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PubMed2006

Comparative phylogeography of coastal limpets across a marine disjunction in New Zealand.

Cook Strait, which separates the North and South Island of New Zealand, has been a transient, but re-occurring feature of the New Zealand land mass throughout the Pleistocene, maintaining its current width and depth for the past 5000 years. Historic land fragmentation coupled with the complex hydrography of the Greater Cook Strait region has created both biogeographic and phylogeographic disjunctions between the North and South Island in several marine species. Here we use mitochondrial cytochrome b DNA sequences of three endemic intertidal limpets, Cellana ornata, Cellana radians and Cellana flava to assess intraspecific phylogeographic patterns across Cook Strait and to look for interspecific concordance of ecological and evolutionary processes among closely related taxa. We sequenced 328-359 bp in 85-321 individuals from 8-31 populations spanning the biogeographic range of the three species. Intraspecific phylogeographic analyses show moderate to strong genetic discontinuity among North and South Island populations due to allopatric fragmentation. This pattern was broadly concordant across the three species and the observed divergence among this group of intertidal limpets (0.3-2.0%) is similar to that of previously studied subtidal organisms. For each species, divergence time calculations suggest contemporary North and South Island lineages diverged from their respective most recent common ancestor approximately 200 000 to 300 000 years before present (bp), significantly earlier than previous estimates in other coastal marine taxa that arose from a miscalculation of divergence time.

Animals↗
PubMed1998

Siberian population of the New Stone Age: mtDNA haplotype diversity in the ancient population from the Ust'-Ida I burial ground, dated 4020-3210 BC by 14C.

On the basis of analysis of mtDNA from skeletal remains, dated by 14C 4020-3210 BC, from the Ust'-Ida I Neolithic burial ground in Cis-Baikal area of Siberia, we obtained genetic characteristics of the ancient Mongoloid population. Using the 7 restriction enzymes for the analysis of site's polymorphism in 16,106-16,545 region of mtDNA, we studied the structure of the most frequent DNA haplotypes, and estimated the intrapopulational nucleotide diversity of the Neolithic population. Comparison of the Neolithic and modern indigeneous populations from Siberia, Mongolia and Ural showed, that the ancient Siberian population is one of the ancestors of the modern population of Siberia. From genetic distance, in the assumption of constant nucleotide substitution rate, we estimated the divergence time between the Neolithic and the modern Siberian population. This divergence time (5572 years ago) is conformed to the age of skeletal remains (5542-5652 years). With use of the 14C dates of the skeletal remains, nucleotide substitution rate in mtDNA was estimated as 1% sequence divergence for 8938-9115 years.

Asian People↗
PubMed2000

Molecular estimates of primate divergences and new hypotheses for primate dispersal and the origin of modern humans.

The concept of recent hominoid divergences has been a mainstay in molecular primatology since the 1970's. However, the ages allocated to the calibration points used to establish these divergence times and the estimates resulting from their application, notably the commonly accepted divergence between Pan (chimpanzees) and Homo 5 million years before present (MYBP), are now palaeontologically refutable. Here we estimate the ages of various primate divergences using three references with a more detailed fossil record than any of the traditional primate calibration points. Our findings suggest that the latter yield datings that are too recent by a factor of about two. For example, our estimates place the divergence between Pan and Homo 10.5-13 MYBP. The revised estimates of primate divergence times suggest a new hypothesis for primate evolution and dispersal: that the divergence between strepsirhines (lorises, lemurs) and anthropoids was contemporary with the break-up of Southern continents about 90 MYBP, with strepsirhines becoming isolated on Madagascar and later dispersing to Africa (and Asia) and anthropoids evolving in South America and subsequently colonizing Africa (and Asia), or possibly North America. In addition we present a new hypothesis, which accommodates the strikingly similar coalescence times for human mitochondrial DNA and the Y-chromosome. This hypothesis posits a common mitochondrial and Y-chromosome bottleneck about 400,000 years ago, associated with the origination of the human 2n = 46 karyotype, obstructing genetic exchange with the 2n = 48 Homo contemporaries.

Africa↗
PubMed2005

Two chloroplast DNA inversions originated simultaneously during the early evolution of the sunflower family (Asteraceae).

The chloroplast DNA (cpDNA) inversion in the Asteraceae has been cited as a classic example of using genomic rearrangements for defining major lineages of plants. We further characterize cpDNA inversions in the Asteraceae using extensive sequence comparisons among 56 species, including representatives of all major clades of the family and related families. We determine the boundaries of the 22-kb (now known as 22.8 kb) inversion that defines a major split within the Asteraceae, and in the process, we characterize the second and a new, smaller 3.3-kb inversion that occurs at one end of the larger inversion. One end point of the smaller inversion is upstream of the trnE-UUC gene, and the other end point is located between the trnC-GCA and rpoB genes. Although a diverse sampling of Asteraceae experienced substantial length variation and base substitution during the long evolutionary history subsequent to the inversion events, the precise locations of the inversion end points are identified using comparative sequence alignments in the inversion regions. The phylogenetic distribution of two inversions is identical among the members of Asteraceae, suggesting that the inversion events likely occurred simultaneously or within a short time period shortly after the origin of the family. Estimates of divergence times based on ndhF and rbcL sequences suggest that two inversions originated during the late Eocene (38-42 MYA). The divergence time estimates also suggest that the Asteraceae originated in the mid Eocene (42-47 MYA).

Amino Acid Sequence↗
PubMed2025

Comparative Phylogenetics Reveal Clade-specific Drivers of Recombination Rate Evolution Across Vertebrates.

Meiotic recombination is an integral cellular process, required for the production of viable gametes. Recombination rate is a fundamental genomic parameter, modulating genomic responses to selection. Our increasingly detailed understanding of its molecular underpinnings raises the prospect that we can gain insight into trait divergence by examining the molecular evolution of recombination genes from a pathway perspective, as in mammals, where protein-coding changes in later stages of the recombination pathway are connected to divergence in intra-clade recombination rate. Here, we leverage increased availability of avian and teleost genomes to reconstruct the evolution of the recombination pathway across two additional vertebrate clades: birds, which have higher and more variable rates of recombination and similar divergence times to mammals, and teleost fish, which have much deeper divergence times. Rates of molecular evolution of recombination genes are highly correlated between vertebrate clades and significantly elevated compared to control panels, suggesting that they experience similar selective pressures. Avian recombination genes are significantly more likely to exhibit signatures of positive selection than other clades, unrestricted to later stages of the pathway. Signatures of positive selection in genes linked to recombination rate variation in mammalian populations and those with signatures of positive selection across the avian phylogeny are highly correlated. In contrast, teleost fish recombination genes have significantly less evidence of positive selection despite high intra-clade recombination rate variability. Gaining clade-specific understanding of patterns of variation in recombination genes can elucidate drivers of recombination rate and thus, factors influencing genetic diversity, selection efficacy, and species divergence.

Animals↗
PubMed1996

Continental breakup and the ordinal diversification of birds and mammals.

The classical hypothesis for the diversification of birds and mammals proposes that most of the orders diverged rapidly in adaptive radiations after the Cretaceous/Tertiary (K/T) extinction event 65 million years ago. Evidence is provided by the near-absence of fossils representing modern orders before the K/T boundary. However, fossil-based estimates of divergence time are known to be conservative because of sampling biases, and some molecular/time estimates point to earlier divergences among orders. In an attempt to resolve this controversy, we have estimated times of divergence among avian and mammalian orders with a comprehensive set of genes that exhibit a constant rate of substitution. Here we report molecular estimates of divergence times that average about 50-90% earlier than those predicted by the classical hypothesis, and show that the timing of these divergences coincides with the Mesozoic fragmentation of emergent land areas. This suggests that continental breakup may have been an important mechanism in the ordinal diversification of birds and mammals.

Animals↗
PubMed2026

Genomic Footprints of Historical Introgression Between Ancient Lineages of Wild Oryza AA-Genome Species With Widely Separated Contemporary Distributions.

Phylogenetic incongruence is increasingly recognized as pervasive, yet the extent to which reticulate evolution occurs between groups separated by substantial geographical distances and deep phylogenetic divergence remains poorly characterized. In the Oryza AA-genome group-a model for plant speciation and domestication-the traditional bifurcation model posits that Australian Oryza meridionalis and African Oryza longistaminata occupy basal branches, distinct from the more recently diversified monophyletic clade comprising Asian and other African lineages, including major cultivars. However, recent evidence from endogenous viral sequences has hinted at unexpected genetic relatedness between African O. longistaminata and Asian Oryza sativa, which are geographically and phylogenetically distant. Here, we conducted a genome-wide survey across 11 Oryza species to systematically identify genomic regions exhibiting phylogenetic incongruence. Widespread phylogenetic discordance was observed, notably involving genomic segments in which O. longistaminata showed phylogenetic proximity to Asian species, contradicting their established deep divergence. To distinguish between introgression and incomplete lineage sorting, we performed four-taxon ABBA-BABA tests, which provided statistical support for introgression. Furthermore, divergence time estimates for these incongruent regions were younger than the species divergence times, suggesting historical introgression between the ancestors of lineages that are currently separated by vast geographical distances. Systematic assessments indicated that potential analytical artifacts, such as compositional bias and substitution saturation, were unlikely to explain the observations. These convergent lines of evidence suggest that ancient introgression had occurred between currently geographically separated and evolutionarily divergent Oryza lineages, leaving detectable footprints across their modern genomes.

Oryza↗
PubMed1994

Molecular systematics of hystricognath rodents: evidence from the mitochondrial 12S rRNA gene.

Nucleotide sequence variation among 22 representatives of 14 families of hystricognathid rodents was examined using an 814-bp region of the mitochondrial 12S ribosomal RNA (rRNA) gene composing domains I-III. The purpose of this study was twofold. First, the phylogenetic relationships among Old World phiomorph (primarily African) and New World caviomorph (primarily South American) families were investigated, with a special emphasis on testing hypotheses pertaining to the origin of New World families and the identification of major monophyletic groups. Second, divergence times derived from molecular data were compared to those suggested by the fossil record. The resultant 12S rRNA gene phylogeny, analyzed separately and in combination with other morphological and molecular data, supported a monophyletic Caviomorpha. This finding is counter to the idea of a multiple origin for the South American families. The most strongly supported relationships within the Caviomorpha were a monophyletic Octodontoidea (containing five families) and the placement of New World porcupines (family Erethizontidae) as the most divergent family. Although comparisons to other data were more equivocal, the most parsimonious 12S rRNA trees also supported a monophyletic Phiomorpha that could be subdivided into two major groups, a clade containing the Thryonomyoidea (Thryonomyidae and Petromuridae) plus Bathyergidae and the more divergent Hystricidae (Old World porcupines). No significant differences in rates of 12S rRNA gene divergence were observed for hystricognathids in comparison to other rodent groups. Although time since divergence estimates were influenced by the fossil dates chosen to calibrate absolute rates, the overall divergence times derived from both transversions only and Kimura corrected distances and calibrations using two independent dates revealed a divergence time between Old and New World groups dating in the Eocene.

Africa↗
PubMed1980

A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.

Some simple formulae were obtained which enable us to estimate evolutionary distances in terms of the number of nucleotide substitutions (and, also, the evolutionary rates when the divergence times are known). In comparing a pair of nucleotide sequences, we distinguish two types of differences; if homologous sites are occupied by different nucleotide bases but both are purines or both pyrimidines, the difference is called type I (or "transition" type), while, if one of the two is a purine and the other is a pyrimidine, the difference is called type II (or "transversion" type). Letting P and Q be respectively the fractions of nucleotide sites showing type I and type II differences between two sequences compared, then the evolutionary distance per site is K = -(1/2) ln [(1-2P-Q) square root of 1-2Q]. The evolutionary rate per year is then given by k = K/(2T), where T is the time since the divergence of the two sequences. If only the third codon positions are compared, the synonymous component of the evolutionary base substitutions per site is estimated by K'S = -(1/2) ln (1-2P-Q). Also, formulae for standard errors were obtained. Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.

Animals↗
PubMed1995

A measure of population subdivision based on microsatellite allele frequencies.

A new measure of the extent of population subdivision as inferred from allele frequencies at microsatellite loci is proposed and tested with computer simulations. This measure, called R(ST), is analogous to Wright's F(ST) in representing the proportion of variation between populations. It differs in taking explicit account of the mutation process at microsatellite loci, for which a generalized stepwise mutation model appears appropriate. Simulations of subdivided populations were carried out to test the performance of R(ST) and F(ST). It was found that, under the generalized stepwise mutation model, R(ST) provides relatively unbiased estimates of migration rates and times of population divergence while F(ST) tends to show too much population similarity, particularly when migration rates are low or divergence times are long [corrected].

Alleles↗
PubMed2000

Likelihood analysis of ongoing gene flow and historical association.

We develop a Monte Carlo-based likelihood method for estimating migration rates and population divergence times from data at unlinked loci at which mutation rates are sufficiently low that, in the recent past, the effects of mutation can be ignored. The method is applicable to restriction fragment length polymorphisms (RFLPs) and single nucleotide polymorphisms (SNPs) sampled from a subdivided population. The method produces joint maximum-likelihood estimates of the migration rate and the time of population divergence, both scaled by population size, and provides a framework in which to test either for no ongoing gene flow or for population divergence in the distant past. We show the method performs well and provides reasonably accurate estimates of parameters even when the assumptions under which those estimates are obtained are not completely satisfied. Furthermore, we show that, provided that the number of polymorphic loci is sufficiently large, there is some power to distinguish between ongoing gene flow and historical association as causes of genetic similarity between pairs of populations.

Alleles↗
PubMed2005

Molecular clocks and geological dates: cytochrome b of Anolis extremus substantially contradicts dating of Barbados emergence.

Even though molecular clocks vary in rate to some extent, they are widely used and very important in a range of evolutionary studies, not least in interpreting cause and colonization in phylogeography. Evolutionists may use island age and emergence to give the earliest possible date for colonization by a species and hence give the lower limit in a molecular clock calibration. The geology of the Lesser Antilles is well studied and Barbados, although composed of some ancient rocks, is thought to have emerged only about 1 million years ago (Ma). The cytochrome b mitochondrial gene is the most widely used gene in vertebrate phylogeography, and generally evolves at a rate of 1-2% per million years (Myr) for poikilothermic vertebrates. Divergence measured across almost all of this gene in the endemic anole (Anolis extremus) reveals a mean patristic distance of approximately 8.3% between this clade and its sister, together with distinct divergence and phylogeographical structure within Barbados. The divergence time, estimated by a range of procedures using four calibration points, is not in the least compatible with the proposed geological time of emergence of Barbados. Hence, either the molecular clock rate does not apply to the Barbadian anole population, or the geological dating of the emergence of Barbados is erroneous. The compatibility of geological times and molecular divergence of this complex on Martinique, together with relative rates tests comparing the rates on Barbados and Martinique, do not suggest atypical clock rates. The question of whether Barbados emerged much earlier than is currently thought, or whether the molecular clock assumptions are inappropriate, remains open.

Animals↗
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↗
PubMed2000

Phylogeny of taxaceae and cephalotaxaceae genera inferred from chloroplast matK gene and nuclear rDNA ITS region.

Phylogeny of the Taxaceae genera and the monotypic family Cephalotaxaceae has been extraordinarily controversial. In this paper chloroplast matK genes and nuclear ITS sequences were determined for all six genera of the two families and representatives of other conifer families. Analysis using either the nonsynonymous sites or the deduced amino acid sequences of matK genes strongly indicates that taxad genera and Cephalotaxaceae are monophyletic, with the Taxodiaceae/Cupressaceae clade as their sister group. Cephalotaxus is basal to the taxad genera, among which two clades, Torreya/Amentotaxus and Taxus/Pseudotaxus/Austrotaxus, are resolved. They correspond to Janchen's two tribes, Torreyeae and Taxeae. In Taxeae, Austrotaxus is the first to branch off. Analyses of the nuclear ITS sequence data corroborated the topology of the matK gene tree. These results refute the views that Cephalotaxaceae has no alliance with Taxaceae and that Austrotaxus and Amentotaxus should be excluded from the Taxaceae. We estimated the divergence time between the Taxodiaceae/Cupressaceae and the Cephalotaxaceae/Taxaceae clades to be 192-230 Myr ago and the divergence time between taxads and Cephalotaxus to be 149-179 Myr ago. Soon after the latter divergence event, within 6-8 Myr, the two taxad tribes originated. In conclusion, our data do not support Florin's claim that taxads could be traced to Devonian psilophytes (359-395 Myr ago).

Base Sequence↗
PubMed1993

Molecular evolution of the Adh1 locus in the genus Zea.

We sampled DNA sequences from the locus encoding alcohol dehydrogenase 1 (alcohol:NAD+ oxidoreductase, EC 1.1.1.1). Our sample represents Adh1 alleles from a wide geographic distribution of Zea mays (maize) and two species of teosinte (Zea luxurians and Zea diploperennis). Using these and previously published sequences, we analyze the molecular evolution of Adh1 in the genus Zea. We perform tests to characterize recombination and identify the putative parents of the recombinant Adh1-Cm allele. We also perform tests for selection but are unable to detect either a selective sweep or strong balancing selection at the Adh1 locus. We estimate that divergence times between teosinte and some maize alleles are approximately 1 million years, whereas divergence times between distantly related maize alleles are approximately 2 million years. We conclude that the common ancestor to the genus Zea was polymorphic at the Adh1 locus. On the basis of previous estimates of nucleotide diversity at other maize loci, it appears that the common ancestor to the genus Zea was polymorphic at many loci.

Alcohol Dehydrogenase↗
PubMed2005

Molecular dating: ape bones agree with chicken entrails.

Molecular time estimates, especially those that employed the 310 million years ago (Mya) date of mammal-bird divergence as the calibration point, were criticized in recent publications. In this article, we estimate the divergence time of primates and rodents, primates and artiodactyls and the different great ape species by using two independent calibration-time ranges and maximally conservative error estimates. We observed a variation of approximately +/-15-20% for most of the molecular time estimates in the 10-100 Mya range. The estimated range of the primate-rodent divergence time, 84-121 Mya, includes the date obtained with the 310 million years calibration point (110 Mya). We conclude that molecular time estimates remain useful tools of evolutionary biology, although utmost caution is required when interpreting the results.

Animals↗
PubMed1992

Crocodilian evolution: insights from immunological data.

The quantitative immunological technique of microcomplement fixation was used to examine serum albumin evolution among members of the order Crocodylia. The cross-reactivity of the albumin antisera and antigens employed in this study had been examined previously using the qualitative technique of immunodiffusion. The phylogenetic conclusions derived from these two data sets are highly congruent, including support of the families Alligatoridae and Crocodylidae, with the placement of Gavialis as the sister taxon of Tomistoma. Both methods provide similar information on the relative amounts of amino acid sequence divergence between albumin molecules; however, the data obtained from microcomplement fixation comparisons are more discriminating than those derived from immunodiffusion. The estimated divergence times within the Crocodylia derived from the fossil record are examined in light of divergence times predicted by the microcomplement fixation-based albumin clock. The traditional phylogenetic placement of Gavialis outside the remaining extant crocodilians is inconsistent with all molecular data sets and we suggest that a careful reexamination of both the extant and the fossil morphological data is warranted.

Alligators and Crocodiles↗
PubMed2004

Temporal diversification of Mesoamerican cichlid fishes across a major biogeographic boundary.

The Mexican Neovolcanic Plateau sharply divides the vertebrate fauna of Mesoamerica where the climate of both the neotropics and temperate North America gradually blend. Only a few vertebrate groups such as the Heroine cichlids, distributed from South America to the Rio Grande in North America, are found both north and south of the Neovolcanic Plateau. To better understand the geography and temporal diversification of cichlids at this geologic boundary, we used mitochondrial DNA sequences of the cytochrome b (cyt b) gene to reconstruct the relationships of 52 of the approximately 80 species of Heroine cichlids in Mesoamerica. Our analysis suggests several cichlids in South America should be considered as part of the Mesoamerican Heroine clade because they and the cichlids north of the Isthmus of Panama are clearly supported as monophyletic with respect to all other Neotropical cichlids. We also recovered a group containing species in Paratheraps+Paraneetroplus+Vieja as the sister clade to Herichthys. Herichthys is the only cichlid clade north of the Mexican Plateau and it is monophyletic. Non-parametric rate smoothing of cichlid cyt b sequence resulted in an estimated divergence time of approximately 6 million years for Herichthys. This temporal diversification is concordant with divergence times estimated for anurans in the genus Bufo, a group that exhibits a similar geographic distribution. Our results indicate the 5-million-year-old extension of the Mexican Neovolcanic Plateau to the Gulf Coast of Mexico has strongly influenced the current transition between the vertebrate faunas of the Neotropics and Nearctic.

Animals↗