The annual cycle for whimbrel populations using the Western Atlantic Flyway

Many long-distance migratory birds use habitats that are scattered across continents and confront hazards throughout the annual cycle that may be population-limiting. Identifying where and when populations spend their time is fundamental to effective management. We tracked 34 adult whimbrels (Numenius phaeopus) from two breeding populations (Mackenzie Delta and Hudson Bay) with satellite transmitters to document the structure of their annual cycles. The two populations differed in their use of migratory pathways and their seasonal schedules. Mackenzie Delta whimbrels made long (22,800 km) loop migrations with different autumn and spring routes. Hudson Bay whimbrels made shorter (17,500 km) and more direct migrations along the same route during autumn and spring. The two populations overlap on the winter grounds and within one spring staging area. Mackenzie Delta whimbrels left the breeding ground, arrived on winter grounds, left winter grounds and arrived on spring staging areas earlier compared to whimbrels from Hudson Bay. For both populations, migration speed was significantly higher during spring compared to autumn migration. Faster migration was achieved by having fewer and shorter stopovers en route. We identified five migratory staging areas including four that were used during autumn and two that were used during spring. Whimbrels tracked for multiple years had high (98%) fidelity to staging areas. We documented dozens of locations where birds stopped for short periods along nearly all migration routes. The consistent use of very few staging areas suggests that these areas are integral to the annual cycle of both populations and have high conservation value.

Genome wide association mapping of yield and other agronomic traits in rice: Narrative literature review

Based on previous recombination actions and LD (linkage disequilibrium) throughout the genome, genome wide association mapping studies often are employed to find Quantitative trait locus in varied collections of crop germplasm. Generally, diverse panel’s genotyped using high density Single nucleotide polymorphism (SNP) panels are used to test a broad variety of haplotypes and alleles, as well as to track recombination divisions throughout the genome. GWAS, on the other hand, have rarely been used in breeding populations. We studied association mapping for agricultural parameters such as yield and its constituents in a breeding inhabitants of top irrigated tropical rice progenies so that the findings could be used to breeding more directly than those from a diverse panel. GWAS was undertaken with the specific purpose of accelerating selection in the breeding population, and the sample was genotyped with 71,710 Single nucleotide polymorphisms using genotyping-by-sequencing. We found 52 Quantitative trait locus QTL for 11 agronomic characteristics using this breeding panel, including substantial impact Quantitative trait loci (QTLs) for flowering period as well as grain width, grain length, grain length-breadth ratio. Furthermore we discovered haplotypes that may be applied to choose plants for our population with smaller stature (plant height), fast blooming time, with high yield, demonstrating the value of association mapping for advising breeding choices in breeding populations. Furthermore, we explore at how genomic-assisted selection models might be built using the newly discovered important Single nucleotide polymorphisms (SNPs) and deep insight into the genetic structure of these quantitative traits.

Population specific annual cycles and migration strategies in a leap-frog migrant

A common migratory pattern in birds is that northerly breeding populations migrate to more southerly non-breeding sites compared to southerly breeding populations (leap-frog migration). Not only do populations experience differences in migration distances, but also different environmental conditions, which may vary spatiotemporally within their annual cycles, creating distinctive selective pressures and migratory strategies. Information about such adaptations is important to understand migratory drivers and evolution of migration patterns. We use light-level geolocators and citizen science data on regional spring arrivals to compare two populations of common ringed plover Charadrius hiaticula breeding at different latitudes. We (1) describe and characterize the annual cycles and (2) test predictions regarding speed and timing of migration. The northern breeding population (NBP) wintered in Africa and the southern (SBP) mainly in Europe. The annual cycles were shifted temporally so that the NBP was always later in all stages. The SBP spent more than twice as long time in the breeding area, but there was no difference in winter. The NBP spent more time on migration in general. Spring migration speed was lower in the SBP compared to autumn speed of both populations, and there was no difference in autumn and spring speed in the NBP. We also found a larger variation in spring arrival times across years in the SBP. This suggests that a complex interaction of population specific timing and variation of breeding onset, length of breeding season, and proximity to the breeding area shape the annual cycle and migratory strategies. Significance statement Migration distance, climate, and the resulting composition of the annual cycle are expected to influence migration strategies and timing in birds. Testing theories regarding migration behaviours are challenging, and intraspecific comparisons over the full annual cycle are still rare. Here we compare the spatiotemporal distributions of two latitudinally separated populations of common ringed plovers using light-level geolocators. We found that there was a larger long-term variation in first arrival dates and that migration speed was slower only in spring in a temperate, short-distance migratory population, compared to an Arctic, long-distance migratory population. This suggests that a complex interaction of population specific timing and variation of breeding onset, length of breeding season and proximity to the breeding area shape the annual cycle and migratory behaviours.

Tree selection and use by the polyphagous xylophage Anoplophora glabripennis (Coleoptera: Cerambycidae) in Canada

Two breeding populations of the non-native Asian longhorned beetle (Anoplophora glabripennis Motschulsky), a pest of broadleaf trees in its native China, were discovered in Ontario in 2003 and 2013, respectively. Both populations were eradicated by removing all trees injured by the beetle and all uninjured trees deemed at high risk of injury. We used data collected during this removal to study host selection. Signs of A. glabripennis injury were observed on 732 stems from seven (i.e., Acer, Salix, Populus, Betula, Ulmus, Fraxinus and Tilia) of the 45 tree genera available. Complete beetle development was confirmed on only the first four of these seven genera. Most signs of injury were on the genus Acer and on trees with a diameter at 130 cm above ground ranging between 15 cm and 40 cm. On most trees, the lowest sign of injury was within three meters of the ground or within 40% of tree height. Tree height explained 63% of the variance in the location of the lowest sign of injury. Initial attacks were typically near the middle of the tree and expanded both upward and downward with successive attacks over time. We discuss how these findings could improve survey efforts for A. glabripennis.

Conservation Genomics Reveals Low Connectivity Among Populations of Threatened Roseate Terns in the Atlantic Basin

While the effects of barriers to dispersal such as population declines, habitat fragmentation, and geographic distance have been well-documented in terrestrial wildlife, factors impeding the dispersal of highly vagile taxa such as seabirds are less well understood. The roseate tern (Sterna dougallii) is a globally distributed seabird species, but populations tend to be both fragmented and small, and the species is declining across most of its range. Within the Atlantic Basin, past work has shown differentiation among roseate terns breeding on different continents, but these results were generated with a limited number of microsatellite markers. Relationships between breeding populations in the Northwestern Atlantic and the Caribbean have never been analyzed. We evaluated population structuring of roseate tern populations in North America and the Azores using both microsatellite markers and single-nucleotide polymorphisms generated through targeted sequencing of Ultra-conserved Elements. For both marker types, we found significant genetic differentiation among all 3 populations and evidence for moderate contemporary unidirectional gene flow from the Caribbean to the Azores, but not among other populations. Within the Caribbean metapopulation, we found high rates of unidirectional migration from the Virgin Islands to Florida, potentially indicative of movement from source population to sink or an artifact of dispersal among other unsampled populations in the Caribbean region. These observations have significance for species persistence in the Atlantic, as our results suggest that loss of genetic diversity within populations is unlikely to be buffered by inflow of new alleles from other breeding populations.

Evaluation of Drought Tolerance in Maize Inbred Lines Selected from the Shaan A Group and Shaan B Group

Drought is one of the most prevailing abiotic stresses affecting the growth, development, and productivity of maize. Knowledge of drought tolerance could help in maize improvement. However, less research has been done to comprehensively evaluate the drought tolerance of maize inbred lines. We used 27 elite maize inbred lines selected from Shaan A group and Shaan B group breeding populations to estimate their drought tolerance in 3 years 2 locations under normal field conditions and low irrigation. Using principal component analysis (PCA) and GGE biplots, all inbred lines, including the controls, could be divided into four types. Ten lines could be categorized as the high-yield drought-resistant type (‘KB081’, ‘KA105’, ‘KB417’, ‘KB215’, ‘KB-7’, ‘2013KB-37’, ‘KA203’, ‘2012KA-34’, ‘KA225’, and ‘91227’) because of their stability and wide adaptability. Compared with the controls, a large proportion of the inbred lines selected from Shaan A and Shaan B breeding populations demonstrated higher drought resistance. Our results suggest that multi-year drought screening can be used as a tool to improve the drought resistance of maize inbred lines and provide a scientific basis for making better use of the Shaan A and Shaan B maize inbred lines to breed new varieties and to identify existing drought-resistant maize varieties.

A Semi-Automatic Workflow to Extract Irregularly Aligned Plots and Sub-Plots: A Case Study on Lentil Breeding Populations

Plant breeding experiments typically contain a large number of plots, and obtaining phenotypic data is an integral part of most studies. Image-based plot-level measurements may not always produce adequate precision and will require sub-plot measurements. To perform image analysis on individual sub-plots, they must be segmented from plots, other sub-plots, and surrounding soil or vegetation. This study aims to introduce a semi-automatic workflow to segment irregularly aligned plots and sub-plots in breeding populations. Imagery from a replicated lentil diversity panel phenotyping experiment with 324 populations was used for this study. Image-based techniques using a convolution filter on an excess green index (ExG) were used to enhance and highlight plot rows and, thus, locate the plot center. Multi-threshold and watershed segmentation were then combined to separate plants, ground, and sub-plot within plots. Algorithms of local maxima and pixel resizing with surface tension parameters were used to detect the centers of sub-plots. A total of 3489 reference data points was collected on 30 random plots for accuracy assessment. It was found that all plots and sub-plots were successfully extracted with an overall plot extraction accuracy of 92%. Our methodology addressed some common issues related to plot segmentation, such as plot alignment and overlapping canopies in the field experiments. The ability to segment and extract phenometric information at the sub-plot level provides opportunities to improve the precision of image-based phenotypic measurements at field-scale.

Evolutionary and Ecological Explanations for the Elevational Flexibility of Several East African Bird Species Complexes

Africa’s montane areas are broken up into several large and small units, each isolated as forest-capped “sky islands” in a “sea” of dry lowland savanna. Many elements of their biota, including montane forest birds, are shared across several disjunct mountains, yet it has been difficult to rigorously define an Afromontane forest avifauna, or determine its evolutionary relationships with the birds of the surrounding lowland forests. In order to trace the historical relationship between lowland and highland avifaunas, we review cases of species or groups of closely related species with breeding populations at different elevations, and use phylogeographic methods to explore the historical connections between such populations within the biodiversity hotspot of East Africa. The study reveals several idiosyncratic patterns, but also a prominent number of cases of gene flow between populations in southern areas, mainly around the Malawi Rift, and mountains and coastal forests to the north, close to the equator. This may reflect more continuous past distributions through northern Mozambique and coastal Tanzania, or seasonal migrations between areas with different rainfall regimes. Over time, these distributional dynamics have resulted in a higher persistence of lineages, and an accumulation of forest-dependent lineages within the Eastern Arc Mountains of Tanzania and the northern part of the coastal forest mosaic.

Spatial and temporal differences in migration strategies among endangered European Greater Spotted Eagles Clanga clanga

Summary Understanding connectivity between migratory bird breeding and wintering grounds is essential for range-wide planning of conservation activities. We used GPS tracking to explore the migration of 28 ‘Endangered’ Greater Spotted Eagles, Clanga clanga from three remaining European breeding populations towards their wintering range, and to identify population and sex-specific patterns in selection of wintering sites. The tracked eagles wintered in three continents, 46% in Africa (mostly Eastern Sahel), 43% across southern Europe (mostly Greece) and 11% in Asia (the Middle East). Migratory connectivity was weak (rM = 0.16), and the population spread across the wintering range was large (1,917 km). The three studied populations differed in their migration strategy, with northerly, Estonian breeders all wintering in Southern Europe, and Polish and Belarusian breeders divided between Southern Europe and Africa. Migration strategy was different between Belarusian males and females, with males more likely to winter in Africa than Europe, and on average, migrating 2,500 km further south than females. Migration to Africa took longer, but was partly compensated by higher migration speeds. Greater Spotted Eagles wintered in wetland sites throughout their wintering range, with 15 of 29 birds wintering in internationally or nationally protected sites (including 12 Ramsar sites). Nearly a third of European winterers stayed in the same Greek national park, perhaps indicating a limitation of suitable sites in Europe due to wetland loss or degradation. This highlights the importance of protected wetlands to this species, but also shows their vulnerability to future wetland degradation. Only two of 14 wintering sites in Africa were under protection, showing a potential mismatch between protection of females and males in their wintering grounds.

The Southern Ocean Exchange: porous boundaries between humpback whale breeding populations in southern polar waters

Humpback whales (Megaptera novaeangliae) are a cosmopolitan species and perform long annual migrations between low-latitude breeding areas and high-latitude feeding areas. Their breeding populations appear to be spatially and genetically segregated due to long-term, maternally inherited fidelity to natal breeding areas. In the Southern Hemisphere, some humpback whale breeding populations mix in Southern Ocean waters in summer, but very little movement between Pacific and Atlantic waters has been identified to date, suggesting these waters constituted an oceanic boundary between genetically distinct populations. Here, we present new evidence of summer co-occurrence in the West Antarctic Peninsula feeding area of two recovering humpback whale breeding populations from the Atlantic (Brazil) and Pacific (Central and South America). As humpback whale populations recover, observations like this point to the need to revise our perceptions of boundaries between stocks, particularly on high latitude feeding grounds. We suggest that this “Southern Ocean Exchange” may become more frequent as populations recover from commercial whaling and climate change modifies environmental dynamics and humpback whale prey availability.