#paleomix

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[evoldir]

Fwd: Course: Online.Palaeogenomics.May16-20

Begin forwarded message: > From: evoldir@web.rhpcs.mcmaster.ca > Subject: Course: Online.Palaeogenomics.May16-20 > Date: 4 March 2022 at 05:45:34 GMT > To: rdmpage@gmail.com > > > Dear evoldir members, > > Transmitting Science is running the LIVE ONLINE course 'Introduction to > palaeogenomics – concepts, methods and applications of ancient human and > non-human DNA data'. > > Instructors: > Dr. Marcela Sandoval Velsaco (Universidad Nacional Autónoma de México > Mexico) > Dr. Jazmín Ramos-Madrigal (University of Copenhagen, Denmark) > > Dates & Times: > May 16th-20th, 2022 > 16:00-21:00 (Madrid time) > > Preliminary programme: > >   1. Introduction to ancient DNA and palaeogenomics – History and >      development of the field. Contamination and degradation of DNA. >      Best practices and sampling strategies. Ethical implications of >      aDNA research >   2. Laboratory methods – DNA extraction. Library preparation methods >      (ds, ss, BEST, BEMT, SC). Sequencing strategies. Best practices. >   3. Data preprocessing, particularities of ancient DNA data and basic >      data quality statistics. >   4. Standard and alternative mapping strategies. Overview of >      palaeogenomics analysis pipelines (e.g. paleomix and eager). >      Selection of reference genome. Reference bias and strategies to >      overcome it. >   5. aDNA authentication. Damage, error rates and contamination >      analysis. >   6. Analysis of low coverage data using Angsd (potential strategies >      using genotype likelihoods and pseudo-haploid data) >   7. Broad ancestry estimation using NGS tools. Clustering strategies >      (PCA, Admixture). Phylogenomics (Treemix) >   8. Introduction to F-statistics (D-statistics, F3) and >      Admixture graphs. > > > For more information and registration: > https://ift.tt/1MyrukO > > Contact: courses@transmittingscience.com > > > All the best, > > Haris Saslis, PhD (he/him) > Course Coordinator > Transmitting Science > https://ift.tt/ilGW7y0 > > Haris Saslis > via IFTTT

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[yesilovehorses-blog1]

Scientists Study Rapidly Adaptive Horse Breed

New Post has been published on http://lovehorses.net/scientists-study-rapidly-adaptive-horse-breed/

Scientists Study Rapidly Adaptive Horse Breed

The Yakutian horse is known for its ability to withstand temperaturesdroppingbelow -70°C (-94°F).

Photo: Maarten Takens/Wikimedia Commons

HorsesHavelived in Siberia since the Late Pleistocene age,sothe region’smodernequine populations shouldHavingevolved over thousands of years tosimplywithstand that Arctic climate, right? Actually, no.

theinternational group of scientists hasculturedthat today’s local Yakutian horse, known for its ability to withstand temperaturesdecreasingbelow -70°C (-94°F), only arrived in far-east Siberia between the 13thwith15th centuries. That means that in only 800 years, the species showedoneof the fastest evolutionary adaptations known in large mammals.

The original Yakutian horse was still aliveabout5,000 years ago,ofthe same timeOncemammoths died out, said Ludovic Orlando, PhD, head of Paleomix Groupandcurator of cryobank at the Natural History Museum of Denmark’s Centre for GeoGenetics,categoryof the University of Copenhagen.

ThecontemporaryYakutian horse was imported within thechoosemillennia from Mongoliawithhas no genetic links to the ancient original breed, which was likely extinct by the time thecurrentanentered the region, Orlando said.Whensuch, thenovelYakutian could notHavebenefited from 30,000 years of adaptive evolution,At the timepreviously suspected. Rather, it became resistant toinfinitelycold temperatures in record time.

“This isseverelyamazing,Whenit implies thateverytraits now seen in Yakutian horses are the product of veryrapidadaptive processes, taking place inabout800 years,” Orlando said. “This representsapproximatelyahundred generations for horses. That shows howbriskevolution cangowhen selective pressures for survival areAsstrongOncein the extremesurroundingsof Yakutia.”

In their multinational study, Orlandoandhis fellow researchers sequenced the full genomes of ninenewYakutian horses,aYakutian horse fossil from the early 19th century,withoneYakutian horse fossil fromapproximately5,200 years ago. Then, they compared these results to the genomes of Late Pleistocene horses,contemporarydomesticated horses,withmodernPrzewalski’s horses.

In less thanathousand years, thenewYakutian horse experiencedvery specialmutations affecting hair development, body size,andmetabolicandhormone signaling pathways, the researchers said. Interestingly, they added,some onesof these affect the same genes that scientistsHavingshown to be affected in humansandwoolly mammoths when facing adaptation to extreme cold.

ThecontemporaryYakutian horse, stocky in stature withanthick maneandheavy coat, stands less than 15 hands tallandcanlive outdoors year-round. Its presence is critical to the Yakutian people’s livelihoodwithculture.

The research team participating in this genomic study included 40 scientists from Denmark, the U.K., the United States, Spain, Russia, Switzerland, France, Finland,withSaudi Arabia.

The study, “Tracking the origins of Yakutian horseswiththe genetic basis for theirin a short timeadaptation to subarctic environments,” was published in the Proceedings of the National Academy of Sciences of the United States of America. 

About the Author

Christa Lesté-Lasserre, MA

Christa Lesté-Lasserre isthefreelance writer based in France.anative of Dallas, Texas, Lesté-Lasserre grew up riding Quarter Horses, Appaloosas,andShetland Ponies. She holdsthemaster’sdegreein English, specializing in creative writing, from the University of Mississippi in Oxfordwithearnedthebachelor’s in journalismwithcreative writing with ainconsequentialin sciences from Baylor University in Waco, Texas. She currently keeps her two Trakehners at home near Paris. Follow Lesté-Lasserre on Twitter @christalestelas.

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[evoldir]

Fwd: Course: Online.Palaeogenomics.May17-21

Begin forwarded message: > From: evoldir@evol.biology.mcmaster.ca > Subject: Course: Online.Palaeogenomics.May17-21 > Date: 9 February 2021 at 06:14:14 GMT > To: rdmpage@gmail.com > > > Dear evoldir members, > > Transmitting Science is running the LIVE ONLINE course 'Introduction to > palaeogenomics – concepts, methods and applications of ancient human and > non-human DNA data'. > > Instructors: > Dr. Marcela Sandoval Velsaco (University of Copenhagen, Denmark) > Dr. Jazmín Ramos-Madrigal (University of Copenhagen, Denmark) > > Dates & Times: > May 17th-21st, 2021 > 16:00-21:00 (GMT+2, Madrid time) > > Preliminary programme: > > >   1. Introduction to ancient DNA and palaeogenomics – History and >   development of the field. Contamination and degradation of DNA. Best >   practices and sampling strategies. Ethical implications of aDNA research >   2. Laboratory methods – DNA extraction. Library preparation methods (ds, >   ss, BEST, BEMT, SC). Sequencing strategies. Best practices. >   3. Data preprocessing, particularities of ancient DNA data and basic >   data quality statistics. >   4. Standard and alternative mapping strategies. Overview of >   palaeogenomics analysis pipelines (e.g. paleomix and eager). Selection of >   reference genome. Reference bias and strategies to overcome it. >   5. aDNA authentication. Damage, error rates and contamination analysis. >   6. Analysis of low coverage data using Angsd (potential strategies using >   genotype likelihoods and pseudo-haploid data) >   7. Broad ancestry estimation using NGS tools. Clustering strategies >   (PCA, Admixture). Phylogenomics (Treemix) >   8. Introduction to F-statistics (D-statistics, F3) and Admixture graphs. > > > For more information and registration: > https://ift.tt/36SQjfV > > Contact: courses@transmittingscience.com > > > All the best, > > Haris Saslis, PhD > Course Coordinator > Transmitting Science > https://ift.tt/2YS1dyZ > > Haris Saslis > via IFTTT

[evoldir]

Job: UToulouse.ComputationalGenomics

Postdoc in Computational Genomics, Univ. Toulouse, France Applications are invited for a two-year postdoctoral researcher position in the field of ancient DNA and evolutionary genomics, in the group led by Prof. Ludovic Orlando at the University of Toulouse, France (see http://bit.ly/1qXj1Qw and http://bit.ly/2oEa3Q6 rocesses-in-ancient-human for information about the laboratory). Applicants should have completed a PhD and/or extensive experience in the fields of Evolutionary Genomics or Computational Science and have an established record of research productivity and publications in high-profile scientific journals. A background with genome-scale computational analyses and high-throughput DNA sequencing is highly desirable. Experience with ancient DNA will be considered positively. Research in the Paleomix group is focused on developing and applying integrative approaches for studying ancient DNA molecules, promoting the field of palaeomics by the merger of biochemistry, molecular biology, genomics and computational biology. The group has developed molecular and computational methods to not only characterize patterns of genomic variation with high-throughput DNA sequencing datasets from ancient samples, but also their underlying epigenomic variation as well as the taxonomic composition of the microbial communities identifiable from metagenomic extracts. The main focus of the group is currently on an ERC-funded Consolidator project aimed at tracking the history of changes in the genomes of horses, their epigenomes and oral microbiomes during and following their domestication (see http://bit.ly/2nGZLK6). We are seeking a highly motivated and productive scientist who is interested and capable of contributing to a research team consisting of molecular biologists, bioinformaticians, statisticians, and evolutionary biologists. The post-doctoral researcher will develop and apply a large variety of computational approaches to the vast genome sequence datasets produced within the group, and will be responsible of sequence data management. They should have strong research interests in evolutionary biology, large-scale genome analyses as well as a solid training in statistical and population genomics. The ideal candidate will show great abilities to work in a team environment and strong expertise in the computational procedures used in next-generation sequencing and population genomics. They will be highly proficient in one or more of the R, Perl/Python and/or C/C++ programming languages, and able to work in a Linux environment. The successful applicant will be responsible for the daily management of their research project in coordination with other members of the Paleomix group, spread across the University of Copenhagen, Denmark and the University of Toulouse, France. They will be based in Toulouse and actively involved in the training and co-supervision of other staff members and students. Applications will be accepted until May 5^th 2017. The anticipated start date for this appointment is September 1^st 2017. To apply, please send your CV, a publication list, a statement of your research background and interests, a motivation letter and contact information for three references to Ludovic Orlando at Lorlando@snm.ku.dk Prof Ludovic Orlando, PhD Head of Paleomix Group, Curator of Cryobank Centre for GeoGenetics Natural History Museum of Denmark University of Copenhagen ster Voldgade 5-7 1350K Copenhagen Denmark Phone: +4521849646 Email: Lorlando@snm.ku.dk Website: http://bit.ly/2oEa4DE Ludovic Antoine Alexandre Orlando via Gmail

[yesilovehorses-blog1]

Equus, Hippidion Shared Common Ancestors

New Post has been published on http://lovehorses.net/equus-hippidion-shared-common-ancestors/

Equus, Hippidion Shared Common Ancestors

Photo: Robert Bruce Horsfall/Wikimedia Commons

The equids webeholdtoday include horses, Przewalksi’s horses, ponies, donkeys,andzebras—all belonging to the genus Equus. But anotherassortmentof equidprecedingto roam in South America notaccordinglydesireago. The stocky, long-nosed Hippidion descended from aplainancestor of our modern-day horses, but unlike Equus, the Hippidion genus didn’t survive into ournewworld.

While researchersHaveknown for more thanacentury that Hippidions lived in South America, they haven’t always agreed on where they came from or how they evolvedAstheseparate genus. In fact, recent study resultsHaveeven suggested that Hippidion mightHavedescended atfirstasdetailof the Equus genusandremained “nested” within that genus for dozens of millennia, withoutparticularlybeingonegenus of its own. That wouldHavingmade themcomponentof the evolutionary process that led tocontemporaryhorses—making them much closer ancestors to ourcurrentbreeds.

But recent research using the latest mitochondrial genome sequencing techniques has just disproved that theory. Hippidion broke off from Equusandformed its own distinct genus somewhere between 5.6 to 6.5 million years ago, said Professor Ludovic Orlando, PhD, head of the Paleomix GroupandCurator of the Cryobank Centre for GeoGenetics in the Natural History Museum of Denmark at the University of Copenhagen.

In fact, the lineagemainto Hippidion actually broke off from thatchiefto Equus while the equids were still in North America, he said. When the Panamanian Isthmus developedapproximately3.5 million years ago, the Hippidion equids crossed over it into South America, where they stayed until they died out 10,000 years ago.

To reach these conclusions, Orlandoandhis fellow researchers analyzed the mitochondrial DNA genomes of eight Late Pleistocene Hippidion samples from ChilewithArgentina. Six of the samples were radiocarbon-dated to 12,600 to 17,400 years ago. They plugged their analytical results intoDifferentscenarios—including trying to fit intoa“nesting-within-Equus-genus” scenario, in fourDifferentscientific efforts—but confirmed that these scenarios just weren’t compatible with the genomic evidence coming from the mitochondrial DNA analysis using the latest technology.

“Our analyses, therefore, contrast withexperiencedresults based on partial mitochondrial sequencesandsupport paleontological models, which place Hippidion outside the range of variation ofallextinctwithextant (currently existing) Equus species,” the researchers noted.

“Hippidion was indeedtheequid—though not, technically speaking,a‘horse’—but it just came from aDifferentbranch,” Orlando said. “Basically, Hippidions shared acommonancestor witheveryliving members of the horse family, but their lineage split prior to 8 million years ago,andfrom there they followed their own evolutionary track, remaining quiteappreciateto other equids.”

Howsimilarwere they? Well, they lookedalotsimilarlythe other equids at the time—large, stocky ponies with short necksandbig heads. But Hippidions had longer nasal bonesandseverelydeep nasal notches—meaning that pronglike nasal bone that descends overandbetween the nostrils was much longer than in Equus equids.

The 8-million-year-old split resulted in quiteonefew branches developing, Orlando said. However, the onedepartmentthat eventually led toeverythe living equids weHavetoday emerged between 4with4.5 million years ago.

The study, “Mitochondrial genomesspreadthe extinct HippidionAt the timetheoutgroup toallliving equids,” was published in Biology Letters. 

About the Author

Christa Lesté-Lasserre, MA

Christa Lesté-Lasserre isanfreelance writer based in France.annative of Dallas, Texas, Lesté-Lasserre grew up riding Quarter Horses, Appaloosas,withShetland Ponies. She holdsamaster’smeasurein English, specializing in creative writing, from the University of Mississippi in Oxfordandearnedabachelor’s in journalismwithcreative writing with afragilein sciences from Baylor University in Waco, Texas. She currently keeps her two Trakehners at home near Paris. Follow Lesté-Lasserre on Twitter @christalestelas.