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3,655 results for “Structural data”
Data from: Fuelwood sustainability revisited: integrating size structure and resprouting into a spatially realistic fuelshed model
Much concern has been expressed about the sustainability of fuelwood harvesting in Africa. Most models predict that demand will outstrip supply within a few decades, resulting in severe deforestation. However, despite substantial impacts of harvesting on woody vegetation structure, the 'fuelwood crisis' predicted since the 1970s has not materialized. We propose that this is at least partially because regeneration through coppicing has been poorly accounted for in most models. We developed a local fuelwood model that is demographically and spatially explicit, and that incorporates coppice dynamics. The model simulates the dynamics of multiple stem size classes (seedling, sapling, pole and adult), the harvesting decisions of villagers based on fuelwood availability and village demand across the landscape. Importantly, we specify size-dependent coppice production of cut stems, and the probability of progression of coppice shoots into larger size classes, after accounting for self-thinning of shoots. In general, our model projections for a rural South African savanna system suggest that current levels of harvesting (barring changes in human population size) are relatively sustainable. Declines in total woody biomass were predicted to be modest (˜20%), and the loss of intact stems of sapling size was predicted to be more than offset by increases in coppiced stems. Synthesis and applications. The results from our local fuelwood model clearly demonstrate that the impact of deforestation and wood removal on tree populations and wood resources is strongly influenced by the resprouting ability of trees. This highlights the importance of considering coppice dynamics when assessing the sustainability of wood harvesting. Our model is not system specific, and can be transferred to other systems, with the relevant parameters and geographic information system layers specified. Because of the transferability of this model, it can help address key international concerns about deforestation and sustainable fuelwood management.
Data from: Male-biased dispersal causes intersexual differences in the subpopulation structure of the gray-sided vole
The genetic structure of gray-sided voles was investigated at a spatial scale of 2 km using mtDNA sequences. The control region (674bp) of 162 voles was sequenced and 18 haplotypes were identified. Within 0.5-ha trapping plots (n = 8), the number of haplotypes and gene diversity was significantly greater in males than in females. The fixation index among plots for females (F GP = 0.241) was 3 times as large as that for males (0.075), implying male-biased dispersal. A simulation analysis showed that the observed genetic structure in males could be generated by modifying the observed haplotype distribution of females by adding the effects of local male dispersal. Half of the pairwise F GP (15/28) showed significant differentiation in females, whereas almost none (1/28) were significant in males. Isolation by distance was observed in females, whereas no clear spatial pattern was observed in males. Most pairwise F GP for females were not significant in the short- and intermediate-distance classes (≤1.0 km) as with those for males, whereas all showed significant differentiation in the long-distance class (>1.0 km) for females, but not for males. These findings indicate that the extent of subpopulations within which individuals interact differs between sexes.
Data from: Spatio-temporal changes in the structure of an Australian frog hybrid zone: a 40 year perspective
Spatio-temporal studies of hybrid zones provide an opportunity to test evolutionary hypotheses of hybrid zone maintenance and movement. We conducted a landscape genetics study on a classic hybrid zone of the south-eastern Australian frogs, Litoria ewingii and L. paraewingi. This hybrid zone has been comprehensively studied since the 1960s, providing the unique opportunity to directly assess changes in hybrid zone structure across time. We compared both mtDNA and male advertisement call data from two time periods (present and 1960s). Clinal analysis of the coincidence (same centre) and concordance (same width) of these traits indicated that the centre of the hybrid zone has shifted 1 km south over the last 40 years, although the width of the zone and the rate of introgression remained unchanged. The low frequency of hybrids, the strong concordance of clines within a time period and the small but significant movement across the study period despite significant anthropogenic changes through the region, suggest the hybrid zone is a tension zone located within a low density trough. Hybrid zone movement has not been considered common in the past but our findings highlight that it should be considered a crucial component to our understanding of evolution.
Data from: Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates
The cheetah (Acinonyx jubatus) has been described as a species with low levels of genetic variation. This has been suggested to be the consequence of a demographic bottleneck 10 000–12 000 years ago (ya) and also led to the assumption that only small genetic differences exist between the described subspecies. However, analysing mitochondrial DNA and microsatellites in cheetah samples from most of the historic range of the species we found relatively deep phylogeographic breaks between some of the investigated populations, and most of the methods assessed divergence time estimates predating the postulated bottleneck. Mitochondrial DNA monophyly and overall levels of genetic differentiation support the distinctiveness of Northern-East African cheetahs (Acinonyx jubatus soemmeringii). Moreover, combining archaeozoological and contemporary samples, we show that Asiatic cheetahs (Acinonyx jubatus venaticus) are unambiguously separated from African subspecies. Divergence time estimates from mitochondrial and nuclear data place the split between Asiatic and Southern African cheetahs (Acinonyx jubatus jubatus) at 32 000–67 000 ya using an average mammalian microsatellite mutation rate and at 4700–44 000 ya employing human microsatellite mutation rates. Cheetahs are vulnerable to extinction globally and critically endangered in their Asiatic range, where the last 70–110 individuals survive only in Iran. We demonstrate that these extant Iranian cheetahs are an autochthonous monophyletic population and the last representatives of the Asiatic subspecies A. j. venaticus. We advocate that conservation strategies should consider the uncovered independent evolutionary histories of Asiatic and African cheetahs, as well as among some African subspecies. This would facilitate the dual conservation priorities of maintaining locally adapted ecotypes and genetic diversity.
Data from: RAD-seq reveals genetic structure of the F2-generation of natural willow hybrids (Salix L.) and a great potential for interspecific introgression
Background: Hybridization of species with porous genomes can eventually lead to introgression via repeated backcrossing. The potential for introgression between species is reflected by the extent of segregation distortion in later generation hybrids. Here we studied a population of hybrids between Salix purpurea and S. helvetica that has emerged within the last 30 years on a glacier forefield in the European Alps due to secondary contact of the parental species. We used 5,758 biallelic SNPs produced by RAD sequencing with the aim to ascertain the predominance of backcrosses (F1 hybrid x parent) or F2 hybrids (F1 hybrid x F1 hybrid) among hybrid offspring. Further, the SNPs were used to study segregation distortion in the second hybrid generation. Results: The analyses in STRUCTURE and NewHybrids revealed that the population consisted of parents and F1 hybrids, whereas hybrid offspring consisted mainly of backcrosses to either parental species, but also some F2 hybrids. Although there was a clear genetic differentiation between S. purpurea and S. helvetica (FST = 0.24), there was no significant segregation distortion in the backcrosses or the F2 hybrids. Plant height of the backcrosses resembled the respective parental species, whereas F2 hybrids were more similar to the subalpine S. helvetica. Conclusions: The co-occurrence of the parental species and the hybrids on the glacier forefield, the high frequency of backcrossing, and the low resistance to gene flow via backcrossing make a scenario of introgression in this young hybrid population highly likely, potentially leading to the transfer of adaptive traits. We further suggest that this willow hybrid population may serve as a model for the evolutionary processes initiated by recent global warming.
Data from: Genetic structure, admixture, and invasion success in a Holarctic defoliator, the gypsy moth (Lymantria dispar, Lepidoptera: Erebidae)
Characterizing the current population structure of potentially invasive species provides a critical context for identifying source populations and for understanding why invasions are successful. Non-native populations inevitably lose genetic diversity during initial colonization events, but subsequent admixture among independently introduced lineages may increase both genetic variation and adaptive potential. Here we characterize the population structure of the gypsy moth (Lymantria dispar Linnaeus), one of the world's most destructive forest pests. Native to Eurasia and recently introduced to North America, the current distribution of gypsy moth includes forests throughout the temperate region of the northern hemisphere. Analyses of microsatellite loci and mitochondrial DNA sequences for 1738 individuals identified four genetic clusters within L. dispar. Three of these clusters correspond to the three named subspecies; North American populations represent a distinct fourth cluster, presumably a consequence of the population bottleneck and allele frequency change that accompanied introduction. We find no evidence that admixture has been an important catalyst of the successful invasion and range expansion in North America. However, we do find evidence of ongoing hybridization between subspecies and increased genetic variation in gypsy moth populations from Eastern Asia, populations that now pose a threat of further human-mediated introductions. Finally, we show that current patterns of variation can be explained in terms of climate and habitat changes during the Pleistocene, a time when temperate forests expanded and contracted. Deeply diverged matrilines in Europe imply that gypsy moths have been there for a long time and are not recent arrivals from Asia.
Data from: Strong spatial structure, Pliocene diversification and cryptic diversity in the Neotropical dry forest spider Sicarius cariri
The Brazilian Caatinga is part of the seasonally dry tropical forests, a vegetation type disjunctly distributed throughout the Neotropics. It has been suggested that during Pleistocene glacial periods, these dry forests had a continuous distribution, so that these climatic shifts may have acted as important driving forces of the Caatinga biota diversification. To address how these events affected the distribution of a dry forest species, we chose Sicarius cariri, a spider endemic to the Caatinga, as a model. We studied the phylogeography of one mitochondrial and one nuclear gene and reconstructed the paleodistribution of the species using modelling algorithms. We found two allopatric and deeply divergent clades within S. cariri, suggesting that this species as currently recognized might consist of more than one independently evolving lineage. Sicarius cariri populations are highly structured, with low haplotype sharing among localities, high fixation index and isolation by distance. Models of paleodistribution, Bayesian reconstructions and coalescent simulations suggest that this species experienced a reduction in its population size during glacial periods, rather than the expansion expected by previous hypotheses on the paleodistribution of dry forest taxa. In addition to that, major splits of intraspecific lineages of S. cariri took place in the Pliocene. Taken together, these results indicate S. cariri has a complex diversification history dating back to the Tertiary, suggesting the history of dry forest taxa may be significantly older than previously thought.
Data from: Genetic diversity, population structure and ancestral origin of Australian wheat
Since the introduction of wheat into Australia by the First Fleet settlers, germplasm from different geographical origins has been used to adapt wheat to the Australian climate through selection and breeding. In this paper, we used 482 cultivars, representing the breeding history of bread wheat in Australia since 1840, to characterize their diversity and population structure and to define the geographical ancestral background of Australian wheat germplasm. This was achieved by comparing them to a global wheat collection using in-silico chromosome painting based on SNP genotyping. The global collection involved 2,335 wheat accessions which was divided into 23 different geographical subpopulations. However, the whole set was reduced to 1,544 accessions to increase the differentiation and decrease the admixture among different global subpopulations to increase the power of the painting analysis. Our analysis revealed that the structure of Australian wheat germplasm and its geographic ancestors have changed significantly through time, especially after the Green Revolution. Before 1920, breeders used cultivars from around the world, but mainly Europe and Africa, to select potential cultivars that could tolerate Australian growing conditions. Between 1921 and 1970, a dependence on African wheat germplasm became more prevalent. Since 1970, a heavy reliance on International Maize and Wheat Improvement Center (CIMMYT) germplasm has persisted. Combining the results from linkage disequilibrium, population structure and in-silico painting revealed that the dependence on CIMMYT materials has varied among different Australian Sstates, has shrunken the germplasm effective population size and produced larger linkage disequilibrium blocks. This study documents the evolutionary history of wheat breeding in Australia and provides an understanding for how the wheat genome has been adapted to local growing conditions. This information provides a guide for industry to assist with maintaining genetic diversity for long-term selection gains and to plan future breeding programs.
Data from: Biogeography in a continental island: population structure of the relict endemic centipede Craterostigmus tasmanianus (Chilopoda, Craterostigmomorpha) in Tasmania using 16S rRNA and COI
We used 16S ribosomal RNA (rRNA) and cytochrome c oxidase subunit I (COI) sequence data to investigate the population structure in the centipede Craterostigmus tasmanianus Pocock, 1902 (Chilopoda: Craterostigmomorpha: Craterostigmidae) and to look for possible barriers to gene flow on the island of Tasmania, where C. tasmanianus is a widespread endemic. We first confirmed a molecular diagnostic character in 28S rRNA separating Tasmanian Craterostigmus from its sister species Craterostigmus crabilli (Edgecombe and Giribet 2008) in New Zealand and found no shared polymorphism in this marker for the 2 species. In Tasmania, analysis of molecular variance analysis showed little variation at the 16S rRNA and COI loci within populations (6% and 13%, respectively), but substantial variation (56% and 48%, respectively) among populations divided geographically into groups. We found no clear evidence of isolation by distance using a Mantel test. Bayesian clustering and gene network analysis both group the C. tasmanianus populations in patterns which are broadly concordant with previously known biogeographical divisions within Tasmania, but we did not find that genetic distance varied in a simple way across cluster boundaries. The coarse-scale geographical sampling on which this study was based should be followed in the future by sampling at a finer spatial scale and to investigate genetic structure within clusters and across cluster boundaries.
Data from: Landscape resistance and habitat combine to provide an optimal model of genetic structure and connectivity at the range margin of a small mammal
We evaluated the effect of habitat and landscape characteristics on the population genetic structure of the white-footed mouse. We develop a new approach that uses numerical optimization to define a model that combines site differences and landscape resistance to explain the genetic differentiation between mouse populations inhabiting forest patches in southern Québec. We used ecological distance computed from resistance surfaces with Circuitscape to infer the effect of the landscape matrix on gene flow. We calculated site differences using a site index of habitat characteristics. A model that combined site differences and resistance distances explained a high proportion of the variance in genetic differentiation and outperformed models that used geographical distance alone. Urban and agriculture related land uses were, respectively, the most and the least resistant landscape features influencing gene flow. Our method detected the effect of rivers and highways as highly resistant linear barriers. The density of grass and shrubs on the ground best explained the variation in the site index of habitat characteristics. Our model indicates that movement of white-footed mouse in this region is constrained along routes of low resistance. Our approach can generate models that may improve predictions of future northward range expansion of this small mammal.
Data from: Seascape continuity plays an important role in determining patterns of spatial genetic structure in a coral reef fish
Detecting patterns of spatial genetic structure (SGS) can help identify intrinsic and extrinsic barriers to gene flow within metapopulations. For marine organisms such as coral reef fishes, identifying these barriers is critical to predicting evolutionary dynamics and demarcating evolutionarily significant units for conservation. In this study, we adopted an alternative hypothesis-testing framework to identify the patterns and predictors of SGS in the Caribbean reef fish Elacatinus lori. First, genetic structure was estimated using nuclear microsatellites and mitochondrial cytochrome b sequences. Next, clustering and network analyses were applied to visualize patterns of SGS. Finally, logistic regressions and linear mixed models were used to identify the predictors of SGS. Both sets of markers revealed low global structure: mitochondrial ΦST = 0.12, microsatellite FST = 0.0056. However, there was high variability among pairwise estimates, ranging from no differentiation between sites on contiguous reef (ΦST = 0) to strong differentiation between sites separated by ocean expanses ≥ 20 km (maximum ΦST = 0.65). Genetic clustering and statistical analyses provided additional support for the hypothesis that seascape discontinuity, represented by oceanic breaks between patches of reef habitat, is a key predictor of SGS in E. lori. Notably, the estimated patterns and predictors of SGS were consistent between both sets of markers. Combined with previous studies of dispersal in E. lori, these results suggest that the interaction between seascape continuity and the dispersal kernel plays an important role in determining genetic connectivity within metapopulations.
Data from: Genetic structure reveals a history of multiple independent origins followed by admixture in the allopolyploid weed Salsola ryanii
It has recently become clear that many invasive species have evolved in situ via hybridization or polyploidy from progenitors which themselves are introduced species. For species formed by hybridization or polyploidy, genetic diversity within the newly formed species is influenced by the number of independent evolutionary origins of the species. For recently formed species, an analysis of genetic structure can provide insight into the number of independent origin events involved in the formation of the species. For a putative invasive allopolyploid species, the number of origins involved in the species formation, the genetic diversity present within these origins, and the level of gene flow between independent origins determines the genetic composition of the neospecies. Here we analyze the genetic structure of the newly formed allopolyploid species, Salsola ryanii, a tumbleweed which evolved within the last 20–100 years in California. We utilize the genetic structure analysis to determine that this new species is the result of at least three independent allopolyplodization events followed by gene flow between the descendants of independent origins.
Data from: Wildfire alters the structure and seasonal dynamics of nocturnal pollen-transport networks
Wildfires drive global biodiversity patterns and affect plant–pollinator interactions, and are expected to become more frequent and severe under climate change. Post‐fire plant communities often have increased floral abundance and diversity, but the effects of wildfires on the ecological process of pollination are poorly understood. Nocturnal moths are globally important pollinators, but no previous study has examined the effects of wildfire on nocturnal pollination interactions. We investigated the effects of wildfire on nocturnal pollen‐transport networks. We analysed the abundance and species richness of moths and flowers, and the structure of these networks, at three burned and three unburned sites in Portugal for two years, starting eight months after a large fire. Nocturnal pollen‐transport networks had lower complexity and robustness following the fire than at nearby unburned sites. Overall, 70% of individual moths carried pollen, and moths were found to be transporting pollen from 83% of the flower species present. Burned sites had significantly more abundant flowers, but less abundant and species‐rich moths. Individual moths transported more pollen in summer at burned sites, but less in winter; however, total pollen transport by the moth assemblage at burned sites was just 20% of that at unburned sites. Interaction turnover between burned and unburned networks was high. Negative effects of fire upon moths will likely permeate to other taxa through loss of mutualisms. Therefore, if wildfires become more frequent under climate change, community resilience may be eroded. Understanding the responses of ecological networks to wildfire can inform management that promotes resilience and facilitates whole‐ecosystem conservation.
Data from: The Atlantic-Mediterranean watershed, river basins and glacial history shape the genetic structure of Iberian poplars
Recent phylogeographic studies in several organisms have elucidated the varied effects of Pleistocene glaciations and of Pre-Pleistocene events on populations from glacial refuge areas. This study investigates those effects in riparian trees (Populus spp.), whose particular features may convey enhanced resistance to climate fluctuations. We analysed the phylogeographic structure of white, black and grey poplars (44, 13 and two populations, respectively) in the Iberian Peninsula using plasmid DNA microsatellites and sequences, we assessed fine-scale spatial genetic structure and the extent of clonality in four white and one grey poplar populations using nuclear microsatellites and we determined quantitative genetic differentiation (Q_ST) for growth traits among populations and river systems in white poplar. Black poplar displayed higher regional diversity and lower differentiation than white poplar, reflecting its higher cold-tolerance. In white poplar, the Atlantic and Mediterranean drainage basins but also river basins were strongly differentiated, indicating confinement to the lower river courses during glacial periods and moderate gene exchange along coastlines. In this species, the northern Iberian river basins had lower diversity, fewer private haplotypes and larger clonal assemblies than the southern basins, indicating a stronger effect of glaciations in the north. The dependence of white poplar on phreatic water was evidenced by stronger isolation by distance among river basins than within them. Despite strong genetic structure and frequent asexual propagation in white poplar, some growth traits displayed adaptive divergence between drainage and river basins (Q_ST > F_ST), highlighting the remarkable capacity of riparian tree populations to adapt to regional environmental conditions.
Data from: High genotypic diversity and strong spatial structure in populations of Trifolium alpestre with low seed production
The studies on clonal plant populations indicate that the proportion between clonal and sexual reproduction may be highly variable, depending on the biological characteristics of species and the ecological conditions of habitats. We focused on the genotypic diversity of Trifolium alpestre populations in Estonia. We assayed the genetic diversity, spatial genotypic structure and diversity with the use of allozyme markers. Populations revealed high levels of genotypic diversity and showed strong spatial structure of MLGs. The values of genetic diversity were moderately high. Spatially aggregated, identical genotypes spread up to 15 meters along the linear transects and in 4 m2 plots indicate extensive clonal propagation in populations. However, numerous unique and small-sized clones in transects and quadrates reflect significant contribution from the sexual reproduction. The spatially and temporarily stochastic soil disturbances have evidently opened new opportunities for the successful sexual reproduction from the permanent soil seed bank and have thus avoided the losses of genotypic and genetic diversity. The seed production in all populations during the three study years was low, in average up to 1.5-2.4 seeds per shoot. The almost total lack of seed set from all 57 bagged flower heads of genets grown in a common garden indicates that T. alpestre needs pollinators for the seed production.
Data from: Climate change alters the structure of arctic marine food webs due to poleward shifts of boreal generalists
Climate-driven poleward shifts, leading to changes in species composition and relative abundances, have been recently documented in the Arctic. Among the fastest moving species are boreal generalist fish which are expected to affect arctic marine food web structure and ecosystem functioning substantially. Here, we address structural changes at the food web level induced by poleward shifts via topological network analysis of highly resolved boreal and arctic food webs of the Barents Sea. We detected considerable differences in structural properties and link configuration between the boreal and the arctic food webs, the latter being more modular and less connected. We found that a main characteristic of the boreal fish moving poleward into the arctic region of the Barents Sea is high generalism, a property that increases connectance and reduces modularity in the arctic marine food web. Our results reveal that habitats form natural boundaries for food web modules, and that generalists play an important functional role in coupling pelagic and benthic modules. We posit that these habitat couplers have the potential to promote the transfer of energy and matter between habitats, but also the spread of pertubations, thereby changing arctic marine food web structure considerably with implications for ecosystem dynamics and functioning.
Data from: Genetic resources of teak (Tectona grandis Linn. f.) – strong genetic structure among natural populations
Twenty-nine provenances of teak (Tectona grandis Linn. f.) representing the full natural distribution range of the species were genotyped with microsatellite DNA markers to analyse genetic diversity and population genetic structure. Provenances originating from the semi-moist east coast of India had the highest genetic diversity while provenances from Laos showed the lowest. In the eastern part of the natural distribution area, comprising Myanmar, Thailand and Laos, there was a strong clinal decrease in genetic diversity the further east the provenance was located. Overall, the pattern of genetic diversity supports the hypothesis that teak has its centre of origin in India, from where it spread eastwards. The analysis of molecular variance (AMOVA) gave an overall highly significant F st value of 0.227—population pairwise F st values were in the range 0.01–0.48. Applying the G″st differentiation parameter, the estimated overall differentiation was 0.632, implying a strong genetic structure among populations. A neighbour-joining (NJ) tree, using the pairwise population matrix of G″st values as input, contained three distinct groups: (1) the eight provenances from Thailand and Laos, (2) the Indian provenances from the dry interior and the moist west coast and (3) the provenances from northern Myanmar. The provenances from southern Myanmar were placed close to the root of the tree together with the three provenances from the semi-moist east coast of India. A Bayesian cluster analysis using the STRUCTURE software gave very similar results, with three main clusters, each containing two sub-clusters, while Bayesian cluster analysis in the Geneland software, exploiting the spatial coordinates of the provenances, resulted in five clusters in accordance with the former results. The implications of the findings for conservation and use of genetic resources of the species are discussed.
Data from: The interaction of phylogeny and community structure: linking the community composition and trait evolution of clades
Aim. Community phylogenetic studies use information about species' evolutionary relationships to understand the ecological processes of community assembly. A central premise of the field is that species' evolution maps onto ecological patterns, and phylogeny reveals something more than species' traits alone about ecological mechanisms structuring communities such as environmental filtering, competition, and facilitation. We argue, therefore, that there is a need to better understand and model the interaction of phylogeny with species' traits and community composition. Innovation. We outline a new approach that identifies clades that are eco-phylogenetically clustered or overdispersed, and then assesses whether those clades have different rates of trait evolution. Eco-phylogenetic theory would predict that the traits of clustered or overdispersed clades might have evolved differently, either in terms of tempo (fast or slow) or mode (e.g., under constraint or neutrally). We suggest that modelling the evolution of independent trait data in these clades represents a strong test of whether there is an association between species' ecological co-occurrence patterns and evolutionary history. Main conclusions. Using an empirical dataset of mammals from around the world, we identify two clades of rodents whose species tend not to co-occur in the same local assemblages (are phylogenetically overdispersed), and then find independent evidence of slower rates of body mass evolution in these clades. Our approach, which assumes nothing about the mode of species' trait evolution but rather seeks to explain it using ecological information, presents a new way to examine eco-phylogenetic structure.
Data from: Shaping species with ephemeral boundaries: the distribution and genetic structure of the desert tortoise (Gopherus morafkai) in the Sonoran Desert region
Aim: We examine the role biogeographical features played in the evolution of Morafka's desert tortoise (Gopherus morafkai) and test the hypothesis that G. morafkai maintains genetically distinct lineages associated with different Sonoran Desert biomes. Increased knowledge of the past and present distribution of the Sonoran Desert region's biota provides insight into the forces that drive and maintain its biodiversity. Location: Sonoran Desert biogeographical region; Sonora and Sinaloa, Mexico and Arizona, USA. Methods: We examined wild tortoises from Mexico (n = 155) and Arizona (n = 78), spanning their known distribution. We used mtDNA sequences to reconstruct matrilineal relationships and 25 microsatellite (STR) loci for Bayesian analyses of gene flow. We performed clinal analyses on both mtDNA and STR loci to determine the position and amount of introgression where lineages co-occur. We used GIS to assess the association of genetic structuring with ecological features. We used these data in a hypothesis-driven approach to assess different models of how genetic diversity is maintained and distributed in G. morafkai. Results: Gopherus morafkai was found to comprise genetically and geographically distinct 'Sonoran' and 'Sinaloan' lineages. Both lineages occurred in a relatively narrow zone of overlap in Sinaloan thornscrub, where it transitions into Sonoran desertscrub. Limited introgression occurred at the contact zone. The best-fit model suggests that these lineages diverged in parapatry where the distribution of genotypes is environment-dependent and introgression is inhibited by exogenous selection. Main conclusions: The historically shifting ecotone between tropical deciduous forest and Sonoran desertscrub appears to be a boundary that fostered divergence between parapatric lineages of tortoises. The sharp genetic cline between the two lineages suggests that periods of isolation in temporary refugia due to Pleistocene climatic cycling influenced divergence. Despite incomplete reproductive isolation, the Sonoran and Sinaloan lineages of G. morafkai are on separate evolutionary trajectories.
Data from: Habitat-driven population structure of bottlenose dolphins, Tursiops truncatus, in the North-East Atlantic
Despite no obvious barrier to gene flow, historical environmental processes and ecological specializations can lead to genetic differentiation in highly mobile animals. Ecotypes emerged in several large mammal species as a result of niche specializations and/or social organization. In the North-West Atlantic, two distinct bottlenose dolphin (Tursiops truncatus) ecotypes (i.e. 'coastal' and 'pelagic') have been identified. Here, we investigated the genetic population structure of North-East Atlantic (NEA) bottlenose dolphins on a large scale through the analysis of 381 biopsy-sampled or stranded animals using 25 microsatellites and a 682-bp portion of the mitochondrial control region. We shed light on the likely origin of stranded animals using a carcass drift prediction model. We showed, for the first time, that coastal and pelagic bottlenose dolphins were highly differentiated in the NEA. Finer-scale population structure was found within the two groups. We suggest that distinct founding events followed by parallel adaptation may have occurred independently from a large Atlantic pelagic population in the two sides of the basin. Divergence could be maintained by philopatry possibly as a result of foraging specializations and social organization. As coastal environments are under increasing anthropogenic pressures, small and isolated populations might be at risk and require appropriate conservation policies to preserve their habitats. While genetics can be a powerful first step to delineate ecotypes in protected and difficult to access taxa, ecotype distinction should be further documented through diet studies and the examination of cranial skull features associated with feeding.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.