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.
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.
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.
Understanding genetic variation and structure, adaptive genetic variation and its relationship with environmental factors is of great significance to understand how plants adapt to climate change and design effective conservation and management strategies. The objective of this study was to (I) investigate the genetic diversity and structure by AFLP markers in 36 populations of R. aureum from northeast China, (Ⅱ) reveal the relative contribution of geographical and environmental impacts on the distribution and genetic diﬀerentiation of R. aureum; (Ⅲ) identify outlier loci under selection and evaluate the association between outlier loci and environmental factors and (Ⅳ) exactly calculate development trend of population of R. aureum，as it is confronted with severe climate change and to provide information for designing eﬀective conservation and management strategies. We found high genetic variation (I = 0.584) and diﬀerentiation among populations (ΦST = 0.711) and moderate levels of genetic diversity within populations of R. aureum. A significant relationship between genetic distance and environmental distance was identified, which suggested that the differentiation of diﬀerent populations was the caused by environmental factors. Using BayeScan and Dfdist, 42 outlier loci identified and most of the outlier loci are associated with climate or relief factors, suggesting that these loci are linked to genes that are involved in the adaptability of R. aureum to environment. Species distribution models (SDM) showed that climate warming will cause a significant reduction of suitable area for R. aureum especially under the RCP 85 scenario. Our results help to understand the potential response of R. auruem to climatic changes, and provide new perspectives for R. auruem resource management and conservation strategies.
How and why species range size varies along spatial gradients is fundamental yet controversial topics in biogeography. To advance our understanding on these questions and to provide insight into biological conservation, we assessed the elevational variations in vascular plants range size for different life form and biogeographical affinities, and explored the main drivers underlying above variations in the longest valley in China's Himalayas---the Gyirong Valley. Elevational range sizes of vascular plants were documented by 96 sampling plots along 12 elevational bands of 300-m ranging from 1800 to 5400 m above sea level. We assessed the elevational variations in range size by averaging the range size of all species within each elevational band. We then related range size to climate, disturbance, competition factors and the mid-domain effect, and explored the relative importance of aforementioned factors in explaining the range size variations using the Random Forest model. Total 545 vascular plants were documented by our sampling plots along the elevational gradient. Out of 545 plants, 158, 387, 337 and 112 were woody, herbaceous, temperate and tropical species respectively. Range size of each groups of vascular plants shown uniform increasing trends along the elevational gradient which are in accordance with the prediction of Rapoport's rule. Climate was the main driver for the increasing trends of vascular plants range size in the Gyirong Valley. Climate variability hypothesis and mean climate condition hypothesis were both supported to jointly explain such climate-range size relationship. Our results reinforce previous notion that Rapoport's rule applies to where the influence of climate is most pronounced, and call for close attention to the impact of climate change in order to prevent range contraction and even extinction under global warming.
The mechanisms of forest seed dispersal and regeneration of various altered forest ecosystems are complemented by the action of carnivores. The objective of this study was to evaluate the role of endozoochoric and diploendozoochoric mammals in the dispersal, scarification, and germination of seeds in two different forest ecosystems: temperate forest (TF) and dry tropical forest (DTF). A direct search and scat collection were carried out to determine dispersing agents and the abundance and richness of seeds in the Protected Natural Area, Sierra Fría, Aguascalientes, Mexico. Viability was evaluated by means of X-rays and a germination test using an optical densitometry. In addition, thickness measurements and observations were made on the surfaces of the testas by a scanning electron microscopy. In the TF, four plant species were dispersed, mainly Arctostaphylos pungens (P < 0.05), by four mammals, where the gray fox dispersed the highest average (66.8 ± 68.2; P < 0.05) and diploendozoochory was detected in bobcat scats associated with rabbit hair (Sylvilagus floridanus). The DTF presented higher abundance and richness of species, where Myrtillocactus geometrizans had the highest abundance (2680 ± 4423) and the coati (P < 0.05) dispersed the highest number of seeds (8639 ± 12203). In both types of forest, endozoochory and diploendozoochory did not affect the viability, the thickness of the testas, or the germination of any species of seeds. These results suggest that dispersing carnivores adapt to the abundance and richness of seeds in the forests they inhabit, thus developing an important ecological function by dispersing, scarifying and promoting the selective germination of seeds with thick testas in TF and thin testas in DTF.
Diapause is an adaptive dormancy strategy by which arthropods endure extended periods of adverse climatic conditions. Seasonal variation in larval diapause initiation and duration in Ostrinia furnacalis influences adult mating generation number (voltinism) across different local environments. The degree of mating period overlap between sympatric voltine ecotypes influence hybridization level, but impacts on O. furnacalis population genetic structure and evolution of divergent adaptive phenotypes remains uncertain. Genetic differentiation was estimated between voltine ecotypes collected from 8 locations. Mitochondrial haplotypes were significantly different between historically allopatric univoltine and bivoltine locations. Haplotypes from sympatric locations were clustered more-closely to bivoltine locations, but influenced by local demographics. Additionally, analyses of single nucleotide polymorphism (SNP) genotypes implicate voltinism, as opposed to geographic distance, as contributing to low, but significant levels of variation among voltine ecotypes. Regardless, only 11 of 257 SNP loci were predicted to be under selection, suggesting population genetic homogenization except at loci proximal to factors putatively responsible for locally adaptive or voltinism-specific traits. These findings provide evidence that divergent voltine ecotypes may be maintained in allopatric and sympatric areas despite relatively high rates of nuclear gene flow, yet influence of voltinism on maintenance of observed haplotype divergence remains unresolved.
1. Species are not genetically homogeneous, as the genetic structure among populations is related to the degree of isolation amongst them, such as isolation-by-distance, isolation-by-barrier and isolation-by-environment. 2. To decipher the isolation processes that drive population structuring in Jenynsia lineata we analyzed 221 sequences of the mitochondrial cytochrome c oxidase I gene (COI), which came from 19 localities. Jenynsia lineata is a small viviparous fish that inhabits a wide range of habitats in South America. Then, we examined the influence of the three most common types of isolation to explain the genetic variation found in this species. 3. Our results revealed a marked structuration, with three groups: i) La Plata/Desaguadero Rivers (sampling sites across Argentina, Uruguay, and Southern Brazil), ii) Central Argentina, and iii) Northern Argentina. A distance-based redundancy analysis including the explanatory variables geographical distances, altitude, latitude, basin, was able to explain up to 65% of the genetic structure. A variance partitioning analysis showed that the two most important variables underlying the structuration in J. lineata were altitude (isolation-by-environment) and type of basin (isolation-by-barrier). 4. Our results show that in this species, the processes of population diversification are complex and are not limited to a single mechanism. Population-structuring may lead to population reproductive isolation and ultimately to speciation. 5. This study demonstrated that the process of diversification of populations is complex and is not limited to a single mechanism. The processes that play a prominent role in this study could explain the high rate of diversity that characterizes freshwater fish species. And these processes in turn are the basis for possible speciation events.
Population size is a central parameter for conservation, however monitoring abundance is often problematic for threatened marine species. Despite substantial investment in research, many marine species remain data-poor resulting in uncertain population forecasts and restricting the evaluation of past and present conservation actions. Such is the case for the white shark (Carcharodon carcharias), a highly mobile apex predator for whom population monitoring is a conservation priority following substantial declines recorded through the 20th century. Here, we estimate the effective number of breeders that successfully contribute offspring in one reproductive cycle (Nb) providing a snapshot of recent reproductive effort in an east-Australian New Zealand population of white shark. Nb was estimated over four consecutive age cohorts (2010, 2011, 2012, 2013) using two genetic estimators (linkage-disequilibrium; LD and sibship assignment; SA) based on genetic data derived from two types of genetic markers (single-nucleotide-polymorphisms; SNPs and microsatellite loci). While estimates of Nb using different marker types produced comparable estimates, microsatellite loci were the least precise. The LD and SA estimates of Nb within cohorts using SNPs were comparable, for example the 2013 age-cohort Nb(SA) was 289 (95%CI 200-461) and Nb(LD) was 208.5 (95%CI 116.4-712.7). We show that over the time period studied Nb was stable and ranged between 206.1(±45.9) and 252.0(±46.7) per year using a combined estimate of Nb(SA+LD) from SNP loci, and a simulation approach showed that in this population effective population size (Ne) per generation can be expected to be larger than Nb per reproductive cycle. This study demonstrates how breeding population size can be monitored over time to provide insight into the effectiveness of recovery and conservation measures for the white shark, where the methods described here may be applicable to other data-poor species of conservation concern.
The evolutionary origins and hybridization patterns of Canis species in North America has been hotly debated for the past 30 years. Disentangling ancestry and timing of hybridization in Great Lakes wolves, eastern Canadian wolves, red wolves, and eastern coyotes is most often partitioned into a 2-species model that assigns all ancestry to grey wolves and/or coyotes, and a 3-species model that includes a third, North American evolved eastern wolf genome. The proposed models address recent or sometimes late Holocene hybridization events but have largely ignored Pleistocene era opportunities for hybridization that may have impacted the current mixed genomes in eastern Canada and the United States. Here, we re-analyze contemporary and ancient mitochondrial DNA genomes with Bayesian phylogenetic analyses to more accurately estimate divergence dates among lineages. We combine that with a review of the literature on Late Pleistocene Canis distributions to illuminate opportunities for ancient hybridization events between extinct Beringian grey wolves (C. lupus) and extinct large wolf-like coyotes (C. latrans orcutti) that we propose as a potentially unrecognized source of introgressed genomic variation within contemporary Canis genomes. These events speak to the potential origins of contemporary genomes and provide a new perspective on Canis ancestry, but do not influence/negate current conservation priorities of dwindling wolf populations with unique genomic signatures and key ecologically critical roles.
1. The Cormack-Jolly-Seber (CJS) model and its extensions have been widely applied to the study of animal survival rates in open populations. The model assumes that individuals within the population of interest have independent fates. It is, however, highly unlikely that a pair of animals which have formed a long-term pairing have dissociated fates. 2. We examine a model extension which allows animals who have formed a pair-bond to have correlated survival and recapture fates. Using the proposed extension to generate data, we conduct a simulation study exploring the impact that correlated fate data has on inference from the CJS model. We compute Monte Carlo estimates for the bias, range, and standard errors of the parameters of the CJS model for data with varying degrees of survival correlation between mates. Furthermore, we study the likelihood ratio test of gender effects within the CJS model by simulating densities of the deviance. Finally, we estimate the variance inflation factor for CJS models that incorporate sex-specific heterogeneity. 3. Our study shows that correlated fates between mated animals may result in underestimated standard errors for parsimonious models, significantly deflated likelihood ratio test statistics, and underestimated values of the variance inflation factor for models taking sex-specific effects into account. 4. Underestimated standard errors can result in lowered coverage of confidence intervals. Moreover, deflated test statistics will provide overly conservative test results. Finally, underestimated variance inflation factors can lead researchers to make incorrect conclusions about the level of extra-binomial variation present in their data.
1. Landscape change is a key driver of biodiversity declines due to habitat loss and fragmentation, but spatially shifting resources can also facilitate range expansion and invasion. Invasive populations are reproductively successful, and landscape change may buoy this success. 2. We show how modelling the spatial structure of reproductive success can elucidate the mechanisms of range shifts and sustained invasions for mammalian species with attendant young. We use an example of white-tailed deer (deer; Odocoileus virginianus) expansion in the Nearctic boreal forest, a North American phenomenon implicated in severe declines of threatened woodland caribou (Rangifer tarandus). 3. We hypothesized that deer reproductive success is linked to forage subsidies provided by extensive landscape change via resource extraction. We measured deer occurrence using data from 62 camera-traps in northern Alberta, Canada, over three years. We weighed support for multiple competing hypotheses about deer reproductive success using multi-state occupancy models and generalized linear models in an AIC-based model selection framework. 4. Spatial patterns of reproductive success were best explained by features associated with petroleum exploration and extraction, which offer early seral vegetation resource subsidies. Effect sizes of anthropogenic features eclipsed natural heterogeneity by two orders of magnitude. We conclude that deer populations are likely buffered from overwinter mortality by landscape change, wherein early seral forage subsidies support high springtime reproductive success to offset or exceed winter losses. 5. Synthesis and Applications. Modelling spatial structuring in reproductive success can become a key goal of remote camera-based global networks, yielding ecological insights into mechanisms of invasion and range shifts to inform effective decision-making for global biodiversity conservation.