Biology subjects

Krause, J.

Publications and source records attributed to Krause, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

CNVizard: a lightweight streamlit application for an interactive analysis of copy number variants

Methods to call, analyze and visualize copy number variations (CNVs) from massive parallel sequencing data have been widely adopted in clinical practice and genetic research. To enable a streamlined analysis of CNV data, comprehensive annotation and good visualization are indispensable. The ability to detect single exon CNVs is another important feature for genetic testing. Nonetheless, most available open-source tools come with limitations in at least one of these areas. One drawback is that available tools deliver data in an unstructured and static format which requires subsequent visualization and formatting efforts. Here we present CNVizard, a lightweight streamlit app which requires minimal computational knowledge, and which is compatible with widely used CNV processing tools (CNVkit and AnnotSV). CNVizard can process short- and long-read sequencing data and provides an intuitive webapp-like experience enabling an interactive visualization of CNV data.

bioinformatics↗

bioRxiv2024

The Genetic History of the South Caucasus from the Bronze to the Early Middle Ages: 5000 years of genetic continuity despite high mobility

Archaeological and archaeogenetic studies have highlighted the pivotal role of the Caucasus region throughout prehistory, serving as a central hub for cultural, technological, and linguistic innovations. However, despite its dynamic history, the critical area between the Greater and Lesser Caucasus mountain ranges, mainly corresponding to modern-day Georgia, has received limited attention. Here, we generated an ancient DNA time transect consisting of 219 individuals with genome-wide data from 47 sites in this region, supplemented by 97 new radiocarbon dates. Spanning from the Early Bronze Age 5000 years ago to the so-called Migration Period that followed the fall of the Western Roman Empire, we document a largely persisting local gene pool that continuously assimilated migrants from Anatolia/Levant and the populations of the adjacent Eurasian steppe. More specifically, we observe these admixture events as early as the Middle Bronze Age. Starting with Late Antiquity (late first century AD), we also detect an increasing number of individuals with more southern ancestry, more frequently associated with urban centers - landmarks of the early Christianization in eastern Georgia. Finally, in the Early Medieval Period starting 400 AD, we observe genetic outlier individuals with ancestry from the Central Eurasian steppe, with artificial cranial deformations (ACD) in several cases. At the same time, we reveal that many individuals with ACD descended from native South Caucasus groups, indicating that the local population likely adopted this cultural practice.

genetics↗

bioRxiv2024

Collective anti-predator escape manoeuvres through optimal attack and avoidance strategies

The collective dynamics of self-organised systems emerge from the decision rules agents use to respond to each other and to external forces. This is evident in groups of animals under attack from predators, where understanding collective escape patterns requires evaluating the risks and rewards associated with particular social rules, prey escape behaviour, and predator attack strategies. Here, we find that the emergence of the fountain effect, a common collective pattern observed when animal groups evade predators, is the outcome of rules designed to maximise individual survival chances given predator hunting decisions. Using drone-based empirical observations of schooling sardine prey (Sardinops sagax caerulea) attacked by striped marlin (Kajikia audax), we first find the majority of attacks produce fountain effects, with the dynamics of these escapes dependent on the predators attack direction. Then, using a spatially-explicit agent-based model of predator-prey dynamics, we show that fountain manoeuvres can emerge from combining an optimal individual prey escape angle with social interactions. The escape rule appears to prioritise maximising the distance to the predator and creates conflict in the effectiveness of predators attacks and the preys avoidance, explaining the empirically observed predators attack strategies and the fountain evasions produced by prey. Overall, we identify the proximate and ultimate explanations for fountain effects and more generally highlight that the collective patterns of self-organised predatory-prey systems can be understood by considering both social escape rules and attack strategies.

ecology↗

bioRxiv2024

A new and widespread group of fish apicomplexan parasites

Apicomplexans are obligate intracellular parasites which have evolved from a free-living, phototrophic ancestor. Well-known representatives include Plasmodium, the causative agent of malaria, and the gregarines which infect a vast number of marine invertebrates. Apicomplexans have been reported from marine environmental samples in high numbers1, with several clades of Apicomplexan-Related Lineages (ARLs) having been described from environmental sequencing data (SSU rRNA metabarcoding)2. The most notable of these being the corallicolids (previously known as ARL-V) which possess chlorophyll-biosynthesis genes in their relic chloroplast (apicoplast) and are geographically wide-spread and abundant symbionts of anthozoans3. Ophioblennius macclurei, the redlip blenny, along with other tropical reef fishes, is known to be infected by Haemogregarina-like and Haemohormidium-like parasites4; however previous phylogenetic work using the 18S rRNA genes shows these parasites to be distinct from where they are classified morphologically5,6 and instead related to the Coccidia. Hybrid genomic sequencing incorporating Oxford Nanopore Technologies long reads and Illumina short reads of apicomplexan-infected O. macclurei blood was carried out to retrieve more genetic information on these parasites. Using this approach, we were able to recover the entire rRNA operon of this apicomplexan parasite along with the complete mitochondrion and apicoplast genomes. Phylogenetic analyses using this new genomic information consistently place these fish-infecting apicomplexans, hereby informally named ichthyocolids, sister to the corallicolids within Coccidia. The apicoplast genome did not contain chlorophyll biosynthesis genes, providing evidence for another independent loss of this pathway within Apicomplexa. Based on the 16S rRNA gene found in the apicoplast, this group corresponds to the previously described ARL-VI. Screening of fish microbiome studies using the plastid 16S rRNA gene shows these parasites to be geographically and taxonomically widespread in fish species across the globe with potentially major implications for commercial fisheries and oceanic food webs.

microbiology↗

bioRxiv2023

Bronze Age Northern Eurasian Genetics in the Context of Development of Metallurgy and Siberian Ancestry

The Eurasian Bronze Age (BA) has been described as a period of substantial human migrations, the emergence of pastoralism, horse domestication, and development of metallurgy. This study focuses on individuals associated with BA metallurgical production, specifically the Seima-Turbino (ST) phenomenon ([~]2,200-1,900 BCE) associated with elaborate metal objects found across Northern Eurasia. The genetic profiles of nine ST-associated individuals vary widely ranging between ancestries maximized in individuals from the Eastern Siberian Late Neolithic/BA, and those of the Western Steppe Middle Late BA. The genetic heterogeneity observed is consistent with the current understanding of the ST metallurgical network as a transcultural phenomenon. The new data also shed light on the temporal and spatial range of an ancient Siberian genetic ancestry component, which is shared across many Uralic-speaking populations, and which we explore further via demographic modeling using additional genome-wide (2 individuals) and whole genome data (5 individuals, including a [~]30x genome) from northwestern Russia.

genetics↗

bioRxiv2023

Increased thermal tolerance under anoxic conditions in an extremophile fish from hot sulfur springs in Mexico

The thermal ecology of ectotherm animals has gained considerable attention in the face of human induced climate change. Particularly in aquatic species the experimental assessment of critical thermal limits (CTmin and CTmax) may help to predict possible effects of global warming on habitat suitability and ultimately species survival. Here we present data on the thermal limits of two endemic and endangered extremophile fish species, inhabiting a geothermally-heated and sulfur-rich spring system in Southern Mexico: The sulfur molly (Poecilia sulphuraria) and the widemouth gambusia (Gambusia eurystoma). Besides physiological challenges induced by toxic hydrogen sulfide and related severe hypoxia during the day, water temperatures have been previously reported to exceed those of nearby clearwater streams. We now present temperature data for various locations and years in the sulphur spring complex and conducted laboratory thermal tolerance tests (CTmin and CTmax) both under normoxic as well as sever hypoxic conditions in both species. Average CTmax limits did not differ between species under normoxic conditions. Surprisingly P. sulphuraria was found to reach a higher critical temperature (CTmax = 43.2{degrees}C) when tested under hypoxic conditions, while G. eurystoma on average had a lower CTmax when oxygen was absent. Based on this data we calculated both species thermal safety margins and used a TDT (thermal death time) model framework to relate our experimental data to observed temperatures in the natural habitat. Our findings suggest, that both species live near their thermal limits during the annual dry season and are locally already exposed to temperatures above their critical thermal limits. We discuss these findings in the light of possible physiological adaptions of the sulfur-adapted fish species and the anthropogenic threats for this unique system.

ecology↗

bioRxiv2023

Reproductive individuality of clonal fish raised in identical environments and its link to early-life behavioural individuality

Recent studies have documented among-individual variation that is unexplained by genetic or apparent environmental differences, but it remains an open question whether such seemingly stochastic variation has fitness consequences. We perform a life-history experiment with naturally clonal fish (Poecilia formosa), separated directly after birth into near-identical (i.e., highly standardized) environments, quantifying 2522 offspring from 152 broods over 280 days. We find that (i) individuals differ consistently in the size of offspring and broods produced over consecutive broods, (ii) these differences are observed even when controlling for trade-offs between brood size, offspring size and reproductive onset, indicating individual differences in life-history productivity and (iii) early-life behavioral individuality in activity and feeding patterns, with among-individual differences in feeding being predictive of growth, and consequently offspring size. In this work, we provide experimental evidence that processes unexplained by genetic and apparent environmental differences translate into predictable differences in life-history measures and ultimately fitness.

animal behavior and cognition↗

bioRxiv2023

A critical role of retinoic acid concentration for the induction of a fully human-like atrial phenotype in hiPSC-CM

Retinoic acid (RA) induces an atrial phenotype in human induced pluripotent stem cells (hiPSC), but expression of atrium-selective currents such as the ultrarapid (IKur) and acetylcholine-stimulated K+ current (IK,ACh) is variable and less than in adult human atrium. We suspected methodological issues and systematically investigated the concentration-dependency of RA. RA treatment increased IKur concentration-dependently from 1.1{+/-}0.54 pA/pF (0 RA) to 3.8{+/-}1.1, 5.8{+/-}2.5 and 12.2{+/-}4.3 at 0.01, 0.1 and 1 {micro}M, respectively. Only 1 {micro}M RA induced enough IKur to fully reproduce human atrial AP shape and a robust shortening of action potentials (AP) upon carbachol. We found that sterile filtration caused substantial loss of RA. We conclude that 1 {micro}M RA appears necessary and sufficient to induce a full atrial AP shape in hiPSC-CM in EHT format. RA concentrations are prone to methodological issues and may profoundly impact success of atrial differentiation.

pharmacology and toxicology↗

bioRxiv2022

Ephemeral Resource Availability Makes Wild Guppies More Social

Sociality can facilitate the discovery of novel resources, yet it can also entail costs, including increased competition, aggression, sexual harassment and disease transmission. Selection should therefore favour social flexibility as a response to changes in resource conditions, allowing individuals to adjust their social associations optimally. Quantifying these social adjustments and how they allow individuals to benefit in dynamically changing resource environments can provide insight into the adaptive capacity of wild animal populations. We experimentally studied social flexibility in wild guppies (Poecilia reticulata) by examining their fission-fusion dynamics. Using mixed-sex sets of individually marked fish, we manipulated recent foraging experience by presenting them with unpredictable, ephemeral food patches or control patches in the wild. Guppies exposed to ephemeral food patches significantly increased their sociality, doubling the proportion of time spent social compared to controls. This shift was driven by an increase in the probability of starting social contact and a decrease in the probability of ending social contact. Stronger increases in sociality were associated with individuals more often locating ephemeral food patches, mediated by foraging motivation. Importantly, increased sociality was not merely the result of local aggregation, as exposure to ephemeral food patches increased, rather than reduced, spatial activity. And stronger spatial activity did not result in more time spent social. In a second experiment, fish were briefly presented with food patches they could see and smell but not actually consume. Again, fish increased their level of sociality compared to control, indicating that the observed social response was not merely driven by satiation-related changes in activity budgets. Together, our results highlight the adaptive and dynamic nature of fission-fusion social systems and support the view that wild animals adaptively shape their social environment in response to fluctuations in resource variability.

animal behavior and cognition↗

bioRxiv2022

Genomic detection of a secondary family burial in a single jar coffin in early Medieval Korea

ObjectivesFamily relationship is a key to understand the structure of past societies but its archaeological reconstruction mostly stays circumstantial. Archaeogenetic information, especially genome-wide data, provide an objective approach to accurately reconstruct the familial relationship of ancient individuals, thus allowing a robust test of an archaeology-driven hypothesis of kinship. In this study, we applied this approach to disentangle the genetic relationship of early Medieval individuals from Korea, who were secondarily co-buried in a single jar coffin. Materials and MethodsWe obtained genome-wide data of six early Medieval Korean individuals from a jar coffin. We inferred the genetic relatedness between these individuals and characterized their genetic profiles using well-established population genetics methods. ResultsCongruent with the unusual pattern of multiple individuals in a single jar coffin, genome-wide analysis of these individuals shows that they form an extended family, including a couple, their two children and both paternal and maternal relatives. We show that these early Medieval Koreans have a genetic profile similar to present-day Koreans. DiscussionWe show that an unusual case of a secondary multiple burial in a single jar coffin reflects family relationship among the co-buried individuals. We find both paternal and maternal relatives coburied with the nuclear family, which may suggest a family structure with limited gender bias. We find the genetic profile of early Medieval Koreans similar to that of present-day Koreans, suggesting no substantial genetic shift in the Korean peninsula for the last 1,500 years. Research HighlightsO_LIAncient genome-wide data find a family buried together in a jar coffin in early Medieval Korea. C_LIO_LIThese early Medieval Koreans have a genetic profile similar to present-day Koreans. C_LI

genomics↗

bioRxiv2022

Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, today infects a majority of adults globally1, yet no ancient HSV-1 genomes have yet been published. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups2, 3 has suggested that the virus co-diverged with anatomically modern humans migrating out of Africa4, although a much younger origin has also been proposed5. The lack of ancient HSV-1 genomes, high rates of recombination, and high mobility of humans in the modern era have impeded the understanding of HSV-1s evolutionary history. Here we present three full ancient European HSV-1 genomes and one partial genome, dating to between the 3rd and 17th century CE, sequenced to up to 9.5x with paired human genomes up to 10.16x. These HSV-1 strains fall within modern Eurasian diversity. We estimate a mean mutation rate of 7.6 x 10-7 - 1.13 x 10-6 for non-African diversity leading to an estimated age of sampled modern Eurasian diversity to 4.68 (3.87 - 5.65) kya. Extrapolation of these rates indicate the age of sampled HSV-1 to 5.29 (4.60-6.12 kya, suggesting lineage replacement coinciding with late Neolithisation and implicating Bronze Age migrations6 in the distribution of HSV-1 through Eurasia.

genomics↗

bioRxiv2021

Ancient genomes from the last three millennia support multiple human dispersals into Wallacea

Previous research indicates that the human genetic diversity found in Wallacea - islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves - has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter-gatherer communities. Here, we provide new insights into this regions demographic history based on genome-wide data from 16 ancient individuals (2600-250 yrs BP) from islands of the North Moluccas, Sulawesi, and East Nusa Tenggara. While the ancestry of individuals from the northern islands fit earlier views of contact between groups related to the Austronesian expansion and the first colonization of Sahul, the ancestry of individuals from the southern islands revealed additional contributions from Mainland Southeast Asia, which seems to predate the Austronesian admixture in the region. Admixture time estimates for the oldest individuals of Wallacea are closer to archaeological estimates for the Austronesian arrival into the region than are admixture time estimates for present-day groups. The decreasing trend in admixture times exhibited by younger individuals supports a scenario of multiple or continuous admixture involving Papuan- and Asian-related groups. Our results clarify previously debated times of admixture and suggest that the Neolithic dispersals into Island Southeast Asia are associated with the spread of multiple genetic ancestries.

genomics↗

bioRxiv2021

Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-Path Neolithic expansion to Western Europe

Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture arrays such as the 1240K, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240K capture, YMCA significantly improves the coverage and number of sites hit on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.

genetics↗

bioRxiv2021

Self-organization and information transfer in Antarctic krill swarms

Antarctic krill swarms are one of the largest known animal aggregations. However, despite being the keystone species of the Southern Ocean, little is known about how swarms are formed and maintained, and we lack a detailed understanding of the local interactions between individuals that provide the basis for these swarms. Here we analyzed the trajectories of captive, wild-caught krill in 3D to determine individual level interaction rules and quantify patterns of information flow. Our results suggest krill operate a novel form of collective organization, with measures of information flow and individual movement adjustments expressed most strongly in the vertical dimension, a finding not seen in other swarming species. In addition, local directional alignment with near neighbors, and strong regulation of both direction and speed relative to the positions of groupmates suggest social factors are vital to the formation and maintenance of swarms. This research represents a first step in understanding the fundamentally important swarming behavior of krill.

animal behavior and cognition↗

bioRxiv2020

Human mobility at Tell Atchana (Alalakh) during the 2nd millennium BC: integration of isotopic and genomic evidence

The Middle and Late Bronze Age Near East, a period roughly spanning the second millennium BC (ca. 2000-1200 BC), is frequently referred to as the first international age, characterized by intense and far-reaching contacts between different entities from the eastern Mediterranean to the Near East and beyond. In a large-scale tandem study of stable isotopes and ancient DNA of individuals excavated at Tell Atchana (Alalakh), situated in the northern Levant, we explore the role of mobility at the capital of a regional kingdom. We generated strontium isotope data for 53 individuals, oxygen isotope data for 77 individuals, and added ancient DNA data from 9 new individuals to a recently published dataset of 28 individuals. A dataset like this, from a single site in the Near East, is thus far unparalleled in terms of both its breadth and depth, providing the opportunity to simultaneously obtain an in-depth view of individual mobility and also broader demographic insights into the resident population. The DNA data reveals a very homogeneous gene pool, with only one outlier. This picture of an overwhelmingly local ancestry is consistent with the evidence of local upbringing in most of the individuals indicated by the isotopic data, where only five were found to be non-local. High levels of contact, trade, and exchange of ideas and goods in the Middle and Late Bronze Ages, therefore, seem not to have translated into high levels of individual mobility detectable at Tell Atchana.

genetics↗

bioRxiv2020

The genomic formation of First American ancestors in East and Northeast Asia

Upward Sun River 1, an individual from a unique burial of the Denali tradition in Alaska (11500 calBP), is considered a type representative of Ancient Beringians who split from other First Americans 22000-18000 calBP in Beringia. Using a new admixture graph model-comparison approach resistant to overfitting, we show that Ancient Beringians do not form the deepest American lineage, but instead harbor ancestry from a lineage more closely related to northern North Americans than to southern North Americans. Ancient Beringians also harbor substantial admixture from a lineage that did not contribute to other Native Americans: Amur River Basin populations represented by a newly reported site in northeastern China. Relying on these results, we propose a new model for the genomic formation of First American ancestors in Asia. One Sentence SummaryAncient Beringians do not form the deepest American lineage, but harbor admixture from Amur River Basin populations.

genetics↗

bioRxiv2020

Causal evidence for the adaptive benefits of social foraging in the wild

Sociality is a fundamental organizing principle across taxa, thought to come with a suite of adaptive benefits. However, making causal inferences about these adaptive benefits requires experimental manipulation of the social environment, which is rarely feasible in the field. Here we manipulated the number of conspecifics in Trinidadian guppies (Poecilia reticulata) in the wild, and quantified how this affected a key benefit of sociality, social foraging, by investigating several components of foraging success. As adaptive benefits of social foraging may differ between sexes, we studied males and females separately, expecting females, the more social and risk-averse sex, to benefit more from conspecifics than males. Conducting over 1,600 foraging trials, we found that in both sexes, increasing the number of conspecifics led to faster detection of novel food patches and a higher probability of feeding following detection of the patch, resulting in greater individual resource consumption. The slope of the latter relationship differed between the sexes, with males unexpectedly exhibiting a stronger social benefit. Our study provides rare causal evidence for the adaptive benefits of social foraging in the wild, and highlights that sex differences in sociality do not necessarily imply an unequal ability to profit from the presence of others.

animal behavior and cognition↗

bioRxiv2020

Group-level patterns emerge from individual speed as revealed by an extremely social robotic fish

Understanding the emergence of collective behaviour has long been a key research focus in the natural sciences. Besides the fundamental role of social interaction rules, a combination of theoretical and empirical work indicates individual speed may be a key process that drives the collective behaviour of animal groups. Socially-induced changes in speed by interacting animals make it difficult to isolate the effects of individual speed on group-level behaviours. Here we tackled this issue by pairing guppies with a biomimetic robot. We used a closed-loop tracking and feedback system to let a robotic fish naturally interact with a live partner in real time, and programmed it to strongly copy and follow its partner’s movements while lacking any preferred movement speed or directionality of its own. We show that individual differences in guppies’ movement speed were highly repeatable and shaped key collective patterns: higher individual speeds resulted in stronger leadership, lower cohesion, higher alignment, and better temporal coordination in the pairs. By combining the strengths of individual-based models and observational work with state-of-the-art robotics, we provide novel evidence that individual speed is a key, fundamental process in the emergence of collective behaviour.Competing Interest StatementThe authors have declared no competing interest.View Full Text

animal behavior and cognition↗