Female Scarcity and Natal Dispersal Differences Between Sexes Among Bellbirds (Anthornis melanura)

Sex ratio imbalances in wild bird populations have been a challenge for wildlife managers for decades. Differences between sexes during natal dispersal has long been thought to promote sex ratio imbalances. Natal dispersal distances may differ between sexes because of competition for food and space, or intrasexual competition and aggression. I investigated natal dispersal and intrasexual competition as mechanisms for a sex ratio imbalance in a small, translocated population of a New Zealand honeyeater, the bellbird (Anthornis melanura) in the Karori Wildlife Sanctuary- Zealandia, Wellington, New Zealand. I analysed long term records of population size and structure to document annual variation in sex ratios since the reintroduction of bellbirds to Zealandia. Radio telemetry was used to track the 2008/2009 cohort of bellbirds for five months after fledging to observe movements and distances travelled from their hatching location. Observations at a supplemental food source that was used by both adults and fledglings, were used to study intrasexual competition and aggression. Dispersal distances did not differ between the sexes for any of the measurement types used. Males did however significantly dominate the use of a supplemental food source and were significantly more aggressive around this food source, which is most likely responsible for the lower feeding rate among females. Therefore, I conclude that the sex ratio imbalance in the bellbird population in Zealandia may not result from a difference in natal dispersal, but from males dominating a supplemental food source, raising their population and fitness over that of females

Comparing energy and water use of aqueous and gas‐based metalworking fluids

Gas‐based metalworking fluids (MWFs) have been proposed as alternative coolants and lubricants in machining operations to mitigate concerns surrounding water use and pollution, industrial hygiene, occupational health, and performance limitations associated with water‐based (aqueous) MWFs that are ubiquitously used in the metals manufacturing industry. This study compares the primary energy and water use associated with the consumptive use, delivery, and disposal of aqueous MWFs with three gas‐based MWFs in the literature—minimum quantity lubricant‐in‐compressed air (MQL), liquid/gaseous N2, and liquid/supercritical CO2. The comparison accounts for reported differences in machining performance in peer‐reviewed experimental studies across several machining processes and materials. The analysis shows that despite the reported improvement in tool life with N2 and CO2‐based MWFs, the electricity‐ and water‐intensive separation and purification processes for N2 and CO2 lead to their higher primary energy and water use per volume of material machined relative to water‐based MWFs. Although MQL is found to have lower primary energy use, significant consumptive water use associated with the vegetable oil commonly used with this MWF leads to higher overall water use than aqueous MWF, which is operated in a recirculative system. Gas‐based MWFs thus shift the water use upstream of the manufacturing plant. Primary energy and water use of gas‐based MWFs could be reduced by focusing on achieving higher material removal rates and throughput compared to aqueous MWF instead of solely targeting improvements in tool life. Additionally, the consumptive use of CO2 and N2 MWFs could be minimized by optimizing their flow rates and delivery to precisely meet the cooling and lubrication needs of specific machining processes instead of flooding the tool and workpiece with these gases. This article met the requirements for a gold–gold JIE data openness badge described at http://jie.click/badges.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/163496/3/jiec12992.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/163496/2/jiec12992-sup-0001-SuppMat.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/163496/1/jiec12992_am.pd

Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads

Despite the power of massively parallel sequencing platforms, a drawback is the short length of the sequence reads produced. We demonstrate that short reads can be locally assembled into longer contigs using paired-end sequencing of restriction-site associated DNA (RAD-PE) fragments. We use this RAD-PE contig approach to identify single nucleotide polymorphisms (SNPs) and determine haplotype structure in threespine stickleback and to sequence E. coli and stickleback genomic DNA with overlapping contigs of several hundred nucleotides. We also demonstrate that adding a circularization step allows the local assembly of contigs up to 5 kilobases (kb) in length. The ease of assembly and accuracy of the individual contigs produced from each RAD site sequence suggests RAD-PE sequencing is a useful way to convert genome-wide short reads into individually-assembled sequences hundreds or thousands of nucleotides long

Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences

Advances in sequencing technology provide special opportunities for genotyping individuals with speed and thrift, but the lack of software to automate the calling of tens of thousands of genotypes over hundreds of individuals has hindered progress. Stacks is a software system that uses short-read sequence data to identify and genotype loci in a set of individuals either de novo or by comparison to a reference genome. From reduced representation Illumina sequence data, such as RAD-tags, Stacks can recover thousands of single nucleotide polymorphism (SNP) markers useful for the genetic analysis of crosses or populations. Stacks can generate markers for ultra-dense genetic linkage maps, facilitate the examination of population phylogeography, and help in reference genome assembly. We report here the algorithms implemented in Stacks and demonstrate their efficacy by constructing loci from simulated RAD-tags taken from the stickleback reference genome and by recapitulating and improving a genetic map of the zebrafish, Danio rerio

Naturalistic experimental designs as tools for understanding the role of genes and the environment in prevention research

Before genetic approaches were applied in experimental studies with human populations, they were used by animal and plant breeders to observe, and experimentally manipulate, the role of genes and environment on specific phenotypic or behavioral outcomes. For obvious ethical reasons, the same level of experimental control is not possible in human populations. Nonetheless, there are natural experimental designs in human populations that can serve as logical extensions of the rigorous quantitative genetic experimental designs used by animal and plant researchers. Applying concepts such as cross-fostering and common garden rearing approaches from the life science discipline, we describe human designs that can serve as naturalistic proxies for the controlled quantitative genetic experiments facilitated in life sciences research. We present the prevention relevance of three such human designs: (1) children adopted at birth by parents to whom they are not genetically related (common garden approach); (2) sibling designs where one sibling is reared from birth with unrelated adoptive parents and the other sibling is reared from birth by the biological mother of the sibling pair (cross-fostering approach); and (3) in vitro fertilization designs, including egg donation, sperm donation, embryo donation, and surrogacy (prenatal cross-fostering approach). Each of these designs allows for differentiation of the effects of the prenatal and/or postnatal rearing environment from effects of genes shared between parent and child in naturalistic ways that can inform prevention efforts. Example findings from each design type are provided and conclusions drawn about the relevance of naturalistic genetic designs to prevention science

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

Single nucleotide polymorphism (SNP) discovery and genotyping are essential to genetic mapping. There remains a need for a simple, inexpensive platform that allows high-density SNP discovery and genotyping in large populations. Here we describe the sequencing of restriction-site associated DNA (RAD) tags, which identified more than 13,000 SNPs, and mapped three traits in two model organisms, using less than half the capacity of one Illumina sequencing run. We demonstrated that different marker densities can be attained by choice of restriction enzyme. Furthermore, we developed a barcoding system for sample multiplexing and fine mapped the genetic basis of lateral plate armor loss in threespine stickleback by identifying recombinant breakpoints in F2 individuals. Barcoding also facilitated mapping of a second trait, a reduction of pelvic structure, by in silico re-sorting of individuals. To further demonstrate the ease of the RAD sequencing approach we identified polymorphic markers and mapped an induced mutation in Neurospora crassa. Sequencing of RAD markers is an integrated platform for SNP discovery and genotyping. This approach should be widely applicable to genetic mapping in a variety of organisms

So, You Want to Use Next-Generation Sequencing in Marine Systems? Insight from the Pan-Pacific Advanced Studies Institute

The emerging field of next-generation sequencing (NGS) is rapidly expanding capabilities for cutting edge genomic research, with applications that can help meet marine conservation challenges of food security, biodiversity loss, and climate change. Navigating the use of these tools, however, is complex at best. Furthermore, applications of marine genomic questions are limited in developing nations where both marine biodiversity and threats to marine biodiversity are most concentrated. This is particularly true in Southeast Asia. The first Pan-Pacific Advanced Studies Institute (PacASI) entitled “Genomic Applications to Marine Science and Resource Management in Southeast Asia” was held in July 2012 in Dumaguete, Philippines, with the intent to draw together leading scientists from both sides of the Pacific Ocean to understand the potential of NGS in helping address the aforementioned challenges. Here we synthesize discussions held during the PacASI to provide perspectives and guidance to help scientists new to NGS choose among the variety of available advanced genomic methodologies specifically for marine science questions