1.Ectomycorrhizal (ECM) roots are evolutionary strategies of plants for effective nutrient uptake under varying abiotic conditions. Formation and morphological differentiations of ECM roots are important strategies in foraging environments. However, little is known on how such strategies mediate the nutrients of the below- and aboveground tissues and the balances among nutrient elements across environmental gradients. 2.We studied the function of ECM symbiosis in Abies faxoniana across its distributional range in Southwest China. The effects of differential ECM strategies, i.e. the contact exploration type, the short-distance exploration type, and the medium-distance exploration type, and root tips functional traits, etc., on root and foliar N and P and N:P ratio were examined across natural environmental gradients. 3.The ECM symbionts preferentially facilitated P uptake in A. faxoniana under both N and P limitations. The uptakes of N and P were primarily promoted by the effectiveness of ECM roots, e.g. ECM root tips per unit biomass, superficial area of ECM root tips, the ratio of living and dead root tips, but negatively related to the ECM proliferations and morphological differentiations. Generally, plant N and P nutrients were always promoted by the contact exploration type, while negatively affected by the short-distance exploration type in A. faxoniana. Root and foliar N and P nutrients were expected to be affected by the medium-distance exploration type in dynamics. Especially, root P limitation could be relieved when the frequency of medium-distance exploration type up to c.15%, whilst root N limitation was strengthen when the frequency of medium-distance exploration type over 20%. 4.We suggest that both below- and above-ground nutritional traits of host tree species could be strongly affected by ECM symbiosis in natural environments. The ECM strategies responding to environmental conditions significantly affect the plant nutrient uptakes and trade-offs. ECM soil exploration types are the great supplementary mechanisms for plant nutrient uptake.
1. Bat abundance, diversity and behaviour can be monitored by capturing bats for identification and measurement in the hand, but this has several disadvantages. These include disturbance to the bats, which limits the frequency with which captures can be made at an individual capture site, and potentially alters the behaviours being studied. 2. Passive recording and automated analysis and identification of bat calls offers an alternative, non-invasive approach to monitoring bats. In this study, we examine the effectiveness of acoustic monitoring in comparison with capture-based monitoring of seasonal swarming behaviour among several species of Myotis bats in southern Britain. 3. We show that both approaches have advantages and disadvantages for different tasks, but can be viewed as complementary methods for addressing different types of research questions. 4. We applied these complementary approaches, together with observations from infra-red video monitoring, to describe seasonal, overnight and species-specific variation in swarming behaviour in a multi-species community of Myotis bats. 5. In our study of swarming behaviour, capture and examination of bats in the hand was necessary for measuring sex ratios, reproductive status, and even for confirmation of species identification for some difficult to separate taxa. Capture is also an essential aspect of tagging bats for individual identification and tracking studies. 6. Passive acoustic monitoring is a valuable non-invasive method for continuous monitoring of within-night, seasonal and between-year variation in the abundance of bat calls. These can be used as an index of variation in relative abundance within -- but not between -- bat species.
Texas horned lizards (Phrynosoma cornutum) have a number of ways to avoid predation, including camouflage, sharp cranial horns, flattening of the body, and the ability to squirt blood from the eyes. These characteristics and their relatively low survival rates in the wild suggests these lizards are under high predation pressure. These lizards have been declining in much of their eastern range due to increased urbanization, agriculture, and loss of prey species. However, they can be still be found in some small south Texas towns where they can reach densities that are much higher (~50 lizards/ha) than in natural areas (~4-10 lizards/ha). We hypothesized that one reason for the high densities observed in these towns may be due to reduced predation pressure. We used model Texas horned lizards to test whether predation levels were lower in two south Texas towns than on a nearby ranch. We constructed models from urethane foam, a material that is ideal for preserving marks left behind by predators. Models (n = 126) and control pieces of foam (n = 21) were left in the field for 9 days in each location in early and late summer and subsequent predation marks were categorized by predator taxa. We observed significantly more predation attempts on the models than on controls and significantly fewer attempts in town (n = 1) compared to the ranch (n = 60). On the ranch, avian predation attempts appear to be common especially when the models did not match the color of the soil. Our results suggest that human modified environments that have suitable habitat and food resources may provide a refuge for some prey species like horned lizards from predators.
Connectivity of marine populations is shaped by complex interactions of biological and physical processes across the seascape. The influence of environmental features on the genetic structure of populations has key implications to the dynamics and persistence of populations, and an understanding of spatial scales and patterns of connectivity is crucial for management and conservation. This study employed a seascape genetics approach combining larval dispersal modeling and population genomic analysis based on RADseq to examine environmental factors influencing patterns of genetic structure and connectivity for a highly-dispersive mud crab, Scylla olivacea (Herbst, 1796) in the Sulu Sea. Dispersal simulations reveal widespread but asymmetric larval dispersal influenced by persistent southward and westward surface circulation features in the Sulu Sea. Despite potential for widespread dispersal, significant genetic differentiation was detected among eight Sulu Sea populations based on 1,655 single-nucleotide polymorphism (SNP) markers (FST = 0.0057, p = 0.001) and a subset of 1,643 putatively neutral SNP markers (FST = 0.0042, p = 0.001). Oceanography influences genetic structure, as redundancy analysis (RDA) revealed significant contribution of asymmetric ocean currents to neutral genetic variation (R2adj = 0.133; p = 0.035). Genetic structure may also reflect demographic factors, with divergent populations characterized by low effective population sizes (Ne < 50). Pronounced latitudinal genetic structure was recovered for loci putatively under selection (FST = 0.2390, p = 0.001), significantly correlated with variability in mean sea surface temperatures during peak spawning months of S. olivacea (R2adj = 0.763; p = 0.041), suggesting putative signatures of selection and local adaptation of early life history stages to thermal clines. This study contributes to the growing body of literature documenting population genetic structure and local adaptation for highly-dispersive marine species, and provides information useful for spatial management of the fishery resource.
Aim: In theory, long-distance dispersal (LDD) outside a species’ range contributes to genetic divergence. However, previous studies have not discriminated this process from vicariant speciation in migratory bird species. We conducted an integrative phylogeographic approach to test the LDD hypothesis, which predicts that a Japanese migratory bird subspecies diverged from a population in the coastal region of the East China Sea (CRECS) via LDD over the East China Sea (ECS). Location: East Asia Taxon: Brown Shrike (Lanius cristatus) Methods: Both a haplotype network and a multi-locus gene network of its three subspecies were reconstructed to examine from which continental population the Japanese subspecies diverged. A species distribution model (SDM) for the Japanese subspecies was constructed using bioclimatic variables under the maximum entropy algorithm. It was projected to the climate of the last glacial maximum (LGM) to infer the candidate source area of colonisation. A migratory route of the Japanese subspecies, which possibly reflects a candidate past colonisation route, was tracked by light-level geolocators. Results: Molecular phylogenetic networks suggest that the Japanese subspecies diverged from a population in the CRECS. The SDM inferred that the emerged continental shelf of the ECS and the present CRECS were suitable breeding areas for the Japanese subspecies during the LGM. A major migratory route for the Japanese subspecies was inferred between the CRECS and the Japanese archipelago across the ECS. Main conclusions: Our integrative approach supported the LDD hypothesis for divergence of the Japanese subspecies of the Brown Shrike. Shrinkage and expansion of the ECS may have been responsible for successful colonisation and isolation of the new population. Vicariance was inferred for divergence of the subspecies in the northeast Asian continent from the Japanese population. Our framework provides a new phylogeographic scenario in this region, and discriminating LDD and vicariance models should improve our understanding of the phylogeographic histories of migratory species.
Comparisons of 3D shapes have recently been applied to diverse anatomical structures using landmarking techniques. However discerning evolutionary patterns can be challenging for structures lacking homologous landmarks. We used alpha shape analyses to quantify vaginal shape complexity in 40 marine mammal specimens including cetaceans, pinnipeds, and sirenians. We explored phylogenetic signal and the potential roles of natural and sexual selection on vaginal shape evolution. Complexity scores were consistent with qualitative observations. Cetaceans had a broad range of alpha complexities, while pinnipeds were comparatively simple and sirenians were complex. Intraspecific variation was found. Three-dimensional surface heat maps revealed that shape complexity was driven by invaginations and protrusions of the vaginal wall. Phylogenetic signal was weak and metrics of natural selection (relative neonate size) and sexual selection (relative testes size, sexual size dimorphism, and penis morphology) did not explain vaginal complexity patterns. Additional metrics, such as penile shape complexity, may yield interesting insights into marine mammal genital coevolution. We advocate for the use of alpha shapes to discern patterns of evolution that would otherwise not be possible in 3D anatomical structures lacking homologous landmarks.
1. Species distribution modelling, which allows users to predict the spatial distribution of species with the use of environmental covariates, has become increasingly popular, with many software platforms providing tools to fit species distribution models. However, the species observations used in species distribution models can have varying levels of quality and can have incomplete information, such as uncertain species identity. 2. In this paper, we develop two algorithms to reclassify observations with unknown species identities which simultaneously predict different species distributions using spatial point processes. We compare the performance of the different algorithms using different initializations and parameters with models fitted using only the observations with known species identity through simulations. 3. We show that performance varies with differences in correlation among species distributions, species abundance, and the proportion of observations with unknown species identities. Additionally, some of the methods developed here outperformed the models that didn't use the misspecified data. 4. These models represent an helpful and promising tool for opportunistic surveys where misidentification happens or for the distribution of species newly separated in their taxonomy.
1. Patterns in, and the underlying dynamics of, species cooccurrence is of interest in many ecological applications. Unaccounted for, imperfect detection of the species can lead to misleading inferences about the nature and magnitude of any interaction. A range of different parameterisations have been published that could be used with the same fundamental modelling framework that accounts for imperfect detection, although each parameterisation has different advantages and disadvantages. 2. We propose a parameterisation based on log-linear modelling that does not require a species hierarchy to be defined (in terms of dominance), and enables a numerically robust approach for estimating covariate effects. 3. Conceptually the parameterisation is equivalent to using the presence of species in the current, or a previous, time period as predictor variables for the current occurrence of other species. This leads to natural, ’symmetric’, interpretations of parameter estimates. 4. The parameterisation can be applied to many species, in either a maximum-likelihood or Bayesian estimation framework. We illustrate the method using camera trapping data collected on three mesocarnivore species in South Texas.
1. A time-consuming challenge faced by ecologists is the extraction of meaningful data from camera trap images to inform ecological management. Automated object detection solutions are increasingly, however, most are not sufficiently robust to be deployed on a large scale due to lack of location invariance across sites. This prevents optimal use of ecological data and results in significant resource expenditure to annotate and retrain object detectors. 2. In this study, we aimed to (a) assess the value of publicly available image datasets including FlickR and iNaturalist (FiN) when training deep learning models for camera trap object detection (b) develop a for training location invariant object detection models and (c) explore the use of small subsets of camera trap images for optimization training. 3. We collected and annotated 3 datasets of images of striped hyena, rhinoceros and pig, from FiN, and used transfer learning to train 3 object detection models in the task of animal detection. We compared the performance of these models to that of 3 models trained on the Wildlife Conservation Society and Camera CATalogue datasets, when tested on out of sample Snapshot Serengeti datasets. Furthermore, optimized the FiN models via infusion of small subsets of camera trap images to increase robustness for challenging detection cases. 4. In all experiments, the mean Average Precision (mAP) of the FiN models was significantly higher (82.33-88.59%) than that achieved by the models trained only on camera trap datasets (38.5-66.74%). The infusion of camera trap images into FiN training further improved mAP, with increases ranging from 1.78-32.08%. 5. Ecology researchers can use FiN images for training robust, location invariant, out-of-the-box, deep learning object detection solutions for camera trap image processing. This would allow AI technologies to be deployed on a large scale in ecological applications. Datasets and code related to this study are open source and available at: https://github.com/ashep29/infusion
For nearly all organisms, dispersal is a fundamental life history trait that can shape their ecology and evolution. Variation in dispersal capabilities within a species exists and can influence population genetic structure and ecological interactions. In fungus-gardening (attine) ants, co-dispersal of ants and mutualistic fungi is crucial to the success of this obligate symbiosis. Female-biased dispersal (and gene flow) may be favored in attines because virgin queens carry the responsibility of dispersing the fungi, but a paucity of research has made this conclusion difficult. Here, we investigate dispersal of the fungus-gardening ant Trachymyrmex septentrionalis using a combination of maternally- (mitochondrial DNA) and biparentally-inherited (microsatellites) markers. We found three distinct, spatially isolated mitochondrial DNA haplotypes. Two were found in the Florida panhandle and the other was found in the Florida peninsula. In contrast, biparental markers illustrated significant gene flow across this region and minimal spatial structure. The differential patterns uncovered from mitochondrial DNA and microsatellite markers suggest that most long-distance ant dispersal is male-biased and that females (and concomitantly the fungus) have more limited dispersal capabilities. Consequently, the limited female dispersal is likely an important bottleneck for the fungal symbiont. This bottleneck could slow fungal genetic diversification, which has significant implications for both ant hosts and fungal symbionts regarding population genetics, species distributions, adaptive responses to environmental change, and coevolutionary patterns.
We examined whether the presence or absence of different environmental stressors influenced the reproductive potential of a saltmarsh species - Plantago maritima. We focused on total seed output, seed quality and biomass of progeny. So far, there are no studies trying to answer the question of how different saltmarsh management affects the quality of seed in saltmarsh species. For the purposes of the study, plots subjected to light mowing, light or heavy grazing, trampling or rooting were designated in three nature reserves in Poland. On each plot, the abundance of infructescences per sq. metre was calculated. Mature infructascences were collected and their length and no of fruit capsules were measured. The seeds obtained from fruit capsules were weighted and sown in controlled conditions. The germination rate and the final germination percentage were calculated. A representative number of sprouts were grown. After a period of two months, the specimens were harvested and their total dry mass was measured. It was found that heavy grazing had the greatest effect on all of the studied characteristics. The presence of this factor resulted in shorter infructescences with a smaller number of fruit capsules. However, this phenomenon was compensated by the higher abundance of infructescences per sq. metre. At the same time seeds produced by grazed specimens were significantly lighter. Intensive trampling by people affected specimens in a similar way to heavy grazing, while mowing and rooting had less impact on the considered characteristics. Although a positive correlation between seed mass and germination success was found, the altogether lower seed mass had a negligible effect on germination parameters. Also, the differences in seed parameters did not affect dry mass of obtained progeny grown in lab conditions.
A rapid biodiversity assessment of insects and associated Laboulbeniales fungi was conducted over the course of five nights in August, 2018 at two central Florida lakes: Lake Eustis and the nearby protected and restored National Natural Landmark, Emeralda Marsh Conservation Area (EMCA), which encompasses a portion of Lake Griffin. These locations were selected because Lake Eustis was surveyed for Laboulbeniales in 1897 by mycologist Dr. Roland Thaxter, but has not since been investigated. Because Lake Eustis has been urbanized, with the lake perimeter almost entirely altered by human development, the site offers a look into Laboulbeniales diversity across a 121 year timeline, before and after human development. By surveying Lake Eustis and EMCA, a modern case study comparison of Laboulbeniales and insect diversity between a developed and unrestored system and a protected and restored system is made. A total of 4,022 insects were collected during the rapid assessment. Overall, insect abundance was greater at EMCA, with 3,001 insects collected, compared to 1,021 insects collected from Eustis. Though family level insect richness was comparable between sites, with 55 families present at EMCA and 56 at Eustis, 529 out of 3,001 (17.6%) of the insects collected at EMCA were hosts to parasitic Laboulbeniales fungi whereas only 2 out of 1,021 (0.19%) collected from Eustis were infected. There were 16 species of Laboulbeniales found at EMCA compared to only one at Eustis. The current number of Laboulbeniales species documented at Eustis was incredibly depauperate compared to the 27 species recorded by Thaxter in 1897, suggesting the possibility of utilizing Laboulbeniales as indicators of ecosystem health. A figure displaying host-parasite records and a species list of Laboulbeniales fungi is compiled and updated occurrence records for species of Ceratomyces and Hydrophilomyces are provided.
The range of the Canada lynx (Lynx canadensis) has contracted substantially from its historical range prior to the 19th century. Using harvest records, we found that the southern range of the lynx in Ontario in the late 1940s collapsed and then in a short period of time increased to its largest extent in the mid-1960s where the lynx range spread south of the boreal forest for a decade. After this expansion the southern range contracted northwards beginning in the 1970s. Most recently, there has been a slight expansion between 2010-2017. We have attributed these dynamics on the southern range periphery to the fluctuation of the boreal lynx population in the core of the species’ range. In addition, connectivity to boreal lynx populations and snow depth seemed to condition whether the lynx expanded into an area. However, we did not find any evidence that would suggest that these changes were due to anthropogenic disturbances or competition. The boreal lynx population does not reach numbers as it once did, consequently we likely will not see large expansions of the southern lynx range as in the mid-1960s. Our results suggest that southern lynx range in Ontario have been driven by the magnitude of the boreal lynx population cycle, connectivity to the boreal forest and snow conditions. Therefore, it is quite unlikely that southern lynx population in the Great Lakes will ever recover, since the warming climate and forestry practices are causing a northward contraction of the boreal forest and likely with it the core lynx populations.
Third generation sequencing technologies, such as Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), have gained popularity over the last years. These platforms can generate millions of long read sequences. This is not only advantageous for genome sequencing projects, but also for amplicon-based high-throughput sequencing experiments, such as DNA barcoding. However, the relatively high error rates associated with these technologies still pose challenges for generating high quality consensus sequences. Here we present NGSpeciesID, a program which can generate highly accurate consensus sequences from long-read amplicon sequencing technologies, including ONT and PacBio. The tool includes clustering of the reads to help filter out contaminants or reads with high error rates and employs polishing strategies specific to the appropriate sequencing platform. We show that NGSpeciesID produces consensus sequences with improved usability by minimizing preprocessing and software installation and scalability by enabling rapid processing of hundreds to thousands of samples, while maintaining similar consensus accuracy as current pipelines
The Magdalena River in Colombia and its floodplain lakes are key ecosystems for the subsistence of Colombian society. Yet, hydrologic regulation, pollution, deforestation and climate change are threatening its ecological integrity. To understand how these floodplain lakes respond over decadal-centennial scales to natural and anthropogenic stressors, we selected two shallow lakes with varying degree of connectivity to the River and assessed their historical ecological and limnological change through a multi-proxy analysis of diatoms, geochemistry and lake’s morphometric variation resulting from extreme periods of high floods and droughts. The reconstruction of the more isolated San Juana Lake covered the last c.500 years. It showed riverine-flooded conditions from c.1555-1741 characterised by high detrital inputs, reductive conditions, and dominance of planktonic diatoms. From c.1758-1954, the riverine meander became disconnected, conveying into a marsh-like environment rich in aerophil diatoms and organic matter. The current lake was then formed around the mid 1960s and a diverse lake-associated diatom flora developed. Lake waters became more oxygenated, while sedimentation and nutrients increased through time since the lake formation. The reconstruction for Barbacoas Lake, a waterbody directly connected to the Magdalena River, spanned the last 60 years and showed alternating riverine-wetland-lake conditions dominated by planktonic and benthic diatoms respectively. An exception was however observed, during a prolonged period of low rainfall between 1989-1992, where the lake almost desiccated and where aerophil diatoms prevailed. Inferences of flood magnitudes and river connectivity in the lakes were supported by parallel increases in Zr/Fe (flooding) and detrital inputs (Ti/Ca) along with decreases in sedimentary OM. We proposed that lake hydrological connectivity to the Magdalena River is a main factor controlling lake long-term responses to human pressures. Highly connected lakes may respond more acutely to ENSO events while isolated lakes might be more sensitive to local land-use changes.
1. Understanding how ecosystem engineers influence other organisms has long been a goal of ecologists. Woodpeckers select nesting sites with high food availability and will excavate and then abandon multiple cavities throughout their lifetime. These cavities are crucial to secondary cavity nesting birds (SCB) that are otherwise limited by the availability of naturally occurring cavities. 2. Our study examined the influence of food resources on the nest site location and home-range size of woodpeckers, and the subsequent influence of woodpeckers on the nesting success of SCB. 3. Using five years of avian point count data to locate golden-fronted woodpeckers (GFWO), we correlated insect availability with GFWO home range size, determined differences in insect availability between GFWO occupied and unoccupied sites, and compared nesting success for the GFWO and common SCB in south Texas. We used model averaging to fit species-specific logistic regression models to predict nest success based on cavity metrics across all species. 4. Sites occupied by GFWO had a higher biomass of insects in orders Coleoptera, Hymenoptera, and Orthoptera than unoccupied sites, and there was a negative correlation between the availability of these insect orders and home-range size. GFWO nest success increased with vegetation cover and lower levels of tree decay. SCB had higher levels of nesting success in abandoned GFWO, and in trees with lower levels of nest tree decay. 5. Our results suggest that SCB may be drawn to nest in abandoned woodpecker cavities where they have higher rates of nest success compared to natural cavities. Additionally, the prevalence for GFWO to excavate cavities in trees with lower levels of decay contradicts previous literature, and may indicate a novel temperature trade-off, with live trees requiring more energy to excavate, but providing increased protection from high breeding season temperatures in arid and semi-arid areas.
Tilia cordata Mill. is a valuable tree species enriching the ecological values of the coniferous dominated boreal forests in northerly Europe. Following the historical decline, spreading of Tilia sp. is challenged by the elevated inbreeding and habitat fragmentation. We aimed to identify the main factors affecting the genetic potential of Tilia cordata for natural expansion by studying the geographical distribution of genetic diversity of Tilia cordata in semi-boreal forests of Lithuania. We used 14 genomic microsatellite markers to genotype 543 individuals from 23 wild growing populations of Tilia cordata in Lithuania. We found that Tilia cordata retained high levels of genetic diversity (population Fis = 0 to 0.15, Ho = 0.53 to 0.69, He = 0.56 to 0.75). AMOVA, Bayesian clustering and Monmonier’s barrier detection indicate weak but significant differentiation among the populations (Fst = 0.037***) into geographically interpretable clusters of (a) western Lithuania with high genetic heterogeneity but low genetic diversity, bottleneck effects, (b) peaking values of genetic diversity of Tilia cordata on rich and most soils of midland lowland, and (c) the most differentiated populations on poor soils of the coolest north-eastern highland possessing the highest rare alle frequency but elevated inbreeding and bottleneck effects, presumably, due to sub-structuring. We conclude that the genepool of Tilia cordata in Lithuania contains (a) the autochthonous populations of high genetic diversity representing the pre-historical genepools, that can be promoted, and (b) the escapes from urban sources of low diversity, that must be contained.
Exploring vegetation distribution spatial patterns facilitates understanding how biodiversity addresses the potential threat of future climate variability, especially for highly diverse and threatened tropical plant communities, but few empirical studies have been performed over various environmental scales. In this study, we used species-based and phylogeny-based methods to analyze the α- and β-diversity pattern variation in Dacrydium pectinatum communities and its key drivers along elevation and geographical gradients across three national nature reserves in Bawangling, Diaoluoshan and Jianfengling. Our study indicates that the species and phylogenetic α-diversity patterns presented consistent decreasing with elevation, with the peak occurring at low elevations. Environmental filtering caused by decreases in limiting factors, such as temperature, precipitation, soil organic matter, soil phosphorus, and light, is the main reason for the decline in diversity at high elevations, whereas low-elevation areas are affected by various factors, such as environmental filtering and similarity limitations. Species and phylogenetic β-diversity changes are closely related to environmental filtering and dispersal limitation, but the latter is key in community assembly at the heterogeneous spatial scale. In conclusion, combining species-based and phylogeny-based methods to explore the biogeographic patterns of tropical plant communities helps provide convincing evidence and confirms that the relative contributions of niche and neutral theory in the assembly process vary along environmental gradients. Though the D. pectinatum community constitute a floristically integrated unit, the genetic relationships between species are relatively far, and co-evolution to promote species coexistence is difficult when faced with habitat pressure. Hence, we believe that species coexistence in tropical plant communities requires mild environmental conditions, and low temperatures, precipitation, soil nutrients and light will aggravate environmental filtering and species competition. We also recommend strengthening the construction and management of nature reserves and the exploration of biodiversity formation mechanisms, which are crucial for biodiversity conservation in endangered tropical plant communities.