Yielded Age Estimates Research Articles

A biochronological date of 3.6 million years for "Little Foot" (StW 573, Australopithecus prometheus from Sterkfontein, South Africa).

A debate has developed with regard to geological ages of hominin fossils attributed to Australopithecus africanus and Australopithecus prometheus in South African Plio-Pleistocene cave deposits. For the Sterkfontein caves (Members 2 and 4), cosmogenic nuclide isochron (10Be/26Al) dating has yielded age estimates ranging from 3.4 to 3.7 million years ago (Ma). However, biochronological approaches using nonhominin primates suggest an alternative age range between 2 and 2.6 Ma. Based on a new method of hominin biochronology, Thackeray and Dykes have recognized that Sterkfontein Member 4 has a mean age of 2.76 Ma associated with a wide range (circa 2.0-3.5 Ma). In this study, the Sterkfontein skull and skeleton (StW 573), nicknamed "Little Foot" from Member 2 and attributed to A. prometheus, is reassessed. A regression model applied to estimate its age provides a hypothesized date of 3.6 Ma, which compares favorably with the existing cosmogenic dates.

Корневые структуры Даригангского и Витимского вулканических полей Японско-Байкальского геодинамического коридора: Соотношения источников позднекайнозойских магматических расплавов и современных локальных низкоскоростных аномалий в верхней мантии

In the Dariganga volcanic field of southeastern Mongolia, mainly basalt and tephrite melts with a MgO content of 5–11 wt. % and La/Yb ratio 7–40, derived from the mantle region of transition from the asthenosphere to the lithosphere, erupted in the last 14 million years. Basanite melts with a high MgO content (11–15.8 wt. %) and phonotephrite melts with a high La/Yb ratio (40–54) played a special role. Some basanites erupted after melting of the material of a residual slab source with a high potential temperature (Tp = 1489 °C) in the time interval of 10–5 million years ago, others due to melting of an OIB-like source at Tp up to 1423 °C about 4–3 million years ago. Phonotephrites resulted from low-temperature degassing of mantle fluids during the Quaternary. For the sources of basanites and phonotephrites, Pb-isotope age estimates yield age estimates for the protomantle (4.47 and 4.45 Ga, respectively) and age-modified mantle (3.11 and 2.74 Ga, respectively). We suggest that Quaternary degassing of mantle fluids with phonotephrite eruptions in the Dariganga volcanic field is reflected in the generation of the local East Mongolian anomaly of low S-wave velocities in the upper mantle on the SSW flank of the Japan-Baikal geodynamic corridor and that similar mechanism of Quaternary degassing of mantle fluids is responsible for the formation of the local North Baikal low-velocity root structure of the Vitim volcanic field at the axial part of the geodynamic corridor. High-Mg rocks (basanites and picrobasalts) of the latter volcanic field has been shifted relative to the root structure by 300 km in the last 16 million years.

Characterizing chloroplast genomes and inferring maternal divergence of the Triticum–Aegilops complex

The Triticum (wheat)–Aegilops (goatgrass) complex has been extensively studied, but the evolutionary history of polyploid wheats has not been fully elucidated. The chloroplast (cp) with maternal inheritance and homoplasy can simplify the sequence-based evolutionary inferences, but informative inferences would require a complete and accurate cp genome sequence. In this study, 16 cp genomes representing five Aegilops and 11 Triticum species and subspecies were sequenced, assembled and annotated, yielding five novel circular cp genome sequences. Analyzing the assembled cp genomes revealed no marked differences in genome structure and gene arrangement across the assayed species. A polymorphism analysis of 72 published cp genome sequences representing 10 Aegilops and 15 Triticum species and subspecies detected 1183 SNPs and 1881 SSRs. More than 80% SNPs detected resided on the downstream and upstream gene regions and only 2.78% or less SNPs were predicted to be deleterious. The largest nucleotide diversity was observed in the short single-copy genomic region. Relatively weak selection pressure on cp coding genes was detected. Different phylogenetic analyses confirmed that the maternal divergence of the Triticum–Aegilops complex had three deep lineages each representing a diploid species with nuclear A, B, or D genome. Dating the maternal divergence yielded age estimates of divergence that matched well with those reported previously. The divergence between emmer and bread wheats occurred at 8200–11,200 years ago. These findings are useful for further genomic studies, provide insight into cp genome evolvability and allow for better understanding of the maternal divergence of the Triticum–Aegilops complex.

Iconographic and archaeometric studies on the rock art at Musayqira, Al‐Quwaiyah Governorate, central Saudi Arabia

AbstractWe investigated the rock art (petroglyphs) in the Al‐Quwaiyah Governorate (Saudi Arabia) with focus on the Musayqira site. Iconographic analysis showed a broad variety of human depictions, game animals (ibex, ass, ostrich, lion, etc.), domestic animals (cattle, camel, horse, dog, etc.), inscriptions and abstract symbols. Archaeometric measurements by pXRF provided the areal densities of Mn on petroglyphs and intact rock varnish. Varnish accumulation rates were derived from Mn density measurements on inscriptions of known approximate age. Applying these rates to varnish densities on the petroglyphs yielded age estimates. Some of the rock art was incised in fracture fill rather than true varnish, complicating the interpretation of the data. The combination of iconographic and archaeometric data indicated multiple phases of rock art creation, corresponding to the Late Neolithic, Bronze Age, Iron Age, and Islamic Period, with different artistic traditions, reflecting changing socioeconomic and ecological conditions.

Rock art dating by 230Th/234U analysis: an appraisal of Chinese case studies

A reconsideration of the application of 230Th/234U analysis to thin accretionary skins of re-precipitated carbonate to secure minimum or maximum ages for physically related rock art suggests that the controversy it has created can be resolved. A program to test the method’s results indicates that such calcite skins tend to yield age estimates that are too high, particularly from Pleistocene samples. Although the controversy about such results has escalated in recent years, it had initially become apparent several decades ago. Here, two case studies of Chinese rock art, in Heilongjiang and Yunnan Provinces, are presented. Potential error sources accounting for the discrepancies are proposed. Some cautionary measures are presented to prevent the promotion of sensational but ultimately erroneous rock art age estimates deriving from this method.

Growth estimates of Caribbean reef sponges on a shipwreck using 3D photogrammetry

The growth rates and ages of many benthic marine organisms are poorly understood, complicating our understanding of ecosystem change. This is particularly true for sponges, which are morphologically diverse and lack indicators of annual growth. In this study, we used emerging technologies to measure volume, surface area, and approximate age of 16 sponge species on the Tibbetts shipwreck off Cayman Brac, Caribbean Sea. Photogrammetry was used to determine the volume of individual sponges on the wreck surface, and a time series of YouTube videos was amassed in order to approximate the greatest possible age of the sponges as 8.74 y. Applying the volume measurements to an existing growth equation for the Caribbean sponge Aiolochroia crassa yielded age estimates of 5.2–10.4 y for the largest individuals of the 16 species. Specific growth rates were then calculated for 7 species from the Tibbetts and 8 species from a second shipwreck (Spiegel Grove, Key Largo, FL). Subsequent growth forecasts from these 15 species corroborate a resource trade-off between growth and the production of chemical defenses. Shipwrecks and other anthropogenic structures can be an important source of demographic information for benthic organisms, provided that certain assumptions about their provenance and history can be met.

Life history of the deep-water persimmon eelpout (Eucryphycus californicus, family: Zoarcidae), and its use of drift vegetation as an ecological subsidy

The Persimmon Eelpout (Eucryphycus californicus) is a relatively unknown, deep-sea fish inhabiting temperate marine waters on the west coast of North America. Using samples collected in the mid-1970s, the most recent targeted sampling for this species, we present basic life history attributes, and an analysis of the relationship between E. californicus and drift macrophyte habitat in the Monterey Canyon, California, USA. A diet analysis revealed that the fish consumes predominantly small crustaceans, especially amphipods and copepods, including species that associate with drift macrophyte habitat. Otoliths were analyzed to yield age estimates ranging from 0 to 6 years, and growth was modeled showing a maximum length of 203 mm for males and 271 mm for females. An analysis of the reproductive ecology of E. californicus showed that like many deep-sea fishes, females lay relatively few, large eggs. The species exhibits a protracted spawning period, and females spawn with only one functional ovary. Empirical information presented in this paper and anecdotal evidence shows that E. californicus likely relies on drift algae and seagrasses, a habitat subsidy exported to the deep-sea environment from adjacent kelp forest ecosystems, for shelter and to concentrate food resources. This example of a species dependent on an ecosystem subsidy adds to our knowledge regarding the effects of cross-ecosystem connectivity in the marine environment, and furthers our understanding of the ecology of the deep-sea macrofaunal assemblage in Monterey Bay.

The stratigraphy and chronology of the fluvial sediments at Warsash, UK: implications for the Palaeolithic archaeology of the River Test

This paper reports new fieldwork at Warsash which clarifies the terrace stratigraphic framework of the Palaeolithic archaeology of the region. Sections were recorded in former gravel pits and at coastal locations, supplemented by the use of ground penetrating radar and luminescence dating techniques. The region’s extensive borehole archive was also analysed to produce a revised terrace stratigraphy at Warsash and for the Test valley as a whole. At Warsash, some of the sediments previously identified as the Mottisfont/Lower Warsash Terrace are reassigned to the Hamble, Belbin/Upper Warsash and Ganger Wood/Mallards Moor Terraces. A luminescence dating programme, using test procedures not utilised in earlier dating studies in the region, yielded age estimates for the Hamble and Mottisfont/Lower Warsash Terraces at Warsash and also highlighted the complicated nature of the fluvial sediments of the River Test, suggesting that published luminescence ages for these deposits should be treated with some caution. This study indicates that the data used to construct terrace stratigraphies also requires careful assessment. The use of bedrock height and sediment thickness data produces more coherent long profile correlations than those produced by terrace surface data alone. The revised terrace stratigraphy provides the framework for the Palaeolithic archaeology at Warsash and clarifies correlations within and between archaeologically important sediments of the Test Valley, enabling it to contribute to discussions on the Lower-Middle Pleistocene settlement history of southern Britain.

UV-extended E-MILES stellar population models: young components in massive early-type galaxies

We present UV-extended E-MILES stellar population synthesis models covering the spectral range 1680-50000A at moderately high resolution. We employ the NGSL space-based stellar library to compute spectra of single-age, single-metallicity stellar populations in the wavelength range from 1680 to 3540A. These models represent a significant improvement in resolution and age/metallicity coverage over previous studies based on earlier space-based libraries. These model spectra were joined with those we computed in the visible using MILES, and other empirical libraries for redder wavelengths. The models span the metallicity range -1.79<[M/H]<+0.26 and ages above 30 Myr, for a suite of IMF types with varying slopes. We focus on the behaviour of colours, spectra and line-strength indices in the UV range as a function of relevant stellar population parameters. Whereas some indices strengthen with increasing age and metallicity, as most metallicity indicators in the visible, other indices peak around 3 Gyr for metal-rich stellar populations, such as Mg at 2800A. Our models provide reasonably good fits to the integrated colours and most line-strengths of the stellar clusters of the Milky-Way and LMC. Our full-spectrum fits in the UV range for a representative set of ETGs of varying mass yield age and metallicity estimates in very good agreement with those obtained in the optical range. The comparison of UV colours and line-strengths of massive ETGs with our models reveals the presence of young stellar components, with ages in the range 0.1-0.5 Gyr and mass fractions 0.1-0.5%, on the top of an old stellar population.

Xes-Xen thermochronology of the Rayner metamorphic complex, Enderby Land (East Antarctica, Molodezhnaya Station Area)

The Xes-Xen dating of zircons from rocks of the Rayner Complex of the Enderby Land at the Molodezhnaya Station area (coast of the Alasheyev Bight) yielded age estimates of 550 ± 50 and 1040 ± 30 Ma. The metamorphic rocks of the Rayner Complex record two main events: first, the crystallization of the magmatic protoliths of charnockitic and enderbitic gneisses and, second, superimposed structural and metamorphic alterations under conditions transitional from the amphibolite to granulite facies (metamorphism manifested regionally in the rocks of the Rayner Complex). The most reliable Xes-Xen age estimates for magmatic zircons from the charnockitic and enderbitic gneisses correspond to the Grenville stage of the development of the Rayner Complex (∼1.0 Ga). The Xe isotopic systematics of metamorphic zircons reflect a pan-African stage in the evolution of the Rayner Complex (600–550 Ma). Pan-African events are reflected in the U-Xe isotope system in two cases: if metamorphic zircons crystallized at the same time (which probably resulted in the formation of a plateau in the Xes-Xen age spectrum) and if the initial isotopic systems were disturbed (which resulted in a decrease in apparent age toward low-temperature gas fractions). It is important that secondary alterations and a decrease in apparent ages to 600–550 Ma affected only those components (i.e., caused xenon release only from those traps) that were unstable under the maximum metamorphic temperatures and yielded Tcl values lower than 750°C (conditions transitional from the amphibolite to granulite facies). At a higher xenon retention, “primary” isotopic systems are preserved. Consequently, the age of metamorphism transitional between the amphibolite and granulite facies can be estimated at 600–550 Ma on the basis of Xes-Xen dating. In general, the results of our study indicate that the age of regional metamorphism of the Rayner complex at the Molodezhnaya area is approximately 600–550 Ma rather than ∼1.0 Ga, as was previously supposed.

Age-at-death estimation of pathological individuals: A complementary approach using teeth cementum annulations

Bioarchaeologists rely on accurate estimations of age-at-death. Clearly, some pathological conditions are associated with gross morphological changes in the skeleton that could impact the effectiveness of age-at-death estimation (i.e. methods based on the pelvis, fourth rib, dental attrition, and cranial stenosis). The magnitude of this problem has not been widely studied due to a paucity of pathological skeletons of known age. We assessed age-at death for three individuals affected by bone dysplasias (achondroplasia, residual rickets, osteogenesis imperfecta) using cementum annulations and several osseous age indicators. We predicted osseous indicators that are based on gross morphological changes would yield age estimates discrepant from the cementochronology. Results demonstrated considerable differences in age estimates between morphological and histological techniques suggesting a need for additional research on the effects of pathology on the accuracy of morphological methods. Conversely, we addressed the proposition that cementum annulations will be inappropriate for age estimation in cases of chronic and severe rhino-maxillary infection and periodontitis. We assessed age-at-death for one individual with leprosy and found no indication the disease process affected cementum formation or preservation. The results of this research indicate the potential value of cementochronology in cases where skeletal pathological conditions constrain the usefulness of traditional age estimation approaches.

Poster #M27 SERIOUS OBSTETRIC COMPLICATIONS CONTRIBUTE TO RISK FOR HIPPOCAMPAL DYSFUNCTION DURING RECOGNITION MEMORY

Magnetic and seismic surveys were carried out in the Blake—Bahama Basin. The magnetic survey delineates low-amplitude anomalies in the Jurassic quiet zone that can be correlated with anomalies found elsewhere in the western North Atlantic (M26, M27 and M28). A spreading rate of 2.25 cm/yr was derived from anomalies M22 through M25 and extrapolated into the Jurassic, giving a Callovian age for M26 and M27 and Bathonian for M28 (150, 154 and 159 m.y., respectively). The seismic survey traces the major sedimentary horizons and basement in the vicinity of DSDP site 391. Sonobuoy data were used to convert reflection time to depth for correlation with the drilling results. A deep reflector not penetrated at site 391 is designated as horizon D. Basement at site 391 lies 1800 m subbottom, just within reach of the drill. Extrapolation of the sedimentation rate estimated for the lower 400 m of the drill hole yielded age estimates of 156 m.y. for horizon D and 160 m.y. for basement.

A Comparison of Different Age Estimation Methods for the Northern Snakehead

AbstractWe used otoliths, scales, pectoral fins, dorsal fins, basioccipital bones, opercular bones, interopercular bones, vertebrae, teeth, and cleithra sampled from 221 known‐age Northern Snakeheads Channa argus argus representing five age‐groups to determine and compare age estimation methods for this species. Results showed that accuracy of age estimation methods varied among structures: 85.68% of otoliths, 68.91% of scales, 49.25% of pectoral fin rays, and 27.67% of opercular bones yielded age estimates that were consistent with the actual fish ages. Ages determined from other structures, such as interopercular bones, dorsal fins, basioccipital bones, and vertebrae, had lower rates of agreement (&lt;20%) with actual ages. The current results suggest that age estimation with otoliths, especially sagittal otoliths, is the most accurate method for use with Northern Snakeheads. Furthermore, analysis of scales can be used as a supplementary approach, especially for younger (age &lt; 3) Northern Snakeheads.Received March 14, 2013; accepted June 27, 2013

U–Pb dating of zircon in hydrothermally altered rocks of the Kawerau Geothermal Field, Taupo Volcanic Zone, New Zealand

Crystallisation-age spectra have been obtained by SIMS techniques (SHRIMP-RG) on zircons from altered volcanic units penetrated by drillholes at Kawerau Geothermal Field in the central Taupo Volcanic Zone (TVZ), New Zealand. Drillholes penetrate 700–1300m of volcanic rocks and sediments before reaching the basement Mesozoic greywacke. Twenty-seven samples of altered volcanic lithologies and two surficial, fresh rock units have been studied in order to constrain ages of the major stratigraphic units. Within the volcanic/sedimentary pile the oldest in-situ ignimbrites that can be widely correlated have ages of ~1.45Ma. Between them and the basement greywacke is a variable thickness of sediments, mostly greywacke gravels and minor volcaniclastic units, reflecting localised basinal deposition associated with strike–slip faulting. Two ignimbrites within this sequence yield age estimates of c. 2.4 and 2.1Ma, consistent with these being distal southern Coromandel Volcanic Zone deposits, pre-dating TVZ activity. Below the regional marker plane of the 0.32Ma Matahina ignimbrite, three main ignimbrite groups occur, with ages around 1.45Ma, 1.0Ma and 0.6–0.5Ma, which are separated by sediment-dominated intervals and andesite volcanics. All of these ignimbrites represent marker horizons from other volcanic centres and do not reflect the presence of local magmatic heat sources.Numerous bodies of coherent rhyolite, previous labelled as Caxton and Onepu rhyolites, have been intersected at all pre-Matahina ignimbrite levels (including within the basement greywacke) and reflect earlier local magmatic heat sources. Our geochronological data resolve these rock bodies into three packages. The youngest is represented by the surficial rhyodacite Onepu domes, 40Ar/39Ar dated at 0.138±0.007Ma. U–Pb ages on zircons from dome material yield a spectrum that can be matched (consistent with petrography) with two dikes intersected at 880m and 2.67km depth, and with an estimated age of 0.15±0.01Ma (Onepu Formation). The older two packages consist of older crystal rich (~15%) and younger crystal-poor (~5%) rhyolite, here grouped as Caxton Formation and with eruption/intrusion age of 0.36±0.03Ma. The shallowest Caxton rhyolite bodies are interpreted to be domes, whilst deeper intersections are inferred to be sills based on the lateral extents relative to thicknesses.Net subsidence rates inferred from depths to key units do not reflect the present-day situation. Modern rates of subsidence (2±1mm/yr) associated with TVZ rifting processes can have been active for no more than ~50,000years, based on elevation differences of the Matahina ignimbrite top surface. An inferred change in intrusion geometry from sill (Caxton) to dike (Onepu) indicates a change in principal stress orientations reflecting onset of the modern Whakatane Graben. This change is dated at ~0.37Ma in coastal sedimentary sequences 23km to the north of Kawerau, consistent with our age data. Although previously interpreted to be a long-lived system, the modern Kawerau Geothermal Field is a Holocene entity reflecting the rejuvenation of magmatic heat flux associated with Putauaki volcano superimposed on an area of multiple reactivated fault structures, sporadic magmatism and variable rates of subsidence.

Iceberg discharge to the Chukchi shelf during the Younger Dryas

The extent of glaciation in northwestern Alaska, the source of sediment supply to the Chukchi shelf and slope, and the movement of sea ice and icebergs across the shelf during the last glacial maximum (LGM) remain poorly constrained. Here we present geophysical and geological data from the outer Chukchi margin that reveal a regionally extensive, heavily ice-scoured surface ∼ 5–8 m below the modern seafloor. Radiocarbon dating of this discrete event yields age estimates between 10,600 and 11,900 14C yr BP, indicating the discharge event occurred during the Younger Dryas. Based on mineralogy of the ice-rafted debris, the icebergs appear to be sourced from the northwestern Alaskan margin, which places important constraints on the ice extent in northern Alaska during the LGM as well as existing circulation models for the region.

Electron spin resonance dating of South Australian megafauna sites*

In recent years, there has been much debate about the timing of the Late Pleistocene extinction of the Australian megafauna. Some studies postulated a rapid, continental-wide extinction at around 46 000 years ago and that the arrival of humans in Australia, rather than climatic fluctuations, was the main cause for the demise of the megafauna. We have applied electron spin resonance (ESR) dating to a series of teeth from megafauna sites in South Australia, where young ages were expected. During this study, a number of unexpected problems were encountered. These were mainly related to the fact that ESR age assessments on fossil teeth are critically dependent on a realistic reconstruction of the post-mortem uranium uptake into the dental tissues. At virtually all sites, conventional, routine ESR dating, based on the parametric early and linear U-uptake models, would have led to grossly erroneous results. Most teeth were analysed for U-series isotopes with laser ablation ICP-MS, and the results were used to calculate combined U-series ESR age estimates. Only one of the 24 teeth analysed conformed to the commonly applied early and linear U-uptake models. At one of the sites, we found for the first time clear evidence of uranium leaching from dentine. Detailed laser ablation scans revealed that, in contrast to large mammals outside Australia, marsupial tooth enamel does not seem to contain a barrier layer close to the outer surface that blocks uranium diffusion into the enamel. As a consequence, uranium migrates into the enamel layer from both the outside and the inside via the dentine, which makes marsupial teeth generally less well suited for ESR dating. It was particularly difficult to obtain age estimates for the site of Black Creek Swamp, where the sediments contained extreme U-series disequilibrium, and the teeth had unexpectedly accumulated very high U-concentrations (up to 700 ppm in dentine) within a few thousand years. Although most of the sites contained reworked teeth, none of the samples yielded age estimates that were significantly younger than the proposed extinction window of about 40 000–51 000 years.

Age and growth in olive ridley seaturtles (Lepidochelys olivacea) from the North‐central Pacific: a skeletochronological analysis

AbstractThe olive ridley is the most abundant seaturtle species in the world but little is known of the demography of this species. We used skeletochronological data on humerus diameter growth changes to estimate the age of North Pacific olive ridley seaturtles caught incidentally by pelagic longline fisheries operating near Hawaii and from dead turtles washed ashore on the main Hawaiian Islands. Two age estimation methods [ranking, correction factor (CF)] were used and yielded age estimates ranging from 5 to 38 and 7 to 24 years, respectively. Rank age‐estimates are highly correlated (r = 0.93) with straight carapace length (SCL), CF age estimates are not (r = 0.62). We consider the CF age‐estimates as biologically more plausible because of the disassociation of age and size. Using the CF age‐estimates, we then estimate the median age at sexual maturity to be around 13 years old (mean carapace size c. 60 cm SCL) and found that somatic growth was negligible by 15 years of age. The expected age‐specific growth rate function derived using numerical differentiation suggests at least one juvenile growth spurt at about 10–12 years of age when maximum age‐specific growth rates, c. 5 cm SCL year−1, are apparent.

THE AGE OF THE ANGIOSPERMS: A MOLECULAR TIMESCALE WITHOUT A CLOCK

The age of the angiosperms has long been of interest to botanists and evolutionary biologists. Many early efforts to date the age of the angiosperms and evolutionary divergences within the angiosperm clade using a molecular clock have yielded age estimates that are grossly inconsistent with the fossil record. We investigated the age of angiosperms using Bayesian relaxed clock (BRC) and penalized likelihood (PL) approaches. Both of these methods allow the incorporation of multiple fossil constraints into the optimization procedure. The BRC method allows a range of values for among-lineage rate of substitution, from a nearly clocklike behavior to a condition in which each branch is allowed an optimal substitution rate, and also accounts for variation in molecular evolution across multiple genes. A topology derived from an analysis of genes from all three plant genomes for 71 taxa was used as a backbone. The effects on age estimates of different genes, single-gene versus concatenated datasets, and the inclusion and assumptions of fossils as age constraints were examined. In addition, the influence of prior distributions on estimates of divergence times was also explored. These results indicate that widely divergent age estimates can result from the different methods (198-139 million years ago), different sources of data (275-122 million years ago), and the inclusion of temporal constraints to topologies. Most dates, however, are between 180-140 million years ago, suggesting a Middle Jurassic-Early Cretaceous origin of flowering plants, predating the oldest unequivocal fossil angiosperms by about 45-5 million years. Nonetheless, these dates are consistent with other recent studies that have used methods that relax the assumption of a strict molecular clock and also agree with the hypothesis that the angiosperms may be somewhat older than the fossil record indicates.

THE AGE OF THE ANGIOSPERMS: A MOLECULAR TIMESCALE WITHOUT A CLOCK

The age of the angiosperms has long been of interest to botanists and evolutionary biologists. Many early efforts to date the age of the angiosperms and evolutionary divergences within the angiosperm clade using a molecular clock have yielded age estimates that are grossly inconsistent with the fossil record. We investigated the age of angiosperms using Bayesian relaxed clock (BRC) and penalized likelihood (PL) approaches. Both of these methods allow the incorporation of multiple fossil constraints into the optimization procedure. The BRC method allows a range of values for among-lineage rate of substitution, from a nearly clocklike behavior to a condition in which each branch is allowed an optimal substitution rate, and also accounts for variation in molecular evolution across multiple genes. A topology derived from an analysis of genes from all three plant genomes for 71 taxa was used as a backbone. The effects on age estimates of different genes, single-gene versus concatenated datasets, and the inclusion and assumptions of fossils as age constraints were examined. In addition, the influence of prior distributions on estimates of divergence times was also explored. These results indicate that widely divergent age estimates can result from the different methods (198–139 million years ago), different sources of data (275–122 million years ago), and the inclusion of temporal constraints to topologies. Most dates, however, are between 180–140 million years ago, suggesting a Middle Jurassic-Early Cretaceous origin of flowering plants, predating the oldest unequivocal fossil angiosperms by about 45–5 million years. Nonetheless, these dates are consistent with other recent studies that have used methods that relax the assumption of a strict molecular clock and also agree with the hypothesis that the angiosperms may be somewhat older than the fossil record indicates.

Comprehensive analysis of two Alu Yd subfamilies.

Alu elements have inserted in the human genome throughout primate evolution. A small number of Alu insertions have occurred after the divergence of humans from nonhuman primates and therefore should not be present in nonhuman primate genomes. Most of these recently integrated Alu elements are contained with a series of discrete Alu subfamilies that are related to each other based upon diagnostic nucleotide substitutions. We have extracted members of the Alu Yd subfamily that are derivatives of the Alu Y subfamily that share a common 12-bp deletion that defines the Yd lineage from the draft sequence of the human genome. Analysis of the Yd Alu elements resulted in the recovery of two new Alu subfamilies, Yd3 and Yd6, which contain a total of 295 members (198 Yd3 and 97 Yd6). DNA sequence analysis of each of the Alu Yd subfamilies yielded age estimates of 8.02 and 1.20 million years old for the Alu Yd3 and Yd6 subfamilies, respectively. Two hundred Alu Yd3 and Yd6 loci were screened using polymerase chain reaction (PCR) assays to determine their phylogenetic origin and associated levels of human genomic diversity. The Alu Yd3 subfamily appears to have started amplifying relatively early in primate evolution and continued propagating albeit at a low level as many of its members are found in a variety of hominoid (humans, greater and lesser ape) genomes. Only two of the elements are polymorphic in the human genome and absent from the genomes of nonhuman primates. By contrast all of the members of the Alu Yd6 subfamily are restricted to the human genome, with 12% of the elements representing insertion polymorphisms in human populations. A single Alu Yd6 locus contained an independent parallel forward insertion of a paralogous Alu Sq sequence in the owl monkey. These Alu subfamilies are a source of genomic fossil relics for the study of primate phylogenetics and human population genetics.