Intergenic DNA sequences from the human X chromosome reveal high rates of global gene flow

<p>Abstract</p> <p>Background</p> <p>Despite intensive efforts devoted to collecting human polymorphism data, little is known about the role of gene flow in the ancestry of human populations. This is partly because most analyses have applied one of two simple models of population structure, the island model or the splitting model, which make unrealistic biological assumptions.</p> <p>Results</p> <p>Here, we analyze 98-kb of DNA sequence from 20 independently evolving intergenic regions on the X chromosome in a sample of 90 humans from six globally diverse populations. We employ an isolation-with-migration (IM) model, which assumes that populations split and subsequently exchange migrants, to independently estimate effective population sizes and migration rates. While the maximum effective size of modern humans is estimated at ~10,000, individual populations vary substantially in size, with African populations tending to be larger (2,300–9,000) than non-African populations (300–3,300). We estimate mean rates of bidirectional gene flow at 4.8 × 10^-4/generation. Bidirectional migration rates are ~5-fold higher among non-African populations (1.5 × 10^-3) than among African populations (2.7 × 10^-4). Interestingly, because effective sizes and migration rates are inversely related in African and non-African populations, population migration rates are similar within Africa and Eurasia (e.g., global mean Nm = 2.4).</p> <p>Conclusion</p> <p>We conclude that gene flow has played an important role in structuring global human populations and that migration rates should be incorporated as critical parameters in models of human demography.</p

Radiolysis of Solid-State Nitrogen Heterocycles Provides Clues to Their Abundance in the Early Solar System

We studied the radiolysis of a wide variety of N-heterocycles, including many of biological importance, and find that the majority are remarkably stable in the solid-state when subjected to large doses of ionizing gamma radiation from a 60Co source. Degradation of N-heterocycles as a function of dose rate and total dose was measured using high performance liquid chromatography with UV detection. Many N-heterocycles show little degradation when γ-irradiated up to a total dose of ~1 MGy, which approximates hundreds of millions of years’ worth of radiation emitted in meteorite parent bodies due to slow radionuclide decay. Extrapolation of these results suggests that these N-heterocyclic compounds would be stable in dry parent bodies over solar system time-scales. We suggest that the abundance of these N-heterocycles as measured presently in carbonaceous meteorites is largely reflective of their abundance at the time aqueous alteration stopped in their parent bodies, and the absence of certain compounds in present-day samples is either due to the formation mechanisms or degradation which occurred during periods of aqueous alteration or thermal metamorphism

Sex-Biased Evolutionary Forces Shape Genomic Patterns of Human Diversity

Comparisons of levels of variability on the autosomes and X chromosome can be used to test hypotheses about factors influencing patterns of genomic variation. While a tremendous amount of nucleotide sequence data from across the genome is now available for multiple human populations, there has been no systematic effort to examine relative levels of neutral polymorphism on the X chromosome versus autosomes. We analyzed ∼210 kb of DNA sequencing data representing 40 independent noncoding regions on the autosomes and X chromosome from each of 90 humans from six geographically diverse populations. We correct for differences in mutation rates between males and females by considering the ratio of within-human diversity to human-orangutan divergence. We find that relative levels of genetic variation are higher than expected on the X chromosome in all six human populations. We test a number of alternative hypotheses to explain the excess polymorphism on the X chromosome, including models of background selection, changes in population size, and sex-specific migration in a structured population. While each of these processes may have a small effect on the relative ratio of X-linked to autosomal diversity, our results point to a systematic difference between the sexes in the variance in reproductive success; namely, the widespread effects of polygyny in human populations. We conclude that factors leading to a lower male versus female effective population size must be considered as important demographic variables in efforts to construct models of human demographic history and for understanding the forces shaping patterns of human genomic variability

Untangling Tales of Tropical Sardines: Local Knowledge From Fisheries in Timor-Leste

Tropical sardines (Family Clupeidae) are an important component of many marine fisheries in the Indo-West Pacific region. In Timor-Leste, a small, less-developed country within this region, ‘sardiña’ are some of the more commonly caught and consumed fish. Yet there is little published information from Timor-Leste about the species composition of these fisheries, nor their biology or ecology. We document the knowledge of Timorese fishers on nine locally distinguished sardine types that contribute to fisheries, and relate these to at least nine species: four species of ‘Flat-bodied Sardinellas’ (Sardinella subg. Clupeonia spp.), one species of ‘Round-bodied Sardinella’ (Sardinella subg. Sardinella lemuru), two species of ‘Tropical Pilchards’ (Amblygaster spp.) and a ‘Tropical Herring’ species (Herklotsichthys quadrimaculatus), all from the Clupeidae family; and one Dussumieria species from the Dussumieriidae family. We record variations in local sardine names across the country and document aspects of fishers’ knowledge relevant to understanding and managing the fisheries, including local sardine species’ seasonality, habitat, movements, interannual variation, as well as post-harvest characteristics in relation to perishability. In general, local names relate more closely with groups of species than individual species, although some names also distinguish fish size within species-groups. The local knowledge identified in this study has immediate application to inform fisheries monitoring and management, and to identify areas for future research. Notably, Timorese fishers recognize and make use of the strong association between some sardine species-groups and seasonally turbid river plumes. While further research is required to understand the underlying mechanisms of this association, this emphasizes the need to consider coastal fisheries and fisher livelihood impacts when assessing any plans or proposals that may alter river flow or water quality. Fishers also recognize migratory behavior of some sardine species, in particular the Flat bodied Sardinellas (S. gibbosa and others) along the north-west coast of Timor-Leste and across the border into Indonesian West Timor. Such insights complicate and need to be accounted for in initiatives for co-management or community-based management of Timor-Leste’s coastal waters and their fisheries

Autosomal Resequence Data Reveal Late Stone Age Signals of Population Expansion in Sub-Saharan African Foraging and Farming Populations

BACKGROUND:A major unanswered question in the evolution of Homo sapiens is when anatomically modern human populations began to expand: was demographic growth associated with the invention of particular technologies or behavioral innovations by hunter-gatherers in the Late Pleistocene, or with the acquisition of farming in the Neolithic? METHODOLOGY/PRINCIPAL FINDINGS:We investigate the timing of human population expansion by performing a multilocus analysis of > or = 20 unlinked autosomal noncoding regions, each consisting of approximately 6 kilobases, resequenced in approximately 184 individuals from 7 human populations. We test the hypothesis that the autosomal polymorphism data fit a simple two-phase growth model, and when the hypothesis is not rejected, we fit parameters of this model to our data using approximate Bayesian computation. CONCLUSIONS/SIGNIFICANCE:The data from the three surveyed non-African populations (French Basque, Chinese Han, and Melanesians) are inconsistent with the simple growth model, presumably because they reflect more complex demographic histories. In contrast, data from all four sub-Saharan African populations fit the two-phase growth model, and a range of onset times and growth rates is inferred for each population. Interestingly, both hunter-gatherers (San and Biaka) and food-producers (Mandenka and Yorubans) best fit models with population growth beginning in the Late Pleistocene. Moreover, our hunter-gatherer populations show a tendency towards slightly older and stronger growth (approximately 41 thousand years ago, approximately 13-fold) than our food-producing populations (approximately 31 thousand years ago, approximately 7-fold). These dates are concurrent with the appearance of the Late Stone Age in Africa, supporting the hypothesis that population growth played a significant role in the evolution of Late Pleistocene human cultures

Phylogeny, diversification, and biogeography of a hemiclonal hybrid system of native Australian freshwater fishes (Gobiiformes:Gobioidei: Eleotridae: Hypseleotris)

BACKGROUND: Carp gudgeons (genus Hypseleotris) are a prominent part of the Australian freshwater fish fauna, with species distributed around the western, northern, and eastern reaches of the continent. We infer a calibrated phylogeny of the genus based on nuclear ultraconserved element (UCE) sequences and using Bayesian estimation of divergence times, and use this phylogeny to investigate geographic patterns of diversification with GeoSSE. The southeastern species have hybridized to form hemiclonal lineages, and we also resolve relationships of hemiclones and compare their phylogenetic placement in the UCE phylogeny with a hypothesis based on complete mitochondrial genomes. We then use phased SNPs extracted from the UCE sequences for population structure analysis among the southeastern species and hemiclones. RESULTS: Hypseleotris cyprinoides, a widespread euryhaline species known from throughout the Indo-Pacific, is resolved outside the remainder of the species. Two Australian radiations comprise the bulk of Hypseleotris, one primarily in the northwestern coastal rivers and a second inhabiting the southeastern region including the Murray–Darling, Bulloo-Bancannia and Lake Eyre basins, plus coastal rivers east of the Great Dividing Range. Our phylogenetic results reveal cytonuclear discordance between the UCE and mitochondrial hypotheses, place hemiclone hybrids among their parental taxa, and indicate that the genus Kimberleyeleotris is nested within the northwestern Hypseleotris radiation along with three undescribed species. We infer a crown age for Hypseleotris of 17.3 Ma, date the radiation of Australian species at roughly 10.1 Ma, and recover the crown ages of the northwestern (excluding H. compressa) and southeastern radiations at 5.9 and 7.2 Ma, respectively. Range-dependent diversification analyses using GeoSSE indicate that speciation and extinction rates have been steady between the northwestern and southeastern Australian radiations and between smaller radiations of species in the Kimberley region and the Arnhem Plateau. Analysis of phased SNPs confirms inheritance patterns and reveals high levels of heterozygosity among the hemiclones. CONCLUSIONS: The northwestern species have restricted ranges and likely speciated in allopatry, while the southeastern species are known from much larger areas, consistent with peripatric speciation or allopatric speciation followed by secondary contact. Species in the northwestern Kimberley region differ in shape from those in the southeast, with the Kimberley species notably more elongate and slender than the stocky southeastern species, likely due to the different topographies and flow regimes of the rivers they inhabit

Using resource graphs to represent conceptual change

We introduce resource graphs, a representation of linked ideas used when reasoning about specific contexts in physics. Our model is consistent with previous descriptions of resources and coordination classes. It can represent mesoscopic scales that are neither knowledge-in-pieces or large-scale concepts. We use resource graphs to describe several forms of conceptual change: incremental, cascade, wholesale, and dual construction. For each, we give evidence from the physics education research literature to show examples of each form of conceptual change. Where possible, we compare our representation to models used by other researchers. Building on our representation, we introduce a new form of conceptual change, differentiation, and suggest several experimental studies that would help understand the differences between reform-based curricula.Comment: 27 pages, 14 figures, no tables. Submitted for publication to the Physical Review Special Topics Physics Education Research on March 8, 200

A Polynesian Motif on the Y Chromosome: Population Structure in Remote Oceania

This is the publisher's version, also available electronically from http://digitalcommons.wayne.edu/humbiol/vol79/iss5/5/.The Polynesian motif, a mitochondrial DNA marker of ancestral Polynesian communities, has filled a critical role in reconstructions of remote Oceanic history. Although the motif provides an effective narrative for Polynesian females, no equivalent male history is available from paternal lineages. Here, we describe a Y-chromosome binary polymorphism with absolute Polynesian affinity. We illustrate its unique spatial and temporal connections to early Polynesian communities, and through an analysis of associated short tandem repeat variation, we describe the first clear genealogic structure within Polynesia. Unlike the eastern and western regions advocated by archeology, we identify a tripartite structure comprising interaction spheres in the west (Tonga and Samoa), center (Tahiti), and east (Rapanui/Easter Island). Such patterning, a product of early regional contact and subsequent isolation, signals the conflicting roles of mobility and seclusion in Polynesian prehistory

Alternative conservation outcomes from aquatic fauna translocations: Losing and saving the Running River rainbowfish

1. The translocation of species outside their natural range is a threat to aquatic biodiversity globally, especially freshwater fishes, as most are not only susceptible to predation and competition but readily hybridize with congeners. 2. Running River rainbowfish (RRR, Melanotaenia sp.) is a narrow-ranged, small-bodied freshwater fish that recently became threatened and was subsequently listed as Critically Endangered, owing to introgressive hybridization and competition following the translocation of a congeneric species, the eastern rainbowfish (Melanotaenia splendida). 3. To conserve RRR, wild fish were taken into captivity, genetically confirmed as pure representatives, and successfully bred. As the threat of introgression with translocated eastern rainbowfish could not be mitigated, a plan was devised to translocate captive raised RRR into unoccupied habitats within their native catchment, upstream of natural barriers. The translocation plan involved careful site selection and habitat assessment, predator training (exposure to predators prior to release), soft release (with a gradual transition from captivity to nature), and post-release monitoring, and this approach was ultimately successful. 4. Two populations of RRR were established in two previously unoccupied streams above waterfalls with a combined stream length of 18 km. Post-release monitoring was affected by floods and low sample sizes, but suggested that predation and time of release are important factors to consider in similar conservation recovery programmes for small-bodied, short-lived fishes

Quantitative Membrane Loading of Polymer Vesicles

We utilize a series of structurally homologous, multi-porphyrin-based, fluorophores (PBFs) in order to explore the capacity of polymer vesicles (polymersomes) to stably incorporate large hydrophobic molecules, non-covalently within their thick lamellar membranes. Through aqueous hydration of dry, uniform thin-films of amphiphilic polymer and PBF species deposited on Teflon, self-assembled polymersomes are readily generated incorporating the hydrophobic fluorophores in prescribed molar ratios within their membranes. The size-dependent spectral properties of the PBFs allow for ready optical verification (via steady-state absorption and emission spectroscopy) of the extent of vesicle membrane loading and enable delineation of intermembranous molecular interactions. The resultant effects of PBF membrane-loading on polymersome thermodynamic and mechanical stability are further assessed by cryogenic transmission electron microscopy (cryo-TEM) and micropipet aspiration, respectively. We demonstrate that polymersomes can be loaded at up to 10 mol/wt% concentrations, with hydrophobic molecules that possess sizes comparable to those of large pharmaceutical conjugates (e.g. ranging 1.4–5.4 nm in length and Mw = 0.7–5.4 kg mol–1), without significantly compromising the robust thermodynamic and mechanical stabilities of these synthetic vesicle assemblies. Due to membrane incorporation, hydrophobic encapsulants are effectively prevented from self-aggregation, able to be highly concentrated in aqueous solution, and successfully shielded from deleterious environmental interactions. Together, these studies present a generalized paradigm for the generation of complex multi-functional materials that combine both hydrophilic and hydrophobic agents, in mesoscopic dimensions, through cooperative self-assembly