Gene function conservation is crucial in molecular ecology, especially for key traits like growth and maturation in teleost fish. The vgll3 and six6 genes are known to influence age-at-maturity in Atlantic salmon, but their impact on other fish species is poorly understood. Here, we investigated the association of vgll3 and six6 in the domestication of gilthead seabream and European seabass, both undergoing selective breeding for growth-related traits in the Mediterranean. We analysed two different sets of samples using two different genotyping approaches. The first dataset comprised farmed and wild populations from Greece, genotyped for SNPs within the genomic range of the two genes (“gene-level genotyping”). The second dataset examined 300k to 600k SNPs located in the chromosomes of the two genes, derived from a meta-analysis of a Pool-Seq experiment involving farmed and wild populations distributed widely across the Mediterranean (“chromosome-level genotyping”). The gene-level analysis revealed a significant effect of domestication on both genes in each species. This finding was partially supported by the chromosome-level analysis, identifying highly differentiated regions associated with domestication at varying distances from the candidate genes. Noteworthy genomic features were found, such as a CpG island in gilthead seabream and novel candidate genes in European seabream, warranting further investigation. These findings support a putative role of vgll3 and six6 in the maturation and growth of gilthead seabream and European seabass, emphasizing the need for further research on their conserved function.
Despite belonging to the most abundant and widespread genus of freshwater fishes in the region, the carp gudgeons of eastern Australia (genus Hypseleotris) have proved taxonomically and ecologically problematic to science since the 19th century. Several molecular studies and a recent taxonomic revision have now shed light on the complex biology and evolutionary history that underlies this group. These studies have demonstrated that carp gudgeons include a sexual/unisexual complex (five sexual species plus an assortment of hemiclonal lineages), many members of which also co-occur with an independent sexual relative, the western carp gudgeon (H. klunzingeri). Here we fill yet another knowledge gap for this important group by presenting a detailed molecular phylogeographic assessment of the western carp gudgeon across its entire and extensive geographic range. We use a suite of nuclear genetic markers (SNPs and allozymes) plus a matrilineal genealogy (cytb) to demonstrate that H. klunzingeri s.l. also displays considerable taxonomic and phylogeographic complexity. All molecular datasets concur in recognizing the presence of multiple candidate species, two instances of historic between-species admixture, and the existence of a natural hybrid zone between two of the three candidate species found in the Murray Darling Basin. We also discuss the major phylogeographic patterns evident within each taxon. Together these analyses provide a robust molecular, taxonomic, and distributional framework to underpin future morphological and ecological investigations on this prominent member of regional freshwater ecosystems in eastern Australia.
1) Clustering is indispensable in the quest for robust vegetation classification schemes which aim to partition continua to summarise and communicate pattern. However, clustering solutions are sensitive to methods and data and are therefore unstable, a feature which is usually attributed to noise. Viewed through a central-tendency lens, noise is defined as the degree of departure from type, which is problematic since vegetation types are abstractions of continua and so noise can only be quantified relative to a particular solution to hand. Graph theory models the structure of vegetation data based on the interconnectivity of samples. Through a graph-theoretic lens, the causes of instability can be quantified in absolute terms via the degree of connectivity among objects. 2) We simulated incremental increases in sampling intensity in a dataset over five iterations and assessed classification stability across successive solutions derived using algorithms implementing, respectively, models of central-tendency and interconnectivity. We used logistic regression to model the likelihood of a sample changing groups between iterations as a function of distance to centroid and degree of interconnectivity. 3) Our results show that the degree to which samples are interconnected is a more powerful predictor of instability than the degree to which they deviate from their nearest centroid. The removal of weakly interconnected samples resulted in more stable classifications, although solutions with many clusters were apparently inherently less stable than those with few clusters, and improvements in stability flowing from the removal of outliers declined as the number of clusters increased. 4) Our results reinforce the fact that clusters abstracted from continuous data are inherently unstable, and that the quest for stable, fine-scale classifications from large regional datasets is illusory. Nevertheless, our results show that using models better suited to the analysis of continuous data may yield more stable classifications of the available data.
Livebearing fishes are a standard model for studying the effect of predation on prey biology. Numerous studies have found differences in life history, sexual selection, behavior, and morphology between populations of the same species that co-occur with predators and those that do not. Alfaro cultratus is a livebearing fish with populations in different predation environments, but unlike other livebearers, this species also has an extreme body shape that is laterally compressed. Given this unusual morphology, we asked if predation environment would still predict overall body shape, as has been documented in other species. We collected specimens from both predator and no-predator sites in Costa Rica. We used a geometric morphometrics analysis to determine if body shape is affected by the predation environment while controlling for size and river gradient. Body shape does indeed differ between predation environments; however, the observed differences contrast with the patterns found in other livebearer systems. Alfaro cultratus in predation environments had deeper and shorter bodies and deeper caudal peduncles than those found in environments without dominant fish predators.
Body size shifts in ectotherms are mostly attributed to the Temperature Size Rule stating that warming speeds up initial growth rate but leads to smaller size when food availability does not limit growth. Nevertheless, climate warming can decrease food availability, which can influence growth, fecundity and survival. However, the interactive effects of temperature and food availability on life history traits have been mostly studied in small invertebrate species. In contrast, we have limited information on how temperature and food availability jointly influence life history traits in vertebrate predators and how changes in different life history traits combines to influence population demography. We investigated the independent and interactive effects of temperature and food availability on traits of the medaka fish Oryzias latipes. We used our empirical estimates of vital rates as input parameters of an Integral Projection model to predict how modifications in vital rates translate into population demography. Our results confirm that warming leads to a higher initial growth rate and lower size leading to crossed growth curves between the two temperatures. Food-restricted fish were smaller than ad libitum fed fish throughout the experiment. Fish reared at 30 °C matured younger, had smaller size at maturity, had a higher fecundity but had a shorter life span than fish reared at 20 °C. Food restriction increased survival under both temperature conditions. Warming reduces generation time and increases mean fitness in comparison to the cold treatments. Food restriction increased generation time and fitness in the cold treatment but had no effect in the warm treatment. Our results highlight the importance of accounting for the interaction between temperature and food availability to understand how body size shifts can affects vital rates and population demography. This is of importance in the context of global warming as resources are predicted to change with increasing temperatures.
Since the analysis of animal behavior is a central element of ethology and ecology, it is not surprising that a great deal of research has been conducted describing the behavior of various ungulates. Most studies were conducted during the daylight hours, thus much less is known about nocturnal behavior. Detailed analyses of nocturnal behavior have only been conducted for very prominent ungulates such as giraffes, elephants, or livestock, and the nocturnal rhythms exhibited by many ungulates remain unknown. In the present study, the nocturnal rhythms of 192 individuals of 18 ungulate species from 20 European zoos are studied with respect to the behavioral positions standing, lying - head up, and lying - head down (the typical REM sleep position). Differences between species of the orders Perissodactyla and Cetartiodactyla, as well as between individuals of different age were found. However, no differences with respect to the sex were seen. Most species showed a significant increase in the proportion of lying during the night. In addition, the time between two events of “lying down” was studied in detail. A high degree of rhythmicity with respect to this quantity was found in all species. The proportion of lying in such a period was greater in Cetartidactyla than in Perissodactyla, and greater in juveniles than in adults.
Climate suitability analyses based on ecological niche modeling provide a powerful tool for biological control practitioners to assess the likelihood of establishment of different candidate agents prior to their introduction in the field. These same analyses could also be performed to understand why some agents establish more easily than others. The release of three strains of Aphalara itadori (Shinji) (Hemiptera: Pysllidae), each from a different source locality in Japan, for the biological control of invasive knotweed species, Reynoutria spp. Houtt. (Caryophyllales: Polygonaceae), provides an important opportunity to compare the utility of climate suitability analyses for identifying potential climate-based limitations for successful biological control introductions. Here we predict climate suitability envelopes for three target species of knotweed in Europe and two target species of knotweed in North America and compare these suitability estimates for each of these species to the source localities of each A. itadori strain. We find that source locality of one strain, the Kyushu strain, has little-to-no suitability compared to other locations in Japan based on knotweed records from Europe, supporting an earlier study based on North American Japanese knotweed records. The source locality of a second strain, the Murakami strain, was predicted to have medium-to-high suitability based on records of knotweeds from North America. In contrast, European records of R. bohemica Chrtek & Chrtková and R. sachalinensis (F. Schmidt) Nakai predicted no suitability for this locality compared to other locations in Japan, while European records for R. japonica Houtt. predicted low suitability. The source locality of the final strain, the Hokkaido strain, was predicted as having medium-to-high suitability based on knotweed records of all examined species from both North America and Europe.
As an island endemic with a decreasing population, the Critically Endangered Grenada Dove Leptotila wellsi is threatened by accelerated loss of genetic diversity resulting from ongoing habitat fragmentation. Small, threatened populations are difficult to sample directly but advances in molecular methods mean that non-invasive samples can be used. We performed the first assessment of genetic diversity of populations of Grenada Dove by a) assessing mtDNA genetic diversity in the only two areas of occupancy on Grenada, b) defining the number of haplotypes present at each site and c) evaluating evidence of isolation between sites. We used non-invasively collected samples from two locations: Mt Hartman (n=18) and Perseverance (n=12). DNA extraction and PCR were used to amplify 1,751 bps of mtDNA from two mitochondrial markers: NADH dehydrogenase 2 (ND2) and Cytochrome b (Cyt b). Haplotype diversity (h) of 0.4, a nucleotide diversity (π) of 0.4 and two unique haplotypes were identified within the ND2 sequences; one haplotype was identified within the Cyt b sequences. Of the two haplotypes identified; the most common haplotype (haplotype A = 73.9%) was observed at both sites and the other (haplotype B = 26.1%) was unique to Perseverance. Our results show low mitochondrial genetic diversity, a non-expanding population and clear evidence for genetically isolated populations. The Grenada Dove needs urgent conservation action, including habitat protection and potentially augmentation of gene flow by translocation in order to increase genetic resilience and diversity with the ultimate aim of securing the long-term survival of this Critically Endangered species.
The nests of ground-nesting birds rely heavily on camouflage for their survival, and predation pressures, often linked to human activity, are a major source of mortality. Numerous ground-nesting bird populations are in decline, so understanding the effects of camouflage on their nesting behaviour is of relevance to their conservation concern. Habitat three-dimensional (3D) geometry together with predator visual abilities, viewing distance, and viewing angle determine whether a nest is either visible, occluded or too far away to detect. While this link is intuitive, few studies have investigated how fine-scale geometry is likely to help defend nests from different predator guilds. We quantified nest visibility based on 3D occlusion, camouflage, and predator visual modelling in northern lapwing, Vanellus Vanellus, on different land management regimes. Lapwings selected local backgrounds that had a higher 3D complexity at a spatial scale greater than their entire clutches compared to nearby control sites. Importantly, our findings show that habitat geometry – rather than predator visual acuity restricts nest visibility to terrestrial predators, and that an open field would actually be perceived as a closed habitat to a terrestrial predator searching for nests on the ground. Taken together with lapwings’ careful nest site selection, our findings highlight the importance of considering habitat geometry for understanding the evolutionary ecology and management of conservation sites for ground-nesting birds.
Urbanization processes are taking place at a very high rate, especially in Africa, these. At the same time, a number of small mammal species, be they native of invasive, take advantage of these human-induced habitat modifications. They represent commensal communities of organisms that cause a number of inconveniences to humans, including as potential reservoirs of zoonotic diseases. We studied via live trapping and habitat characterization such commensal small mammal communities in small villages to large cities of Senegal, to try understand how the species share this particular space. Seven major species were recorded, with exotic invasive house mice (Mus musculus) and black rats (Rattus rattus) dominating in numbers. The shrew Crocidura olivieri appeared as the main and more widespread native species, while native rodent species (Mastomys natalensis, M. erythroleucus, Arvicanthis niloticus and Praomys daltoni) were less abundant and/or more localized. Habitat preferences, compared between species in terms of room types and characteristics, showed differences between house mice, black rats and M. natalensis especially. Niche (habitat component) breadth and overlap were measured. Among invasive species, the house mouse showed a larger niche breadth than the black rat, and overall, all species displayed high overlap values. Co-occurrence patterns were studied at the locality and local scales. The latter show cases of aggregation (between the black rat and native species, for instance) and of segregation (as between the house mouse and the black rat in Tambacounda, or between the black rat and M. natalensis in Kédougou). While updating information on commensal small mammal distribution in Senegal, a country submitted to a dynamic process of invasion by the black rat and the house mouse, we bring original information on how species occupy and share the commensal space, and make predictions on the evolution of these communities in a period of ever-accelerating global changes.
Poyang Lake is an essential natural wetland in the Yangtze River basin and plays a vital role in maintaining the ecosystem function and ecological security in the middle and lower reaches of the Yangtze River. However, the relative importance and spatial heterogeneity of the impacts of human activities and land use changes on ecological security needs to be further explored. Here, we analyzed the habitat quality level around Poyang Lake in 2022 and explored the factors of habitat quality change from a geographical perspective. The land use structure changes around the Poyang Lake basin from 2000 to 2022 were quantitatively analyzed, and then the relative importance and spatial heterogeneity of each factor on ecological security changes were investigated using geographic probes. The results show that (1) The worst quality habitat (0–0.1) consists mainly of construction land (1624.9 km2) with an area of 1634.64 km2; (2) Construction land continues to increase with the most significant change, and the dynamic land use attitude is 0.47. Grassland and mudflats have the greatest decrease. The increase in cultivated land in different periods is mainly due to the shift of water surface and forest land; (3) Wetland land use change drivers are more influenced by the interaction of socioeconomic factors. The explanatory degrees of the interaction between population density and total year-end population and population density and administrative area are greater than 0.84. The data are greater than the explanatory degrees of every single factor, indicating that the land use change is mainly coupled with population density, total year-end population, and administrative area. These results reveal that human activities influence the degradation of wetlands around the Poyang Lake area. This study has significant reference value for coordinating human–land relationships in Poyang Lake, optimizing land management policy, and improving the sustainable development of cities
With global climates changing rapidly, animals must adapt to new environmental conditions with altered weather and phenology. Key to adapting to these new conditions is adjusting the timing of reproduction to maximize fitness. Using a long-term dataset on a wild population of yellow-bellied marmots (Marmota flaviventer) at the Rocky Mountain Biological Laboratory (RMBL), we investigated how the timing of reproduction changed with changing spring conditions over the past 50 years. Marmots are hibernators with a four-month active season. It is thus crucial to reproduce early enough in the season to have time to prepare for hibernation, but not too early so as snow cover prevents access to food. Importantly, climate change in this area has increased spring temperatures by 5 oC and decreased spring snowpack by 50 cm over the past 50 years. We evaluated how female marmots adjust the timing of their reproduction in response to the changing conditions and estimated the importance of both genetic variance and plasticity in the variation in this timing. We showed that, within a year, the timing of reproduction is not as tightly linked to the date a female emerges from hibernation as previously thought. We reported a positive effect of spring snowpack but not of spring temperature on the timing of reproduction. We found inter-individual variation in the timing of reproduction, including low heritability, but not in its response to changing spring conditions. There was directional selection for earlier pup emergence date since it increased the number and proportion of pups surviving their first winter. Taken together, the timing of marmot reproduction might evolve via natural selection, however, plastic changes will also be extremely important as long as plasticity is not limited. Further, future studies on the marmots should not operate under the assumption that females reproduce immediately following their emergence.
The subgenus Aschizomys belongs to the genus Alticola (Central Asian mountain vole) and consists of two species: Alticola macrotis and Alticola lemminus. Phylogenetic relationships within the subgenus Aschizomys remain obscure due to limited sampling, an insufficient number of molecular markers used in phylogenetic studies, and paraphyly observed on mitochondrial trees. In this work, to infer reliable phylogenetic relationships and evaluate putative scenarios of ancient hybridization within the subgenus, we applied double-digest restriction site–associated DNA paired-end (quaddRAD) sequencing to 20 DNA samples (20 individuals), including five species of the genus Alticola, and dated the divergence of cytochrome b (cytb) lineages within Aschizomys using a “second calibration” approach. We showed monophyly of the two species on the basis of thousands of nuclear loci and demonstrated traces of introgression also in the nuclear genome. Observed paraphyly in cytb could be explained by an introgression event rather than incomplete lineage sorting. This explanation was confirmed by an analysis of the cytb divergence time. Overall, our results support the hypothesis of extensive migration of the Aschizomys species during the Late Pleistocene, with this migration leading to population divergence and introgression. We expect our article to become a starting point for a series of rigorous studies on the population history of the genus Alticola as a whole.
Early life adversity predicts shorter adult lifespan in several animal taxa. Yet, work on long-lived primate populations suggests the evolution of mechanisms that contribute to resiliency and long lives despite early life insults. Here, we tested associations between individual and cumulative early life adversity and lifespan on rhesus macaques at the Cayo Santiago Biological Field Station using 50 years of demographic data. We performed sex-specific survival analyses at different life stages to contrast short-term effects of adversity (i.e., infant survival) with long-term effects (i.e., adult survival). Rhesus macaques exposed to adversity at birth suffered a significant increase in mortality risk during infancy with both individual and cumulative adversities having the highest impact among affected females. However, when considering adult lifespan, affected males showed higher vulnerability to both individual and cumulative adversities early in life. Our study shows profound immediate effects of insults at birth on female infant cohorts and suggests that affected female adults are more robust (i.e., viability selection). In contrast, adult males who experienced harsh conditions early in life showed an increased mortality risk at older ages as expected from hypotheses of long-term effects of individual, as well as cumulative, adversity early in life. Our study reveals that mortality risk during infancy is mainly driven by the type of adversity, rather than their accumulation at birth. However, cumulative adversity seems to play a major role in adult survival. Our analysis suggests sex-specific selection pressures on life histories and highlights the need for studies addressing the effects of early life adversity across multiple life stages. This information is critical for planning life stage-specific strategies of conservation interventions.
Animal dietary choices help understand a species’ feeding niche and are particularly relevant in conservation management. In this study, we aimed to gather knowledge on food niche and the foraging ecology of the Grizzled Giant Squirrel (Ratufa macroura) in Chinnar Wildlife Sanctuary, Southern Western Ghats, Kerala, India. Specifically, the objectives were to identify food composition, the seasonal variation in food choice and feeding technique. Through focal animal sampling, the Grizzled Giant Squirrel in Chinnar Wildlife Sanctuary was found to feed on 30 plant species belonging to 18 families. The most utilized plant family was Fabaceae, with eight species, followed by Moraceae (four species) and Anacardiaceae (two species). The feeding species included 22 trees, four climbers, one liana, one paraphyte, one shrub and one succulent species. The maximum duration of feeding was observed on Bauhinia racemosa (19.79%), followed by Tamarindus indica (14.08%) and Nothopegia beddomei (9.89%). The squirrel’s choice of diet was primarily affected by the availability of food tree species and food items rather than the season and non-tree species also have been reported from the diet of Grizzled Giant Squirrel. Even though the Grizzled Giant Squirrel shows plasticity in the food niche, the availability of mature trees and plants appears important for its conservation in the fragmented riparian forest in the Western Ghats, southern India.
The management objectives of many protected areas must meet the dual mandates of protecting biodiversity while providing recreational opportunities. Balancing these mandates is made difficult by constraints on monitoring trends in the status of biodiversity and impacts of recreation. Using detections from 45 camera traps deployed between July 2019 and September 2021, we assessed the potential impacts of recreation on spatial and temporal habitat use for 8 medium- and large-bodied terrestrial mammals in an isolated alpine protected area: Cathedral Provincial Park, Canada. We hypothesized that some wildlife perceive a level of threat from people, such that they avoid ‘risky times’ or ‘risky places’ associated with human activity. Other species may benefit from associating with people, be it through access to anthropogenic resource subsidies or filtering of competitors/predators that are more human-averse (i.e., human shield hypothesis). Specifically, we predicted that large carnivores would show the greatest segregation from people while mesocarnivores and ungulates would associate spatially with people. We found spatial co-occurrence between ungulates and recreation, consistent with the human shield hypothesis, but did not see the predicted negative relationship between larger carnivores and humans, except for coyotes (Canis latrans). Temporally, all species other than cougars (Puma concolor) had activity patterns significantly different from that of recreationists, suggesting potential displacement in the temporal niche. Wolves (Canis lupus) and mountain goats (Oreamnos americanus) showed shifts in temporal activity away from people on recreation trails relative to off-trail areas, providing further evidence of potential displacement. Our results highlight the importance of monitoring spatial and temporal interactions between recreation activities and wildlife communities, in order to ensure the effectiveness of protected areas in an era of increasing human impacts.
1.- There is a strong decrease in liana diversity along latitudinal and altitudinal gradients at global scale, and there is a marked difference in liana diversity between tropical and temperate ecosystems. From these observations it has been proposed that cold temperatures would restrict the liana ecological patterns, because of the vulnerability of their vascular system to freezing-thaw embolism. 2.- Our aim was to establish the functional mechanism behind the loss of liana diversity along a latitudinal temperature gradient. We evaluate the ecological liana performance as the apical growth rate in ten liana species, and functional traits associated with efficiency (maximum hydraulic conductivity and percentage of lost conductivity) and the safety (vessel diameter, vessel density, wood density and root pressure) of water transport. 4.- We found that in the southern site (colder) of the latitudinal gradient lianas species the have low performance, with a 5-fold decrease in their apical growth rate compared to the northern sites (warmer). These would be consequence of a much lower water transport efficiency (26.1-fold decrease) respect to liana species that inhabit northern (warmer) sites, as an outcome of a higher freezing-thaw embolism (37.5% of PLC) and reduction of vessel diameter (3 times narrower). 5.- These results are unmistakable evidence that cold temperature restricts liana performance, in cold environment liana species exhibit a strong decrease in performance, a low efficiency and higher safety of water transport. On the other hand, in warmer sites, we found that liana species exhibit functional strategies associated with higher performance, higher efficiency and low safety of water transport capacity. This trade-off between efficiency and safety of water transport and their effect over performance would explain the latitudinal pattern of liana diversity
Ecological interactions between parasites and their hosts play a fundamental role in evolutionary processes. Selection pressures are exerted on parasites and their hosts, usually resulting in high levels of specificity. Such is the case of ectoparasitic bat-flies, but how large-scale spatial gradients affect the dynamics of their interactions with their bat hosts is still unknown. In the present study, we investigated interaction patterns between bats and their ectoparasitic flies (Streblidae and Nycteribiidae), both presenting their peak of diversity in the Neotropical region, along a latitudinal gradient. Using network analyses and parasitic indices, grounded on the latitudinal diversity gradient theory, we evaluated how spatial gradients affect species interactions and parasitic indices at the macroscale level, predicting that interaction networks should become richer in species, leading to increases in network modularity, size, and specialization, and to a decrease in nestedness and connectance. We conducted a literature review, focusing on studies done in the Neotropical region, and data of our own authorship. We obtained a richness of 97 species of bats parasitized by 128 species of ectoparasitic flies, distributed into 57 interaction networks between latitudes 29ºS and 19ºN in the Neotropic. Network metrics and parasitic indices varied along the latitudinal gradient, with changes in richness of bats and their ectoparasitic flies and in the structure of their interactions; network specialization, modularity and connectance increase with latitude, while network size decreases with latitude. Regions closer to the equator had higher parasite loads. Our results show that interaction networks metrics present a latitudinal gradient and that such interactions, when observed at a local scale, hide variations that only become perceptible at larger scales. In this way, ectoparasites such as bat flies are not only influenced by the ecology and biology of their hosts, but by other environmental factors acting directly on their distribution and survival.