Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry

© 2019 The Author(s). Background: Baboons (genus Papio) and geladas (Theropithecus gelada) are now generally recognized as close phylogenetic relatives, though morphologically quite distinct and generally classified in separate genera. Primate specific Alu retrotransposons are well-established genomic markers for the study of phylogenetic and population genetic relationships. We previously reported a computational reconstruction of Papio phylogeny using large-scale whole genome sequence (WGS) analysis of Alu insertion polymorphisms. Recently, high coverage WGS was generated for Theropithecus gelada. The objective of this study was to apply the high-Throughput poly-Detect method to computationally determine the number of Alu insertion polymorphisms shared by T. gelada and Papio, and vice versa, by each individual Papio species and T. gelada. Secondly, we performed locus-specific polymerase chain reaction (PCR) assays on a diverse DNA panel to complement the computational data. Results: We identified 27,700 Alu insertions from T. gelada WGS that were also present among six Papio species, with nearly half (12,956) remaining unfixed among 12 Papio individuals. Similarly, each of the six Papio species had species-indicative Alu insertions that were also present in T. gelada. In general, P. kindae shared more insertion polymorphisms with T. gelada than did any of the other five Papio species. PCR-based genotype data provided additional support for the computational findings. Conclusions: Our discovery that several thousand Alu insertion polymorphisms are shared by T. gelada and Papio baboons suggests a much more permeable reproductive barrier between the two genera then previously suspected. Their intertwined evolution likely involves a long history of admixture, gene flow and incomplete lineage sorting

Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine

[This corrects the article DOI: 10.1186/s13054-016-1208-6.]

An Environmentally Ineffective Way to Increase Resource Productivity: Evidence from the Italian Case on Transferring the Burden Abroad

Policy has so far not taken full advantage of the tools offered by the “material flows” school of thought. Resource Productivity (RP) is amongst the normative concepts currently popular among policy makers the nearest one to Material Input Per Service unit (MIPS). However, the RP concept falls substantially short of the MIPS idea, as it puts resource use in relation to the monetary value of production, while MIPS makes reference to services actually delivered by the products. Moreover, the indicator currently used by the European Commission for monitoring RP lacks in life-cycle perspective, which is essential in the MIPS concept. The present paper illustrates, by using Italian case evidence, some of the current RP indicator shortcomings and it discusses a possible alternative, by introducing the life-cycle perspective. In Italy, RP has grown faster than both energy and labour productivity since 1980. This apparently shows that Italy is moving in the right direction. However, a deeper and more extensive analysis regarding the country’s natural resource requirements is necessary before a conclusion can be drawn about the sustainability of the Italian socio-economic process. Therefore, on the one hand we disaggregate material consumption (i.e., the denominator of RP) into its components; on the other hand we extend the analysis to overall material requirements, including indirect material flows associated with international trade. These analyses, although limited to used materials (i.e., to resource requirements in Raw Material Equivalents), demonstrate that the Italian success in increasing RP is largely due to the transferring abroad of material flows and ecological burden

Выбросы парниковых газов, ресурсопользование и экологическая эффективность экономики с точки зрения жизненного цикла

This paper illustrates the results of two environmentally extended input-output applications based on environmental-economic accounts concerning the attribution of environmental flows to final demand. First, total (direct and indirect) GHG emissions of the Italian vertically integrated industries from 1995 to 2008 are presented, including emissions avoided thanks to final and intermediate imports. In this case, the classical IO domestic technology assumption is conveniently integrated with supplementary data in consideration of the inexistence or non-representativeness of some primary industries in Italy. Then, estimates of the Italian material flows in terms of Raw Material Equivalents (RME) for the period 2000-2010 are presented building on the ongoing Eurostat RME project. RME indicators provide a valuable methodological improvement with respect to the current EW-MFA aggregate indicators, as they overcome the asymmetry between the heterogeneous parts by which the indicators currently in use are produced (flows from nature and traded flows). In order to derive such estimates, the environmental-economic accountingframework is fully exploited: the link between direct and indirect demand for raw materials on the one hand, and the final use of products on the other hand, is established through Leontiefs inter-industry interdependence model. The paper also proposes an in-depth analysis of the possible use of demand-based measures in the derivation of productivity indicators, focussing on resource productivity. In a policy setting where indirectflows are not neglected, raising carbon or resource productivity by transferring abroad of potential environmental burden is recognised as not being environmentally effective, i. e. as not leading to a reduction of pressures on a global scale. Moreover, we argue that the indicators used to measure productivity should use figures from National Accounts and from Environmental Satellite Accounts coherently.В статье представлены результаты расчетов двух вариантов применения модели «затраты-выпуск», учитывающей экологическую составляющую и основанной на эколого-экономических счетах, отражающих включение экологических потоков в конечный спрос. Во-первых, представлен общий объем выбросов (как прямых, так и непрямых) парниковых газов вертикально интегрированных промышленных отраслей Италии за период с 1995 по 2008 г., включая и те выбросы, которые не были произведены по причине импорта продуктов конечного и промежуточного использования. В этом случае классическая модель "затраты-выпуск", предполагающая учет отечественной технологии, хорошо интегрирована с дополнительными данными, учитывающими фактически не существующие или не представленные в Италии отрасли промышленности. Кроме того, даны оценки материальных потоков в Италии, а именно сырьевых эквивалентов, за период с 2000 по 2010 г., построенные в рамках реализации текущего проекта Евростата. Использование показателей сырьевых эквивалентов оказывает положительное влияние на методологию расчета агрегированных показателей текущих счетов потоков материалов в масштабах экономики (СПМ- МЭ), так как благодаря им преодолевается асимметрия между разнородными частями, на основе которых в настоящее время строятся эти агрегированные показатели (природные источники и потоки торгуемых товаров). Для получения такого рода оценок необходимо в полной мере использовать систему эколого-экономических счетов: связь между прямым и косвенным спросом на сырье, с одной стороны, и конечным использованием товаров - с другой, устанавливается через модель межотраслевого баланса Леонтьева. В статье также предложен углубленный анализ возможности использования измерений на основе спроса для построения показателей продуктивности, в частности показателей ресурсной продуктивности. Делается вывод о том, что политика, в которой учитываются непрямые потоки, а углеродная или ресурсная продуктивность повышается путем перемещения за границу потенциальной экологической нагрузки, является экологически неэффективной, так как не приводит к снижению воздействия на окружающую среду в глобальном масштабе. Авторы также утверждают, что для показателей, применяемых для измерения продуктивности, следует использовать согласованные данные из национальных счетов и сателлитных экологических счетов

Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry

Background: Baboons (genus Papio) and geladas (Theropithecus gelada) are now generally recognized as close phylogenetic relatives, though morphologically quite distinct and generally classified in separate genera. Primate specific Alu retrotransposons are well-established genomic markers for the study of phylogenetic and population genetic relationships. We previously reported a computational reconstruction of Papio phylogeny using large-scale whole genome sequence (WGS) analysis of Alu insertion polymorphisms. Recently, high coverage WGS was generated for Theropithecus gelada. The objective of this study was to apply the high-Throughput "poly-Detect" method to computationally determine the number of Alu insertion polymorphisms shared by T. gelada and Papio, and vice versa, by each individual Papio species and T. gelada. Secondly, we performed locus-specific polymerase chain reaction (PCR) assays on a diverse DNA panel to complement the computational data. Results: We identified 27,700 Alu insertions from T. gelada WGS that were also present among six Papio species, with nearly half (12,956) remaining unfixed among 12 Papio individuals. Similarly, each of the six Papio species had species-indicative Alu insertions that were also present in T. gelada. In general, P. kindae shared more insertion polymorphisms with T. gelada than did any of the other five Papio species. PCR-based genotype data provided additional support for the computational findings. Conclusions: Our discovery that several thousand Alu insertion polymorphisms are shared by T. gelada and Papio baboons suggests a much more permeable reproductive barrier between the two genera then previously suspected. Their intertwined evolution likely involves a long history of admixture, gene flow and incomplete lineage sorting

Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis

Background: Alu elements are primate-specific retroposons that mobilize using the enzymatic machinery of L1 s. The recently completed baboon genome project found that the mobilization rate of Alu elements is higher than in the genome of any other primate studied thus far. However, the Alu subfamily structure present in and specific to baboons had not been examined yet. Results: Here we report 129 Alu subfamilies that are propagating in the genome of the olive baboon, with 127 of these subfamilies being new and specific to the baboon lineage. We analyzed 233 Alu insertions in the genome of the olive baboon using locus specific polymerase chain reaction assays, covering 113 of the 129 subfamilies. The allele frequency data from these insertions show that none of the nine groups of subfamilies are nearing fixation in the lineage. Conclusions: Many subfamilies of Alu elements are actively mobilizing throughout the baboon lineage, with most being specific to the baboon lineage

Papio Baboon species indicative alu elements

The genus of Papio (baboon) has six recognized species separated into Northern and Southern clades, each comprised of three species distributed across the African continent. Geographic origin and phenotypic variants such as coat color and body size have commonly been used to identify different species. The existence of multiple hybrid zones, both ancient and current, have complicated efforts to characterize the phylogeny of Papio baboons. More recently, mitochondrial DNA (mtDNA) and Y-chromosome genetic markers have been utilized for species identification with particular focus on the hybrid zones. Alu elements accumulate in a random manner and are a novel source of identical by descent variation with known ancestral states for inferring population genetic and phylogenetic relationships. As part of the Baboon Genome Analysis Consortium, we assembled an Alu insertion polymorphism database of nearly 500 Papio-lineage specific insertions representing all six species and performed population structure and phylogenetic analyses. In this study, we have selected a subset of 48 species indicative Alu insertions and demonstrate their utility as genetic systems for the identification of baboon species within Papio. Individual elements from the panel are easy to genotype and can be used in a hierarchical fashion based on the original level of uncertainty. This Alu-48 panel should serve as a valuable tool during the maintenance of pedigree records in captive populations and assist in the forensic identification of fossils and potential hybrids in the wild