Beyond multiregional and simple out-of-Africa models of human evolution

info:eu-repo/semantics/publishedVersio

Female and Male Perspectives on the Neolithic Transition in Europe:Clues from Ancient and Modern Genetic Data

The arrival of agriculture into Europe during the Neolithic transition brought a significant shift in human lifestyle and subsistence. However, the conditions under which the spread of the new culture and technologies occurred are still debated. Similarly, the roles played by women and men during the Neolithic transition are not well understood, probably due to the fact that mitochondrial DNA (mtDNA) and Y chromosome (NRY) data are usually studied independently rather than within the same statistical framework. Here, we applied an integrative approach, using different model-based inferential techniques, to analyse published datasets from contemporary and ancient European populations. By integrating mtDNA and NRY data into the same admixture approach, we show that both males and females underwent the same admixture history and both support the demic diffusion model of Ammerman and Cavalli-Sforza. Similarly, the patterns of genetic diversity found in extant and ancient populations demonstrate that both modern and ancient mtDNA support the demic diffusion model. They also show that population structure and differential growth between farmers and hunter-gatherers are necessary to explain both types of data. However, we also found some differences between male and female markers, suggesting that the female effective population size was larger than that of the males, probably due to different demographic histories. We argue that these differences are most probably related to the various shifts in cultural practices and lifestyles that followed the Neolithic Transition, such as sedentism, the shift from polygyny to monogamy or the increase of patrilocality

Signals of recent spatial expansions in the grey mouse lemur (Microcebus murinus)

<p>Abstract</p> <p>Background</p> <p>Pleistocene events have shaped the phylogeography of many taxa worldwide. Their genetic signatures in tropical species have been much less explored than in those living in temperate regions. We analysed the genetic structure of a Malagasy primate species, a mouse lemur with a wide distribution (<it>M. murinus)</it>, in order to investigate such phylogeographic processes on a large tropical island. We also evaluated the effects of anthropogenic pressures (fragmentation/deforestation) and natural features (geographic distance, rivers) on genetic structure in order to complement our understanding of past and present processes of genetic differentiation.</p> <p>Results</p> <p>The analysis of the mitochondrial D-loop sequences of 195 samples from 15 study sites (10 from a continuous forest and five from isolated forest fragments) from two adjacent Inter-River-Systems (IRSs) revealed that forest fragmentation and the river restrict gene flow, thereby leading to an increased genetic differentiation between populations beyond the effect of isolation-by-distance. Demographic simulations detected signals of two successive spatial expansions that could be preliminarily dated to the late Pleistocene and early Holocene. The haplotype network revealed geographic structure and showed deep molecular divergences within and between the IRSs that would be congruent with a two-step colonization scenario.</p> <p>Conclusions</p> <p>This study supports the hypothesis of a relatively recent spatial expansion of the grey mouse lemur in northwestern Madagascar, which may also explain why this taxon, in contrast to its congeners, has not yet undergone allopatric speciation in the studied area and possibly across its presently wide range.</p

Genetic diversity in Tetrachaetum elegans, a mitosporic aquatic fungus.

Tetrachaetum elegans Ingold is a saprobic aquatic hyphomycete for which no sexual stage has yet been described. It occurs most commonly during the initial decay of tree leaves in temperate freshwater habitats and typically sporulates under water. Dispersal of the aquatic fungus takes place primarily in the water column and has a large passive component. Differences in substrate composition (e.g. quality of leaf litter) may also play a role in the distribution of different species or genotypes. The population genetic structure of T. elegans was studied using amplified fragment length polymorphism (AFLP) multilocus fingerprints. The populations were isolated from the leaf litter of three different tree genera, sampled in nine streams distributed throughout a mixed deciduous forest. Molecular markers were developed for 97 monosporic isolates using four selective primer pairs. A total of 247 fragments were scored, of which only 32 were polymorphic. Significant stream differentiation was detected for the isolates considered in this study. Analysis of molecular variance revealed that 20% of the genetic variation observed was the result of differences between streams. No correlation between genetic and geographical distances was found but a few multilocus genotypes were observed in different locations. Altogether these results suggest that environmental barriers play a role in the population structure of this aquatic fungus. No clear-cut effect of leaf litter composition on genetic variation could be demonstrated. Finally, tests of linkage disequilibrium between the 32 polymorphic AFLP loci as well as simulations did not provide a final answer regarding clonality in T. elegans. Indeed, it was possible to reject linkage equilibrium at different sampling levels and show that full linkage was unlikely

Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle

Iberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical space. While genomic data are accumulating for most commercial cattle, it is still lacking for these primitive breeds. Whole genome data is key to understand the consequences of historic breed formation and the putative role of earlier admixture events in the observed diversity patterns.info:eu-repo/semantics/publishedVersio

Forest type influences population densities of nocturnal lemurs in Manompana, Northeastern Madagascar

Forest loss, fragmentation, and anthropization threaten the survival of forest species all over the world. Shifting agriculture is one of these threatening processes in Madagascar. However, when its cycle is halted and the land is left to regenerate, the resulting growth of secondary forest may provide a viable habitat for folivorous and omnivorous lemur species. We aimed to identify the response of nocturnal lemurs to different successional stages of regenerating secondary, degraded mature, and mature forest across a mosaic-type landscape. We surveyed four nocturnal lemur species (Avahi laniger, Microcebus cf. simmonsi, Allocebus trichotis, and Daubentonia madagascariensis) in four forest types of varying habitat disturbance in northeastern Madagascar. We estimated densities in mature and regenerating secondary forest for the eastern woolly lemur (Avahi laniger) and mouse lemur (Microcebus cf. simmonsi), two sympatric species with folivorous and omnivorous diets respectively. We did not estimate densities of Allocebus trichotis and Daubentonia madagascariensis owing to small sample size; however, we observed both species exclusively in mature forest. We found higher population densities of A. laniger and M. cf. simmonsi in secondary than in mature forest, showing the potential of regenerating secondary forest for lemur conservation. Several environmental factors influenced the detectability of the two lemur species. While observer and habitat type influenced detection of the eastern woolly lemur, canopy height and vine density influenced detection of mouse lemurs. Understanding how different species with different diets interact with anthropogenically impacted habitat will aid future management decisions for the conservation of primate species

Conservation Status and Abundance of the Crowned Sifaka (Propithecus coronatus)

The crowned sifaka (Propithecus coronatus) is Endangered. It has a large but highly fragmented distribution; its known range extends from the Betsiboka River in the north of Madagascar, to the Mahavavy River in the north-west, and down to the Tsiribihina River in the south-west. The species lives in forest habitats that are highly and increasingly fragmented and are continuously suffering perturbations and destruction. In order to carry out effective conservation measures targeting P. coronatus, its conservation status needs to be updated so that measures can be taken before anthropogenic or natural environmental changes lead to the extirpation of the species in most of its forests. We (i) identified forest fragments where the species is still present and (ii) using the line-transect “Distance” sampling method, estimated the population size and density in the principal remaining forest fragments in the northern part of its range, including both protected and unprotected areas. We visited most of the forests in the northern part of its range in order to update the current area of occupancy, and to rate the state of its forests using a qualitative “forest quality index.” Our survey results have shown that (i) a large number of forests have disappeared or decreased in size in the last 10 years, and (ii) population densities vary considerably among forest fragments (ranging from 49 to 309 individuals per km²), with some very high densities in forests located along the Mahavavy River and in the Antrema area. Their abundance in the area surveyed is likely to be between 4,226 and 36,672 individuals, and most probably above 10,000. It is difficult to extrapolate from these estimates to the total abundance across the species’ entire range, but we estimate that it is likely to be large, probably between 130,000 and 220,000 individuals. Unfortunately, many field observations suggest that its populations continue to decline at a high rate due to habitat loss and hunting, and we argue for the re-evaluation of the conservation status from Endangered A2cd to Endangered A4acd, and the need to survey the rest of the range of P.coronatus.FCT grant: (SFRH/BD/64875/2009), Institut Français de la Biodiversité, Programme Biodiversité de l’Océan Indien (ref.CD-AOOI-07-003), the GDRI Madagascar, the "Laboratoire d’Excellence" (LABEX) entitled TULIP: (ANR -10-LABX-41), Instituto Gulbenkian de Ciência, “Optimus Alive!” Biodiversity grant, University of Mahajanga, Département de Biologie Animale et Ecologie, Fanamby NGO

Comparing maternal genetic variation across two millennia reveals the demographic history of an ancient human population in southwest Turkey

More than two decades of archaeological research at the site of Sagalassos, in southwest Turkey, resulted in the study of the former urban settlement in all its features. Originally settled in late Classical/early Hellenistic times, possibly from the later fifth century BCE onwards, the city of Sagalassos and its surrounding territory saw empires come and go. The Plague of Justinian in the sixth century CE, which is considered to have caused the death of up to a third of the population in Anatolia, and an earthquake in the seventh century CE, which is attested to have devastated many monuments in the city, may have severely affected the contemporary Sagalassos community. Human occupation continued, however, and Byzantine Sagalassos was eventually abandoned around 1200 CE. In order to investigate whether these historical events resulted in demographic changes across time, we compared the mitochondrial DNA variation of two population samples from Sagalassos (Roman and Middle Byzantine) and a modern sample from the nearby town of Ağlasun. Our analyses revealed no genetic discontinuity across two millennia in the region and Bayesian coalescence-based simulations indicated that a major population decline in the area coincided with the final abandonment of Sagalassos, rather than with the Plague of Justinian or the mentioned earthquake.Belgian Programme on Interuniversity Poles of Attraction grant: (IAP 07/09, http://iap-cores.be/); University of Leuven grant: (GOA 13/04); KU Leuven BOF Centre of Excellence Financing on ‘Centre for Archaeological Sciences 2–New methods for research in demography and interregional exchange’; Research Foundation Flanders (FWO) grants: (Projects G.0562.11, G.0637.15); Leverhulme Trust (UK) grant:(F/00212/AM); Institute of History of Leiden University

Taxonomy, geographic variation and population genetics of Bornean and Sumatran orangutans

This chapter reviews the published data and discusses the taxonomy and population genetics of orangutans. The orangutan was traditionally classified as two separate subspecies, Pongo pygmaeus pygmaeus in Borneo and P. p. abelii in Sumatra. Recent molecular data have suggested a re-classification into two separate species: P. pygmaeus in Borneo and P. abelii in Sumatra. Moreover, three subspecies have been described on Borneo Island: P. p. pygmaeus in Sarawak and west Kalimantan, P. p. morio in Sabah and east Kalimantan and P. p. wurmbii in central and south Kalimantan. Despite this, little is known about the intra-subspecific variation between isolated Bornean populations and among the Sumatran populations. More data are needed, which should include a large sampling of all geographically separated populations in Borneo and Sumatra in order to provide a more complete genetic information database