Ozgur Taskent
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ozgurtaskent.bsky.social
Ozgur Taskent
@ozgurtaskent.bsky.social
130 followers 240 following 10 posts
post-doctoral researcher @METU/ODTU @CompEvo
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Reposted by Ozgur Taskent
nature.com
Nature research paper: An ancient recombination desert is a speciation supergene in placental mammals

go.nature.com/47UiBWa
An ancient recombination desert is a speciation supergene in placental mammals - Nature
Deep learning methods identified a large and evolutionarily conserved X-linked low recombination region in placental mammals that serves as both a barrier to gene flow in hybridizing lineages and an accurate phylogenomic marker.
go.nature.com
November 14, 2025 at 2:03 PM
Reposted by Ozgur Taskent
arkeofili.bsky.social
Neandertaller Yok Olmadı, Bir Parçamız Haline Geldi

arkeofili.com/neandertalle...
Neandertaller Yok Olmadı, Bir Parçamız Haline Geldi - Arkeofili
Neandertaller tek bir olayla veya soykırımla dünyadan yok olmak yerine, modern insan popülasyonunun bir parçası hâline geldi.
arkeofili.com
November 14, 2025 at 8:36 AM
Reposted by Ozgur Taskent
hansonmark.bsky.social
We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing:

a 🧵 1/n

Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...
A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision. A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.
November 11, 2025 at 11:52 AM
Reposted by Ozgur Taskent
mollyprz.bsky.social
An empirical approach to evaluating the prevalence of long-lived balancing selection in humans--and important limitations. Work by @hannahmm.bsky.social
November 11, 2025 at 7:14 PM
Reposted by Ozgur Taskent
moorjanipriya.bsky.social
Exciting new study led by @ekerdoncuff.bsky.social and @meaghanmarohn.bsky.social on the evolution of Lactase Persistence in South Asia.
www.biorxiv.org/content/10.1...
Revisiting the Evolution of Lactase Persistence: Insights from South Asian Genomes
Lactase persistence (LP), the ability to digest lactose from milk into adulthood, is a classic example of natural selection in humans. Multiple mutations upstream of the LCT gene are associated with L...
www.biorxiv.org
November 7, 2025 at 2:33 PM
Reposted by Ozgur Taskent
mootspoints.bsky.social
How time, climate, and storage shape DNA survival in herbarium specimens - and why plants from the tropics face tougher odds 🌿🧬
#AncientDNA
www.biorxiv.org/content/10.1...
November 4, 2025 at 8:32 PM
ozgurtaskent.bsky.social
www.biorxiv.org/content/10.1...
Principal Components Analysis fails to recover phylogenetic structure in hominins
Objectives: Paleoanthropologists often utilize geometric morphometrics and principal components analysis (PCA) to interpret shape variation within the hominin fossil record. It is common practice to i...
www.biorxiv.org
November 1, 2025 at 3:19 PM
Reposted by Ozgur Taskent
merondun.bsky.social
Our new @science.org paper is out! Cuckoos and hosts are locked in a coevolutionary arms race over egg mimicry.

But how are these egg types inherited, and could this drive speciation? We sequenced hundreds of genomes to find out!

doi.org/10.1126/scie...

🧵1/6
Genomic architecture of egg mimicry and its consequences for speciation in parasitic cuckoos
Host-parasite arms races facilitate rapid evolution and can fuel speciation. Cuculus cuckoos are deceptive egg mimics that exhibit a broad diversity of counterfeit egg phenotypes, representing host-ad...
doi.org
October 30, 2025 at 7:15 PM
Reposted by Ozgur Taskent
genetics-gsa.bsky.social
The latest issue of #G3journal features work from @trstngnthr.bsky.social, @amygoldberg.bsky.social, @jgschraiber.bsky.social, where they benchmarked methods for estimating ancestry proportions under mapping bias and present adjusted genotype-likelihoods to mitigate its impact. buff.ly/9ET69CA
October 30, 2025 at 6:04 PM
Reposted by Ozgur Taskent
yuvalsim.bsky.social
Why do complex traits differ in their genetic architecture?
In our new PLOS Biology paper, we will try to convince you that two simple scaling laws drive differences in the number, effect sizes and frequencies of causal variants affecting complex traits.

Thread:
journals.plos.org/plosbiology/...
Simple scaling laws control the genetic architectures of human complex traits
Genome-wide association studies have revealed that the genetic architectures of complex traits vary widely. This study shows that differences in architectures of highly polygenic traits arise mainly f...
journals.plos.org
October 24, 2025 at 1:51 AM
ozgurtaskent.bsky.social
great study (www.biorxiv.org/content/10.1...), but what they considered weak selection (s=[0.005-0.05]) translates to 2Nes=[100-1000], for which their model has low power of detection, and which is in the range of strong selection here: academic.oup.com/mbe/article/....
The persistence and loss of hard selective sweeps amid ancient human admixture
The extent to which human adaptations have persisted throughout history despite strong eroding demographic events such as admixture, genetic drift, and fluctuations in selection pressures remains unkn...
www.biorxiv.org
October 23, 2025 at 6:11 PM
Reposted by Ozgur Taskent
rebeccasear.bsky.social
Have been looking forward to seeing this come out. The fundamental population problem is: what is a population?
October 23, 2025 at 4:02 PM
Reposted by Ozgur Taskent
biorxivpreprint.bsky.social
Antiviral reverse transcriptases reveal the evolutionary origin of telomerase https://www.biorxiv.org/content/10.1101/2025.10.16.682844v1
October 16, 2025 at 9:18 PM
Reposted by Ozgur Taskent
biorxiv-evobio.bsky.social
The persistence and loss of hard selective sweeps amid ancient human admixture https://www.biorxiv.org/content/10.1101/2025.10.14.682443v1
October 15, 2025 at 7:32 AM
Reposted by Ozgur Taskent
mbeisen.bsky.social
Finally, someone has solved a real problem with AI! No more having to take a paper in the format for a journal that rejected you, and reformat it for a new journal. Well done!! formatmypaper.com
October 15, 2025 at 6:33 AM
Reposted by Ozgur Taskent
plosbiology.org
Genetic architectures of #ComplexTraits vary widely. @yuvalsim.bsky.social @jkpritch.bsky.social @gs2747.bsky.social &co show these diffs arise from mutational target size & heritability per site; when controlled for, all tested traits have similar architectures @plosbiology.org 🧪 plos.io/47mZXqT
Heritability and target size underlie differences between trait architectures: examples for three traits. Top: Height (blue) and platelet crit (red) have the same heritability per site h2/L, but height has a much higher mutational target size L. This results in many more hits for height (1533) than for platelet crit (648) (2 left panels). However, the marginal distributions of effect sizes, MAFs, and z-scores of hits are nearly identical for the two traits (3 right panels). Middle: Height (blue) and FEV1 (gold) differ in h2/L, but have similar L. Consequently, the joint distribution of z-scores and MAFs of their hits are markedly different (2 left panels), as are the marginal distributions of hit effect sizes, MAFs and z-scores (right). Bottom: After scaling by their respective , and imposing the more stringent scaled significance threshold (corresponding to FEV1) for both traits, the joint distribution of z-scores and MAFs of their hits (2 left panels) and the corresponding marginal distributions (3 right panels) are highly similar.
October 14, 2025 at 7:53 AM
Reposted by Ozgur Taskent
aprilwei.bsky.social
Excited to preprint our latest work (w/ Drew DeHaas, Zhibai Jia, Leo Speidel) on using ARGs for demographic inference. w/ applications using data from 1000 Genomes Project. www.biorxiv.org/content/10.1...
Inference of complex demographic history using composite likelihood based on whole-genome genealogies
Accurate parametric inference on complex demographic models is a continuing challenge in population genetics. Ancestral recombination graphs (ARGs) provide richer information than simple population ge...
www.biorxiv.org
October 8, 2025 at 2:48 PM
Reposted by Ozgur Taskent
biorxiv-genetic.bsky.social
Comprehensive gene heritability estimation reveals the genetic architecture of rare coding variants underlying complex traits https://www.biorxiv.org/content/10.1101/2025.10.07.681018v1
October 8, 2025 at 2:33 PM
Reposted by Ozgur Taskent
rosafernandez.bsky.social
How did animals repeatedly conquer land? 🌊➡️⛰️ We analysed ~1,000 gene repertoires (24M genes!) from all animal phyla to uncover how this happened. Work led by @gemmaeling.bsky.social & Klara Eleftheriadi, both first coauthors of this titanic effort!
www.biorxiv.org/content/10.1...
Independent genomic trajectories shape adaptation to life on land across animal lineages
How animals repeatedly adapted to life on land is a central question in evolutionary biology. While terrestrialisation occurred independently across animal phyla, it remains unclear whether shared gen...
www.biorxiv.org
October 7, 2025 at 7:27 AM
Reposted by Ozgur Taskent
drmlharris.bsky.social
Ahead of tomorrow’s #NobelPrize announcement, I went on a deep dive in search of the most obscure physics Nobel Prizes in history. That means it's time for a thread on...🧵

PHYSICS NOBEL PRIZES YOU’VE NEVER HEARD OF – PART 1

(1/n)
A photo of the Matterhorn rising above an Alpine landscape. The colours are a little washed out, but do not appear artificially tinted
October 6, 2025 at 3:22 PM
Reposted by Ozgur Taskent
arkeofili.bsky.social
Karahantepe’de İlk Defa İnsan Yüzlü Dikilitaş Bulundu

arkeofili.com/karahanteped...
Karahantepe'de İlk Defa İnsan Yüzlü Dikilitaş Bulundu - Arkeofili
12.000 yıl öncesinden bir yüz: Karahantepe’de ilk kez insan yüzü taşıyan T-dikilitaş ortaya çıktı. Peki bu ne anlama geliyor?
arkeofili.com
October 6, 2025 at 12:57 PM
Reposted by Ozgur Taskent
anaignatieva.bsky.social
Delighted that our paper about the distribution of genomic spans of clades/edges in genealogies (ARGs), and using this for detecting inversions and other SVs (and other phenomena that cause local disruption of recombination) is out in MBE academic.oup.com/mbe/article/... (1/n)
The Length of Haplotype Blocks and Signals of Structural Variation in Reconstructed Genealogies
Abstract. Recent breakthroughs have enabled the accurate inference of large-scale genealogies. Through modelling the impact of recombination on the correla
academic.oup.com
October 3, 2025 at 9:54 AM
Reposted by Ozgur Taskent
biorxivpreprint.bsky.social
Accurate and efficient phylogenetic inference through end-to-end deep learning https://www.biorxiv.org/content/10.1101/2025.09.30.679045v1
October 2, 2025 at 7:47 PM
Reposted by Ozgur Taskent
biorxiv-evobio.bsky.social
Population genomic scan of endogenous retrovirus insertions revealed cryptic drivers of selective sweep in wild house mouse genomes https://www.biorxiv.org/content/10.1101/2025.09.23.678169v1
September 25, 2025 at 10:32 AM
Reposted by Ozgur Taskent
biorxivpreprint.bsky.social
Generative continuous time model reveals epistatic signatures in protein evolution https://www.biorxiv.org/content/10.1101/2025.09.17.676821v1
September 20, 2025 at 4:48 PM