Ice Age refugia and Quaternary extinctions: An issue of Quaternary evolutionary palaeoecology a b... more Ice Age refugia and Quaternary extinctions: An issue of Quaternary evolutionary palaeoecology a b s t r a c t Quaternary palaeoecology, as a discipline, involves the analysis of a large range of fossil organisms from the last ca. 2 million years. This paper considers the role that these Quaternary records can take in better understanding the evolution of those organisms. We also discuss the surprisingly low uptake of evolutionary biology in Quaternary palaeoecological studies. This leads us to encourage an advance on both these fronts with a greater degree of collaboration with phylogeographic and ancient DNA researchers. These discussions accompany a summary of a special issue of Quaternary Science Reviews representing the proceedings of the XVII INQUA held in Cairns Australia in 2007. This special issue includes papers on a wide variety of Quaternary evolutionary palaeoecological and population dynamic subjects including extinct Pacific Island palm trees, Beringian beetles, Scandinavian trees, and the effects on human and animal populations of an extraterrestrial impact event in the Late Glacial of North America.
Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various g... more Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various genes and taxa. Recent studies based on population-level and pedigree data have produced remarkably high estimates of mutation rate, which strongly contrast with substitution rates inferred in phylogenetic (species-level) studies. Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (,1-2 Myr) mutation rate and the low, long-term substitution rate. The relationship between the age of the calibration and the rate of change can be described by a vertically translated exponential decay curve, which may be used for correcting molecular date estimates. The phylogenetic substitution rates in mitochondria are approximately 0.5% per million years for avian protein-coding sequences and 1.5% per million years for primate protein-coding and d-loop sequences. Further analyses showed that purifying selection offers the most convincing explanation for the observed relationship between the estimated rate and the depth of the calibration. We rule out the possibility that it is a spurious result arising from sequence errors, and find it unlikely that the apparent decline in rates over time is caused by mutational saturation. Using a rate curve estimated from the d-loop data, several dates for last common ancestors were calculated: modern humans and Neandertals (354 ka; 222-705 ka), Neandertals (108 ka; 70-156 ka), and modern humans (76 ka; 47-110 ka). If the rate curve for a particular taxonomic group can be accurately estimated, it can be a useful tool for correcting divergence date estimates by taking the rate decay into account. Our results show that it is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution.
ing observations with the initiation of a reaction [for example, temperature jump and photochemic... more ing observations with the initiation of a reaction [for example, temperature jump and photochemical or electrochemical (9, 11) generation of a reactant], one can follow each molecule as it reacts to see how confined spaces and low concentrations affect reaction rates and equilibrium in order to compare those measurements with macroscopic measurements. The temporal resolution of the open-shutter experiment can be further improved with higher speed A/D cameras (4 MHz is commercially available) or by imaging narrow subframes. If the frame rate is increased to Ͼ10 kHz (16), then movies can be taken to construct trajectories (14, 15) in free solutions.
Secondary structure models are an important step for aligning sequences, understanding probabilit... more Secondary structure models are an important step for aligning sequences, understanding probabilities of nucleotide substitutions, and evaluating the reliability of phylogenetic reconstructions.
The Pleistocene was a dynamic period for Holarctic mammal species, complicated by episodes of gla... more The Pleistocene was a dynamic period for Holarctic mammal species, complicated by episodes of glaciation, local extinctions, and intercontinental migration. The genetic consequences of these events are difficult to resolve from the study of present-day populations. To provide a direct view of population genetics in the late Pleistocene, we measured mitochondrial DNA sequence variation in seven permafrost-preserved brown bear (Ursus arctos) specimens, dated from 14,000 to 42,000 years ago. Approximately 36,000 years ago, the Beringian brown bear population had a higher genetic diversity than any extant North American population, but by 15,000 years ago genetic diversity appears similar to the modern day. The older, genetically diverse, Beringian population contained sequences from three clades now restricted to local regions within North America, indicating that current phylogeographic patterns may provide misleading data for evolutionary studies and conservation management. The late Pleistocene phylogeographic data also indicate possible colonization routes to areas south of the Cordilleran ice sheet.
Two groups of flightless ratite birds existed in New Zealand during the Pleistocene: the kiwis an... more Two groups of flightless ratite birds existed in New Zealand during the Pleistocene: the kiwis and the moas. The latter are now extinct but formerly included 11 species. We have enzymatically amplified and sequenced approximately 400 base pairs of the mitochondrial 12S rRNA gene from bones and soft tissue remains of four species of moas as well as eight other species of ratite birds and a tinamou. Contrary to expectation, the phylogenetic analysis shows that the kiwis are more closely related to Australian and African ratites than to the moas. Thus, New Zealand probably was colonized twice by ancestors of ratite birds.
Zoogeographic, palaeontological and biochemical data support a Southern Hemisphere origin for pas... more Zoogeographic, palaeontological and biochemical data support a Southern Hemisphere origin for passerine birds, while accumulating molecular data suggest that most extant avian orders originated in the mid-Late Cretaceous. We obtained DNA sequence data from the nuclear c-myc and RAG-1 genes of the major passerine groups and here we demonstrate that the endemic New Zealand wrens (Acanthisittidae) are the sister taxon to all other extant passerines, supporting a Gondwanan origin and early radiation of passerines. We propose that (i) the acanthisittids were isolated when New Zealand separated from Gondwana (ca. 82-85 Myr ago), (ii) suboscines, in turn, were derived from an ancestral lineage that inhabited western Gondwana, and (iii) the ancestors of the oscines (songbirds) were subsequently isolated by the separation of Australia from Antarctica. The later spread of passerines into the Northern Hemisphere reflects the northward migration of these former Gondwanan elements.
The distribution of postmortem damage in mitochondrial DNA retrieved from 37 ancient human DNA sa... more The distribution of postmortem damage in mitochondrial DNA retrieved from 37 ancient human DNA samples was analyzed by cloning and was compared with a selection of published animal data. A relative rate of damage (r v ) was calculated for nucleotide positions within the human hypervariable region 1 (HVR1) and cytochrome oxidase subunit III genes. A comparison of damaged sites within and between the regions reveals that damage hotspots exist and that, in the HVR1, these correlate with sites known to have high in vivo mutation rates. Conversely, HVR1 subregions with known structural function, such as MT5, have lower in vivo mutation rates and lower postmortem-damage rates. The postmortem data also identify a possible functional subregion of the HVR1, termed "low-diversity 1," through the lack of sequence damage. The amount of postmortem damage observed in mitochondrial coding regions was significantly lower than in the HVR1, and, although hotspots were noted, these did not correlate with codon position. Finally, a simple method for the identification of incorrect archaeological haplogroup designations is introduced, on the basis of the observed spectrum of postmortem damage.
Molecular studies have the potential to shed light on the origin of the animal phyla by providing... more Molecular studies have the potential to shed light on the origin of the animal phyla by providing independent estimates of the divergence times, but have been criticized for failing to account adequately for variation in rate of evolution. A method of dating divergence times from molecular data addresses the criticisms of earlier studies and provides more realistic, but wider, confidence intervals. The data are not compatible with the Cambrian explosion hypothesis as an explanation for the origin of metazoan phyla, and provide additional support for an extended period of Precambrian metazoan diversification. The fossil dates used to form pairs of sequences were (in millions of years before present):
Short term selection for recombination among mutually antagonistic species, Nature 328, 66-68 32 ... more Short term selection for recombination among mutually antagonistic species, Nature 328, 66-68 32 Müller, H.J. (1964) The relation of recombination to mutational advance, Mutat. Res. 1, 2-9 33 Howard, R.S. and Lively, C.M. (1994) Parasitism, mutation accumulation and the maintenance of sex, Nature 367, 554-557 Experimental evidence for the adaptive value of sexual reproduction, Genetica 72, 151-159 45 Kondrashov, A.S. and Yampolsky, L.Y. (1996) High genetic variability under the balance between symmetric mutation and fluctuating stabilizing selection, Genet. A molecular-clock date for the origin of the animal phyla, Lethaia 15, 199-205 10 Janke, A. et al. (1994) The marsupial mitochondrial genome and the evolution of placental mammals, Genetics 137, 243-256 11 Doolittle, R.F. et al. (1996) Determining divergence times of the major kingdoms of living organisms with a protein clock, Science 271, 470-477 REVIEWS 155
Ice Age refugia and Quaternary extinctions: An issue of Quaternary evolutionary palaeoecology a b... more Ice Age refugia and Quaternary extinctions: An issue of Quaternary evolutionary palaeoecology a b s t r a c t Quaternary palaeoecology, as a discipline, involves the analysis of a large range of fossil organisms from the last ca. 2 million years. This paper considers the role that these Quaternary records can take in better understanding the evolution of those organisms. We also discuss the surprisingly low uptake of evolutionary biology in Quaternary palaeoecological studies. This leads us to encourage an advance on both these fronts with a greater degree of collaboration with phylogeographic and ancient DNA researchers. These discussions accompany a summary of a special issue of Quaternary Science Reviews representing the proceedings of the XVII INQUA held in Cairns Australia in 2007. This special issue includes papers on a wide variety of Quaternary evolutionary palaeoecological and population dynamic subjects including extinct Pacific Island palm trees, Beringian beetles, Scandinavian trees, and the effects on human and animal populations of an extraterrestrial impact event in the Late Glacial of North America.
Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various g... more Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various genes and taxa. Recent studies based on population-level and pedigree data have produced remarkably high estimates of mutation rate, which strongly contrast with substitution rates inferred in phylogenetic (species-level) studies. Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (,1-2 Myr) mutation rate and the low, long-term substitution rate. The relationship between the age of the calibration and the rate of change can be described by a vertically translated exponential decay curve, which may be used for correcting molecular date estimates. The phylogenetic substitution rates in mitochondria are approximately 0.5% per million years for avian protein-coding sequences and 1.5% per million years for primate protein-coding and d-loop sequences. Further analyses showed that purifying selection offers the most convincing explanation for the observed relationship between the estimated rate and the depth of the calibration. We rule out the possibility that it is a spurious result arising from sequence errors, and find it unlikely that the apparent decline in rates over time is caused by mutational saturation. Using a rate curve estimated from the d-loop data, several dates for last common ancestors were calculated: modern humans and Neandertals (354 ka; 222-705 ka), Neandertals (108 ka; 70-156 ka), and modern humans (76 ka; 47-110 ka). If the rate curve for a particular taxonomic group can be accurately estimated, it can be a useful tool for correcting divergence date estimates by taking the rate decay into account. Our results show that it is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution.
ing observations with the initiation of a reaction [for example, temperature jump and photochemic... more ing observations with the initiation of a reaction [for example, temperature jump and photochemical or electrochemical (9, 11) generation of a reactant], one can follow each molecule as it reacts to see how confined spaces and low concentrations affect reaction rates and equilibrium in order to compare those measurements with macroscopic measurements. The temporal resolution of the open-shutter experiment can be further improved with higher speed A/D cameras (4 MHz is commercially available) or by imaging narrow subframes. If the frame rate is increased to Ͼ10 kHz (16), then movies can be taken to construct trajectories (14, 15) in free solutions.
Secondary structure models are an important step for aligning sequences, understanding probabilit... more Secondary structure models are an important step for aligning sequences, understanding probabilities of nucleotide substitutions, and evaluating the reliability of phylogenetic reconstructions.
The Pleistocene was a dynamic period for Holarctic mammal species, complicated by episodes of gla... more The Pleistocene was a dynamic period for Holarctic mammal species, complicated by episodes of glaciation, local extinctions, and intercontinental migration. The genetic consequences of these events are difficult to resolve from the study of present-day populations. To provide a direct view of population genetics in the late Pleistocene, we measured mitochondrial DNA sequence variation in seven permafrost-preserved brown bear (Ursus arctos) specimens, dated from 14,000 to 42,000 years ago. Approximately 36,000 years ago, the Beringian brown bear population had a higher genetic diversity than any extant North American population, but by 15,000 years ago genetic diversity appears similar to the modern day. The older, genetically diverse, Beringian population contained sequences from three clades now restricted to local regions within North America, indicating that current phylogeographic patterns may provide misleading data for evolutionary studies and conservation management. The late Pleistocene phylogeographic data also indicate possible colonization routes to areas south of the Cordilleran ice sheet.
Two groups of flightless ratite birds existed in New Zealand during the Pleistocene: the kiwis an... more Two groups of flightless ratite birds existed in New Zealand during the Pleistocene: the kiwis and the moas. The latter are now extinct but formerly included 11 species. We have enzymatically amplified and sequenced approximately 400 base pairs of the mitochondrial 12S rRNA gene from bones and soft tissue remains of four species of moas as well as eight other species of ratite birds and a tinamou. Contrary to expectation, the phylogenetic analysis shows that the kiwis are more closely related to Australian and African ratites than to the moas. Thus, New Zealand probably was colonized twice by ancestors of ratite birds.
Zoogeographic, palaeontological and biochemical data support a Southern Hemisphere origin for pas... more Zoogeographic, palaeontological and biochemical data support a Southern Hemisphere origin for passerine birds, while accumulating molecular data suggest that most extant avian orders originated in the mid-Late Cretaceous. We obtained DNA sequence data from the nuclear c-myc and RAG-1 genes of the major passerine groups and here we demonstrate that the endemic New Zealand wrens (Acanthisittidae) are the sister taxon to all other extant passerines, supporting a Gondwanan origin and early radiation of passerines. We propose that (i) the acanthisittids were isolated when New Zealand separated from Gondwana (ca. 82-85 Myr ago), (ii) suboscines, in turn, were derived from an ancestral lineage that inhabited western Gondwana, and (iii) the ancestors of the oscines (songbirds) were subsequently isolated by the separation of Australia from Antarctica. The later spread of passerines into the Northern Hemisphere reflects the northward migration of these former Gondwanan elements.
The distribution of postmortem damage in mitochondrial DNA retrieved from 37 ancient human DNA sa... more The distribution of postmortem damage in mitochondrial DNA retrieved from 37 ancient human DNA samples was analyzed by cloning and was compared with a selection of published animal data. A relative rate of damage (r v ) was calculated for nucleotide positions within the human hypervariable region 1 (HVR1) and cytochrome oxidase subunit III genes. A comparison of damaged sites within and between the regions reveals that damage hotspots exist and that, in the HVR1, these correlate with sites known to have high in vivo mutation rates. Conversely, HVR1 subregions with known structural function, such as MT5, have lower in vivo mutation rates and lower postmortem-damage rates. The postmortem data also identify a possible functional subregion of the HVR1, termed "low-diversity 1," through the lack of sequence damage. The amount of postmortem damage observed in mitochondrial coding regions was significantly lower than in the HVR1, and, although hotspots were noted, these did not correlate with codon position. Finally, a simple method for the identification of incorrect archaeological haplogroup designations is introduced, on the basis of the observed spectrum of postmortem damage.
Molecular studies have the potential to shed light on the origin of the animal phyla by providing... more Molecular studies have the potential to shed light on the origin of the animal phyla by providing independent estimates of the divergence times, but have been criticized for failing to account adequately for variation in rate of evolution. A method of dating divergence times from molecular data addresses the criticisms of earlier studies and provides more realistic, but wider, confidence intervals. The data are not compatible with the Cambrian explosion hypothesis as an explanation for the origin of metazoan phyla, and provide additional support for an extended period of Precambrian metazoan diversification. The fossil dates used to form pairs of sequences were (in millions of years before present):
Short term selection for recombination among mutually antagonistic species, Nature 328, 66-68 32 ... more Short term selection for recombination among mutually antagonistic species, Nature 328, 66-68 32 Müller, H.J. (1964) The relation of recombination to mutational advance, Mutat. Res. 1, 2-9 33 Howard, R.S. and Lively, C.M. (1994) Parasitism, mutation accumulation and the maintenance of sex, Nature 367, 554-557 Experimental evidence for the adaptive value of sexual reproduction, Genetica 72, 151-159 45 Kondrashov, A.S. and Yampolsky, L.Y. (1996) High genetic variability under the balance between symmetric mutation and fluctuating stabilizing selection, Genet. A molecular-clock date for the origin of the animal phyla, Lethaia 15, 199-205 10 Janke, A. et al. (1994) The marsupial mitochondrial genome and the evolution of placental mammals, Genetics 137, 243-256 11 Doolittle, R.F. et al. (1996) Determining divergence times of the major kingdoms of living organisms with a protein clock, Science 271, 470-477 REVIEWS 155
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