scholarly journals Genome-wide markers redeem the lost identity of a heavily managed gamebird

2021 ◽  
Vol 288 (1947) ◽  
Author(s):  
Giovanni Forcina ◽  
Qian Tang ◽  
Emilie Cros ◽  
Monica Guerrini ◽  
Frank E. Rheindt ◽  
...  
Keyword(s):  
Management Practices ◽  
Natural Populations ◽  
Introgressive Hybridization ◽  
Alectoris Rufa ◽  
Evolutionary Potential ◽  
Biodiversity Crisis ◽  
Genome Wide ◽  
Intraspecific Structure ◽  
Intensively Managed ◽  
Chukar Partridge

Heavily managed wildlife may suffer from genetic homogenization and reshuffling of locally adapted genotypes with non-native ones. This phenomenon often affects natural populations by reducing their evolutionary potential and speeding up the ongoing biodiversity crisis. For decades, the red-legged partridge ( Alectoris rufa ), an intensively managed gamebird of conservation concern and considerable socio-economic importance, has been subjected to extensive releases of farm-reared hybrids with the chukar partridge ( Alectoris chukar ) and translocations irrespective of subspecific affinity. These practices have led to serious concerns that the genetic integrity and biogeographic structure of most red-legged partridge populations are irreversibly affected, as suggested by previous studies based on few genetic markers. Using over 168 000 genome-wide loci and a sampling across the entire A. rufa range, we detected unexpectedly limited and spatially uneven chukar introgression as well as significant intraspecific structure. We demonstrate that species widely feared to have irretrievably lost their genetic identity are likely to be much less affected by unsuitable management practices than previously assumed. Our results spell the need for a radical re-think on animal conservation, possibly restoring native status to populations long treated as compromised. Our study exemplifies how the application of innovative conservation-genomic methods is key to solving wildlife management problems dealing with introgressive hybridization worldwide.

scholarly journals The Genetic Architecture of Ovariole Number in Drosophila melanogaster: Genes with Major, Quantitative, and Pleiotropic Effects

2017 ◽  
Vol 7 (7) ◽  
pp. 2391-2403 ◽  
Author(s):  
Amanda S Lobell ◽  
Rachel R Kaspari ◽  
Yazmin L Serrano Negron ◽  
Susan T Harbison
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Natural Populations ◽  
Direct Role ◽  
Genome Wide ◽  
A Genome ◽  
Fitness Trait ◽  
Sleep Parameters ◽  
Activity Behavior ◽  
Ovariole Number

Abstract Ovariole number has a direct role in the number of eggs produced by an insect, suggesting that it is a key morphological fitness trait. Many studies have documented the variability of ovariole number and its relationship to other fitness and life-history traits in natural populations of Drosophila. However, the genes contributing to this variability are largely unknown. Here, we conducted a genome-wide association study of ovariole number in a natural population of flies. Using mutations and RNAi-mediated knockdown, we confirmed the effects of 24 candidate genes on ovariole number, including a novel gene, anneboleyn (formerly CG32000), that impacts both ovariole morphology and numbers of offspring produced. We also identified pleiotropic genes between ovariole number traits and sleep and activity behavior. While few polymorphisms overlapped between sleep parameters and ovariole number, 39 candidate genes were nevertheless in common. We verified the effects of seven genes on both ovariole number and sleep: bin3, blot, CG42389, kirre, slim, VAChT, and zfh1. Linkage disequilibrium among the polymorphisms in these common genes was low, suggesting that these polymorphisms may evolve independently.

Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations ofPopulus trichocarpa

2014 ◽  
Vol 203 (2) ◽  
pp. 535-553 ◽  
Author(s):  
Athena D. McKown ◽  
Jaroslav Klápště ◽  
Robert D. Guy ◽  
Armando Geraldes ◽  
Ilga Porth ◽  
...  
Keyword(s):  
Natural Populations ◽  
Genome Wide Association ◽  
Trait Variation ◽  
Genome Wide

To what extent do microsatellite markers reflect genome-wide genetic diversity in natural populations?

2008 ◽  
Vol 17 (17) ◽  
pp. 3808-3817 ◽  
Author(s):  
ÜLO VÄLI ◽  
ANNIKA EINARSSON ◽  
LISETTE WAITS ◽  
HANS ELLEGREN
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Natural Populations ◽  
Genome Wide

scholarly journals Elevated virulence of an emerging viral genotype as a driver of honeybee loss

2016 ◽  
Vol 283 (1833) ◽  
pp. 20160811 ◽  
Author(s):  
Dino P. McMahon ◽  
Myrsini E. Natsopoulou ◽  
Vincent Doublet ◽  
Matthias Fürst ◽  
Silvio Weging ◽  
...  
Keyword(s):  
Emerging Infectious Diseases ◽  
Genetic Identity ◽  
Accurate Identification ◽  
Deformed Wing Virus ◽  
Species Decline ◽  
Biodiversity Crisis ◽  
Pathogen Virulence ◽  
Population Loss ◽  
Genome Wide

Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo . The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline.

scholarly journals Population Genetics and Evolution Analysis Reveal Diversity and Origin of Ammopiptanthus in China.

2021 ◽  
Author(s):  
Guai-qiang Chai ◽  
Yizhong Duan ◽  
Peipei Jiao ◽  
Zhongyu Du ◽  
Furen Kang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Association Studies ◽  
Natural Populations ◽  
Principal Component ◽  
Nucleotide Polymorphisms ◽  
Future Design ◽  
Ammopiptanthus Nanus ◽  
Genome Wide

Abstract Background：Elucidating and revealing the population genetic structure, genetic diversity and recombination is essential for understanding the evolution and adaptation of species. Ammopiptanthus, which is an endangered survivor from the Tethys in the Tertiary Period, is the only evergreen broadleaf shrub grown in Northwest of China. However, little is known about its genetic diversity and underlying adaptation mechanisms. Results：Here, 111 Ammopiptanthus individuals collected from fifteen natural populations in estern China were analyzed by means of the specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) detected by SLAF-seq, genetic diversity and markers associated with climate and geographical distribution variables were identified. The results of genetic diversity and genetic differentiation revealed that all fifteen populations showed medium genetic diversity, with PIC values ranging from 0.1648 to 0.3081. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Phylogenetic analysis showed that NX-BG and NMG-DQH of fifteen populations have the highest homology，while the genetic structure analysis revealed that these Ammopiptanthus germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in each group. In addition, the genome-wide linkage disequilibrium (LD) and principal component analysis showed that Ammopiptanthus nanus had a more diverse genomic background, and all genetic populations were clearly distinguished, although different degrees of introgression were detected in these groups. Conclusion：Our study could provide guidance to the future design of association studies and the systematic utilization and protection of the genetic variation characterizing the Ammopiptanthus.

scholarly journals Genome-wide characterization of genetic diversity and population structure of Valeriana officinalis L.

2019 ◽  
Author(s):  
Maja Boczkowska ◽  
Katarzyna Bączek ◽  
Olga Kosakowska ◽  
Anna Rucińska ◽  
Wiesław Podyma ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Genomics ◽  
Natural Populations ◽  
Valeriana Officinalis ◽  
Wild Populations ◽  
Genetic Fingerprint ◽  
Genome Wide ◽  
Species Population ◽  
Outcrossing Species

Abstract Background: Valeriana officinalis L. is one of the most important medicinal plant with a mild sedative, nervine, antispasmodic and relaxant effect. Despite a substantial number of studies on this species, population genomics has not yet been analyzed. The main aim of this study was: characterization of genetic variation of natural populations of V. officinalis in Poland and comparison of variation of wild populations and the cultivated form using Next Generation Sequencing based DArTseq technique. We also would like to establish foundations for genetic monitoring of the species in the future and to develop genetic fingerprint profile for samples deposited in gene bank and in natural sites in order to assess the degree of their genetic integrity and population structure preservation in the future.Results: The major and also the most astounding result of our work is the low level of observed heterozygosity of individual plants from natural populations despite the fact that the species is widespread in the studied area. Inbreeding, in naturally outcrossing species such as valerian, decreases the reproductive success. The analysis of the population structure indicated the potential presence of metapopulation in a broad area of Poland and the formation of a distinct gene pool in Bieszczady Mountains. The results also indicate the presence of individuals of the cultivated form in natural populations in the region where the species is cultivated for the needs of the pharmaceutical industry and this could lead to structural and genetic imbalance in wild populations.Conclusions: The DArTseq technology can be applied effectively in genetic studies of V. officinalis. The genetic variability of wild populations is in fact significantly lower than assumed. Individuals from the cultivated population are found in the natural environment and their impact on wild populations should be monitored.

scholarly journals The crucial role of genome-wide genetic variation in conservation

2021 ◽  
Vol 118 (48) ◽  
pp. e2104642118
Author(s):  
Marty Kardos ◽  
Ellie E. Armstrong ◽  
Sarah W. Fitzpatrick ◽  
Samantha Hauser ◽  
Philip W. Hedrick ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Environmental Changes ◽  
Population Viability ◽  
Adaptive Potential ◽  
Biodiversity Crisis ◽  
Genome Wide ◽  
Simulation Based ◽  
Functional Genetic Variation

The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation biology has placed too much focus on conserving genome-wide genetic variation, and that the field should instead focus on managing the subset of functional genetic variation that is thought to affect fitness. Here, we critically evaluate the feasibility and likely benefits of this approach in conservation. We find that population genetics theory and empirical results show that conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential from driving populations toward extinction. Focusing conservation efforts on presumably functional genetic variation will only be feasible occasionally, often misleading, and counterproductive when prioritized over genome-wide genetic variation. Given the increasing rate of habitat loss and other environmental changes, failure to recognize the detrimental effects of lost genome-wide genetic variation on long-term population viability will only worsen the biodiversity crisis.

scholarly journals Distribution and Demographics of Fuchsia Excorticata, Nelson Lakes National Park

2021 ◽  
Author(s):  
◽  
Edward Rex Lancelot Bartholomew
Keyword(s):  
National Park ◽  
Animal Species ◽  
Management Practices ◽  
Reference Area ◽  
Reference Sites ◽  
Ecological Changes ◽  
Significant Difference ◽  
Management Area ◽  
Intensively Managed ◽  
Reference Areas

<p>The small tree Fuchsia excorticata (Onagraceae) is found on disturbed riparian sites throughout New Zealand. Spatial distribution and  demographic changes in populations of F. excorticata were surveyed in the Rotoiti Nature Recovery Project (RNRP) area, and an associated non-treatment reference area, Nelson Lakes National Park, over the period 2005 to 2007. The RNRP is an intensively managed "mainland island" project in mixed beech (Nothofagus) forest, pest animal species especially possums (Trichosurus vulpecula), rodents, and mustelids are controlled. The aim of this study was to survey the condition of F. excorticata in the managed and reference areas to determine if any differences could be detected between the populations over time. The only significant (p<0.05) difference between the two areas was in sapling abundance, which was higher in the RNRP management area. This was tentatively attributed to pest management; however the concurrence of complex  environmental influences, and a lack of management replication, prevented a simple interpretation of the data. There was no significant difference in recruitment, growth, mortality, and tree or seedling abundance  between the managed and reference areas. Growth rate, especially of saplings, was significantly greater at lower elevations in the RNRP managed area, however the inverse held for the reference area. Mammalian herbivory was light; the main affect being to restrict seedling growth through hedging. Periodic heavy flooding was responsible for much of the mortality, however many newly disturbed sites were rapidly populated with fuchsia seedlings. The need for rigour in establishing ecologically comparable reference sites for comparative studies was evident. There were inherent difficulties in establishing causal relationships between ecological changes and management practices where management was not replicated geographically.</p>

scholarly journals Spatio-temporal ecological and evolutionary dynamics in natural butterfly populations

2017 ◽  
Vol 40 ◽  
pp. 31-36
Author(s):  
Zachariah Gompert ◽  
Lauren Lucas
Keyword(s):  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Distance Sampling ◽  
Spatial And Temporal Variation ◽  
Insect Community ◽  
Long Term Study ◽  
Greater Yellowstone Area ◽  
Genome Wide ◽  
Spatio Temporal

Long term studies of wild populations indicate that natural selection can cause rapid and dramatic changes in traits, with spatial and temporal variation in the strength of selection a critical driver of genetic variation in natural populations. In 2012, we began a long term study of genome-wide molecular evolution in populations of the butterfly Lycaeides ideas in the Greater Yellowstone Area (GYA). We aimed to quantify the role of environment-dependent selection on evolution in these populations. Building on previous work, in 2017 we collected new samples, incorporated distance sampling, and surveyed the insect community at each site. We also defined the habitat boundary at anew, eleventh site. Our preliminary analyses suggest that both genetic drift and selection are important drivers in this system.   Featured photo from Figure 1 in report.

Hybridization in leopard frogs (Rana pipiens complex): terrestrial performance of newly metamorphosed hybrid and parental genotypes in field enclosures

2001 ◽  
Vol 79 (9) ◽  
pp. 1552-1558 ◽  
Author(s):  
Matthew J Parris
Keyword(s):  
Growth Rates ◽  
Life Histories ◽  
Parental Species ◽  
Natural Populations ◽  
Life Cycles ◽  
Natural Hybridization ◽  
Evolutionary Potential ◽  
Leopard Frogs ◽  
Rana Blairi ◽  
Advanced Generation

Terrestrial ecology has been largely neglected in the study of amphibian life histories because it is difficult to manipulate most species during the terrestrial stage. I examined the terrestrial performance of Rana blairi, Rana sphenocephala, and four hybrid (two F1 and two advanced generation) genotypes in replicated experimental enclosures to test for differences in traits related to juvenile terrestrial fitness. I produced all genotypes by means of artificial fertilizations using frogs collected from natural populations in central Missouri, and juvenile frogs were obtained from larvae reared in experimental ponds. Following metamorphosis, froglets were raised in single-genotype groups in terrestrial enclosures through the first overwintering. The proportion surviving did not vary among genotypes, but the power to detect significant differences was low. F1 hybrid genotypes BS and SB demonstrated significantly higher growth rates than either parental species or advanced-generation hybrid genotypes. Observation of growth rates of advanced-generation hybrids equal to those of the parental species, and heterosis in F1 hybrids for growth rate, suggests that natural hybridization between R. blairi and R. sphenocephala can produce novel and relatively fit hybrid genotypes. Direct measurement of multiple fitness components for hybrid and parental genotypes is critical for assessing the evolutionary potential of natural hybridization in organisms with complex life cycles.

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