pinecone/core-2020-05-10-deduplication huggingface dataset:
Pteropus lylei primarily forages in residential areas in Kandal, Cambodia

Bats are the second most species‐rich Mammalian order and provide a wide range of ecologically important and economically significant ecosystem services. Nipah virus is a zoonotic emerging infectious disease for which pteropodid bats have been identified as a natural reservoir. In Cambodia, Nipah virus circulation has been reported in Pteropus lylei, but little is known about the spatial distribution of the species and the associated implications for conservation and public health. We deployed Global Positioning System (GPS) collars on 14 P. lylei to study their movements and foraging behavior in Cambodia in 2016. All of the flying foxes were captured from the same roost, and GPS locations were collected for 1 month. The habitats used by each bat were characterized through ground‐truthing, and a spatial distribution model was developed of foraging sites. A total of 13,643 valid locations were collected during the study. Our study bats flew approximately 20 km from the roost each night to forage. The maximum distance traveled per night ranged from 6.88–105 km and averaged 28.3 km. Six of the 14 bats visited another roost for at least one night during the study, including one roost located 105 km away. Most foraging locations were in residential areas (53.7%) followed by plantations (26.6%). Our spatial distribution model confirmed that residential areas were the preferred foraging habitat for P. lylei, although our results should be interpreted with caution due to the limited number of individuals studied. Synthesis and applications: Our findings suggest that the use of residential and agricultural habitats by P. lylei may create opportunities for bats to interact with humans and livestock. They also suggest the importance of anthropogenic habitats for conservation of this vulnerable and ecologically important group in Cambodia. Our mapping of the probability of occurrence of foraging sites will help identification of areas where public awareness should be promoted regarding the ecosystem services provided by flying foxes and potential for disease transmission through indirect contact
Genetic diversity and phylogenetic analysis of the native mountain ponies of Britain and Ireland reveal a novel rare population

Winton, C. L., Hegarty, M. J., McMahon, R., Slavov, G. T., McEwan, N. R., Davies-Morel, M. C. G., Morgan, C. T., Powell, W., Nash, D. M. (2013). Genetic diversity and phylogenetic analysis of the native mountain ponies of Britain and Ireland reveal a novel rare population. Ecology and Evolution, 3 (4), 934?947.The conservation of unique populations of animals is critical in order to preserve valuable genetic diversity and, where populations are free-living, maintain their irreplaceable influence upon habitat ecology. An accurate assessment of genetic diversity and structure within and between populations is crucial in order to design and implement conservation strategies in natural and domesticated species. Moreover, where it is possible to identify relic populations that are related to a structured breed an ideal opportunity presents itself to model processes that reveal historical factors that have shaped genetic diversity. The origins of native UK mountain and moorland ponies are uncertain, but they may have directly descended from prehistoric populations and potentially harbour specific adaptations to the uplands of Britain and Ireland. To date, there have been no studies of population structure and genetic diversity present within a free-living group of ponies in the Carneddau mountain range of North Wales. Herein, we describe the use of microsatellites and SNPs together with analysis of the mitochondrial control region to quantify the extent and magnitude of genetic diversity present in the feral Carneddau pony and relate this to several recognised British and Irish pony breeds. Our results establish that the feral Carneddau ponies represent a unique and distinctive population that merits recognition as a defined population and conservation priority. We discuss the implications for conservation of this population as a unique pool of genetic diversity adapted to the British uplands and potentially of particular value in maintaining the biodiversity of these habitats.preprintPeer reviewe
Gene flow in the green mirid, Creontiades dilutus (Hemiptera: Miridae), across arid and agricultural environments with different host plant species

Creontiades dilutus (Stål), the green mirid, is a polyphagous herbivorous insect endemic to Australia. Although common in the arid interior of Australia and found on several native host plants that are spatially and temporally ephemeral, green mirids also reach pest levels on several crops in eastern Australia. These host-associated dynamics, distributed across a large geographic area, raise questions as to whether (1) seasonal fluctuations in population size result in genetic bottlenecks and drift, (2) arid and agricultural populations are genetically isolated, and (3) the use of different host plants results in genetic differentiation. We sequenced a mitochondrial COI fragment from individuals collected over 24 years and screened microsatellite variation from 32 populations across two seasons. The predominance of a single COI haplotype and negative Tajima D in samples from 2006/2007 fit with a population expansion model. In the older collections (1983 and 1993), a different haplotype is most prevalent, consistent with successive population contractions and expansions. Microsatellite data indicates recent migration between inland sites and coastal crops and admixture in several populations. Altogether, the data suggest that long-distance dispersal occurs between arid and agricultural regions, and this, together with fluctuations in population size, leads to temporally dynamic patterns of genetic differentiation. Host-associated differentiation is evident between mirids sampled from plants in the genus Cullen (Fabaceae), the primary host, and alternative host plant species growing nearby in arid regions. Our results highlight the importance of jointly assessing natural and agricultural environments in understanding the ecology of pest insects.J. P. Hereward, G. H. Walter, P. J. DeBarro, A. J. Lowe, & C. Rigino
Cenozoic climate change and diversification on the continental shelf and slope: evolution of gastropod diversity in the family Solariellidae (Trochoidea)

Recent expeditions have revealed high levels of biodiversity in the tropical deep-sea, yet little is known about the age or origin of this biodiversity, and large-scale molecular studies are still few in number. In this study, we had access to the largest number of solariellid gastropods ever collected for molecular studies, including many rare and unusual taxa. We used a Bayesian chronogram of these deep-sea gastropods (1) to test the hypothesis that deep-water communities arose onshore, (2) to determine whether Antarctica acted as a source of diversity for deep-water communities elsewhere and (3) to determine how factors like global climate change have affected evolution on the continental slope. We show that although fossil data suggest that solariellid gastropods likely arose in a shallow, tropical environment, interpretation of the molecular data is equivocal with respect to the origin of the group. On the other hand, the molecular data clearly show that Antarctic species sampled represent a recent invasion, rather than a relictual ancestral lineage. We also show that an abrupt period of global warming during the Palaeocene Eocene Thermal Maximum (PETM) leaves no molecular record of change in diversification rate in solariellids and that the group radiated before the PETM. Conversely, there is a substantial, although not significant increase in the rate of diversification of a major clade approximately 33.7 Mya, coinciding with a period of global cooling at the Eocene–Oligocene transition. Increased nutrients made available by contemporaneous changes to erosion, ocean circulation, tectonic events and upwelling may explain increased diversification, suggesting that food availability may have been a factor limiting exploitation of deep-sea habitats. Tectonic events that shaped diversification in reef-associated taxa and deep-water squat lobsters in central Indo-West Pacific were also probably important in the evolution of solariellids during the Oligo-Miocene
Species-time-area and phylogenetic-time-area relationships in tropical tree communities

The species-area relationship (SAR) has proven to be one of the few strong generalities in ecology. The temporal analog of the SAR, the species-time relationship (STR), has received considerably less attention. Recent work primarily from the temperate zone has aimed to merge the SAR and the STR into a synthetic and unified species-time-area relationship (STAR) as originally envisioned by Preston (1960). Here we test this framework using two tropical tree communities and extend it by deriving a phylogenetic-time-area relationship (PTAR). The work finds some support for Preston's prediction that diversity-time relationships, both species and phylogenetic, are sensitive to the spatial scale of the sampling. Contrary to the Preston's predictions we find a decoupling of diversity-area and diversity-time relationships in both forests as the time period used to quantify the diversity-area relationship changes. In particular, diversity-area and diversity-time relationships are positively correlated using the initial census to quantify the diversity-area relationship, but weakly or even negatively correlated when using the most recent census. Thus, diversity-area relationships could forecast the temporal accumulation of biodiversity of the forests, but they failed to back-cast the temporal accumulation of biodiversity suggesting a decoupling of space and time
Mate choice for genetic compatibility in the house mouse

In house mice, genetic compatibility is influenced by the t haplotype, a driving selfish genetic element with a recessive lethal allele, imposing fundamental costs on mate choice decisions. Here, we evaluate the cost of genetic incompatibility and its implication for mate choice in a wild house mice population. In laboratory reared mice, we detected no fertility (number of embryos) or fecundity (ability to conceive) costs of the t, and yet we found a high cost of genetic incompatibility: heterozygote crosses produced 40% smaller birth litter sizes because of prenatal mortality. Surprisingly, transmission of t in crosses using +/t males was influenced by female genotype, consistent with postcopulatory female choice for + sperm in +/t females. Analysis of paternity patterns in a wild population of house mice showed that +/t females were more likely than +/+ females to have offspring sired by +/+ males, and unlike +/+ females, paternity of their offspring was not influenced by +/t male frequency, further supporting mate choice for genetic compatibility. As the major histocompatibility complex (MHC) is physically linked to the t, we investigated whether females could potentially use variation at the MHC to identify male genotype at the sperm or individual level. A unique MHC haplotype is linked to the t haplotype. This MHC haplotype could allow the recognition of t and enable pre- and postcopulatory mate choice for genetic compatibility. Alternatively, the MHC itself could be the target of mate choice for genetic compatibility. We predict that mate choice for genetic compatibility will be difficult to find in many systems, as only weak fertilization biases were found despite an exceptionally high cost of genetic incompatibility
Geographic mode of speciation in a mountain specialist avian family endemic to the Palearctic

Mountains host greater avian diversity than lowlands at the same latitude due to their greater diversity of habitats stratified along an elevation gradient. Here we test whether this greater ecological heterogeneity promotes sympatric speciation.
We selected accentors (Prunellidae), an avian family associated with mountains of the Palearctic, as a model system. Accentors differ in their habitat/elevation preferences and south-central Siberia and Himalayan regions each host 6 of the 13 species in the family. We used sequences of the mtDNA ND2 gene and the intron 9 of the Z chromosome specific ACO1 gene to reconstruct a complete species-level phylogeny of Prunellidae. The tree based on joint analysis
of both loci was used to reconstruct the family’s biogeographic history and to date the diversification events. We also analyzed the relationship between the node age and sympatry, to determine the geographic mode of speciation in
Prunellidae. Our data suggest a Miocene origin of Prunellidae in the Himalayan region. The major division between alpine species (subgenus Laiscopus) and species associated with shrubs (subgenus Prunella) and initial diversification
events within the latter happened within the Himalayan region in the Miocene and Pliocene. Accentors colonized other parts of the Palearctic during the Pliocene-Pleistocene transition. This spread across the Palearctic resulted in rapid
diversification of accentors. With only a single exception dating to 0.91 Ma, lineages younger than 1.5 Ma are allopatric. In contrast, sympatry values for older nodes are >0. There was no relationship between node age and range symmetry. Allopatric speciation (not to include peripatric) is the predominant geographic mode of speciation in Prunellidae despite the favorable conditions
for ecological diversification in the mountains and range overlaps among species
Climate change impact on seaweed meadow distribution in the North Atlantic rocky intertidal

The North-Atlantic has warmed faster than all other ocean basins and climate change scenarios predict sea surface temperature isotherms to shift up to 600km northwards by the end of the 21st century. The pole-ward shift has already begun for many temperate seaweed species that are important intertidal foundation species. We asked the question: Where will climate change have the greatest impact on three foundational, macroalgal species that occur along North-Atlantic shores: Fucus serratus, Fucus vesiculosus, and Ascophyllum nodosum? To predict distributional changes of these key species under three IPCC (Intergovernmental Panel on Climate Change) climate change scenarios (A2, A1B, and B1) over the coming two centuries, we generated Ecological Niche Models with the program MAXENT. Model predictions suggest that these three species will shift northwards as an assemblage or unit and that phytogeographic changes will be most pronounced in the southern Arctic and the southern temperate provinces. Our models predict that Arctic shores in Canada, Greenland, and Spitsbergen will become suitable for all three species by 2100. Shores south of 45 degrees North will become unsuitable for at least two of the three focal species on both the Northwest- and Northeast-Atlantic coasts by 2200. If these foundational species are unable to adapt to the rising temperatures, they will lose their centers of genetic diversity and their loss will trigger an unpredictable shift in the North-Atlantic intertidal ecosystem
Population genetic patterns among social groups of the endangered Central American spider monkey (Ateles geoffroyi) in a human-dominated landscape

Spider monkeys (Genus: Ateles) are a widespread Neotropical primate with a highly plastic socioecological strategy. However, the Central American species, Ateles geoffroyi, was recently re-listed as endangered due to the accelerated loss of forest across the subcontinent. There is inconsistent evidence that spider monkey populations could persist when actively protected, but their long-term viability in unprotected, human-dominated landscapes is not known. We analyzed noninvasive genetic samples from 185 individuals in 14 putative social groups on the Rivas Isthmus in southwestern Nicaragua. We found evidence of weak but significant genetic structure in the mitochondrial control region and in eight nuclear microsatellite loci plus negative spatial autocorrelation in Fst and kinship. The overall pattern suggests strong localized mating and at least historical female-biased dispersal, as is expected for this species. Heterozygosity was significantly lower than expected under random mating and lower than that found in other spider monkey populations, possibly reflecting a recent decline in genetic diversity and a threat from inbreeding. We conclude that despite a long history of human disturbance on this landscape, spider monkeys were until recently successful at maintaining gene flow. We consider the recent decline to be further indication of accelerated anthropogenic disturbance, but also of an opportunity to conserve native biodiversity. Spider monkeys are one of many wildlife species in Central America that is threatened by land cover change, and an apt example of how landscape-scale conservation planning could be used to ensure long-term persistence
Getting the biggest birch for the bang: restoring and expanding upland birchwoods in the Scottish Highlands by managing red deer

High deer populations threaten the conservation value of woodlands and grasslands, but predicting the success of deer culling, in terms of allowing vegetation to recover, is difficult. Numerical simulation modeling is one approach to gain insight into the outcomes of management scenarios. We develop a spatially explicit model to predict the responses of Betula spp. to red deer (Cervus elaphus) and land management in the Scottish Highlands. Our model integrates a Bayesian stochastic stage-based matrix model within the framework of a widely used individual-based forest simulation model, using data collected along spatial and temporal gradients in deer browsing. By initializing our model with the historical spatial locations of trees, we find that densities of juvenile trees (<3 m tall) predicted after 9–13 years closely match counts observed in the field. This is among the first tests of the accuracy of a dynamical simulation model for predicting the responses of tree regeneration to herbivores. We then test the relative importance of deer browsing, ground cover vegetation, and seed availability in facilitating landscape-level birch regeneration using simulations in which we varied these three variables. We find that deer primarily control transitions of birch to taller (>3 m) height tiers over 30 years, but regeneration also requires suitable ground cover for seedling establishment. Densities of adult seed sources did not influence regeneration, nor did an active management scenario where we altered the spatial configuration of adults by creating “woodland islets”. Our results show that managers interested in maximizing tree regeneration cannot simply reduce deer densities but must also improve ground cover for seedling establishment, and the model we develop now enables managers to quantify explicitly how much both these factors need to be altered. More broadly, our findings emphasize the need for land managers to consider the impacts of large herbivores rather than their densities
Forecasting deforestation and carbon emissions in tropical developing countries facing demographic expansion: A case study in Madagascar

Anthropogenic deforestation in tropical countries is responsible for a significant part of global carbon dioxide emissions in the atmosphere. To plan efficient climate change mitigation programs (such as REDD+, Reducing Emissions from Deforestation and forest Degradation), reliable forecasts of deforestation and carbon dioxide emissions are necessary. Although population density has been recognized as a key factor in tropical deforestation, current methods of prediction do not allow the population explosion that is occurring in many tropical developing countries to be taken into account. Here, we propose an innovative approach using novel computational and statistical tools, including R/GRASS scripts and the new phcfM R package, to model the intensity and location of deforestation including the effect of population density. We used the model to forecast anthropogenic deforestation and carbon dioxide emissions in five large study areas in the humid and spiny-dry forests of Madagascar. Using our approach, we were able to demonstrate that the current rapid population growth in Madagascar (+3.39% per year) will significantly increase the intensity of deforestation by 2030 (up to +1.17% per year in densely populated areas). We estimated the carbon dioxide emissions associated with the loss of aboveground biomass to be of 2.24 and 0.26 tons per hectare and per year in the humid and spiny-dry forest, respectively. Our models showed better predictive ability than previous deforestation models (the figure of merit ranged from 10 to 23). We recommend this approach to reduce the uncertainty associated with deforestation forecasts. We also underline the risk of an increase in the speed of deforestation in the short term in tropical developing countries undergoing rapid population expansion. (Résumé d'auteur
Invasion genetics of vendace (Coregonus albula (L.)) in the Inari-Pasvik watercourse: revealing the origin and expansion pattern of a rapid colonization event

Species invasions can have wide-ranging biological and socio-economic effects and are generally unwanted by legislation. Identification of the source population as well as the ecology and genetics of both the invader population and the receiving community is of crucial importance. The rapid invasion of a small coregonid fish vendace (Coregonus albula) in a major northern European subarctic watercourse has resulted in a labile ecological situation in the receiving community. The ecological impact of the invasion has been thoroughly documented, but the genetics of the invasion remains to be explored. We analyzed the genetic diversity and divergence patterns among the two possible source populations from southern Finnish Lapland and three colonists populations within the Inari-Pasvik watercourse using ten microsatellite loci in order to (i) identify the most likely source of the invasion, (ii) reveal the dispersal pattern and genetic structure of the secondary expansion, and (iii) to investigate whether the initial introduction and the secondary expansion were associated with founder effects. We revealed that repeated translocation of vendace from Lake Sinettäjärvi into a tributary lake of L. Inari in 1964–1966 is the most plausible source for the invasion. Both the initial introduction and the secondary expansion were found not to be associated with significant founder effects. The secondary expansion followed a stepping stone pattern and the source and colonist populations of this expansion have undergone rapid genetic divergence within a period of 15–35 years (ca. 8–17 generations). The rapid divergence may be contributed to lack of gene flow among the source and colonist populations due to the extensive hydroelectric damming in the watercourse. Multiple introductions and substantial genetic variation in combination with the boom-and-bust population development of the species thus likely counteracted the founder effects as well as fueled the rapid establishment and expansion of this species within the Inari-Pasvik watercourse