Strategies for keeping dairy cows and calves together - a cross-sectional survey study

Although it is still most common to rear dairy calves separately from adult cattle, the interest in pro-longed contact between dairy calves and lactating cows during early life is increasing. Previous research has documented positive effects of cow-calf contact (CCC) on for example early calf growth and udder health of suckled cows, but also negative effects such as increased separation distress and reduced weight gains after weaning. The aim of this study was to use information from European farms with prolonged cow-calf contact to identify innovative solutions to common challenges for CCC farms. Commercial dairy farms that kept calves with adult lactating cows for seven days or more after birth were invited to participate, and interviews were performed with 104 farmers from six countries. During interviews, information about farm management, calf rearing, farmers' perception of animal health on their farm, and farmers' drivers and barriers for implementing CCC were collected. We found that CCC was practised in a large variety of housing and management systems, and that calves could be reared together with their dam, with foster cows, or using a combination of the two. The contact period varied considerably (7-305 days) between farms and about 25% of the farms manually milk fed the calves during parts of the milk feeding period. Daily contact time varied between farms, from 30 minutes per day to permanent contact except at milking. Behaviours indicative of separation distress, most commonly vocalisation in cows and calves, were reported by 87% of the farmers. Strategies to alleviate separation distress, for example simultaneous gradual weaning and separation, were used on some farms. Building constraints were most often mentioned as a barrier for implementing CCC. Our findings suggest that CCC is practised in a variety of commonly used husbandry systems. Reported challenges were primarily related to weaning and separation, and to building constraints; these aspects should be areas of future research.@2022 The Authors. Published by Elsevier B.V. on behalf of The Animal Consortium. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/)

Discovery and population genomics of structural variation in a songbird genus

Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly- and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (~530,000 years) cis-acting 2.25-kb LTR retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping

Revising mtDNA haplotypes of the ancient Hungarian conquerors with next generation sequencing

As part of the effort to create a high resolution representative sequence database of the medieval Hungarian conquerors we have resequenced the entire mtDNA genome of 24 published ancient samples with Next Generation Sequencing, whose haplotypes had been previously determined with traditional PCR based methods. We show that PCR based methods are prone to erroneous haplotype or haplogroup determination due to ambiguous sequence reads, and many of the resequenced samples had been classified inaccurately. The SNaPshot method applied with published ancient DNA authenticity criteria is the most straightforward and cheapest PCR based approach for testing a large number of coding region SNP-s, which greatly facilitates correct haplogroup determination

Unmanned aircraft systems as a new source of disturbance for wildlife: A systematic review.

The use of small Unmanned Aircraft Systems (UAS; also known as "drones") for professional and personal-leisure use is increasing enormously. UAS operate at low altitudes (<500 m) and in any terrain, thus they are susceptible to interact with local fauna, generating a new type of anthropogenic disturbance that has not been systematically evaluated. To address this gap, we performed a review of the existent literature about animals' responses to UAS flights and conducted a pooled analysis of the data to determine the probability and intensity of the disturbance, and to identify the factors influencing animals' reactions towards the small aircraft. We found that wildlife reactions depended on both the UAS attributes (flight pattern, engine type and size of aircraft) and the characteristics of animals themselves (type of animal, life-history stage and level of aggregation). Target-oriented flight patterns, larger UAS sizes, and fuel-powered (noisier) engines evoked the strongest reactions in wildlife. Animals during the non-breeding period and in large groups were more likely to show behavioral reactions to UAS, and birds are more prone to react than other taxa. We discuss the implications of these results in the context of wildlife disturbance and suggest guidelines for conservationists, users and manufacturers to minimize the impact of UAS. In addition, we propose that the legal framework needs to be adapted so that appropriate actions can be undertaken when wildlife is negatively affected by these emergent practices

Strategies for keeping dairy cows and calves together – a cross-sectional survey study

Although it is still most common to rear dairy calves separately from adult cattle, the interest in prolonged contact between dairy calves and lactating cows during early life is increasing. Previous research has documented positive effects of cow-calf contact (CCC) on for example early calf growth and udder health of suckled cows, but also negative effects such as increased separation distress and reduced weight gains after weaning. The aim of this study was to use information from European farms with prolonged cow-calf contact to identify innovative solutions to common challenges for CCC farms. Commercial dairy farms that kept calves with adult lactating cows for seven days or more after birth were invited to participate, and interviews were performed with 104 farmers from six countries. During interviews, information about farm management, calf rearing, farmers’ perception of animal health on their farm, and farmers’ drivers and barriers for implementing CCC were collected. We found that CCC was practised in a large variety of housing and management systems, and that calves could be reared together with their dam, with foster cows, or using a combination of the two. The contact period varied considerably (7–305 days) between farms and about 25% of the farms manually milk fed the calves during parts of the milk feeding period. Daily contact time varied between farms, from 30 minutes per day to permanent contact except at milking. Behaviours indicative of separation distress, most commonly vocalisation in cows and calves, were reported by 87% of the farmers. Strategies to alleviate separation distress, for example simultaneous gradual weaning and separation, were used on some farms. Building constraints were most often mentioned as a barrier for implementing CCC. Our findings suggest that CCC is practised in a variety of commonly used husbandry systems. Reported challenges were primarily related to weaning and separation, and to building constraints; these aspects should be areas of future research

Whole-genome sequencing for an enhanced understanding of genetic variation among South Africans

The Southern African Human Genome Programme is a national initiative that aspires to unlock the unique genetic character of southern African populations for a better understanding of human genetic diversity. In this pilot study the Southern African Human Genome Programme characterizes the genomes of 24 individuals (8 Coloured and 16 black southeastern Bantu-speakers) using deep whole-genome sequencing. A total of ~16 million unique variants are identified. Despite the shallow time depth since divergence between the two main southeastern Bantu-speaking groups (Nguni and Sotho-Tswana), principal component analysis and structure analysis reveal significant (p < 10−6) differentiation, and FST analysis identifies regions with high divergence. The Coloured individuals show evidence of varying proportions of admixture with Khoesan, Bantu-speakers, Europeans, and populations from the Indian sub-continent. Whole-genome sequencing data reveal extensive genomic diversity, increasing our understanding of the complex and region-specific history of African populations and highlighting its potential impact on biomedical research and genetic susceptibility to disease

A Critical Analysis of Atoh7 (Math5) mRNA Splicing in the Developing Mouse Retina

The Math5 (Atoh7) gene is transiently expressed during retinogenesis by progenitors exiting mitosis, and is essential for ganglion cell (RGC) development. Math5 contains a single exon, and its 1.7 kb mRNA encodes a 149-aa polypeptide. Mouse Math5 mutants have essentially no RGCs or optic nerves. Given the importance of this gene in retinal development, we thoroughly investigated the possibility of Math5 mRNA splicing by Northern blot, 3′RACE, RNase protection assays, and RT-PCR, using RNAs extracted from embryonic eyes and adult cerebellum, or transcribed in vitro from cDNA clones. Because Math5 mRNA contains an elevated G+C content, we used graded concentrations of betaine, an isostabilizing agent that disrupts secondary structure. Although ∼10% of cerebellar Math5 RNAs are spliced, truncating the polypeptide, our results show few, if any, spliced Math5 transcripts exist in the developing retina (<1%). Rare deleted cDNAs do arise via RT-mediated RNA template switching in vitro, and are selectively amplified during PCR. These data differ starkly from a recent study (Kanadia and Cepko 2010), which concluded that the vast majority of Math5 and other bHLH transcripts are spliced to generate noncoding RNAs. Our findings clarify the architecture of the Math5 gene and its mechanism of action. These results have implications for all members of the bHLH gene family, for any gene that is alternatively spliced, and for the interpretation of all RT-PCR experiments

Population genomics of speciation and admixture

The application of population genomics to the understanding of speciation has led to the emerging field of speciation genomics. This has brought new insight into how divergence builds up within the genome during speciation and is also revealing the extent to which species can continue to exchange genetic material despite reproductive barriers. It is also providing powerful new approaches for linking genotype to phenotype in admixed populations. In this chapter, we give an overview of some of the methods that have been used and some of the novel insights gained. We also outline some of the pitfalls of the most commonly used methods and possible problems with interpretation of the results

The Beaker phenomenon and the genomic transformation of northwest Europe

From around 2750 to 2500 bc, Bell Beaker pottery became widespread across western and central Europe, before it disappeared between 2200 and 1800 bc. The forces that propelled its expansion are a matter of long-standing debate, and there is support for both cultural diffusion and migration having a role in this process. Here we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain’s gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries