitors to the generation of the three-dimensional tubuloalveolar structure of the mammary tree produced in vivo, we propose a model in which the commitment to the luminal versus the myoepithelial lineage may play a determining role in the generation of alveoli and ducts.

Animals↗
PubMed2006

Genome histories clarify evolution of the expansin superfamily: new insights from the poplar genome and pine ESTs.

Expansins comprise a superfamily of plant cell wall-loosening proteins that has been divided into four distinct families, EXPA, EXPB, EXLA and EXLB. In a recent analysis of Arabidopsis thaliana and Oryza sativa expansins, we proposed a further subdivision of the families into 17 clades, representing independent lineages in the last common ancestor of monocots and eudicots. This division was based on both traditional sequence-based phylogenetic trees and on position-based trees, in which genomic locations and dated segmental duplications were used to reconstruct gene phylogeny. In this article we review recent work concerning the patterns of expansin evolution in angiosperms and include additional insights gained from the genome of a second eudicot species, Populus trichocarpa, which includes at least 36 expansin genes. All of the previously proposed monocot-eudicot orthologous groups, but no additional ones, are represented in this species. The results also confirm that all of these clades are truly independent lineages. Furthermore, we have used position-based phylogeny to clarify the history of clades EXPA-II and EXPA-IV. Most of the growth of the expansin superfamily in the poplar lineage is likely due to a recent polyploidy event. Finally, some monocot-eudicot clades are shown to have diverged before the separation of the angiosperm and gymnosperm lineages.

Arabidopsis↗
PubMed2004

Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (gamma-Proteobacteria).

Standard methods of phylogenetic reconstruction are based on models that assume homogeneity of nucleotide composition among taxa. However, this assumption is often violated in biological data sets. In this study, we examine possible effects of nucleotide heterogeneity among lineages on the phylogenetic reconstruction of a bacterial group that spans a wide range of genomic nucleotide contents: obligately endosymbiotic bacteria and free-living or commensal species in the gamma-Proteobacteria. We focus on AT-rich primary endosymbionts to better understand the origins of obligately intracellular lifestyles. Previous phylogenetic analyses of this bacterial group point to the importance of accounting for base compositional variation in estimating relationships, particularly between endosymbiotic and free-living taxa. Here, we develop an approach to compare susceptibility of various phylogenetic reconstruction methods to the effects of nucleotide heterogeneity. First, we identify candidate trees of gamma-Proteobacteria groEL and 16S rRNA using approaches that assume homogeneous and stationary base composition, including Bayesian, maximum likelihood, parsimony, and distance methods. We then create permutations of the resulting candidate trees by varying the placement of the AT-rich endosymbiont Buchnera. These permutations are evaluated under the nonhomogeneous and nonstationary maximum likelihood model of Galtier and Gouy, which allows equilibrium base content to vary among examined lineages. Our results show that commonly used phylogenetic methods produce incongruent trees of the Enterobacteriales, and that the placement of Buchnera is especially unstable. However, under a nonhomogeneous model, various groEL and 16S rRNA phylogenies that separate Buchnera from other AT-rich endosymbionts (Blochmannia and Wigglesworthia) have consistently and significantly higher likelihood scores. Blochmannia and Wigglesworthia appear to have evolved from secondary endosymbionts, and represent an origin of primary endosymbiosis that is independent from Buchnera. This application of a nonhomogeneous model offers a computationally feasible way to test specific phylogenetic hypotheses for taxa with heterogeneous and nonstationary base composition.

Animals↗
PubMed2002

Is cladogenesis heritable?

The heritability of speciation rates and extinction risks is a crucial parameter in models of macroevolution, but little direct evidence has been available to assess the occurrence, strength, or generality of this heritability. We tested for heritability using correlations between ancestral and descendent branch lengths in phylogenetic trees, an approach first applied to a bird phylogeny by Harvey et al. (1991, pages 123-137 in Genes in ecology [R. J. Berry et al., eds.], Blackwell Scientific, Oxford). We applied Harvey et al.'s test to some of the largest DNA sequence-based phylogenetic analyses published to date for plants, insects, fungi, and bacteria. If one of two parent lineages splits first and if this is the case for any heritable reason, then on average we expect its daughter lineages to also split first. We also used a randomization procedure to assess significance of branch length heritability. Using maximum parsimony and maximum likelihood branch lengths and trees made ultrametric after nonparametric rate smoothing or by enforcing a molecular clock, we found a pattern for most clades consistent with heritable net cladogenesis. Heritability of cladogenesis may be a general phenomenon, detectable across a large number of lineages and a broad range of taxa.

Animals↗
PubMedDate not supplied

The Wilhelmine E. Key 2001 Invitational Lecture. Estimation of divergence times for a few mammalian and several primate species.

Statistical methods for estimating divergence times by using multiprotein gamma distances are discussed. When a large number of proteins are used, even a small degree of deviation from the molecular clock hypothesis can be detected. In this case, one may use the stem-lineage method for estimating divergence times. However, the estimates obtained by this method are often similar to those obtained by the linearized tree method. Application of these methods to a dataset of 104 proteins from several vertebrate species indicated that the divergence times between humans and mice and between mice and rats are about 96 and 33 million years (MY) ago, respectively. These estimates were obtained by assuming that birds and mammals diverged 310 MY ago. Similarly application of the methods to the protein sequence data from primate species indicated that the human lineage separated from the chimpanzee, gorilla, Old World monkeys, and New World monkeys about 6.0, 7.0, 23.0, and 33.0 MY ago, respectively. In this case the use of two calibration points, that is, the divergence time (13 MY ago) between humans and orangutans and between primates and artiodactyls (90 MY ago) gave essentially the same estimates.

Animals↗
PubMed2004

Evolutionary relationships, cospeciation, and host switching in avian malaria parasites.

We used phylogenetic analyses of cytochrome b sequences of malaria parasites and their avian hosts to assess the coevolutionary relationships between host and parasite lineages. Many lineages of avian malaria parasites have broad host distributions, which tend to obscure cospeciation events. The hosts of a single parasite or of closely related parasites were nonetheless most frequently recovered from members of the same host taxonomic family, more so than expected by chance. However, global assessments of the relationship between parasite and host phylogenetic trees, using Component and ParaFit, failed to detect significant cospeciation. The event-based approach employed by TreeFitter revealed significant cospeciation and duplication with certain cost assignments for these events, but host switching was consistently more prominent in matching the parasite tree to the host tree. The absence of a global cospeciation signal despite conservative host distribution most likely reflects relatively frequent acquisition of new hosts by individual parasite lineages. Understanding these processes will require a more refined species concept for malaria parasites and more extensive sampling of parasite distributions across hosts. If parasites can disperse between allopatric host populations through alternative hosts, cospeciation may not have a strong influence on the architecture of host-parasite relationships. Rather, parasite speciation may happen more often in conjunction with the acquisition of new hosts followed by divergent selection between host lineages in sympatry. Detailed studies of the phylogeographic distributions of hosts and parasites are needed to characterize these events.

Animals↗
PubMed1999

Different models, different trees: the geographic origin of PTLV-I.

Using nucleotide sequences from three genomic regions of the human and simian T-cell lymphotropic virus type I (HTLV-I/STLV-I)-consisting of 69 sequences from a 140-bp segment of the pol region, 98 sequences from a 503-bp segment of the LTR, and 154 sequences from a 386-bp segment of the env region-we tested two hypotheses concerning the geographic origin and evolution of STLV-I and HTLV-I. First, we tested the assumption of equal rates of evolution along STLV-I and HTLV-I lineages using a likelihood ratio test to ascertain whether current levels of genomic diversity can be used to determine ancestry. We demonstrated that unequal rates of evolution along HTLV-I and STLV-I lineages have occurred throughout evolutionary time, thus calling into question the use of pairwise distances to assign ancestry. Second, we constructed phylogenetic trees using multiple phylogenetic techniques to test for the geographic origin of STLV-I and HTLV-I. Using the principle of likelihood, we chose a statistically justified model of evolution for each data set. We demonstrated the utility of the likelihood ratio test to determine which model of evolution should be chosen for phylogenetic analyses, revealing that using different models of evolution produces conflicting results, and neither the hypothesis of an African origin nor the hypothesis of an Asian origin can be rejected statistically. Our best estimates of phylogenetic relationships, however, support an African origin of PTLV for each gene region.

Animals↗
PubMed2003

Molecular circumscription of the hornworts (Anthocerotophyta) based on the chloroplast DNA trnL-trnF region.

In phylogenetic trees generated from partial trnL(UAA) intron sequences, the hornworts (represented by nine species from the genera Anthoceros, Dendroceros, Megaceros, Notothylas and Phaeoceros) are resolved as a monophyletic group and are separated from the clades of mosses, liverworts and tracheophytes. A secondary structure of the trnL(UAA) intron of Anthoceros agrestis is presented, displaying the arrangement of the stem-loop regions P1-P9. Compensatory base-pair changes (coevolutionary sites) are detected in regions P4/5 and P9 within the hornwort sequences. The original homology of the most variable region, P8, cannot be detected anymore due to the extremely fast divergent evolution of this segment in the major land plant groups. Similarly, a high sequence divergence occurs in the trnL-trnF intergenic spacer. Apart from synapomorphic substitutions in the trnL(UAA) intron, the hornworts are characterised by a large P6 region consisting of many repetitive elements. The molecular data therefore support the hornworts as representing an independent land plant lineage (Anthocerotophyta). Although relationships between hornworts and the other land plant groups remain unresolved in the trnL(UAA) intron trees, it is rather unlikely that bryophytes are monophyletic in their traditional circumscription, i.e. comprising hornworts, mosses and liverworts.

Anthocerotophyta↗
PubMed2002

Differences in pyrenoid morphology are correlated with differences in the rbcL genes of members of the Chloromonas lineage (volvocales, chlorophyceae).

Chloromonas is distinguished from Chlamydomonas primarily by the absence of pyrenoids, which are structures that are present in the chloroplasts of most algae and are composed primarily of the CO2-fixing enzyme Rubisco. In this study we compared sequences of the rbcL (Rubisco large subunit-encoding) genes of pyrenoid-less Chloromonas species with those of closely related pyrenoid-containing Chlamydomonas species in the "Chloromonas lineage" and with those of 45 other green algae. We found that the proteins encoded by the rbcL genes had a much higher level of amino acid substitution in members of the Chloromonas lineage than they did in other algae. This kind of elevated substitution rate was not observed, however, in the deduced proteins encoded by two other chloroplast genes that we analyzed: atpB and psaB. The rates of synonymous and nonsynonymous nucleotide substitutions in the rbcL genes indicate that the rapid evolution of these genes in members of the Chloromonas lineage is not due to relaxed selection (as it presumably is in parasitic land plants). A phylogenetic tree based on rbcL nucleotide sequences nested two Chlamydomonas species as a "pyrenoid-regained" clade within a monophyletic Chloromonas "pyrenoid-lost" clade. Character-state optimization with this tree suggested that the loss and the regain of pyrenoids were accompanied by eight synapomorphic amino acid replacements in the Rubisco large subunit, four of which are positioned in the region involved in its dimerization. However, both the atpB and the psaB sequence data gave robust support for a rather different set of phylogenetic relationships in which neither the "pyrenoid-lost" nor the "pyrenoid-regained" clade was resolved. The appearance of such clades in the rbcL-based tree may be an artifact of convergent evolutionary changes that have occurred in a region of the large subunit that determines whether Rubisco molecules will aggregate to form a visible pyrenoid.

Amino Acid Substitution↗