scholarly journals Conservation Genomic Analyses of African and Asiatic Cheetahs (Acinonyx jubatus) Across Their Current and Historical Species Range

2020 ◽  
Author(s):  
Stefan Prost ◽  
Ana Paula Machado ◽  
Julia Zumbroich ◽  
Lisa Preier ◽  
Sarita Mahtani-Williams ◽  
...  
Keyword(s):  
Mhc Class Ii ◽  
Conservation Status ◽  
Nuclear Data ◽  
East African ◽  
Acinonyx Jubatus ◽  
Original Distribution ◽  
Genome Wide ◽  
Genome Wide Data ◽  
In The Wild ◽  
Uncertain Future

SummaryCheetahs (Acinonyx jubatus) are majestic carnivores and the fastest land animals; yet, they are quickly heading towards an uncertain future. Threatened by habitat loss, human-interactions and illegal trafficking, there are only approximately 7,100 individuals remaining in the wild. Cheetahs used to roam large parts of Africa, and Western and Southern Asia. Today they are confined to about 9% of their original distribution. To investigate their genetic diversity and conservation status, we generated genome-wide data from historical and modern samples of all four currently recognized subspecies, along with mitochondrial DNA (mtDNA) and major histo-compatibility complex (MHC) data. We found clear genetic differentiation between the sub-species, thus refuting earlier assumptions that cheetahs show only little population differentiation. Our genome-wide nuclear data indicate that cheetahs from East Africa may be more closely related to A. j. soemmeringii than they are to A. j. jubatus. This supports the need for further research on the classification of cheetah subspecies, as East African cheetahs are currently included in the Southern Africa subspecies, A. j. jubatus. We detected stronger inbreeding in individuals of the Critically Endangered A. j. venaticus (Iran) and A. j. hecki (Northwest Africa), and show that overall genome-wide heterozygosity in cheetah is lower than that reported for other threatened and endangered felids, such as tigers and lions. Furthermore, we show that MHC class II diversity in cheetahs is generally higher than previously reported, but still lower than in other felids. Our results provide new and important information for efficient genetic monitoring, subspecies assignments and evidence-based conservation policy decisions.

scholarly journals Phylogenomic Reconstruction of the Neotropical Poison Frogs (Dendrobatidae) and Their Conservation

Diversity ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 126 ◽  
Author(s):  
Wilson X. Guillory ◽  
Morgan R. Muell ◽  
Kyle Summers ◽  
Jason L. Brown
Keyword(s):  
Bayesian Methods ◽  
Evolutionary History ◽  
Conservation Status ◽  
Nuclear Data ◽  
Nuclear Markers ◽  
Poison Frog ◽  
Sequence Capture ◽  
Genome Wide ◽  
Frog Species ◽  
History Of

The evolutionary history of the Dendrobatidae, the charismatic Neotropical poison frog family, remains in flux, even after a half-century of intensive research. Understanding the evolutionary relationships between dendrobatid genera and the larger-order groups within Dendrobatidae is critical for making accurate assessments of all aspects of their biology and evolution. In this study, we provide the first phylogenomic reconstruction of Dendrobatidae with genome-wide nuclear markers known as ultraconserved elements. We performed sequence capture on 61 samples representing 33 species across 13 of the 16 dendrobatid genera, aiming for a broadly representative taxon sample. We compare topologies generated using maximum likelihood and coalescent methods and estimate divergence times using Bayesian methods. We find most of our dendrobatid tree to be consistent with previously published results based on mitochondrial and low-count nuclear data, with notable exceptions regarding the placement of Hyloxalinae and certain genera within Dendrobatinae. We also characterize how the evolutionary history and geographic distributions of the 285 poison frog species impact their conservation status. We hope that our phylogeny will serve as a backbone for future evolutionary studies and that our characterizations of conservation status inform conservation practices while highlighting taxa in need of further study.

scholarly journals Iran’s roads: mitigating the most serious threat to the critically endangered Asiatic cheetah Acinonyx jubatus venaticus

2017 ◽  
Author(s):  
Jamshid Parchizadeh ◽  
Maria Gatta ◽  
Roberta Bencini ◽  
Ali Turk Qashqaei ◽  
Mohammad Ali Adibi ◽  
...  
Keyword(s):  
Road Network ◽  
Conservation Status ◽  
Critically Endangered ◽  
Evidence Based ◽  
Acinonyx Jubatus ◽  
Vehicle Collisions ◽  
Crossing Structures ◽  
In The Wild ◽  
Wildlife Populations ◽  
High Level

AbstractWildlife-vehicle collisions are an important cause of mortality for many species, and the number of collisions is expected to grow rapidly as the global road network quickly expands over the next few decades. Wildlife-vehicle collisions also have the potential to be extremely detrimental to small wildlife populations, such as the critically endangered Asiatic cheetah (Acinonyx jubatus venaticus), with only 43 individuals remaining in the wild. We assessed the spatial distribution of road mortalities between 2004 and 2016 to identify roadkill hotspots involving Asiatic cheetahs in Iran using network kernel density estimation. A total of sixteen cheetah fatalities due to wildlife-vehicle collisions were recorded, and we identified six road fragments as roadkill hotspots. Efforts to reduce wildlife-cheetah collisions should be targeted in the densest hotspots. We review the options available to achieve this, and we recommend a strategic shift away from the ineffective warning signage currently used, and instead suggest adopting an evidence-based approach focusing on installing wildlife crossing structures in conjunction with fencing in roadkill hotspots. These measures will help to enhance the conservation status of the Asiatic cheetah, as the current high level of mortality of Asiatic cheetahs on Iran’s roads could have potentially dramatic impacts on this critically endangered subspecies.

scholarly journals Genetic analysis of amyotrophic lateral sclerosis identifies contributing pathways and cell types

2021 ◽  
Vol 7 (3) ◽  
pp. eabd9036
Author(s):  
Sara Saez-Atienzar ◽  
Sara Bandres-Ciga ◽  
Rebekah G. Langston ◽  
Jonggeol J. Kim ◽  
Shing Wan Choi ◽  
...  
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Membrane Trafficking ◽  
Molecular Mechanisms ◽  
Cell Types ◽  
Polygenic Risk Score ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Data Driven Approach ◽  
Single Nucleus ◽  
Lateral Sclerosis

Despite the considerable progress in unraveling the genetic causes of amyotrophic lateral sclerosis (ALS), we do not fully understand the molecular mechanisms underlying the disease. We analyzed genome-wide data involving 78,500 individuals using a polygenic risk score approach to identify the biological pathways and cell types involved in ALS. This data-driven approach identified multiple aspects of the biology underlying the disease that resolved into broader themes, namely, neuron projection morphogenesis, membrane trafficking, and signal transduction mediated by ribonucleotides. We also found that genomic risk in ALS maps consistently to GABAergic interneurons and oligodendrocytes, as confirmed in human single-nucleus RNA-seq data. Using two-sample Mendelian randomization, we nominated six differentially expressed genes (ATG16L2, ACSL5, MAP1LC3A, MAPKAPK3, PLXNB2, and SCFD1) within the significant pathways as relevant to ALS. We conclude that the disparate genetic etiologies of this fatal neurological disease converge on a smaller number of final common pathways and cell types.

scholarly journals Ancient genomic time transect from the Central Asian Steppe unravels the history of the Scythians

2021 ◽  
Vol 7 (13) ◽  
pp. eabe4414
Author(s):  
Guido Alberto Gnecchi-Ruscone ◽  
Elmira Khussainova ◽  
Nurzhibek Kahbatkyzy ◽  
Lyazzat Musralina ◽  
Maria A. Spyrou ◽  
...  
Keyword(s):  
Bronze Age ◽  
Iron Age ◽  
Gene Pools ◽  
Social Rules ◽  
Eurasian Steppe ◽  
Central Asian ◽  
Genome Wide ◽  
Genome Wide Data ◽  
History Of ◽  
First Millennium

The Scythians were a multitude of horse-warrior nomad cultures dwelling in the Eurasian steppe during the first millennium BCE. Because of the lack of first-hand written records, little is known about the origins and relations among the different cultures. To address these questions, we produced genome-wide data for 111 ancient individuals retrieved from 39 archaeological sites from the first millennia BCE and CE across the Central Asian Steppe. We uncovered major admixture events in the Late Bronze Age forming the genetic substratum for two main Iron Age gene-pools emerging around the Altai and the Urals respectively. Their demise was mirrored by new genetic turnovers, linked to the spread of the eastern nomad empires in the first centuries CE. Compared to the high genetic heterogeneity of the past, the homogenization of the present-day Kazakhs gene pool is notable, likely a result of 400 years of strict exogamous social rules.

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 Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry

Nature ◽  
2021 ◽  
Vol 592 (7853) ◽  
pp. 253-257 ◽  
Author(s):  
Mateja Hajdinjak ◽  
Fabrizio Mafessoni ◽  
Laurits Skov ◽  
Benjamin Vernot ◽  
Alexander Hübner ◽  
...  
Keyword(s):  
Family History ◽  
East Asia ◽  
Late Pleistocene ◽  
Modern Human ◽  
Human Migration ◽  
Upper Palaeolithic ◽  
Modern Humans ◽  
Genome Wide ◽  
Genome Wide Data

AbstractModern humans appeared in Europe by at least 45,000 years ago1–5, but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago6, and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bacho Kiro Cave, Bulgaria1,2. They are the earliest Late Pleistocene modern humans known to have been recovered in Europe so far, and were found in association with an Initial Upper Palaeolithic artefact assemblage. Unlike two previously studied individuals of similar ages from Romania7 and Siberia8 who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations. This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia. Moreover, we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common.

scholarly journals Commercialization of Aframomum spp. in Africa: a Systematic Review of Literature and Supporting Botanical Vouchers

2021 ◽  
Author(s):  
Ronja Hermiene Maria Knippers ◽  
Sandrine Gallois ◽  
Tinde van Andel
Keyword(s):  
Literature Review ◽  
Conservation Status ◽  
Future Research ◽  
East African ◽  
African Countries ◽  
Wild Resources ◽  
Living Material ◽  
Specific Species ◽  
Material Information

AbstractAframomum (Zingiberaceae) is a genus of plants native to tropical Africa that are sold on African markets as spices and traditional medicine. Not all species of Aframomum are equally abundant or widespread, and no overview exists of the specific species traded or the quality of the species identifications in publications referencing the sale of Aframomum. Through a systematic literature review, we show that 14 species of Aframomum are sold in 15 African countries. The majority of the studies were done in Nigeria and Cameroon and A. melegueta was the most frequently reported species in trade. A. kayserianum was the only commercialized species with confirmed conservation issues. Our literature review shows extensive knowledge gaps regarding the commercialization of Aframomum in Africa. Most studies did not include herbarium vouchers, or only used market-sourced plant material, which impedes the possibilities for species verifications. Additionally, most East African countries were devoid of relevant research. These gaps can be bridged by future research in East Africa and voucher collection from living material. Information on the conservation status of traded Aframomum species can be obtained by population studies on wild resources and documenting local domestication efforts, as the cultivation of marketed species tends to relieve the pressure from wild resources.

scholarly journals Genome-Wide Patterns of Homozygosity Reveal the Conservation Status in Five Italian Goat Populations

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1510
Author(s):  
Salvatore Mastrangelo ◽  
Rosalia Di Gerlando ◽  
Maria Teresa Sardina ◽  
Anna Maria Sutera ◽  
Angelo Moscarelli ◽  
...  
Keyword(s):  
Conservation Status ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Local Populations ◽  
Genomic Technologies ◽  
Fitness Traits ◽  
Genome Wide ◽  
Breeding Schemes ◽  
Genomic Inbreeding

The application of genomic technologies has facilitated the assessment of genomic inbreeding based on single nucleotide polymorphisms (SNPs). In this study, we computed several runs of homozygosity (ROH) parameters to investigate the patterns of homozygosity using Illumina Goat SNP50 in five Italian local populations: Argentata dell’Etna (N = 48), Derivata di Siria (N = 32), Girgentana (N = 59), Maltese (N = 16) and Messinese (N = 22). The ROH results showed well-defined differences among the populations. A total of 3687 ROH segments >2 Mb were detected in the whole sample. The Argentata dell’Etna and Messinese were the populations with the lowest mean number of ROH and inbreeding coefficient values, which reflect admixture and gene flow. In the Girgentana, we identified an ROH pattern related with recent inbreeding that can endanger the viability of the breed due to reduced population size. The genomes of Derivata di Siria and Maltese breeds showed the presence of long ROH (>16 Mb) that could seriously impact the overall biological fitness of these breeds. Moreover, the results confirmed that ROH parameters are in agreement with the known demography of these populations and highlighted the different selection histories and breeding schemes of these goat populations. In the analysis of ROH islands, we detected harbored genes involved with important traits, such as for milk yield, reproduction, and immune response, and are consistent with the phenotypic traits of the studied goat populations. Finally, the results of this study can be used for implementing conservation programs for these local populations in order to avoid further loss of genetic diversity and to preserve the production and fitness traits. In view of this, the availability of genomic data is a fundamental resource.

scholarly journals Molecular Characterization of the Common Snook, Centropomus undecimalis (Bloch, 1792) in the Usumacinta Basin

Diversity ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 347
Author(s):  
Jazmín Terán-Martínez ◽  
Rocío Rodiles-Hernández ◽  
Marco A. A. Garduño-Sánchez ◽  
Claudia Patricia Ornelas-García
Keyword(s):  
Molecular Characterization ◽  
Conservation Status ◽  
Nuclear Data ◽  
Important Species ◽  
Common Snook ◽  
Mitochondrial Data ◽  
Haplotypic Diversity ◽  
Genetic Diversity And Structure ◽  
Genetic Clusters ◽  
The Common

The common snook is one of the most abundant and economically important species in the Usumacinta basin in the Gulf of Mexico, which has led to overfishing, threatening their populations. The main goal of the present study was to assess the genetic diversity and structure of the common snook along the Usumacinta River in order to understand the population dynamics and conservation status of the species. We characterized two mitochondrial markers (mtCox1 and mtCytb) and 11 microsatellites in the Usumacinta basin, which was divided into three zones: rainforest, floodplain and river delta. The mitochondrial data showed very low diversity, showing some haplotypic diversity differences between the rainforest and delta zones. In contrast, we consistently recovered two genetic clusters in the Usumacinta River basin with the nuclear data in both the DAPC and STRUCTURE analyses. These results were consistent with the AMOVA analyses, which showed significant differences among the genetic clusters previously recovered by DAPC and STRUCTURE. In terms of diversity distribution, the floodplain zone corresponded to the most diverse zone according to the mitochondrial and nuclear data, suggesting that this is a transition zone in the basin. Our results support the relevance of the molecular characterization and monitoring of the fishery resources at the Usumacinta River to better understand their connectivity, which could help in their conservation and management.

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