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PubMed1991

Molecular evolution of the psi eta-globin gene locus: gibbon phylogeny and the hominoid slowdown.

An 8.4-kb genomic region spanning both the psi eta-globin gene locus and flanking DNA was sequenced from the common gibbon (Hylobates lar). In addition, sequencing of the entire orthologous region from galago (Galago crassicaudatus) was completed. The gibbon and galago sequences, along with published orthologous sequences from 10 other species, were aligned. These noncoding nucleotide sequences represented four human alleles, four apes (chimpanzee, gorilla, organgutan, and gibbon), an Old World monkey (rhesus monkey), two New World monkeys (spider and owl monkeys), tarsier, two strepsirhines (galago and lemur), and goat. Divergence and maximum parsimony analyses of the psi eta genomic region first groups humans and chimpanzees and then, at progressively more ancient branch points, successively joins gorillas, orangutans, gibbons, Old World monkeys, New World monkeys, tarsiers, and strepsirhines (the lemuriform-lorisiform branch of primates). This cladistic pattern supports the taxonomic grouping of all extant hominoids into family Hominidae, the division of Hominidae into subfamilies Hylobatinae (gibbons) and Homininae, the division of Homininae into tribes Pongini (orangutans) and Hominini, and the division of Hominini into subtribes Gorillina (gorillas) and Hominina (chimpanzees and humans). The additional gibbon and galago sequence data provide further support for the occurrence of a graded evolutionary-rate slowdown in the descent of simian primates, with the slowing rate being more pronounced in the great-ape and human lineages than in the gibbon or monkey lineages. A comparison of global versus local molecular clocks reveals that local clock predictions, when focused on a specific number of species within a narrow time frame, provide a more accurate estimate of divergence dates than do those of global clocks.

Animals↗
PubMed2001

Out of Africa: origins of the Taenia tapeworms in humans.

Phylogenetic and divergence date analyses indicate that the occurrence of Taenia tapeworms in humans pre-dates the development of agriculture, animal husbandry and domestication of cattle (Bos spp.) or swine (Sus scrofa). Taeniid tapeworms in Africa twice independently colonized hominids and the genus Homo prior to the origin of modern humans. Dietary and behavioural shifts, from herbivory to scavenging and carnivory, as early Homo entered the carnivore guild in the Pliocene/Pleistocene, were drivers for host switching by tapeworms to hominids from carnivores including hyaenids and felids. Parasitological data provide a unique means of elucidating the historical ecology, foraging behaviour and food habits of hominids during the diversification of Homo spp.

Africa↗
PubMed2003

Exhaustive sample set among Viverridae reveals the sister-group of felids: the linsangs as a case of extreme morphological convergence within Feliformia.

Although molecular studies have helped to clarify the phylogeny of the problematic family Viverridae, a recent phylogenetic investigation based on cytochrome b (cyt b) has excluded the Asiatic linsangs (genus Prionodon) from the family. To assess the phylogenetic position of the Asiatic linsangs within the Feliformia, we analysed an exhaustive taxonomic sample set with cyt b and newly produced transthyretin intron I sequences (TR-I-I). TR-I-I alone and cyt b +TR-I-I combined (maximum-likelihood analysis) highly support the position of Asiatic linsangs as sister-group of the Felidae. The estimation of minimum divergence dates from molecular data suggests a splitting event ca. 33.3 million years (Myr) ago, which lends support to historical assertions that the Asiatic linsangs are "living fossils" that share a plesiomorphic morphotype with the Oligocene feliform Paleoprionodon. The African linsang is estimated to appear more than 20 Myr later and represents the sister-group of the genus Genetta. Our phylogenetic results illustrate numerous morphological convergences of "diagnostic" characters among Feliformia that might be problematic for the identification of fossil taxa. The morphotype reappearance from the Asiatic to the African linsangs suggests that the genome of the Feliformia conserved its potential ability of expression for a peculiar adaptive phenotype throughout evolution, in this case arboreality and hypercarnivory in tropical forest.

Animals↗
PubMed2005

A molecular phylogeny for bats illuminates biogeography and the fossil record.

Bats make up more than 20% of extant mammals, yet their evolutionary history is largely unknown because of a limited fossil record and conflicting or incomplete phylogenies. Here, we present a highly resolved molecular phylogeny for all extant bat families. Our results support the hypothesis that megabats are nested among four major microbat lineages, which originated in the early Eocene [52 to 50 million years ago (Mya)], coincident with a significant global rise in temperature, increase in plant diversity and abundance, and the zenith of Tertiary insect diversity. Our data suggest that bats originated in Laurasia, possibly in North America, and that three of the major microbat lineages are Laurasian in origin, whereas the fourth is Gondwanan. Combining principles of ghost lineage analysis with molecular divergence dates, we estimate that the bat fossil record underestimates (unrepresented basal branch length, UBBL) first occurrences by, on average, 73% and that the sum of missing fossil history is 61%.

Africa↗
PubMed2006

The late Miocene radiation of modern Felidae: a genetic assessment.

Modern felid species descend from relatively recent (<11 million years ago) divergence and speciation events that produced successful predatory carnivores worldwide but that have confounded taxonomic classifications. A highly resolved molecular phylogeny with divergence dates for all living cat species, derived from autosomal, X-linked, Y-linked, and mitochondrial gene segments (22,789 base pairs) and 16 fossil calibrations define eight principal lineages produced through at least 10 intercontinental migrations facilitated by sea-level fluctuations. A ghost lineage analysis indicates that available felid fossils underestimate (i.e., unrepresented basal branch length) first occurrence by an average of 76%, revealing a low representation of felid lineages in paleontological remains. The phylogenetic performance of distinct gene classes showed that Y-chromosome segments are appreciably more informative than mitochondrial DNA, X-linked, or autosomal genes in resolving the rapid Felidae species radiation.

Africa↗
PubMed2005

Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA.

We sequenced 28 million base pairs of DNA in a metagenomics approach, using a woolly mammoth (Mammuthus primigenius) sample from Siberia. As a result of exceptional sample preservation and the use of a recently developed emulsion polymerase chain reaction and pyrosequencing technique, 13 million base pairs (45.4%) of the sequencing reads were identified as mammoth DNA. Sequence identity between our data and African elephant (Loxodonta africana) was 98.55%, consistent with a paleontologically based divergence date of 5 to 6 million years. The sample includes a surprisingly small diversity of environmental DNAs. The high percentage of endogenous DNA recoverable from this single mammoth would allow for completion of its genome, unleashing the field of paleogenomics.

Animals↗
PubMed2005

Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies.

The length of the human generation interval is a key parameter when using genetics to date population divergence events. However, no consensus exists regarding the generation interval length, and a wide variety of interval lengths have been used in recent studies. This makes comparison between studies difficult, and questions the accuracy of divergence date estimations. Recent genealogy-based research suggests that the male generation interval is substantially longer than the female interval, and that both are greater than the values commonly used in genetics studies. This study evaluates each of these hypotheses in a broader cross-cultural context, using data from both nation states and recent hunter-gatherer societies. Both hypotheses are supported by this study; therefore, revised estimates of male, female, and overall human generation interval lengths are proposed. The nearly universal, cross-cultural nature of the evidence justifies using these proposed estimates in Y-chromosomal, mitochondrial, and autosomal DNA-based population divergence studies.

Adolescent↗
PubMed1996

Pattern and timing of evolutionary divergences among hominoids based on analyses of complete mtDNAs.

We have examined and dated primate divergences by applying a newly established molecular/ paleontological reference, the evolutionary separation between artiodactyls and cetaceans anchored at 60 million years before present (MYBP). Owing to the morphological transformations coinciding with the transition from terrestrial to aquatic (marine) life and the large body size of the animals (which makes their fossils easier to find), this reference can be defined, paleontologically, within much narrower time limits compared to any local primate calibration marker hitherto applied for dating hominoid divergences. Application of the artiodactyl/ cetacean reference (A/C-60) suggests that hominoid divergences took place much earlier than has been concluded previously. According to a homogeneous-rate model of sequence evolution, the primary hominoid divergence, i.e., that between the families Hylobatidae (gibbons) and Hominidae, was dated at approximately 36 MYBP. The corresponding dating for the divergence between Pongo (orangutan) and Gorilla-Pan (chimpanzee) -Homo is approximately 24.5 MYBP, that for Gorilla vs Homo-Pan is approximately 18 MYBP, and that for Homo vs Pan approximately 13.5 MYBP. The split between Sumatran and Bornean orangutans was dated at approximately 10.5 MYBP and that between the common and pygmy chimpanzees at approximately 7 MYBP. Analyses of a single gene (cytochrome b) suggest that the divergence within the Catarrhini, i.e., between Hominoidea and Old World monkeys (Cercopithecoidea), took place > 40 MYBP; that within the Anthropoidea, i.e., between Catarrhini and Platyrrhini (New World monkeys), > 60 MYBP; and that between Anthropoidea and Prosimii (lemur), approximately 80 MYBP. These separation times are about two times more ancient than those applied previously as references for the dating of hominoid divergences. The present findings automatically imply a much slower evolution in hominoid DNA (both mitochondrial and nuclear) than commonly recognized.

Animals↗
PubMed2005

Placing confidence limits on the molecular age of the human-chimpanzee divergence.

Molecular clocks have been used to date the divergence of humans and chimpanzees for nearly four decades. Nonetheless, this date and its confidence interval remain to be firmly established. In an effort to generate a genomic view of the human-chimpanzee divergence, we have analyzed 167 nuclear protein-coding genes and built a reliable confidence interval around the calculated time by applying a multifactor bootstrap-resampling approach. Bayesian and maximum likelihood analyses of neutral DNA substitutions show that the human-chimpanzee divergence is close to 20% of the ape-Old World monkey (OWM) divergence. Therefore, the generally accepted range of 23.8-35 millions of years ago for the ape-OWM divergence yields a range of 4.98-7.02 millions of years ago for human-chimpanzee divergence. Thus, the older time estimates for the human-chimpanzee divergence, from molecular and paleontological studies, are unlikely to be correct. For a given the ape-OWM divergence time, the 95% confidence interval of the human-chimpanzee divergence ranges from -12% to 19% of the estimated time. Computer simulations suggest that the 95% confidence intervals obtained by using a multifactor bootstrap-resampling approach contain the true value with >95% probability, whether deviations from the molecular clock are random or correlated among lineages. Analyses revealed that the use of amino acid sequence differences is not optimal for dating human-chimpanzee divergence and that the inclusion of additional genes is unlikely to narrow the confidence interval significantly. We conclude that tests of hypotheses about the timing of human-chimpanzee divergence demand more precise fossil-based calibrations.

Animals↗
PubMed2000

The power of relative rates tests depends on the data.

One of the most useful features of molecular phylogenetic analyses is the potential for estimating dates of divergence of evolutionary lineages from the DNA of extant species. But lineage-specific variation in rate of molecular evolution complicates molecular dating, because a calibration rate estimated from one lineage may not be an accurate representation of the rate in other lineages. Many molecular dating studies use a "clock test" to identify and exclude sequences that vary in rate between lineages. However, these clock tests should not be relied upon without a critical examination of their effectiveness at removing rate variable sequences from any given data set, particularly with regard to the sequence length and number of variable sites. As an illustration of this problem we present a power test of a frequently employed triplet relative rates test. We conclude that (1) relative rates tests are unlikely to detect moderate levels of lineage-specific rate variation (where one lineage has a rate of molecular evolution 1.5 to 4.0 times the other) for most commonly used sequences in molecular dating analyses, and (2) this lack of power is likely to result in substantial error in the estimation of dates of divergence. As an example, we show that the well-studied rate difference between murid rodents and great apes will not be detected for many of the sequences used to date the divergence between these two lineages and that this failure to detect rate variation is likely to result in consistent overestimation the date of the rodent-primate split.

Evolution, Molecular↗
PubMed1989

Relationships of the chromosomal species in the Eurasian mole rats of the Spalax ehrenbergi group as determined by DNA-DNA hybridization, and an estimate of the spalacid-murid divergence time.

DNA-DNA hybridization was used to measure the average genomic divergence among the four chromosomal species of the Eurasian mole rats belonging to the Spalax ehrenbergi complex (Rodentia: Spalacidae). The percent nucleotide substitutions in the single-copy nuclear DNA among the species ranged from 0 to 5%, suggesting that speciation has occurred with minor genomic changes in these animals. The youngest chromosomal species appear to differ by 0.2-0.6% base pair mismatch, which is only between one and three base differences in a 500-bp fragment. The interspecific values of percent nucleotide differences permit the recognition of two well-separated speciation events in the S. ehrenbergi complex, the older (of Lower Pleistocene age) having isolated the chromosomal species 2n = 54 before the divergence of the three other species. DNA-DNA hybridization was also used to compare the Spalacinae (Eurasian mole rats), Murinae (Old World rats and mice), and Arvicolinae (voles and lemmings). These data enabled us to estimate the time of divergence of the spalacids at ca. 19 million years ago. The dates of divergence among the other rodent lineages, as predicted by DNA hybridization results, agree well with paleontological data. These dates of divergence are obtained by the relation between geological time and single-copy nuclear DNA change, a relation that was calibrated by Catzeflis et al. (1987) through the use of fossil Arvicolinae and Murinae data.

Animals↗
PubMed2003

Molecular identification of natural hybrids between Trichinella nativa and Trichinella T6 provides evidence of gene flow and ongoing genetic divergence.

To date, there are no data available on the population genetics of Trichinella due to the lack of genetic markers and the difficulty of working with such small parasites. In the Arctic region of North America and along the Rocky Mountains, there exist two genotypes of Trichinella, Trichinella nativa and Trichinella T6, respectively, which are well differentiated by biochemical and molecular characters. However, both are resistant to freezing, show other common biological characters (e.g. low or no infectivity to rodents and swine) and produce fertile F1 offspring upon interbreeding. To data, these two genotypes have been considered allopatric. In this study, we detected both genotypes in wolves of the same wolf packs in Alaska, suggesting sympatry. A single GTT trinucleotide present in the ITS-2 sequence of T. nativa but not in Trichinella T6 was used as a genetic marker to study gene flow for this character in both a murine infection model and in larvae from naturally-infected Alaskan wolves. Only F1 larvae originating from a cross between T. nativa male and Trichinella T6 female were able to produce F2 offspring. Larvae (F1) originating from a cross between Trichinella T6 male and T. nativa female were not reproductively viable. As expected, all F1 larvae showed a heterozygote pattern for the GTT character upon heteroduplex analysis; however, within the F2 population, the number of observed heterozygotes (n=52) was substantially higher than expected (n=39.08), as supported by the F(is) index, and was not in the Hardy-Weinberg equilibrium. Larvae from two of the 16 Trichinella positive Alaskan wolves, showed the Trichinella T6 pattern or the T. nativa/Trichinella T6 hybrid pattern. Our data demonstrate that T. nativa and Trichinella T6 live in sympatry at least in Alaskan wolves, where T. nativa occurs more frequently (69%) than Trichinella T6 (31%). One explanation for this phenomenon is that glacial periods may have caused a geographical relocation, colonisation and independent evolution of T. nativa within the Rocky Mountains, resulting in a bifurcation of the freeze-resistant genotype. Additional studies will be required to test this hypothesis.

Alaska↗
PubMed2000

Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies.

Molecular methods as applied to the biogeography of single species (phylogeography) or multiple codistributed species (comparative phylogeography) have been productively and extensively used to elucidate common historical features in the diversification of the Earth's biota. However, only recently have methods for estimating population divergence times or their confidence limits while taking into account the critical effects of genetic polymorphism in ancestral species become available, and earlier methods for doing so are underutilized. We review models that address the crucial distinction between the gene divergence, the parameter that is typically recovered in molecular phylogeographic studies, and the population divergence, which is in most cases the parameter of interest and will almost always postdate the gene divergence. Assuming that population sizes of ancestral species are distributed similarly to those of extant species, we show that phylogeographic studies in vertebrates suggest that divergence of alleles in ancestral species can comprise from less than 10% to over 50% of the total divergence between sister species, suggesting that the problem of ancestral polymorphism in dating population divergence can be substantial. The variance in the number of substitutions (among loci for a given species or among species for a given gene) resulting from the stochastic nature of DNA change is generally smaller than the variance due to substitutions along allelic lines whose coalescence times vary due to genetic drift in the ancestral population. Whereas the former variance can be reduced by further DNA sequencing at a single locus, the latter cannot. Contrary to phylogeographic intuition, dating population divergence times when allelic lines have achieved reciprocal monophyly is in some ways more challenging than when allelic lines have not achieved monophyly, because in the former case critical data on ancestral population size provided by residual ancestral polymorphism is lost. In the former case differences in coalescence time between species pairs can in principle be explained entirely by differences in ancestral population size without resorting to explanations involving differences in divergence time. Furthermore, the confidence limits on population divergence times are severely underestimated when those for number of substitutions per site in the DNA sequences examined are used as a proxy. This uncertainty highlights the importance of multilocus data in estimating population divergence times; multilocus data can in principle distinguish differences in coalescence time (T) resulting from differences in population divergence time and differences in T due to differences in ancestral population sizes and will reduce the confidence limits on the estimates. We analyze the contribution of ancestral population size (theta) to T and the effect of uncertainty in theta on estimates of population divergence (tau) for single loci under reciprocal monophyly using a simple Bayesian extension of Takahata and Satta's and Yang's recent coalescent methods. The confidence limits on tau decrease when the range over which ancestral population size theta is assumed to be distributed decreases and when tau increases; they generally exclude zero when tau/(4Ne) > 1. We also apply a maximum-likelihood method to several single and multilocus data sets. With multilocus data, the criterion for excluding tau = 0 is roughly that l tau/(4Ne) > 1, where l is the number of loci. Our analyses corroborate recent suggestions that increasing the number of loci is critical to decreasing the uncertainty in estimates of population divergence time.

Animals↗
PubMed2005

Evolution of mitochondrial uncoupling proteins: novel invertebrate UCP homologues suggest early evolutionary divergence of the UCP family.

Current hypothesis about the evolution of uncoupling proteins (UCPs) proposed by suggests that UCP4 is the earliest form of UCP ancestral to all other UCP orthologues. However, this hypothesis is difficult to reconcile with a narrow tissue distribution of UCP4 (which is a brain-specific isoform), suggesting highly specialized rather than anfcestral function for this protein. We searched for UCP2, UCP3, and UCP5 homologues in invertebrate genomes using amplification with degenerate primers designed against UCP2-specific conserved sequences and/or BLASTP search with stringent ad hoc criteria to distinguish between homologues and orthologues of different UCPs. Our study identified invertebrate UCP homologues similar to UCP2 and 3 (which we termed UCP6) and an invertebrate homologue of UCP5. Phylogenetic analysis indicates that there are at least three clades of UCPs in invertebrates, which are closely related to vertebrate UCP1-3, UCP4, and UCP5, respectively, and shows early evolutionary divergence of UCPs, which pre-dates the divergence of protostomes and deuterostomes. It also suggests that the newly identified UCP6 proteins from invertebrates are ancestral to the vertebrate UCP1, UCP2, and UCP3, and that divergence of these three vertebrate orthologues occurred late in evolution of the vertebrates. This study refutes the hypothesis of Hanak and Jezek (2001) that UCP4 is an ancestral form for all UCPs, and shows early evolutionary diversification of this protein family, which corresponds to their proposed functional diversity in regulation of proton leak, antioxidant defense and apoptosis.

Amino Acid Sequence↗
PubMed1996

The "Phoca standard": an external molecular reference for calibrating recent evolutionary divergences.

Comparison of the complete mitochondrial DNA (mtDNA) of the high-Arctic ringed seal (Phoca hispida) and the sub-Arctic harbour (P. vitulina) and grey (Halichoerus grypus) seals shows that they are genetically equidistant from one another. We relate the evolutionary divergence of the three species to expanding glaciation in the Arctic Basin and establish, in conjunction with mtDNA data, a standard reference for calibration of recent divergence events among mammalian taxa. In the present study, we apply the "Phoca standard" to the dating of divergences within the hominid phylogenetic tree. After determining the relative rates of substitution over all mitochondrial protein-coding genes in the different evolutionary lineages, we estimate that humans and chimpanzees diverged from each other 6.1 Mya (95% confidence limits: 5.2-6.9 Mya). The corresponding lower-limit divergence between common chimpanzee, Pan troglodytes, and pygmy chimpanzee, P. paniscus, occurred 3 (2.4-3.6) Mya, and the primary split within the P. troglodytes complex 1.6 (1.3-2.0) Mya. The analyses suggest that the split between Gorilla and Pan/Homo occurred 8.4 (7.3-9.4) Mya. They also suggest that Pongo (orangutan) and the lineage leading to gorillas, chimpanzees, and humans diverged 18.1 (16.5-19.6) Mya. The present analysis is independent of the hominid paleontological record and inferential morphological interpretations and thus is a novel approach to the lower-limit dating of recent divergences.

Animals↗
PubMed1979

Myoglobin of the shark Heterodontus portusjacksoni: isolation and amino acid sequence.

Myoglobin isolated from red muscle of the shark H. portusjacksoni was purified by ion-exchange chromatography on sulfopropyl-Sephadex and gel-filtration. Amino acid analysis and sequence determination showed 148 amino acid residues. The amino terminal residue is acetylated as shown by mass spectrographic analysis of N-terminal peptides. There is a deletion of four residues at the amino terminal end as well as one residue in the CD interhelical area relative to other myoglobins. The complete amino acid sequence has been determined following digestion with trypsin, chymotrypsin, pepsin and staphylococcal protease. Sequences of the purified peptides were determined by the dansyl-Edman procedure. The amino acid sequence showed approximately 85 differences from mammalian, monotreme and bird myoglobins. The date of divergence of the shark H. portusjacksoni from these other orders was estimated at 450 +/- 16 million years, based on the number of amino acid differences between species and allowing for multiple mutations during the evolutionary period. This estimate agrees well with similar estimates made using alpha- and beta-globin sequences, in contrast to widely differing estimates of dates of divergence for monotremes using the same three globin chains. Compared with myoglobins from species previously studied, there are many more differences in amino acid sequences, and in many positions residues are found that are more characteristic of alpha- and beta-globins, suggesting a conservation of residues over a long period of evolutionary time. There are fewer stabilizing hydrogen bonds and salt-linkages than in other myoglobins.

Amino Acid Sequence↗
PubMed2004

Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes.

We estimated the dates of the monocot-dicot split and the origin of core eudicots using a large chloroplast (cp) genomic dataset. Sixty-one protein-coding genes common to the 12 completely sequenced cp genomes of land plants were concatenated and analyzed. Three reliable split events were used as calibration points and for cross references. Both the method based on the assumption of a constant rate and the Li-Tanimura unequal-rate method were used to estimate divergence times. The phylogenetic analyses indicated that nonsynonymous substitution rates of cp genomes are unequal among tracheophyte lineages. For this reason, the constant-rate method gave overestimates of the monocot-dicot divergence and the age of core eudicots, especially when fast-evolving monocots were included in the analysis. In contrast, the Li-Tanimura method gave estimates consistent with the known evolutionary sequence of seed plant lineages and with known fossil records. Combining estimates calibrated by two known fossil nodes and the Li-Tanimura method, we propose that monocots branched off from dicots 140-150 Myr ago (late Jurassic-early Cretaceous), at least 50 Myr younger than previous estimates based on the molecular clock hypothesis, and that the core eudicots diverged 100-115 Myr ago (Albian-Aptian of the Cretaceous). These estimates indicate that both the monocot-dicot divergence and the core eudicot's age are older than their respective fossil records.

Chloroplasts↗