The biogeographical distribution of diversity among populations of threatened mammalian species is generally investigated through population genetics. However, intraspecific phenotypic diversity is rarely assessed beyond taxonomy-focused linear measurements or qualitative descriptions. Here, we use a technique widely used in the evolutionary sciences – geometric morphometrics – to characterize shape diversity in the skull of an endangered marsupial, the northern quoll, across its 5,000 km distribution range along the northern Australian coast. Skull shape is a proxy of feeding, behaviour, and phenotypic differentiation, allowing us to ask if populations can be distinguished and if patterns of variation indicate adaptability to changing environmental conditions. We analysed skull shape in 101 individuals across the four mainland populations and several islands. We assessed the contribution of population, size, sex, rainfall, temperature, and latitude/longitude to skull shape variation through Principal Components, Procrustes ANOVA, and variation partitioning analyses. Regardless of land area inhabited, northern quoll populations harbour similar amounts of broadly overlapping skull shape variation. Size predicted skull shape best, coinciding with braincase size variation and differences in the cheekbone shape. Size-adjusted population differences explained less variation with far smaller effect sizes, relating to changes in insertion areas of masticatory muscles, as well as the upper muzzle and incisor region. Climatic and geographic variables contributed little or nothing. Strikingly, the vast majority of shape variation - 76% - remained unexplained. Our results suggest a uniform within-species scope for shape variation, possibly due to phenotypic plasticity or allometric constraints. The lack of local adaptation indicates that cross-breeding between populations will not reduce local morphological skull (and probably general musculoskeletal) adaptation because none exists. However, the potential for heritable morphological variation (e.g. specialization to local diets) seems exceedingly limited. We conclude that 3D geometric morphometrics can provide a comprehensive, statistically rigorous phenomic contribution to genetics-based conservation studies.
The Sanjiang Plain is the biggest freshwater wetland locating within northeastern China. Due to climate change and human activities, that wetland has degraded to a successional gradient from the original flooded wetland to dry shrub vegetation and a forest area with lower ground water level, resulting in changes in soil microbiologic structure and functions. The present study investigated the microbial diversity and community structure in relation to soil properties along this gradient. The soil physic-chemical properties changed significantly with degradation. The Shannon variety of soil fungi as well as bacteria varied significantly with successional stage (both P < 0.05). The community structures of soil bacteria and fungi in the early successional stages (i.e., the wetland) were significantly structured via total phosphorus, available nitrogen and total nitrogen concentrations in soils, while those in the later successional stages (i.e., forests) were significantly structured by soil organic carbon, soil pH and available phosphorus concentrations. Our results indicated that variations in the soil environment affected soil microbial communities along a successional gradient from wetland to forests are mainly. These outcomes indicate that above ground plant composition is a forceful determinant of the structure as well as functions of bacterial and fungal communities, might finally causing substantial alterations in ecosystem activity.
Phenotypic diversity, or disparity, can be explained by simple genetic drift or, if functional constraints are strong, by selection for ecologically relevant phenotypes. We here studied phenotypic disparity in head shape in aquatic snakes. We investigated whether conflicting selective pressures related to different functions have driven shape diversity and explore whether similar phenotypes may give rise to the same functional output (i.e. many-to-one mapping of form to function). We focused on the head shape of aquatically foraging snakes as they fulfil several fitness-relevant functions and show a large amount of morphological variability. We used 3D surface scanning and 3D geometric-morphometrics to compare the head shape of 62 species in a phylogenetic context. We first tested whether diet specialization and size are drivers of head shape diversification. Next, we tested for many-to-one mapping by comparing the hydrodynamic efficiency of head shapes characteristic of the main axis of variation in the dataset. We 3D printed these shapes and measured the forces at play during a frontal strike. Our results show that diet and size explain only a small amount of shape variation. Shapes did not functionally converge as more specialized aquatic species evolved a more efficient head shape than others. The shape disparity observed could thus reflect a process of niche specialization under a stabilizing selective regime.
Many eusocial insects, including ants, show complex colony structures, distributions, and reproductive strategies. In the ant Vollenhovia emeryi Wheeler (Hymenoptera: Myrmicinae), queens and males are produced clonally, while sterile workers arise sexually, unlike other ant species and Hymenopteran insects in general. Furthermore, there is a wing length polymorphism in the queen caste. Despite its ecological and evolutionary importance, little is known about the population dynamics and structure of this ant species, which may provide insight into its unique reproductive mode and polymorphic traits. We performed in-depth analyses of ant populations from Korea, Japan, and North America using three mitochondrial genes (COI, COII, and Cytb). The long-winged (L) morph is predominant in Korean populations, and the short-winged (S) morph is very rare. Interestingly, all L morphs were infected with Wolbachia, while all Korean S morphs lacked Wolbachia, demonstrating a novel association between a symbiont and a phenotypic trait. A phylogenetic analysis revealed that the S morph is derived from the L morph. We propose that the S morph is associated with potential resistance to Wolbachia infection, and that Wolbachia infection does not influence clonal reproduction.
The identification of the mechanisms underlying co-occurrence patterns of species is a way to identify which processes (niche, neutral or both) structure metacommunities. In this paper, our goals are to identify patterns of co-occurrence in neotropical stream fish and determine which processes structure the metacommunity and the gradients that underlie this structure. Our results pointed out that the metacommunity formed by the total pool of species is structured by a nested pattern (Hyperdispersed Species Loss) of co-occurrence and the mass effect mechanism. On the other hand, a set of core species displays a Clementisian pattern and is structured by the species sorting mechanism. Both, hyperdispersed species loss and the Clementisian patterns point to a discrete set of communities in the metacommunity. These communities could be isolated by physicochemical conditions, or physical barriers, like dams or waterfalls.
Marine food webs are highly compartmentalized and characterizing the trophic niches among consumers is important for predicting how impact from human activities affect the structuring and functioning of marine food webs. Biomarkers such as bulk stable isotopes have proven to be powerful tools to elucidate trophic niches, but they may lack in resolution, particularly when spatio-temporal variability in a system is high. To close this gap, we investigated whether carbon isotope (δ13C) patterns of essential amino acids (EAAs), also termed δ13AA fingerprints, can characterize niche differentiation in a highly dynamic marine system. We tested the ability of δ13AA fingerprints to differentiate trophic niches among six functional groups and ten individual species in the Baltic Sea. We also tested whether fingerprints of the common zooplanktivorous fishes, herring and sprat, differ among four Baltic Sea regions with different biochemical conditions and phytoplankton assemblages. Additionally, we investigated how these results compared to bulk C and N isotope data for the same sample set. We found significantly different δ13AA fingerprints among all six functional groups. Species differentiation was in comparison less distinct, due to partial convergence of the species’ fingerprints within functional groups. Herring and sprat displayed region specific δ13AA fingerprints indicating that this approach could be used as a migratory marker. Bulk isotope data had a lower power to differentiate between trophic niches, but may provide more easily interpretable information about relative trophic position than the fingerprints. We conclude that δ13AA fingerprinting has a strong potential to advance our understanding of ecological niches, and trophic linkages from producers to higher trophic levels in dynamic marine systems. Given how management practices of marine resources and habitats are reshaping the structure and function of marine food webs, implementing new and powerful tracer methods are urgently needed to improve the knowledge base for policy makers.
Coral reef fish larvae are tiny, exceedingly numerous, and hard to track. They are also highly capable, equipped with swimming and sensory abilities that may influence their dispersal trajectories. Despite the importance of larval input to the dynamics of a population, we remain reliant on indirect insights to the processes influencing larval behaviour and transport. Here, we used genetic data (300 independent single nucleotide polymorphisms) derived from a light trap sample of a single recruitment event of Dascyllus abudafur in the Red Sea (N=168 settlers). We analysed the genetic composition of the larvae and assessed whether kinship among these was significantly different from random as evidence for cohesive dispersal during the larval phase. We simulated many iterations of similar-sized recruitment cohorts to compare the expected kinship composition relative to our empirical data. The high number of siblings within the empirical cohort strongly suggests cohesive dispersal among larvae. This work highlights the utility of kinship analysis as a means of inferring dynamics during the pelagic larval phase.
The sharp rise in anthropogenic activities and climate change have caused the extensive degradation of grasslands worldwide, jeopardising ecosystem function and threatening human well-being. Toxic weeds have been constantly spreading in recent decades; indeed, their occurrence is considered to provide an early sign of land degeneration. Policy makers and scientific researchers often focus on the negative effects of toxic weeds, such as how they inhibit forage growth, kill livestock and cause economic losses. However, toxic weeds can have several potentially positive ecological impacts on grasslands, such as promoting soil and water conservation, improving nutrient cycling and biodiversity conservation, and protecting pastures from excessive damage by livestock. We reviewed the literature to detail the adaptive mechanisms underlying toxic weeds and to provide new insight into their roles in degraded grassland ecosystems. The findings highlight that the establishment of toxic weeds may provide a self-protective strategy of degenerated pastures that does not require special interventions. Consequently, policy makers, managers and other personnel responsible for managing grasslands need to take appropriate actions to assess the long-term trade-offs between the development of animal husbandry and the maintenance of ecological services provided by grasslands.
Fluorescent pseudomonads represent one of the largest groups of bacteria inhabiting the surfaces of plants, but their genetic composition in planta is poorly understood. Here, we examined the population structure and diversity of fluorescent pseudomonads isolated from sugar beet grown at two geographic locations (Oxford, UK and Auckland, New Zealand). To seek evidence for niche adaptation, bacteria were sampled from three types of leaves (immature, mature and senescent) and then characterized using a combination of genotypic and phenotypic analysis. We first performed multilocus sequence analysis (MLSA) of three housekeeping genes (gapA, gltA, acnB) in a total of 152 isolates (96 from Oxford, 56 from Auckland). The concatenated sequences were grouped into 81 sequence types and 22 distinct operational taxonomic units (OTUs). Significant levels of recombination were detected, particularly for the Oxford isolates (rate of recombination to mutation (r/m) = 5.23 for the whole population). Subsequent ancestral analysis performed in STRUCTURE found evidence of six ancestral populations, and their distributions significantly differed between Oxford and Auckland strains. Next, the ability to grow on 95 carbon sources was assessed using the BiologTM GN2 microtiter plates. A distance matrix was generated from the raw growth data (A660) and subjected to multidimensional scaling (MDS) analysis. There was a significant correlation between the substrate utilization profiles and MLSA genotypes. Both phenotypic and genotypic analyses indicated presence of a geographic structure for strains from Oxford and Auckland. Significant differences were genotypically detected between strains isolated from immature versus mature/senescent leaves. The fluorescent pseudomonads thus showed an ecotypic population structure, suggestive of adaptation to both geographical and local plant environments.
European starlings (Sturnus vulgaris) represent one of the most widespread and problematic avian invasive species in the world. Understanding their unique population history and current population dynamics can contribute to conservation efforts and clarify how evolutionary processes play out over short timescales. European starlings were introduced to Central Park, New York in 1890, and from a founding group of about 100 birds, they have expanded across North America with a current population of approximately 200 million. There were also multiple introductions in Australia in the mid-19th century, and at least one introduction in South Africa in the late 19th century. Independent introductions on these three continents provide a robust system to investigate invasion genetics. In this study, we compare mitochondrial diversity in European starlings from North America, Australia and South Africa, and a portion of the native range in the United Kingdom. Of the three invasive ranges, the North American population shows the highest haplotype diversity and evidence of both sudden demographic and spatial expansion. Comparatively, the Australian population shows the lowest haplotype diversity, but also shows evidence for sudden demographic and spatial expansion. South Africa is intermediate to the other invasive populations in genetic diversity but does not show evidence of demographic expansion. In previous studies, population genetic structure was found in Australia, but not in South Africa. Here we find no evidence of population structure in North America. Although all invasive populations share haplotypes with the native range, only one haplotype is shared between invasive populations. This suggests these three invasive populations represent independent subsamples of the native range. The structure of the haplotype network implies that the native range sampling does not comprehensively characterize the genetic diversity there. This study represents the most geographically widespread analysis of European starling population genetics to date.
Abstract: Sensitivity to bitter tastes provides animals with an important means of interacting with their environment and thus, influences their dietary preferences. Genetic variants encoding functionally distinct receptor types contribute to variation in bitter taste sensitivity. Our previous study showed that two nonsynonymous sites, A52V and Q296H, in the TAS2R20 gene are directionally selected in giant pandas from the Qinling Mountains, which are speculated to be the causative base-pair changes of Qinling pandas for the higher preference for bamboo leaves in comparison with other pandas. Here, we used functional expression in engineered cells to identify agonists of pTAS2R20 (i.e. giant panda’s TAS2R20) and interrogated the differences in perception in the in vitro responses of pTAS2R20 variants to the agonists. Our results show that pTAS2R20 is specifically activated by quercitrin and that pTAS2R20 variants exhibit differences in the sensitivity of their response to the agonist. Compared to pTAS2R20 in pandas from other areas, the receptor variant with A52V and Q296H, which is most commonly found in Qinling pandas, confers a significantly decreased sensitivity to quercitrin. We subsequently quantified the quercitrin content of the leaves of bamboo distributed in the Qinling Mountains, which was found to be significantly higher than that of the leaves of bamboo from panda habitats in other areas. Our results suggest that the decreased sensitivity to quercitrin in Qinling pandas results in higher-quercitrin-containing bamboo leaves to be tasting less bitter to them and thus, influences their dietary preference. This study illustrates the genetic adaptation of Qinling pandas to their environments and provides a fine example of the functional effects of directional selection in the giant panda.
The search for mates and food is mediated by volatile chemicals. Insects sense food odorants and sex pheromones through odorant receptors (ORs) and pheromone receptors (PRs), which are expressed in olfactory sensory neurons. Investigating the receptive range of these receptors instructs the identification of behaviourally relevant chemicals. Studying orthologous receptors and their ligands across taxa affords insights into the role of chemical communication in reproductive isolation and phylogenetic divergence. The female sex pheromone of green budworm moth Hedya nubiferana (Lepidoptera, Totricidae) is a blend of two unsaturated acetates, only a blend of both elicits male attraction. Females also produce codlemone, which is the sex pheromone of another tortricid, codling moth Cydia pomonella. Codlemone also attracts green budworm moth males. Concomitantly, green budworm and codling moth males are attracted to the food plant volatile pear ester. A congruent behavioural response to the same pheromone and plant volatile in two tortricid species suggests co-occurrence of dedicated odorant receptors. In codling moth, one PR is tuned to both compounds, the sex pheromone codlemone and the plant volatile pear ester. Our phylogenetic analysis finds that green budworm moth expresses an orthologous PR gene. Shared ancestry, and high levels of amino acid identity and sequence similarity, in codling and green budworm moth PRs offers an explanation for parallel attraction of both species to the same compounds. A conserved olfactory channel for a sex pheromone and host plant volatile substantiates the alliance of social and habitat signals in insect chemical communication. Field attraction assays confirm that in silico investigations of odorant receptors afford powerful predictions for an efficient identification of behaviour-modifying semiochemicals, for an improved understanding of the mechanisms of host plant attraction in insect herbivores and for the further development of sustainable insect control.
The capacity of some yeasts to extract energy from single sugars, generating CO2 and ethanol (=fermentation), even in the presence of oxygen is known as the Crabtree effect. This phenomenon represents an important adaptation as it allowed the utilization of the ecological niche given by modern fruits, an abundant source of food that emerged in the terrestrial environment in the Cretaceous. However, identifying the evolutionary events that triggered fermentative capacity in Crabtree positive species is challenging, as microorganisms do not leave fossil evidence. Thus, key innovations should be inferred based only on traits measured under culture conditions. Here, we reanalyzed data form a common-garden experiment where several proxies of fermentative capacity were recorded in Crabtree positive and negative species, representing yeast’s phylogenetic diversity. In particular, we applied the “lasso-OU” algorithm which detects points of adaptive shifts, provided trait values representing a given performance measure. We tested whether multiple events or a single event explains the actual fermentative capacity of yeasts. According to the lasso-OU procedure, evolutionary changes in the three proxies of fermentative capacity that we considered (i.e., glycerol production, ethanol yield and respiratory quotient) are consistent with a single evolutionary episode (a whole-genomic duplication, WGD), instead of a series of small genomic rearrangements. Thus, the WGD appears as the key event behind the diversification of fermentative yeasts, which by increasing gene dosage and maximized their capacity of energy extraction for exploiting the new ecological niche provided by single sugars.
Euterpe edulis (Arecaceae) Mart has high ecological and economic importance providing food resources for more than 58 species of birds and 20 species of mammals, including humans. E. edulis is the second most explored non-timber product from Brazilian Atlantic Forest. Due to overexploitation and destruction of habitats, E. edulis is threatened by extinction. E. edulis populations have large morphological variations, with individuals having green, red or yellow leaf sheath. However, no study has related phenotypic distinctions between populations and their levels of genetic structure. Thus, this study aimed to evaluate the diversity and genetic structure of different E. edulis morphotypes. We sampled 250 adult individuals in eight populations with the different morphotypes. Using 14 microsatellite markers, we access genetic diversity through population genetic parameters calculated in the GenAlex program and the diveRsity package in R. We used the Wilcoxon test to verify population bottlenecks and the genetic distance of Nei and Bayesian analysis for genetic clusters. The eight populations showed low allele richness, low heterogeneity observed and high inbreeding values (f). In addition, six of the eight populations experienced genetic bottlenecks, which would partly explain the low genetic diversity in populations. Cluster analysis identified two clusters (K=2), with green morphotype genetically distinguishing from yellow and red morphotypes. Thus, we show, for the first time, a strong genetic structure among E. edulis morphotypes even for geographically close populations.
Competitive interactions between distantly related clades could cause complementary diversity patterns of these clades over large spatial scales. One such example might be ants and birds in the eastern Himalaya; ants are very common at low elevations but almost absent at mid-elevations where the abundance of other arthropods and insectivorous bird diversity peaks. Here, we ask if ants at low elevations could compete with birds for arthropod prey. Specifically, we studied the impact of the Asian weaver ant (Oecophylla smaragdina), a common aggressive ant at low elevations. Diet analysis using molecular methods demonstrate extensive diet overlap between weaver ants and songbirds at both low and mid-elevations. Trees without weaver ants have greater non-ant arthropod abundance and leaf damage. Experimental removal of weaver ants results in an increase in the abundance of non-ant arthropods. Notably, numbers of Coleoptera and Lepidoptera were most affected by removal experiments and were prominent components of both bird and weaver ant diets. Our results suggest that songbirds and weaver ants might potentially compete with each other for arthropod prey at low elevations, thereby contributing to lower insectivorous bird diversity at low elevations in eastern Himalaya. Competition with ants may shape vertebrate diversity patterns across broad biodiversity gradients.
1. Bitterlings are small freshwater fish that use long ovipositors to place eggs in host mussels and have morphological adaptations to increase larval survival. The most well-known adaptations are the minute tubercles on the skin surface of larvae, which are developed in early-stage larvae with weak swimming ability and disappear in free-swimming larvae before they leave the host mussel. 2. In the present study, a comprehensive analysis of the developmental stages of Rhodeus pseudosericeus larvae, their morphological and physiological characteristics, their migration inside mussels, and the development of minute tubercle are presented as direct evidence of the morphological function of the minute tubercles. These tubercles began to develop 1 day after hatching (formation stage), grew for 2–5 days (growth stage), reached the peak height after 6–7 days (peak stage), abruptly reduced in height after 8–10 days (abrupt reduction stage), and went through a final gradual reduction (reduction stage) until completely disappearing 27 days after hatching (disappearance stage). 3. The larvae remained in the mussels’ interlamellar space of the gill demibranchs until 10 days after hatching, and began to migrate to mussels’ suprabranchial cavity 11 days after hatching. At this time, the larvae had clear components of heart rate and caudal fin began to develop. At 24 days after hatching, the minute tubercles had almost disappeared, and some individuals were observed swimming out of the mussels. 4. The experiment results herein presented prove that the minute tubercles are a first direct evidence that the bitterling larvae are morphologically adapted to prevent premature ejection from the mussel.
Resource polymorphism is a ubiquitous phenomenon in vertebrates and may represent a critical intermediate stage in speciation. Freshwater lakes in high-altitude areas represent a natural system for understanding resource polymorphism in fishes in diverse lacustrine environments and a few co-distributed species. We report resource polymorphism in a cyprinid fish, Schizopygopsis thermalis, in Lake Amdo Tsonak Co, a headwater lake in the upper Salween River system. Two morphs, planktivorous and benthivorous, were identified according to geometric morphological and traditional linear traits. The planktivorous morph exhibits a longer head and lower jaw, larger asymptotic standard length (L∞), lower growth rate (k) and higher growth performance index (φ) than the benthivorous morph. With respect to descriptive traits, the planktivorous morph possesses a terminal mouth and a highly developed mucus cavity in the cheek and chin, while the benthivorous morph is characterized by an inferiorly positioned mouth with a sharpened horny edge on the lower jaw. Our results indicate that distinct pelagic-benthic resources and low interspecific competition in the lake drove the initial differentiation of the two morphs and that partial spatial reproductive isolation might maintain and reinforce the differences between them.
Maintenance of a portfolio of adaptive alleles may provide resilience of populations to natural environmental variability. We used Pacific ocean perch (POP; Sebastes alutus) to test for the maintenance of adaptive variation across overlapping generations. POP are a long-lived species characterized by widespread larval dispersal in their first year and a longevity of over 100 years. In order to understand how early marine dispersal affects POP survival and population structure, we used Restriction Site Associated DNA sequencing (RADseq) to obtain 11,146 single-nucleotide polymorphisms (SNPs) from 401 young-of-the-year (YOY) POP collected during surveys conducted in 2014 (19 stations) and 2015 (4 stations) in the eastern Gulf of Alaska. Population clustering analysis showed that the POP samples represented four distinct ancestral populations mixed throughout the sampling area. Based on prior work on larval dispersal of POP, these larvae are most likely from distinct parturition locations that are mixing during their pelagic dispersal life stage. Latent factor mixed models revealed that POP larvae face significant selection during their first year at sea, which were specific to the year of their birth. Thus each adult cohort’s genetic composition is heavily influenced by the environmental conditions experienced during their first year at sea. Long-lived species relying on broadcast spawning strategies may therefore be uniquely resilient to environmental variability by maintaining a portfolio of cohort-specific adaptive genotypes, and age truncation due to overfishing of older cohorts may have detrimental effect on the population viability.