Molecular Genetics of Spectral Tuning in New World Monkey Color Vision

Although most New World monkeys have only one X-linked photopigment locus, many species have three polymorphic alleles at the locus. The three alleles in the squirrel monkey and capuchin have spectral peaks near 562, 550, and 535 nm, respectively, and the three alleles in the marmoset and tamarin have spectral peaks near 562, 556, and 543 nm, respectively. To determine the amino acids responsible for the spectral sensitivity differences among these pigment variants, we sequenced all exons of the three alleles in each of these four species. From the deduced amino acid sequences and the spectral peak information and from previous studies of the spectral tuning of X-linked pigments in humans and New World monkeys, we estimated that the Ala → Ser, Ile → Phe, Gly → Ser, Phe → Tyr, and Ala → Tyr substitutions at residue positions 180, 229, 233, 277, and 285, respectively, cause spectral shifts of about 5, −2, −1, 8, and 15 nm. On the other hand, the substitutions His → Tyr, Met → Val or Leu, and Ala → Tyr at positions 116, 275, and 276, respectively, have no discernible spectral tuning effect, though residues 275 and 276 are inside the transmembrane domains. Many substitutions between Val and Ile or between Val and Ala have occurred in the transmembrane domains among the New World monkey pigment variants but apparently have no effect on spectral tuning. Our study suggests that, in addition to amino acid changes involving a hydroxyl group, large changes in residue size can also cause a spectral shift in a visual pigment. Received: 17 July 1997 / Accepted: 7 December 1997     

Evolution of Microsatellite Alleles in Four Species of Mice (Genus Apodemus)

Microsatellite length variation was investigated at a highly variable microsatellite locus in four species of Apodemus. Information obtained from microsatellite allele sequences was contrasted with allele sizes, which included 18 electromorphs. Additional analysis of a 400-bp unique sequence in the flanking region identified 26 different haplotype sequences or ``true' alleles in the sample. Three molecular mechanisms, namely, (1) addition/deletion of repeats, (2) substitutions and indels in the flanking region, and (3) mutations interrupting the repeat, contributed to the generation of allelic variation. Size homoplasy can be inferred for alleles within populations, from different populations of the same species, and from different species. We propose that microsatellite flanking sequences may be informative markers for investigating mutation processes in microsatellite repeats as well as phylogenetic relationships among alleles, populations, and species. Received: 3 November 1999 / Accepted: 2 May 2000     

Microsatellite Evolution: Testing the Ascertainment Bias Hypothesis

Previous studies suggest the median allele length of microsatellites is longest in the species from which the markers were derived, suggesting that an ascertainment bias was operating. We have examined whether the size distribution of microsatellite alleles between sheep and cattle is source dependent using a set of 472 microsatellites that can be amplified in both species. For those markers that were polymorphic in both species we report a significantly greater number of markers (P < 0.001) with longer median allele sizes in sheep, regardless of microsatellite origin. This finding suggests that any ascertainment bias operating during microsatellite selection is only a minor contributor to the variation observed. Received: 6 January 1997 / Accepted: 19 May 1997     

Unexpected Conservation of the X-Linked Color Vision Gene in Nocturnal Prosimians: Evidence from Two Bush Babies

Bush babies have had a long history of nocturnal life and it would be interesting to know whether their color vision genes have become degenerate. Therefore, we used PCR techniques to sequence the X-linked pigment gene of two of these nocturnal prosimians: Galago senegalensis and Otolemur garnettii. Southern hybridization of genomic DNA of G. senegalensis showed a single X-linked pigment gene. Interestingly, the deduced pigment sequences of the two bush babies are identical. By comparing the X-linked pigments of bush baby, human, squirrel monkey, and marmoset, 38 variable positions were identified. At those positions that may cause a spectral shift, the bush baby pigment has identical or biochemically similar residues to those of the marmoset cone pigment with a spectral peak of 543 nm. This result is consistent with the estimate of 544–545 nm for the spectral peak of the X-linked pigment of Otolemur crassicaudatus, which is closely related to Otolemur garnettii. The neighbor-joining tree of mammalian X-linked pigments showed a significantly shorter branch in the bush baby lineage than in other primate lineages. A relative rate test showed that the nonsynonymous substitution rate of the bush baby X-linked pigment gene is about three times slower than that of the human red pigment gene, though the synonymous substitution rates of the two genes are similar. The slower nonsynonymous rate in the bush baby lineage suggests that the bush baby X-linked pigment gene is under functional constraints, in spite of its nocturnal life. Two radical changes at positions in the intradiskal surface next to the sixth transmembrane domain were observed in the X-linked cone pigment of bush babies but not in other primates. They are changes from Ala to Ser and from Asn to His, which are similar in function to the corresponding residues in rhodopsins. These two changes may be of importance for dim light sensitivity, which is consistent with our proposal that the evolution of the bush baby X-linked pigment gene is under selective pressure. In addition, the 2.5% divergence in introns 2 and 5 of the X-linked pigment gene between the two bush babies supports their classification into two separate genera. Received: 30 November 1996 / Accepted: 17 June 1997     

Ancient Origin of the Null Allele se 428 of the Human ABO-Secretor Locus (FUT2)

In human populations, a null allele having several nucleotide differences from the wild-type allele is segregating at the FUT2 locus (the ABO-Secretor locus) encoding α(1,2)fucosyltransferase. To estimate the age of the most recent common ancestor (MRCA) of these two alleles, we sequenced FUT2 homologues from chimpanzee, gorilla, orangutan, and green monkey. Since we did not detect acceleration or any heterogeneity in the substitution rate at this locus among these species, the age of the MRCA was estimated to be around 3 MYA, assuming the divergence time of human and chimpanzee to be 5 MYA. We developed a simple test to examine whether or not the old age of the MRCA of the FUT2 is consistent with that expected for two divergent neutral alleles sampled from a random mating population. An application of the test to the data at FUT2 indicated that the age of the MRCA is too old to be explained by the simple neutral assumptions, although our test depends on accurate estimation of the divergence time of human and chimpanzee in units of twice the human population size. Various possibilities including balancing selection are discussed to explain this old age of the MRCA. Received: 9 May 1999 / Accepted: 20 September 1999     

Allelic Diversity at the het-c Locus in Neurospora tetrasperma Confirms Outcrossing in Nature and Reveals an Evolutionary Dilemma for Pseudohomothallic Ascomycetes

Vegetative cells of the filamentous ascomycete Neurospora tetrasperma are typically heterokaryotic, possessing haploid nuclei of both A and a mating types. As a consequence, N. tetrasperma is self-fertile. This life cycle, referred to as pseudohomothallism, clearly derives from true heterothallism of the type exhibited by related species such as N. crassa. Occasional homokaryotic, single-mating-type (heterothallic) isolates occur; in the laboratory, such strains can be outcrossed. The potential for outcrossing in N. tetrasperma raises the question of how this organism avoids heterokaryon incompatibility. Heterokaryon incompatability in vegetatively growing fungi is controlled by multiple loci. Two strains must be identical at each het locus (11 in N. crassa) to form a stable heterokaryon. Prior to the present survey, it seemed plausible that N. tetrasperma avoids heterokaryon incompatibility by maintaining compatible allele combinations through continual selfing. A survey of het-c variation among wild-type isolates in this study demonstrated that N. tetrasperma outcrosses in nature and that such matings can result in incompatible combinations of het-c alleles. Whereas individual wild-type isolates are invariably homoallelic for het-c, closely related strains may possess functionally different het-c alleles, which predate the origin of N. tetrasperma. Therefore, pseudohomothallic ascomycetes such as N. tetrasperma face an apparent evolutionary dilemma: the benefits of outcrossing must be balanced against the fact that matings can produce unstable heterokaryons and disrupt the pseudohomothallic life cycle. Received: 22 October 1999 / Accepted: 7 September 2000     

Evolutionary History of MHC Class I Genes in the Mammalian Order Perissodactyla

We carried out an analysis of partial sequences from expressed major histocompatibility complex (MHC) class I genes isolated from a range of equid species and more distantly related members of the mammalian order Perissodactyla. Phylogenetic analysis revealed a minimum of six groups, five of which contained genes and alleles that are found in equid species and one group specific to the rhinoceros. Four of the groups contained only one, or very few sequences, indicating the presence of relatively nonpolymorphic loci, while another group contained the majority of the equid sequences identified. These data suggest that a diversification of MHC genes took place after the split between the Equidae and the Rhinocerotidae yet before the speciation events within the genus Equus. Received: 17 November 1998 / Accepted: 7 April 1999     

Evaluation of Sequence Variation and Selection in the Bindin Locus of the Red Sea Urchin, Strongylocentrotus franciscanus

Recent evidence suggests that gamete recognition proteins may be subjected to directed evolutionary pressure that enhances sequence variability. We evaluated whether diversity enhancing selection is operating on a marine invertebrate fertilization protein by examining the intraspecific DNA sequence variation of a 273-base pair region located at the 5′ end of the sperm bindin locus in 134 adult red sea urchins (Strongylocentrotus franciscanus). Bindin is a sperm recognition protein that mediates species-specific gamete interactions in sea urchins. The region of the bindin locus examined was found to be polymorphic with 14 alleles. Mean pairwise comparison of the 14 alleles indicates moderate sequence diversity (p-distance = 1.06). No evidence of diversity enhancing selection was found. It was not possible to reject the null hypothesis that the sequence variation observed in S. franciscanus bindin is a result of neutral evolution. Statistical evaluation of expected proportions of replacement and silent nucleotide substitutions, observed versus expected proportions of radical replacement substitutions, and conformance to the McDonald and Kreitman test of neutral evolution all indicate that random mutation followed by genetic drift created the polymorphisms observed in bindin. Observed frequencies were also highly similar to results expected for a neutrally evolving locus, suggesting that the polymorphism observed in the 5′ region of S. franciscanus bindin is a result of neutral evolution. Received: 19 June 1998 / Accepted: 2 August 2000     

Variation of Microsatellite Size Homoplasy Across Electromorphs, Loci, and Populations in Three Invertebrate Species

Size homoplasy was analyzed at microsatellite loci by sequencing electromorphs, that is, variants of the same size (base pairs). This study was conducted using five interrupted and/or compound loci in three invertebrate species, the honey bee Apis mellifera, the bumble bee Bombus terrestris, and the freshwater snail Bulinus truncatus. The 15 electromorphs sequenced turned out to hide 31 alleles (i.e., variants identical in sequence). Variation in the amount of size homoplasy was detected among electromorphs and loci. From one to seven alleles were detected per electromorph, and one locus did not show any size homoplasy in both bee species. The amount of size homoplasy was related to the sequencing effort, since the number of alleles was correlated with the number of copies of electromorphs sequenced, but also with the molecular structure of the core sequence at each locus. Size homoplasy within populations was detected only three times, meaning that size homoplasy was detected mostly among populations. We analyzed population structure, estimating F _st and a genetic distance, based on either electromorphs or alleles. Whereas little difference was found in A. mellifera, uncovering size homoplasy led to a more marked population structure in B. terrestris and B. truncatus. We also showed in A. mellifera that the detection of size homoplasy may alter phylogenetic reconstructions. Received: 21 July 1997 / Accepted: 29 January 1998     

Absence of Protein Polymorphism in the Ras Genes of Drosophila melanogaster

Sequence analysis of 27 alleles of each of the three Ras-related genes in Drosophila melanogaster indicates that they all have low levels of polymorphism but may experience slightly different evolutionary pressures. No amino acid replacement substitutions were indicated in any of the sequences, or in the sibling species D. simulans and D. mauritiana. The Dras1 gene, which is the major ras homologue in Drosophila, has less within-species variation in D. melanogaster relative to the amount of divergence from the sibling species than does Dras2, although the contrast was not significant by the HKA test. Dras2 appears to be maintaining two classes of haplotype in D. melanogaster, one of which is closer to the alleles observed in the sibling species, suggesting that this is not likely to be a pseudogene despite the absence of a mutant phenotype. Although differences in level of expression may affect the function of the genes, it is concluded that genetic variation in the Ras signal transduction pathways cannot be attributed to catalytic variation in the Ras proteins. Received: 5 November 1998 / Accepted: 26 March 1999     

The Geographic Distribution of Monoamine Oxidase Haplotypes Supports a Bottleneck During the Dispersion of Modern Humans from Africa

Every genetic locus mingles the information about the evolutionary history of the human species with the history of its own evolution. Therefore, to address the question of the origin of humans from a genetic point of view, evolutionary histories from many genetic loci have to be gathered and compared. We have studied two genes residing on the X chromosome encoding monoamine oxidases A and B (MAOA and MAOB). Both genes have been suggested to play a role in psychiatric and/or behavioral traits. To search for DNA variants of the MAO genes, the sequences of exonic and flanking intronic regions of these two genes were determined in a group of Swedish males. The sequence analysis revealed several novel polymorphisms in the MAO genes. Haplotypes containing high-frequency MAOA polymorphisms were constructed, and their frequencies were determined in additional samples from Caucasian, Asian, and African populations. We found two common haplotypes with similar frequencies in Caucasian and Asian populations. However, only one of them was also the most frequent haplotype in Africans, while the other haplotype was present in only one Kenyan male. This profound change in haplotype frequencies from Africans to non-Africans supports a possible bottleneck during the dispersion of modern humans from Africa. Received: 19 April 2000 / Accepted: 9 October 2000     

Six Opsins from the Butterfly Papilio glaucus: Molecular Phylogenetic Evidence for Paralogous Origins of Red-Sensitive Visual Pigments in Insects

It has been hypothesized that the UV-, blue-, and green-sensitive visual pigments of insects were present in the common ancestor of crustaceans and insects, whereas red-sensitive visual pigments evolved later as a result of convergent evolution. This hypothesis is examined with respect to the placement of six opsins from the swallowtail butterfly Papilio glaucus (PglRh1–6) in relationship to 46 other insect, crustacean, and chelicerate opsin sequences. All basal relationships established with maximum parsimony analysis except two are present in the distance and maximum likelihood analyses. In all analyses, the six P. glaucus opsins fall into three well-supported clades, comprised, respectively, of ultraviolet (UV), blue, and long-wavelength (LW) pigments, which appear to predate the radiation of the insects. Lepidopteran green- and red-sensitive visual pigments form a monophyletic clade, which lends support to the hypothesis from comparative physiological studies that red-sensitive visual pigments in insects have paralogous origins. Polymorphic amino acid sites (180, 197, 277, 285, 308), which are essential for generating the spectral diversity among the vertebrate red- and green-sensitive pigments are notably invariant in the Papilio red- and green-sensitive pigments. Other major tuning sites must be sought to explain the spectral diversification among these and other insect visual pigments. Received: 6 December 1999 / Accepted: 3 April 2000     

Multiple Origins of Cyclodiene Insecticide Resistance in Tribolium castaneum (Coleoptera: Tenebrionidae)

The number of origins of pesticide resistance-associated mutations is important not only to our understanding of the evolution of resistance but also in modeling its spread. Previous studies of amplified esterase genes in a highly dispersive Culex mosquito have suggested that insecticide resistance-associated mutations (specifically a single-gene duplication event) can occur a single time and then spread throughout global populations. In order to provide data for resistance-associated point mutations, which are more typical of pesticide mechanisms as a whole, we studied the number of independent origins of cyclodiene insecticide resistance in the red flour beetle Tribolium castaneum. Target-site insensitivity to cyclodienes is conferred by single point mutations in the gene Resistance to dieldrin (Rdl), which codes for a subunit of a γ-aminobutyric acid (GABA) receptor. These point mutations are associated with replacements of alanine 302 which render the receptor insensitive to block by the insecticide. We collected 141 strains of Tribolium worldwide and screened them for resistance. Twenty-four strains contained resistant individuals. After homozygosing 23 of these resistance alleles we derived a nucleotide sequence phylogeny of the resistant strains from a 694-bp section of Rdl, encompassing exon 7 (which contains the resistance-associated mutation) and part of a flanking intron. The phylogeny also included six susceptible alleles chosen at random from a range of geographical locations. Resistance alleles fell into six clades and three clades contained both resistant and susceptible alleles. Although statistical analysis provided support at only the 5–6% level, the pattern of variation in resistance alleles is more readily explained by multiple independent origins of resistance than by spread of a single resistance-associated mutation. For example, two resistance alleles differed from two susceptible alleles only by the resistance-associated mutation itself, suggesting that they form the susceptible ancestors and that resistance arose independently in several susceptible backgrounds. This suggests that in Tribolium Rdl, de novo mutations for resistance have arisen independently in several populations. Identical alleles were found in geographically distant regions as well, also implying that some Rdl alleles have been exported in stored grain. These differences from the Culex study may stem both from differences in the population genetics of Tribolium versus that of mosquitoes and differences in mutation rates associated with point mutations versus gene duplication events. The Tribolium data therefore suggest that multiple origins of insecticide resistance (associated with specific point mutations) may be more common than the spread of single events. These findings have implications for the way in which we model the evolution and spread of insecticide resistance genes and also suggest that parallel adaptive substitutions may not be uncommon in phyletic evolution. Received: 14 October 1998 / Accepted: 4 January 1999     

MHC (Major Histocompatibility Complex)-DRB Genes and Polymorphisms in Common Marmoset

A New World monkey, the common marmoset (Callithrix jacchus), will be used as a preclinical animal model to study the feasibility of cell and gene therapy targeting immunological and hematological disorders. For elucidating the immunogenetic background of common marmoset to further studies, in the present study, polymorphisms of MHC-DRB genes in this species were examined. Twenty-one Caja-DRB exon 2 alleles, including seven new ones, were detected by means of subcloning and the polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) methods followed by nucleotide sequencing. Based on the alignment of these allele sequences, we designed two pairs of specific primers and established a PCR-SSCP method for DNA-based histocompatibility typing of the common marmoset. According to the family segregation data and phylogenetic analyses, we presumed that Caja-DRB alleles could be classified into five different loci. Southern blotting analysis also supported the existence of multiple DRB loci. The patterns of nucleotide substitutions suggests that positive selection operates in the antigen-recognition sites of Caja-DRB genes. Received: 18 February 2000 / Accepted: 17 May 2000     

The Codon-Degeneracy Model of Molecular Evolution

Mitochondrial genetic codons can be categorized by four patterns of nucleotide-site degeneracy based on varying combinations of twofold- or nondegenerate sites at first codon positions and twofold- or fourfold-degenerate sites at third codon positions. Herein, a model of molecular evolution is introduced that uses these patterns to calculate expected substitution frequencies for each codon position and substitution type relative to overall number of synonymous or nonsynonymous substitutions. Regions of the pocket gopher cytochrome oxidase subunit I (COI) and cytochrome b (cyt-b) genes are analyzed using this model. Chi-square distributions are used to produce relative goodness-of-fit (GF) scores for measuring the difference between substitution frequencies predicted by the codon-degeneracy model (CDM), and frequencies inferred using a well-supported phylogenetic tree of closely related species. The GF scores for expected and observed synonymous (GF_syn= 0.429, p= 0.807) and nonsynonymous (GF_ns= 2.309, p= 0.679) substitution frequencies resulted in a failure to reject the CDM as a null hypothesis for the molecular evolution of COI and cyt-b in pocket gophers. Alternative tree topologies and calculations of transition bias for these data result in higher GF scores. Received: 25 March 1999 / Accepted: 17 September 1999     

Sequence diversity and molecular evolution of the merozoite surface antigen 2 of plasmodium falciparum

Eleven new alleles of the Plasmodium falciparum merozoite surface antigen 2 (MSA2) from Papua New Guinea were analyzed by direct sequencing of polymerase chain reaction (PCR) products. We have used the sequence information to trace the molecular evolution of MSA2. The repeats of ten alleles belonging to the 3D7 allelic family differed considerably in size, nucleotide sequence, and repeat copy number. In the repeat region of these new alleles, codon usage was extremely biased with an exclusive use of NNT codons. Another new allele sequenced belonged to the FC27 family and confirmed the family-specific conserved structure of 96 and 36 bp repeats. In order to assess sequence microheterogeneity within samples defined as the same genotype by restriction fragment length polymorphism (RFLP), we have analyzed single-strand conformation polymorphism (SSCP) of different samples of the most frequent allele (D10 of the FC27 family) in the study population. No sequence heterogeneity could be detected within the repeat region. Based on analysis of the repeat regions in both allelic families, we discuss the hypothesis of a different evolutionary strategy being represented by each of the allelic families. Received: 8 February 1995 / Accepted: 24 March 1997     

Analysis of Orthologous Retrovirus-Like Elements in the White-Footed Mouse,Peromyscus leucopus

Three loci in the genome of the white-footed mouse, Peromyscus leucopus, were examined for the presence or absence of orthologous copies of the retrovirus-like element mys using polymerase chain reaction. We examined these loci in 28 mice collected throughout the P. leucopus species range. Mys insertions were present in only one of the individuals examined at the mys-1 and mys-7 loci. Conversely, the mys-6 element was found in several individuals, but the presence of this element was limited to northern latitudes. Because the long terminal repeats (LTRs) of a given element are expected to be identical at the time of retrotransposition into the genome, and to accumulate changes over evolutionary time, within-element LTR sequence comparisons can be used to estimate the relative age of insertions. Within-element LTR differences are greater in mys-6 than in mys-1 or mys-7. The LTRs from orthologous mys-6 elements of six mice were sequenced. The alignment revealed 13 of the 22 differences between the right and left LTRs that were shared by all orthologous mys-6 sites, suggesting that relative to its time of insertion into the genome, mys-6 has only recently spread across the northern part of the species range. Received: 23 January 1996 / Accepted: 24 April 1996     

Speciation Versus Phenotypic Plasticity in Coral Inhabiting Barnacles: Darwin's Observations in an Ecological Context

Speciation and phenotypic plasticity are two extreme strategic modes enabling a given taxon to populate a broad ecological niche. One of the organismal models which stimulated Darwin's ideas on speciation was the Cirripedia (barnacles), to which he dedicated a large monograph. In several cases, including the coral-inhabiting barnacle genera Savignium and Cantellius (formerly Pyrgoma and Creusia, respectively), Darwin assigned barnacle specimens to morphological ``varieties' (as opposed to species) within a genus. Despite having been the subject of taxonomic investigations and revisions ever since, the significance of these varieties has never been examined with respect to host-associated speciation processes. Here we provide evidence from molecular (12S mt rDNA sequences) and micromorphological (SEM) studies, suggesting that these closely related barnacle genera utilize opposite strategies for populating a suite of live-coral substrates. Cantellius demonstrates a relatively low genetic variability, despite inhabiting a wide range of corals. The species C. pallidus alone was found on three coral families, belonging to distinct higher-order classification units. In contrast, Savignium barnacles exhibit large between- and within-species variations with respect to both micromorphology and DNA sequences, with S. dentatum ``varieties' clustering phylogenetically according to their coral host species (all of which are members of a single family). Thus, whereas Savignium seems to have undergone intense host-associated speciation over a relatively narrow taxonomic range of hosts, Cantellius shows phenotypic plasticity over a much larger range. This dichotomy correlates with differences in life-history parameters between these barnacle taxa, including host-infestation characteristics, reproductive strategies, and larval trophic type. Received: 18 January 1999 / Accepted: 9 May 1999     

The association between HLA-A alleles and an Alu dimorphism near HLA-G

The AluYb8 sequences are a subfamily of short interspersed Alu retroelements that have been amplified within the human genome during recent evolutionary time and are useful polymorphic markers for studies on the origin of human populations. We have identified a new member of the Yb8 subfamily, AluyHG, located between the HLA-H and -G genes and 88-kb telomeric of the highly polymorphic HLA-A gene within the alpha block of the major histocompatibility complex (MHC). The AluyHG element was characterised with a view to examining the association between AluyHG and HLA-A polymorphism and reconstructing the history of the MHC alpha block. A specific primer pair was designed for a simple PCR assay to detect the absence or presence (dimorphism) of the AluyHG element within the DNA samples prepared from a panel of 46 homozygous cell-lines containing complete or recombinant ancestral haplotypes (AH) of diverse ethnic origin and 92 Caucasoid and Asian subjects on which HLA-A typing was available. The AluyHG insertion was most strongly associated with HLA-A2 and, to a lesser degree with HLA-A1, -A3, -A11, and A-19. The gene frequency of the AluyHG insertion for 146 Caucasians and 94 Chinese-Han was 0.30 and 0.32 and there was no significant difference between the observed and expected frequencies. The results of the association studies and the phylogenetic analysis of HLA-A alleles suggest that the AluyHG sequence was integrated within the progenitor of HLA-A2, but has been transferred by recombination to other human ancestral populations. In this regard, the dimorphic AluyHG element is an important diagnostic marker for HLA association studies and could help in elucidating the evolution and functions of the MHC alpha block and polymorphism within and between ancestral haplotypes. Received: 7 December 2000 / Accepted: 28 February 2001