Find research datasets worth reusing

Data from: Matching geographical assignment by stable isotopes with African non-breeding sites of Barn swallows Hirundo rustica tracked by geolocation

Knowledge on whereabouts within the annual cycle of migratory species is prerequisite for many aspects in ecology and biological conservation. Spatial assignments of stable isotopes archived in tissues allows for later inference on sites where the specific tissue had been grown.. It has been rarely tested whether spatial assignments match directly tracked non-breeding residences, especially for migratory songbirds. We here compare assignments of stable isotopes from feathers of Palaearctic Barn swallows Hirundo rustica with their African non-breeding residence sites tracked by geolocation. Assignments based on δ2H, δ13C and δ15N isotope compositions delineate three main non-breeding regions: a main cluster in central Africa, a second in West Africa, and the third cluster in Northern Africa. Using δ13C, δ15N only, non-breeding sites ranged from clusters in West/Southwest Africa to South East Africa with a centre in Central Africa. The non-breeding areas (50% and 75% Kernel density estimates, KDE) of the birds tracked by geolocation stretched from West Africa via central Africa to southern Africa. We found little overlap of 0.3% (assuming an 1:1 odds ratio) to 1.4 % (3:1 odds ratio) in the three element assignments and KDEs for only 2 and 13 individuals out of 32 birds. Assignment maps for two elements (δ13C, δ15N) and KDEs showed higher consistencies with an overlap of 3.6 and 8.5% for 12 and 18 birds. We argue that the low matching between stable isotope assignments and non-breeding sites in our study arise from insufficient baseline data for Africa (concerning both isoscapes and specific discrimination functions). However, other factors like aerial foraging habit of the species, and a potential mismatch of non-breeding site location and the spatial origin of aerial plankton might further hamper accurate assignments. Finally we call for concerted analyses of tissues i.e. feathers and claws of birds which are grown at known sites across the continent and from species with various ecological requirements (diverse habitats, foraging behaviours, and diet compositions) to establish isoscapes for general applicability.

Data from: Social control of reproduction and breeding monopolization in the eusocial snapping shrimp Synalpheus elizabethae

Understanding why individuals within altruistic societies forego reproduction to raise others' offspring has fascinated scientists since Darwin. Although worker polymorphism is thought to have evolved only in sterile workers, worker subcastes appear to be common among social invertebrates and vertebrates. We asked whether sterility accompanies eusociality and morphological differentiation in snapping shrimps (Synalpheus) - the only known marine eusocial group. We show that workers in S. elizabethae are reproductively totipotent, and that female — but not male — gonadal development and mating are mediated by the presence of a queen, apparently without physical aggression. In queenless experimental colonies, a single immature female worker typically became ovigerous, and no female workers matured in colonies with a resident queen. Thus, eusocial shrimp workers retain reproductive totipotency despite signs of morphological specialization. The failure of most female workers to mature is instead facultative and mediated by the presence of the queen, ensuring her reproductive monopoly.

opencc-zeroOct 2019View details →

Data from: A high-density exome capture genotype-by-sequencing panel for forestry breeding in Pinus radiata

Development of genome-wide resources for application in genomic selection or genome-wide association studies, in the absences of full reference genomes, present a challenge to the forestry industry, where longer breeding cycles could benefit from the accelerated selection possible through marker-based breeding value predictions. In particular, large conifer megagenomes require a strategy to reduce complexity, whilst ensuring genome-wide coverage is achieved. Using a transcriptome-based reference template, we have successfully developed a high density exome capture genotype-by-sequencing panel for radiata pine (Pinus radiata D.Don), capable of capturing in excess of 80,000 single nucleotide polymorphism (SNP) markers with a minor allele frequency above 0.03 in the population tested. This represents approximately 29,000 gene models from a core set of 48,914 probes. A set of 704 SMP markers capable of pedigree reconstruction and differentiating individual genotypes were tested within two full-sib mapping populations. While as few as 70 markers could reconstruct parentage in almost all cases, the impact of missing genotypes was noticeable in several offspring. Therefore, sets of 60 sets of 110 randomly selected SNP markers were compared for both parentage reconstruction and clone differentiation. The performance in parentage reconstruction showed little variation over 60 iterations. However, there was notable variation in discriminatory power between closely related individuals, indicating a higher density SNP marker panel may be required to elucidate hidden relationships in complex pedigrees.

Data from: Sex-specific arrival times on the breeding grounds: hybridizing migratory skuas provide empirical support for the role of sex ratios

In migratory animals, protandry (earlier arrival of males on the breeding grounds) prevails over protogyny (females preceding males). In theory, sex differences in timing of arrival should be driven by the operational sex ratio, shifting toward protogyny in female-biased populations. However, empirical support for this hypothesis is, to date, lacking. To test this hypothesis, we analyzed arrival data from three populations of the long-distance migratory south polar skua (Catharacta maccormicki). These populations differed in their operational sex ratio caused by the unidirectional hybridization of male south polar skuas with female brown skuas (Catharacta antarctica lonnbergi). We found that arrival times were protandrous in allopatry, shifting toward protogyny in female-biased populations when breeding in sympatry. This unique observation is consistent with theoretical predictions that sex-specific arrival times should be influenced by sex ratio and that protogyny should be observed in populations with female-biased operational sex ratio.

opencc-zeroDec 2018View details →

Data from: Experimental traffic noise attracts birds during the breeding season

Understanding how anthropogenic disturbance affects animal behavior is challenging because observational studies often involve co-occurring disturbances (e.g., noise, lighting, and roadways), and laboratory experiments often lack ecological validity. During the 2016 and 2017 avian breeding seasons, we investigated the effects of anthropogenic noise and light on the singing and spatial behavior of wild birds by independently manipulating the presence of each type of disturbance at 89 sites in an otherwise undisturbed boreal forest in Labrador, Canada. Each treatment was surrounded by an 8-channel microphone array that recorded and localized avian vocalizations throughout the manipulation. We analyzed the effects of noise and light on the timing of the first vocalizations of each species at each array during the dawn chorus, and on the proximity of the vocalizing birds to the disturbance when those songs were produced. We analyzed all species combined, and then conducted separate analyses for the six most common species: Boreal Chickadee, Dark-eyed Junco, Ruby-crowned Kinglet, Swainson's Thrush, White-throated Sparrow, and Yellow-rumped Warbler. When all species were analyzed together, we found that traffic noise attracted vocalizing birds. There was some evidence that light repelled birds, but this evidence was inconsistent. In our species-specific analyses, Yellow-rumped Warbler sang earlier in response to noise; Swainson's Thrush was attracted to noise and the combination of noise and light, but repelled by light alone. Our study provides some of the first experimental evidence of the independent and combined effects of traffic noise and light on the vocal and spatial behavior of wild birds, and suggests that breeding birds may be attracted to noisy roads where they could be exposed to additional forms of disturbance.

opencc-zeroJul 2019View details →

Data from: Low-load pathogen spillover predicts shifts in skin microbiome and survival of a terrestrial-breeding amphibian

Wildlife disease dynamics are strongly influenced by the structure of host communities and their symbiotic microbiota. Conspicuous amphibian declines associated with the waterborne fungal pathogen Batrachochytrium dendrobatidis (Bd) have been observed in aquatic-breeding frogs globally. However, less attention has been given to cryptic terrestrial-breeding amphibians that have also been declining in tropical regions. By experimentally manipulating multiple tropical amphibian assemblages harboring natural microbial communities, we tested whether Bd spillover from naturally infected aquatic-breeding frogs could lead to Bd amplification and mortality in our focal terrestrial-breeding host: the pumpkin toadlet Brachycephalus pitanga. We also tested whether the strength of spillover could vary depending on skin bacterial transmission within host assemblages. Terrestrial-breeding toadlets acquired lethal spillover infections from neighboring aquatic hosts and experienced dramatic but generally non-protective shifts in skin bacterial composition primarily attributable to their Bd infections. In contrast, aquatic-breeding amphibians maintained mild Bd infections and higher survival, with shifts in bacterial microbiomes that were unrelated to Bd infections. Our results indicate that Bd spillover from even mildly infected aquatic-breeding hosts may lead to dysbiosis and mortality in terrestrial-breeding species, underscoring the need to further investigate recent population declines of terrestrial-breeding amphibians in the tropics.

Data from: Individual variation in parental workload and breeding productivity in female European starlings: is the effort worth it?

We analyzed individual variation in work load (nest visit rate) during chick-rearing, and the consequences of this variation in terms of breeding productivity, in a highly synchronous breeder, the European starling (Sturnus vulgaris) focusing on female birds. There was marked (10- to 16-fold) variation in total, female and male nest visit rates, among individuals, but individual variation in female nest visit rate was independent of environment (rainfall, temperature) and metrics of individual quality (laying date, clutch size, amount of male provisioning help), and was only weakly associated with chick demand (i.e., day 6 brood size). Female nest visit rate was independent of date and experimentally delayed birds provisioned at the same rate as peak-nesting birds; supporting a lack of effect of date per se. Brood size at fledging was positively but weakly related to total nest visit rate (male + female), with >fivefold variation in nest visit rate for any given brood size, and in females brood size at fledging and chick mass at fledging were independent of female nest visit rate, that is, individual variation in workload was not associated with higher productivity. Nevertheless, nest visit rate in females was repeatable among consecutive days (6–8 posthatching), and between peak (first) and second broods, but not among years. Our data suggest that individual females behave as if committed to a certain level of parental care at the outset of their annual breeding attempt, but this varies among years, that is, behavior is not fixed throughout an individual's life but represents an annually variable decision. We suggest females are making predictable decisions about their workload during provisioning that maximizes their overall fitness based on an integration of information on their current environment (although these cues currently remain unidentified).

opencc-zeroJun 2019View details →

Data from: Seasonality in spatial distribution: climate and land use have contrasting effects on the species richness of breeding and wintering birds

Aim: Many studies have examined large-scale distributions of various taxa and their drivers, emphasizing the importance of climate, topography, and land-use. Most studies have dealt with distributions over a single season or annually without considering seasonality. However, animal distributions and their drivers can differ among seasons because many animals migrate to suitable climates and areas with abundant prey resources. We aim to clarify seasonality in bird distributions and their drivers. Location: Japan. Methods: We examined the effects of climate (annual mean temperature, snow depth), topography (elevation), and land use (extent of surrounding habitat) on bird species richness, in the breeding and wintering seasons separately, using nationwide data (254 forest and 43 grassland sites, respectively). We separately analyzed the species richness of all species, residents, short-, and long-distance migrants in forests and grasslands. Results: In the breeding season, the annual mean temperature negatively affected all groups (except for forest and grassland residents), and the extent of surrounding habitat positively affected many groups. By contrast, in the wintering season, temperature positively affected all groups (except for forest residents), and the extent of surrounding habitat positively affected only grassland long-distance migrants. In both seasons, the species richness of forest and grassland residents was high in regions of moderate and high temperature, respectively. Moreover, snow depth negatively affected all forest groups in the wintering season. Mapping expected species richness suggested that regions with different climates served as habitats for different groups during different seasons. Main conclusions: All regions were important bird habitats depending on the season, reflecting the contrasting effects of temperature across seasons. In the breeding season, surrounding land-use was also an important driver. To understand the seasonal role that each region and environment plays in maintaining species/communities, a large-scale study considering both environmental seasonality and species distribution is needed.

Data from: Wintering areas predict age-related breeding phenology in a migratory passerine bird

Understanding connections between breeding, stopover and wintering grounds for long-distance migratory birds can provide important insight into factors influencing demography and the strength of carry-over effects among various periods of the annual cycle. Using previously described, multi-isotope (δ13C, δ15N, δ2H) feather isoscapes for Africa, we identified the most probable wintering areas for house martins (Delichon urbica) breeding at Badajoz in southwestern Spain. We identified two most-probable wintering areas differing in latitude in West Africa. We found that the probability to winter in the northern region was related to age and sex of individuals. Specifically, experienced males (i.e., two years or older) winter in the northern area with a greater probability than experienced females, whereas first-year females winter in the northern area with a greater probability than first-year males. In addition, wintering area was correlated with breeding phenology, with individuals wintering in the northern area initiating their clutches earlier than those wintering in the southern area. For birds wintering in the northern area, there was no relationship between age and clutch initiation date. In contrast, young birds wintering in the southern area initiated their clutches earlier than experienced birds wintering in this area. There was no significant correlation between wintering area and clutch size or the number of fledglings produced. We hypothesize that the relationship among social status, population density and winter habitat quality should be the most important driver of the carry-over effect we found for this population

Data from: Aquatic insects rich in omega-3 fatty acids drive breeding success in a widespread bird

Ecologists studying bird foraging ecology have generally focused on food quantity over quality. Emerging work suggests that food quality, in terms of highly unsaturated omega-3 fatty acids (HUFA), can have equally important effects on performance. HUFA, which are present in aquatic primary producers, are all but absent in vascular plants, and HUFA content is also correspondingly higher in aquatic insects. Here, we show that Tree Swallow (Tachycineta bicolor) chicks rapidly accumulate HUFA from food during the nestling period. Using data sampled over 24 years, we also show that Tree Swallow breeding success is positively associated with the availability of HUFA-rich aquatic insects. Variation in aquatic insect biomass during chick development was a strong predictor of fledging success, while variation in terrestrial insects had little effect on fledging success. Our results highlight the potential for nutritional mismatches between insectivores and high-quality prey to affect avian reproductive performance.

Data from: Fine-scale genetic structure and helping decisions in a cooperatively breeding bird

In animal societies, characteristic demographic and dispersal patterns may lead to genetic structuring of populations, generating the potential for kin selection to operate. However, even in genetically structured populations, social interactions may still require kin discrimination for cooperative behaviour to be directed towards relatives. Here, we use molecular genetics and long-term field data to investigate genetic structure in an adult population of long-tailed tits Aegithalos caudatus, a cooperative breeder in which helping occurs within extended kin networks, and relate this to patterns of helping with respect to kinship. Spatial autocorrelation analyses reveal fine-scale genetic structure within our population, such that related adults of either sex are spatially clustered following natal dispersal, with relatedness among nearby males higher than that among nearby females, as predicted by observations of male-biased philopatry. This kin structure creates opportunities for failed breeders to gain indirect fitness benefits via redirected helping, but crucially, most close neighbours of failed breeders are unrelated and help is directed towards relatives more often than expected by indiscriminate helping. These findings are consistent with the effective kin discrimination mechanism known to exist in long-tailed tits, and support models identifying kin selection as the driver of cooperation.

Data from: Habitat preference facilitates successful early breeding in an open-cup nesting songbird

Selecting breeding habitats that ameliorate environmental limits on fitness and facilitate successful reproduction should benefit individual animals. This is particularly true in the temperate zone, where breeding early in a season presents a unique series of environmental challenges that can limit an individual's fitness. While many studies document links between habitat quality and reproductive success, few identify the cues used to assess habitat quality or the components of reproduction most influenced by occupying higher quality habitat, particularly during the early breeding season. We used detailed spatial maps and observations of all early season nesting attempts in an insular song sparrow (Melospiza melodia) population over 38 years to estimate the influence of nest-site preference on reproductive success and to test whether relative microclimate or food availability may act as cues for early season site selection. Female sparrows in preferred early season nest sites had earlier laying dates, exhibited more energetically efficient incubation behaviour and produced more offspring that recruited to the population than those nesting in less-preferred sites. Preference for potential nesting sites was positively related to leaf damage by Lepidopteran larvae, an indicator of food abundance, negatively related to early season microclimate, likely due to greater vegetation cover, and unrelated to site-specific plant phenology. Our findings show that breeding in preferred, high-quality habitat may offer females a fitness advantage by facilitating early laying and the production of offspring more likely to recruit to the population at a lower potential reproductive cost to the parent. We provide a clear demonstration of potential links between habitat preference and quality and their contributions to the ecology and life history of animals in seasonal environments.

Data from: Breeding relationships in Macaronesian Tolpis (Asteraceae-Cichorieae): F1 hybrid pollen fertility within and among populations from the Azores, Canary Islands and Madeira

The pollen fertility of F1 hybrids, ranging from progeny within natural populations to synthetic hybrids between species of Tolpis from three archipelagos in Macaronesia, was determined. Pollen fertility of F1 hybrids of inter-archipelago crosses from the Azores, Canaries, and Madeira were generally lower than crosses between populations or species in the same archipelagos. Lower pollen fertility was pronounced in hybrids between plants from the Canaries and the other archipelagos, which is concordant with a more distant phylogenetic relationship between the Canaries, and the Azores and Madeira. Lower average pollen fertility was seen between plants from different as compared to the same clades in the Canary Islands. However, low pollen fertilities were also detected between plants from some populations/species in the same archipelagos, and even among progeny of individual maternal plants. Some hybrids with reduced fertility had meiotic irregularities, suggesting chromosomal rearrangements; in other cases meiosis appeared normal. Results indicate that postzygotic isolating factors evolved subsequent to the divergence of Tolpis in the three archipelagos, but there are hybrid sterility factors among plants within each of the archipelagos, and even within some natural populations. Phylogenetic relationships in the Canary Islands indicate that divergence has occurred within the last million years. Present results implicate postzygotic factors as reproductive barriers facilitating population divergence and speciation in Macaronesian Tolpis.

opencc-zeroDec 2015View details →

Data from: Tick infestation of chicks in a seabird colony varies with local breeding synchrony, local nest density and habitat structure

Parasites are a major risk for group-living animals and seabirds are notoriously susceptible to ectoparasite infestations because they commonly nest in dense colonies. Ticks parasitize seabirds across all biogeographical regions and they can be particularly harmful to nestlings, but the ecological factors that affect their transmission to chicks are little studied and poorly understood. Here we show that abundance of tick larvae in blue-footed booby (Sula nebouxii) broods varies with local nest synchrony and density, and also with habitat structure: abundance increased with local breeding synchrony, was linearly and quadratically related to local nest density, and was highest toward the southern end of the study area which has suitable (boulder-rich) habitat for ticks. Also, with increasing chick age infestation first increased and then declined. The results of this study highlight how local physical and social environmental factors influence infestation of seabird nestlings by ticks.

Data from: Individuality in northern lapwing migration and its link to timing of breeding

We tracked eight adult northern lapwings, Vanellus vanellus, (six females and two males) from a Dutch breeding colony by light-level geolocation year-round, three of them for multiple years. We show that birds breeding virtually next to each other may choose widely separated wintering grounds, stretching from nearby the colony west towards the UK and Ireland, and southwest through France into Iberia and Morocco. However, individual lapwings appeared relatively faithful to a chosen wintering area, and timing of outward and homeward migration can be highly consistent between years. Movements of migratory individuals were usually direct and fast, with some birds covering distances of approximately 2000 km within 2 to 4 days of travel. The two males wintered closest and returned earliest to the breeding colony. The female lapwings returned well before the onset of breeding, spending a pre-laying period of 19 to 54 days in the wider breeding area. Despite the potential for high migration speeds, the duration that birds were absent from the breeding area increased with distance to wintering areas, a pattern which was mainly driven by an earlier outward migration of birds heading for more distant wintering grounds. Moreover, females that overwintered closer to colony bred earlier. A large variation in migration strategies found even within a single breeding colony has likely supported the species' responsiveness to recent climate change as evidenced by a shortened migration distance and an advanced timing of reproduction in Dutch lapwings since the middle of the 20th century.

Data from: Genetic pedigree analysis of the pilot breeding program for the rediscovered Galapagos giant tortoise from Floreana island

An aim of many captive breeding programs is to increase population sizes for reintroduction and establishment of self-sustaining wild populations. Genetic analyses play a critical role in these programs: monitoring genetic variation, identifying the origin of individuals, and assigning parentage to track family sizes. Here we use genetic pedigree analyses to examine three seasons of a pilot breeding program for the Floreana island Galapagos giant tortoise, C. niger, that had been declared extinct for ~150 years until individuals with mixed ancestry were recently discovered. We determined that eight of nine founding individuals were assigned parentage to at least one of 130 offspring produced, though there was considerable reproductive skew. In addition, we observed that genetic diversity of the progeny was lower than that of the founders. Despite the observed reproductive skew, we did not see evidence for assortative mating based on relatedness, but there was a trend towards reduced fitness when more related individuals bred. Finally, we found that the majority of progeny had ancestry assigned to the Floreana species (mean±SE = 0.51±0.02), though individual estimates varied. The success of these pilot seasons bodes well for a larger breeding program to help restore the previously extinct tortoise from Floreana island. Future efforts should continue to monitor for reproductive skew and assortative mating in order to maintain allelic diversity. We would also recommend forming smaller breeding groups and rotating individuals among them to prevent long-term reproductive skew among pairs.

opencc-zeroDec 2013View details →

Data from: The impacts of inbreeding, drift, and selection on genetic diversity in captive breeding populations

The goal of captive breeding programs is often to maintain genetic diversity until reintroductions can occur. However, due in part to changes that occur in captive populations, approximately one-third of reintroductions fail. We evaluated genetic changes in captive populations using microsatellites and mtDNA. We analyzed six populations of white-footed mice that were propagated for 20 generations using two replicates of three protocols: random mating (RAN), minimizing mean kinship (MK), and selection for docility (DOC). We found that MK resulted in the slowest loss of microsatellite genetic diversity compared to RAN and DOC. However, the loss of mtDNA haplotypes was not consistent among replicate lines. We compared our empirical data to simulated data and found no evidence of selection in the MK lines although some evidence of selection in the RAN lines was present. Our results suggest that although the effects of drift may not be fully mitigated, MK reduces the loss of alleles due to inbreeding more effectively than random mating or docility selection. Therefore, MK should be preferred for captive breeding. Furthermore, our simulations show that incorporating microsatellite data into the MK framework reduced the magnitude of drift, which may have applications in long-term or extremely genetically depauperate captive populations.

Data from: Genetic diversity, breed composition and admixture of Kenyan domestic pigs

The genetic diversity of African pigs, whether domestic or wild has not been widely studied and there is very limited published information available. Available data suggests that African domestic pigs originate from different domestication centers as opposed to international commercial breeds. We evaluated two domestic pig populations in Western Kenya, in order to characterize the genetic diversity, breed composition and admixture of the pigs in an area known to be endemic for African swine fever (ASF). One of the reasons for characterizing these specific populations is the fact that a proportion of indigenous pigs have tested ASF virus (ASFv) positive but do not present with clinical symptoms of disease indicating some form of tolerance to infection. Pigs were genotyped using either the porcine SNP60 or SNP80 chip. Village pigs were sourced from Busia and Homabay counties in Kenya. Because bush pigs (Potamochoerus larvatus) and warthogs (Phacochoerus spp.) are known to be tolerant to ASFv infection (exhibiting no clinical symptoms despite infection), they were included in the study to assess whether domestic pigs have similar genomic signatures. Additionally, samples representing European wild boar and international commercial breeds were included as references, given their potential contribution to the genetic make-up of the target domestic populations. The data indicate that village pigs in Busia are a non-homogenous admixed population with significant introgression of genes from international commercial breeds. Pigs from Homabay by contrast, represent a homogenous population with a "local indigenous' composition that is distinct from the international breeds, and clusters more closely with the European wild boar than African wild pigs. Interestingly, village pigs from Busia that tested negative by PCR for ASFv genotype IX, had significantly higher local ancestry (>54%) compared to those testing positive, which contained more commercial breed gene introgression. This may have implication for breed selection and utilization in ASF endemic areas. A genome wide scan detected several regions under preferential selection with signatures for pigs from Busia and Homabay being very distinct. Additionally, there was no similarity in specific genes under selection between the wild pigs and domestic pigs despite having some broad areas under similar selection signatures. These results provide a basis to explore possible genetic determinants underlying tolerance to infection by ASFv genotypes and suggests multiple pathways for genetically mediated ASFv tolerance given the diversity of selection signatures observed among the populations studied.

opencc-zeroDec 2015View details →

Data from: Insights into the genetic relationships and breeding patterns of the African tea germplasm based on nSSR markers and cpDNA sequences

Africa is one of the key centers of global tea production. Understanding the genetic diversity and relationships of cultivars of African tea is important for future targeted breeding efforts for new crop cultivars, specialty tea processing, and to guide germplasm conservation efforts. Despite the economic importance of tea in Africa, no research work has been done so far on its genetic diversity at a continental scale. Twenty-three nSSRs and three plastid DNA regions were used to investigate the genetic diversity, relationships, and breeding patterns of tea accessions collected from eight countries of Africa. A total of 280 African tea accessions generated 297 alleles with a mean of 12.91 alleles per locus and a genetic diversity (HS) estimate of 0.652. A STRUCTURE analysis suggested two main genetic groups of African tea accessions which corresponded well with the two tea types Camellia sinensis var. sinensis and C. sinensis var. assamica, respectively, as well as an admixed "mosaic" group whose individuals were defined as hybrids of F2 and BC generation with a high proportion of C. sinensis var. assamica being maternal parents. Accessions known to be C. sinensis var. assamica further separated into two groups representing the two major tea breeding centers corresponding to southern Africa (Tea Research Foundation of Central Africa, TRFCA), and East Africa (Tea Research Foundation of Kenya, TRFK). Tea accessions were shared among countries. African tea has relatively lower genetic diversity. C. sinensis var. assamica is the main tea type under cultivation and contributes more in tea breeding improvements in Africa. International germplasm exchange and movement among countries within Africa was confirmed. The clustering into two main breeding centers, TRFCA, and TRFK, suggested that some traits of C. sinensis var. assamica and their associated genes possibly underwent selection during geographic differentiation or local breeding preferences. This study represents the first step toward effective utilization of differently inherited molecular markers for exploring the breeding status of African tea. The findings here will be important for planning the exploration, utilization, and conservation of tea germplasm for future breeding efforts in Africa.

Data from: Growth gains from selective breeding in a spruce hybrid zone do not compromise local adaptation to climate

Hybrid zones contain extensive standing genetic variation that facilitates rapid responses to selection. The Picea glauca x P. engelmannii hybrid zone in western Canada is the focus of tree breeding programs that annually produce ~90 million reforestation seedlings. Understanding the direct and indirect effects of selective breeding on adaptive variation is necessary to implement assisted gene flow polices in Alberta and British Columbia that match these seedlings with future climates. We decomposed relationships among hybrid ancestry, adaptive traits and climate to understand the implications of selective breeding for climate adaptations and assisted gene flow strategies. The effects of selection on associations among hybrid index estimated from ~6500 SNPs, adaptive traits, and provenance climates were assessed for ~2400 common garden seedlings. Hybrid index differences between natural and selected seedlings within breeding zones were small in Alberta (average +2%), but larger and more variable in BC (average -7 %, range -24% to +1%), slightly favoring P. glauca ancestry. The average height growth gain of selected seedlings over natural seedlings within breeding zones was 36% (range 12% to 86%). Clines in growth with temperature-related variables were strong, but differed little between selected and natural populations. Seedling hybrid index and growth trait associations with evapotranspiration-related climate variables were stronger in selected than in natural seedlings, indicating possible pre-adaptation to drier future climates. Associations among cold hardiness, hybrid ancestry and cold-related climate variables dominated signals of local adaptation that were preserved in breeding populations. Strong hybrid ancestry-phenotype-climate associations suggest that assisted gene flow will be necessary to match interior spruce breeding populations with shifting future climates. The absence of antagonistic selection responses among traits and maintenance of cold adaptation in selected seedlings suggests breeding populations can be safely redeployed using assisted gene flow prescriptions similar to those of natural populations.