Variation in inbreeding rates across the range of Northern Spotted Owls (\u3ci\u3eStrix occidentalis caurina\u3c/i\u3e): Insights from over 30 years of monitoring data

Inbreeding has been difficult to quantify in wild populations because of incomplete parentage information. We applied and extended a recently developed framework for addressing this problem to infer inbreeding rates in Northern Spotted Owls (Strix occidentalis caurina) across the Pacific Northwest, USA. Using pedigrees from 14,187 Northern Spotted Owls, we inferred inbreeding rates for 14 types of matings among relatives that produce pedigree inbreeding coefficients of F=0.25 or F=0.125. Inbreeding was most common in the Washington Cascades, where an estimated 15% of individuals are inbred. Inbreeding was lowest in western Oregon (3.5%) and northern California (2.7%), and intermediate for the Olympic Peninsula of Washington (6.1%). Estimates from the Olympic Peninsula were likely underestimates because of small sample sizes and the presence of few pedigrees capable of resolving inbreeding events. Most inbreeding resulted from matings between full siblings or half siblings, although a high rate of inbreeding from mother–son pairs was identified in the Olympic Peninsula. Geographic variation in inbreeding rates may reflect population declines and bottlenecks that have been detected in prior investigations. We show that there is strong selection against inbred birds. Only 3 of 44 inbred birds were later identified as parents (6.8%), whereas 2,823 of 10,380 birds that represented a comparable cross section of the data were later seen as reproducing parents (27.2%). Habitat loss and competition with Barred Owls (S. varia) remain primary threats to Northern Spotted Owls. However, given the negative consequences of inbreeding, Spotted Owl populations in Washington with suitable habitat and manageable numbers of Barred Owls may benefit from translocations of individuals from Oregon and California to introduce new genetic variation and reduce future inbreeding events. La endogamia ha sido dif´ıcil de cuantificar en las poblaciones silvestres debido a la falta de informaci ´on sobre los parentescos. Aplicamos y extendimos un marco conceptual recientemente desarrollado para encarar el problema de inferir las tasas de endogamia en Strix occidentalis caurina a trav´es del noroeste del Pac´ıfico, EEUU. Usando los pedigr´ıes provenientes de 14187 individuos, inferimos las tasas de endogamia para 14 tipos de apareamiento entre parientes que producen coeficientes de endogamia de pedigr´ı de F=0.25 o F=0.125. La endogamia fue ma´s com´un en las Cascadas de Washington, donde se estima que 15% de los individuos son endoga´micos. La endogamia fue menor en el oeste de Oreg´on (3.5%) y el norte de California (2.7%), e intermedia en la Pen´ınsula Ol´ımpica de Washington (6.1%). Las estimaciones de la Pen´ınsula Ol´ımpica fueron probablemente subestimadas debido a los peque ˜nos tama ˜nos de muestreo y a la presencia de pocos pedigr´ıes capaces de resolver los eventos de endogamia. La mayor´ıa de la endogamia result ´o de los apareamientos entre hermanos completos o medios hermanos, aunque se identific ´o una alta tasa de endogamia en parejas madre/hijo en la Pen´ınsula Ol´ımpica. La variaci ´on geogra´ fica en las tasas de endogamia puede reflejar disminuciones poblacionales y cuellos de botella que han sido detectados en investigaciones previas. Mostramos que hay una fuerte selecci ´on contra las aves endoga´micas. Solo tres de 44 aves endoga´micas fueron ma´s tarde identificadas como progenitores (6.8%), mientras que 2823 de 10380 aves que representaron una secci ´on transversal comparable de datos fueron vistas ma´s tarde como progenitores reproductivos (27.2%). La p´erdida de ha´bitat y la competencia con Strix varia sigue siendo la principal amenaza para S. o. caurina. Sin embargo, dadas las consecuencias negativas de la endogamia, las poblaciones de S. occidentalis en Washington con ha´bitat adecuado y n´umeros manejables de Strix varia pueden beneficiarse de traslocaciones de individuos de Oreg´on y California para introducir nueva variaci ´on gen´etica y reducir futuros eventos de endogamia

Evolution of cooperation without reciprocity

A long-standing problem in biological and social sciences is to understand the conditions required for the emergence and maintenance of cooperation in evolving populations. For many situations, kin selection(1) is an adequate explanation, although kin-recognition may still be a problem. Explanations of cooperation between non-kin include continuing interactions that provide a shadow of the future (that is, the expectation of an ongoing relationship) that can sustain reciprocity(2-4), possibly supported by mechanisms to bias interactions such as embedding the agents in a two-dimensional space(4-6) or other context-preserving networks(7). Another explanation, indirect reciprocity(8), applies when benevolence to one agent increases the chance of receiving help from others. Here we use computer simulations to show that cooperation can arise when agents donate to others who are sufficiently similar to themselves in some arbitrary characteristic. Such a characteristic, or 'tag', can be a marking, display, or other observable trait. Tag-based donation can lead to the emergence of cooperation among agents who have only rudimentary ability to detect environmental signals and, unlike models of direct(3,4) or indirect reciprocity(9,10), no memory of past encounters is required.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62686/1/414441a0.pd

Effects of APETALA2 on embryo, endosperm, and seed coat development determine seed size in Arabidopsis

Arabidopsis APETALA2 (AP2) controls seed mass maternally, with ap2 mutants producing larger seeds than wild type. Here, we show that AP2 influences development of the three major seed compartments: embryo, endosperm, and seed coat. AP2 appears to have a significant effect on endosperm development. ap2 mutant seeds undergo an extended period of rapid endosperm growth early in development relative to wild type. This early expanded growth period in ap2 seeds is associated with delayed endosperm cellularization and overgrowth of the endosperm central vacuole. The subsequent period of moderate endosperm growth is also extended in ap2 seeds largely due to persistent cell divisions at the endosperm periphery. The effect of AP2 on endosperm development is mediated by different mechanisms than parent-of-origin effects on seed size observed in interploidy crosses. Seed coat development is affected; integument cells of ap2 mutants are more elongated than wild type. We conclude that endosperm overgrowth and/or integument cell elongation create a larger postfertilization embryo sac into which the ap2 embryo can grow. Morphological development of the embryo is initially delayed in ap2 compared with wild-type seeds, but ap2 embryos become larger than wild type after the bent-cotyledon stage of development. ap2 embryos are able to fill the enlarged postfertilization embryo sac, because they undergo extended periods of cell proliferation and seed filling. We discuss potential mechanisms by which maternally acting AP2 influences development of the zygotic embryo and endosperm to repress seed size

Genomic Analysis of Parent-of-Origin Allelic Expression in Arabidopsis thaliana Seeds

Differential expression of maternally and paternally inherited alleles of a gene is referred to as gene imprinting, a form of epigenetic gene regulation common to flowering plants and mammals. In plants, imprinting primarily occurs in the endosperm, a seed tissue that supports the embryo during its growth and development. Previously, we demonstrated that widespread DNA demethylation at remnants of transposable elements accompanies endosperm development and that a subset of these methylation changes are associated with gene imprinting. Here we assay imprinted gene expression genome-wide by performing high-throughput sequencing of RNA derived from seeds of reciprocal intraspecific crosses. We identify more than 200 loci that exhibit parent-of-origin effects on gene expression in the endosperm, including a large number of transcription factors, hormone biosynthesis and response genes, and genes that encode regulators of epigenetic information, such as methylcytosine binding proteins, histone methyltransferases, and chromatin remodelers. The majority of these genes are partially, rather than completely, imprinted, suggesting that gene dosage regulation is an important aspect of imprinted gene expression

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

Genome-wide associations for birth weight and correlations with adult disease

Birth weight (BW) has been shown to be influenced by both fetal and maternal factors and in observational studies is reproducibly associated with future risk of adult metabolic diseases including type 2 diabetes (T2D) and cardiovascular disease. These life-course associations have often been attributed to the impact of an adverse early life environment. Here, we performed a multi-ancestry genome-wide association study (GWAS) meta-analysis of BW in 153,781 individuals, identifying 60 loci where fetal genotype was associated with BW ($\textit{P}$  < 5 × 10$^{-8}$). Overall, approximately 15% of variance in BW was captured by assays of fetal genetic variation. Using genetic association alone, we found strong inverse genetic correlations between BW and systolic blood pressure ($\textit{R}$ $_{g}$ = -0.22, $\textit{P}$  = 5.5 × 10$^{-13}$), T2D ($\textit{R}$ $_{g}$ = -0.27, $\textit{P}$  = 1.1 × 10$^{-6}$) and coronary artery disease ($\textit{R}$ $_{g}$ = -0.30, $\textit{P}$  = 6.5 × 10$^{-9}$). In addition, using large -cohort datasets, we demonstrated that genetic factors were the major contributor to the negative covariance between BW and future cardiometabolic risk. Pathway analyses indicated that the protein products of genes within BW-associated regions were enriched for diverse processes including insulin signalling, glucose homeostasis, glycogen biosynthesis and chromatin remodelling. There was also enrichment of associations with BW in known imprinted regions ($\textit{P}$ = 1.9 × 10$^{-4}$). We demonstrate that life-course associations between early growth phenotypes and adult cardiometabolic disease are in part the result of shared genetic effects and identify some of the pathways through which these causal genetic effects are mediated.For a full list of the funders pelase visit the publisher's website and look at the supplemetary material provided. Some of the funders are: British Heart Foundation, Cancer Research UK, Medical Research Council, National Institutes of Health, Royal Society and Wellcome Trust