Long distance migration is a major factor driving local adaptation at continental scale in Coho Salmon

Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across its entire North American range. We hypothesized that extensive spatial variation in environmental conditions and the species homing behavior may promote the establishment of local adaptation. We genotyped 7,829 individuals representing 217 sampling locations at more than 100,000 high-quality RADseq loci to investigate how recombination might affect the detection of loci putatively under selection and took advantage of the precise description of the demographic history of the species from our previous work to draw accurate population genomic inferences about local adaptation. Results indicated that genetic differentiation scans and genetic-environment association analyses were both significantly affected by variation in recombination rate as low recombination regions displayed an increased number of outliers. By taking these confounding factors into consideration, we revealed that migration distance was the primary selective factor driving local adaptation and partial parallel divergence among distant populations. Moreover, we identified several candidates SNP associated with long distance migration and altitude including a gene known to be involved in adaptation to altitude in other species. The evolutionary implications of our findings are discussed along with conservation applications.

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Influence of environmental factors on the genetic variation of the aquatic macrophyte Ranunculus subrigidus on the Qinghai-Tibetan Plateau

BMC Evolutionary Biology ◽

10.1186/s12862-019-1559-0 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 2

Author(s):

Zhigang Wu ◽

Xinwei Xu ◽

Juan Zhang ◽

Gerhard Wiegleb ◽

Hongwei Hou

Keyword(s):

Genetic Diversity ◽

Tibetan Plateau ◽

Environmental Factors ◽

Local Adaptation ◽

Aquatic Macrophyte ◽

Spatial Genetic Structure ◽

Long Distance ◽

Elevation Gradients ◽

Mantel Tests ◽

Genetic Patterns

Abstract Background Due to the environmental heterogeneity along elevation gradients, alpine ecosystems are ideal study objects for investigating how ecological variables shape the genetic patterns of natural species. The highest region in the world, the Qinghai-Tibetan Plateau, is a hotspot for the studies of evolutionary processes in plants. Many large rivers spring from the plateau, providing abundant habitats for aquatic and amphibious organisms. In the present study, we examined the genetic diversity of 13 Ranunculus subrigidus populations distributed throughout the plateau in order to elucidate the relative contribution of geographic distance and environmental dissimilarity to the spatial genetic pattern. Results A relatively low level of genetic diversity within populations was found. No spatial genetic structure was suggested by the analyses of molecular variance, Bayesian clustering analysis and Mantel tests. Partial Mantel tests and multiple matrix regression analysis showed a significant influence of the environment on the genetic divergence of the species. Both climatic and water quality variables contribute to the habitat heterogeneity of R. subrigidus populations. Conclusions Our results suggest that historical processes involving long-distance dispersal and local adaptation may account for the genetic patterns of R. subrigidus and current environmental factors play an important role in the genetic differentiation and local adaptation of aquatic plants in alpine landscapes.

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Gene expression clines reveal local adaptation and associated trade-offs at a continental scale

Scientific Reports ◽

10.1038/srep32975 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 14

Author(s):

Damiano Porcelli ◽

Anja M. Westram ◽

Marta Pascual ◽

Kevin J. Gaston ◽

Roger K. Butlin ◽

...

Keyword(s):

Gene Expression ◽

Local Adaptation ◽

Continental Scale ◽

Trade Offs

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Structure and Migration in U.S. Blumeria graminis f. sp. tritici Populations

Phytopathology ◽

10.1094/phyto-03-15-0066-r ◽

2016 ◽

Vol 106 (3) ◽

pp. 295-304 ◽

Cited By ~ 7

Author(s):

Christina Cowger ◽

Ryan Parks ◽

Evsey Kosman

Keyword(s):

Ssr Markers ◽

Large Scale ◽

Isolation By Distance ◽

Blumeria Graminis ◽

Snp Markers ◽

Eastern United States ◽

Long Distance ◽

Continental Scale ◽

South Central ◽

Haplotypic Diversity

While wheat powdery mildew occurs throughout the south-central and eastern United States, epidemics are especially damaging in the Mid-Atlantic states. The structure of the U.S. Blumeria graminis f. sp. tritici population was assessed based on a sample of 238 single-spored isolates. The isolates were collected from 16 locations in 12 states (18 site-years) as chasmothecial samples in 2003 or 2005, or as conidial samples in 2007 or 2010. DNA was evaluated using nine single nucleotide polymorphism (SNP) markers in four housekeeping genes, and 10 simple sequence repeat (SSR) markers. The SSR markers were variably polymorphic, with allele numbers ranging from 3 to 39 per locus. Genotypic diversity was high (210 haplotypes) and in eight of the site-years, every isolate had a different SSR genotype. SNP haplotypic diversity was lower; although 15 haplotypes were identified, the majority of isolates possessed one of two haplotypes. The chasmothecial samples showed no evidence of linkage disequilibrium (P = 0.36), while the conidial samples did (P = 0.001), but the two groups had nearly identical mean levels of genetic diversity, which was moderate. There was a weakly positive relationship between genetic distance and geographic distance (R2 = 0.25, P = 0.001), indicating modest isolation by distance. Most locations in the Mid-Atlantic and Great Lakes regions clustered together genetically, while Southeast locations formed a distinct but adjacent cluster; all of these were genetically separated from Southern Plains locations and an intermediate location in Kentucky. One-way migration was detected at a rate of approximately five individuals per generation from populations west of the Appalachian Mountains to those to the east, despite the fact that the Atlantic states experience more frequent and damaging wheat mildew epidemics. Overall, the evidence argues for a large-scale mosaic of overlapping populations that re-establish themselves from local sources, rather than continental-scale extinction and re-establishment, and a low rate of long-distance dispersal roughly from west to east, consistent with prevailing wind directions.

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Movement and mortality of Australian pelicans (Pelecanus conspicillatus) banded at inland and coastal breeding sites in South Australia

Pacific Conservation Biology ◽

10.1071/pc14925 ◽

2015 ◽

Vol 21 (4) ◽

pp. 271 ◽

Cited By ~ 1

Author(s):

Gregory R. Johnston ◽

Maxwell H. Waterman ◽

Clare E. Manning

Keyword(s):

South Australia ◽

Population Declines ◽

Long Distance ◽

Breeding Sites ◽

Continental Scale ◽

South Eastern ◽

Eastern Australia ◽

Causes Of Mortality ◽

Conservation Concern ◽

South Eastern Australia

Globally, pelican populations have decreased, with three species being of conservation concern. Australian pelicans (Pelecanus conspicillatus) are not regarded as endangered, but have declined across south-eastern Australia. Information on their movements and causes of mortality are required to interpret the importance of these regional declines to the species’ global population. We explored patterns of movement and causes of mortality by analysing recoveries from 14 615 Australian pelicans banded over 37 years between 1969 and 2006. Data from 243 leg band recoveries showed that Australian pelicans move distances of up to 3206 km, and travel across the species’ entire geographic range, within a year of fledging. We found little evidence for the popular notion that these birds move en masse from the coast to inland areas in response to flooding rains. Maximum recorded age of a banded Australian pelican was 15 years. The banding data suggest that the regional pelican declines could reflect long-distance movements rather than an overall population response. However, a concentration of band returns from south-eastern Australia where the declines have been recorded, and the high incidence of human-induced deaths (16.4%) suggest otherwise. Accurate assessment of population trends in long-lived, long-distance nomads such as Australian pelicans requires assessment at a continental scale. Our results emphasise the importance of knowledge about fundamental aspects of a species’ biology for accurate interpretation of regional population declines.

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Environmental correlates of genetic variation in the invasive and largely panmictic European starling in North America

10.1101/643858 ◽

2019 ◽

Cited By ~ 1

Author(s):

Natalie R. Hofmeister ◽

Scott J. Werner ◽

Irby J. Lovette

Keyword(s):

North America ◽

Local Adaptation ◽

North American ◽

Winter Season ◽

Bird Species ◽

Genomic Diversity ◽

Rapid Expansion ◽

Continental Scale ◽

High Dispersal ◽

Local Selection

ABSTRACTPopulations of invasive species that colonize and spread in novel environments may differentiate both through demographic processes and local selection. European starlings (Sturnus vulgaris) were introduced to New York in 1890 and subsequently spread throughout North America, becoming one of the most widespread and numerous bird species on the continent. Genome-wide comparisons across starling individuals and populations can identify demographic and/or selective factors that facilitated this rapid and successful expansion. We investigated patterns of genomic diversity and differentiation using reduced-representation genome sequencing (ddRADseq) of 17 winter-season starling populations. Consistent with this species’ high dispersal rate and rapid expansion history, we found low geographic differentiation and few FST outliers even at a continental scale. Despite starting from a founding population of approximately 180 individuals, North American starlings show only a moderate genetic bottleneck, and models suggest a dramatic increase in effective population size since introduction. In genotype-environment associations we found that ∼200 single-nucleotide polymorphisms are correlated with temperature and/or precipitation against a background of negligible genome- and range-wide divergence. Local adaptation in North American starlings may have evolved rapidly even in this wide-ranging and evolutionarily young population. This survey of genomic signatures of expansion in North American starlings is the most comprehensive to date and complements ongoing studies of world-wide local adaptation in these highly dispersive and invasive birds.

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Surveillance of airborne plant disease dissemination at continental scale using air mass trajectory analysis and network theory

10.1101/2021.06.04.447025 ◽

2021 ◽

Author(s):

Andrea Radici ◽

Davide Martinetti ◽

Daniele Bevacqua

Keyword(s):

Stem Rust ◽

Disease Surveillance ◽

Plant Disease ◽

Disease Outbreaks ◽

Plant Diseases ◽

Long Distance ◽

Continental Scale ◽

Prophylactic Measures ◽

Spatio Temporal ◽

Meteorological Features

Sustainable management of plant disease outbreaks in agriculture is one of the main challenges of the next years to restore economic and environmental viability of farming practices. Improving early-detection capabilities and disease surveillance is increasingly seen as an obligate step to design appropriate and effective prophylactic measures. In this context, plant diseases caused by wind-dispersed pathogens represent a peculiar case of study, since they are particularly complex and hard to observe directly, especially if compared to other dissemination means, and demand for a multidisciplinary approach to be dealt with. Wind dispersal could imply a geographic differentiation in pathogens spreading potential, due to the emerging of local meteorological features. In this work we analyze the spatio-temporal patterns of wind connectivity in Europe and the Mediterranean basin in order to identify possible pathways of Puccinia graminis spores, the causal agent of stem rust of wheat. By running backwards Lagrangian simulations merging a biological layer coupled with a pathogen viability model, we investigate possible long-distance connections between regions in the study area across different seasons. We characterized these regions in terms of network centrality indicators to identify possible spreaders of stem rust of wheat, founding that Central and Western European regions appears to provide highest connectivity for the spread of P. graminis.

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Tracking dragons: stable isotopes reveal the annual cycle of a long-distance migratory insect

Biology Letters ◽

10.1098/rsbl.2018.0741 ◽

2018 ◽

Vol 14 (12) ◽

pp. 20180741 ◽

Cited By ~ 19

Author(s):

Michael T. Hallworth ◽

Peter P. Marra ◽

Kent P. McFarland ◽

Sara Zahendra ◽

Colin E. Studds

Keyword(s):

Annual Cycle ◽

Life Histories ◽

First Generation ◽

Isotope Analysis ◽

Science Data ◽

Long Distance ◽

Anax Junius ◽

Migration Timing ◽

Continental Scale ◽

Insect Migration

Insect migration is globally ubiquitous and can involve continental-scale movements and complex life histories. Apart from select species of migratory moths and butterflies, little is known about the structure of the annual cycle for migratory insects. Using stable-hydrogen isotope analysis of 852 wing samples from eight countries spanning 140 years, combined with 21 years of citizen science data, we determined the full annual cycle of a large migratory dragonfly, the common green darner ( Anax junius ). We demonstrate that darners undertake complex long-distance annual migrations governed largely by temperature that involve at least three generations. In spring, the first generation makes a long-distance northbound movement (further than 650 km) from southern to northern range limits, lays eggs and dies. A second generation emerges and returns south (further than 680 km), where they lay eggs and die. Finally, a third resident generation emerges, reproducing locally and giving rise to the cohort that migrates north the following spring. Since migration timing and nymph development are highly dependent on temperature, continued climate change could lead to fundamental changes in the biology for this and similar migratory insects.

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Effectiveness of the system of protected areas of Lombardy (Northern Italy) in preserving breeding birds

Bird Conservation International ◽

10.1017/s095927091700017x ◽

2017 ◽

Vol 28 (3) ◽

pp. 475-492 ◽

Cited By ~ 2

Author(s):

BEATRICE SICURELLA ◽

VALERIO ORIOLI ◽

GUIDO PINOLI ◽

ROBERTO AMBROSINI ◽

LUCIANO BANI

Keyword(s):

Protected Areas ◽

Human Activities ◽

Biological Diversity ◽

Temporal Trends ◽

Bird Species ◽

Northern Italy ◽

Sustainable Land Use ◽

Long Distance ◽

Ecological Processes ◽

Continental Scale

SummaryNetworks of protected areas (PAs) where human activities are allowed at different degrees are fundamental to ensure the long-term conservation of biological diversity and ecological processes. However, studies aimed at assessing their effectiveness, focusing on several species simultaneously are scarce. We assessed the effectiveness of the system of protected areas (PAs) of Lombardy, Northern Italy, in conserving bird populations by comparing the changes from 1992 to 2013 in the occurrence of 54 breeding bird species censused in areas classified in different protection categories, namely Nature Reserves (NRs), areas designed predominantly for the protection of nature; Regional Parks (RPs), naturally valuable areas where human activities, including intensive agriculture, are allowed; and non-protected areas (NPAs). Overall, occurrence of common birds increased in Lombardy in the last 20 years and farmland and long-distance migrants (LDMs), which suffered sharp declines at a continental scale, showed stable and increasing trends, respectively. These trends were, however, the balance between those of species whose occurrence markedly increased, and those of species that dramatically declined. Species occurred more often in PAs than in NPAs, while temporal trends in occurrence were significantly more positive in RPs than in both NRs and NPAs. Hence, PAs seemed effective in preserving common bird communities. Occurrence of woodland and short-distance migrant species was higher in PAs than in NPAs, while occurrence of farmland species and LDMs was similar in all protection categories. PAs of Lombardy appear therefore effective only in protecting some categories of birds. Farmland and LDM birds would benefit more from ecologically sustainable land-use policies aiming at improving agro-ecosystem biodiversity than from protected areas.

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Conserving the Diversity of Ecological Interactions: The Role of Two Threatened Macaw Species as Legitimate Dispersers of “Megafaunal” Fruits

Diversity ◽

10.3390/d12020045 ◽

2020 ◽

Vol 12 (2) ◽

pp. 45 ◽

Cited By ~ 3

Author(s):

José L. Tella ◽

Fernando Hiraldo ◽

Erica Pacífico ◽

José A. Díaz-Luque ◽

Francisco V. Dénes ◽

...

Keyword(s):

Biodiversity Loss ◽

Ecological Interactions ◽

Large Mammals ◽

Species Dispersal ◽

Long Distance ◽

Continental Scale ◽

Palm Species ◽

Dispersal Events ◽

Prevailing View

The extinction of ecological functions is increasingly considered a major component of biodiversity loss, given its pervasive effects on ecosystems, and it may precede the disappearance of the species engaged. Dispersal of many large-fruited (>4 cm diameter) plants is thought to have been handicapped after the extinction of megafauna in the Late Pleistocene and the recent defaunation of large mammals. We recorded the seed dispersal behavior of two macaws (Anodorhynchus hyacinthinus and Anodorhynchus leari) in three Neotropical biomes, totaling >1700 dispersal events from 18 plant species, 98% corresponding to six large-fruited palm species. Dispersal rates varied among palm species (5%–100%). Fruits were moved to perches at varying distances (means: 17–450 m, maximum 1620 m). Macaws also moved nuts after regurgitation by livestock, in an unusual case of tertiary dispersal, to distant perches. A high proportion (11%–75%) of dispersed nuts was found undamaged under perches, and palm recruitment was confirmed under 6%–73% of the perches. Our results showed that these macaws were legitimate, long-distance dispersers, and challenge the prevailing view that dispersal of large-fruited plants was compromised after megafauna extinction. The large range contraction of these threatened macaws, however, meant that these mutualistic interactions are functionally extinct over large areas at a continental scale.

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