scholarly journals Genomic variation and population histories of spotted (Strix occidentalis) and barred (S. varia) owls

2020 ◽  
Author(s):  
Naoko T. Fujito ◽  
Zachary R. Hanna ◽  
Michal Levy-Sakin ◽  
Rauri C. K. Bowie ◽  
Pui-Yan Kwok ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Keystone Species ◽  
Genomic Variation ◽  
F1 Hybrids ◽  
Suitable Habitat ◽  
High Coverage ◽  
Strix Occidentalis ◽  
Strix Varia ◽  
Intermediate Morphology ◽  
Species Specific

AbstractSpotted owls (SO, Strix occidentalis) are a keystone species inhabiting old-growth forests in Western North America. In recent decades, their populations have declined due to ongoing reductions in suitable habitat caused by logging, wildfires, and competition with the congeneric barred owl (BO, Strix varia). The northern spotted owl (subspecies S. o. caurina) has been listed as “threatened” under the Endangered Species Act since 1990. Here we present a comprehensive look at genetic variation to elucidate the population histories of SO and invading western BO. Specifically, we present an improved SO genome assembly, based on 10x and Bionano Genomics data, along with 51 high-coverage whole-genome sequences including 11 SO from two subspecies (caurina and occidentalis), 25 BO, 2 confirmed and 13 potential hybrids. We identified potential hybrids based on intermediate morphology and found them to be a mixture of pure BO, F1 hybrids, and F1 x BO backcrosses. Unlike previous studies reporting asymmetries in the species-specific genders of the parents of F1 hybrids, we did not observe any significant asymmetry. Within species, we found that Western BO genetic variation is not simply a subset of the genetic variation in Eastern BO, suggesting that the two groups have been genetically isolated for longer (thousands of years) than previously suspected (80-130 years). Similarly, we found evidence of substantial genetic differentiation between the two SO subspecies. Finally, our analyses suggest that Northern SO experienced a moderate population bottleneck around the end of the last glaciation, while BO population sizes have always been large.

scholarly journals Genetic Variation Within Two Sympatric Spotted Gum Eucalypts Exceeds Between Taxa Variation

2008 ◽  
Vol 57 (1-6) ◽  
pp. 249-256 ◽  
Author(s):  
J. W. Ochieng ◽  
M. Shepherd ◽  
P. R. Baverstock ◽  
G. Nikles ◽  
D. J. Lee ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Allele Frequency ◽  
Population Stratification ◽  
East Coast ◽  
Population Substructure ◽  
Cherry Tree ◽  
Separate Species ◽  
Intermediate Morphology ◽  
Species Specific ◽  
A Site

AbstractPopulation substructure and hybridization, among other factors, have the potential to cause erroneous associations in linkage disequilibrium (LD) mapping. Two closely related spotted gum eucalypts, Corymbia variegata and C. henryi (Myrtaceae) occur in sympatry in the east coast of Australia and potentially interbreed. They are morphologically similar but are distinguished as separate species based on capsule and foliage size. To determine whether they hybridize in nature and its implications for LD mapping, we investigated the level of molecular divergence between the two species at two sympatric locations separated by 300 kilometres. Very few individuals of intermediate morphology were identified, despite the two species occurring only metres apart. Analysis of genetic structure using 12 microsatellite loci showed that genetic differentiation between populations of the same species at different locations (FST= 0.07 for both species; p = 0.0001) was significantly higher than that observed between species at each location (mean FST= 0.02 and 0.04 for Cherry tree and Bunyaville respectively; p = 0.0001; all Mann-Whitney U-test p ≤ 0.01). No species-specific alleles or significant allele frequency differences were detected within a site, suggesting recurr#ent local gene flow between the two species. The lack of significant allele frequency differences implies no population stratification along taxonomic lines. This suggested that there is little concern for cryptic hybridization when sampling from sites of sympatry for LD mapping.

scholarly journals Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kelly B. Klingler ◽  
Joshua P. Jahner ◽  
Thomas L. Parchman ◽  
Chris Ray ◽  
Mary M. Peacock
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Sierra Nevada ◽  
Spatial Genetic Structure ◽  
Spatial Scales ◽  
Thermal Sensitivity ◽  
Genomic Variation ◽  
Genome Wide ◽  
A Genome ◽  
American Pika

Abstract Background Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada. Results Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θW = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θW = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θW = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide. Conclusions Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

scholarly journals Genome diversity in Ukraine

GigaScience ◽  
2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Taras K Oleksyk ◽  
Walter W Wolfsberger ◽  
Alexandra M Weber ◽  
Khrystyna Shchubelka ◽  
Olga T Oleksyk ◽  
...  
Keyword(s):  
Sequence Data ◽  
Copy Number Variations ◽  
Genomic Variation ◽  
High Coverage ◽  
Genome Data ◽  
New Information ◽  
Genome Wide ◽  
Public Data ◽  
Genome Wide Data ◽  
Multiple Samples

Abstract Background The main goal of this collaborative effort is to provide genome-wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals representing major regions of Ukraine that were consented for public data release. BGISEQ-500 sequence data and genotypes by an Illumina GWAS chip were cross-validated on multiple samples and additionally referenced to 1 sample that has been resequenced by Illumina NovaSeq6000 S4 at high coverage. Results The genome data have been searched for genomic variation represented in this population, and a number of variants have been reported: large structural variants, indels, copy number variations, single-nucletide polymorphisms, and microsatellites. To our knowledge, this study provides the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for medical research in a large understudied population. Conclusions Our results indicate that the genetic diversity of the Ukrainian population is uniquely shaped by evolutionary and demographic forces and cannot be ignored in future genetic and biomedical studies. These data will contribute a wealth of new information bringing forth a wealth of novel, endemic and medically related alleles.

scholarly journals Intraspecific genomic variation and local adaptation in a young hybrid species

2019 ◽  
Author(s):  
Angélica Cuevas ◽  
Mark Ravinet ◽  
Glenn-Peter Sætre ◽  
Fabrice Eroukhmanoff
Keyword(s):  
Genetic Variation ◽  
Local Adaptation ◽  
Climatic Variation ◽  
Genomic Variation ◽  
Population Divergence ◽  
Parent Species ◽  
Evolutionary Potential ◽  
Variable Environment ◽  
Hybrid Species ◽  
Species Population

ABSTRACTHybridization increases genetic variation, hence hybrid species may have a strong evolutionary potential once their admixed genomes have stabilized and incompatibilities have been purged. Yet, little is known about how such hybrid lineages evolve at the genomic level following their formation, in particular the characteristics of their adaptive potential, i.e. constraints and facilitations of diversification. Here we investigate how the Italian sparrow (Passer italiae), a homoploid hybrid species, has evolved and locally adapted to its variable environment. Using restriction site-associated DNA sequencing (RAD-seq) on several populations across the Italian peninsula, we evaluate how genomic constraints and novel genetic variation have influenced population divergence and adaptation. We show that population divergence within this hybrid species has evolved in response to climatic variation. As in non-hybrid species, climatic differences may even reduce gene flow between populations, suggesting ongoing local adaptation. We report outlier genes associated with adaptation to climatic variation, known to be involved in beak morphology in other species. Most of the strongly divergent loci among Italian sparrow populations seem not to be differentiated between its parent species, the house and Spanish sparrow. Within the parental species, population divergence has occurred mostly in loci where different alleles segregate in the parent species, unlike in the hybrid, suggesting that novel combinations of parental alleles in the hybrid have not necessarily enhanced its evolutionary potential. Rather, our study suggests that constraints linked to incompatibilities may have restricted the evolution of this admixed genome, both during and after hybrid species formation.

scholarly journals Ongoing production of low-fitness hybrids limits range overlap between divergent cryptic species

2021 ◽  
Author(s):  
Else K. Mikkelsen ◽  
Darren Irwin
Keyword(s):  
First Generation ◽  
Sex Chromosome ◽  
Genomic Variation ◽  
F1 Hybrids ◽  
The Pacific ◽  
Species Pairs ◽  
Genetic Clusters ◽  
Range Overlap ◽  
Female Specific

AbstractContact zones between recently-diverged taxa provide opportunities to examine the causes of reproductive isolation and to examine the processes that determine whether two species can coexist over a broad region. The Pacific Wren (Troglodytes pacificus) and the Winter Wren (Troglodytes hiemalis) are two morphologically similar songbird species that started diverging about 4 million years ago, older than most sister species pairs. The ranges of these species come into narrow contact in western Canada, where the two species remain distinct in sympatry. To assess evidence for differentiation, hybridization, and introgression in this system, we examined variation in over 250,000 single nucleotide polymorphism markers distributed across the genomes of the two species. The two species formed highly divergent genetic clusters, consistent with long-term differentiation. In a set of 75 individuals from allopatry and sympatry, two first-generation hybrids (i.e., F1’s) were detected, indicating only moderate levels of assortative mating between these taxa. We found no recent backcrosses or F2’s or other evidence of recent breeding success of F1 hybrids, indicating very low or zero fitness of F1 hybrids. Examination of genomic variation shows evidence for only a single backcrossing event in the distant past. The sizeable rate of hybridization combined with very low fitness of F1 hybrids is expected to result in a population sink in the contact zone, largely explaining the narrow overlap of the two species. If such dynamics are common in nature, they could explain the narrow range overlap often observed between pairs of closely related species. Additionally, we present evidence for a rare duplication of a large chromosomal segment from an autosome to the W chromosome, the female-specific sex chromosome in birds.

scholarly journals Using Detection Dogs to Conduct Simultaneous Surveys of Northern Spotted (Strix occidentalis caurina) and Barred Owls (Strix varia)

PLoS ONE ◽  
2012 ◽  
Vol 7 (8) ◽  
pp. e42892 ◽  
Author(s):  
Samuel K. Wasser ◽  
Lisa S. Hayward ◽  
Jennifer Hartman ◽  
Rebecca K. Booth ◽  
Kristin Broms ◽  
...  
Keyword(s):  
Strix Occidentalis ◽  
Strix Varia ◽  
Strix Occidentalis Caurina ◽  
Barred Owls

scholarly journals Does The Presence of Barred Owls Suppress the Calling Behavior of Spotted Owls?

The Condor ◽  
2006 ◽  
Vol 108 (4) ◽  
pp. 760-769 ◽  
Author(s):  
Michelle L. Crozier ◽  
Mark E. Seamans ◽  
R. J. GutiÉRrez ◽  
Peter J. Loschl ◽  
Robert B. Horn ◽  
...  
Keyword(s):  
Calling Behavior ◽  
Field Observations ◽  
Spotted Owl ◽  
Strix Occidentalis ◽  
Response Data ◽  
Strix Varia ◽  
Spotted Owls ◽  
Strix Occidentalis Caurina ◽  
Northern Spotted Owls ◽  
Barred Owls

Abstract Abstract Barred Owls (Strix varia) have expanded their range throughout the ranges of Northern (Strix occidentalis caurina) and California Spotted Owls (S. o. occidentalis). Field observations have suggested that Barred Owls may be behaviorally dominant to Spotted Owls. Therefore, we conducted a test of behavioral dominance by assessing responsiveness of Spotted Owls to conspecific calls when they were in the simulated presence (i.e., imitation of Barred Owl vocalizations) of a Barred Owl. We hypothesized that Spotted Owls would be less likely to respond to conspecific calls in areas where Barred Owls were common. We used a binary 2 × 2 crossover experimental design to examine male Spotted Owl responses at 10 territories randomly selected within two study areas that differed in abundance of Barred Owls. We also conducted a quasi experiment at four study areas using response data from any Spotted Owl (male or female) detected following exposure to Barred Owl calls. We inferred from the crossover experiment that the simulated presence of a Barred Owl might negatively affect Spotted Owl responsiveness. Both subspecies of Spotted Owl responded less to Spotted Owl calls after exposure to Barred Owl calls, Northern Spotted Owls responded less frequently in areas having higher numbers of Barred Owls, and California Spotted Owls responded less frequently than Northern Spotted Owls overall.

scholarly journals Are Barred Owls Displacing Spotted Owls?

The Condor ◽  
2003 ◽  
Vol 105 (1) ◽  
pp. 45-53 ◽  
Author(s):  
Elizabeth G. Kelly ◽  
Eric D. Forsman ◽  
Robert G. Anthony
Keyword(s):  
Pacific Northwest ◽  
Current Status ◽  
Spotted Owl ◽  
Strix Occidentalis ◽  
Strix Varia ◽  
The Pacific ◽  
Spotted Owls ◽  
Before And After ◽  
Strix Occidentalis Caurina ◽  
Barred Owls

Abstract Barred Owls (Strix varia) have expanded their range into the Pacific Northwest, and anecdotal evidence suggests that they may be displacing the federally threatened Northern Spotted Owl (Strix occidentalis caurina). Our objectives were to describe the current status of Barred Owls in Oregon and compare occupancy of Spotted Owls in historic Spotted Owl territories before and after Barred Owls were first detected in those territories. Between 1974 and 1998, we estimated that 706 different Barred Owl territories were located in Oregon. From 1989–1998 an average of 60 new Barred Owl territories were located in Oregon each year. In Spotted Owl demographic study areas in Oregon and Washington, Barred Owl detections increased at Spotted Owl territories from 1987–1999. Occupancy of Spotted Owl territories declined after Barred Owls were detected within 0.80 km of the territory center. When Barred Owls were detected 0.81–2.40 km from Spotted Owl territory centers, occupancy of Spotted Owls was only marginally less than at territories without Barred Owls. This suggests that the frequency and intensity of interactions between the two species is negatively associated with distance between them. Our results suggest that land managers and regulatory agencies should regard Barred Owls as a threat to Spotted Owls, particularly if Barred Owls continue to increase in number as they have during the past 25 years. ¿Está Strix varia Desplazando a Strix occidentalis caurina? Resumen. Desde su expansión hacia el Pacífico Noroeste, existe evidencia anecdótica de que Strix varia podría estar desplazando a S. occidentalis caurina. Nuestros objetivos fueron describir el estatus actual de S. varia en Oregon y comparar la ocurrencia de S. occidentalis caurina en sus territorios históricos antes y después de que S. varia se detectó por primera vez en dichos territorios. Entre 1974 y 1998, estimamos que se confirmaron 706 territorios diferentes de S. varia en Oregon. Entre 1989 y 1998, se localizaron en promedio 60 nuevos territorios de S. varia anualmente. En áreas con estudios demográficos de S. occidentalis caurina en Oregon y Washington, las detecciones de S. varia en territorios de S. occidentalis caurina se incrementaron entre 1987 y 1999. En comparación con territorios sin S. varia, la ocupación de territorios de S. occidentalis caurina disminuyó luego de que se detectaron individuos de S. varia a menos de 0.80 km del centro del territorio. Cuando se detectaron individuos de S. varia entre 0.81 y 2.40 km del centro de los territorios, la ocupación de éstos fue sólo marginalmente menor que en territorios sin S. varia. Esto sugiere que la frecuencia e intensidad de la interacción entre las dos especies está asociada con la distancia entre ellas. Nuestros resultados sugieren que las autoridades ambientales y de regulación deben considerar a S. varia como una amenaza para S. occidentalis caurina, particularmente si los números de S. varia se siguen incrementando como en los últimos 25 años.

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