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opencc-zeroJul 2020View details →

Data from: Population structure, connectivity and demographic history of an apex marine predator, the bull shark Carcharhinus leucas

Knowledge of population structure, connectivity and effective population size remains limited for many marine apex predators, including the bull shark Carcharhinus leucas. This large-bodied coastal shark is distributed worldwide in warm temperate and tropical waters, and uses estuaries and rivers as nurseries. As an apex predator, the bull shark likely plays a vital ecological role within marine food webs, but is at risk due to inshore habitat degradation and various fishing pressures. We investigated the bull shark's global population structure and demographic history by analysing the genetic diversity of 370 individuals from 11 different locations using 25 microsatellite loci and three mitochondrial genes (CR, nd4, cytb). Both types of markers revealed clustering between sharks from the Western Atlantic and those from the Western Pacific and the Western Indian Ocean, with no contemporary gene flow. Microsatellite data suggested low differentiation between the Western Indian Ocean and the Western Pacific, but substantial differentiation was found using mitochondrial DN A. Integrating information from both types of markers and using Bayesian computation with a random forest procedure (ABC-RF), this discordance was found to be due to a complete lack of contemporary gene flow. High genetic connectivity was found both within the Western Indian Ocean and within the Western Pacific. In conclusion, these results suggest important structuring of bull shark populations globally with important gene flow occurring along coastlines , highlighting the need for management and conservation plans on regional scales rather than oceanic basin scale.

Data from: Cascading effects of climate variability on the breeding success of an edge population of an apex predator

1. Large-scale environmental forces can influence biodiversity at different levels of biological organization. Climate, in particular, is often associated to species distributions and diversity gradients. However, its mechanistic link to population dynamics is still poorly understood. 2. Here, we unraveled the full mechanistic path by which a climatic driver, the Atlantic trade winds, determines the viability of a bird population. 3. We monitored the breeding population of Eleonora's falcons in the Canary Islands for over a decade (2007-2017) and integrated different methods and data to reconstruct how the availability of their prey (migratory birds) is regulated by trade winds. We tracked foraging movements of breeding adults using GPS, monitored departure of migratory birds using weather radar, and simulated their migration trajectories using an individual-based, spatially explicit model. 4. We demonstrate that regional easterly winds regulate the flux of migratory birds that is available to hunting falcons, determining food availability for their chicks and consequent breeding success. By reconstructing how migratory birds are pushed towards the Canary Islands by trade winds, we explain most of the variation (up to 86%) in annual productivity for over a decade. 5. This study unequivocally illustrates how a climatic driver can influence local-scale demographic processes, while providing novel evidence of wind as a major determinant of population fitness in a top predator. 06-Jul-2020

Data from: Post‐glacial establishment of locally adapted fish populations over a steep salinity gradient

Studies of colonization of new habitats that appear from rapidly changing environments are interesting and highly relevant to our understanding of divergence and speciation. Here, we analyse phenotypic and genetic variation involved in the successful establishment of a marine fish (sand goby, Pomatoschistus minutus) over a steep salinity drop from 35 PSU in the North Sea (NE Atlantic) to two PSU in the inner parts of the post-glacial Baltic Sea. We first show that populations are adapted to local salinity in a key reproductive trait, the proportion of motile sperm. Thereafter, we show that genome variation at 22,190 single nucleotide polymorphisms (SNPs) shows strong differentiation among populations along the gradient. Sequences containing outlier SNPs and transcriptome sequences, mapped to a draft genome, reveal associations with genes with relevant functions for adaptation in this environment but without overall evidence of functional enrichment. The many contigs involved suggest polygenic differentiation. We trace the origin of this differentiation using demographic modelling and find the most likely scenario is that at least part of the genetic differentiation is older than the Baltic Sea and is a result of isolation of two lineages prior to the current contact over the North Sea–Baltic Sea transition zone.

Data from: Salinity stress increases the severity of ranavirus epidemics in amphibian populations

The stress-induced susceptibility hypothesis, which predicts chronic stress weakens immune defenses, was proposed to explain increasing infectious disease-related mass mortality and population declines. Previous work characterized wetland salinization as a chronic stressor to larval amphibian populations. Thus, we combined field observations with experimental exposures quantifying epidemiological parameters to test the role of salinity stress in the occurrence of ranavirus-associated mass mortality events. Despite ubiquitous pathogen presence (94%), populations exposed to salt runoff had slightly more frequent ranavirus related mass mortality events, more lethal infections, and 117-times greater pathogen environmental DNA. Experimental exposure to chronic elevated salinity (0.8-1.6 g/L Cl-) reduced tolerance to infection, causing greater mortality at lower doses. We found a strong negative relationship between splenocyte proliferation and corticosterone in ranavirus-infected larvae at a moderate elevation of salinity, supporting glucocorticoid-medicated immunosuppression, but not at high salinity. Salinity alone reduced proliferation further at similar corticosterone levels and infection intensities. Finally, larvae raised in elevated salinity had 10-times more intense infections and shed 5-times as much virus with similar viral decay rates, suggesting increased transmission. Our findings illustrate how a small change in habitat quality leads to more lethal infections and potentially greater transmission efficiency, increasing the severity of ranavirus epidemics.

Data from: Deep Divergence between Island Populations in Lichenized Fungi

Macaronesia is characterized by a high degree of endemism and represents a noteworthy system to study the evolutionary history of populations and species. Here, we compare the population-genetic structure in three lichen-forming fungi, the widespread Lobaria pulmonaria and two Macaronesian endemics, L. immixta and L. macaronesica, based on microsatellites. We utilize population genetic approaches to explore population subdivision and evolutionary history of these taxa on the Canary Islands, Madeira, Azores, and the western Iberian Peninsula. A common feature in all species was the deep divergence between populations on the Azores, a pattern expected by the large geographic distance among islands. For both endemic species, there was a major split between archipelagos. In contrast, in the widespread L. pulmonaria, divergent individuals were distributed across multiple archipelagos, suggesting a complex evolutionary history involving repeated migration between islands and mainland.

Data from: Multi-scale spatial genetic structure within and between populations of wild cherry trees in nuclear genotypes and chloroplast haplotypes

Spatial genetic structure (SGS) of plants mainly depends on the effective population size and gene dispersal. Maternally inherited loci are expected to have higher genetic differentiation between populations and more intensive SGS within populations than biparentally inherited loci because of smaller effective population sizes and fewer opportunities of gene dispersal in the maternally inherited loci. We investigated biparentally inherited nuclear genotypes and maternally inherited chloroplast haplotypes of microsatellites in 17 tree populations of three wild cherry species under different conditions of tree distribution and seed dispersal. As expected, inter-population genetic differentiation was 6–9 times higher in chloroplast haplotypes than in nuclear genotypes. This difference indicated that pollen flow 4–7 times exceeded seed flow between populations. However, no difference between nuclear and chloroplast loci was detected in within-population SGS intensity due to their substantial variation among the populations. The SGS intensity tended to increase as trees became more aggregated, suggesting that tree aggregation biased pollen and seed dispersal distances toward shorter. The loss of effective seed dispersers, Asian black bears, did not affect the SGS intensity probably because of mitigation of the bear loss by other vertebrate dispersers and too few tree generations after the bear loss to alter SGS. The findings suggest that SGS is more variable in smaller spatial scales due to various ecological factors in local populations.

Data from: Multi-population seedling and soil transplants show possible responses of a common tropical montane tree species (Weinmannia bangii) to climate change

A possible response of many plant species to global warming is migration to higher elevations. However, these migrations may not be required if species can tolerate higher temperatures, or may be prevented if there are other factors such as changes in soil conditions that make upslope areas unsuitable. We used a set of 3-year field transplant experiments in the remote Peruvian Andes to simulate two possible responses of an abundant tropical montane cloudforest tree species (Weinmania bangii) to global warming: (1) "upward migration", in which case seedlings of W. bangii's were grown at their current elevation/temperature but in soils transplanted from higher elevations; and (2) "migration failure", in which case seedlings were transplanted downslope along with their home soils into areas that are 1°C or 2°C warmer. We conducted separate experiments with populations from the upper/leading edge, middle and lower/trailing edges of W. bangii's elevational/thermal range to assess the influence of local adaptation on responses to changes in temperature or soil. We found that seedling survival and growth were not affected by changes in soil conditions, regardless of the origin population. However, seedling survival decreased with temperature. A simulated warming of 1°C caused a significant reduction in the survival of seedlings transplanted from the mid-range population, and 2°C warming caused a severe decrease in the survival of seedlings transplanted from both the mid-range and bottom-edge populations. Synthesis. Our findings reveal that rising temperatures are a serious threat to plants, especially in populations growing in the hotter portion of their species' range. At least in the case of W. bangii, novel soil conditions will not limit the establishment or growth of seedlings at higher elevations. As such, decreases in the survivorship at lower elevations may be offset through upward migrations as temperatures continue to increase.

Data from: Curation: heat stress responses and population genetics of the kelp Laminaria digitata (Phaeophyceae) across latitudes reveal differentiation among North Atlantic populations

We aim to understand the thermal plasticity of a coastal foundation species across its latitudinal distribution by assessing physiological responses to high temperature stress in the kelp Laminaria digitata in combination with population genetic characteristics. We <a>hypothesize</a> that Arctic and cold-temperate populations are less heat resilient than warm-temperate populations. Using meristems of natural L. digitata populations from six locations ranging between Kongsfjorden, Spitsbergen (79°N), and Quiberon, France (47°N), we performed a common-garden heat stress experiment applying 15°C to 23°C over eight days. We assessed growth, quantum yield, carbon and nitrogen storage, and xanthophyll pigment contents as response traits. Population connectivity and genetic diversity were analysed with microsatellite markers to relate heat resilience to genetic features and phylogeography. Microsatellite genotyping revealed all sampled populations to be genetically distinct, underlying strong hierarchical structuring between and within southern and northern clades. Genetic diversity was lowest in the isolated population of the North Sea island of Helgoland and highest in Roscoff in the English Channel. Results from the heat stress experiment suggest that the upper temperature limit of L. digitata is nearly identical across its distribution range, but subtle differences we<a>re </a>revealed for the two populations currently at their warm limits. They respectively <a>show</a> a significant advantage in growth at 19°C and 21°C (Quiberon) and a lack of stress responses in photosynthetic quantum yield and xanthophyll pigments at 23°C (Helgoland). In addition, quantum yield indicated the highest heat sensitivity in L. digitata from the northernmost population in Spitsbergen. All together, these results support the hypothesis of moderate local differentiation across L. digitata's European distribution, whereas effects are likely too weak to ameliorate the species' capacity to withstand ocean warming and marine heatwaves at the southern range edge.

opencc-zeroOct 2019View details →

Data from: New and Old World phylogeography of pumpkinseed (Lepomis gibbosus): the North American origin of introduced populations in Europe

To determine the origin of introduced European populations of pumpkinseed (Lepomis gibbosus) – a freshwater sunfish, native to eastern North America that has spread across western and central Europe – we investigated the phylogeography of the species by sequencing the mitochondrial NADH subunit 1 gene. A total of 543 pumpkinseed were sampled from 32 sites across the native range of the species, and from 19 sites covering much of its introduced European range. The presence and geographic distribution of two distinct clades in North American populations were discovered, suggesting that pumpkinseed survived the Pleistocene glaciations in two refugia (Atlantic and Mississippian). Analyses of mitochondrial variation revealed that European pumpkinseed may have been introduced to Europe from at least two distinct sources, but from the Atlantic drainages of North America only, which is consistent with historical records. Within Europe, haplotype distributions of pumpkinseed lend support to the entry of non-native fishes into Iberia via the so-called 'Perpignan–Barcelona corridor'. European populations possessed lower genetic diversity than populations from North America, suggesting that low genetic diversity may not preclude a species from establishing and spreading into new environments outside of their native range.

Data from: Selection on multiple sexual signals in two Central- and Eastern-European populations of the barn swallow

Variation in intensity and targets of sexual selection on multiple traits has been suggested to play a major role in promoting phenotypic differentiation between populations, although the divergence in selection may depend on year, local conditions or age. In this study, we quantified sexual selection for two putative sexual signals across two Central- and East-European barn swallow (Hirundo rustica rustica) populations from Czech Republic and Romania over multiple years. We then related these differences in selection to variation in sexual characters among barn swallow populations. Our results show that tail length and ventral colouration vary between populations, sexes and age classes (first-time breeders vs. experienced birds). We found that selection on tail length was stronger in first-time breeders than in experienced birds and in males than in females in the Romanian population, while these differences between age groups and sexes were weak in Czech birds. We suggest that the populational difference in selection on tail length might be related to the differences in breeding conditions. Our results show that ventral colouration is darker (i.e. has lower brightness) in the Romanian than in the Czech population, and in experienced birds and males compared with first-time breeders and females, respectively. The sexual difference in ventral colouration may suggest sexual selection on this trait, which is supported by the significant directional selection of ventral colouration in first-time breeding males on laying date. However, after controlling for the confounding effect of wing length and tarsus length, the partial directional selection gradient on this trait turned non-significant, suggesting that the advantage of dark ventral colouration in early breeding birds is determined by the correlated traits of body size. These findings show that ventral colouration may be advantageous over the breeding season, but the underlying mechanism of this relationship is not clarified.

opencc-by-4.0Jun 2020View details →

zenodo36/100

A genomic data set of single‐nucleotide polymorphisms (SNPs) generated by ddRAD tag sequencing in Q. petraea (Matt.) Liebl. populations from Central-Eastern Europe and Balkan Peninsula

This genomic dataset provides highly variable single-nucleotide polymorphism (SNP) markers from georeferenced natural Quercus petraea (Matt.) Liebl. populations collected in Bulgaria, Hungary, Romania, Serbia, Bosnia and Herzegovina, Kosovo and Albania. These SNP loci can be used to assess genetic diversity, differentiation, population structure, and can also be used to detect signatures of selection and local adaptation.

zenodo36/100

Raw data : Population Dynamics and Yield Loss Assessment for Pea Aphid (Homoptera: Aphididae) on Lentil in Morocco

Raw data to describes the population fluctuation of pea aphid over different seasons and their effects on yield loss in Morocco.

opencc-by-4.0Sep 2020View details →

opencc-zeroSep 2020View details →

Data from: Consequences of past and present harvest management in a declining flyway population of common eiders Somateria mollissima

1. Harvested species population dynamics are shaped by the relative contribution of natural and harvest mortality. Natural mortality is usually not under management control, so managers must continuously adjust harvest rates to prevent overexploitation. Ideally, this requires regular assessment of the contribution of harvest to total mortality and how this affects population dynamics. 2. To assess the impact of hunting mortality on the dynamics of the rapidly declining Baltic/Wadden Sea population of common eiders Somateria mollissima we first estimated vital rates of ten study colonies over the period 1970–2015. By means of a multi-event capture-recovery model we then used the cause of death of recovered individuals to estimate proportions of adult females that died due to hunting or other causes. Finally, we adopted a stochastic matrix population modelling approach based on simulations to investigate the effect of past and present harvest regulations on changes in flyway population size and composition. 3. Results showed that even the complete ban on shooting females implemented in 2014 in Denmark, where most hunting takes place was not enough to stop the population decline given current levels of natural female mortality. Despite continued hunting of males our predictions suggest that the proportion of females will continue to decline unless natural mortality of the females is reduced. 4. Although levels of natural mortality must decrease to halt the decline of this population, we advocate that the current hunting ban on females is maintained while further investigations of factors causing increased levels of natural mortality among females are undertaken. 5. Synthesis and applications. At the flyway scale, continuous and accurate estimates of vital rates and the relative contribution of harvest versus other mortality causes are increasingly important as the population effect of adjusting harvest rates is most effectively evaluated within a model-based adaptive management framework.

opencc-zeroSep 2020View details →

Code and data for: Familiarity breeds success: pairs that meet earlier experience increased breeding performance in a wild bird population

This is a Data package that contains three separate datasets and the analysis code for a manuscript 'Familiarity breeds success: pairs that meet earlier experience increased breeding performance in a wild bird population '. The first Dataset (pairs_data_2007_10) and the second dataset (pairs_data_2011_14) contain the data used to analyse the influence of meeting time of a pair of Great tits (i.e. month in the first dataset, week in the second dataset, when a pair was first detected in a flock together) on different components of breeding success of a pair. The third dataset (meeting_and_divorce) was used to analyse whether meeting time of a pair (in winter prior to the breeding season t) influence the probability of a pair to stay together or separate (divorce) to the following breeding season (t+1).

opencc-zeroSep 2020View details →

Data from: Integrating population genetics to define conservation units from the core to the edge of Rhinolophus ferrumequinum western range

The greater horseshoe bat (Rhinolophus ferrumequinum) is among the most widespread bat species in Europe but it has experienced severe declines, especially in Northern Europe. This species is listed Near Threatened in the European IUCN Red List of Threatened Animals and it is considered to be highly sensitive to human activities and particularly to habitat fragmentation. Therefore, understanding the population boundaries and demographic history of populations of this species is of primary importance to assess relevant conservation strategies. In this study, we used 17 microsatellite markers to assess the genetic diversity, the genetic structure and the demographic history of R. ferrumequinum colonies in the western part of its distribution. We identified one large population showing high levels of genetic diversity and large population size. Lower estimates were found in England and northern France. Analyses of clustering and isolation by distance suggested that the Channel and the Mediterranean seas could impede R. ferrumequinum gene flow. These results provide important information to improve the delineation of R. ferrumequinum management units. We suggest that a large management unit corresponding to the population ranging from Spanish Basque country to northern France must be considered. Particular attention should be given to mating territories as they seem to play a key role in maintaining the high levels of genetic mixing between colonies. Smaller management units corresponding to English and northern France colonies must also be implemented. These insular or peripheral colonies could be at higher risk of extinction in a near future.

opencc-zeroJul 2020View details →

Data from: Changes in age-structure over four decades were a key determinant of population growth rate in a long-lived mammal

1. A changing environment directly influences birth and mortality rates, and thus population growth rates. However, population growth rates in the short-term are also influenced by population age-structure. Despite its importance, the contribution of age-structure to population growth rates has rarely been explored empirically in wildlife populations with long-term demographic data. 2. Here, we assessed how changes in age-structure influenced short-term population dynamics in a semi-captive population of Asian elephants (Elephas maximus). 3. We addressed this question using a demographic dataset of female Asian elephants from timber camps in Myanmar spanning 45 years (1970-2014). First, we explored temporal variation in age-structure. Then, using annual matrix population models, we used a retrospective approach to assess the contributions of age-structure and vital rates to short-term population growth rates with respect to the average environment. 4. Age-structure was highly variable over the study period, with large proportions of juveniles in the years 1970 and 1985, and made a substantial contribution to annual population growth rate deviations. High adult birth rates between 1970-1980 would have resulted in large positive population growth rates, but these were prevented by a low proportion of reproductive-aged females. 5. We highlight that an understanding of both age-specific vital rates and age-structure is needed to assess short-term population dynamics. Furthermore, this example from a human-managed system suggests that the importance of age-structure may be accentuated in populations experiencing human disturbance where age-structure is unstable, such as those in captivity or for endangered species. Ultimately, changes to the environment drive population dynamics by influencing birth and mortality rates, but understanding demographic structure is crucial for assessing population growth.

Data from: Tetranychus evansi spider mite populations suppress tomato defences to varying degrees

Plant defence suppression is an offensive strategy of herbivores, in which they manipulate plant physiological processes to increase their performance. Paradoxically, defence suppression does not always benefit the defence-suppressing herbivores, because lowered plant defences can also enhance the performance of competing herbivores and can expose herbivores to increased predation. Suppression of plant defence may therefore entail considerable ecological costs depending on the presence of competitors and natural enemies in a community. Hence, we hypothesize that the optimal magnitude of suppression differs among locations. To investigate this, we studied defence suppression across populations of Tetranychus evansi spider mites, a herbivore from South America that is an invasive pest of solanaceous plants including cultivated tomato, Solanum lycopersicum, in other parts of the world. We measured the level of expression of defence marker genes in tomato plants after infestation with mites from eleven different T. evansi populations. These populations were chosen across a range of native (South American) and non-native (other continents) environments and from different host plant species. We found significant variation at three out of four defence marker genes, demonstrating that T. evansi populations suppress jasmonic acid- and salicylic acid-dependent plant signalling pathways to varying degrees. While we found no indication that this variation in defence suppression was explained by differences in host plant species, invasive populations tended to suppress plant defence to a smaller extent than native populations. This may reflect either the genetic lineage of T. evansi - as all invasive populations we studied belong to one linage and both native populations to another - or the absence of specialized natural enemies in invasive T. evansi populations.

Data from: Dispersal patterns in a medium-density Irish badger population: implications for understanding the dynamics of tuberculosis transmission.

European badgers (Meles meles) are group-living mustelids implicated in the spread of bovine tuberculosis (TB) to cattle and act as a wildlife reservoir for the disease. In badgers, only a minority of individuals disperse from their natal social group. However, dispersal may be extremely important for the spread of TB, as dispersers could act as hubs for disease transmission. We monitored a population of 139 wild badgers over seven years in a medium-density population (1.8 individuals/ km2). GPS-tracking collars were applied to 80 different individuals. Of these, we identified 25 dispersers, 14 of which were wearing collars as they dispersed. This allowed us to record the process of dispersal in much greater detail than ever before. We show that dispersal is an extremely complex process, and measurements of straight-line distance between old and new social groups can severely underestimate how far dispersers travel. Assumptions of straight-line travel can also underestimate direct and indirect interactions and the potential for disease transmission. For example, one female disperser which eventually settled 1.5 km from her natal territory travelled 308 km and passed through 22 different territories during dispersal. Knowledge of badgers'ranging behaviour during dispersal is crucial to understanding the dynamics of TB transmission, and for designing appropriate interventions, such as vaccination.

Data from: Whole-genome analyses provide no evidence for dog introgression in Fennoscandian wolf populations

Hybridisation and admixture can threaten the genetic integrity of populations and be of particular concern to endangered species. Hybridisation between grey wolves and dogs has been documented in many wolf populations worldwide and is a prominent example of human-mediated hybridisation between a domesticated species and its wild relative. We analysed whole-genome sequences from >200 wolves and >100 dogs to study admixture in Fennoscandian wolf populations. A principal component analysis of genetic variation as well as Admixture showed that wolves and dogs were well separated, without evidence for introgression. Analyses of local ancestry revealed that wolves had <1% mixed ancestry, levels comparable to the degree of mixed ancestry in many dogs, and likely not resulting from recent wolf-dog hybridisation. We also show that the founders of the Scandinavian wolf population were genetically inseparable from Finnish and Russian Karelian wolves, pointing at the geographical origin of contemporary Scandinavian wolves. Moreover, we found Scandinavian-born animals among wolves sampled in Finland, demonstrating bi-directional gene flow between the Scandinavian peninsula and eastern countries. The low incidence of admixture between wolves and dogs in Fennoscandia may be explained by that feral dogs are rare in this part of Europe, and that careful monitoring and management act to remove hybrids before they backcross into wolf populations.

Data from: Contrasting population structure and demographic history of cereal aphids in different environmental and agricultural landscapes

Single Nucleotide Polymorphisms files and phylogonetic trees of S. miscanthi samples collected in China and S. avenae from the UK used to study the population genetics analyses of these species. These are: China_samples_vcf.zip: dataset of SNPs from S. miscanthi sampled in 10 populations of China obtained using FreeBayes (in vcf format). China_samples_vcf_filtered.zip: SNPs from S. miscanthi after filtering the file China_samples_vcf.zip using vcftools (max-missing 0.75, minDP 3, mac 3, minQ 30, remove-indels, thin 2000, max-missing 0.9, thin 5000). This file was used in all population genetic analyses of the Chinese populations in the paper, transforming to the appropriate formats. China_samples_SNPs.fas: fasta file of phased SNPs used to estimate the phylogeny of S. miscanthi haplotypes using RAxML. China_RAxML_phylogeny_newick.tre: RAxML phylogenetic tree in newick format obtained with China_samples_SNPs.fas. England_samples_vcf.zip: dataset of SNPs from S. avenae sampled in 12 populations of England obtained using FreeBayes (in vcf format). England_samples_vcf_filtered.zip: SNPs from S. avenae after filtering the file England_samples_vcf.zip using vcftools (max-missing 0.5, mac 3, minQ 30, minDP 3, max-missing 0.5, exclude individuals with 50% missing data, max-missing 0.75, remove-indels, thin 2000). This file was used in all population genetic analyses of the English populations in the paper, transforming the vcf to the corresponding formats. England_samples_SNPs.fas: fasta file of phased SNPs. England_samples_SNPs_polymorphic.fas: fasta file of phased SNPs used in the phylogenetic reconstruction of S. avenae haplotypes using RAxML. This file is the same as England_samples_SNPs.fas after removing sites which were not polymorphic (e.g. a site that contains N and T in different samples is not considered polymorphic for RAxML and has to be removed) England_RAxML_phylogeny_newick.tre: RAxML phylogenetic tree in newick format obtained with England_samples_SNPs_polymorphic.fas.