The molecular evolution of ZFY-related genes in birds and mammals

Summary We report the isolation and nucleotide sequence determination of clones derived from five ZFY-related zinc-finger genes from birds and mammals. These sequences are analyzed with reference to the previously published human genes, ZFX and ZFY, and mouse genes, Zfx, Zfa, Zfy-1, and Zfy-2. The analysis indicates that ZFY-related genes are highly conserved in birds and mammals, and that the rate of nucleotide substitution in the Y-linked genes is not as high as predicted. However, the mouse Zfy-1 and Zfy-2 genes are markedly divergent members of the ZFY gene family; we suggest this relates to X-inactivation of the mouse gene Zfx.     

Three patterns of mitochondrial DNA nucleotide divergence in the meadow vole,Microtus pennsylvanicus

Summary The DNA sequence was determined for the cytochrome c oxidase II (COII), tRNA^Lys, and ATPase 8 genes from the mitochondrial genome of the meadow vole, Microtus pennsylvanicus. When compared to other rodents, three different patterns of evolutionary divergence were found. Nucleotide variation in tRNA^Lys is concentrated in the TC loop. Nucleotide variation in the COII gene in three genera of rodents (Microtus, Mus, Rattus) consists predominantly of transitions in the third base positions of codons. The predicted amino acid sequence in highly conserved (>92% similarity). Analysis of the ATPase 8 gene among four genera (Microtus, Cricetulus, Mus, Rattus) revealed more detectable transversions than transitions, many fixed first and second position mutations, and considerable amino acid divergence. The rate of nucleotide substitution at nonsynonymous sites in the ATPase 8 gene is 10 times the rate in the COII gene. In contrast, the estimated absolute mutation rate as determined by analysis of nucleotide substitutions at fourfold degenerate sites probably is the same for the two genes. The primary sequences of the ATPase 8 and COII peptides are constrained differently, but each peptide is conserved in terms of predicted secondary-level configuration.     

Small mammal seed consumption in the Karoo,South Africa: further evidence for divergence in desert biotic processes

Summary Annual seed consumption by a small mammal community in the semi-arid Karoo, South Africa, was calculated using population, biomass and dietary estimates and published estimates of field metabolic rate. The community comprised a macroscelid elephant shrew Macroscelides proboscideus, and two rodents Gerbillurus paeba and Desmodillus auricularis. Only G. paeba consumed seed during the study, and then in low amounts (annual mean = 0.4% of diet, insects = 53%, herbage = 47%), with M. proboscideus and D. auriocularis consuming mainly insects (88%) and herbage (90%), respectively. Energy requirements for the G. paeba population averaged 568 kJ ha^–1 day^–1. Total seed consumption was estimated to be 140 g ha^–1, or 155 000 seeds ha^–1 which represents 0.5% of the annual seed production for this site. These levels of granivory by small mammals are significantly lower than those recorded for North American deserts, and raises the question as to why granivory varies between these systems. These findings also refute the hypothesis that as a result of the harshness and similarity of physical conditions in deserts, the properties of desert communities are convergent.     

A mixed relaxed clock model

Over recent years, several alternative relaxed clock models have been proposed in the context of Bayesian dating. These models fall in two distinct categories: uncorrelated and autocorrelated across branches. The choice between these two classes of relaxed clocks is still an open question. More fundamentally, the true process of rate variation may have both long-term trends and short-term fluctuations, suggesting that more sophisticated clock models unfolding over multiple time scales should ultimately be developed. Here, a mixed relaxed clock model is introduced, which can be mechanistically interpreted as a rate variation process undergoing short-term fluctuations on the top of Brownian long-term trends. Statistically, this mixed clock represents an alternative solution to the problem of choosing between autocorrelated and uncorrelated relaxed clocks, by proposing instead to combine their respective merits. Fitting this model on a dataset of 105 placental mammals, using both node-dating and tip-dating approaches, suggests that the two pure clocks, Brownian and white noise, are rejected in favour of a mixed model with approximately equal contributions for its uncorrelated and autocorrelated components. The tip-dating analysis is particularly sensitive to the choice of the relaxed clock model. In this context, the classical pure Brownian relaxed clock appears to be overly rigid, leading to biases in divergence time estimation. By contrast, the use of a mixed clock leads to more recent and more reasonable estimates for the crown ages of placental orders and superorders. Altogether, the mixed clock introduced here represents a first step towards empirically more adequate models of the patterns of rate variation across phylogenetic trees.This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.     

Evolutionary timescale of monocots determined by the fossilized birth‐death model using a large number of fossil records

Although the phylogenetic relationships between monocot orders are sufficiently understood, a timescale of their evolution is needed. Several studies on molecular clock dating are available, but their results have been biased by their calibration schemes. Recently, the fossilized birth‐death model, a type of Bayesian dating method, was proposed, and it does not require prior calibration and allows the use all available fossils. Using this model, we conducted divergence‐time estimations of monocots to explore their evolutionary timeline without calibration bias. This is the first application of this model to seed plants. The dataset contained the matK and rbcL chloroplast genes of 118 monocot genera covering all extant orders. We employed information from 247 monocot fossils, which exceeded previous dating analyses that used a maximum of 12 monocot fossils. The crown group of monocots was dated to approximately the Late Jurassic–Early Cretaceous periods, and most extant monocot orders were estimated to diverge throughout the Early Cretaceous. Our results overlapped with the divergence time of insect lineages, such as beetles and flies, suggesting an association with pollinators in early monocot evolution. In addition, we proposed three new orders based on divergence time: Orchidales separated from Asparagales and Tofieldiales and Arales separated from Aslimatales.     

Carbon isotope evidence for recent climate‐related enhancement of CO 2 assimilation and peat accumulation rates in Antarctica

Signy Island, maritime Antarctic, lies within the region of the Southern Hemisphere that is currently experiencing the most rapid rates of environmental change. In this study, peat cores up to 2 m in depth from four moss banks on Signy Island were used to reconstruct changes in moss growth and climatic characteristics over the late Holocene. Measurements included radiocarbon dating (to determine peat accumulation rates) and stable carbon isotope composition of moss cellulose (to estimate photosynthetic limitation by CO ₂ supply and model CO ₂ assimilation rate). For at least one intensively ¹⁴C‐dated Chorisodontium aciphyllum moss peat bank, the vertical accumulation rate of peat was 3.9 mm yr^?1 over the last 30 years. Before the industrial revolution, rates of peat accumulation in all cores were much lower, at around 0.6–1 mm yr^?1. Carbon‐13 discrimination (Δ), corrected for background and anthropogenic source inputs, was used to develop a predictive model for CO ₂ assimilation. Between 1680 and 1900, there had been a gradual increase in Δ, and hence assimilation rate. Since 1800, assimilation has also been stimulated by the changes in atmospheric CO ₂ concentration, but a recent decline in Δ (over the past 50–100 years) can perhaps be attributed to documented changes in temperature and/or precipitation. The overall increase in CO ₂ assimilation rate (¹³C proxy) and enhanced C accumulation (¹⁴C proxy) are consistent with warmer and wetter conditions currently generating higher growth rates than at any time in the past three millennia, with the decline in Δ perhaps compensated by a longer growing season.     

中国古人类遗址年代学的研究进展与问题

我国丰富的古人类遗存为研究东亚乃至全球古人类起源、迁徙和演化提供了重要的基础材料与数据。对已发表的2000多处旧石器时代古人类遗址年代学数据的整理和统计分析发现,绝大多数遗址目前仍缺少基本的年代学数据,不足20%的遗址开展过测年,仅10%左右具有相对可靠的年代学数据,只有极少数开展了多种测年方法的交叉定年。对于80多处出土古人类化石的遗址,亦过半存在明显的年代学争议。我们对一些古人类遗址中的常见各种复杂的同沉积和沉积后改造现象进行了详细分析,探讨了我国测年平台和测年队伍建设、考古发掘以及年代学采样与测年方法学等方面存在的问题,及其对遗址年代学研究的可能影响。基于此,笔者提出改善我国古人类年代学研究现状的可能措施,希望可以抛砖引玉,引发对该研究领域更多的关注和思考。     

Molecular evidence for Gondwanan origins of multiple lineages within a diverse Australasian gecko radiation

Aim Gondwanan lineages are a prominent component of the Australian terrestrial biota. However, most squamate (lizard and snake) lineages in Australia appear to be derived from relatively recent dispersal from Asia (< 30 Ma) and in situ diversification, subsequent to the isolation of Australia from other Gondwanan landmasses. We test the hypothesis that the Australian radiation of diplodactyloid geckos (families Carphodactylidae, Diplodactylidae and Pygopodidae), in contrast to other endemic squamate groups, has a Gondwanan origin and comprises multiple lineages that originated before the separation of Australia from Antarctica. Location Australasia. Methods Bayesian (beast ) and penalized likelihood rate smoothing (PLRS) (r 8s ) molecular dating methods and two long nuclear DNA sequences (RAG‐1 and c‐mos) were used to estimate a timeframe for divergence events among 18 genera and 30 species of Australian diplodactyloids. Results At least five lineages of Australian diplodactyloid geckos are estimated to have originated > 34 Ma (pre‐Oligocene) and basal splits among the Australian diplodactyloids occurred c. 70 Ma. However, most extant generic and intergeneric diversity within diplodactyloid lineages appears to post‐date the late Oligocene (< 30 Ma). Main conclusions Basal divergences within the diplodactyloids significantly pre‐date the final break‐up of East Gondwana, indicating that the group is one of the most ancient extant endemic vertebrate radiations east of Wallace’s Line. At least five Australian lineages of diplodactyloid gecko are each as old or older than other well‐dated Australian squamate radiations (e.g. elapid snakes and agamids). The limbless Pygopodidae (morphologically the most aberrant living geckos) appears to have radiated before Australia was occupied by potential ecological analogues. However, in spite of the great age of the diplodactyloid radiation, most extant diversity appears to be of relatively recent origin, a pattern that is shared with other Australian squamate lineages.     

Older than New Caledonia emergence? A molecular phylogenetic study of the eneopterine crickets (Orthoptera: Grylloidea)

Aim A New Caledonian insect group was studied in a world‐wide phylogenetic context to test: (1) whether local or regional island clades are older than 37 Ma, the postulated re‐emergence time of New Caledonia; (2) whether these clades show evidence for local radiations or multiple colonizations; and (3) whether there is evidence for relict taxa with long branches in phylogenetic trees that relate New Caledonian species to geographically distant taxa. Location New Caledonia, south‐west Pacific. Methods We sampled 43 cricket species representing all tribes of the subfamily Eneopterinae and 15 of the 17 described genera, focusing on taxa distributed in the South Pacific and around New Caledonia. One nuclear and three mitochondrial genes were analysed using Bayesian and parsimony methods. Phylogenetic divergence times were estimated using a relaxed clock method and several calibration criteria. Results The analyses indicate that, under the most conservative dating scenario, New Caledonian eneopterines are 5–16 million years old. The largest group in the Pacific region dates to 18–29 Ma. New Caledonia has been colonized in two phases: the first around 10.6 Ma, with the subsequent diversification of the endemic genus Agnotecous, and the second with more recent events around 1–4 Ma. The distribution of the sister group of Agnotecous and the lack of phylogenetic long branches in the genus refute an assumption of major extinction events in this clade and the hypothesis of local relicts. Main conclusions Our phylogenetic studies invalidate a simple scenario of local persistence of this group in New Caledonia since 80 Ma, either by survival on the New Caledonian island since its rift from Australia, or, if one accepts the submergence of New Caledonia, by local island‐hopping among other subaerial islands, now drowned, in the region during periods of New Caledonian submergence.