Reduction In Population Size Research Articles

Does restoring apex predators to food webs restore ecosystems? Large carnivores in Yellowstone as a model system

AbstractModification of food webs is a frequent cause of shifts in ecosystem states that resist reversal when the food web is restored to its original condition. We used the restoration of the large carnivore guild including gray wolves (Canis lupis), cougars (Felis concolor), and grizzly bears (Ursus arctos horribilis) to the northern range of Yellowstone National Park as a model system to understand how ecosystems might resist reconfiguration after the restoration of apex predators to the food web. The absence of wolves, cougars, and grizzly bears for nearly a century from the northern range was the primary cause of dramatic changes in riparian plant communities. Willows (Salix spp.) were suppressed in height by intense browsing by the dominant herbivore, elk (Cervus canadensis). The loss of activity by beavers (Castor canadensis) coincided with the loss of tall willows. We hypothesized that intense elk browsing interrupted the mutualism between willow and beavers: ecosystem engineering by beavers was a critical component of willow habitat and tall willows were a critical component of habitat for beavers. This interruption made riparian communities resilient to the disturbance caused by the restoration of apex predators. We hypothesized further that reductions in elk browsing attributable to reductions in elk population size were not sufficient to prevent the suppression of willow growth. To test these hypotheses, we conducted a 20‐year, factorial experiment that crossed simulated beaver dams with the exclusion of browsing. We found that willows grew to heights expected for restored communities only in the presence of dams and reduced browsing. Willows experiencing ambient conditions remained well below this expectation. We found no difference in heights or growth rates of willows in experimental controls and willows in 21 randomly chosen sites, confirming that the results of the experiment were representative of range‐wide conditions. A reorganized community of large herbivores was implicated in the suppression of willow growth. We conclude that the restoration of large carnivores to the food web failed to restore riparian plant communities on Yellowstone's northern range, supporting the hypothesis that this ecosystem is in an alternative stable state caused primarily by the extirpation of apex predators during the early 20th century.

GENETIC APPROACH OF THE COIBA ISLAND HOWLER MONKEY Alouatta coibensis coibensis FROM PANAMA, AND ITS CONSERVATION IMPLICATIONS

Studies on genetic diversity are key to conservation management because they may determine the resilience of primate populations under environmental and anthropogenic changes. Herein, we studied genetic diversity and connectivity in a population sample of the Coiba island howler monkey Alouatta coibensis coibensis from Coiba island in Panama. We collected 14 faecal samples from individuals at two sites on the northern and north-eastern sides of the island at the Gambute and Los Pozos trails, respectively. DNA was extracted from these samples, and partial sequences of cytochrome oxidase I (COI) were obtained and used as molecular markers to determine genetic diversity. Haplotypic diversity estimates ranged from 0.68 to 0.80 and from 0.0026 to 0.0041 for nucleotide diversity. Genetic connectivity based on reduced genetic distances and nonsignificant Hudson Snn test values suggests elevated connectivity between sites and the existence of a single population with good variability. Demographic history data identified positive Tajimas D as an indication of population contraction and reduced population size in this species. These results will be the baseline for establishing a better understanding of population structure, genetic health, connectivity patterns and reproductive behaviour along the largest island of the Central American Pacific. This information will allow scientists to understand and better evaluate the conservation status of this primate, confirming good availability of genetic flow even for this population living in isolation.

The genome of the black-footed cat: Revealing a rich natural history and urgent conservation priorities for small felids.

Habitat degradation and loss of genetic diversity are common threats faced by almost all of today's wild cats. Big cats, such as tigers and lions, are of great concern and have received considerable conservation attention through policies and international actions. However, knowledge of and conservation actions for small wild cats are lagging considerably behind. The black-footed cat, Felis nigripes, one of the smallest felid species, is experiencing increasing threats with a rapid reduction in population size. However, there is a lack of genetic information to assist in developing effective conservation actions. A de novo assembly of a high-quality chromosome-level reference genome of the black-footed cat was made, and comparative genomics and population genomics analyses were carried out. These analyses revealed that the most significant genetic changes in the evolution of the black-footed cat are the rapid evolution of sensory and metabolic-related genes, reflecting genetic adaptations to its characteristic nocturnal hunting and a high metabolic rate. Genomes of the black-footed cat exhibit a high level of inbreeding, especially for signals of recent inbreeding events, which suggest that they may have experienced severe genetic isolation caused by habitat fragmentation. More importantly, inbreeding associated with two deleterious mutated genes may exacerbate the risk of amyloidosis, the dominant disease that causes mortality of about 70% of captive individuals. Our research provides comprehensive documentation of the evolutionary history of the black-footed cat and suggests that there is an urgent need to investigate genomic variations of small felids worldwide to support effective conservation actions.

Calcium stress reduces the reproductive capacity and pathogenicity of the pine wood nematode (Bursaphelenchus xylophilus) by inhibiting oxidative phosphorylation reaction

The continuous use of chemical pesticides to control nematodes could result in the developing of pesticide-resistant nematodes. Novel nucleic acid pesticides are becoming the focus of pesticide research due to their strong specificity, high efficiency, and environmental friendliness. However, the limited known biochemical targets restrict the development of target pesticides for nematodes. The calcium stress experiments on pine wood nematodes (PWN) showed that 100 mmol/L Ca2+ resulted in longitudinal depression on the PWN body wall, reduced oviposition, and increased corrected mortality. To enrich the biological targets of nematode pesticides, we further investigated the response mechanism of PWN to calcium stress at the molecular level. Differentially expressed gene analysis showed that genes involved in the oxidative phosphorylation (OXPHOS) pathway were significantly enriched. RNA interference results of 6 key genes belonging to four mitochondrial complex I (BXNDUFA2), III (BXQCR8), IV (BXCOX17), V (BXV-ATPaseB, BXV-ATPaseE, BXV-ATPaseε) in non-stressed nematodes showed reduction in PWN oviposition, population size, feeding ability, and pathogenicity. The BXNDUFA2 gene interference had the highest inhibitory impact by decreasing the oviposition from 31.00 eggs to 6.75 eggs and PWN population size from 8.27 × 103 nematodes to 1.64 × 103 nematodes, respectively. Interestingly, RNA interference of these 6 key genes in calcium-stressed nematodes also led to increased mortality and decreased oviposition of PWN. In summary, calcium stress inhibited the reproductive capacity of PWN by down-regulating key genes BXNDUFA2, BXQCR8, BXV-ATPaseB, BXV-ATPaseE, BXV-ATPaseε, and BXCOX17, thereby reducing the pathogenicity. The current results enrich the RNAi targets in PWN and provide a scientific basis for developing novel nucleic nematicides.

Genetic diversity, gene flow, and landscape resistance in a pond-breeding amphibian in agricultural and natural forested landscapes in Norway.

Genetic diversity is a key part of biodiversity, threatened by human activities that lead to loss of gene flow and reduction of effective population sizes. Gene flow is a result of both landscape connectivity and demographic processes determining the number of dispersing individuals in space and time. Thus, the effect of human impact on processes determining the level of genetic diversity must be interpreted in the context of basic ecological conditions affecting survival and recruitment. When the intensity of human impact and habitat suitability correlate, the effect on genetic diversity and gene flow may be challenging to predict. We compared genetic diversity, gene flow and landscape resistance in two contrasting landscapes in Norway for the pond-breeding amphibian Triturus cristatus: a highly human-impacted, agricultural landscape with ecologically productive habitats, and a forested landscape with less productive habitats and lower levels of human impact. Our results show that genetic diversity was higher and gene flow lower within the forested landscape. Microclimatic moisture conditions and vegetation cover were important determinants of landscape resistance to gene flow within both landscapes. There were indications that landscape resistance was increased by minor roads in the forested landscape, which was not the case for the agricultural landscape, suggesting a higher vulnerability to human interference within the landscape matrix for the populations in less productive habitats. Our findings suggest that the effect of human impact on genetic diversity may not be straightforward but modulated by the ecological conditions underlying local demographic processes. Populations within both landscapes seem to be vulnerable to loss of genetic diversity, but due to different mechanisms. This has implications for the choice of relevant management actions, that is, increasing population stability may be more relevant within an agricultural landscape still permeable for dispersal, while conserving dispersal corridors may be more appropriate in the forested landscape, to avoid isolation and increased genetic drift.

Demographic responses of oceanic island birds to local and regional ecological disruptions revealed by whole-genome sequencing.

Disentangling the effects of ecological disruptions operating at different spatial and temporal scales in shaping past species' demography is particularly important in the current context of rapid environmental changes driven by both local and regional factors. We argue that volcanic oceanic islands provide useful settings to study the influence of past ecological disruptions operating at local and regional scales on population demographic histories. We investigate potential drivers of past population dynamics for three closely related species of passerine birds from two volcanic oceanic islands, Reunion and Mauritius (Mascarene archipelago), with distinct volcanic history. Using ABC and PSMC inferences from complete genomes, we reconstructed the demographic history of the Reunion Grey White-eye (Zosterops borbonicus (Pennant, 1781)), the Reunion Olive White-eye (Z. olivaceus (Linnaeus, 1766)) and the Mauritius Grey White-eye (Z. mauritianus (Gmelin, 1789)) and searched for possible causes underlying similarities or differences between species living on the same or different islands. Both demographic inferences strongly support ancient and long-term expansions in all species. They also reveal different trajectories between species inhabiting different islands, but consistent demographic trajectories in species or populations from the same island. Species from Reunion appear to have experienced synchronous reductions in population size during the Last Glacial Maximum, a trend not seen in the Mauritian species. Overall, this study suggests that local events may have played a role in shaping population trajectories of these island species. It also highlights the potential of our conceptual framework to disentangle the effects of local and regional drivers on past species' demography and long-term population processes.

Landscape structure does not hinder the dispersal of an invasive herbivorous mammal in the New Caledonian biodiversity hotspot

Biological invasions are a major threat to biodiversity and have particularly devastating impacts on island ecosystems. The New Caledonia archipelago is considered a biodiversity hotspot due to its diverse native flora. Javan rusa deer (Rusa timorensis) were introduced to New Caledonia in 1870 and the population consists of several hundred thousand individuals today. They directly threaten rare endemic species and affect the composition and structure of the vegetation. While a rusa deer management plan has identified ten priority areas for deer control operations, removing deer could be offset by the dispersal of animals back into the control areas. Here, we genotyped 628 rusa deer using 16 microsatellite markers to analyse the genetic structure of the animals in New Caledonia. We aimed to assess fine-scale genetic structure, to identify natural barriers to deer movement and to assess functional connectivity by optimising individual-based landscape resistance models. Our results suggested that rusa deer formed a single genetic population on the main New Caledonian island. The isolation-by-distance pattern suggested that female dispersal was limited, whereas males had larger dispersal distances. We assessed functional connectivity using different genetic distance metrics and all models performed poorly (mR2 ≤ 0.0043). Landscape features thus hardly affected deer movement. The characteristics of our results suggested that they were not an artefact of the colonisation history of the species. Achieving an effective reduction of deer population sizes in specific management areas will be difficult because of the deer’s high dispersal capabilities and impossible without very substantial financial investment.

Predicting the small strain shear modulus of sands and sand-fines binary mixtures using machine learning algorithms

This study aims to develop several novel machine learning (ML) evolutionary algorithms for the prediction of small strain shear modulus (Gmax) of clean sands and sand-fines binary mixtures. To this end, five key features of isotropic confining pressure (p), void ratio (e), uniformity coefficient (Cu), particle shape descriptor (ρ), and non-plastic fines content (FC) are adopted as the inputs to artificial neural network (ANN) models as well as genetic programming (GP) algorithm so as to render the maximum shear modulus of granular soils as the output. Accordingly, a comprehensive dataset containing 1055 Gmax data points is exploited to develop ML simulations. The validity of ML-based models in estimating the Gmax of clean sands and sand-silt mixtures is rigorously examined through various statistical indices and measurement criteria. The results show that a novel ML model utilizing ANN-Levenberg Marquardt (LM) in conjunction with an evolutionary optimization method named Success History-based Adaptive Differential Evolution with Linear population size reduction (LSHADE) is capable of predicting Gmax data with a very high precision rendering R2 values of 0.9833, 0.9841, 0.9802, and 0.9835 for the whole, training, validation, and test datasets, respectively. Meanwhile, using the well-established GP algorithm, a new practical model is proposed to predict the Gmax of clean sands and sand-fines mixtures containing non-cohesive silt inclusion with R2 values of 0.9323, 0.9351, and 0.9312 for the whole, training, and test datasets, respectively. Finally, the proposed models of ANN-LSHADE-LM and GP are shown to be appreciably superior, in terms of accuracy, to all commonly used empirical correlations in the literature for Gmax estimation.

Trouble in the trawls: Is bycatch in trawl fisheries preventing the recovery of sawfish? A case study using the US population of smalltooth sawfish, Pristis pectinata

All five species of sawfish (Family Pristidae), are among the most threatened families of elasmobranchs, and face significant threats from fishing, in particular trawl fisheries, and habitat loss. Unfortunately, there is little data on the level of sawfish taken in trawl fisheries outside Australia and the United States and case studies from these areas can provide a “risk analysis” for populations elsewhere. In the United States, bycatch risk for smalltooth sawfish is significantly higher for the southeast shrimp trawl fishery than all other fisheries assessed. Using new estimates of life history and population size, an updated population viability model was developed and trajectories using different scenarios of initial population sizes, fishery catches and post-release mortality were projected for 100 years. The simulated population trajectories for the assumed initial population sizes and fishing mortality ranged between population extinction, quasi-extinction, to a slight reduction in population size and in some cases the population continuing to recover. The most pessimistic scenarios were when the initial population was lowest and post-release mortality in the shrimp trawl fishery was highest. Quasi-extinction for some scenarios was between 6.9 and 22.8 years. While some scenarios suggest that smalltooth sawfish still can recover despite the potential for shrimp trawl fishing mortality, key input variables for these optimistic scenarios is the initial population size and the true level of fishing mortality. This uncertainty highlights the importance of improving our understanding of sawfish life history, captures in fisheries and their associated post-release mortality.

Intensive sea urchin harvest rescales Paracentrotus lividus population structure and threatens self-sustenance.

The harvest of the edible sea urchin Paracentrotus lividus is intensively practiced in some regions of the Western Mediterranean Sea. The removal of the largest individuals can determine an overall reduction in population size and a size class truncation that can lead to a drastic drop the self-sustenance. The aim of this study is to evaluate the variability of the population reproductive potential across 5 years in one of the main harvest hotspots of Sardinia (Western Mediterranean Sea). The breeding stock consists of commercial and under-commercial size individuals which were sampled on a monthly basis to estimate their GonadoSomatic Index (GSI) and the Individual Gamete Output (IGO). In addition, the reproductive potential of the population-Total Gamete Output (TGO)-was calculated across the 5-year period in relation with the variation of the density of the breeding stock. During the last year, the reproductive potential was also estimated in a well-conserved population of a nearby Marine Protected Area. No significant variability in GSI and IGO was found over the 5 years nor when compared with the ones of protected population in the last year. However, the intensive harvest drastically rescaled the population body-size: although density of the commercial size class remained low, density of the under-commercial size-class halved from the beginning to the end of the study. Accordingly, the proportional decrease of their gamete output contribution led to a 40% loss of the reproductive potential of the whole population in the 5-year period. Interestingly, despite the loss of reproductive potential due to the decrease of the breeding stock density, the average values of IGO slightly increased across the years leading to the highest Annual Gamete Output (AGO) during the fourth year of sampling. This positive pattern could suggest a mechanism of reproductive investments of the survivors in terms of gonad production rate or increase in spawning intensity. This work provides evidence of the direct effect of size-selective harvesting on the rapid loss of population self-sustenance. Furthermore, it lays new prospective for future research of the indirect effects of the rescaling population body-size in functional traits of the sea urchin P. lividus and that could become important for both, sustainable exploitation and ecosystem conservation management.

Importance of Genetic-Fitness Correlations for the Conservation of Amphibians.

Endangered animals suffer from isolation of their habitats. Isolation leads to a reduction in population size as well as a decrease in genetic diversity and a concomitant increase in the risk of extinction. Amphibians are the most endangered vertebrate class. Besides habitat loss, fragmentation and isolation, amphibians are threatened by emerging diseases e.g., chytrid fungus or Ranavirus. By employing experiments, researchers investigate whether changes in genetic diversity within or among isolated populations affect amphibian fitness. While genetic diversity estimates are based on molecular markers, typically microsatellites, fitness is mostly measured as tadpole performance in rearing experiments often under varying environmental conditions. Tadpole performances (e.g., body mass, growth rate and survival) have been found to be negatively affected by low genetic diversity, as several studies have found a positive association between genetic diversity and these fitness traits. Moreover, infection with pathogens also seems to be more likely in individuals or populations with lower genetic diversity. Overall, these genetic-fitness correlations seem to be more pronounced or detectable in smaller, declining populations but not in larger populations. Genomic studies, which sample a larger fraction of the genome, are still scarce in the conservation genetic literature on amphibians. These are likely to increase in upcoming years and may reveal adaptive variants that protect against dangerous pathogens or environmental changes. Altogether, genetic-fitness correlation studies should be a priority in order to develop effective management plans for the genetic rescue of isolated, imperilled amphibian populations.

Impact of Holocene environmental change on the evolutionary ecology of an Arctic top predator.

The Arctic is among the most climatically sensitive environments on Earth, and the disappearance of multiyear sea ice in the Arctic Ocean is predicted within decades. As apex predators, polar bears are sentinel species for addressing the impact of environmental variability on Arctic marine ecosystems. By integrating genomics, isotopic analysis, morphometrics, and ecological modeling, we investigate how Holocene environmental changes affected polar bears around Greenland. We uncover reductions in effective population size coinciding with increases in annual mean sea surface temperature, reduction in sea ice cover, declines in suitable habitat, and shifts in suitable habitat northward. Furthermore, we show that west and east Greenlandic polar bears are morphologically, and ecologically distinct, putatively driven by regional biotic and genetic differences. Together, we provide insights into the vulnerability of polar bears to environmental change and how the Arctic marine ecosystem plays a vital role in shaping the evolutionary and ecological trajectories of its inhabitants.

Depredation influences anglers’ perceptions on coastal shark management and conservation in the United States Gulf of Mexico

Overfishing, habitat degradation, and climate change have caused declines in shark populations throughout the world’s oceans. However, in the United States Gulf of Mexico (GoM), populations of several coastal shark species are starting to stabilize following decades of successful regulations and enforcement. The stabilization of coastal shark populations, coupled with increases in recreational fishing effort, has the potential to escalate human-wildlife interactions. The most often reported conflict is shark depredation, the partial or complete removal of a hooked species by a shark. Reported increases in shark depredation within the last several years have begun to erode angler support for shark conservation, potentially undermining decades of previous work. To address these concerns, we implemented a GoM-wide online survey to characterize the impact of depredation on recreational reef fish anglers’ fishing satisfaction and perceptions of shark management and conservation. Our results revealed that most recreational anglers in the GoM have witnessed depredation but have not changed their fishing behaviors. In contrast, anglers’ viewpoints on managing shark populations were split between reducing population sizes and maintaining current population levels. As coastal shark populations in the GoM continue to recover, shark depredation is likely to increase. Consequently, efforts to characterize anglers’ satisfaction and perceptions are a critical component of future shark conservation initiatives.

A comparative study of evolutionary computation and swarm-based methods applied to color quantization

Color Quantization (CQ) is a complex and hard problem because selecting the best set of colors from many available colors and using that set to obtain a good quality image is an NP-complete problem. The use of evolutionary computation and swarm-based methods to solve search and optimization problems has increased dramatically in recent years. This article compares some of these methods in order to solve the CQ problem. The following methods were used to generate CQ images: Particle swarm optimization, Artificial bee colony, Adaptive differential evolution, Success-history based adaptive differential evolution (with and without linear population size reduction), Cuckoo search, Firefly algorithm and Shuffled-frog leaping algorithm. For the first two methods, two variants were considered. Thus, a total of ten metaheuristics were compared with four classical CQ methods (Variance-based, Median-cut, Binary splitting and Wu’s methods) applying them to a set of benchmark images and considering four different palette sizes (32, 64, 128, and 256 colors). Three error measures were considered to compare the methods: the mean squared error, the mean absolute error and the peak signal-to-noise ratio. Some of the swarm-based methods analyzed include a recently proposed CQ method using ants. Although they have a slow computational speed in the experimental studies, the ant-based methods are significantly better than all other methods according to the Wilcoxon signed rank test. In general, despite their speed, classical methods underperform the other ten methods both qualitatively and quantitatively.

Estimating the impact of the illegal trade of primates in Mexico: a potential threat to wildlife.

The primates of Mexico, Ateles geoffroyi, Alouatta palliata, and Alouatta pigra, are seriously threatened by habitat loss, fragmentation, and illegal hunting and trade. Very little is known about the extent of illegal trade and its impacts on declining primate populations. Our study proposes a potential method based on estimating the number of individuals that die in the trade before being detected and those that probably cannot be detected. This facilitates estimating the number of animals extracted and allows an assessment of how trafficking impacts their populations. We derive estimates from seizure data of primates in Mexico between 2010 and 2019. To do this, we created wildlife detection rates and mortality rates from the existing literature (scientific articles, journalistic articles, and notes) to estimate the number of primates that die during capture, transport, and sale and the number of trafficked primates that were not detected by Mexican authorities. We estimate that 946 primates were removed from the wild for the pet trade each year (spider monkey Ateles geoffroyi= 854; black howler monkeys Alouatta pigra= 38, mantled howler monkey Alouatta palliata= 54). The annual reduction in population size caused by trafficking was greatest for Ateles geoffroyi (2.2%), followed by Alouatta pigra (1.3%), and Alouatta palliata (0.4%). Our estimates show the percentage of impacts that trafficking has on Mexican primate populations. Nevertheless, trade has the potential to impact declining populations and still must be addressed.

Genetic Variability of Tabebuia rosea (Bignoniaceae) from Plantations and Remnant Populations in the Mayan Forest

In Neotropical regions, plantations and remnant forest populations of native trees coexist in a highly fragmented matrix and may be affected by isolation and reduction in population size, leading to genetic structure, inbreeding, and genetic bottlenecks that reduce the population’s genetic diversity. Tabebuia rosea variability in the Mayan Forest was studied by genotyping 30 trees from three plantations and three remnant natural populations using simple sequence repeats (SSRs) and inter-simple sequence repeats (ISSRs). Ho-SSR estimates were lower than He; the mean inbreeding coefficient was 0.07 and did not differ among populations, but was eight times higher in plantations than in remnant populations. Using ISSR data, the individuals were assigned to k = 5 and k = 4 clusters under admixture without and with geographic information used as priors in Bayesian analysis assignments. Genetic differentiation estimated with the Bayesian estimator II (0.0275 ± 0.0052) was significantly different from 0, but FST was not (0.0985 ± 0.1826), while paired FST among populations ranged from 0.05 up to 0.16. Only one remnant population displayed evidence of a genetic bottleneck. T. rosea displays a genetic structure in which the isolated remnant forest populations show moderate inbreeding levels.

Conservation genomics of Dioon holmgrenii (Zamiaceae) reveals a history of range expansion, fragmentation, and isolation of populations

Many Cycad species may not survive the current extinction crisis, despite belonging to the oldest living seed plant lineage. Conservation of endangered and threatened species will require a combination of in situ and ex situ programs, both of which will benefit from better knowledge of species’ population genetic structure, as will assessments of threatened status. Here we develop a cost-effective method of obtaining population-level genomic data from across the range of the Mexican cycad, Dioon holmgreni, and use these data to characterize the genetic structure and diversity of the species. We also reconstruct aspects of the demographic history of the species and evaluate the taxonomic cohesion of populations across the range using genomic and morphological data. We find that D. holmgrenii harbors moderate genetic diversity across genetically and geographically isolated populations that each possess a substantial percentage of private alleles. We further find that the history of this species likely includes a widespread range expansion followed by fragmentation due to population contraction. These results argue for conservation of all populations and their unique alleles but also suggest an unexpected ability of this species to maintain genetic diversity despite dramatic reductions in population size.

Genus-Wide Transcriptional Landscapes Reveal Correlated Gene Networks Underlying Microevolutionary Divergence in Diatoms.

Marine microbes like diatoms make up the base of marine food webs and drive global nutrient cycles. Despite their key roles in ecology, biogeochemistry, and biotechnology, we have limited empirical data on how forces other than adaptation may drive diatom diversification, especially in the absence of environmental change. One key feature of diatom populations is frequent extreme reductions in population size, which can occur both in situ and ex situ as part of bloom-and-bust growth dynamics. This can drive divergence between closely related lineages, even in the absence of environmental differences. Here, we combine experimental evolution and transcriptome landscapes (t-scapes) to reveal repeated evolutionary divergence within several species of diatoms in a constant environment. We show that most of the transcriptional divergence can be captured on a reduced set of axes, and that repeatable evolution can occur along a single major axis of variation defined by core ortholog expression comprising common metabolic pathways. Previous work has associated specific transcriptional changes in gene networks with environmental factors. Here, we find that these same gene networks diverge in the absence of environmental change, suggesting these pathways may be central in generating phenotypic diversity as a result of both selective and random evolutionary forces. If this is the case, these genes and the functions they encode may represent universal axes of variation. Such axes that capture suites of interacting transcriptional changes during diversification improve our understanding of both global patterns in local adaptation and microdiversity, as well as evolutionary forces shaping algal cultivation.

Evidence of site-specific and male-biased germline mutation rate in a wild songbird.

Germline mutations are the ultimate source of genetic variation and the raw material for organismal evolution. Despite their significance, the frequency and genomic locations of mutations, as well as potential sex bias, are yet to be widely investigated in most species. To address these gaps, we conducted whole-genome sequencing of 12 great reed warblers (Acrocephalus arundinaceus) in a pedigree spanning three generations to identify single-nucleotide de novo mutations (DNMs) and estimate the germline mutation rate. We detected 82 DNMs within the pedigree, primarily enriched at CpG sites, but otherwise randomly located along the chromosomes. Furthermore, we observed a pronounced sex bias in DNM occurrence, with male warblers exhibiting three times more mutations than females. After correction for false negatives and adjusting for callable sites, we obtained a mutation rate of 7.16 × 10-9 mutations per site per generation (m/s/g) for the autosomes, and 5.10 × 10-9 m/s/g for the Z chromosome. To demonstrate the utility of species-specific mutation rates, we applied our autosomal mutation rate in models reconstructing the demographic history of the great reed warbler. We uncovered signs of drastic population size reductions pre-dating the last glacial period (LGP), and reduced gene flow between western and eastern populations during the LGP. In conclusion, our results provide one of the few direct estimates of the mutation rate in wild songbirds and evidence for male-driven mutations in accordance with theoretical expectations.

Promotion of plasmid maintenance by heterogeneous partitioning of microbial communities.

Transferable plasmids play a critical role in shaping the functions of microbial communities. Previous studies suggested multiple mechanisms underlying plasmid persistence and abundance. Here, we focus on the interplay between heterogeneous community partitioning and plasmid fates. Natural microbiomes often experience partitioning that creates heterogeneous local communities with reduced population sizes and biodiversity. Little is known about how population partitioning affects the plasmid fate through the modulation of community structure. By modeling and experiments, we show that heterogeneous community partitioning can paradoxically promote the persistence of a plasmid that would otherwise not persist in a global community. Among the local communities created by partitioning, a minority will primarily consist of members able to transfer the plasmid fast enough to support its maintenance by serving as a local plasmid haven. Our results provide insights into plasmid maintenance and suggest a generalizable approach to modulate plasmid persistence for engineering and medical applications.