Ignoring heterozygous sites biases phylogenomic estimates of divergence times: implications for the evolutionary history of Microtus voles

Phylogenetic reconstruction of the evolutionary history of closely related organisms may be difficult because of the presence of unsorted lineages and of a relatively high proportion of heterozygous sites that are usually not handled well by phylogenetic programs. Genomic data may provide enough fixed polymorphisms to resolve phylogenetic trees, but the diploid nature of sequence data remains analytically challenging. Here, we performed a phylogenomic reconstruction of the evolutionary history of the common vole (Microtus arvalis) with a focus on the influence of heterozygosity on the estimation of intraspecific divergence times. We used genome-wide sequence information from 15 voles distributed across the European range. We provide a novel approach to integrate heterozygous information in existing phylogenetic programs by repeated random haplotype sampling from sequences with multiple unphased heterozygous sites. We evaluated the impact of the use of full, partial, or no heterozygous information for tree reconstructions on divergence time estimates. All results consistently showed four deep and strongly supported evolutionary lineages in the vole data. These lineages undergoing divergence processes split only at the end or after the last glacial maximum based on calibration with radiocarbon-dated paleontological material. However, the incorporation of information from heterozygous sites had a significant impact on absolute and relative branch length estimations. Ignoring heterozygous information led to an overestimation of divergence times between the evolutionary lineages of M. arvalis. We conclude that the exclusion of heterozygous sites from evolutionary analyses may cause biased and misleading divergence time estimates in closely related taxa.

A history of civilisation in Palestine

R. A. S. Macalister

Late Glacial and Holocene environmental history of the Pirin Mountains (SW Bulgaria): a paleolimnological study of Lake Dalgoto (2310 m)

Diatoms, Cladocera, and chironomids preserved in the sediments of Lake Dalgoto were studied to reconstruct the history of the lake ecosystem in the context of the vegetation history as represented by the pollen stratigraphy. Younger Dryas silty sediments at the base of the core are characterized by low diversity of aquatic organisms. The transition to the Holocene is indicated by a sharp change from silt to clay-gyttja. The migration and expansion of trees at lower elevations between 10200 and 8500 14C-yr BP, along with higher diversities and concentrations of aquatic organisms and the decreased proportion of north-alpine diatoms, point to rapidly rising summer temperatures. After 6500 14C-yr BP the expansion of Pinus mugo in the catchment coincides with signs of natural eutrophication as recorded by an increase of planktonic diatoms. In the late Holocene (4000–0 14C-yr BP) Pinus peuce and Abies are reduced and Picea expands. Cereal grains and disturbance indicators suggest late-Holocene human modification of the vegetation.

Middle to Late Holocene vegetation history of the Upper Engadine (Swiss Alps): the role of man and fire

o reconstruct the vegetation and fire history of the Upper Engadine, two continuous sediment cores from Lej da Champfèr and Lej da San Murezzan (Upper Engadine Valley, southeastern Switzerland) were analysed for pollen, plant macrofossils, charcoal and kerogen. The chronologies of the cores are based on 38 radiocarbon dates. Pollen and macrofossil data suggest a rapid afforestation with Betula, Pinus sylvestris, Pinus cembra, and Larix decidua after the retreat of the glaciers from the lake catchments 11,000 cal years ago. This vegetation type persisted until ca. 7300 cal b.p. (5350 b.c.) when Picea replaced Pinus cembra. Pollen indicative of human impact suggests that in this high-mountain region of the central Alps strong anthropogenic activities began during the Early Bronze Age (3900 cal b.p., 1950 b.c.). Local human settlements led to vegetational changes, promoting the expansion of Larix decidua and Alnus viridis. In the case of Larix, continuing land use and especially grazing after fire led to the formation of Larix meadows. The expansion of Alnus viridis was directly induced by fire, as evidenced by time-series analysis. Subsequently, the process of forest conversion into open landscapes continued for millennia and reached its maximum at the end of the Middle Ages at around 500 cal b.p. (a.d. 1450).

Good reproducibility of heart rate variability after orthostatic challenge in patients with a history of acute coronary syndrome

BACKGROUND: Several parameters of heart rate variability (HRV) have been shown to predict the risk of sudden cardiac death (SCD) in cardiac patients. There is consensus that risk prediction is increased when measuring HRV during specific provocations such as orthostatic challenge. For the first time, we provide data on reproducibility of such a test in patients with a history of acute coronary syndrome. METHODS: Sixty male patients (65+/-8years) with a history of acute coronary syndrome on stable medication were included. HRV was measured in supine (5min) and standing (5min) position on 2 occasions separated by two weeks. For risk assessment relevant time-domain [standard deviation of all R-R intervals (SDNN) and root mean squared standard differences between adjacent R-R intervals (RMSSD)], frequency domain [low-frequency power (LF), high-frequency power (HF) and LF/HF power ratio] and short-term fractal scaling component (DF1) were computed. Absolute reproducibility was assessed with the standard errors of the mean (SEM) and 95% limits of random variation, and relative reproducibility by the intraclass correlation coefficient (ICC). RESULTS: We found comparable SEMs and ICCs in supine position and after an orthostatic challenge test. All ICCs were good to excellent (ICCs between 0.636 and 0.869). CONCLUSIONS: Reproducibility of HRV parameters during orthostatic challenge is good and comparable with supine position.

The palaeoecological history of the Praz-Rodet bog (Swiss Jura) based on pollen, plant macrofossils and testate amoebae (Protozoa)

Stratigraphy, radiocarbon dating and analyses of pollen, plant macrofossils and testate amoebae were used to reconstruct the development and ecology of a small raised bog in a karst-dominated landscape in the Swiss Jura Mountains. Special focus was on past vegetation and on the history of Pinus rotundata in relation to anthropogenic and climatic influences. Testate amoebae were used to reconstruc-t past local soil pH and water-table depth. The inferred development of the Praz-Rodet bog typifies a classic hydroseral tefrestrialization of a small basin. Two features are specific for this site. First, the bog was much wetter than today for a long period; according to our hypothesis, this only changed as a consequence of human activities. Second, two hiatuses are present at the coring location (Younger Dryas--early Preboreal, and 4700-2800 cal. yr BP), the former probably caused by low lake productivity due to cold temperatures and the latter by the erosional activity of the adjacent small river. The date of 2800 cal. yr BP for renewed peat accumulation may be related to climatic change (Subboreal-Subatlantic transition). Pollen indicators failed to show one hiatus: an apparently complete pollen sequence is therefore no guarantee of an uninterrupted sediment accumulation. Evidence of early minor human impact on the vegetation in the Joux Valley dates back to c. 6850 calendar years, congruous with the early Neolithic in the Jura Mountains. The history of Pinuis rotindata appears to be more complex than previously believed. Human activity is clearly responsible for the present abundance of this species, but the tree was naturally present on the bog long before the first evidence of important human disturbance of the site (1500 cal. yr BP). It is suggested that, in karst-dominated landscapes, dense forests growing on mineral soils around raised bogs may significantly reduce summer evapotranspiration by acting as windbreaks. Forest clearance results in increased evapotranspiration, causing a lowering of the water table on the bog and a modification of the vegetation cover. This hypothesis has implications for the management of similar small raised bogs in karst-dominated landscape.

Influence of human impact and bedrock differences on the vegetational history of the Insubrian Southern Alps

Vegetation history for the study region is reconstructed on the basis of pollen, charcoal and AMS14C investigations of lake sediments from Lago del Segrino (calcareous bedrock) and Lago di Muzzano (siliceous bedrock). Late-glacial forests were characterised byBetula andPinus sylvestris. At the beginning of the Holocene they were replaced by temperate continental forest and shrub communities. A special type of temperate lowland forest, withAbies alba as the most important tree, was present in the period 8300 to 4500 B.P. Subsequently,Fagus, Quercus andAlnus glutinosa were the main forest components andA. alba ceased to be of importance.Castanea sativa andJuglans regia were probably introduced after forest clearance by fire during the first century A.D. On soils derived from siliceous bedrock,C. sativa was already dominant at ca. A.D. 200 (A.D. dates are in calendar years). In limestone areas, however,C. sativa failed to achieve a dominant role. After the introduction ofC. sativa, the main trees were initially oak (Quercus spp.) and later the walnut (Juglans regia). Ostrya carpinifolia became the dominant tree around Lago del Segrino only in the last 100–200 years though it had spread into the area at ca. 5000 cal. B.C. This recent expansion ofOstrya is confirmed at other sites and appears to be controlled by human disturbances involving especially clearance. It is argued that these forests should not be regarded as climax communities. It is suggested that under undisturbed succession they would develop into mixed deciduous forests consisting ofFraxinus excelsior, Tilia, Ulmus, Quercus and Acer.

Vegetation and fire history of coastal north-eastern Sardinia (Italy) under changing Holocene climates and land use

Little is known about the vegetation and fire history of Sardinia, and especially the long-term history of the thermo-Mediterranean belt that encompasses its entire coastal lowlands. A new sedimentary record from a coastal lake based on pollen, spores, macrofossils and microscopic charcoal analysis is used to reconstruct the vegetation and fire history in north-eastern Sardinia. During the mid-Holocene (c. 8,100–5,300 cal bp), the vegetation around Stagno di Sa Curcurica was characterised by dense Erica scoparia and E. arborea stands, which were favoured by high fire activity. Fire incidence declined and evergreen broadleaved forests of Quercus ilex expanded at the beginning of the late Holocene. We relate the observed vegetation and fire dynamics to climatic change, specifically moister and cooler summers and drier and milder winters after 5,300 cal bp. Agricultural activities occurred since the Neolithic and intensified after c. 7,000 cal bp. Around 2,750 cal bp, a further decline of fire incidence and Erica communities occurred, while Quercus ilex expanded and open-land communities became more abundant. This vegetation shift coincided with the historically documented beginning of Phoenician period, which was followed by Punic and Roman civilizations in Sardinia. The vegetational change at around 2,750 cal bp was possibly advantaged by a further shift to moister and cooler summers and drier and milder winters. Triggers for climate changes at 5,300 and 2,750 cal bp may have been gradual, orbitally-induced changes in summer and winter insolation, as well as centennial-scale atmospheric reorganizations. Open evergreen broadleaved forests persisted until the twentieth century, when they were partly substituted by widespread artificial pine plantations. Our results imply that highly flammable Erica vegetation, as reconstructed for the mid-Holocene, could re-emerge as a dominant vegetation type due to increasing drought and fire, as anticipated under global change conditions.