PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs

Summary: The analysis of genetic data often requires a combination of several approaches using different and sometimes incompatible programs. In order to facilitate data exchange and file conversions between population genetics programs, we introduce PGDSpider, a Java program that can read 27 different file formats and export data into 29, partially overlapping, other file formats. The PGDSpider package includes both an intuitive graphical user interface and a command-line version allowing its integration in complex data analysis pipelines. Availability: PGDSpider is freely available under the BSD 3-Clause license on http://cmpg.unibe.ch/software/PGDSpider/ Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

Methane Emissions of Differently Fed Dairy Cows and Corresponding Methane and Nitrogen Emissions from their Manure during Storage

This study investigated the effects of supplementing 40 g lauric acid (C12) kg-1 dry matter (DM) in feed on methane emissions from early-lactating dairy cows and the associated effects on methane, nitrous oxide and ammonia release from the manure during storage. Stearic acid (C18), a fatty acid without assumed methane-suppressing potential in the digestive tract of ruminants, was added at 40 g kg-1 DM to a control diet. The complete feed consisted of forage and concentrate in a ratio of 1.5:1 (DM basis). The manure was stored for 14 weeks either as complete slurry or, separately, as urine-rich slurry and farmyard manure representing two common storage systems. Methane release of the cows, as measured in respiratory chambers, was lower with C12 by about 20%, but this was mostly resulting from a reduced feed intake and, partly, from a lower rate of fibre digestion. As milk yield declined less than feed intake, methane emission per kg of milk was significantly lower with C12 (11.4 g) than with C18 (14.0 g). Faeces of C12-fed cows had a higher proportion of undigested fibre and accordingly methane release from their manure was higher compared with the manure obtained from the C18-fed cows. Overall, manure-derived methane accounted for8.2% and 15.4% of total methane after 7 and 14 weeks of storage, respectively. The evolution of methane widely differed between manure types and dietary treatments, with a retarded onset of release in complete slurry particularly in the C12 treatment. Emissions of nitrous oxide were lower in the manures from the C12 treatment. This partially compensated for the higher methane release from the C12 manure with respect to the greenhouse gas potential. The total greenhouse gas potential (cow and manure together) accounted for 8.7 and 10.5 kg equivalents of CO2 cow-1 d-1with C12 and C18, respectively. At unaffected urine-N proportion ammonia and total nitrogen losses from stored manure were lower with C12 than with C18 corresponding to the differences in feed and nitrogen intake. The present results suggest that manure storage significantly contributes to total methane emission from dairy husbandry, and that the identification of effective dietary mitigation strategies has to consider both the digestive tract of the animals and the corresponding manur

Batch effects in a multiyear sequencing study: false biological trends due to changes in read lengths

High-throughput sequencing is a powerful tool, but suffers biases and errors that must be accounted for to prevent false biological conclusions. Such errors include batch effects; technical errors only present in subsets of data due to procedural changes within a study. If overlooked and multiple batches of data are combined, spurious biological signals can arise, particularly if batches of data are correlated with biological variables. Batch effects can be minimized through randomization of sample groups across batches. However, in long-term or multiyear studies where data are added incrementally, full randomization is impossible, and batch effects may be a common feature. Here, we present a case study where false signals of selection were detected due to a batch effect in a multiyear study of Alpine ibex (Capra ibex). The batch effect arose because sequencing read length changed over the course of the project and populations were added incrementally to the study, resulting in nonrandom distributions of populations across read lengths. The differences in read length caused small misalignments in a subset of the data, leading to false variant alleles and thus false SNPs. Pronounced allele frequency differences between populations arose at these SNPs because of the correlation between read length and population. This created highly statistically significant, but biologically spurious, signals of selection and false associations between allele frequencies and the environment. We highlight the risk of batch effects and discuss strategies to reduce the impacts of batch effects in multiyear high-throughput sequencing studies

Claw and limb disorders in 12 Norwegian beef-cow herds

<p>Abstract</p> <p>Background</p> <p>The main aim of the study was to assess the prevalence of claw and limb disorders in Norwegian beef-cow herds.</p> <p>Methods</p> <p>Twenty-six herds with ≥15 cow-years were selected by computerized systematic assignment from the three most beef cattle-dense regions of Norway. The study population consisted of 12 herds with 28 heifers and 334 cows. The animals were trimmed and examined once by claw trimmers during the late winter and spring of 2003. The seven claw trimmers had been taught diagnosing and recording of claw lesions. Environment, feeding and management routines, age and breed, culling and carcass characteristics were also recorded.</p> <p>Results</p> <p>Lameness was recorded in 1.1% of the animals, and only in hind claws. Pericarpal swellings were recorded in one animal and peritarsal lesions in none. In total, claw and limb disorders including lameness were recorded in 29.6% of the animals, 4.1% with front and 28.2% with hind limb disorders, respectively. Most lesions were mild. Laminitis-related claw lesions were recorded in 18.0% of the animals and infectious lesions in 16.6%. The average claw length was 84 mm in front claws and 89 mm in hind claw. Both laminitis-related and infectious claw lesions were more prevalent with increasing age. Carcasses from animals with claw and limb disorders were on average 34 kg heavier than carcasses from animals without such disorders (p = 0.02). Our results also indicate association between some management factors and claw lesions.</p> <p>Conclusion</p> <p>The study shows that the prevalence of lameness was low in 12 Norwegian beef-cow herds compared to beef-cattle herds in other countries and also that there were less claw and limb disorders in these herds compared to foreign dairy-cattle herds. The prevalence of lameness and white-line fissures was approximately the same as in Norwegian dairy herds whereas less dermatitis, heel-horn erosions, haemorrhages of the sole and the white line and sole ulcers were recorded.</p

Rapid niche expansion by selection on functional genomic variation after ecosystem recovery

It is well recognized that environmental degradation caused by human activities can result in dramatic losses of species and diversity. However, comparatively little is known about the ability of biodiversity to re-emerge following ecosystem recovery. Here, we show that a European whitefish subspecies, the gangfisch Coregonus lavaretus macrophthalmus, rapidly increased its ecologically functional diversity following the restoration of Lake Constance after anthropogenic eutrophication. In fewer than ten generations, gangfisch evolved a greater range of gill raker numbers (GRNs) to utilize a broader ecological niche. A sparse genetic architecture underlies this variation in GRN. Several co-expressed gene modules and genes showing signals of positive selection were associated with GRN and body shape. These were enriched for biological pathways related to trophic niche expansion in fishes. Our findings demonstrate the potential of functional diversity to expand following habitat restoration, given a fortuitous combination of genetic architecture, genetic diversity and selection

Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

Background: Climatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-third of the world’s tortoise genera. The distribution of Psammobates tentorius (Kuhl, 1820) covers two of the 25 biodiversity hotspots in the world, the Succulent Karoo and Cape Floristic Region. The highly diverged P. tentorius represents an excellent model species for exploring biogeographic and radiation patterns of reptiles in Southern Africa. Results: We investigated genetic structure and radiation patterns against temporal and spatial dimensions since the Miocene in the Psammobates tentorius species complex, using multiple types of DNA markers and niche modelling analyses. Cladogenesis in P. tentorius started in the late Miocene (11.63–5.33 Ma) when populations dispersed from north to south to form two geographically isolated groups. The northern group diverged into a clade north of the Orange River (OR), followed by the splitting of the group south of the OR into a western and an interior clade. The latter divergence corresponded to the intensifcation of the cold Benguela current, which caused western aridifcation and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fuctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by diferent climatic parameters, and that the niches difered substantially among the clades of the northern group but were similar among clades of the southern group. Conclusion: Climatic shifts, and biome and geographic changes were possibly the three major driving forces shaping cladogenesis and genetic structure in Southern African tortoise species. Our results revealed that the cladogenesis of the P. tentorius species complex was probably shaped by environmental cooling, biome shifts and topographic uplift in Southern Africa since the late Miocene. The Last Glacial Maximum (LGM) may have impacted the distribution of P. tentorius substantially. We found the taxonomic diversify of the P. tentorius species complex to be highest in the Greater Cape Floristic Region. All seven clades discovered warrant conservation attention, particularly Ptt-B–Ptr, Ptt-A and Pv-

Histopathology of dairy cows' hooves with signs of naturally acquired laminitis

O objetivo deste trabalho foi investigar as alterações histológicas no casco de vacas leiteiras sem e com lesões de laminite, naturalmente, adquirida. Utilizaram-se animais de descarte sem lesões macroscópicas no casco (G1 n=9) e com lesões macroscópicas associadas à laminite sem (G2 n=23), ou com claudicação (G3 n=7). Após o abate, amostras da junção derme-epiderme das regiões solear, axial e dorsal do casco foram obtidas e processadas, histologicamente, nas colorações de HE e PAS. Avaliou-se, semiquantitativamente, às cegas e por um mesmo pesquisador, congestão, hemorragia e infiltrado inflamatório na derme das regiões solear, axial e dorsal. Avaliou-se infiltrado inflamatório na lâmina dermal das regiões axial e dorsal. A morfologia das células epidermais e a presença de irregularidades em três regiões do comprimento da membrana basal (MB) foram examinadas na coloração de PAS. Os escores das lesões nas diferentes regiões do casco no mesmo grupo e nos diferentes grupos para cada região do casco foram comparados através de análises não paramétricas (P<0,05). Infiltrado inflamatório na derme de todas as regiões do casco foi detectado em todos os grupos sem diferença estatística (P>0,05). Vacas sem lesões macroscópicas secundárias à laminite (G1) apresentaram escores de inflamação e alteração de células epidermais semelhantes aos dos grupos com lesões de laminite, sugerindo a existência de fase prodrômica para a doença em bovinos. A MB apresentou irregularidades com intensidade variável ao longo de seu comprimento (P<0,05), porém, sem diferença entre grupos (P>0,05). O padrão de irregularidades na MB encontrado não foi relatado até o momento e não se assemelha ao colapso de MB descrito em equinos e bovinos com laminite induzida. Concluiu-se que, mesmo na ausência de lesões macroscópicas no casco causadas por laminite, vacas leiteiras apresentam lesões histológicas compatíveis com inflamação da junção derme-epiderme como em animais afetados. A membrana basal de bovinos sem e com lesões de laminite apresenta irregularidades com distribuição irregular ao longo de seu comprimento que precisam ser melhor estudadas

The Migration State in the Global South: Nationalizing, Developmental and Neoliberal Models of Migration Management

How do states in the Global South manage cross-border migration? This article identifies Hollifield’s “migration state” as a useful tool for comparative analysis yet notes that in its current version the concept is limited, given its focus on economic immigration in advanced liberal democracies. We suggest a framework for extending the “migration state” concept by introducing a typology of nationalizing, developmental, and neoliberal migration management regimes. The article explains each type and provides illustrative examples drawn from a range of case studies. To conclude, it discusses the implications of this analysis for comparative migration research, including the additional light it sheds on the migration management policies of states in the Global North

Evolution of sex determination and heterogamety changes in section Otites of the genus Silene

Abstract Switches in heterogamety are known to occur in both animals and plants. Although plant sex determination systems probably often evolved more recently than those in several well-studied animals, including mammals, and have had less time for switches to occur, we previously detected a switch in heterogamety in the plant genus Silene: section Otites has both female and male heterogamety, whereas S. latifolia and its close relatives, in a different section of the genus, Melandrium (subgenus Behenantha), all have male heterogamety. Here we analyse the evolution of sex chromosomes in section Otites, which is estimated to have evolved only about 0.55 MYA. Our study confirms female heterogamety in S. otites and newly reveals female heterogamety in S. borysthenica. Sequence analyses and genetic mapping show that the sex-linked regions of these two species are the same, but the region in S. colpophylla, a close relative with male heterogamety, is different. The sex chromosome pairs of S. colpophylla and S. otites each correspond to an autosome of the other species, and both differ from the XY pair in S. latifolia. Silene section Otites species are suitable for detailed studies of the events involved in such changes, and our phylogenetic analysis suggests a possible change from female to male heterogamety within this section. Our analyses suggest a possibility that has so far not been considered, change in heterogamety through hybridization, in which a male-determining chromosome from one species is introgressed into another one, and over-rides its previous sex-determining system