Towards a Socio-Economic Model for Southwest Asian Cereal Domestication

Mechanisms of selection for domestication traits in cereals and other annual plants are commonly explained from agro-technological and genetic perspectives. Since archaeobotanical data showed that domestication processes were slow and protracted, research focused on genetic constraints and hypothetical ‘non-selective’ management regimes to explain the low selection rates. I argue that these factors only partially explain the observed patterns and develop a model that contextualises the archaeobotanical data in their socio-economic settings. I propose that developments towards individual storage by small household units and the gradual increase in storage capacities with the development of extended households represent key factors for establishing the conditions for selection, as these practices isolated individually managed and stored cereal subpopulations and gradually reduced the need to replenish grain stocks with grains from unmanaged populations. This genetic isolation resulted in stronger and more persistent selection rates and facilitated the genetic fixation of domestication traits on a population level. Moreover, individual storage facilities within buildings reflect gradual developments towards households as the social units that mobilised agricultural labour, which negotiated new sharing principles over cultivated resources and drove the intensification of cultivation practices. In this sense, selection rates and the slow domestication process can be understood as a function of limited food sharing networks and increased labour-inputs into early arable environments—socio-economic processes that also unfolded gradually over a protracted period of time.

Morphological, Karyological and Phylogenetic Analyses of three Artemisia species that Around the Van Lake in Turkey

Artemisia is one of the biggest genera in the family Asteraceae, with around 500-600 taxa at specific and sub-specific levels and organised in five subgenera. Due to the high number of taxa, a lot taxonomists are trying to solve the problem of its classification and phylogeny but its natural classification still has not been achieved.The aim of this study is to try to solve the problematic systematic relationship between three different Artemisia species growing in close proximity to each other in the light of morphological, karyological and molecular data.The roots, stems, leaves, flowers structures of the plant samples collected from different populations belong to these species were investigated within the framework of morphological studies. Additionally, the chromosome counts and karyotype analysises of these species were made and idiograms were drawn in the karyological studies. In the context of phylogenetic studies, ITS and trn regions of 22 individuals belonging to 3 taxa were studied. It has been found that there is complete speciation genetic isolation mechanism between the species A. spicigera, A. taurica and A. fragrans that inhibit gene flow. A. fragrans and A. spicigera species are very similar to each other in terms of morphological characteristics. However, since populations of the species a fragrans are otopolyploid, the dimensional values of their morphological squares are larger than those of the species A. spicigera.This study is important as it is the first molecular based study relating with some species of Artemisia growing naturally in Turkey.

Differences in microhabitat and morphology of two sympatric congeneric species Palaquium maliliensis and Palaquium obovatum in the education forest of Hasanuddin University

Two species of Palaquium (P. maliliensis and P. obovatum) were found coexist in same habitat in the educational forest of Hasanuddin University (Unhas). Two or more species are living in a habitat could be formed from similar parent through genetic isolation process without geographic isolation and was classified as sympatric congeneric species. So far, sympatric congeneric species is still controversial among researchers. Based on this case, the purpose of this study was to determine the microhabitat and morphological differences between the two species. The methods of the study were conducted by purposively selecting 21 samples of P. maliliensis and 20 samples of P. obovatum at the tree level. In each samples found, the microhabitat characteristics (topographic position and slope) and morphological characteristics (leaf, buttress root, and morphological in general) were observed. Morphological measurement data were analyzed with correlation test for intra-species variable and real difference test for inter-species variable. This study concluded that the slope was one of the major microhabitat factors that has driven the process of sympatric speciation between P. maliliensis and P. obovatum. In morphological characteristics, differences between P. maliliensis and P. obovatum appeared in the form of leaves.

Anthropogenic restocking of gharial individuals prevents genetic isolation of gharial population in Girwa River, India by geographic barriers imposed by a barrage

Gharial (Gavialis gangeticus) is a critically endangered fresh water crocodile endemic to the Indian subcontinent. The species has suffered > 95% decline in population and habitat size. A small population of gharials comprising of 50 breeding adults is resident in a 20 Km stretch of the River Girwa in Katerniaghat wildlife sanctuary, India. Gharials in this 20 Km stretch have been genetically isolated since 1976 by a barrage that functions as a barrier to gene flow. A captive rear and release program has been initiated since 1979 under Project Crocodile for restocking declining wild gharial populations. Thousands of gharial eggs were collected from gharial populations at Girwa and Chambal Rivers. Hatchlings from the collected eggs were captive reared at a common location in Kukrail Gharial Centre, India and released back to multiple gharial populations including the isolated population at Girwa. This restocking programme was not preceded by a genetic screening of captive animals or wild populations to identify genetic diversity and genetic structure of both captive and wild animals. In this study we investigate whether release of captive reared gharials into the resident population at Girwa River has prevented genetic isolation caused due to barriers imposed by the barrage. Using a combination of empirical analysis using microsatellite markers and a systematic review of data from previous workers on molecular characterization of gharial populations, we analysed genetic differentiation in gharial populations at Girwa and Chambal. We found similar genetic variability in gharial populations of Girwa and Chambal. There was low inter population genetic differentiation and evidences of genetic migration between the two populations. Our findings indicate that anthropogenic intervention via release of captive animals has compensated for the genetic isolation in Girwa population caused by the barrage.

Mate choice enhances post-zygotic barriers to gene flow via ancestry bundling

Hybridization and subsequent genetic introgression are now known to be common features of the histories of many species, including our own. Following hybridization, post-zygotic selection tends to purge introgressed DNA genome-wide. While mate choice can prevent hybridization in the first place, it is also known to play an important role in post-zygotic selection against hybrids, and thus the purging of introgressed DNA. However, this role is usually thought of as a direct one: a mating preference for conspecifics reduces the sexual fitness of hybrids, reducing the transmission of introgressed ancestry. Here, we explore a second, indirect role of mate choice as a barrier to gene flow. Under assortative mating, parents covary in their ancestry, causing ancestry to be "bundled" in their offspring and later generations. This bundling effect increases ancestry variance in the population, enhancing the efficiency with which post-zygotic selection purges introgressed DNA. Using whole-genome simulations, we show that the bundling effect can comprise a substantial portion of mate choice's overall effect as a postzygotic barrier to gene flow, and that it is driven by ancestry covariances both between and within maternally and paternally inherited genomes. Using estimates of the strength of assortative mating in avian hybrid zones, we calculate that the bundling effect of mate choice may increase the amount of purging of introgressed DNA by 40-80%, contributing substantially to the genetic isolation of species.

Landscape configuration of an Amazonian island-like ecosystem drives population structure and genetic diversity of a habitat-specialist bird

Context Amazonian white-sand ecosystems (campinas) are open vegetation patches which form a natural island-like system in a matrix of tropical rainforest. Due to a clear distinction from the surrounding matrix, the spatial characteristics of campina patches may affect the genetic diversity and composition of their specialized organisms, such as the small and endemic passerine Elaenia ruficeps. Objectives To estimate the relative contribution of the current extension, configuration and geographical context of campina patches to the patterns of genetic diversity and population structure of E. ruficeps. Methods We sampled individuals of E. ruficeps from three landscapes in central Amazonia with contrasting campina spatial distribution, from landscapes with large and connected patches to landscapes with small and isolated patches. We estimated population structure, genetic diversity, and contemporary and historical migration within and among the three landscapes and used landscape metrics as predictor variables. Furthermore, we estimated genetic isolation by distance and resistance within landscapes. Results We identified three genetically distinct populations with asymmetrical gene flow among landscapes and a decreasing migration rate with distance. Within each landscape, we found low differentiation without genetic isolation by distance nor by resistance. In contrast, we found differentiation and spatial correlation between landscapes. Conclusions Together with previous studies, the population dynamics of E. ruficeps suggests that both regional context and landscape structure shape the connectivity among populations of campina specialist birds. Also, the spatial distribution of Amazonian landscapes, together with their associated biota, has changed in response to climatic changes in the Late Pleistocene.

An in-depth analysis of the mitochondrial phylogenetic landscape of Cambodia

Cambodia harbours a variety of human aboriginal populations that have scarcely been studied in terms of genetic diversity of entire mitochondrial genomes. Here we present the matrilineal gene pool of 299 Cambodian refugees from three different ethnic groups (Cham, Khmer, and Khmer Loeu) deriving from 16 Cambodian districts. After establishing a DNA-saving high-throughput strategy for mitochondrial whole-genome Sanger sequencing, a HaploGrep based workflow was used for quality control, haplogroup classification and phylogenetic reconstruction. The application of diverse phylogenetic algorithms revealed an exciting picture of the genetic diversity of Cambodia, especially in relation to populations from Southeast Asia and from the whole world. A total of 224 unique haplotypes were identified, which were mostly classified under haplogroups B5a1, F1a1, or categorized as newly defined basal haplogroups or basal sub-branches of R, N and M clades. The presence of autochthonous maternal lineages could be confirmed as reported in previous studies. The exceptional homogeneity observed between and within the three investigated Cambodian ethnic groups indicates genetic isolation of the whole population. Between ethnicities, genetic barriers were not detected. The mtDNA data presented here increases the phylogenetic resolution in Cambodia significantly, thereby highlighting the need for an update of the current human mtDNA phylogeny.

Genetic isolation by distance underlies color pattern divergence in red-eyed treefrogs (Agalychnis callidryas)

Investigating the spatial distribution of genetic and phenotypic variation can provide insights into the evolutionary processes that shape diversity in natural systems. We characterized patterns of genetic and phenotypic diversity to learn about drivers of color-pattern diversification in red-eyed treefrogs (Agalychnis callidryas) in Costa Rica. Along the Pacific coast, red-eyed treefrogs have conspicuous leg color patterning that transitions from orange in the north to purple in the south. We measured phenotypic variation of frogs across Pacific sites, with increased sampling at sites where the orange-to-purple transition occurs. At the transition zone, we discovered the co-occurrence of multiple color-pattern morphs. To explore possible causes of this variation, we generated a SNP dataset with RAD sequencing to analyze population genetic structure, measure genetic diversity, and infer the processes that mediate genotype-phenotype dynamics. We investigated how patterns of genetic relatedness correspond with individual measures of color pattern along the coast, including testing for the role of hybridization in geographic regions where orange and purple phenotypic groups co-occur. We found no evidence that color-pattern polymorphism in the transition zone arose through recent hybridization or introgression. Instead, a strong pattern of genetic isolation by distance (IBD) indicates that color-pattern variation was retained through other processes such as ancestral color polymorphisms, ancient secondary contact or generated by novel mutations. We found that color phenotype changes along the Pacific coast more than would be expected from geographic distance alone. Combined, our results suggest the possibility of selective pressures acting on color pattern at a small geographic scale.