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opencc-zeroApr 2022View details →

Data from: Breeding heat tolerant orchardgrass germplasm for summer persistence in high temperature stress environments of the southeastern United States

This is digital research data corresponding to a published manuscript, Breeding heat tolerant orchardgrass germplasm for summer persistence in high temperature stress environments of the southeastern United States, in Crop Science, Volume 61, p. 1915 - 1925. Orchardgrass (Dactylis glomerata L.) could serve as a cool-season perennial in southeastern production systems, but often does not behave as a true perennial under high temperature stress conditions of the region. This work sought to develop heat-tolerant orchardgrass germplasm through recurrent phenotypic selection (RPS) that would both reduce secondary seed dormancy caused by high soil temperatures and improve stand persistence over summer months. Selection was conducted in a growth chamber 40/30 °C (12/12 h, light/darkness), with germinated seedlings subjected to an additional 2–3 weeks of 40/30 °C conditions. The base germplasm (Cycle 0) and selected individuals (Cycles 1–3) were transplanted into the field, then harvested for seed. Forty-degree germination tests compared mean cumulative germination, velocity of germination within 8 days (VOG8), and realized heritability. Stand persistencewas assessed 1 year after transplanting.

Breeding status shapes territoriality and vocalization patterns in spotted owls

Vocal territory defense can vary within a species due to many factors such as sex and breeding status, influencing territory size and thus population density across a landscape. Therefore, understanding what influences variation in territorial vocalizations can help to illuminate trade-offs between territoriality and other life history demands, which benefits our general understanding of animal ecology as well as helps to inform emerging passive acoustic monitoring approaches. Here, we investigated how sex and breeding status affected territoriality and vocal behavior in the California spotted owl (Strix occidentalis occidentalis) in the Sierra Nevada, California, USA, using high-resolution acoustic/GPS tags. We discovered that territorial vocal behavior was related to breeding status and to a lesser extent sex. Breeding owls with fledged young had a less diverse vocal repertoire, produced fewer and quieter territorial calls, and typically called only when close to their nest. Males were also more likely to engage in territorial calling than females. Breeding spotted owls also maintained significantly smaller territories—but utilized larger home ranges—than non-breeding individuals. Our results suggest that breeding spotted owls may reduce their investment in territorial behaviors to mitigate the demands and risks associated with rearing young. Further, our results have important implications for the passive acoustic monitoring of spotted owls and, more broadly, highlight the utility of using multiple call types to detect species of interest.

Associated data files and scripts for 'Ancestry-inclusive dog genomics challenges popular breed stereotypes'

Behavioral genetics in dogs has focused on modern breeds, isolated subgroups <200 years old with distinctive physical, and, purportedly, behavioral characteristics. We interrogated breed stereotypes by surveying owners of 18,371 purebred and mixed-breed dogs, and densely genotyping (~45 million markers) a subset of 2,155 dogs. Most behavioral traits are heritable (h2>25%), and admixture patterns in mixed-breed dogs can reveal breed propensities. However, breed poorly predicts an individual purebred dog's behavioral phenotype, explaining just 9% of variation. Using genome-wide association, we identify 11 loci significantly associated with howling and other behaviors, and show characteristic breed behaviors are genetically complex. Behavior-associated loci are not unusually differentiated in modern breeds, but breed propensities do align, albeit weakly, with ancestral function. We propose behaviors now perceived as characteristic of modern breeds likely derive from thousands of years of polygenic adaptation predating breed formation, with modern breeds distinguished primarily by aesthetic, not behavioral, traits.

Breeding biology of two populations of Chinese penduline tits

The phenotypes and breeding behavior in one species may be different between populations. The local environments, social interactions can all lead to some variations in life history. The thorough investigations of breeding biology over populations can provide insights for us to understand the evolution and diversifications of breeding systems and phenotypic traits from multiple perspectives other than drawing monotonous associations between a factor and a trait. In this study, we explored two Chinese penduline populations, Liaohekou (LHK) and Xianghai (XH), both in the northeast of China located 550 km away from each other. A comparative study of the breeding biology was carried on in the two populations. We found that the climate has no obvious difference in these two populations but has different habitats. Nest emergence and egg-laying were earlier in the more northern population XH. Males in XH has a lower chance of pairing up with a female and exhibit mainly biparental care pattern instead uniparental care that we reported in LHK. The chick fledgling success in the biparental care nests was higher than in the uniparental care nests in XH, but no difference to the uniparental care nests in LHK. Besides, the penduline tits in the two populations were also significantly different in their wing length, tail length and beak shape. These incongruences suggested different food availability, adult sex ratio and migration distances of the two populations. Future studies should experimentally investigate the joint influences of breeding perspectives on the evolution of parental care and mating system.

Large scale across-breed genome-wide association study reveals a variant in HMGA2 associated with inguinal cryptorchidism risk in dogs

Cryptorchidism is the most common congenital sex development disorder in dogs. Despite this, little progress has been made in understanding its genetic background. Extensive genetic testing of dogs through consumer and veterinary channels using a high-density SNP genotyping microarray coupled with links to clinical records presents the opportunity for a large-scale genome-wide association study to elucidate the molecular risk factors associated with cryptorchidism in dogs. Using an inter-breed genome-wide association study approach, a significant statistical association on canine chromosome 10 was identified, with the top SNP pinpointing a variant of HMGA2 previously associated with adult weight variance. In further analysis we show that incidence of cryptorchidism is skewed towards smaller dogs in concordance with the identified variant's previous association with adult weight. This study represents the first putative variant to be associated with cryptorchidism in dogs.

Territory-level temperature influences breeding phenology and reproductive output in three forest passerine birds

Temperature plays an important role in determining the breeding phenology of birds in temperate climates, with higher spring temperatures associated with earlier breeding. However, the effect of localised territory-scale temperature variations is poorly understood, with relationships between temperature and breeding phenology mostly studied using coarse-grained climatic indices. Here, we interpolate spring temperatures recorded at 150 m2 grid intersections encompassing 417 ha of forest to examine the influence of territory-scale temperature, and its interaction with mean annual temperature, on territory selection, breeding phenology, clutch size and fledging success for three co-occurring single-brooded passerine birds using data from 672 nests over four years. All species exhibited significant trends in reproductive traits associated with territory-scale temperature. Pied flycatchers Ficedula hypoleuca settled in cooler territories first, where they raised more fledglings. Blue tits Cyanistes caeruleus laid larger clutches in warmer territories in warm years and always laid earlier at warmer territories irrespective of annual temperature variation. Contrastingly, pied flycatcher and wood warbler Phylloscopus sibilatrix breeding phenology was earlier at warmer territories in cool years and cooler territories in warm years, with wood warbler clutch size responding similarly to this interaction. Greater previous breeding experience and increased higher rates of historical territory occupancy (territory quality) also predicted earlier breeding phenology and higher fledging success for pied flycatchers. We suggest that the migratory pied flycatcher and wood warbler are best synchronised with their prey availability in cooler years at a local population level. However resident blue tits match local phenology across all years, which is potentially advantageous under warmer predicted climate change scenarios. We conclude that temperature at the territory scale can be an important driver of settlement and breeding phenology and influence reproductive traits.

opencc-zeroDec 2021View details →

Data from: A trait‒environment relationship approach to participatory plant breeding for organic agriculture

The extent of intraspecific variation in trait‒environment relationships is an open question with limited empirical support in crops. In organic agriculture, with high environmental heterogeneity, this knowledge could guide breeding programs to optimize crop attributes. We propose a three-dimensional framework involving crop performance, crop traits, and environmental axes to uncover the multidimensionality of trait‒environment relationships within a crop. We modeled instantaneous photosynthesis (Asat) and water-use efficiency (WUE) as functions of four phenotypic traits, three soil variables, five carrot (D. carota) varieties, and their interactions in a national participatory plant breeding program involving a suite of farms across Canada. We used these interactions to describe the resulting 12 trait‒environment relationships across varieties. We found one significant trait‒environment relationship for Asat (taproot tissue density‒soil phosphorus), which was consistent across varieties. For WUE, we found that three relationships (petiole diameter‒soil nitrogen, petiole diameter‒soil phosphorus, and leaf area‒soil phosphorus) varied significantly across varieties. As a result, WUE was maximized by different combinations of trait values and soil conditions depending on the variety. Our three-dimensional framework supports the identification of functional traits behind the differential responses of crop varieties to environmental variation and thus guides breeding programs to optimize crop attributes from an eco-evolutionary perspective.

Data from: Interannual consistency of migration phenology is season- and breeding region-specific in North American Golden Eagles

Avian migrants can adjust the time they depart for migration and arrive at their destination (i.e. phenology) based on environmental conditions, the period of the annual cycle, and the distance of migration. Our study shows that interannual consistency (an indicator of the strength of adjustments) in migration schedule of Golden Eagles (Aquila chrysaetos) in North America was greatest in boreal spring migration and the breeding regions of eastern Canada, suggesting that migration schedule is partly environmentally driven. Using multi-year GPS tracks of 83 adults breeding in three spatially distant regions (Alaska, northeast Canada, and southeast Canada), we quantified the interannual consistency of migration timing with variations within individuals tracked across multiple years and among-individuals and repeatability (r) of migration schedule, duration, and wintering latitude by breeding regions and seasons. By comparing regions and seasons, we found that consistency was highest (r > 0.85) for the schedule of the boreal spring migration in eastern Canada while Alaska had the lowest value (r < 0.15). Since seasonal consistency of migration schedule was only detected in eastern Canada, we conclude that seasonal features are not the main constraint on consistency of migration schedule. While regional differences in consistency were not related to differences in migratory distances, they could be the result of genetic or habitat differences. We also found that warmer temperatures than the decadal average at the region of departure delayed the start of boreal spring migration by ~10 days and advanced boreal autumn migration by ~20 days. It suggests that warmer temperatures would reduce residence time on breeding grounds, which is contrary to expectations and trends found in other studies. Wide variations in migratory strategies across a species distribution can add to the lists of challenges for conservation yet such variations can give migrants the capacity to acclimate to environmental changes.

Population changes in a whale breeding ground revealed by citizen science noninvasive genetics unique microsatellite profiles of southern right whales

Historical exploitation, and a combination of current anthropogenic impacts, such as climate change and habitat degradation, impact the population dynamics of marine mammalian megafauna. Right whales (Eubalaena spp.) are large cetaceans recovering from hunting, whose reproductive and population growth rate appear to be impacted by climate change. We apply noninvasive genetic methods to monitor southern right whale (E. australis, SRW) and test the application of noninvasive genetics to minimise the observer effects on the population. Our aim is to describe population structure, and interdecadal and interannual changes to assess species status in the Great Acceleration period of Anthropocene. As a basis for population genetic analyses, we collected samples from sloughed skin during post-migration epidermal moult. Considering the exploration-exploitation dilemma, we collaborated with whale-watching companies, as part of a citizen science approach and to reduce ad hoc logistic operations and biopsy equipment. We used mitochondrial and microsatellite data and population genetic tools. We report for the first time the genetic composition and differentiation of the Namibian portion of the range. Population genetic parameters suggest that South Africa hosts the largest population. This corresponds with higher estimates of current gene flow from Africa compared to older samples. We have observed considerable interannual variation in population density at the breeding ground and an interdecadal shift in genetic variability, evidenced by an increase in the point estimate inbreeding. Clustering analyses confirmed differentiation between the Atlantic and Indo-Pacific, presumably originating during the ice ages. We show that population monitoring of large whales, essential for their conservation management, is feasible using noninvasive sampling within non-scientific platforms. Observed patterns are concurrent to changes of movement ecology and decline in reproductive success of the South African population, probably reflecting a large-scale restructuring of pelagic marine food webs.

Evolutionary determinants of non-seasonal breeding in wild chacma baboons

Animal reproductive phenology varies from strongly seasonal to non-seasonal, sometimes among closely related or sympatric species. While the extent of reproductive seasonality is often attributed to environmental seasonality, this fails to explain many cases of non-seasonal breeding in seasonal environments. We investigated the evolutionary determinants of non-seasonal breeding in a wild primate, the chacma baboon (Papio ursinus), living in a seasonal environment with high climatic unpredictability. We tested three hypotheses proposing that non-seasonal breeding has evolved in response to (1) climatic unpredictability, (2) reproductive competition between females favoring birth asynchrony, and (3) individual, rank-dependent variations in optimal reproductive timing. We found strong support for an effect of reproductive asynchrony modulated by rank: (i) birth synchrony is costly to subordinate females, lengthening their interbirth intervals, (ii) females alter their reproductive timings (fertility periods and conceptions) in relation to previous conceptions in the group, and (iii) the reported effect of birth synchrony on interbirth intervals weakens the intensity of reproductive seasonality at the population level. This study emphasizes the importance of sociality in mediating the evolution of reproductive phenology in group-living organisms, a result of broad significance for understanding key demographic parameters driving population responses to increase climatic fluctuations.

Mating traits and fitness components in two breeding designs in Drosophila serrata

Misalignment between male and female interests over mating creates inter-locus sexual conflict that is known to drive the coevolution of reproductive traits. Males and females also share the majority of their genome, which may cause these traits to genetically covary between the sexes and experience intra-locus sexual conflict where beneficial alleles in one sex are costly when expressed in the other. Traits expressed during mating may uniquely be subject to both intra- and interlocus sexual conflict. Here, we use a biologically repeated quantitative genetic experiment to test whether intra-locus sexual conflict is operating on mating latency, and copulation duration in the polyandrous fruit-fly Drosophila serrata. Mating latency and copulation duration were both heritable in males but not in females, and within sex and across-sex genetic correlations among the traits were all small. We found no significant genetic covariance between any measured mating behaviours and fitness components, nor between male and female fitness, suggesting that these traits are not under strong selection. Our study, therefore, finds little evidence of ongoing intra-locus sexual conflict over these traits. One explanation for our result is that these mating traits have historically been under strong selection, which has exhausted their genetic variation, making it difficult to detect selection in these populations. Keywords: mating latency, copulation duration, quantitative genetics, sexual conflict, Drosophila serrata, multivariate analyses, cuticula.

opencc-by-4.0May 2022View details →

zenodo36/100

Evolution of allele frequencies in the cattle breed Asturiana de los Valles

Genotype data for 153 animals from the Asturiana de los Valles bovine breed, with birth dates from 1980 to 2013. These genotypes were obtained from 3 different sources:  - 88 sires were genotyped using the Illumina’s BovineSNP50 v.2 chip; the resulting data are provided at plink ped/map format (asturiana_50K.tar.xz). - 50 animals (25 sires and 25 dams) were genotyped using the Illumina’s Bovine High Density BeadChip 770K SNP; the resulting data are provided at plink ped/map format (asturiana_800K.tar.xz). - 15 sires were sequenced on a HiSeq 3,000; the resulting genotype calls are provided at vcf format (asturiana_WGS_SNP.vcf.gz). Boitard et al (2021) combined these 3 datasets in order to detect recent and historical selection signatures in this breed. The scripts used for this analysis can be found at https://github.com/sboitard/Asturiana_analysis.

Wildfire influences individual growth and breeding dispersal, but not survival and recruitment in a montane amphibian

Global wildfire regimes are changing rapidly, with widespread increases in the size, frequency, duration, and severity of wildfires. Whereas the effects of wildfire on ecological state variables such as occupancy, abundance, and species diversity are relatively well-documented, changes in population vital rates (e.g., survival, recruitment) and individual responses (e.g., growth, movement) to wildfire are more limited because of the detailed information needed on the same individuals both pre- and post-fire. We capitalized on the 2018 Roosevelt wildfire, which occurred during our six-year (2015–2020) capture-mark-recapture study of boreal toads (Anaxyrus boreas boreas; n = 1415) in the Bridger-Teton National Forest, USA, to evaluate the responses of population vital rates and individual metrics to wildfire. We employed robust design capture-recapture models to compare the growth, dispersal, survival, and recruitment of adult boreal toads pre- and post-fire at burned versus unburned sites. At burned locations, growth increased two-years post-fire compared with the year directly following wildfire and was higher two-years post-fire than any other interval during our study period. Boreal toads dispersed to alternative breeding patches more at burned sites than unburned sites and dispersal increased two-years post-fire compared with the year directly following wildfire. Annual survival and recruitment did not differ between pre- and post-fire years nor among pre-fire years, the year following wildfire, and two-years post-fire. We demonstrate that, in certain contexts, dispersal can play a major role in changes to state variables (e.g., abundance) after wildfire, as opposed to other vital rates such as survival and recruitment. Our study represents an important step towards understanding the biological processes that underlie observed patterns in state variables following wildfire, which ultimately will be critical for the effective management of species in landscapes experiencing shifts in fire activity.

Arrival dates of male and female willow warblers (Phylloscopus trochilus) to their breeding site in Sweden 1979-2016

Protandry is a widespread life-history phenomenon describing how males precede females at the site or state of reproduction. In migratory birds, protandry has important influence on individual fitness, the migratory syndrome and phenological response to climate change. Despite its significance, accurate analyses on the dynamics of protandry using data sets collected at the breeding site, are lacking. Basing our study on records collected daily, spanning a period of 38 years, we aim to investigate protandry dynamics over time in a breeding population of willow warblers (Phylloscopus trochilus). Temporal change in the timing of arrival was analysed in males and females, and protandry (number of days between male and female arrival) was investigate both at population level and within breeding pairs. Our results show advancement in the arrival time to the breeding site in both sexes, but male arrival has advanced to a greater extent, leading to an increase in protandry both at the population level and within breeding pairs. We do not observe any change in sex ratio that could explain the protandry increase, but pronounced temperature change has occurred at the breeding area and along the migratory route. Typically, natural selection opposes earlier arrival in males, but given warmer springs, this counteracting force may be relaxing, enabling an increase in protandry. We discuss whether our results suggests that climate change has caused sex-specific effects, if these could be evolutionary and whether the timing of important life-history stages such as arrival at the breeding site may change at different rates in males and females following environmental shifts.

Benefit of introgression depends on genetic variation in cereal breeding programs

We investigated the benefit from introgression of external lines into a cereal breeding program and strategies that accelerated introgression of the favourable alleles while minimising linkage drag using stochastic computer simulation. We simulated genomic selection for disease resistance and grain yield in two environments with a high level of genotype-by-environment (G×E) for the latter trait, using genomic data of a historical barley breeding program as the base generation. Two populations (existing and external) were created from this base population with different allele frequencies for few (N=10) major and many (N~990) minor simulated disease quantitative trait loci (QTL). The major disease QTL only existed in the external population and lines from the external population were introgressed into the existing population which had minor disease QTL with low, medium, and high allele frequencies. The study revealed that the benefit of introgression depended on the level of genetic variation for the target trait in the existing cereal breeding program. Introgression of external resources into the existing population was beneficial only when the existing population lacked variation in disease resistance or when minor disease QTL were already at medium or high frequency. When minor disease QTL were at low frequencies, no extra genetic gain was achieved from introgression. More benefit in the disease trait was obtained from the introgression if the major disease QTL had larger effect sizes, more selection emphasis was applied on disease resistance, or more external lines were introgressed. While our strategies to increase introgression of major disease QTL were generally successful, most were not able to completely avoid negative impacts on selection for grain yield with the only exception being when major introgression QTL effects were very large. Breeding programs are advised to carefully consider the level of genetic variation in a trait available in their breeding program before deciding to introgress germplasms.

opencc-zeroJun 2021View details →

Study of the genetic and phenotypic variation among wild and cultivated clary sages provides interesting avenues for breeding programs of a perfume, medicinal and aromatic plant

A road-map of the genetic and phenotypic diversities in both crops and their wild-related species can help identifying valuable genetic resources for further crop breeding. The clary sage (Salvia sclarea L.), a perfume, medicinal and aromatic plant, is used for sclareol production and ornamental purposes. Despite its wide use in the field of cosmetics, the phenotypic and genetic diversity of wild and cultivated clary sage remains to be explored. We characterized the genetic and phenotypic variation of a collection of six wild S. sclarea populations from Croatia, sampled along an altitudinal gradient, and of populations of three S. sclarea cultivars. We showed low level of genetic diversity for the two S. sclarea traditional cultivars used for essential oil production and for ornamental purposes, respectively. In contrast, a recent cultivar resulting from new breeding methods, which involve hybridizations among several genotypes rather than traditional recurrent selection and self-crosses over time, showed high genetic diversity. We also observed a marked phenotypic differentiation for the ornamental clary sage compared with other cultivated and wild clary sages. Instead, the two cultivars used for essential oil production, a traditional and a recent, respectively, were not phenotypically differentiated from the wild Croatian populations. Our results also featured some wild populations with high sclareol content and early-flowering phenotypes as good candidates for future breeding programs. This study opens up perspectives for basic research aiming at understanding the impact of breeding methods on clary sage evolution, and highlights interesting avenues for clary breeding programs.

Plasticity in female timing may explain earlier breeding in a North American songbird

Many species have shifted their breeding phenology in response to climate change. Identifying the magnitude of phenological shifts and whether climate-mediated selection drives these shifts is key for determining species' resilience to climate change. Birds are a strong model for studying phenological shifts due to numerous long-term research studies; however, generalities pertaining to drivers of phenological shifts will emerge only as we add study species that differ in life history and geography. We investigated 32 years of reproductive timing in a non-migratory population of dark-eyed juncos (Junco hyemalis). We predicted that plasticity in reproductive timing would allow females to breed earlier in warmer springs. We also predicted that selection would favour earlier breeding, and we asked whether temperatures throughout the breeding season would predict the strength of selection. To test these predictions, we examined temporal changes in the annual median date for reproductive onset (i.e., first egg date), and we used a sliding window analysis to identify monthly spring temperatures driving these patterns. Next, we explored plasticity in reproductive timing and asked whether selection favoured earlier breeding. Lastly, we used a sliding window analysis to identify the time during the breeding season that temperature was most associated with selection favouring earlier breeding. First egg dates occurred earlier over time and strongly covaried with April temperatures. Further, for individual females that bred in more than one year, they typically bred earlier in warmer Aprils, exhibiting plastic responses to April temperature. We also found significant overall selection favouring earlier breeding (i.e., higher relative fitness with earlier first egg dates) and variation in selection for earlier breeding over time. However, temperature across diverse climatic windows did not predict the strength of selection. Our findings provide further evidence for the role of phenotypic plasticity in shifting phenology in response to earlier springs. We provide evidence for the role of selection favouring earlier breeding, regardless of temperature, thus setting the stage for adaptive changes in female breeding phenology. We suggest for multi-brooded birds that advancing first egg dates likely increases the length of the breeding season, and therefore, reproductive success.

High-density genomic characterization of native Croatian sheep breeds

A recent comprehensive genomic analysis based on 50K SNP profiles has shown that the regional Balkan sheep populations have considerable genetic overlap but are distinctly different from surrounding breeds. All eight Croatian sheep breeds were represented by a small number of individuals per breed. Here, we genotyped 220 individuals representing the native Croatian sheep breeds (Istrian Sheep, Krk Island Sheep, Cres Island Sheep, Rab Island Sheep, Lika Pramenka, Pag Island Sheep, Dalmatian Pramenka, Dubrovnik Sheep) and mouflon using the Ovine Infinium® HD SNP BeadChip (606,006 SNPs). In addition, we included publicly available Balkan Pramenka and other Mediterranean sheep breeds. Our analyses revealed the complex population structure of Croatian sheep breeds and their origin and geographic barriers (island versus mainland). Migration patterns confirmed the historical establishment of breeds and the pathways of gene flow. Inbreeding coefficients (FROH > 2 Mb) between sheep populations ranged from 0.025 to 0.070, with lower inbreeding coefficients observed in Dalmatian Pramenka and Pag Island Sheep and higher inbreeding in Dubrovnik sheep. The estimated effective population size ranged from 61 to 1039 for Krk Island Sheep and Dalmatian Pramenka, respectively. Higher inbreeding levels and lower effective population size indicate the need for improved conservation management to maintain genetic diversity in some breeds. Our results will contribute to breeding and conservation strategies of native Croatian sheep breeds.