Semi-automatic selection of summary statistics for ABC model choice

A central statistical goal is to choose between alternative explanatory models of data. In many modern applications, such as population genetics, it is not possible to apply standard methods based on evaluating the likelihood functions of the models, as these are numerically intractable. Approximate Bayesian computation (ABC) is a commonly used alternative for such situations. ABC simulates data x for many parameter values under each model, which is compared to the observed data xobs. More weight is placed on models under which S(x) is close to S(xobs), where S maps data to a vector of summary statistics. Previous work has shown the choice of S is crucial to the efficiency and accuracy of ABC. This paper provides a method to select good summary statistics for model choice. It uses a preliminary step, simulating many x values from all models and fitting regressions to this with the model as response. The resulting model weight estimators are used as S in an ABC analysis. Theoretical results are given to justify this as approximating low dimensional sufficient statistics. A substantive application is presented: choosing between competing coalescent models of demographic growth for Campylobacter jejuni in New Zealand using multi-locus sequence typing data

The guanine nucleotide exchange factor RIC8 regulates conidial germination through Gα proteins in Neurospora crassa.

Heterotrimeric G protein signaling is essential for normal hyphal growth in the filamentous fungus Neurospora crassa. We have previously demonstrated that the non-receptor guanine nucleotide exchange factor RIC8 acts upstream of the Gα proteins GNA-1 and GNA-3 to regulate hyphal extension. Here we demonstrate that regulation of hyphal extension results at least in part, from an important role in control of asexual spore (conidia) germination. Loss of GNA-3 leads to a drastic reduction in conidial germination, which is exacerbated in the absence of GNA-1. Mutation of RIC8 leads to a reduction in germination similar to that in the Δgna-1, Δgna-3 double mutant, suggesting that RIC8 regulates conidial germination through both GNA-1 and GNA-3. Support for a more significant role for GNA-3 is indicated by the observation that expression of a GTPase-deficient, constitutively active gna-3 allele in the Δric8 mutant leads to a significant increase in conidial germination. Localization of the three Gα proteins during conidial germination was probed through analysis of cells expressing fluorescently tagged proteins. Functional TagRFP fusions of each of the three Gα subunits were constructed through insertion of TagRFP in a conserved loop region of the Gα subunits. The results demonstrated that GNA-1 localizes to the plasma membrane and vacuoles, and also to septa throughout conidial germination. GNA-2 and GNA-3 localize to both the plasma membrane and vacuoles during early germination, but are then found in intracellular vacuoles later during hyphal outgrowth

Population growth of Mexican free-tailed bats \u3cem\u3e(Tadarida brasiliensis mexicana)\u3c/em\u3e predates human agricultural activity

Background Human activities, such as agriculture, hunting, and habitat modification, exert a significant effect on native species. Although many species have suffered population declines, increased population fragmentation, or even extinction in connection with these human impacts, others seem to have benefitted from human modification of their habitat. Here we examine whether population growth in an insectivorous bat (Tadarida brasiliensis mexicana) can be attributed to the widespread expansion of agriculture in North America following European settlement. Colonies of T. b. mexicana are extremely large (~106 individuals) and, in the modern era, major agricultural insect pests form an important component of their food resource. It is thus hypothesized that the growth of these insectivorous bat populations was coupled to the expansion of agricultural land use in North America over the last few centuries. Results We sequenced one haploid and one autosomal locus to determine the rate and time of onset of population growth in T. b. mexicana. Using an approximate Maximum Likelihood method, we have determined that T. b. mexicana populations began to grow ~220 kya from a relatively small ancestral effective population size before reaching the large effective population size observed today. Conclusions Our analyses reject the hypothesis that T. b. mexicana populations grew in connection with the expansion of human agriculture in North America, and instead suggest that this growth commenced long before the arrival of humans. As T. brasiliensis is a subtropical species, we hypothesize that the observed signals of population growth may instead reflect range expansions of ancestral bat populations from southern glacial refugia during the tail end of the Pleistocene

Polythiophenes and oligothiophenes in zeolite hosts

The polymerization of different thiophenes in the channels of molecular sieve zeolite hosts is described. Thiophene, 3-methyIthiophene, 2,2'-bithiophene, and terthiophene were introduced into dehydrated proton-, Cu(II)- or Fe(III)-containing zeolites (NaY and Na-mordenite) from organic solvents or vapor-phase. In the large-pore hosts, green-black products are formed from the monomers within several minutes. Spectroscopic characterization (IR, UV-NIR) confirms the formation of oxidized polymer chains in the zeolite channels. UV-Near IR reflectance spectra of the zeolite/polythiophene samples exhibit a broad absorption from 500 to about 2500 nm as the bulk and not the resolved spectra of short oligomers, thus fairly long polymer chains are formed in the zeolites. Conducting polymers can be recovered after dissolution of the zeolite host in HF. 2, 2'-bithiophene and a-terthiophene in acidic H2Y and U^Y zeolites (2 and 6 protons per super cage/ß-cage) yield yellow-green and purple products, respectively. UV-NIR reflectance data indicate that the acidic zeolite hosts oxidize the thiophene oligomers to yield stable radical cations and dications in their channel systems

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

Climate Change Influenced Female Population Sizes through Time across the Indonesian Archipelago

Lying at the crossroads of Asia and the Pacific world, the Indonesian archipelago hosts one of the world’s richest accumulations of cultural, linguistic, and genetic variation. While the role of human migration into and around the archipelago is now known in some detail, other aspects of Indonesia’s complex history are less understood. Here, we focus on population size changes from the first settlement of Indonesia nearly 50 kya up to the historic era. We reconstructed the past effective population sizes of Indonesian women using mitochondrial DNA sequences from 2,104 individuals in 55 village communities on four islands spanning the Indonesian archipelago (Bali, Flores, Sumba, and Timor). We found little evidence for large fluctuations in effective population size. Most communities grew slowly during the late Pleistocene, peaked 15–20 kya, and subsequently declined slowly into the Holocene. This unexpected pattern may reflect population declines caused by the flooding of lowland hunter/gatherer habitat during sea-level rises following the last glacial maximum

A question of scale: Human migrations writ large and small

Several recent papers illustrate the importance of migration and gene flow in molding the patterns of genetic variation observed in humans today. We place the varied demographic processes covered by these terms into a more general framework, and discuss some of the challenges facing attempts to reconstruct past human mobility and determine its influence on our genetic heritage

The complications of ‘hiring a hubby’: gender relations and the commoditisation of home maintenance in New Zealand

This paper examines the commoditization of traditionally male domestic tasks through interviews with handymen who own franchises in the company ‘Hire a Hubby’ in New Zealand and homeowners who have paid for home repair tasks to be done. Discussions of the commoditization of traditionally female tasks in the home have revealed the emotional conflicts of paying others to care as well as the exploitative and degrading conditions that often arise when work takes place behind closed doors. By examining the working conditions and relationships involved when traditionally male tasks are paid for, this paper raises important questions about the valuing of reproductive labour and the production of gendered identities. The paper argues that while working conditions and rates of pay for ‘hubbies’ are better than those for people undertaking commoditized forms of traditionally female domestic labour, the negotiation of this work is still complex and implicated in gendered relations and identities. Working on the home was described by interviewees as an expression of care for family and a performance of the ‘right’ way to be a ‘Kiwi bloke’ and a father. Paying others to do this labour can imply a failure in a duty of care and in the performance of masculinity

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

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