Evaluating purifying selection in the mitochondrial DNA of various mammalian species

Mitochondrial DNA (mtDNA), the circular DNA molecule inside the mitochondria of all eukaryotic cells, has been shown to be under the effect of purifying selection in several species. Traditional testing of purifying selection has been based simply on ratios of nonsynonymous to synonymous mutations, without considering the relative age of each mutation, which can be determined by phylogenetic analysis of this non-recombining molecule. The incorporation of a mutation time-ordering from phylogeny and of predicted pathogenicity scores for nonsynonymous mutations allow a quantitative evaluation of the effects of purifying selection in human mtDNA. Here, by using this additional information, we show that purifying selection undoubtedly acts upon the mtDNA of other mammalian species/genera, namely Bos sp., Canis lupus, Mus musculus, Orcinus orca, Pan sp. and Sus scrofa. The effects of purifying selection were comparable in all species, leading to a significant major proportion of nonsynonymous variants with higher pathogenicity scores in the younger branches of the tree. We also derive recalibrated mutation rates for age estimates of ancestors of these various species and proposed a correction curve in order to take into account the effects of selection. Understanding this selection is fundamental to evolutionary studies and to the identification of deleterious mutations

Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia

There has been a long-standing debate concerning the extent to which the spread of Neolithic ceramics and Malay-Polynesian languages in Island Southeast Asia (ISEA) were coupled to an agriculturally driven demic dispersal out of Taiwan 4000 years ago (4 ka). We previously addressed this question using founder analysis of mitochondrial DNA (mtDNA) control-region sequences to identify major lineage clusters most likely to have dispersed from Taiwan into ISEA, proposing that the dispersal had a relatively minor impact on the extant genetic structure of ISEA, and that the role of agriculture in the expansion of the Austronesian languages was therefore likely to have been correspondingly minor. Here we test these conclusions by sequencing whole mtDNAs from across Taiwan and ISEA, using their higher chronological precision to resolve the overall proportion that participated in the “out-of-Taiwan” mid-Holocene dispersal as opposed to earlier, postglacial expansions in the Early Holocene. We show that, in total, about 20 % of mtDNA lineages in the modern ISEA pool result from the “out-of-Taiwan” dispersal, with most of the remainder signifying earlier processes, mainly due to sea-level rises after the Last Glacial Maximum. Notably, we show that every one of these founder clusters previously entered Taiwan from China, 6–7 ka, where rice-farming originated, and remained distinct from the indigenous Taiwanese population until after the subsequent dispersal into ISEA

Drought-induced photosynthetic inhibition and autumn recovery in two Mediterranean oak species (Quercus ilex and Quercus suber)

Responses of leaf water relations and photosynthesis to summer drought and autumn rewetting were studied in two evergreen Mediterranean oak species, Quercus ilex spp. rotundifolia and Quercus suber. The predawn leaf water potential (ΨlPD), stomatal conductance (gs) and photosynthetic rate (A) at ambient conditions were measured seasonally over a 3-year period. We also measured the photosynthetic response to light and to intercellular CO2 (A/PPFD and A/ Ci response curves) under water stress (summer) and after recovery due to autumn rainfall. Photosynthetic parameters, Vcmax, Jmax and triose phosphate utilization (TPU) rate, were estimated using the Farquhar model. RuBisCo activity, leaf chlorophyll, leaf nitrogen concentration and leaf carbohydrate concentration were also measured. All measurements were performed in the spring leaves of the current year. In both species, the predawn leaf water potential, stomatal conductance and photosynthetic rate peaked in spring, progressively declined throughout the summer and recovered upon autumn rainfall. During the drought period, Q. ilex maintained a higher predawn leaf water potential and stomatal conductance than Q. suber. During this period, we found that photosynthesis was not only limited by stomatal closure, but was also downregulated as a consequence of a decrease in the maximum carboxylation rate (Vcmax) and the light-saturated rate of photosynthetic electron transport (Jmax) in both species. The Vcmax and Jmax increased after the first autumnal rains and this increase was related to RuBisCo activity, leaf nitrogen concentration and chlorophyll concentration. In addition, an increase in the TPU rate and in soluble leaf sugar concentration was observed in this period. The results obtained indicate a high resilience of the photosynthetic apparatus to summer drought as well as good recovery in the following autumn rains of these evergreen oak species

Effects of recent minimum temperature and water deficit increases on Pinus pinaster radial growth and wood density in southern Portugal

Western Iberia has recently shown increasing frequency of drought conditions coupled with heatwave events, leading to exacerbated limiting climatic conditions for plant growth. It is not clear to what extent wood growth and density of agroforestry species have suffered from such changes or recent extreme climate events. To address this question, tree-ring width and density chronologies were built for a Pinus pinaster stand in southern Portugal and correlated with climate variables, including the minimum, mean and maximum temperatures and the number of cold days. Monthly and maximum daily precipitations were also analyzed as well as dry spells. The drought effect was assessed using the standardized precipitation-evapotranspiration (SPEI) multi-scalar drought index, between 1 to 24-months. The climate-growth/density relationships were evaluated for the period 1958-2011. We show that both wood radial growth and density highly benefit from the strong decay of cold days and the increase of minimum temperature. Yet the benefits are hindered by long-term water deficit, which results in different levels of impact on wood radial growth and density. Despite of the intensification of long-term water deficit, tree-ring width appears to benefit from the minimum temperature increase, whereas the effects of long-term droughts significantly prevail on tree-ring density. Our results further highlight the dependency of the species on deep water sources after the juvenile stage. The impact of climate changes on longterm droughts and their repercussion on the shallow groundwater table and P. pinaster’s vulnerability are also discussed. This work provides relevant information for forest management in the semi-arid area of the Alentejo region of Portugal. It should ease the elaboration of mitigation strategies to assure P. pinaster’s production capacity and quality in response to more arid conditions in the near future in the regioninfo:eu-repo/semantics/publishedVersio

Pityriasis versicolor and AIDS

BACKGROUND: Pityriasis versicolor (PV) is a recurrent, chronic infection of the stratum corneum due to Malassezia furfur that is generally asymptomatic and has the potential of leading to fungemia. Acquired Immunodeficiency Syndrome (AIDS) is characterized by a severe cellular depression, which facilitates the occurrence of opportunist infections. OBJECTIVES: Given the immunodepression caused by HIV and risk this entails for the presence of the pathogenic form of M. furfur, this work sought the real differences in PV affecting immunocompetent hosts compared to immunocompromised HIV-patients. PATIENTS AND METHODS: From July 1998 to June 1999, 50 HIV-positive outpatients from the Teaching Hospital were studied. The control group comprised of 50 HIV-negative patients. The protocol for each patient included identification, clinical and laboratory examination. RESULTS: PV was clinically diagnosed in the HIV-positive group in 7 (14%) patients, with the same number in the control group. As for prior history, 12 (24%) patients in the HIV-positive group reported having previously presented PV, the same incidence was found in the control group. CONCLUSIONS: PV was neither more frequent nor more severe in the HIV-immunocompromised group compared to the control group, whereas seborrheic dermatitis was more frequent in the former.FUNDAMENTOS: A pitiríase versicolor é uma infecção crônica recorrente da camada córnea causada pela Malassezia furfur, geralmente assintomática, podendo ser causa de fungemia. A síndrome da imunodeficiência adquirida caracteriza-se por uma importante depressão celular, o que propicia a ocorrência de infecções oportunistas. OBJETIVOS: Dados a imunodepressão causada pelo HIV e o risco da presença de M. furfur em sua forma patogênica no imunocomprometido, realizou-se este trabalho comparativo buscando as reais diferenças da pitiríase versicolor no imunocompetente e no imunodeprimido pelo HIV. PACIENTES E MÉTODOS: Foram avaliados, no período de julho de 1998 a junho de 1999, 50 pacientes HIV positivos do Hospital Universitário da UFJF. Como grupo controle, foram examinados de forma aleatória 50 pacientes soronegativos para HIV. Para cada paciente foi preenchido um protocolo constando de identificação e exames clínicos e laboratoriais. RESULTADOS: A pitiríase versicolor foi diagnosticada clinicamente no grupo HIV positivo em sete (14%) pacientes, resultado coincidente no grupo controle. Quanto ao passado para a pitiríase versicolor, 12 (24%) pacientes já haviam apresentado tal doença no grupo HIV positivo, e igual incidência ocorreu no grupo controle. CONCLUSÕES: A pitiríase versicolor não se mostrou mais freqüente e nem mais agressiva na população imunodeprimida pelo HIV em relação ao grupo controle, enquanto a dermatite seborréica apresentou-se mais freqüente no grupo infectado pelo HIV

Resolving the ancestry of Austronesian-speaking populations

There are two very different interpretations of the prehistory of Island Southeast Asia (ISEA), with genetic evidence invoked in support of both. The “out-of-Taiwan” model proposes a major Late Holocene expansion of Neolithic Austronesian speakers from Taiwan. An alternative, proposing that Late Glacial/postglacial sea-level rises triggered largely autochthonous dispersals, accounts for some otherwise enigmatic genetic patterns, but fails to explain the Austronesian language dispersal. Combining mitochondrial DNA (mtDNA), Y-chromosome and genome-wide data, we performed the most comprehensive analysis of the region to date, obtaining highly consistent results across all three systems and allowing us to reconcile the models. We infer a primarily common ancestry for Taiwan/ISEA populations established before the Neolithic, but also detected clear signals of two minor Late Holocene migrations, probably representing Neolithic input from both Mainland Southeast Asia and South China, via Taiwan. This latter may therefore have mediated the Austronesian language dispersal, implying small-scale migration and language shift rather than large-scale expansion

Composição e abundância de macrófitas num troço do rio Ovelha

As macrófitas fluviais são um grupo relevante para a avaliação ecológica dos rios. Numa amostragem realizada num troço de 100 m do rio Ovelha, localizado a 217 m de altitude, na freguesia de Fornos, Marco de Canaveses, estudou-se a abundância, composição e distribuição das macrófitas. Verificou-se que o troço estudado é pobre em macrófitas, apresentando uma riqueza específica baixa, o que poderá estar relacionado, sobretudo, com o substrato rochoso. Considerando os resultados obtidos é fundamental que, futuramente, sejam estudadas as macrófitas conjuntamente com outros elementos biológicos, no sentido de se proceder a uma correta monitorização do estado ecológico do rio Ovelha.info:eu-repo/semantics/publishedVersio

Mosaic maternal ancestry in the Great Lakes region of East Africa

The Great Lakes lie within a region of East Africa with very high human genetic diversity, home of many ethno-linguistic groups usually assumed to be the product of a small number of major dispersals. However, our knowledge of these dispersals relies primarily on the inferences of historical, linguistics and oral traditions, with attempts to match up the archaeological evidence where possible. This is an obvious area to which archaeogenetics can contribute, yet Uganda, at the heart of these developments, has not been studied for mitochondrial DNA (mtDNA) variation. Here, we compare mtDNA lineages at this putative genetic crossroads across 409 representatives of the major language groups: Bantu speakers and Eastern and Western Nilotic speakers. We show that Uganda harbours one of the highest mtDNA diversities within and between linguistic groups, with the various groups significantly differentiated from each other. Despite an inferred linguistic origin in South Sudan, the data from the two Nilotic-speaking groups point to a much more complex history, involving not only possible dispersals from Sudan and the Horn but also large-scale assimilation of autochthonous lineages within East Africa and even Uganda itself. The Eastern Nilotic group also carries signals characteristic of West-Central Africa, primarily due to Bantu influence, whereas a much stronger signal in the Western Nilotic group suggests direct West-Central African ancestry. Bantu speakers share lineages with both Nilotic groups, and also harbour East African lineages not found in Western Nilotic speakers, likely due to assimilating indigenous populations since arriving in the region ~3000 years ago

The Expanded mtDNA Phylogeny of the Franco-Cantabrian Region Upholds the Pre-Neolithic Genetic Substrate of Basques

The European genetic landscape has been shaped by several human migrations occurred since Paleolithic times. The accumulation of archaeological records and the concordance of different lines of genetic evidence during the last two decades have triggered an interesting debate concerning the role of ancient settlers from the Franco-Cantabrian region in the postglacial resettlement of Europe. Among the Franco-Cantabrian populations, Basques are regarded as one of the oldest and more intriguing human groups of Europe. Recent data on complete mitochondrial DNA genomes focused on macrohaplogroup R0 revealed that Basques harbor some autochthonous lineages, suggesting a genetic continuity since pre-Neolithic times. However, excluding haplogroup H, the most representative lineage of macrohaplogroup R0, the majority of maternal lineages of this area remains virtually unexplored, so that further refinement of the mtDNA phylogeny based on analyses at the highest level of resolution is crucial for a better understanding of the European prehistory. We thus explored the maternal ancestry of 548 autochthonous individuals from various Franco-Cantabrian populations and sequenced 76 mitogenomes of the most representative lineages. Interestingly, we identified three mtDNA haplogroups, U5b1f, J1c5c1 and V22, that proved to be representative of Franco-Cantabria, notably of the Basque population. The seclusion and diversity of these female genetic lineages support a local origin in the Franco-Cantabrian area during the Mesolithic of southwestern Europe, ∼10,000 years before present (YBP), with signals of expansions at ∼3,500 YBP. These findings provide robust evidence of a partial genetic continuity between contemporary autochthonous populations from the Franco-Cantabrian region, specifically the Basques, and Paleolithic/Mesolithic hunter-gatherer groups. Furthermore, our results raise the current proportion (≈15%) of the Franco-Cantabrian maternal gene pool with a putative pre-Neolithic origin to ≈35%, further supporting the notion of a predominant Paleolithic genetic substrate in extant European populations