Genomic analyses reveal range‐wide devastation of sea otter populations

2021 ◽  
Author(s):  
Annabel C. Beichman ◽  
Pooneh Kalhori ◽  
Christopher C. Kyriazis ◽  
Amber A. DeVries ◽  
Sergio Nigenda‐Morales ◽  
...  
Keyword(s):  
Sea Otter ◽  
Genomic Analyses

Characterizing the impact of recovering sea otters on commercially important crabs in California estuaries

2020 ◽  
Vol 655 ◽  
pp. 123-137
Author(s):  
TM Grimes ◽  
MT Tinker ◽  
BB Hughes ◽  
KE Boyer ◽  
L Needles ◽  
...  
Keyword(s):  
Abiotic Factors ◽  
Sea Otter ◽  
Dungeness Crab ◽  
Sea Otters ◽  
Elkhorn Slough ◽  
Enhydra Lutris Nereis ◽  
Crab Abundance ◽  
Population Sizes ◽  
Commercially Important ◽  
The Impact

Protective legislation and management have led to an increase in California’s sea otter Enhydra lutris nereis population. While sea otter recovery has been linked to ecosystem benefits, sea otter predation may negatively affect commercially valuable species. Understanding the potential influence of sea otters is of particular importance as their range expands into estuaries that function as nurseries for commercially valuable species like Dungeness crab Metacarcinus magister. We consider how sea otter predation has affected the abundance and size of juvenile Dungeness crab in Elkhorn Slough, California, USA, and analyzed cancrid crab abundance and size across 4 California estuaries with and without sea otters to understand how biotic and abiotic factors contribute to observed variation in crab size and abundance. We compared trends in southern sea otters relative to Dungeness crab landings in California to assess whether increasing sea otter abundance have negatively impacted landings. In Elkhorn Slough, juvenile Dungeness crab abundance and size have declined since 2012, coinciding with sea otter population growth. However, the impact of sea otters on juvenile Dungeness crab size was habitat-specific and only significant in unvegetated habitat. Across estuaries, we found that cancrid crab abundance and size were negatively associated with sea otter presence. While abiotic factors varied among estuaries, these factors explained little of the observed variation in crab abundance or size. Although we found evidence that sea otters can have localized effects on cancrid crab populations within estuaries, we found no evidence that southern sea otters, at recent population sizes, have negatively impacted Dungeness crab landings in California from 2000-2014.

Technological advances in single-cell genomic analyses

2011 ◽  
Vol 33 (1) ◽  
pp. 17-24 ◽  
Author(s):  
Xing-Hua PAN ◽  
Hai-Ying ZHU ◽  
Sadie L MARJANI
Keyword(s):  
Single Cell ◽  
Technological Advances ◽  
Genomic Analyses

Genomic Analyses Reveal Genetic Adaptations to Tropical Climates in Chickens

2020 ◽  
Author(s):  
Shilin Tian ◽  
Xuming Zhou ◽  
Dejing Zhang ◽  
Chunyou Ning ◽  
Diyan Li ◽  
...  
Keyword(s):  
Genomic Analyses ◽  
Tropical Climates

scholarly journals The historical and contemporary status of the sea otter Enhydra lutris population on Urup Island, southern Kuril Islands

Oryx ◽  
2021 ◽  
pp. 1-6
Author(s):  
Igor Popov ◽  
Alexey Scopin
Keyword(s):  
Total Population ◽  
Kuril Islands ◽  
Sea Otter ◽  
Enhydra Lutris ◽  
Sea Otters ◽  
The Past ◽  
Remote Island ◽  
Contemporary Status ◽  
Wildlife Refuges ◽  
Effective Conservation

Abstract We describe the population of the Еndangered sea otter Enhydra lutris on Urup Island, one of the main wildlife refuges in the southern Kuril Islands of Russia. We reviewed historical and local reports of the sea otter, identified its habitat around the island, and surveyed the coastal waters of the island in 2019. Sea otters were numerous on Urup Island in the past but were hunted excessively and almost exterminated by the 1950s. Since then, sea otter populations have increased, and as the island is almost uninhabited we expected otters to be numerous. This was not the case, and we estimated the total population to be 363 ± SE 126 individuals. Our observation of two skinned carcasses on the shore suggests the low numbers are a result of poaching for the illegal fur trade. The case of Urup Island demonstrates that sea otters require active conservation, as even on a remote island they remain threatened. Establishment of protected areas would be an effective conservation measure for this species, although the suppression of demand for sea otter fur is of the greatest importance.

scholarly journals High-Altitude Adaptation: Mechanistic Insights from Integrated Genomics and Physiology

2021 ◽  
Author(s):  
Jay F Storz
Keyword(s):  
High Altitude ◽  
Hypoxia Inducible Factor ◽  
Feedback Regulation ◽  
Genomic Analyses ◽  
Manipulative Experiments ◽  
Altitude Adaptation ◽  
Mechanisms Of Adaptation ◽  
Physiological Pathways ◽  
Underlying Mechanisms ◽  
Integrated Genomics

AbstractPopulation genomic analyses of high-altitude humans and other vertebrates have identified numerous candidate genes for hypoxia adaptation, and the physiological pathways implicated by such analyses suggest testable hypotheses about underlying mechanisms. Studies of highland natives that integrate genomic data with experimental measures of physiological performance capacities and subordinate traits are revealing associations between genotypes (e.g., hypoxia-inducible factor gene variants) and hypoxia-responsive phenotypes. The subsequent search for causal mechanisms is complicated by the fact that observed genotypic associations with hypoxia-induced phenotypes may reflect second-order consequences of selection-mediated changes in other (unmeasured) traits that are coupled with the focal trait via feedback regulation. Manipulative experiments to decipher circuits of feedback control and patterns of phenotypic integration can help identify causal relationships that underlie observed genotype–phenotype associations. Such experiments are critical for correct inferences about phenotypic targets of selection and mechanisms of adaptation.

scholarly journals Genetic Contribution of Endometriosis to the Risk of Developing Hormone-Related Cancers

2021 ◽  
Vol 22 (11) ◽  
pp. 6083
Author(s):  
Aintzane Rueda-Martínez ◽  
Aiara Garitazelaia ◽  
Ariadna Cilleros-Portet ◽  
Sergi Marí ◽  
Rebeca Arauzo ◽  
...  
Keyword(s):  
Mendelian Randomization ◽  
Clear Cell ◽  
Association Studies ◽  
Epidemiological Data ◽  
Epidemiological Studies ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Genomic Analyses ◽  
Gynecological Disorder ◽  
Robust Evidence

Endometriosis is a common gynecological disorder that has been associated with endometrial, breast and epithelial ovarian cancers in epidemiological studies. Since complex diseases are a result of multiple environmental and genetic factors, we hypothesized that the biological mechanism underlying their comorbidity might be explained, at least in part, by shared genetics. To assess their potential genetic relationship, we performed a two-sample mendelian randomization (2SMR) analysis on results from public genome-wide association studies (GWAS). This analysis confirmed previously reported genetic pleiotropy between endometriosis and endometrial cancer. We present robust evidence supporting a causal genetic association between endometriosis and ovarian cancer, particularly with the clear cell and endometrioid subtypes. Our study also identified genetic variants that could explain those associations, opening the door to further functional experiments. Overall, this work demonstrates the value of genomic analyses to support epidemiological data, and to identify targets of relevance in multiple disorders.

scholarly journals The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Josué Barrera-Redondo ◽  
Guillermo Sánchez-de la Vega ◽  
Jonás A. Aguirre-Liguori ◽  
Gabriela Castellanos-Morales ◽  
Yocelyn T. Gutiérrez-Guerrero ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Population Level ◽  
Growth Hormones ◽  
Comparative Genomic ◽  
Structural Variants ◽  
Closely Related Species ◽  
Level Data ◽  
Genomic Analyses ◽  
Genotype By Sequencing ◽  
Regulation Of Growth

AbstractDespite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study Cucurbita domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of C. argyrosperma across Mexico. We also assembled the first high-quality wild Cucurbita genome. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We found evidence of gene flow between the domesticated and wild subspecies, which likely alleviated the effects of the domestication bottleneck. We uncovered candidate domestication genes that are involved in the regulation of growth hormones, plant defense mechanisms, seed development, and germination. The presence of shared selected alleles with the closely related species Cucurbita moschata suggests domestication-related introgression between both taxa.

Complete chloroplast genomes of Leptodermis scabrida complex: comparative genomic analyses and phylogenetic relationships

Gene ◽  
2021 ◽  
pp. 145715
Author(s):  
Ying Zhang ◽  
Zhengfeng Wang ◽  
Yanan Guo ◽  
Sheng Chen ◽  
Xianyi Xu ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Comparative Genomic ◽  
Chloroplast Genomes ◽  
Genomic Analyses

scholarly journals Integrative analysis of histomorphology, transcriptome and whole genome resequencing identified DIO2 gene as a crucial gene for the protuberant knob located on forehead in geese

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yan Deng ◽  
Shenqiang Hu ◽  
Chenglong Luo ◽  
Qingyuan Ouyang ◽  
Li Li ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Protein Secondary Structure ◽  
Genomic Analysis ◽  
Production Performance ◽  
Genetic Mechanism ◽  
Farm Animals ◽  
Practical Significance ◽  
Genome Resequencing ◽  
Genomic Analyses ◽  
Whole Genome Resequencing

Abstract Background During domestication, remarkable changes in behavior, morphology, physiology and production performance have taken place in farm animals. As one of the most economically important poultry, goose owns a unique appearance characteristic called knob, which is located at the base of the upper bill. However, neither the histomorphology nor the genetic mechanism of the knob phenotype has been revealed in geese. Results In the present study, integrated radiographic, histological, transcriptomic and genomic analyses revealed the histomorphological characteristics and genetic mechanism of goose knob. The knob skin was developed, and radiographic results demonstrated that the knob bone was obviously protuberant and pneumatized. Histologically, there were major differences in structures in both the knob skin and bone between geese owing knob (namely knob-geese) and those devoid of knob (namely non-knob geese). Through transcriptome analysis, 592 and 952 genes differentially expressed in knob skin and bone, and significantly enriched in PPAR and Calcium pathways in knob skin and bone, respectively, which revealed the molecular mechanisms of histomorphological differences of the knob between knob- and non-knob geese. Furthermore, integrated transcriptomic and genomic analysis contributed to the identification of 17 and 21 candidate genes associated with the knob formation in the skin and bone, respectively. Of them, DIO2 gene could play a pivotal role in determining the knob phenotype in geese. Because a non-synonymous mutation (c.642,923 G > A, P265L) changed DIO2 protein secondary structure in knob geese, and Sanger sequencing further showed that the AA genotype was identified in the population of knob geese, and was prevalent in a crossing population which was artificially selected for 10 generations. Conclusions This study was the first to uncover the knob histomorphological characteristics and genetic mechanism in geese, and DIO2 was identified as the crucial gene associated with the knob phenotype. These data not only expand and enrich our knowledge on the molecular mechanisms underlying the formation of head appendages in both mammalian and avian species, but also have important theoretical and practical significance for goose breeding.

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