Biology subjects

Kolodny, O.

Publications and source records attributed to Kolodny, O..

16 recordsLinked to original sources

bioRxiv2025

The double-edged sword of wildlife biodiversity in the agricultural matrix: a case study of reptiles in vineyards

The global pervasiveness of agriculture and its profound effects on biodiversity increasingly mandate developing sustainable agricultural methods to support healthy ecosystems within agricultural landscapes. However, increasing the attractiveness of agricultural landscapes for wildlife may negatively impact biodiversity if animals or their reproduction are adversely affected in such habitats. While the effects of agricultural practices were investigated across various crop types and wildlife species, reptiles remain largely overlooked. Additionally, although reptiles in croplands were monitored throughout the farming season, little attention has been directed towards the effects of harvest at the seasons end. To illustrate the potential impacts of mechanical harvest on wildlife in permanent crops, we present a case-study concerning reptiles in vineyards. We scanned the waste of a medium-sized winery over four nights and found 105 reptiles, 69% of them chameleons. Though chameleons are considered carnivorous, approximately half had consumed grapes, potentially attracted by them. Vineyards, like many crops, offer resources including sugar, water, and shelter, likely attracting many wildlife species. However, mortality during mechanical harvest may be high, potentially rendering such crops an ecological trap. For chameleons the effects may be particularly devastating, as harvest closely precedes the egg-laying season. While our case study focuses on reptiles in vineyards, its implications extend to many species in permanent crops. Ultimately, ecological traps affect biodiversity by attracting animals to habitats in which their fitness is impaired. While preference has been widely discussed in determining trap severity, our case study highlights that considering the traps fitness impact is also crucial. HighlightsO_LIAgricultural landscapes may attract wild animals while increasing their mortality C_LIO_LIMonitoring biodiversity in agriculture must account for the effects of harvest C_LIO_LIChameleons are likely attracted to vineyards but killed just before reproducing C_LIO_LIAgricultural methods and life history interact to determine ecological trap severity C_LIO_LIEcological trap severity is affected both by preference and by fitness effects C_LI

ecology↗

bioRxiv2024

Competition for resources can reshape the evolutionary properties of spatial structure

Many evolving ecosystems have spatial structures that can be conceptualized as networks, with nodes representing individuals or homogeneous subpopulations and links the patterns of interaction and replacement between them. Prior models of evolution on networks do not take ecological niche differences and eco-evolutionary interplay into account. Here, we combine a resource competition model with evolutionary graph theory to study how heterogeneous topological structure shapes evolutionary dynamics under global frequency-dependent ecological interactions. We find that the addition of ecological competition for resources can produce a reversal of roles between amplifier and suppressor networks for deleterious mutants entering the population. Moreover, we show that this effect is a non-linear function of ecological niche overlap and discuss intuition for the observed dynamics using simulations and analytical approximations.

evolutionary biology↗

bioRxiv2024

Toward a unified theory of microbially mediated invasion

Biological invasions pose major ecological and economic threats, and extensive research has been dedicated to understanding and predicting their dynamics. Most studies focus on the biological invasion of single species, and only in recent years has it been realized that multi-species interactions that involve native and invasive host species and their microbial symbionts can play important roles in determining invasion outputs. A theoretical framework that treats these interactions and their impact is lacking. Here we offer such a framework and use it to explore possible dynamics that may emerge from the horizontal sharing of native and non-native microbial symbionts among native and non-native host individuals and species. Thus, for example, invasive plants might benefit from native mycorrhizal networks in the soil, or might be particularly successful if they carry with them parasites to which competing native hosts are susceptible. On the other hand, invasion might be hindered by native parasites that spread from native to invasive individuals. The mathematical framework that we lay out in this study provides a new mechanistic, cohesive, and intuition-enhancing tool for theoretically exploring the ways by which the subtleties of the relationships between hosts and microbes may affect invasion dynamics. We identify multiple pathways through which microbes can facilitate (or prevent) host invasion, microbial invasion, and the invasion of both hosts and their co-introduced microbes. We disentangle invasion outcomes and highlight modalities of ecological dynamics that have so far not been considered in invasion biology. Our work sets the foundations for invasion theory that includes a community-level view of invasive and native hosts as well as their microbial symbionts.

ecology↗

bioRxiv2023

Shifting from correlations to dynamics in the study of human prehistorical resilience to extreme climatic shifts

In recent years there has been a growing body of research on human resilience to extreme climatic shifts in the past. Most studies focus on comparing archaeological records prior to a perceived climatic shift with those after it, to investigate a causal relationship between the two. Although these comparisons are important, they are limited in their potential to facilitate causal understanding of the factors that determined the human response to climate change. We assert that for such understanding, it is necessary to explicitly consider prior processes that could have made certain populations more resilient to the extreme climatic shift. This assertion calls for a new focus on the cultural and demographic dynamics in prehistorical populations, over the generations that preceded the climatic shift. In this article, we lay out several mechanisms of cultural evolution that - together with the experienced climatic dynamics prior to extreme climatic shifts - may have determined populations abilities to cope with them. This endeavor allows us to outline alternative hypotheses regarding what determined the fate of different human groups. These, in turn, may help direct the collection and analysis of archaeological data and to highlight modalities within it that may be helpful for inference of the mechanisms that determined populations resilience to climatic shifts.

ecology↗

bioRxiv2023

Microbiome transfer from native to invasive species may increase invasion risk and shorten invasion lag

In a fast-changing world, understanding how organisms adapt to their environment is a pressing necessity. Research has focused on genetic adaptation, while our understanding of non-genetic modes is still in its infancy. Particularly, the host-associated microbiome may strongly influence an organisms ability to cope with its environment. The presence of certain microbes in the gut, for example, can facilitate the utilization of dietary resources, provide protection from pathogens, and increase resilience to diverse abiotic conditions. However, the role that the microbiome may play in species adaptation to novel challenges is largely unexplored, experimentally as well as theoretically. Here, we study the possibility of such adaptation in invasive species. We present and explore a new hypothesis: Invasive species may rapidly adapt to local conditions by adopting beneficial microbes of similar co-occurring native species. Ironically, due to competition, these native species are also those most likely to suffer from the invaders spread. We formulate a mathematical framework to investigate how the transfer of beneficial microbes between a native and an introduced species can alter their competitive dynamics. We suggest that, non-intuitively, the presence of a related native species may facilitate the success of an invasive species establishment. This occurs when the invaders fitness is strongly influenced by adaptation to local conditions that is provided by microbes acquired from the natives microbiomes. Further, we show that in such cases a delayed acquisition of native microbes may explain the occurrence of an invasion lag, and we discuss biological systems that could lend themselves for the testing of our hypotheses. Overall, our results contribute to broadening the conceptualization of rapid adaptation via microbiome transfer and offer possible insights for designing early intervention strategies for invasive species management during their lag phase.

ecology↗

bioRxiv2023

Using citizen science to protect threatened amphibian populations in urban spaces: ecology, life history, and conservation of green toads and fire salamanders in Jerusalem and Haifa

O_LIThe rapid urbanization processes occurring worldwide are amongst the main factors driving the current biodiversity crisis. In particular, a third of known amphibian species are directly threatened by urbanization. The negation of this threat will require conservation efforts aimed at sustaining viable amphibian populations within the urban landscape, which must be informed by a deep understanding of the way amphibian populations are affected by the unique risk factors of the urban environment. C_LIO_LITo address this need for four populations of amphibians in Israel, we performed a capture-recapture analysis on two datasets. The larger of the two datasets is the result of a multi-year citizen science program focused on two Salamandra infraimmaculata populations within the city of Haifa, Israel. The second dataset is the result of one year of survey following a similar protocol that we performed on two Bufotes variabilis populations within the city of Jerusalem and at a nature reserve near it. Individuals of both species have unique and recognizable dorsal spot patterns, which allowed for noninvasive recapture identification. C_LIO_LIThe results of our analysis provide insights that can guide future conservation of the specific studied population, but our conclusions have wider implications, regarding both the ecology of the studied species and applied conservation science: using the salamander dataset, we developed a method of length-based age estimations for this species and found that the studied salamanders have a prolonged period of increased vulnerability throughout their first years of life, even after reaching sexual maturity. C_LIO_LIAdditionally, the shared conclusions from the two case studies indicate that the creation of fish-containing artificial water bodies in Mediterranean habitats can have detrimental impacts on the resident amphibian populations. C_LIO_LISynthesis and implications: The significance and extent of our results demonstrate the effectiveness of citizen science as a tool for research and conservation in the urban environment. Our findings call for the implementation of management practices that prioritize the protection of urban amphibians and their habitats. By identifying the vulnerability of amphibians during critical life stages and highlighting the negative impacts of fish-containing water bodies, our study contributes to the development of informed conservation policies with implications for urban planning, habitat management, and biodiversity conservation strategies. C_LI

ecology↗

bioRxiv2023

Shedding light on the Ophel biome: The Trans-Tethyan phylogeography of the sulfide shrimp Tethysbaena (Peracarida: Thermosbaenacea) in the Levant

Tethysbaena are small peracarid crustaceans found in extreme environments such as subterranean lakes and thermal springs, represented by endemic species found around the ancient Tethys, including the Mediterranean, Arabian Sea, Mid-East Atlantic, and the Caribbean Sea. Two Tethysbaena species are known from the Levant: T. relicta, inhabiting the Dead Sea-Jordan Rift Valley, and T. ophelicola, found in the Ayyalon cave complex in the Israeli coastal plain, both belonging to the same species-group based on morphological cladistics. Along the biospeleological research of the Levantine subterranean fauna, three biogeographic hypotheses determining their origins were proposed: (1) Pliocenic transgression, (2) Mid-late Miocenic transgression, and (3) The Ophel Paradigm, according to which these are inhabitants of a chemosynthetic biome as old as the Cambrian. We have used mtDNA COI gene and a molecular clock approach to establish the phylogeny and assess the divergence times of the Levantine Tethysbaena. Contrary to prior hypotheses, our results indicate a two-stage colonization pattern: a late Oligocene transgression, through a marine gulf extending from the Arabian Sea, leading to the colonization of T. relicta in the Dead Sea-Jordan Rift Valley, and a Miocene transgression in the emerging Mediterranean region, carrying T. ophelicola to the coastal plain of Israel.

zoology↗

bioRxiv2023

Mutualism at the leading edge: Insights into the eco-evolutionary dynamics of host-symbiont communities during range expansion

The evolution of mutualism between host and symbiont communities plays an essential role in maintaining ecosystem function and should therefore have a pro-found effect on their range expansion dynamics. In particular, the presence of mutualistic symbionts at the leading edge of a host-symbiont community should enhance its propagation in space. We develop a theoretical framework that captures the eco-evolutionary dynamics of host-symbiont communities, to investigate how the evolution of resource exchange may shape community structure during range expansion. We consider a community with symbionts that are mutualistic or parasitic to various degrees, where parasitic symbionts receive the same amount of resource from the host as mutualistic symbionts, but at lower cost. The selective advantage of parasitic symbionts over mutualistic ones is strengthened with resource availability (i.e. with host density), promoting mutualism at the range edges, where host density is low, and parasitism in the population core, where host density is higher. This spatial selection also influences the speed of spread. We find that the host growth rate (which depends on the average benefit provided by the symbionts) is maximal at the range edges, where symbionts are more mutualistic, and that host-symbiont communities with high symbiont density at their core (e.g. resulting from more mutualistic hosts) spread faster into new territories. These results indicate that the expansion of host-symbiont communities is pulled by the hosts but pushed by the symbionts, in a unique push-pull dynamic where both the host and symbionts are active and tightly-linked players.

ecology↗

bioRxiv2022

Modeling effects of inter-group contact on links between population size and cultural complexity

Human populations rely on cultural artifacts and complex cumulative culture for their survival. Populations vary dramatically in the size of their tool repertoires, and the determinants of these cultural repertoire sizes have been the focus of extensive study in recent years. A prominent hypothesis, supported by computational models of cultural evolution, asserts that tool repertoire size increases with population size. However, not all empirical studies seeking to test this hypothesis have found such a correlation; this has led to a contentious and ongoing debate. As a possible resolution to this longstanding controversy, we suggest that accounting for even rare cultural migration events that allow sharing of knowledge between different-sized populations may help explain why a populations size might not always predict its cultural repertoire size. Using an agent-based model to explore different assumptions about the effects of population size and migration on tool repertoires, we find that connectivity of one population to others, particularly to large populations, may significantly boost its tool repertoire size when population interactions lead to cultural exchange. Thus, two populations of identical size may have drastically different tool repertoire sizes, hinging upon their access to other groups knowledge. Intermittent contact between populations boosts cultural repertoire size and still allows for the development of unique tool repertoires that have limited overlap between populations.

evolutionary biology↗

bioRxiv2022

Cultural specialization as a double-edged sword: division into specialized guilds might promote cultural complexity at the cost of higher susceptibility to cultural loss

The transition to specialization of knowledge within populations could have facilitated the accumulation of cultural complexity in humans. Specialization allows populations to increase their cultural repertoire without requiring that members of that population increase their individual capacity to accumulate knowledge. However, specialization also means that domain-specific knowledge can be concentrated in small subsets of the population, making it more susceptible to loss. Here we use a model of cultural evolution to demonstrate that specialized populations can be more sensitive to stochastic loss of knowledge than populations without subdivision of knowledge, and that demographic and environmental changes have an amplified effect on populations with knowledge specialization. Finally, we suggest that specialization can be a double-edged sword; specialized populations may have an advantage in accumulating cultural traits but may also be less likely to expand and establish themselves successfully in new demes due to the increased cultural loss that they experience during the population bottlenecks that often characterize such expansions.

evolutionary biology↗

bioRxiv2022

Explaining the microbial diversity conundrum: can microbiome composition be crucial for host fitness, while highly divergent among healthy individuals?

Recent empirical studies offer conflicting findings regarding the relation between host fitness and the composition of its microbiome, a conflict which we term the microbial {beta} - diversity conundrum: it has been shown that the microbiome is crucial for host wellbeing and survival. At the same time, different healthy individuals microbiome compositions, even in the same population, often differ dramatically, contrary to the notion that a vital trait should be highly conserved. Moreover, gnotobiotic individuals exhibit highly deleterious phenotypes, supporting the notion that the microbiome is paramount to host fitness. However, the introduction of almost arbitrarily selected microbiota into the system often achieves a significant rescue effect of the deleterious phenotypes, even microbiota from soil or phylogenetically distant host species, highlighting an apparent paradox. Here we suggest several solutions to the paradox using a computational framework, simulating the population dynamics of hosts and their microbiomes over multiple generations. The answers, relating to factors such as host population size, the specific mode of contribution of the microbes to host fitness, and the typical microbiome richness, offer solutions to the conundrum by creating scenarios where even when a hosts fitness is determined in full by its microbiome composition, this composition has little or no effect on the natural selection dynamics of the population.

evolutionary biology↗

bioRxiv2021

Short-Term Dairy Elimination and Reintroduction Minimally Perturbs the Gut Microbiota in Self-Reported Lactose Intolerant Adults

One of the outstanding questions regarding the human gut microbiota is how interventions designed to manipulate the microbiota may influence host phenotypic traits. Here, we employed a dietary intervention to probe this question in the context of lactose intolerance. To assess the effects of dairy elimination and reintroduction on the microbiota and host phenotype, we paired fecal 16S rRNA amplicon sequencing with a clinical assay for lactose intolerance, the hydrogen breath test. We studied 12 self-reported mildly lactose intolerant adults, each with tri-weekly collection of fecal samples over a 12-week study period (2 weeks baseline, 4 weeks of dairy elimination, 6 weeks of gradual milk reintroduction) and a hydrogen breath test before and after each phase. We found that although none of the subjects experienced a change in clinically defined status of lactose intolerant or tolerant, most subjects were qualitatively better able to tolerate dairy products with minimal symptoms at the end of the study compared to their baseline. Like clinical status, gut microbiota also resisted modification. Although the mean fraction of the genus Bifidobacterium, a group known to metabolize lactose, increased slightly with dairy reintroduction (from 0.0125 to 0.0206; Wilcoxon P = 0.068), the overall structure of each subjects gut microbiota remained highly individualized and largely stable. Our study is small, but it suggests the possibility of qualitatively improved tolerance in the absence of change in clinically defined tolerance nor major change in the gut microbiota.

microbiology↗

bioRxiv2020

Simplified model assumptions artificially constrain the parameter range in which selection at the holobiont level can occur

Van Vliet & Doebeli (1) (henceforth VVD) present a multi-level selection framework simulating host-microbiome evolutionary dynamics. The model explores the conditions under which the association between hosts and their "helper" microbiome - microbes that developed a trait that provides a benefit to the host at a cost to themselves - is strong enough to allow for selection at the holobiont level. The model is an important contribution to the holobiont debate, making the notion quantifiable and highlighting the involved parameters. In the study, VVD conclude that the parameter space in which selection occurs at the level of the holobiont is extremely restricted (Fig 1). Here we show that this result stems from specific model assumptions. Although these assumptions are reasonable as a modeling starting point, slight biologically-reasonable modifications of the assumptions lead to qualitatively different outcomes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/988766v1_fig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@29fe1org.highwire.dtl.DTLVardef@4ea220org.highwire.dtl.DTLVardef@75e515org.highwire.dtl.DTLVardef@12e9d6_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1.C_FLOATNO VVDs original results - Selection can only act at the holobiont level under stringent conditions. The mean helper frequency is shown as a function of the timescale of the evolutionary dynamics at the microbe level relative to the host generation time and the ratio of vertical to horizontal transmission. Two different levels of sampling variance are shown: the SD of the sampling distribution is 0.02 in A and 0.1 in B; A (top) and B (top) show the results of single simulations, and A (bottom) and B (bottom) show the same data, averaged within discrete bins. C_FIG

evolutionary biology↗

bioRxiv2019

Reconsidering the management paradigm of fragmented populations

Habitat fragmentation and population declines call for informed management of many endangered species. The dominant paradigm for such management focuses on avoiding deleterious inbreeding effects in separated populations, by facilitating migration to maintain connectivity between them, an approach epitomized by the \"one migrant per generation\" rule. We show that this paradigm fails to take into account two important factors. First, it ignores an inherent trade-off: maintaining within-population genetic diversity is at the expense of maintaining global diversity. Migration increases local within-population genetic diversity, but also homogenizes the meta-population, which may lead to erosion of global genetic diversity. Second, this paradigm does not consider that because many fragmented species have declined in numbers only within the last century, they still carry much of the high genetic diversity characteristic of the historically large population. The conservation of a species global diversity, crucial for evolutionarily adaptation to ecological challenges such as epidemics, industrial pollutants, or climate change, is paramount to a species long-term survival. Here we discuss how consideration of these factors can inform management of fragmented populations and provide a framework to assess the impact on genetic diversity of different management strategies. We also propose two alternative management strategies to replace the \"one migrant per generation\" dogma.

ecology↗

bioRxiv2018

Disease and introgression explain the long-lasting contact zone of Modern Humans and Neanderthals and its eventual destabilization

Neanderthals and modern humans both occupied the Levant for tens of thousands of years prior to modern humans spread into the rest of Eurasia and their replacement of the Neanderthals. That the inter-species boundary remained geographically localized for so long is a puzzle, particularly in light of the rapidity of its subsequent movement. We propose that disease dynamics can explain the localization and persistence of the inter-species boundary; in this view, each species carried pathogens to which it was largely immune and tolerant, but that could spread to the other, vulnerable, species, inducing a significant disease burden. Epidemics and endemic diseases along the interspecies boundary would have mitigated against bands of one species migrating into regions dominated by the other species. Together with decreased population densities and limited inter-group interactions due to disease burden, this mechanism could have resulted in a fixed and narrow contact-zone. We further propose, and support with results from dynamical systems models, that genetic introgression, including transmission of alleles related to the immune system, would have gradually allowed the two species to overcome this barrier to pervasive inter-species interaction, leading to the eventual release of the inter-species boundary from its geographic localization. Asymmetries between the two species in the initial size of their associated \"pathogen package\" could have created feedback loops that influenced the rates at which immunity to and tolerance of the novel pathogens were acquired. These asymmetries could have allowed modern humans to overcome the disease burden earlier than Neanderthals, giving them a significant advantage in their subsequent spread into Eurasia, particularly upon interaction with Neanderthal populations that had previously been far from the original contact zone in the Levant.

evolutionary biology↗

bioRxiv2017

Random Drift With A Determined Outcome: A Parsimonious Null Model OfNeanderthal Replacement By Modern Humans Via Neutral Species Drift

The processes that led to the demise of the Neanderthals and their replacement by modern humans have been the object of speculation, research, and heated debate. Most hypotheses fall into one of two categories: one highlights the role of climate change, epidemics, or other environmental pressures in the Neanderthals demise, and the other attributes it to direct or indirect competition with modern humans, who seem to have occupied the same ecological niche. The latter are based on the assumption that modern humans benefited from some selective advantage over Neanderthals that led to the latters extinction. We show that a scenario that includes migration and selectively neutral species drift can explain the Neanderthals replacement and is in line with the archaeological evidence. Our model offers a parsimonious alternative to those that invoke external factors or selective advantage, and can represent a null hypothesis in assessing such alternatives. We show that for a wide range of parameters this hypothesis cannot be rejected. Moreover, we suggest that although selection and environmental factors may or may not have played a role in the interspecies dynamics of the Neanderthals and modern humans, the eventual outcome of these dynamics, the replacement of the Neanderthals, was the result of the hominid migration dynamics at the end of the middle Paleolithic, namely repeated migration of modern humans from Africa into the Levant and Europe.\n\nSignificance statementMultiple factors have been proposed as possible drivers of the extinction of the Neanderthals and their replacement by modern humans circa 40,000 years ago: climate change, epidemics, and - most prominently - a selective advantage, such as superior cognitive capacity of modern humans over Neanderthals. We propose an alternative model that includes only migration of modern humans out of Africa into the Levant and Europe. We show that, given that the two species occupied a similar ecological niche, modern humans were destined to replace the Neanderthals even under a neutral scenario in which neither species has a selective advantage.

evolutionary biology↗