Inference of recombination maps from a single pair of genomes and its application to ancient samples.

Understanding the causes and consequences of recombination landscape evolution is a fundamental goal in genetics that requires recombination maps from across the tree of life. Such maps can be obtained from population genomic datasets, but require large sample sizes. Alternative methods are therefore necessary to research organisms where such datasets cannot be generated easily, such as non-model or ancient species. Here we extend the sequentially Markovian coalescent model to jointly infer demography and the spatial variation in recombination rate. Using extensive simulations and sequence data from humans, fruit-flies and a fungal pathogen, we demonstrate that iSMC accurately infers recombination maps under a wide range of scenarios-remarkably, even from a single pair of unphased genomes. We exploit this possibility and reconstruct the recombination maps of ancient hominins. We report that the ancient and modern maps are correlated in a manner that reflects the established phylogeny of Neanderthals, Denisovans, and modern human populations.

The MIS5 Pietersburg at '28' Bushman Rock Shelter, Limpopo Province, South Africa.

In the past few decades, a diverse array of research has emphasized the precocity of technically advanced and symbolic practices occurring during the southern African Middle Stone Age. However, uncertainties regarding the regional chrono-cultural framework constrain models and identification of the cultural and ecological mechanisms triggering the development of such early innovative behaviours. Here, we present new results and a refined chronology for the Pietersburg, a techno-complex initially defined in the late 1920's, which has disappeared from the literature since the 1980's. We base our revision of this techno-complex on ongoing excavations at Bushman Rock Shelter (BRS) in Limpopo Province, South Africa, where two Pietersburg phases (an upper phase called '21' and a lower phase called '28') are recognized. Our analysis focuses on the '28' phase, characterized by a knapping strategy based on Levallois and semi-prismatic laminar reduction systems and typified by the presence of end-scrapers. Luminescence chronology provides two sets of ages for the upper and lower Pietersburg of BRS, dated respectively to 73±6ka and 75±6ka on quartz and to 91±10ka and 97±10ka on feldspar, firmly positioning this industry within MIS5. Comparisons with other published lithic assemblages show technological differences between the Pietersburg from BRS and other southern African MIS5 traditions, especially those from the Western and Eastern Cape. We argue that, at least for part of MIS5, human populations in South Africa were regionally differentiated, a process that most likely impacted the way groups were territorially and socially organized. Nonetheless, comparisons between MIS5 assemblages also indicate some typological similarities, suggesting some degree of connection between human groups, which shared similar innovations but manipulated them in different ways. We pay particular attention to the end-scrapers from BRS, which represent thus far the earliest documented wide adoption of such tool-type and provide further evidence for the innovative processes characterizing southern Africa from the MIS5 onwards.

Human evolutionary history of Eastern Africa.

Since the discovery of the first hominin fossils, East Africa has been in the spotlight of palaeo-anthropological investigation for its role as a potential cradle of humanity and as a gateway out of Africa. With the advent of the genomic era an ever increasing amount of information has started to complement this notion, and to place the area within a broader, Pan-African scenario. Here we examine the most recent genetic and fossil results that recapitulate the last hundreds of thousands of years of human evolution in the area, and point to a number of uncharted avenues that may complement the emerging scenario in the coming years.

The importance of fine-scale studies for integrating paleogenomics and archaeology.

There has been an undercurrent of intellectual tension between geneticists studying human population history and archaeologists for almost 40 years. The rapid development of paleogenomics, with geneticists working on the very material discovered by archaeologists, appears to have recently heightened this tension. The relationship between these two fields thus far has largely been of a multidisciplinary nature, with archaeologists providing the raw materials for sequencing, as well as a scaffold of hypotheses based on interpretation of archaeological cultures from which the geneticists can ground their inferences from the genomic data. Much of this work has taken place in the context of western Eurasia, which is acting as testing ground for the interaction between the disciplines. Perhaps the major finding has not been any particular historical episode, but rather the apparent pervasiveness of migration events, some apparently of substantial scale, over the past ∼5000 years, challenging the prevailing view of archaeology that largely dismissed migration as a driving force of cultural change in the 1960s. However, while the genetic evidence for `migration' is generally statistically sound, the description of these events as structured behaviours is lacking, which, coupled with often over simplistic archaeological definitions, prevents the use of this information by archaeologists for studying the social processes they are interested in. In order to integrate paleogenomics and archaeology in a truly interdisciplinary manner, it will be necessary to focus less on grand narratives over space and time, and instead integrate genomic data with other form of archaeological information at the level of individual communities to understand the internal social dynamics, which can then be connected amongst communities to model migration at a regional level. A smattering of recent studies have begun to follow this approach, resulting in inferences that are not only helping ask questions that are currently relevant to archaeologists, but also potentially opening up new avenues of research.

Strontium isotopes (87 Sr/86 Sr) in terrestrial ecological and palaeoecological research: empirical efforts and recent advances in continental-scale models.

Strontium (Sr) isotope analysis can provide detailed biogeographical and ecological information about modern and ancient organisms. Because Sr isotope ratios (87 Sr/86 Sr) in biologically relevant materials such as water, soil, vegetation, and animal tissues predominantly reflect local geology, they can be used to distinguish geologically distinct regions as well as identify highly mobile individuals or populations. While the application of Sr isotope analysis to biological research has been steadily increasing, high analytical costs have prohibited more widespread use. Additionally, accessibility of this geochemical tool has been hampered due to limited understanding of (i) the degree to which biologically relevant materials differ in their spatial averaging of 87 Sr/86 Sr ratios, and (ii) how these differences may be affected by lithologic complexity. A recently developed continental-scale model that accounts for variability in bedrock weathering rates and predicts Sr isotope ratios of surface water could help resolve these questions. In addition, if this 'local water' model can accurately predict 87 Sr/86 Sr ratios for other biologically relevant materials, there would be reduced need for researchers to assess regional Sr isotope patterns empirically. Here, we compile 87 Sr/86 Sr data for surface water, soil, vegetation, and mammalian and fish skeletal tissues from the literature and compare the accuracy with which the local water model predicts Sr isotope data among these five materials across the contiguous USA. We find that measured Sr isotope ratios for all five materials are generally close to those predicted by the local water model, although not with uniform accuracy. Mammal skeletal tissues are most accurately predicted, particularly in regions with low variability in 87 Sr/86 Sr predicted by the local water model. Increasing regional geologic heterogeneity increases both the offset and variance between modelled and empirical Sr isotope ratios, but its effects are broadly similar across materials. The local water model thus provides a readily available source of background data for predicting 87 Sr/86 Sr for biologically relevant materials in places where empirical data are lacking. The availability of increasingly high-quality modelled Sr data will dramatically expand the accessibility of this geochemical tool to ecological applications.

Incorporating fossils into hypotheses of insect phylogeny.

Fossils represent stem and crown lineages, and their inclusion in phylogenetic reconstruction influences branch lengths, topology, and divergence time estimation. In addition, paleontological data may inform trends in morphological evolution as well as biogeographic history. Here we review the incorporation of fossils in studies of insect evolution, from morphological analyses to combined 'total evidence' node dating analyses. We discuss challenges associated with fossil based phylogenetics, and suggest best practices for use in tree reconstruction.

The evolution of methods for establishing evolutionary timescales.

The fossil record is well known to be incomplete. Read literally, it provides a distorted view of the history of species divergence and extinction, because different species have different propensities to fossilize, the amount of rock fluctuates over geological timescales, as does the nature of the environments that it preserves. Even so, patterns in the fossil evidence allow us to assess the incompleteness of the fossil record. While the molecular clock can be used to extend the time estimates from fossil species to lineages not represented in the fossil record, fossils are the only source of information concerning absolute (geological) times in molecular dating analysis. We review different ways of incorporating fossil evidence in modern clock dating analyses, including node-calibrations where lineage divergence times are constrained using probability densities and tip-calibrations where fossil species at the tips of the tree are assigned dates from dated rock strata. While node-calibrations are often constructed by a crude assessment of the fossil evidence and thus involves arbitrariness, tip-calibrations may be too sensitive to the prior on divergence times or the branching process and influenced unduly affected by well-known problems of morphological character evolution, such as environmental influence on morphological phenotypes, correlation among traits, and convergent evolution in disparate species. We discuss the utility of time information from fossils in phylogeny estimation and the search for ancestors in the fossil record.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.

[Ancient DNA: Results and Prospects (the 30th Anniversary)].

Evolutionary genetics has reached a new level of research thanks to the opportunity to study the genomes of not only present-day but also of ancient organisms. The obtaining of reliable data when working with ancient DNA is possible only in the case of interdisciplinary collaboration between archaeologists, paleontologists, molecular geneticists, and bioinformaticians. Despite laborious and high-cost technologies, the results never cease to amaze and can not only fill the gaps in the knowledge of the evolutionary history of different species but can also review the existing ideas on population development and dynamics. In this review, we discuss the history of the development of investigative techniques in ancient DNA research and the most striking results of these studies, including the most recent achievements.

Anomalocaris: la supervisión del gigante marino del período Cámbrico / Anomalocaris: The supervision of the marine giant of the Cambrian period

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Paleontology: a new Burgess Shale fauna.

A spectacular Cambrian soft bodied fauna some 40 km from Walcott's original Burgess Shale locality includes over 50 taxa, some 20% new to science. New anatomical evidence from this site will illuminate the evolution of early marine animals.

A paleogenomic perspective on evolution and gene function: new insights from ancient DNA.

The publication of partial and complete paleogenomes within the last few years has reinvigorated research in ancient DNA. No longer limited to short fragments of mitochondrial DNA, inference of evolutionary processes through time can now be investigated from genome-wide data sampled as far back as 700,000 years. Tremendous insights have been made, in particular regarding the hominin lineage. With rare exception, however, a paleogenomic perspective has been mired by the quality and quantity of recoverable DNA. Though conceptually simple, extracting ancient DNA remains challenging, and sequencing ancient genomes to high coverage remains prohibitively expensive for most laboratories. Still, with improvements in DNA isolation and declining sequencing costs, the taxonomic and geographic purview of paleogenomics is expanding at a rapid pace. With improved capacity to screen large numbers of samples for those with high proportions of endogenous ancient DNA, paleogenomics is poised to become a key technology to better understand recent evolutionary events.