We challenge the view that our species, Homo sapiens, evolved within a single population and/or region of Africa. The chronology and physical diversity of Pleistocene human fossils suggest that morphologically varied populations pertaining to the H. sapiens clade lived throughout Africa. Similarly, the African archaeological record demonstrates the polycentric origin and persistence of regionally distinct Pleistocene material culture in a variety of paleoecological settings. Genetic studies also indicate that present-day population structure within Africa extends to deep times, paralleling a paleoenvironmental record of shifting and fractured habitable zones. We argue that these fields support an emerging view of a highly structured African prehistory that should be considered in human evolutionary inferences, prompting new interpretations, questions, and interdisciplinary research directions.

In the last years, a wide range of methods allowing to reconstruct past population size changes from genome-wide data have been developed. At the same time, there has been an increasing recognition that population structure can generate genetic data similar to those produced under models of population size change. Recently, Mazet et al. (Heredity 116:362–371, 2016 ) showed that, for any model of population structure, it is always possible to find a panmictic model with a particular function of population size changes, having exactly the same distribution of T 2 (the coalescence time for a sample of size two) as that of the structured model. They called this function IICR (Inverse Instantaneous Coalescence Rate) and showed that it does not necessarily correspond to population size changes under non-panmictic models. Besides, most of the methods used to analyse data under models of population structure tend to arbitrarily fix that structure and to minimise or neglect population size changes. Here, we extend the seminal work of Herbots (PhD thesis, University of London, 1994 ) on the structured coalescent and propose a new framework, the Non-Stationary Structured Coalescent (NSSC) that incorporates demographic events (changes in gene flow and/or deme sizes) to models of nearly any complexity. We show how to compute the IICR under a wide family of stationary and non-stationary models. As an example we address the question of human and Neanderthal evolution and discuss how the NSSC framework allows to interpret genomic data under this new perspective.

Beyond multiregional and simple out-of-Africa models of human evolution The past half century has seen a move from a multiregionalist view of human origins to widespread acceptance that modern humans emerged in Africa. Here the authors argue that a simple out-of-Africa model is also outdated, and that the current state of the evidence favours a structured African metapopulation model of human origins.

We challenge the view that our species, Homo sapiens, evolved within a single population and/or region of Africa. The chronology and physical diversity of Pleistocene human fossils suggest that morphologically varied populations pertaining to the H. sapiens clade lived throughout Africa. Similarly, the African archaeological record demonstrates the polycentric origin and persistence of regionally distinct Pleistocene material culture in a variety of paleoecological settings. Genetic studies also indicate that present-day population structure within Africa extends to deep times, paralleling a paleoenvironmental record of shifting and fractured habitable zones. We argue that these fields support an emerging view of a highly structured African prehistory that should be considered in human evolutionary inferences, prompting new interpretations, questions, and interdisciplinary research directions.The lineage of Homo sapiens probably originated in Africa at least 500 thousand years ago (ka) [1], and the earliest observed morphological manifestations of this clade appeared by 300 ka [2]. Early H. sapiens fossils do not demonstrate a simple linear progression towards contemporary human morphology. Instead, putative early H. sapiens remains exhibit remarkable morphological diversity and geographical spread. Together with recent archaeological and genetic lines of evidence, these data are consistent with the view that our species originated and diversified within strongly subdivided (i.e., structured) populations, probably living across Africa, that were connected by sporadic gene flow [1,3-8]. This concept of 'African multiregionalism' [1] may also include hybridization between H. sapiens and more divergent hominins (see Glossary) living in different regions [1,[9][10][11][12]. Crucially, such population subdivisions may have been shaped and sustained by shifts in ecological boundaries [7,13,14], challenging the view that our species was endemic to a single region or habitat, and implying an often underacknowledged complexity to our African origins.In this paper we examine and synthesize fossil, archaeological, genetic, and paleoenvironmental data to refine our understanding of the time-depth, character, and maintenance of Pleistocene population structure. In doing so, we attempt to separate data from inference to stress that using models of population structure fundamentally changes interpretations of recent human evolution. HighlightsThe view that Homo sapiens evolved from a single region/population within Africa has been given primacy in studies of human evolution.The constellation of morphological features characterizing H. sapiens is debated. This has strongly impacted on interpretations of recent human origins by variably including or excluding different fossils from interpretative analyses. For example, different morphological criteria and analytical methods have been used to support both a gradual, mosaic-like process of modernization of our species or, conversely, a punctuated speciation (e.g., [1]).Extant human...

1The rapid development of sequencing technologies represents new opportunities for pop-2 ulation genetics research. It is expected that genomic data will increase our ability to re-3 construct the history of populations. While this increase in genetic information will likely 4 help biologists and anthropologists to reconstruct the demographic history of populations, 5 it also represents new challenges. Recent work has shown that structured populations gen-6 erate signals of population size change. As a consequence it is often difficult to determine 7 whether demographic events such as expansions or contractions (bottlenecks) inferred from 8 genetic data are real or due to the fact that populations are structured in nature. Given 9 that few inferential methods allow us to account for that structure, and that genomic data 10 will necessarily increase the precision of parameter estimates, it is important to develop new 11 approaches. In the present study we analyse two demographic models. The first is a model 12 of instantaneous population size change whereas the second is the classical symmetric island 13 model. We (i) re-derive the distribution of coalescence times under the two models for a sam-14 ple of size two, (ii) use a maximum likelihood approach to estimate the parameters of these 15 models (iii) validate this estimation procedure under a wide array of parameter combina- 16 tions, (iv) implement and validate a model choice procedure by using a test. Altogether we show that it is possible to estimate parameters under several models and 18 perform efficient model choice using genetic data from a single diploid individual. 19 20The sheer amount of genomic data that is becoming available for many organisms with the 21 rapid development of sequencing technologies represents new opportunities for population 22 genetics research. It is hoped that genomic data will increase our ability to reconstruct the 23 history of populations (Li and Durbin 2011) and detect, identify and quantify selection 24 (Vitti et al. 2013). While this increase in genetic information will likely help biologists 25 and anthropologists to reconstruct the demographic history of populations, it also exposes 26 old challenges in the field of population genetics. In particular, it becomes increasingly 27 necessary to understand how genetic data observed in present-day populations are influenced 28 by a variety of factors such as population size changes, population structure and gene flow 29 (Nielsen and Beaumont 2009). Indeed, the use of genomic data does not necessary 30 lead to an improvement of statistical inference. If the model assumed to make statistical 31 inference is fundamentally mis-specified, then increasing the amount of data will lead to 32 increased precision for perhaps misleading if not meaningless parameters and will not reveal 33 new insights (Nielsen and Beaumont 2009; Chikhi et al. 2010; Heller et al. 2013). 34For instance, several recent studies have shown that the genealogy of genes sampled from 35 a deme in an isl...

Abstract Mouse lemurs (Microcebus) are a radiation of morphologically cryptic primates distributed throughout Madagascar for which the number of recognized species has exploded in the past two decades. This taxonomic revision has prompted understandable concern that there has been substantial oversplitting in the mouse lemur clade. Here, we investigate mouse lemur diversity in a region in northeastern Madagascar with high levels of microendemism and predicted habitat loss. We analyzed RADseq data with multispecies coalescent (MSC) species delimitation methods for two pairs of sister lineages that include three named species and an undescribed lineage previously identified to have divergent mtDNA. Marked differences in effective population sizes, levels of gene flow, patterns of isolation-by-distance, and species delimitation results were found among the two pairs of lineages. Whereas all tests support the recognition of the presently undescribed lineage as a separate species, the species-level distinction of two previously described species, M. mittermeieri and M. lehilahytsara is not supported – a result that is particularly striking when using the genealogical discordance index (gdi). Non-sister lineages occur sympatrically in two of the localities sampled for this study, despite an estimated divergence time of less than 1 Ma. This suggests rapid evolution of reproductive isolation in the focal lineages, and in the mouse lemur clade generally. The divergence time estimates reported here are based on the MSC calibrated with pedigree-based mutation rates and are considerably more recent than previously published fossil-calibrated relaxed-clock estimates. We discuss the possible explanations for this discrepancy, noting that there are theoretical justifications for preferring the MSC estimates in this case.

Quaternary climatic changes have been invoked as important drivers of species diversification worldwide. However, the impact of such changes on vegetation and animal population dynamics in tropical regions remains debated. To overcome this uncertainty, we integrated high-resolution paleoenvironmental reconstructions from a sedimentary record covering the past 25,000 years with demographic inferences of a forest-dwelling primate species (Microcebus arnholdi), in northern Madagascar. Result comparisons suggest that climate changes through the African Humid Period (15.2 – 5.5 kyr) strongly affected the demographic dynamics of M. arnholdi. We further inferred a population decline in the last millennium which was likely shaped by the combination of climatic and anthropogenic impacts. Our findings demonstrate that population fluctuations in Malagasy wildlife were substantial prior to a significant human impact. This provides a critical knowledge of climatically driven, environmental and ecological changes in the past, which is essential to better understand the dynamics and resilience of current biodiversity.

We investigated the genetic composition of six Canis remains from western Iberia, directly radiocarbon dated to 7,903-7,570 years (cal BP). They were identified as dogs via their archaeological and depositional context, osteometry, and a high percentage of aquatic diet shared with humans. For comparison, genetic data were obtained from an additional 37 Iberian dog remains from the Neolithic to Late Antiquity, as well as two Palaeolithic and a Chalcolithic Canis identified as wolves. Previous data indicated that dog mtDNA haplogroup A (HgA) is prevalent in extant European dogs (>50%), in the Near East and Asia, but rare or absent (<10%) in European Canis older than 3,000 years (cal BP). We found a high frequency (83%) of dog HgA in Mesolithic Iberian dog remains. This is the first report of a high frequency of dog HgA in pre-Neolithic Europe. We show that, contrary to the current view, Canis with HgA did not necessarily arrive in Europe from East-Asia. This phylogeographical difference in HgA frequency demonstrates that genetic differentiation was high prior to, or as a consequence of, domestication which may be linked with pre-Neolithic local processes for Iberian wolf domestication. Our results emphasize that knowledge of both ancient wolves' and early dogs' genetic profiles from the European periphery should improve our understanding of the evolution of the European dog.