Tetraodontiformes is a special group of higher teleosts, with a long and problematic taxonomic history due to their wide distribution and species diversity. It is a difficult task for both professionals and nonprofessionals to accurately identify all species only according to morphological characteristics. DNA barcoding can identify species at the molecular level. In this study, we collected 616 specimens of Tetraodontiformes and their DNA barcodes from the coastal waters of China. According to the morphological characteristics, 50 species were preliminarily identified, belonging to 23 genera, 6. Among them, DNA barcoding analysis showed that Takifugu pseudommus and Takifugu chinensis are the synonyms of Takifugu rubripes. And Lagocephalus wheeleri is the synonym of Lagocephalus Spadiceus. The third important finding is that the species of Takifugu have close genetic relationship. If T. rubripes, T. pseudommus and T. chinensis are taken as one species, the average interspecific genetic distance of Takifugu is 6.21 times of the average intraspecific genetic distance, which does not reach the DNA barcode threshold of more than 10 times proposed by Hebert. Among them, the genetic distance between T. oblongus and T. stictonotus is the largest, 0.045; And between T. bimaculatus and T. flavidus is the smallest, only 0.013. However, species can be clustered into separate clades in the NJ tree. In conclusion, this study provided molecular basis for solving the problem of confusion in the classification of Tetraodontiformes, it found that there are synonym phenomena in the order, and provided molecular evidence for clarifying the valid species names of Lagocephalus Spadiceus and Takifugu rubripes. The results can provide reliable DNA barcoding information for the identification and classification of Tetraodontiformes, and also provide technical support for the development and utilization of puffer fish resources and the identification of the original components of related commodities on the aquatic product market.
Invasive alien species are generally highly fertile and adaptable and can pose a severe threat to the ecological security of invaded localities. Bemisia tabaci (Gennadius) is a rapidly evolving cryptic complex. Among them, Mediterranean (MED) and Middle East–Asia Minor 1 (MEAM1) is the most invasive and widely distributed. To clarify the invasion source, population structure, and genetic differentiation drivers of whitefly populations in Xinjiang, China, we collected B. tabaci from 14 host crops in Xinjiang, China. A total of 453 sequenced cytochrome c oxidase subunit I(COI) fragments were analysed. We used common methods and parameters of genetic analysis, such as phylogenetic analysis, haplotype diversity, and nucleotide diversity, neutrality testing, and mismatch distribution chart analysis to determine the genetic structure and genetic differentiation and explore the origin of the invasion of B. tabaci populations in Xinjiang. The results have shown that global MED and MEAM1 populations are genetically differentiated, and MED has a significant geographical lineage structure at the Xinjiang and global spatial scales. This was the same for the MEAM1 population at the Xinjiang spatial scale. There have been multiple local expansions and founder effects in the MED populations. The MEAM1 population has retained a stable population size with a bottleneck effect. Based on the phylogenetic tree for MED and MEAM1, it has been demonstrated that there have been multiple points and pathways of invasion of B. tabaci and the sources in Xinjiang, China were complex. The sources of MED invasion of MED are likely to be Zhejiang, Hebei, or Shanxi. The source for MEAM1 is complex, and Zhejiang is one of the main invasion sources. This study has shown that host plant differences in open habitats, geographic isolation, and habitat differences were the driving factors for genetic differentiation of B. tabaci populations in Xinjiang, China
Landlocking is a process whereby a population of normally diadromous fish becomes limited to freshwater, potentially leading to behavioural, morphological, and genetic changes, and occasionally speciation. The study of recently landlocked populations can shed light on how populations adapt to environmental change, and how such life-history shifts affect population-genetic structure. Kōaro (Galaxias brevipinnis) is a facultatively diadromous Southern Hemisphere galaxiid fish that frequently becomes landlocked in inland lakes. This study compares seven landlocked kōaro populations to diadromous populations from main and offshore islands of New Zealand. Genotyping-by-sequencing was used to obtain genotypes at 18,813 single nucleotide polymorphism sites for each population. Analyses of population structure revealed that most landlocked populations were genetically highly distinct from one another, as well as from diadromous populations. A few particularly isolated island and lake populations were particularly strongly genetically differentiated. Landscape characteristics were measured to test whether lake elevation, size, or distance from the sea predicted genetic diversity or differentiation from diadromous kōaro. While there were no significant relationships indicating isolation-by-distance or isolation-by-environment, we detected a trend toward lower genetic diversity in lakes at higher elevations. Our findings illustrate the critical role that landlocking can play in the structure of intraspecific genetic diversity within and between populations.
The study of the eukaryotic fraction of the microbiota using a metabarcoding approach is usually hindered by the high host to eukaryotic microbiota DNA ratio in samples. Indeed, the 18S rRNA gene is very similar for both the host and its eukaryotic communities, leading to a preferential amplification of the predominant host DNA when using universal primers. Multiple approaches have been developed to reduce host DNA amplification. One method is based on elongation arrest blocking primers, oligonucleotides modified with a C3 Spacer that stops the advancement of the DNA polymerase at non-conserved regions of a target gene. In this paper, we successfully developed and tested species-specific elongation arrest blocking primers to block the Flag cichlid, Mesonauta festivus, 18S rRNA SSU. Our elongation arrest blocking primers significantly reduced the amount of host DNA amplicons by 66 %. In addition to reducing the amount of sequencing wasted, the blocking primers increased the detectability of potentially dangerous parasitic taxa in fish gut, highlighting the potential of the method for parasitic screening. For instance, we discovered a case of infection by the parasitic ciliate Nyctotherus sp. and detected the presence of a parasitic Trematode and an Amoebae. While our data support the possibility of achieving a complete inhibition of host DNA amplification using elongation arrest blocking primers, more research is still required. Still, there is a need for the development and additional testing of protocols to study the eukaryotic diversity present in fish gut, a slow-growing field of study in comparison to its prokaryotic counterpart.
The behavior of animals potentially affects their survival and reproduction. The activity budget of the Critically Endangered giraffe Giraffa camelopardalis camelopardalis has been investigated in populations across Africa and found to be influenced by body size, diet and sex. Foraging patterns show how an animal chooses to forage in its environment, and is influenced by resource availability, competition and predation risk. The activity budget and foraging patterns of Nubian giraffes vary considerably between ecosystems. The Nubian giraffe is a recently identified subspecies G. camelopardalis camelopardalis). This Critically Endangered giraffes which includes Rothschild’s giraffes, occurs only within Kenya, Uganda, Ethiopia, and Southern Sudan. We observed the behavior of a population of Nubian giraffes in Lake Nakuru National Park, Kenya, to assess seasonal activity budgets and foraging patterns. In the wet and dry seasons, giraffes spent approximately the same amount of time (53 and 57%, respectively) foraging. Movement and resting duration decreased slightly from the dry to the wet season (22 to 20% and 25 to 22%, respectively. Across both seasons, Vachellia xanthophloea (67%), Maytenus senegalensis (19%), and Solanum incanum (9%) made up the bulk of the giraffe’s diet. In the dry season, giraffe additionally foraged on Maerua triphylla (2%), Vachellia gerrardi (2%), and Grewia similis (1%); in the wet season, they added Vachellia abyssinica (2%) and Rhus natalensis (2%) to their diet. The most utilized browsing height was 3.5 m below their average height.. Overall, season did not appear to influence the Nubian giraffe’s activity time budget or foraging patterns in Lake Nakuru National Park. Improved knowledge of the behavioral patterns of this subspecies will allow managers to manage and conserve the species and its habitat better. For instance, planting perennial plants in all vegetation types used by giraffes in the park minimizes browsing pressure on the already over browsed Vachellia.
We use the InVEST model and five periods of land use data from 1980 to 2020 to assess the habitat quality of the Ningxia Hui Autonomous Region in western China, which has characteristics of a typical fragile ecosystem. We further analyze the spatial and temporal characteristics of habitat quality evolution and its relationship with land use and landscape pattern indices to explore the close relationship between regional habitat quality changes and human natural resource conservation and utilization.The research results show that the overall habitat quality of Ningxia Hui Autonomous Region was stable and at a moderate level during the 40 years from 1980 to 2020; Habitat patches with low, high and very high quality occupy a larger proportion of the area, followed by very low and moderate levels. There was a significant spatial aggregation of high and low habitat quality in Ningxia, with high values usually distributed in the northern and southern areas with good natural conditions and low values distributed in areas with frequent human activities and poor natural conditions. The decrease in habitat quality in Ningxia was mainly due to the expansion of cultivated land and construction land, the increase in landscape fragmentation and the resulting decrease in connectivity. On the other hand, due to the implementation of ecological protection measures, such as the project of returning farmland to pasture and grass to forest, the quality of habitats in Ningxia increased. The conclusions of this study support the idea that the conservation of habitat quality in ecologically fragile areas should fully preserve the original natural habitats and reduce the interference of human activities. At the same time, targeted ecological protection policies should be developed to restore the areas where the habitat quality has been damaged and ultimately maintain the stability of biodiversity and ecosystems in ecologically fragile areas.
1. Passive Acoustic Monitoring is emerging as a solution for monitoring species and environmental change over large spatial and temporal scales. However, drawing rigorous conclusions based on acoustic recordings is challenging, as there is no consensus over which approaches and indices are best suited for characterizing marine acoustic environments. 2. We present an alternative to the use of ecoacoustic indices and describe the application of multiple machine learning techniques to the analysis of a large PAM dataset. We combine pre-trained acoustic classification models, dimensionality reduction, and random forest algorithms to demonstrate how machine-learned acoustic features capture different aspects of the marine environment. We processed two PAM databases and conducted 13 trials showing how acoustic features can be used to: i) discriminate between the vocalizations of marine mammals, beginning with high-level taxonomic groups, and extending to detecting differences between conspecifics belonging to distinct populations; ii) discriminating amongst different marine environments; and iii) detecting and monitoring anthropogenic and biological sound sources. 3. Acoustic features and their UMAP projections exhibited good performance in the classification of marine mammal vocalizations. Most of the taxonomic levels investigated here could be classified using the UMAP projections, apart from species that were underrepresented. Both anthropogenic (ships and airguns) and biological (humpback whales) sound sources could also be identified in field recordings. 4. We argue that acoustic feature extraction, visualization, and analysis allows the retention of most of the environmental information contained in PAM recordings, overcoming the limitations encountered when using ecoacoustics indices. Acoustic features are universal, permitting comparisons of results collected from multiple environments. Our approach can be used to simultaneously investigate the macro and micro characteristics of marine soundscapes, with a more objective method and with far less human effort.
Background and aims High-intensity grazing in Mongolian grasslands has led to the general deterioration of biodiversity and ecosystem functioning. Abundant evidence shows that grazing affects the structure and function of grassland ecosystems, especially under overgrazing. Methods We examined the effects of three grazing intensities (0, 1.92, and 3.08 sheep ha-1 a-1) on plant commu-nities, plant and soil C, N and P contents, and plant and soil C:N:P stoichiometry in a desert grassland in different years. Results Grazing did not affect plant coverage, richness, or N:P, and the plant community biomass, litter bio-mass and C:N and C:P were highest under a zero grazing intensity. Soil C:N changed with the year and grazing intensity. However, soil C:P and N:P were higher in 2018 than in 2016 and 2017. Conclusions Our study suggested that grazing promoted the flow of N between plants and the soil, especially at 3.08 sheep ha-1 a-1. Under grazing stress, plants maintained the potential for compensatory growth. Further-more, N was shown to be the limiting fertilizer component for plants growing in this area among the three grazing intensities.
The encroachment of freshwater territories by invasive species is a global issue with its associated co-existence, displacement and facilitation of native species. The blackchin tilapia, Sarotherodon melanotheron is one of the most successful biological invasive species. Data on its apparent ecological consequences on native species are rare in Nigerian inland waters. Based on stomach contents analyses, diets, feeding strategies, and dietary niche breadths of two sympatric invasive S. melanotheron and native Nile tilapia Oreochromis niloticus populations in a tropical domestic water supply were assessed for possible convergence. Both species exhibited generalist feeding strategies subsisting mostly on algae but fish eggs and larvae were conspicuous preys of S. melanotheron. Dietary niche of S. melanotheron was wider than that of O. niloticus. Dietary niche overlap was high and significant between these sympatric species. These findings imply that competitive feeding interactions-including predations on vulnerable early life stages may potentially promote invasion success of S. melanotheron in Eleiyele Reservoir.
Phytoplankton plays a fundamental role in the ecology of ocean systems and is the key player in the global carbon cycle. At a time of global warming, understanding the mechanisms of its adaptation to temperature is therefore of paramount importance. Cosmopolitan planktonic species abundant in different marine environments provide both a unique opportunity and an efficient methodological tool to study the genomic bases of their adaptation. This is the case for the eukaryotic picoalga Bathycoccus prasinos, whose genomic variability we chose to study in temperate and polar oceanic waters. Using multiple metagenomic datasets, we found that ~5% of B. prasinos genomic positions are variable, with an overwhelming majority of biallelic motifs. Cold and temperate waters are clearly associated with changes in variant frequencies, whereas in transitional waters we found more balanced polymorphism at most of these positions. Mesophilic and psychrophilic gene variants are distinguished by only a few amino acid changes located at positions critical for physical and functional protein properties. These results provide new information on the genomic diversity of a cosmopolitan eukaryotic planktonic species and suggest “minimal mutational strategies” related to the properties of specific proteins at different temperatures.
For more than three decades, the Asian turtle crisis has resulted in the decline of every native species in China. For some species, such as the yellow pond turtle (Mauremys mutica), wild populations have dwindled to near functional extinction. Previous studies show there is deep genetic divergence of M. mutica sensu lato between populations north and south of the Pearl River Drainage but no data to show if phylogeographic structure occurs within these two main types. In this study, we found clear phylogeographic structure. In northern types, we found two main clades, corresponding to mainland China and island clades (Taiwan and Yaeyema Islands) with uncorrected p values of 0.00-2.0% divergence in our 2353 bp concatenated mtDNA data set. For the southern types, we found three main clades corresponding to Hainan, Mainland (Vietnam/Guangxi) and the Annam pond turtle (Mauremys annamensis) with divergence ranging from 1.0-1.8% among these three groups. Moreover, the identification of northern and southern types by phenotype was roughly 98% accurate, which, coupling with the deep genetic divergence in mtDNA (5.5-6.7%) and in the 6056 bp nuDNA data set (0.16-0.37%) provide sufficient evidence for northern M. mutica to be an independent species, and individuals from the southern clade should be regarded as subspecies of M. annamensis. Finally, we provide the most comprehensive database to date which can be used to determine the region of origin for captive stock. Making the large captive populations of M. mutica, under the right conditions, potentially valuable for restocking or augmentation of wild populations.
Plants in suburban forests of eastern North America face the dual stressors of high white-tailed deer density and invasion by nonindigenous plants. The combination of chronic deer herbivory and strong competition from invasive plants could alter a plant’s stress- and defense-related secondary chemistry, especially for long-lived juvenile trees in the understory, but this has not been studied. We measured foliar total antioxidants, phenolics, and flavonoids in juveniles of two native trees, Fraxinus pennsylvanica (green ash) and Fagus grandifolia (American beech), growing in six forests in the suburban landscape of central New Jersey, USA. The trees grew in experimental plots that had been subject for 2.5 years to factorial treatments of deer access/exclosure X addition/no addition of the nonindigenous invasive grass Microstegium vimineum (Japanese stiltgrass). As other hypothesized drivers of plant secondary chemistry, we also measured non-stiltgrass herb layer cover, light levels, and water availability. Univariate mixed model analysis of the deer and stiltgrass effects and multivariate structural equation modeling (SEM) of all variables showed that both greater stiltgrass cover and greater deer pressure induced antioxidants, phenolics, and flavonoids, with some variation between species. Deer were generally the stronger factor, and stiltgrass effects were most apparent at high stiltgrass density. SEM also revealed that soil dryness directly increased the chemicals; deer had additional positive, but indirect, effects via influence on the soil; in beech PAR positively affected flavonoids; and herb layer cover had no effect. Juvenile trees’ chemical defense/stress responses to deer and invasive plants can be protective, but also could have a physiological cost, with negative consequences for recruitment to the canopy. Ecological implications for species and their communities will depend on costs and benefits of stress/defense chemistry in the specific environmental context, particularly with respect to invasive plant competitiveness, extent of invasion, local deer density, and deer browse preferences.
Comparing life history traits among populations that have been separated genetically for several hundred thousand years, but live in similar habitats on different continents, may help us understand how ecological and anthropomorphic factors shape life histories. We compared patterns of growth in body length and mass, and the influence of population density, habitat quality (NDVI), and reproduction on age-specific length and mass of male and female brown bears between Alberta, Canada, and Sweden. We found that Swedish females were significantly smaller in both length and mass than Alberta females. Swedish females also reached primiparity earlier and at a smaller mass and length. However, there were no continental differences in the patterns of growth in males. We found strong positive effects of NDVI, but only weak negative effects of population density on female mass and length in both areas. Generally, especially mass of Alberta females was more strongly affected by NDVI and density than for Swedish females. Reproduction had stronger negative effects on female mass in Alberta than in Sweden. We found no effects of NDVI and population density on male mass and body length in both areas. The larger variation in female growth and size between the areas, in contrast to males, may be related to differences in female reproductive investment due to differences in population trends, i.e., earlier reproduction in increasing populations or populations below carrying capacity, or to different selection pressures in the past, potentially due to human persecution. Swedish females exhibited characteristics typical of increasing populations, whereas Alberta females exhibited characteristics typical of stable or decreasing populations. The difference in reproduction investment means that Swedish bears can be harvested at higher rates, whereas Alberta bears must be managed more conservatively.
The Timber Rattlesnake (Crotalus horridus) has a large distribution spanning much of the eastern United States. Because temperature, habitat type, prey composition and abundance, and a variety of other factors may dictate reptile behavior, populations of conspecific species may exhibit behavioral differences across latitudinal and elevational gradients. Using radio telemetry, we tracked 10 adult Timber Rattlesnakes (7 males, 3 females) from May 2016 to June 2017 in southeastern Louisiana to examine the spatial ecology of male and non-gravid female snakes. Mean annual and seasonal home ranges of non-gravid female Timber Rattlesnakes were not statistically different from that of males. Mean seasonal home range sizes and average distances travelled of both sexes was smallest in winter, and had a general increasing trend beginning in spring with a peak in fall. These increases seemed to coincide with the breeding season, taking place from early July until the end of November. Comparison of this study with other studies throughout its distribution could have implications towards future management of conservation for other southern populations of Timber Rattlesnakes.
The Yunnan-Guizhou Plateau (YGP) is characterized by the distinctive isolated habitat of limestone Karst Islands and features the Wumeng Mountains (Mts), which divide the YGP into the two Plateaus of Yunnan and Guizhou. This study aims to assess the effects of past geographic and environmental isolation and climate fluctuation on the flora distribution in the YGP. To this effect, we analyzed the phylogeographical pattern and genetic structure for Myrica nana, a vulnerable species endemic to the YGP, based on chloroplast and nuclear ribosomal DNA sequence. The results suggest that the genetic and haplotype network structures are divided into at least two groups—cpDNA haplotype H2 (or nrDNA haplotypes h1, h2, and the native haplotype) mainly distributed to the east of the Wumeng Mts, and cpDNA haplotype H1 and haplotypes H3–H10 (or nrDNA haplotype h3) distributed to the west of the Wumeng Mts. A deep genetic split was noted within the two groups to reach 25 steps, especially for the cpDNA fragment variation. The east–west divergence reveals the existence of a natural geographical isolation boundary in the form of the Wumeng Mts, which divides the YGP into the Yunnan and Guizhou Plateaus. Therefore, there existed at least two glacial refugia during the Quaternary glacial period, along with a genetic diversity center, and at least two large geographic protection units for the vulnerable species of M. nana, distributed throughout the eastern and western sides of the Wumeng Mts. This study not only clarifies that the phylogeographical pattern and genetic structure for M. nana can be attributed to geographic and environmental isolation and climate fluctuation, but it also proposes an effective strategy to protect vulnerable species and the important wild flora of the YGP.
There is much concern about disruption of endocrine physiology regulated by steroid hormones in humans, other terrestrial vertebrates and fish by industrial chemicals, such as bisphenol A, and pesticides, such as DDT. These endocrine-disrupting chemicals influence steroid-mediated physiology in humans and other vertebrates by competing with steroids for receptor binding sites, disrupting diverse responses involved in reproduction, development and differentiation. Here I discuss that due to evolution of the progesterone receptor (PR) and mineralocorticoid receptor (MR) after ray-finned fish and terrestrial vertebrates diverged from a common ancestor, each receptor evolved to respond to different steroids in ray-finned fish and terrestrial vertebrates. In elephant shark, a cartilaginous fish, ancestral to ray-finned fish and terrestrial vertebrates, both progesterone and 17,20b-dihydroxy-progesterone activate the PR. During the evolution of ray-finned fish and terrestrial vertebrates, the PR in terrestrial vertebrates continued responding to progesterone and evolved to weakly respond to 17,20b-dihydroxy-progesterone. In contrast, the physiological progestin for the PR in zebrafish and other ray-finned fish is 17,20b-dihydroxy-progesterone, and ray-finned fish PR responds weakly to progesterone. The MR in fish and terrestrial vertebrates also diverged to have different responses to progesterone. Progesterone is a potent agonist for elephant shark MR, zebrafish MR and other fish MRs, in contrast to progesterone's opposite activity as an antagonist for aldosterone, the physiological 2 mineralocorticoid for human MR. These different physiological ligands for fish and terrestrial vertebrate PR and MR need to be considered in applying data for their disruption by chemicals in fish and terrestrial vertebrates to each other.
1. Latitudinal diversity gradient (LDG) is the increase in species richness towards the equator and is one of the most consistent patterns in biogeography, where current and historical processes contribute to shape the pattern. 2. Despite that LDG patterns have been described for some insects, the underlying mechanisms associated with community assembly and diversification along modern latitudinal diversity gradient pattern remain unknowledge for many groups. 3. Odonata is an old order of insects that originated during the Carboniferous and has diversified through different eras. Here, we defined co-occurrence based on the presence in ecoregions and 1°×1° grid cells of Odonata species in North America NA, to address their species richness, phylogenetic structure, and species diversification rate along the latitudinal gradient. 4. For the whole order, we found the highest species richness at mid-latitudes, while phylogenetic diversity showed a linear positive pattern along the gradient. Our results showed dragonfly assemblages were clustered along all the gradient, suggesting that environmental filtering sorted the assemblages. Whereas damselfly species assemblages were clustered at mid-latitude and overdispersed into both extremes of gradient, probably community assembly is driving by thermal gradients at mid-latitude, by competitive exclusion at south extreme, and by different origins of the biota at the boreal zone. Our results show that apparently most ancestral lineages of Odonata inhabit tropical zones, where diversified and dispersed to the temperate region, although likely also have been diversified into regions of NA, which might be linked with the highest species richness at mid-latitude for both suborders.