Do albumin clocks run on time?

2020 William Allan Award address: genetics as a way of thinking-cultural inheritance from our teachers

This article is based on the address given by the author at the 2020 virtual meeting of The American Society of Human Genetics (ASHG) on October 26, 2020. The video of the original address can be found at the ASHG website.

EVOLUTION OF ATLANTIC AND PACIFIC COD: LOSS OF GENETIC VARIATION AND GENE EXPRESSION IN PACIFIC COD

An allozyme investigation of 41 protein-coding loci in two morphologically similar fishes, Atlantic and Pacific cod, indicates that Pacific cod experienced a severe population bottleneck that led to the loss of gene diversity and gene expression. Pacific cod possesses a significantly lesser amount of gene diversity (H = 0.032) than Atlantic cod (H = 0.125) and lacks gene expression for Me-3. Allele-frequency distributions differ between species as predicted by neutral theory: Atlantic cod has a U-shaped distribution, which is expected for populations in drift-mutation equilibrium, whereas Pacific cod has a J-shaped distribution with an excess of low-frequency alleles. This excess may be explained by the appearance of new alleles through mutation which have not yet reached intermediate frequencies through drift. The population bottleneck in Pacific cod was most likely associated with founder populations that dispersed into the Pacific Ocean after the Bering Strait opened. Under the molecular-clock hypothesis a Nei genetic distance of 0.415 (based on 41 loci) suggests that Pacific cod dispersed into the Pacific Ocean soon after the Bering Strait opened in the mid-Pliocene, 3.0 to 3.5 million years ago.

Mitochondrial DNA sequences support allozyme evidence for cryptic radiation of New Zealand Peripatoides (Onychophora)

A combination of single-strand conformation polymorphism analysis (SSCP) and sequencing were used to survey cytochrome oxidase I (COI) mitochondrial DNA (mtDNA) diversity among New Zealand ovoviviparous Onychophora. Most of the sites and individuals had previously been analysed using allozyme electrophoresis. A total of 157 peripatus collected at 54 sites throughout New Zealand were screened yielding 62 different haplotypes. Comparison of 540-bp COI sequences from Peripatoides revealed mean among-clade genetic distances of up to 11. 4% using Kimura 2-parameter (K2P) analysis or 17.5% using general time-reversible (GTR + I + Gamma) analysis. Phylogenetic analysis revealed eight well-supported clades that were consistent with the allozyme analysis. Five of the six cryptic peripatus species distinguished by allozymes were confirmed by mtDNA analysis. The sixth taxon appeared to be paraphyletic, but genetic and geographical evidence suggested recent speciation. Two additional taxa were evident from the mtDNA data but neither occurred within the areas surveyed using allozymes. Among the peripatus surveyed with both mtDNA and allozymes, only one clear instance of recent introgression was evident, even though several taxa occurred in sympatry. This suggests well-developed mate recognition despite minimal morphological variation and low overall genetic diversity.

Diagnostic genetic markers and evolutionary relationships among invasive dreissenoid and corbiculoid bivalves in North America: phylogenetic signal from mitochondrial 16S rDNA

Diagnostic genetic markers from 486 aligned nucleotide sequences of mitochondrial 16S ribosomal DNA were developed for the four closely related species of dreissenoid and corbiculoid bivalves that have invaded North America; the zebra mussel Dreissena polymorpha, the quagga mussel D. bugensis, and the dark false mussel Mytilopsis leucophaeata of the superfamily Dreissenoidea, and the Asian clam Corbicula fluminea of the sister superfamily Corbiculoidea. Evolutionary relationships were examined among the four genera and comparisons were made with native Eurasian populations of D. polymorpha and D. bugensis. Tests were conducted for gender-specific mitochondrial lineages, which occur in some other bivalves. Genetic variability and divergence rates were tested between stem (paired) and loop (unpaired) regions of secondary structure. There were 251 variable nucleotide sites, of which 99 were phylogenetically informative. Overall transition to transversion ratio was 0.76:1.00 and both accumulated linearly in stem and loop regions, suggesting appropriate phylogenetic signal. Genetic distance calibration with the fossil record estimated the pairwise sequence divergence as 0. 0057 +/- 0.0004 per million years. Mytilopsis and Dreissena appear to have diverged about 20.7 +/- 2.7 million years ago. D. bugensis and D. polymorpha appear separated by about 13.2 +/- 2.2 million years. No intraspecific variation was found, including between Eurasian and North American populations, among shallow and deep morphotypes of D. bugensis and between the sexes. Restriction endonuclease markers were developed to distinguish among the species at all life history stages, allowing rapid identification in areas of sympatric distribution.

An electrophoretic analysis of phylogeny and evolutionary rates in the genus Partula from the Society Islands

A study of allozymes in 30 species from the three genera of snails in the family Partulidae was undertaken to examine the phylogeny of, and evolutionary rates in, the genus Partula from the Society Islands, French Polynesia. Genetic identities ( I ) between congeneric species are generally high, with 42% of the I values being greater than 0.85, and 24% above 0.90. Levels of allozymic similarity are therefore of little use for inferences about reproductive relationships. Identities between species from the same island are particularly high, and phylogenetic analysis suggests that the radiation of Partula in the Society Islands can be accounted for by a single colonization of each island. In general, the inferred sequence of colonization is consistent with geological information about the origins of these volcanic islands. The phylogeny, and the ages of the islands, suggest an average rate of allozymic divergence (change in Nei’s D ) of 0.126 per million years. The threefold variation in estimated rates of change within Partula , and the comparison of our results with estimates from other taxa, suggest that the ‘molecular clock’ in Partula is erratic.

Evolution of the cytochrome b gene of mammals

With the polymerase chain reaction (PCR) and versatile primers that amplify the whole cytochrome b gene (approximately 1140 bp), we obtained 17 complete gene sequences representing three orders of hoofed mammals (ungulates) and dolphins (cetaceans). The fossil record of some ungulate lineages allowed estimation of the evolutionary rates for various components of the cytochrome b DNA and amino acid sequences. The relative rates of substitution at first, second, and third positions within codons are in the ratio 10 to 1 to at least 33. For deep divergences (greater than 5 million years) it appears that both replacements and silent transversions in this mitochondrial gene can be used for phylogenetic inference. Phylogenetic findings include the association of (1) cetaceans, artiodactyls, and perissodactyls to the exclusion of elephants and humans, (2) pronghorn and fallow deer to the exclusion of bovids (i.e., cow, sheep, and goat), (3) sheep and goat to the exclusion of other pecorans (i.e., cow, giraffe, deer, and pronghorn), and (4) advanced ruminants to the exclusion of the chevrotain and other artiodactyls. Comparisons of these cytochrome b sequences support current structure-function models for this membrane-spanning protein. That part of the outer surface which includes the Qo redox center is more constrained than the remainder of the molecule, namely, the transmembrane segments and the surface that protrudes into the mitochondrial matrix. Many of the amino acid replacements within the transmembrane segments are exchanges between hydrophobic residues (especially leucine, isoleucine, and valine). Replacement changes at first and second positions of codons approximate a negative binomial distribution, similar to other protein-coding sequences. At four-fold degenerate positions of codons, the nucleotide substitutions approximate a Poisson distribution, implying that the underlying mutational spectrum is random with respect to position.

Compositional transitions in the nuclear genomes of cold-blooded vertebrates

The compositional properties of DNAs from 122 species of fishes and from 18 other cold-blooded vertebrates (amphibians and reptiles) were compared with those from 10 warm-blooded vertebrates (mammals and birds) and found to be substantially different. Indeed, DNAs from cold-blooded vertebrates are characterized by much lower intermolecular compositional heterogeneities and CsCl band asymmetries, by a much wider spectrum of modal buoyant densities in CsCl, by generally lower amounts of satellites, as well as by the fact that in no case do buoyant densities reach the high values found in the GC-richest components of DNAs from warm-blooded vertebrates. In the case of fish genomes, which were more extensively studied, different orders were generally characterized by modal buoyant densities that were different in average values as well as in their ranges. In contrast, different families within any given order were more often characterized by narrow ranges of modal buoyant densities, and no difference in modal buoyant density was found within any single genus (except for the genus Aphyosemion, which should be split into several genera). The compositional differences that were found among species belonging to different orders and to different families within the same order are indicative of compositional transitions, which were shown to be essentially due to directional base substitutions. These transitions were found to be independent of geological time. Moreover, the rates of directional base substitutions were found to be very variable and to reach, in some cases, extremely high values, that were even higher than those of silent substitutions in primates. The taxonomic and evolutionary implications of these findings are discussed.

Nuclear and mitochondrial DNA comparisons reveal extreme rate variation in the molecular clock

The discovery that the rate of evolution of vertebrate mitochondrial DNA is rapid, compared to the rate for vertebrate nuclear DNA, has resulted in its widespread use in evolutionary studies. Comparison of mitochondrial and nuclear DNA divergences among echinoid and vertebrate taxa of similar ages indicates that the rapid rate of vertebrate mitochondrial DNA evolution is, in part, an artifact of a widely divergent rate of nuclear DNA evolution. This disparity in relative rates of mitochondrial and nuclear DNA divergence suggests that the controls and constraints under which the mitochondrial and nuclear genomes operate are evolving independently, and provides evidence that is independent of fossil dating for a robust rejection of a generalized molecular clock hypothesis of DNA evolution.

Ancient origin for Hawaiian Drosophilinae inferred from protein comparisons

Immunological comparisons of a larval hemolymph protein enabled us to build a tree relating major groups of drosophiline flies in Hawaii to one another and to continental flies. The tree agrees in topology with that based on internal anatomy. Relative rate tests suggest that evolution of hemolymph proteins has been about as fast in Hawaii as on continents. Since the absolute rate of evolution of hemolymph proteins in continental flies is known, one can erect an approximate time scale for Hawaiian fly evolution. According to this scale, the Hawaiian fly fauna stems from a colonist that landed on the archipelago about 42 million years ago-i.e., before any of the present islands harboring drosophilines formed. This date fits with the geological history of the archipelago, which has witnessed the sequential rise and erosion of many islands during the past 70 million years. We discuss the bearing of the molecular time scale on views about rates of organismal evolution in the Hawaiian flies.

Developmental mutants isolated from wild-caught Xenopus laevis by gynogenesis and inbreeding

Xenopus laevis obtained from indigenous African populations are a rich source of mutants affecting development. Gynogenesis and inbreeding were used to isolate mutants affecting development from wild-caught Xenopus laevis females. Fourteen mutants were recovered from eight females tested. One mutant was recovered from each of two females. This load of 1.875 developmental mutants per female is similar to that found in the axolotl (Ambystoma mexicanum), a urodele amphibian, and is only slightly less than the load of mutants with major developmental effects found in Drosophila and man. These results suggest that the anuran amphibian Xenopus laevis, an ancestrally tetraploid species, has undergone extensive diploidization of developmentally important loci and that gynogenesis and inbreeding of wild-caught animals can provide adequate mutants at diploid loci for developmental genetic studies.

Constant rate of evolution in the antigenicity of glucose 6-phosphate dehydrogenase revealed by the enzyme inhibition method

Rabbit and chicken antisera against pure and impure rat glucose 6-phosphate dehydrogenase (G6PD) samples were prepared, and their inhibition potencies (RIP) were measured against G6PDs from 26 vertebrate and invertebrate species. The results demonstrated that the -logRIP values of antisera against G6PDs from various test species neatly correlate with paleontologically estimated divergence times between rat and the test species. This suggests that the antigenicity of G6PD has evolved at a constant rate. The correlation coefficients were evidently greater with chicken antisera than with rabbit antisera, but did not markedly differ between chicken antisera elicited to pure and impure rat G6PD samples. Based on the data obtained with chicken antisera, it is estimated that lineages which separated 250-300 million years ago differ in their G6PDs by one unit of the -logRIP.

Molecular evolution in Drosophila and the higher Diptera II. A time scale for fly evolution

In this paper, we examine first the steadiness of the rate of evolutionary change in a larval hemolymph protein, LHP, in numerous Drosophila species. We estimated amino acid sequence divergence from immunological distances measured with the quantitative microcomplement fixation technique. Using tests not depending on knowledge of absolute times of divergence, we estimated the variance of the rate of evolutionary change to be at least 4 times as large as that for a process resembling radioactive decay. Thus, the rate of evolution of this protein is as uniform as that of vertebrate proteins. Our analysis indicates no acceleration of protein evolution in the lineages leading to Hawaiian drosophilines. Second, we give an explicit description of a procedure for calculating the absolute value of the mean rate of evolutionary change in this protein. This procedure is suggested for general use in calculating absolute rates of molecular evolution. The mean rate of evolution of LHP is about 1.2 immunological distance units per million years, which probably corresponds to a unit evolutionary period of 4 million years; LHP thus evolves at a rate comparable to that of mammalian hemoglobins. Finally, we utilize the calibrated rate of LHP evolution to derive a time scale of evolution in the Drosophilidae and higher Diptera.

Albumin and Australian Frogs: Molecular Data a Challenge to Speciation Model

Vertebrate speciation in the southwest of Australia has long been viewed as resulting from multiple invasions of eastern source stocks during the Pleistocene. Microcomplement fixation studies of serum albumin evolution in frogs of the genus Heleioporus provide the first hard data on age and phylogenetic relationships among species in this genus and lead to rejection of the multiple invasion model in favor of speciation occurring in Western Australia. The albumin molecular clock was used to estimate that the species divergences in this genus occurred between 4 million to 12 million years ago in the late Tertiary (Pliocene-Miocene), rather than in the Quaternary (the last 2 million years).

Morphometric analysis of the distal humerus of some Cenozoic Catarrhines: the Late Divergence Hypothesis revisited

Washburn's Late Divergence Hypothesis (LDH) makes a series of predictions about the phyletic affinities of extant hominoids and also predicts the locomotor behavior of the "formative ape," the common ancestor to the African apes and humans, and of the earliest hominids. The present study explores some of these predictions in the light of distal humerus morphology. Multivariate analysis of distal humerus metrics, corrected for the within-groups distortion of shape by size, was used to compare a broad sample of 22 modern anthropoid taxa with 15 fossils from the Fayum, Rusinga Island, Ft. Ternan, Neudorf an der March, Kanapoi, Kromdraai, Lake Turkana, and Hadar. The results of this analysis support some aspects of the LDH, while other aspects are unresolved. Specifically, the distal humeri of the large hominoids are very distinct from those of other anthropoids; however, Hylobates is not associated clearly with either hominoids or monkeys. This suggests that "brachiation" (sensu Hylobates) is too specialized a behavior and cannot explain the common set of characteristics known to unify the hominoids. Among the large apes, there is no discrimination that can be made between the African apes and Pongo, and Homo appears only slightly closer to Pongo than to the other apes. This offers little insight into the question of whether humans did, or did not, go through a "knuckle-walking" stage in their ancestry. The Oligocene and Miocene distal humeri sustain Washburn's assertion that the "formative apes" resembled the suspensory quadrupedal platyrrhines like Ateles. The Miocene P. africanus specimen highlights the uniqueness of Hylobates in showing that this fossil "bridges" the morphology of the acrobatic cebids and the morphology of the larger apes; it appears to be clearly "intermediate" between the two groups. Hylobates, by contrast, has affinities with no fossil, does not connect with the apes, and is generally isolated except for its connection with colobines. Among the Plio-Pleistocene fossils, the Hadar sample proves to be quite primitive, and may be close to the point where hominids and pongids diverged. The Kanapoi distal humerus (KP 271), far from being more "human-like" than Australopithecus, clearly associates with the hyperrobust Australopithecines from Lake Turkana. The stratigraphically late Kromdraai distal humerus is the only hominid to be projected near Homo. The Plio-Pleistocene hominids generally evince a pattern consistent with the prediction of a late separation of hominids and pongids. But, the results of this study, like many before it, fail to resolve the central question of whether the last common ancestor of the African apes and humans "knuckle-walked." It is suggested here that this may be an unresolvable problem.