Biology subjects

Krause, J.

Publications and source records attributed to Krause, J..

16 recordsLinked to original sources

bioRxiv2018

Social networks in the presence and absence of visual cues

We compared the social dynamics of two populations of the live-bearing Atlantic molly (Poecilia mexicana) that live in adjacent habitats with very different predator regimes: cave mollies that inhabit a low-predation environment inside a sulfidic cave with a low density of predatory water bugs (Belostoma sp.), and mollies that live directly outside the cave (henceforth called \"surface\" mollies) in a high-predation environment with a high density of fish-eating birds. We filmed the social interactions of marked fish in both environments and analysed their social network dynamics using a Markov model under two different fish densities of 12 and 6 fish per 0.36 m2. As expected, surface mollies spent overall much more time social than cave mollies. This difference in overall social time was a result of surface mollies being less likely to discontinue social contact (once they had a social partner) and being more likely to resume social contact (once alone) than cave mollies. Interestingly surface mollies were also less likely to leave a current social partner than cave mollies. At low density, mollies (in both environments) were expected to show reduced social encounters which should dramatically change their social dynamics. Surface mollies, however, displayed an ability to maintain their social dynamics at low density (primarily by reducing the convex polygon spanned by the group) which was not observed in cave mollies. Despite the fact that we only compared two populations, our data provide a mechanistic explanation for density compensations of social dynamics that have also been observed in other fish species and give an example of how comparisons between the social dynamics of different populations can be made that go beyond conventional network analyses.

animal behavior and cognition↗

bioRxiv2018

Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia

Anatolia was home to some of the earliest farming communities. It has been long debated whether a migration of farming groups introduced agriculture to central Anatolia. Here, we report the first genome-wide data from a 15,000-year-old Anatolian hunter-gatherer and from seven Anatolian and Levantine early farmers. We find high genetic continuity ([~]80-90%) between the hunter-gatherer and early farmers of Anatolia and detect two distinct incoming ancestries: an early Iranian/Caucasus related one and a later one linked to the ancient Levant. Finally, we observe a genetic link between southern Europe and the Near East predating 15,000 years ago that extends to central Europe during the post-last-glacial maximum period. Our results suggest a limited role of human migration in the emergence of agriculture in central Anatolia.

genetics↗

bioRxiv2018

Quorums enable optimal pooling of independent judgements

Majority-voting and the Condorcet Jury Theorem pervade thinking about collective decision-making. Thus, it is typically assumed that majority-voting is the best possible decision mechanism, and that scenarios exist where individually-weak decision-makers should not pool information. Condorcet and its applications implicitly assume that only one kind of error can be made, yet signal detection theory shows two kinds of errors exist, false positives and false negatives. We apply signal detection theory to collective decision-making to show that majority voting is frequently sub-optimal, and can be optimally replaced by quorum decision-making. While quorums have been proposed to resolve within-group conflicts, or manage speed-accuracy trade-offs, our analysis applies to groups with aligned interests undertaking single-shot decisions. Our results help explain the ubiquity of quorum decision-making in nature, relate the use of sub- and super-majority quorums to decision ecology, and may inform the design of artificial decision-making systems.\n\nImpact StatementTheory typically assumes that majority voting is optimal; this is incorrect - majority voting is typically sub-optimal, and should be replaced by sub-majority or super-majority quorum voting. This helps explain the prevalence of quorum-sensing in even the simplest collective systems, such as bacterial communities.

ecology↗

bioRxiv2018

Modern wolves trace their origin to a late Pleistocene expansion from Beringia

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that maintained a wide geographic distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single late Pleistocene population. Both the geographic origin of this ancestral population and how it became widespread remain a mystery. Here we analyzed a large dataset of novel modern and ancient mitochondrial wolf genomes, spanning the last 50,000 years, using a spatially and temporally explicit modeling framework to show that contemporary wolf populations across the globe trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum - a process most likely driven by the significant ecological changes that occurred across the Northern Hemisphere during this period. This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore and provides an insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.

evolutionary biology↗

bioRxiv2018

Guppies prefer to follow large (robot) leaders irrespective of own size

Body size is often assumed to determine how successful an individual can lead others with larger individuals being more likely to lead than smaller ones. However, direct evidence for such a relation is scarce. Furthermore, even if larger individuals are more likely to lead, body size correlates often with specific behavioral patterns (e.g., swimming capacity) and it is thus unclear whether larger individuals are more often followed than smaller ones because they are larger or because they behave in a certain way. To control for behavioral differences among differentially-sized leaders, we used biomimetic robotic fish - Robofish - of different sizes. Robofish is accepted as a conspecific by live guppies (Poecilia reticulata) and provides standardized behaviors irrespective of its size. We specifically asked whether larger leaders are preferentially followed when behavior is controlled for and whether the preferences of followers depend on their own body size or their risk taking behavior ( boldness). We found that live guppies followed larger Robofish leaders closer than smaller ones and this pattern was independent of the followers own body size as well as risk-taking behavior. This is the first study that shows a bigger is better pattern in leadership in shoaling fish that is fully independent of behavioral differences between differentially-sized leaders and followers own size and personality.

animal behavior and cognition↗

bioRxiv2018

Neolithic and Medieval virus genomes reveal complex evolution of Hepatitis B

The hepatitis B virus (HBV) is one of the most widespread human pathogens known today, yet its origin and evolutionary history are still unclear and controversial. Here, we report the analysis of three ancient HBV genomes recovered from human skeletons found at three different archaeological sites in Germany. We reconstructed two Neolithic and one medieval HBV genomes by de novo assembly from shotgun DNA sequencing data. Additionally, we observed HBV-specific peptides using paleo-proteomics. Our results show that HBV circulates in the European population for at least 7000 years. The Neolithic HBV genomes show a high genomic similarity to each other. In a phylogenetic network, they do not group with any human-associated HBV genome and are most closely related to those infecting African non-human primates. These ancient virus forms appear to represent distinct lineages that have no close relatives today and went possibly extinct. Our results reveal the great potential of ancient DNA from human skeletons in order to study the long-time evolution of blood borne viruses.

evolutionary biology↗

bioRxiv2018

Using a robotic fish to investigate individual differences in social responsiveness in the guppy

Responding towards the actions of others is one of the most important behavioral traits whenever animals of the same species interact. Mutual influences among interacting individuals may modulate the social responsiveness seen and thus makes it often difficult to study the level and variation of individuality in responsiveness. Here, biomimetic robots (BRs) that are accepted as conspecifics but controlled by the experimenter can be a useful tool. Studying the interactions of live animals with BRs allows pinpointing the live animals level of responsiveness by removing confounding mutuality. In this paper, we show that live guppies (Poecilia reticulata) exhibit consistent differences among each other in their responsiveness when interacting with a biomimetic fish robot - Robofish - and a live companion. It has been repeatedly suggested that social responsiveness correlates with other individual behavioral traits like risk-taking behavior ( boldness) or activity level. We tested this assumption in a second experiment. Interestingly, our detailed analysis of individual differences in social responsiveness using the Robofish, suggests that responsiveness is an independent trait, not part of a larger behavioral syndrome formed by boldness and activity.

animal behavior and cognition↗

bioRxiv2018

Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe

European history has been shaped by migrations of people, and their subsequent admixture. Recently, evidence from ancient DNA has brought new insights into migration events that could be linked to the advent of agriculture, and possibly to the spread of Indo-European languages. However, little is known so far about the ancient population history of north-eastern Europe, in particular about populations speaking Uralic languages, such as Finns and Saami. Here we analyse ancient genomic data from 11 individuals from Finland and Northwest Russia. We show that the specific genetic makeup of northern Europe traces back to migrations from Siberia that began at least 3,500 years ago. This ancestry was subsequently admixed into many modern populations in the region, in particular populations speaking Uralic languages today. In addition, we show that ancestors of modern Saami inhabited a larger territory during the Iron Age than today, which adds to historical and linguistic evidence for the population history of Finland.

genomics↗

bioRxiv2018

Understanding 6th-Century Barbarian Social Organization and Migration through Paleogenomics

ABSTARCTDespite centuries of research, much about the barbarian migrations that took place between the fourth and sixth centuries in Europe remains hotly debated. To better understand this key era that marks the dawn of modern European societies, we obtained ancient genomic DNA from 63 samples from two cemeteries (from Hungary and Northern Italy) that have been previously associated with the Longobards, a barbarian people that ruled large parts of Italy for over 200 years after invading from Pannonia in 568 CE. Our dense cemetery-based sampling revealed that each cemetery was primarily organized around one large pedigree, suggesting that biological relationships played an important role in these early Medieval societies. Moreover, we identified genetic structure in each cemetery involving at least two groups with different ancestry that were very distinct in terms of their funerary customs. Finally, our data was consistent with the proposed long-distance migration from Pannonia to Northern Italy.

genetics↗

bioRxiv2018

Individual- and population-level drivers of consistent foraging success across environments

Individual foraging is under strong natural selection. Yet, whether individuals differ consistently in their foraging success across environments, and which individual and population-level traits might drive such differences, is largely unknown. We addressed this question in a field experiment, conducting over 1,100 foraging trials with nine subpopulations of guppies, Poecilia reticulata, translocating them across environments in the wild. A-priori, we determined the individual social phenotypes. We show that individuals consistently differed in reaching food, but not control, patches across environments. Social individuals reached more food patches than less social ones and males reached more food patches than females. Overall, individuals were, however, more likely to join females at patches than males, which explains why individuals in subpopulations with relatively more females reached, on average, more food patches. Our results provide rare evidence for individual differences in foraging success across environments, driven by individual and population level (sex ratio) traits.

animal behavior and cognition↗

bioRxiv2017

Paleo-Eskimo genetic legacy across North America

Paleo-Eskimos were the first people to settle vast regions of the American Arctic around 5,000 years ago, and were subsequently joined and largely displaced around 1,000 years ago by ancestors of the present-day Inuit and Yupik. The genetic relationship between Paleo-Eskimos and Native American populations remains uncertain. We analyze ancient and present-day genome-wide data from the Americas and Siberia, including new data from Alaskan Inupiat and West Siberian populations, and the first genome-wide DNA from ancient Aleutian Islanders, ancient northern Athabaskans, and a 4,250-year-old individual of the Chukotkan Ust'-Belaya culture. Employing new methods based on rare allele and haplotype sharing as well as established methods based on allele frequency correlations, we show that Paleo-Eskimo ancestry is widespread among populations who speak Na-Dene and Eskimo-Aleut languages. Using phylogenetic modelling with allele frequency correlations and rare variation, we present a comprehensive model for the complex peopling of North America.

genetics↗

bioRxiv2017

African Nonhuman Primates Are Infected With The Yaws Bacterium Treponema pallidum subsp. pertenue

Treponema pallidum subsp. pertenue (TPE) is the causative agent of yaws. The disease was subject to global eradication efforts in the mid 20th century but reemerged in West Africa, Southern Asia, and the Pacific region. Despite its importance for eradication, detailed data on possible nonhuman disease reservoirs are missing. A number of African nonhuman primates (NHPs) have been reported to show skin ulcerations suggestive of treponemal infection in humans. Furthermore antibodies against Treponema pallidum (TP) have been repeatedly detected in wild NHP populations. While genetic studies confirmed that NHPs are infected with TP strains, subspecies identification was only possible once for a strain isolated in 1966, pinpointing the involvement of TPE. We therefore collected a number of recently isolated simian TP strains and determined eight whole genome sequences using hybridization capture or long-range PCR combined with next-generation sequencing. These new genomes were compared with those of known human TP isolates. Our results show that naturally occurring simian TP strains circulating in three African NHP species all cluster with human TPE strains and show the same genomic structure as human TPE strains. These data indicate that humans are not the exclusive host for the yaws bacterium and that a One Health approach is required to achieve sustainable eradication of human yaws.

microbiology↗

bioRxiv2017

The Genetic History of Northern Europe

Recent ancient DNA studies have revealed that the genetic history of modern Europeans was shaped by a series of migration and admixture events between deeply diverged groups. While these events are well described in Central and Southern Europe, genetic evidence from Northern Europe surrounding the Baltic Sea is still sparse. Here we report genome-wide DNA data from 24 ancient North Europeans ranging from [~]7,500 to 200 calBCE spanning the transition from a hunter-gatherer to an agricultural lifestyle, as well as the adoption of bronze metallurgy. We show that Scandinavia was settled after the retreat of the glacial ice sheets from a southern and a northern route, and that the first Scandinavian Neolithic farmers derive their ancestry from Anatolia 1000 years earlier than previously demonstrated. The range of Western European Mesolithic hunter-gatherers extended to the east of the Baltic Sea, where these populations persisted without gene-flow from Central European farmers until around 2,900 calBCE when the arrival of steppe pastoralists introduced a major shift in economy and established wide-reaching networks of contact within the Corded Ware Complex.

genetics↗

bioRxiv2017

Salmonella enterica genomes recovered from victims of a major 16th century epidemic in Mexico

Indigenous populations of the Americas experienced high mortality rates during the early contact period as a result of infectious diseases, many of which were introduced by Europeans. Most of the pathogenic agents that caused these outbreaks remain unknown. Using a metagenomic tool called MALT to search for traces of ancient pathogen DNA, we were able to identify Salmonella enterica in individuals buried in an early contact era epidemic cemetery at Teposcolula-Yucundaa, Oaxaca in southern Mexico. This cemetery is linked to the 1545-1550 CE epidemic locally known as \"cocoliztli\", the cause of which has been debated for over a century. Here we present two reconstructed ancient genomes for Salmonella enterica subsp. enterica serovar Paratyphi C, a bacterial cause of enteric fever. We propose that S. Paratyphi C contributed to the population decline during the 1545 cocoliztli outbreak in Mexico.\n\nOne Sentence SummaryGenomic evidence of enteric fever identified in an indigenous population from early contact period Mexico.

genomics↗

bioRxiv2017

Recent Regulatory Changes Shaped the Human Facial and Vocal Anatomy

SummaryRegulatory changes are broadly accepted as key drivers of phenotypic divergence. However, identifying regulatory changes that underlie human-specific traits has proven very challenging. Here, we use 63 DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes affecting the face and vocal tract went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-affecting genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract.View Full Text

evolutionary biology↗

bioRxiv2016

The Stone Age Plague: 1000 years of Persistence in Eurasia

Molecular signatures of Yersinia pestis were recently identified in prehistoric Eurasian individuals, thus suggesting Y. pestis caused some form of disease in humans prior to the first historically documented pandemic. Here, we present six new Y. pestis genomes spanning from the European Late Neolithic to the Bronze Age (LNBA) dating from 4,800 to 3,700 BP. We show that all currently investigated LNBA strains form a single genetic clade in the Y. pestis phylogeny that appears to be extinct. Interpreting our data within the context of recent ancient human genomic evidence, which suggests an increase in human mobility during the LNBA, we propose a possible scenario for the spread of Y. pestis during the LNBA: Y. pestis may have entered Europe from Central Eurasia during an expansion of steppe people, persisted within Europe until the mid Bronze Age, and moved back towards Central Eurasia in parallel with subsequent human population movements.

evolutionary biology↗