Capture and return of sexual genomes by hybridogenetic frogs provide clonal genome enrichment in a sexual species

AbstractHybridogenesis is a reproductive tool for sexual parasitism. Hybridogenetic hybrids use gametes from their sexual host for their own reproduction, but sexual species gain no benefit from such matings as their genome is later eliminated. Here, we examine the presence of sexual parasitism in water frogs through crossing experiments and genome-wide data. We specifically focus on the famous Central-European populations where Pelophylax esculentus males (hybrids of P. ridibundus and P. lessonae) live with P. ridibundus. We identified a system where the hybrids commonly produce two types of clonal gametes (hybrid amphispermy). The haploid lessonae genome is clonally inherited from generation to generation and assures the maintenance of hybrids through a process, in which lessonae sperm fertilize P. ridibundus eggs. The haploid ridibundus genome in hybrids received from P. ridibundus a generation ago, is perpetuated as clonal ridibundus sperm and used to fertilize P. ridibundus eggs, yielding female P. ridibundus progeny. These results imply animal reproduction in which hybridogenetic taxa are not only sexual parasites, but also participate in the formation of a sexual taxon in a remarkable way. This occurs through a process by which sexual gametes are being captured, converted to clones, and returned to sexual populations in one generation.

Download Full-text

Age structure, size and growth rate of water frogs from central European natural Pelophylax ridibundus-Pelophylax esculentus mixed populations estimated by skeletochronology

Amphibia-Reptilia ◽

10.1163/156853810791069119 ◽

2010 ◽

Vol 31 (2) ◽

pp. 239-250 ◽

Cited By ~ 10

Author(s):

Małgorzata Socha ◽

Maria Ogielska

Keyword(s):

Parental Species ◽

Rana Esculenta ◽

Breeding Sites ◽

Central European ◽

Water Frog ◽

Water Frogs ◽

Pelophylax Esculentus ◽

Mixed Populations ◽

The Difference ◽

European Water Frog

AbstractCentral European water frog Pelophylax esculentus (formerly known as Rana esculenta) is a natural hybrid between P. lessonae and P. ridibundus. The hybrids reproduce by hybridogenesis and usually share populations with one of the parental species. Natural ridibundus-esculentus (R-E) mixed populations are rare. The population described herein is composed of 80% P. ridibundus and 20% P. esculentus represented by both sexes. We analyzed 159 adults and 228 juveniles. Age of adults collected from breeding sites ranged from 2 to 6 years in males and from 3 to 7 years in females of both taxa. The percentage of individuals older than 5 years was low. Average age of P. ridibundus was higher than that of P. esculentus. In P. ridibundus the average age of females was higher than that of males. In P. esculentus the difference between ages of females and males was not significant. Measurements of yearly radial growth of long bones revealed that the frogs grew intensively before reaching sexual maturity (3 years for females and 2 years for males). In the group of juveniles before I hibernation, P. esculentus were significantly bigger than P. ridibundus, however, there was no difference in body size between both taxa after I hibernation i.e., before the start of a new growth season. Mean LAG-1 diameters were significantly greater in adults P. ridibundus than in juveniles after I hibernation, but not in P. esculentus.

Download Full-text

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

Science Advances ◽

10.1126/sciadv.abd9036 ◽

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.

Download Full-text

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

Science Advances ◽

10.1126/sciadv.abe4414 ◽

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.

Download Full-text

Genome diversity in Ukraine

GigaScience ◽

10.1093/gigascience/giaa159 ◽

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.

Download Full-text

Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry

Nature ◽

10.1038/s41586-021-03335-3 ◽

2021 ◽

Vol 592 (7853) ◽

pp. 253-257 ◽

Cited By ~ 3

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.

Download Full-text

PCR screening for common weak D types shows different distributions in three Central European populations

Transfusion ◽

10.1046/j.1537-2995.2001.41010045.x ◽

2001 ◽

Vol 41 (1) ◽

pp. 45-52 ◽

Cited By ~ 70

Author(s):

Thomas H. Muller ◽

Franz F. Wagner ◽

Andreas Trockenbacher ◽

Nicole I. Eicher ◽

Willy A. Flegel ◽

...

Keyword(s):

Pcr Screening ◽

Central European ◽

European Populations

Download Full-text

Endoparasitic helminths of water frog complex in Poland: do differences exist between the parental species Pelophylax ridibundus and Pelophylax lessonae, and their natural hybrid Pelophylax esculentus?

Helminthologia ◽

10.2478/s11687-011-0020-8 ◽

2011 ◽

Vol 48 (2) ◽

pp. 108-115 ◽

Cited By ~ 4

Author(s):

M. Popiołek ◽

B. Rozenblut-Kościsty ◽

M. Kot ◽

W. Nosal ◽

M. Ogielska

Keyword(s):

20Th Century ◽

Parental Species ◽

Helminth Species ◽

Natural Hybrid ◽

Intensity Of Infection ◽

Water Frog ◽

Pelophylax Ridibundus ◽

Water Frogs ◽

Pelophylax Esculentus ◽

Cosmocerca Ornata

AbstractParasitic fauna of water frogs was mainly studied in the second half of the 20th century. However, these studies were done without differentiation into species and hybrids and pooled the 3 taxa as “water frogs” or “green frogs”. The aim of this study was to make an inventory of helminth species as well as their prevalence and intensity of infection in the two parental species (Pelophylax ridibundus and P. lessonae) and the hybrid (P. esculentus) of water frogs from 3 big populations composed of hundreds or thousands of individuals inhabited natural and seminatural landscapes in Poland. Eight helminth species were found: Polystoma integerrimum, Diplodiscus subclavatus, Opisthoglyphe ranae, Gorgodera cygnoides, Haematoloechus variegatus, Oswaldocruzia filiformis, Cosmocerca ornata and Acanthocephalus ranae. The results were compared with data from other, polish and European studies. Additionally we compared the level of infection among water frog taxa.

Download Full-text

Genome-wide association study for early-onset and morbid adult obesity identifies three new risk loci in European populations

Nature Genetics ◽

10.1038/ng.301 ◽

2009 ◽

Vol 41 (2) ◽

pp. 157-159 ◽

Cited By ~ 454

Author(s):

David Meyre ◽

Jérôme Delplanque ◽

Jean-Claude Chèvre ◽

Cécile Lecoeur ◽

Stéphane Lobbens ◽

...

Keyword(s):

Association Study ◽

Early Onset ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Adult Obesity ◽

Genome Wide ◽

European Populations

Download Full-text

A curated dataset of modern and ancient high-coverage shotgun human genomes

Scientific Data ◽

10.1038/s41597-021-00980-1 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Pierpaolo Maisano Delser ◽

Eppie R. Jones ◽

Anahit Hovhannisyan ◽

Lara Cassidy ◽

Ron Pinhasi ◽

...

Keyword(s):

Sequence Data ◽

Whole Genome ◽

Reference Dataset ◽

High Coverage ◽

Sample Distribution ◽

Human Samples ◽

Human Genomes ◽

Genome Wide ◽

Genome Wide Data ◽

Computationally Intensive

AbstractOver the last few years, genome-wide data for a large number of ancient human samples have been collected. Whilst datasets of captured SNPs have been collated, high coverage shotgun genomes (which are relatively few but allow certain types of analyses not possible with ascertained captured SNPs) have to be reprocessed by individual groups from raw reads. This task is computationally intensive. Here, we release a dataset including 35 whole-genome sequenced samples, previously published and distributed worldwide, together with the genetic pipeline used to process them. The dataset contains 72,041,355 sites called across 19 ancient and 16 modern individuals and includes sequence data from four previously published ancient samples which we sequenced to higher coverage (10–18x). Such a resource will allow researchers to analyse their new samples with the same genetic pipeline and directly compare them to the reference dataset without re-processing published samples. Moreover, this dataset can be easily expanded to increase the sample distribution both across time and space.

Download Full-text