Aim: We have studied population genetic change through time in the Northern dragonhead, Dracocephalum ruyschiana (Lamiaceae); a plant species that has experienced a drastic population decline and habitat loss in Europe. We aimed at adding a historic level to the monitoring of dragonhead by testing a microfluidic SNP array approach on herbarium specimens up to 200 years old and comparing the genomic results with that of modern populations in Norway. We also aimed to gain a more holistic species knowledge to guide monitoring efforts by combining herbarium genomics with ecological niche modelling (ENM). Location: Europe (mainly Norway) Methods: We have applied a microfluidic array consisting of 96 SNP markers on 130 herbarium specimens collected from 1820 to 2008. Obtained genotype data were compared with SNP data from modern samples using various population genetic analyses. We used sample metadata and observational records to model the species’ environmental niche. Results: The SNP array successfully genotyped all included herbarium specimens but was less capable of capturing diversity outside of Norway, which was genetically highly divergent from the Norwegian dragonheads. The historic-modern comparison revealed similar genetic structure in space and limited change through time in Norway. The ENM suggests that dragonhead has not fully achieved its potential distribution in Norway, which is anchored in warmer and drier regions, including areas where it does not occur today. Main conclusions: With the appropriate design procedures, the SNP array technology is promising for genotyping old herbarium specimens; an invaluable source of information from the past. We found no signs of the severe reduction in population size in our temporal genomic data of Norwegian dragonhead. Regardless, the regional populations in Norway are genetically divergent, both from each other and more so from populations outside of Norway, rendering continued protection of all existing populations of the species relevant.
Despite a growing literature-base devoted to documenting biodiversity patterns in cities, little is known about the processes that influence these patterns, and whether they are consistent over time. In particular, numerous studies have identified the capacity of cities to host a rich diversity of plant species. This trend, however, is driven primarily by introduced species, which comprise a large proportion of the urban species pool relative to natives. Using an experimental common garden study, we assessed the relative influence of local assembly processes (i.e., soil environmental filtering and competition from spontaneous urban species) on the taxonomic and functional diversity of native plant communities sampled over four seasons in 2016-2018. Taxonomic and functional diversity exhibited different responses to local processes, supporting the general conclusion that species- and trait-based measures of biodiversity offer distinct insights into community assembly dynamics. Additionally, we found that neither soil nor competition from spontaneous urban species influenced taxonomic or functional composition of native species. Functional composition, however, did shift strongly over time and was driven by community-weighted mean differences in both measured traits (maximum height, Hmax; specific leaf area, SLA; leaf chlorophyll a fluorescence, chl a) and the relative proportions of different functional groups (legumes, annual and biennial-perennial species, C4 grasses, and forbs). In contrast, taxonomic composition only diverged between early and late seasons. Overall, our results indicate that native species are not only capable of establishing and persisting in vacant urban habitats, they can functionally respond to local filtering pressures over time. This suggests that regional dispersal limitation may be a primary factor limiting native species in urban environments. Thus, future regreening and management plans should focus on enhancing the dispersal potential of native plant species in urban environments, in order to achieve set goals for increasing native species diversity and associated ecosystem services in cities.
Stress can be remembered by plants in a form of stress legacy that can alter future phenotypes of previously stressed plants and even phenotypes of their offspring. DNA methylation belongs among the mechanisms mediating the stress legacy. It is however not known for how long the stress legacy is carried by plants. If the legacy is long lasting, it can become maladaptive in situations when parental-offspring environments do not match. We investigated for how long after the last exposure of a parental plant to drought can the phenotype of its clonal offspring be altered. We grew parental plants of three genotypes of Trifolium repens for five months either in control conditions or in control conditions that were interrupted with intense drought periods applied for two months in four different time-slots. We also treated half of the parental plants with a demethylating agent (5-azaC) to test for the potential role of DNA methylation in the stress legacy. Then, we transplanted parental cuttings (ramets) individually to control environment and allowed them to produce offspring ramets for two months. The drought stress experienced by parents affected phenotypes of offspring ramets. The stress legacy resulted in enhanced number of offspring ramets originating from parents that experienced drought stress even 8 weeks before their transplantation to the control environment. 5-azaC altered transgenerational effects on offspring ramets. We confirmed that drought stress can trigger transgenerational effect in T. repens that is very likely mediated by DNA methylation. Most importantly, the stress legacy in parental plants persisted for at least 8 weeks suggesting that the stress legacy can persist in a clonal plant Trifolium repens for relatively long period. We suggest that the stress legacy should be considered in future ecological studies on clonal plants.
Quantifying habitat quality is dependent on measuring a site’s relative contribution to population growth rate. This is challenging for studies of waterbirds, whose high mobility can decouple demographic rates from local habitat conditions and make sustained monitoring of individuals near-impossible. To overcome these challenges, biologists have used many direct and indirect proxies of waterbird habitat quality. However, consensus on what methods are most appropriate for a given scenario is lacking. We undertook a structured literature review of the methods used to quantify waterbird habitat quality, and provide a synthesis of the context-dependent strengths and limitations of those methods. Our structured search of the Web of Science database returned a sample of 398 studies, upon which our review was based. The reviewed studies assessed habitat quality by either measuring habitat attributes (e.g., food abundance, water quality, vegetation structure), or measuring attributes of the waterbirds themselves (e.g., demographic parameters, body condition, behaviour, distribution). Measuring habitat attributes, although they are only indirectly related to demographic rates, has the advantage of being unaffected by waterbird behavioural stochasticity. Conversely, waterbird-derived measures (e.g., body condition, peck rates) may be more directly related to demographic rates than habitat variables, but may be subject to greater stochastic variation (e.g., behavioural change due to presence of conspecifics). Therefore, caution is needed to ensure that the measured variable does influence waterbird demographic rates. This assumption was usually based on ecological theory rather than empirical evidence. Our review highlighted that there is no single best, universally applicable method to quantify waterbird habitat quality. Individual project specifics (e.g., time frame, spatial scale, funding) will influence the choice of variables measured. Where possible, practitioners should measure variables most directly related to demographic rates. Generally, measuring multiple variables yields a better chance of accurately capturing the relationship between habitat characteristics and demographic rates.
1. Harmful algal blooms are increasing in both severity and frequency across the globe. Many bloom-forming species are capable of vertical motility and colony formation. The cyanobacterium Microcystis aeruginosa is a common example of such a species, yet current models poorly predict vertical distributions of M. aeruginosa. 2. To couple the hydrodynamics, buoyancy, and the colony dynamics of Microcystis, we present a system of one-dimensional advection-diffusion-aggregation equations with Smoluchowski aggregation terms. 3. Results indicate Smoluchowski aggregation accurately describes the colony dynamics of M. aeruginosa. Further, transport dynamics are strongly dependent on colony size, and aggregation processes are highly sensitive to algal concentration and wind-induced mixing. Both of these findings have direct consequences to harmful algal bloom formation. 4. While the theoretical framework outlined in this manuscript was derived for M. aeruginosa, both motility and colony formation are common among bloom-forming algae. As such, this coupling of vertical transport and colony dynamics is a useful step for improving forecasts of surface harmful algal blooms.
ABSTRACT: Culture is widely accepted as an important social factor present across a wide range of species. Bears have a culture as defined as behavioral traditions inherited though social learning usually from mothers to offspring. Successful bear cultures can enhance fitness and resource exploitation benefits. In contrast, some bear cultures related to response to humans and human-related foods can be maladaptive and result in reduced fitness and direct mortality. In environments with minimal human influence most bear culture has evolved over generations to be beneficial and well adapted to enhance fitness. However, most bears across the world do not live in areas with minimal human influence and in these areas, bear culture is often changed by bear interactions with humans, usually to the detriment of bear survival. We highlight the importance of identifying unique bear cultural traits that allow efficient use of local resources and the value of careful management to preserve these adaptive cultural behaviors. It is also important to select against maladaptive cultural behaviors that are usually related to humans inorder to reduce human-bear conflicts and high bear mortality. We use examples from Yellowstone National Park to demonstrate how long-term management to reduce maladaptive bear cultures related to humans has resulted in healthy bear populations and a low level of human-bear conflict in spite of a high number of Park visitors in close association with bears.
1. Competition from invasive species is an increasing threat to biodiversity. In Southern California, the western gray squirrel (Sciurus griseus, WGS) is facing increasing competition from the fox squirrel (Sciurus niger, FS), an invasive congener. 2. We used spectral methods to analyze 140 consecutive monthly censuses of WGS and FS within a 11.3 ha section of the California Botanic Garden. Variation in the numbers for both species and their synchrony was distributed across long timescales (> 15 months). 3. After filtering out annual changes, concurrent mean monthly temperatures from nearby Ontario Airport (ONT) yielded a spectrum with a large semiannual peak and significant spectral power at long timescales (> 30 months). Squirrel-temperature cospectra showed significant negative covariation at long timescales (> 35 months) for WGS and smaller significant negative peaks at 6 months for both species. 4. Simulations from a Lotka-Volterra model of two competing species indicates that the risk of extinction for the weaker competitor increases quickly as environmental noise shifts from short to long timescales. 5. We analyzed the timescales of fluctuations in detrended mean annual temperatures for the time period 1915-2014 from 1218 locations across the continental USA. In the last two decades, significant shifts from short timescales to long timescales have occurred, changing from less than 3 years to 4-6 years. 6. Our results indicate that (i) population fluctuations in co-occurring native and invasive tree squirrels are synchronous, occur over long timescales, and may be driven by fluctuations in environmental conditions; (ii) long timescale population fluctuations increase the risk of extinction in competing species, especially for the inferior competitor; and (iii) the timescales of interannual environmental fluctuations may be increasing from recent historical values. These results have broad implications for the impact of climate change on the maintenance of biodiversity.
A study on rodent species diversity and community assemblages in West Mt Kilimanjaro was conducted in seven different habitats, covering two dry and wet seasons. Data were collected using a combination of medium-sized Sherman’s live traps, snap and Havarhart traps, for three consecutive nights. General Linear Models (GLM) were used to analyze the effects of predictors (vegetation attributes, seasonality, soil physical properties, disturbance and altitude) on rodent species richness and abundance. Community structure analysis was conducted in the Primer v6 program and Canonical correspondence analysis for habitat association in PAST. A total of 1,393 individuals from 14 species of rodents were trapped. The most dominant rodent species were Rhabdomys pumilioPraomys delectorum, and Lophuromys verhageni which contributed to 68.86% of the total captures. Lophuromys verhageni occurred across all the habitats and seasons. Moreover, habitat types, seasonality, soil texture, ground cover, and altitude significantly influenced rodent species abundance (P< 0.05). Furthermore, habitat types, seasonality and altitude significantly influenced rodent species richness (F8, 759 = 629.7, p< 0.001, R2 = 0.87). In addition to that, two major rodent communities were formed in different habitats. The results show that rodent species richness, abundance, and community assemblages in Mt Kilimanjaro, are a result of change in vegetation structure along the altitudinal gradients. Therefore, information on habitat requirements of multiple species is crucial for the management and conservation of these communities.
The invasion of a novel host species can create a mismatch in host choice and offspring survival (performance) when native parasitoids attempt to exploit the invasive host without being able to circumvent its resistance mechanisms. Invasive hosts can therefore act as evolutionary trap reducing parasitoids’ fitness and this may eventually lead to their extinction. Yet, escape from the trap can occur when parasitoids evolve behavioural avoidance or a physiological strategy compatible with the trap host, resulting in either host-range expansion or a complete host-shift. We developed an individual based model to investigate which conditions promote parasitoids to evolve behavioural preference that matches their performance, including host-trap avoidance, and which conditions lead to adaptations to the unsuitable hosts. One important aspect of these conditions was reduced host survival during incompatible interaction, where a failed attempt by a parasitoid resulted in host killing. This non-reproductive host mortality had a strong influence on the likelihood of establishment of novel host-parasitoid relationship. Killing unsuitable hosts can constrain adaptation under conditions which in fact promoted adaptation when parasitoids would leave the trap host unharmed and survive parasitoid attack. Moreover, our model revealed that host-search efficiency and genetic variation in host-preference play a key role in the likelihood that parasitoids will include the suboptimal host in their host range, or will evolve behavioural avoidance resulting in specialization and host-range conservation, respectively. Hence, invasive species might change the evolutionarily trajectory of native parasitoid species, which is important for predicting biocontrol ability of native parasitoids towards novel hosts.
In reptiles, reproductive maturity is often determined by size rather than age. Consequently, growth early in life may influence population dynamics through effects on generation time and survival to reproduction. Because reproductive phenology and pre- and post-natal growth are temperature-dependent, environmental conditions may induce multi-species cohort effects on body size in sympatric reptiles. I present evidence of this using ten years of neonatal size data for three sympatric viviparous snakes, Dekay’s Brownsnakes (Storeria dekayi), Red-bellied Snakes (S. occipitomaculata) and Common Gartersnakes (Thamnophis sirtalis). End-of-season neonatal size varied in parallel across species such that snout-vent length was 36-61% greater and mass was 65-223% greater in years when gestating females could achieve higher April-May (vs. June-July or August-September) operative temperatures. Thus, temperature had a larger impact during follicular enlargement and ovulation than during gestation or post-natal growth. Multi-species cohort effects like these may affect population dynamics and increase with climate change.
Sex is one of the important factors affecting gut microbiota. As key predators in agro-forestry ecosystem, many spider species show dramatically different activity habits and nutritional requirements between female and male. However, how sex affects gut microbiota of spiders is still unclear. Therefore, in this study, the compositions and diversities of gut bacteria, based on bacterial 16S rRNA gene sequencing, were compared between female and male Pardosa astrigera. We found that bacterial richness indices (P < 0.05) in female were significantly lower than male, meanwhile, β-diversity showed significantly different between female and male (P < 0.05). The relative abundance of Actinobacteriota and Rhodococcus (belongs to Actinobacteria) were significantly higher in female than male (P < 0.05). Whereas, the relative abundance of Firmicutes and Acinetobacter (belongs to Proteobacteria), Ruminococcus and Fusicatenibacter (all belong to Firmicutes), were significantly higher in male than female (P < 0.05). The results of PICRUSt2 showed that amino acid and lipid metabolisms were significantly higher in female than male (P < 0.05), whereas glycan biosynthesis and metabolism was significantly higher in male than female (P < 0.05). Our results imply that sexual variation is a crucial factor in shaping gut bacterial community in P. astrigera. Male P. astrigera dispersed more widely than the female hence the male had a higher bacterial diversity. While the distinct differences of bacterial composition mainly due to their different nutritional and energy requirements.
Metagenomics - shotgun sequencing of all DNA fragments from a community DNA extract - is routinely used to describe the composition, structure and function of microorganism communities. Advances in DNA sequencing and the availability of genome databases increasingly allow the use of shotgun metagenomics on eukaryotic communities. Metagenomics offers major advances in the recovery of biomass relationships, in comparison to taxonomic marker gene based approaches (metabarcoding). However, little is known about the factors that influence metagenomics data from eukaryotic communities, such as differences among organism groups, properties of reference genomes and genome assemblies. We evaluated how shotgun metagenomics records composition and biomass in artificial soil invertebrate communities. We generated mock communities of controlled biomass ratios from 28 species from all major soil mesofauna groups: mites, springtails, nematodes, tardigrades and potworms. We shotgun-sequenced these communities and taxonomically assigned them with a database of over 270 soil invertebrate genomes. We recovered 90% of the species, and observed relatively high false positive detection rates. We found strong differences in reads assigned to different taxa, with some groups consistently attracting more hits than others. Biomass could be predicted from read counts after considering taxon-specific differences. Larger genomes more complete assemblies consistently attracted more reads than genomes. The GC content of the genome assemblies had no effect on the biomass-read relationships. The results show considerable differences in taxon recovery and taxon specificity of biomass recovery from metagenomic sequence data. Properties of reference genomes and genome assemblies also influence biomass recovery, and they should be considered in metagenomic studies of eukaryotes. We provide a roadmap for investigating factors which influence metagenomics-based eukaryotic community reconstructions. Understanding these factors is timely as accessibility of DNA sequencing, and momentum for reference genomes projects show a future where the taxonomic assignment of DNA from any community sample becomes a reality.
Mutualisms are ubiquitous in nature, provide important ecosystem services, and involve many species of interest for conservation. Theoretical progress on the population dynamics of mutualistic interactions, however, comparatively lagged behind that of trophic and competitive interactions, leading to the impression that ecologists still lack a generalized framework to investigate the population dynamics of mutualisms. Yet, over the last 90 years, abundant theoretical work has accumulated, ranging from abstract to detailed. Here, we review and synthesize historical models of two-species mutualisms. We find that population dynamics of mutualisms are qualitatively robust across derivations, including levels of detail, types of benefit, and inspiring systems. Specifically, mutualisms tend to exhibit stable coexistence at high density and destabilizing thresholds at low density. These dynamics emerge when benefits of mutualism saturate, whether due to intrinsic or extrinsic density-dependence in intraspecific processes, interspecific processes, or both. We distinguish between thresholds resulting from Allee effects, low partner density, and high partner density, and their mathematical and conceptual causes. Our synthesis suggests that there exists a robust population dynamic theory of mutualism that can make general predictions.
Population dynamics are functions of several demographic processes including survival, reproduction, somatic growth, and maturation. The rates or probabilities for these processes can vary by time, by location, and by individual. These processes can co-vary and interact to varying degrees, e.g., an animal can only reproduce when it is in a particular maturation state. Population dynamics models that treat the processes as independent may yield somewhat biased or imprecise parameter estimates, as well as predictions of population abundances or densities. However, commonly used integral projection models (IPMs) typically assume independence across these demographic processes. We examine several approaches for modelling between process dependence in IPMs, and include cases where the processes co-vary as a function of time (temporal variation), co-vary within each individual (individual heterogeneity), and combinations of these (temporal variation and individual heterogeneity). We compare our methods to conventional IPMs, which treat vital rates independent, using simulations and a case study of Soay sheep (Ovis aries). In particular, our results indicate that correlation between vital rates can moderately affect variability of some population-level statistics. Therefore, including such dependent structures is generally advisable when fitting IPMs to ascertain whether or not such between vital rate dependencies exist, which in turn can have subsequent impact on population management or life-history evolution.
The arboreal marsupial Monito del Monte (genus Dromiciops, with two recognized species) is a paradigmatic mammal. It is the sole living representative of the order Microbiotheria, the ancestor lineage of Australian marsupials. Also, this marsupial is the unique frugivorous mammal in the temperate rainforest, being the main seed disperser of several endemic plants of this ecosystem, thus acting as keystone species. Dromiciops is also one of the few hibernating mammals in South America, spending half of the year in a physiological dormancy where metabolism is reduced to 10% of normal levels. This capacity to reduce energy expenditure in winter contrasts with the enormous energy turnover rate they experience in spring and summer. The unique life-history strategies of this living Microbiotheria, characterized by an alternation of life in the slow and fast lanes, putatively represent ancestral traits that permitted these cold-adapted mammals to survive in this environment. Here we describe the ecological role of this emblematic marsupial, summarizing the ecophysiology of hibernation and sociality, actualized phylogeographic relationships, reproductive cycle, trophic relationships, mutualisms, conservation and threats. This marsupial shows high densities, despite presenting slow reproductive rates, a paradox that is explained by the unique characteristics of its three-dimensional habitat. We finally suggest immediate actions to protect these locally abundant but globally threatened species.
Most studies on animals have conducted comparative studies to deduce the possible relationships among developmental stability, canalization and phenotypic plasticity, there is a lack of direct evidence in plants, which should be better study materials. To investigate the correlations among developmental stability, canalization and plasticity in plants, we conducted a field experiment with Abutilon theophrasti, by subjected plants to three densities under infertile vs. fertile soil conditions, and measured leaf size, leaf fluctuating asymmetry (FA), and calculated coefficient of variation among leaves within individuals (CVleaf) and among individuals (CVin) and relative plasticity (PIrel) and its degree in leaf size at three growth stages, to analyze the responses of their correlations to density and how they may vary with soil conditions or growth stages. Results showed a decrease of FA, CVleaf and PIrel and an increase of CVin in leaf size, with increased density. In most cases, there were no correlations among these variables, but negative correlations between CVin and PIrel, positive correlations between FA and PIrel at high density and/or in fertile soil, in infertile soil. It suggested that higher FA may indicate the state of faster growth rather than an indicator of environmental stresses; there are correlations among developmental stability, canalization and plasticity, which may be complex, affected by other factors. The loss of developmental stability may be beneficial for plant response to environmental stresses, while decreased canalization can be either disadvantageous or advantageous, depending on that the size variation results from an increase or decrease of smaller individuals, and whether its correlations with other variables reflect beneficial or adverse environmental effects.
Cordyceps is a large group of entomogenous, medicinally important fungi. In this study, we sequenced, assembled, and annotated the entire mitochondrial genome of O. xuefengensis, in addition to comparing it against three other complete cordyceps mitogenomes that were previously published. Comparative analysis indicated that the four complete mitogenomes are all composed of circular DNA molecules, although their sizes significantly differ due to high variability in intron and intergenic region sizes in the O. sinensis and O. xuefengensis mitogenomes. All mitogenomes contain 14 conserved genes and two ribosomal RNA genes, but varying numbers of tRNA introns. The Ka/Ks ratios for all 14 PCGs and rps3 were all less than 1, indicating that these genes have been subject to purifying selection. Phylogenetic analysis was conducted using concatenated amino acid and nucleotide sequences of the 14 PCGs and rps3 using two different methods (Maximum Likelihood and Bayesian analysis), revealing highly supported relationships between O. xuefengensis and other Ophiocordyceps species, in addition to a close relationship with O. sinensis. Further, the analyses indicated that cox1 and rps3 play important roles in population differentiation. These mitogenomes will allow further study of the population genetics, taxonomy, and evolutionary biology of medicinally important cordyceps species.
Alternative splicing is a molecular mechanism that enables a single gene to encode multiple transcripts and proteins by post-transcriptional modification of pre-RNA molecules. Changes in the splicing scheme of genes can lead to modifications of the transcriptome and the proteome. This mechanism can enable organisms to respond to environmental fluctuations. In this study, we investigated patterns of alternative splicing in the liver of the coral reef fish Acanthochromis polyacanthus in response to the 2016 marine heatwave on the Great Barrier Reef. The differentially spliced (DS; n=40) genes during the onset of the heatwave (i.e. 29.49°C or +1°C from average) were related to essential cellular functions such as the MAPK signaling system, Ca(2+) binding and homeostasis. With the persistence of the heatwave for a period of one month (February to March), 21 DS genes were detected, suggesting that acute warming during the onset of the heatwave is more influential on alternative splicing than the continued exposure to elevated temperatures. After the heatwave, the water temperature cooled to ~24.96°C, and fish showed differential splicing of genes related to cyto-protection and post-damage recovery (n=26). Two-thirds of the DS genes detected across the heatwave were also differentially expressed, revealing that the two molecular mechanisms act together in A. polyacanthus to cope with the acute thermal change. This study exemplifies how splicing patterns of a coral reef fish can be modified by marine heatwaves. Alternative splicing could therefore be a potential mechanism to adjust cellular physiological states under thermal stress and aid coral reef fishes in their response to more frequent acute thermal fluctuations in upcoming decades.