Mountain View
biomedical and healthCAre Data Discovery Index Ecosystem
help Advanced Search
  • CCDC (656,223)
  • UniProt:Swiss-Prot (438,182)
  • BioProject (226,434)
  • Figshare (192,552)
  • PDB (131,204)
  • Dryad (100,545)
  • OmicsDI (78,201)
  • ArrayExpress (69,996)
  • Dataverse (60,303)
  • NeuroMorpho.Org (50,356)
    • SRA (43,089)
    • CIL (10,226)
    • ICPSR (9,857)
    • UKDA (8,799)
    • PeerJ (6,214)
    • GeneNetwork (4,595)
    • Zenodo (4,544)
    • GEO (4,348)
    • ProteomeXchange (3,397)
    • RGD (3,247)
    • PDBe:EMDB (2,367)
    • GEMMA (2,285)
    • GTex (1,622)
    • BMRB (1,490)
    • VectorBase (1,445)
    • NITRCIR (1,391)
    • NeuroVault:Cols (1,154)
    • GND (1,018)
    • dbGaP (979)
    • MorphoBank (828)
    • NURSA (547)
    • Retina (384)
    • MPD (376)
    • Metabolomics (362)
    • NeuroVault:NIDM (353)
    • SBGrid (328)
    • GigaDB (319)
    • SimTK (305)
    • LINCS (287)
    • ImmPort (222)
    • Scientific Data (193)
    • NIDDKCR (151)
    • Epigenomics (128)
    • LSHTM (118)
    • NIMH (98)
    • MITLCP (93)
    • Thieme (87)
    • PhysioBank (82)
    • PeptideAtlas (75)
    • Databrary (74)
    • TCIA (71)
    • CRCNS (71)
    • Ndar Papers (65)
    • openfMRI (55)
    • LSDB (55)
    • CEDAR (54)
    • CXIDB (52)
    • Adaptive Biotechnologies (49)
    • GDC (39)
    • UCSF-CTSI (32)
    • CVRG (29)
    • YPED (27)
    • JHUDMS (23)
    • FDZ-DZA (21)
    • NeuroVault:Atlases (18)
    • Wormbase (11)
    • NSGM (10)
    • NSRR (10)
    • ADA (9)
    • CANDI (3)
    • BILS (1)
    • MBF (1)
    • CTN (51)
    • (5,667)
    • ClinVar (208,560)


If you are having problems using our tools, or if you would just like to send us some feedback, please post your questions on GitHub.

Displaying 20 of 100,545 results for " "
Switch View:
Sorted By:
Title Date Issued Date Released Description
Data from: Covariance among premating, postcopulatory and viability fitness components in Drosophila melanogaster and their influence on paternity measurement
05-15-2012 10-21-2015
In polyandrous mating systems, male fitness depends on success in premating, postcopulatory, and offspring viability episodes of selection. We tracked male success across all of these episodes simultaneously, using transgenic Drosophila melanogaster with ubiquitously expressed green fluorescent protein (i.e., GFP) in a series of competitive and non-competitive matings. This approach permitted us to track paternity-specific viability over all life stages and to distinguish true competitive fertilization success from differential early offspring viability. Relationships between episodes of selection were generally not present when paternity was measured in eggs, however positive correlations between sperm competitive success and offspring viability became significant when paternity was measured in adult offspring. Additionally, we found a significant male × female interaction on hatching success and a lack of repeatability of offspring viability across a focal male's matings, which may underly the limited number of correlations found between episodes of selection.
Data from: Recolonization after habitat restoration leads to decreased genetic variation in populations of a terrestrial orchid
07-13-2012 09-19-2012
Colonization is crucial to habitat restoration projects that rely on the spontaneous regeneration of the original vegetation. However, as a previously declining plant species spreads again, the likelihood of founder effects increases through recurrent population founding and associated serial bottlenecks. We related AFLP genetic variation and fitness of all extant populations of the outcrossing terrestrial orchid Dactylorhiza incarnata in an isolated coastal dune complex to colonization history. Around 1970, D. incarnata suffered a severe bottleneck yet eventually persisted and gradually spread throughout the spatially segregated dune slacks, aided by the restoration of an open vegetation. Genetic assignment demonstrated dispersal to vacant sites from few nearby extant populations and very limited inflow from outside the spatially isolated reserve. Results further indicated that recurrent founding from few local sources resulted in the loss of genetic diversity and promoted genetic divergence (FST=0.35) among populations, but did not influence population fitness. The few local sources initially available and the little gene inflow from outside the study reserve, as a consequence of respectively habitat degradation and spatial isolation, possibly magnified the genetic effects of recurrent population founding.
Data from: Patterns and controlling factors of species diversity in the Arctic Ocean
08-17-2012 10-17-2012
AIM: The Arctic Ocean is one of the last near-pristine regions on Earth and although human activities are expected to impact on Arctic ecosystems, we know very little about baseline patterns of Arctic Ocean biodiversity. This paper aims to describe Arctic Ocean-wide patterns of benthic biodiversity and to explore factors related to the large-scale species diversity patterns. LOCATION: Arctic Ocean. METHODS: We used large ostracode and foraminiferal datasets to describe the biodiversity patterns and apply comprehensive ecological modelling to test the degree to which these patterns are potentially governed by environmental factors, including temperature, productivity, seasonality, ice cover, and others. To test environmental control of the observed diversity patterns, subsets of samples for which all environmental parameters were available were analysed with multiple regression and model averaging. RESULTS: Well-known negative latitudinal species diversity gradients (LSDGs) were found in metazoan Ostracoda, but the LSDGs were unimodal with an intermediate maximum with respect to latitude in protozoan foraminifera. Depth species diversity gradients were unimodal, with peaks in diversity shallower than those in other oceans. Our modelling results showed that several factors are significant predictors of diversity, but the significant predictors were different among shallow marine ostracodes, deep-sea ostracode, and deep-sea foraminifera. MAIN CONCLUSIONS: On the basis of these Arctic Ocean-wide comprehensive datasets, we document large-scale diversity patterns with respect to latitude and depth. Our modelling results suggest that the underlying mechanisms causing these species diversity patterns are unexpectedly complex. The environmental parameters of temperature, surface productivity, seasonality of productivity, salinity, and ice cover are not necessarily mutually exclusive as controlling factors of large-scale diversity patterns, depending on ecological preferences of taxa and oceanographic characteristics of regions. These results suggest that a multiplicity of variables appears to be related to community structure in this system.
Data from: Nuclear markers reveal a complex introgression pattern among marine turtle species on the Brazilian coast
05-24-2012 10-02-2012
A surprisingly high frequency of interspecific sea turtle hybrids have been previously recorded in a nesting site along a short stretch of the Brazilian coast. Mitochondrial DNA data indicated that as much as 43% of the females identified as E. imbricata are hybrids in this area (Bahia State of Brazil). It is a remarkable find, since most of the nesting sites surveyed worldwide, including some in northern Brazil, presents no hybrids, and rare Caribbean sites present no more than 2% of hybrids. Thus, a detailed understanding of the hybridization process is needed to evaluate natural or anthropogenic causes of this regional phenomenon in Brazil, which could be an important factor affecting the conservation of this population. We analyzed a set of 12 nuclear markers to investigate the pattern of hybridization involving three species of sea turtles: hawksbill (Eretmochelys imbricata), loggerhead (Caretta caretta), and olive ridley (Lepidochelys olivacea). Our data indicate that most of the individuals in the crossings L. olivacea × E. imbricata and L. olivacea × C. caretta are F1 hybrids, whereas C. caretta × E. imbricata crossings present F1 and backcrosses with both parental species. In addition, the C. caretta × E. imbricata hybridization seems to be gender and species biased, and we also found one individual with evidence of multispecies hybridization among C. caretta × E. imbricata × Chelonia mydas. The overall results also indicate that hybridization in this area is a recent phenomenon, spanning at least two generations or ~40 years.
Data from: Reciprocal interaction matrix reveals complex genetic and dose-dependent specificity among coinfecting parasites
07-19-2012 04-30-2013
Understanding genetic specificity in factors determining the outcome of host-parasite interactions is especially important as it contributes to parasite epidemiology, virulence, and maintenance of genetic variation. Such specificity, however, is still generally poorly understood. We examined genetic specificity in interactions among coinfecting parasites. In natural populations, individual hosts are often simultaneously infected by multiple parasite species and genotypes that interact. Such interactions could maintain genetic variation in parasite populations if they are genetically specific so that the relative fitness of parasite genotypes varies across host individuals depending on (1) the presence/absence of coinfections and/or (2) the genetic composition of the coinfecting parasite community. We tested these predictions using clones of fish eye flukes Diplostomum pseudospathaceum and Diplostomum gasterostei. We found that interactions among parasites had a strong genetic basis and that this modified genetic variation in infection success of D. pseudospathaceum between single and multiple infections as well as across multiply infected host individuals depending on the genetic identity of the coinfecting D. gasterostei. The relative magnitude of these effects, however, depended on the exposure dose, suggesting that ecological factors can modify genetic interactions between parasites.
Data from: Evolutionary rescue of sexual and asexual populations in a deteriorating environment
05-20-2012 11-06-2012
The environmental change experienced by many contemporary populations of organisms poses a serious risk to their survival. From the theory of evolutionary rescue we predict that the combination of sex and genetic diversity should increase the probability of survival by increasing variation and thereby the probability of generating a type that can tolerate the stressful environment. We tested this prediction by comparing experimental populations of Chlamydomonas reinhardtii that differ in sexuality and in the initial amount of genetic diversity. The lines were serially propagated in an environment where the level of stress caused by salt increased over time from fresh water to the limits of marine conditions. In the long term, the combination of high diversity and obligate sexuality was most effective in supporting evolutionary rescue. Most of the adaptation to high-salt environments in the obligate sexual-high diversity lines had occurred by mid-way through the experiment, indicating that positive genetic correlations of adaptation to lethal stress with adaptation to sublethal stress greatly increased the probability of evolutionary rescue. The evolutionary rescue events observed in this study provide evidence that major shifts in ways of life can arise within short time frames through the action of natural selection in sexual populations.
Data from: Global honey bee viral landscape altered by a parasitic mite
06-08-2012 06-11-2012
Emerging diseases are among the greatest threats to honey bees. Unfortunately, where and when an emerging disease will appear are almost impossible to predict. The arrival of the parasitic Varroa mite into the Hawaiian honey bee population allowed us to investigate changes in the prevalence, load, and strain diversity of honey bee viruses. The mite increased the prevalence of a single viral species, deformed wing virus (DWV), from ~10 to 100% within honey bee populations, which was accompanied by a millionfold increase in viral titer and a massive reduction in DWV diversity, leading to the predominance of a single DWV strain. Therefore, the global spread of Varroa has selected DWV variants that have emerged to allow it to become one of the most widely distributed and contagious insect viruses on the planet.
Data from: Clinal variation in seed traits influencing life cycle timing in Arabidopsis thaliana.
05-09-2012 11-06-2012
Early life history transitions are crucial determining lifetime survival and fecundity. Adaptive evolution in early life history traits involves a complex interplay between the developing plant and its current and future environments. We examined the plant’s earliest life history traits, dissecting an integrated suite of pre-germination processes: primary dormancy, thermal induction of secondary dormancy, and seasonal germination response. We examined genetic variation in the three processes, genetic correlations among the processes, and the scaling of germination phenology with the source populations’ climates. A spring annual life-history was associated with genetic propensities toward both strong primary dormancy and heat-induced secondary dormancy, alone or in combination. Lineages with similar winter and spring annual life-history have both weak primary dormancy and weak thermal dormancy induction. A genetic bias to adopt a spring annual strategy mediated by rapid loss of primary dormancy, and high thermal dormancy induction is associated with a climatic gradient characterized by increasing temperature in summer and rainfall in winter. This study highlights the importance of considering combinations of multiple genetically-based traits along a climatic gradient as adaptive strategies differentiating annual plant life-history strategies. Despite the genetic-climatic cline, there is polymorphism for life-history strategies within population, classically interpreted as bet-hedging in an unpredictable world.
Data from: Two new species of Lecanora sensu stricto (Lecanoraceae, Ascomycota) from east Africa
05-10-2012 02-05-2013
The new sorediate species Lecanora kenyana from Mount Kenya and Lecanora orientoafricana from the Rift Valley in Kenya are described. Lecanora kenyana has red-brown apothecia with a constricted base, a melacarpella–type amphithecium, pulicaris–type epihymenium, a hyaline hypothecium, and contains usnic acid as major constituent. Lecanora orientoafricana is characterized by having a dark hypothecium, pulicaris-type amphithecium, chlarotera-epihymenium, and contains atranorin and gangaleoidin. A phylogenetic analysis using maximum likelihood and a Bayesian approach based on DNA sequence data of mtSSU and ITS rDNA support that both new species belong to Lecanora sensu stricto and cluster with species containing usnic acid or having a dark hypothecium, respectively.
Data from: Independence among physiological traits suggests flexibility in the face of ecological demands on phenotypes
06-11-2012 10-22-2015
Phenotypic flexibility allows animals to adjust their physiology to diverse environmental conditions encountered over the year. Examining how these varying traits covary gives insights into potential constraints or freedoms that may shape evolutionary trajectories. In this study we examined relationships among hematocrit, baseline corticosterone concentration, constitutive immune function and basal metabolic rate in red knot Calidris canutus islandica individuals subjected to experimentally manipulated temperature treatments over an entire annual cycle. If covariation among traits is constrained, we predict consistent covariation within and among individuals. We further predict consistent correlations between physiological and metabolic traits if constraints underlie species level patterns found along the slow-fast pace-of-life continuum. We found no consistent correlations among hematocrit, baseline corticosterone concentration, immune function and basal metabolic rate either within or among individuals. This provides no evidence for constraints limiting relationships among these measures of the cardiovascular, endocrine, immune and metabolic systems in individual red knots. Rather, our data suggest that knots are free to adjust individual parts of their physiology independently. This makes good sense if one places the animal within its ecological context where different aspects of the environment might put different pressures on different aspects of physiology.
Data from: Macroevolutionary and morphofunctional patterns in theropod skulls: a morphometric approach
04-20-2012 02-19-2013
Theropod dinosaurs are one of the most remarkable lineages of terrestrial vertebrates in the Mesozoic, showing high taxonomic and ecological diversity. We investigate the cranial diversity of non-avian theropods and some basal birds, using geometric morphometrics to obtain insights into the evolutionary modifications of the skull. Theropod skulls mostly vary in the shape of the snout and length of the postorbital region (PC 1), with further variation in orbit shape, depth of the postorbital region, and position of the jaw joint (PC 2 and PC 3). These results indicate that the cranial shape of theropods is closely correlated with phylogeny and dietary preference. Skull shapes of non-carnivorous taxa differ significantly from carnivorous taxa, suggesting that dietary preference affects skull shape. Furthermore, we found a significant correlation between the first three PC axes and functional proxies (average maximum stress and an indicator of skull strength). Interestingly, basal birds occupy a large area within the morphospace, indicating a high cranial, and thus also ecological, diversity. However, we could include only a small number of basal avialan species, because their skulls are fragile and there are few good skull reconstructions. Taking the known diversity of basal birds from the Jehol biota into account, the present result might even underestimate the morphological diversity of basal avialans.
Data from: Paternal care: direct and indirect genetic effects of fathers on offspring performance
05-20-2012 11-06-2012
Knowledge of how genetic effects arising from parental care influence the evolution of offspring traits comes almost exclusively from studies of maternal care. However, males provide care in some taxa, and often this care differs from females in quality or quantity. If variation in paternal care is genetically based then, like maternal care and maternal effects, paternal effects may have important consequences for the evolution of offspring traits via indirect genetic effects (IGEs). IGEs and direct-indirect genetic covariances associated with parental care can contribute substantially to total heritability and influence predictions about how traits respond to selection. It is unknown, however, if the magnitude and sign of parental effects arising from fathers are the same as those arising from mothers. We used a reciprocal cross-fostering experiment to quantify environmental and genetic effects of paternal care on offspring performance in the burying beetle, Nicrophorus vespilloides. We found that IGEs were substantial and direct-indirect genetic covariances negative. Combined, these patterns led to low total heritabilities for offspring performance traits. Thus, under paternal care, offspring performance traits are unlikely to evolve in response to selection and, variation in these traits will be maintained in the population despite potentially strong selection on these traits. These patterns are similar to those generated by maternal care, indicating that the genetic effects of care on offspring performance are independent of the caregiver’s sex.
Data from: A parapatric propensity for breeding precludes the completion of speciation in common teal (Anas crecca, sensu lato)
06-21-2012 10-21-2015
Speciation is a process in which genetic drift and selection cause divergence over tSpeciation is a process in which genetic drift and selection cause divergence over time. However, there is no rule dictating the time required for speciation, and even low levels of gene flow hinder divergence, so that taxa may be poised at the threshold of speciation for long periods of evolutionary time. We sequenced mitochondrial DNA (mtDNA) and eight nuclear introns (nuDNA) to estimate genomic levels of differentiation and gene flow between the Eurasian common teal (Anas crecca crecca) and the North American green-winged teal (A. c. carolinensis). These ducks come into contact in Beringia (northeastern Asia and northwestern North America) and have likely done so, perhaps cyclically, since the Pliocene-Pleistocene transition, ~2.6 Ma, when they apparently began diverging. They have diagnosable differences in male plumage and are 6.9% divergent in the mtDNA control region, with only 1 of 58 crecca and 2 of 86 carolinensis having haplotypes grouping with the other. Two nuclear loci were likewise strongly structured between these teal (ΦST > 0.35), but six loci were undifferentiated or only weakly structured (ΦST = 0.0–0.06). Gene flow between crecca and carolinensis was ~1 individual per generation in both directions in mtDNA, but was asymmetrical in nuDNA, with ~1 and ~20 individuals per generation immigrating into crecca and carolinensis, respectively. This study illustrates that species delimitation using a single marker oversimplifies the complexity of the speciation process, and it suggests that even with divergent selection, moderate levels of gene flow may stall the speciation process short of completion.
Data from: Heterozygosity-behaviour correlations in nine-spined stickleback (Pungitius pungitius) populations: contrasting effects at random and functional loci
08-31-2012 10-02-2015
The study of heterozygosity-fitness correlations has a long history in the fields of ecology and evolutionary biology but remains controversial. Recently, it has been shown that the location of markers i.e. their genomic position with respect to their distance from functional loci can be an important factor to be considered in addition to marker number and variability. In this study, we investigated the correlation between individual heterozygosity and behaviour (aggression, boldness and feeding activity) in nine-spined stickleback individuals originating from four populations in two contrasting environments. Offspring of full-sib families raised in a common garden setting were assessed for behaviour and genotyped using 84 microsatellite markers that were either located within or near behaviourally or physiologically important genes (termed ‘functional’) or were randomly selected. No associations were detected with any behavioural trait in any population or over all populations when genetic variability was measured using all markers combined. However, when the markers were separated into three functional categories, several significant associations were observed both with functional markers and random markers in one of the four populations. Contrasting correlations with behaviour were observed when using physiological gene (negative) and random (positive) markers. Upon dividing the physiological gene markers into further subcategories based on their specific physiological functions, a strong relationship between the heterozygosity of markers linked to osmoregulation-related genes and behaviour was revealed in the brackish water population. Our results indicate that both local (physiological) and general (neutral) effects are important in shaping behaviour and that heterozygosity-behaviour correlations are population dependent.
Data from: Behavioral evidence for fruit odor discrimination and sympatric host races of Rhagoletis pomonella flies in the western United States
06-25-2012 11-06-2012
The recent shift of Rhagoletis pomonella (Diptera: Tephritidae) from its native host downy hawthorn, Crataegus mollis, to introduced domesticated apple, Malus domestica, in the eastern U.S. is a model for sympatric host race formation. However, the fly is also present in the western U.S., where it may have been introduced via infested apples within the last 60 years. In addition to apple, R. pomonella also infests two hawthorns in the West, one the native black hawthorn, C. douglasii, and the other the introduced English ornamental hawthorn, C. monogyna. Here, we test for behavioral evidence of host races in the western U.S. through flight tunnel assays of western R. pomonella flies to host fruit volatile blends. We report that western apple, black hawthorn, and ornamental hawthorn flies showed significantly increased levels of upwind directed flight to their respective natal compared to non-natal fruit volatile blends, consistent with host race status. We discuss the implications of the behavioral results for the origin(s) of western R. pomonella, including the possibility that western apple flies were not introduced, but may represent a recent shift from local hawthorn fly populations.
Data from: Ecological constraints on female fitness in a phytophagous insect
08-21-2012 09-25-2012
Although crucial for population demography, our understanding of how and to which relative extent different ecological factors constrain female reproduction suffers from difficulties in studying links between individual behavior, life history and fitness in nature. We here present such data on females in a natural population of the butterfly Leptidea sinapis. The data were combined with climate records and laboratory estimates of life history parameters to predict the relative impact of different ecological constraints on female fitness in the wild. We partitioned effects of male courtship, host plant availability, and temperature on female fitness using simulation models. Results indicate that temperature is the most constraining factor on female fitness, followed by host plant availability, whereas the short-term negative effects of male courtship detected in the field study were less important in models predicting female reproductive success over the entire lifespan. In the simulations females with more reproductive reserves were more limited by the ecological variables. Reproductive physiology and egg laying behavior were therefore predicted to be co-optimized but reach different optima for females of different body sizes, a prediction supported by the empirical data. This study thus highlights the need of studying behavioral and life history variation in orchestration to achieve a more complete picture of both demographic and evolutionary processes in naturally variable and unpredictable environments.
Data from: Millipede taxonomy after 250 years: classification and taxonomic practices in a mega-diverse yet understudied arthropod group
05-15-2012 06-04-2012
BACKGROUND: The arthropod class Diplopoda is a mega-diverse group comprising >12,000 described millipede species. The history of taxonomic research within the group is tumultuous and, consequently, has yielded a questionable higher-level classification. Few higher-taxa are defined using synapomorphies, and the practice of single taxon descriptions lacking a revisionary framework has produced many monotypic taxa. Additionally, taxonomic and geographic biases render global species diversity estimations unreliable. We test whether the ordinal taxa of the Diplopoda are consistent with regards to underlying taxonomic diversity, attempt to provide estimates for global species diversity, and examine millipede taxonomic effort at a global geographic scale. METHODOLOGY/PRINCIPAL FINDINGS: A taxonomic distinctness metric was employed to assess uniformity of millipede ordinal taxa. We found that ordinal-level taxa are not uniform and are likely overinflated with higher-taxa when compared to related groups. Several methods of estimating global species richness were employed (Bayesian, variation in taxonomic productivity, extrapolation from nearly fully described taxa). Two of the three methods provided estimates ranging from 13,413–16,760 species. Variations in geographic diversity show biases to North America and Europe and a paucity of works on tropical taxa. CONCLUSIONS/SIGNIFICANCE: Before taxa can be used in an extensible way, they must be definable with respect to the diversity they contain and the diagnostic characters used to delineate them. The higher classification for millipedes is shown to be problematic from a number of perspectives. Namely, the ordinal taxa are not uniform in their underlying diversity, and millipedes appear to have a disproportionate number of higher-taxa. Species diversity estimates are unreliable due to inconsistent taxonomic effort at temporal, geographic, and phylogenetic scales. Lack of knowledge concerning many millipede groups compounds these issues. Diplopods are likely not unique in this regard as these issues may persist in many other diverse yet poorly studied groups.
Data from: Ant societies buffer individual-level effects of parasite infections
06-18-2012 10-26-2015
Parasites decrease host fitness and can induce changes in host behavior, morphology, and physiology. When parasites exploit social insects, they influence not only infected individuals but the society as a whole. Workers of the ant Temnothorax nylanderi are an intermediate host for the cestode Anomotaenia brevis. We studied a heavily parasitized population and found that while parasite infection had strong and diverse consequences for individual workers, colony fitness remained unchanged. On the individual level, we uncovered differences among the three worker types: infected and healthy workers from parasitized colonies and healthy workers from non-parasitized colonies. Infected workers were smaller than healthy ones and had, as parasite load increased, smaller heads. Behavioral changes extended to all workers from parasitized colonies, which were less active but groomed more. Healthy workers from parasitized colonies showed behavioral patterns intermediate to those of infected workers and healthy workers from non-parasitized colonies. Despite the lower activity level, an important fitness parameter - per-worker productivity - remained unaltered in parasitized colonies. However, the investment strategies of parasitized colonies changed as their sex ratio became male-biased and male body size increased. In short, ant colonies can buffer the drain of resources by the parasite despite strong effects on individual workers.
Data from: Patterns and persistence of larval retention and connectivity in a marine fish metapopulation
08-14-2012 10-26-2015
Connectivity, the demographic linking of local populations through the dispersal of individuals, is one of the most poorly understood processes in population dynamics, yet has profound implications for conservation and harvest strategies. For marine species with pelagic larvae, direct estimation of connectivity remains logistically challenging and has mostly been limited to single snapshots in time. Here, we document seasonal and interannual patterns of larval dispersal in a metapopulation of the coral reef fish Amphiprion polymnus. A 3-year record of larval trajectories within and among nine discrete local populations from an area of approximately 35 km was established by determining the natal origin of settled juveniles through DNA parentage analysis. We found that spatial patterns of both self-recruitment and connectivity were remarkably consistent over time, with a low level of self-recruitment at the scale of individual sites. Connectivity among sites was common and multidirectional in all years and was not significantly influenced by seasonal variability of predominant surface current directions. However, approximately 75% of the sampled juveniles could not be assigned to parents within the study area, indicating high levels of immigrations from sources outside the study area. The data support predictions that the magnitude and temporal stability of larval connectivity decreases significantly with increasing distance between subpopulations, but increases with the size of subpopulations. Given the considerable effort needed to directly measure larval exchange, the consistent patterns suggest snapshot parentage analyses can provide useful dispersal estimates to inform spatial management decisions.
Data from: Phylogeography of speciation: allopatric divergence and secondary contact between outcrossing and selfing Clarkia
07-31-2012 09-26-2012
The origins of hybrid zones between parapatric taxa have been of particular interest for understanding the evolution of reproductive isolation and the geographic context of species divergence. One challenge has been to distinguish between allopatric divergence (followed by secondary contact) versus primary intergradation (parapatric speciation) as alternative divergence histories. Here we use complementary phylogeographic and population genetic analyses to investigate the recent divergence of two subspecies of Clarkia xantiana and the formation of a hybrid zone within the narrow region of sympatry. We tested alternative phylogeographic models of divergence using ABC (approximate Bayesian computation) and found strong support for a secondary contact model and little support for a model allowing for gene flow throughout the divergence process (i.e. primary intergradation). Two independent methods for inferring the ancestral geography of each subspecies, one based on probabilistic character state reconstructions and the other on paleodistribution modeling, also support a model of divergence in allopatry and range expansion leading to secondary contact. The membership of individuals to genetic clusters suggests geographic substructure within each taxon where allopatric and sympatric samples are primarily found in separate clusters. We also observed coincidence and concordance of genetic clines across three types of molecular markers, which suggests that there is a strong barrier to gene flow. Taken together, our results provide evidence for allopatric divergence followed by range expansion leading to secondary contact. The location of refugial populations and the directionality of range expansion are consistent with expectations based on climate change since the last glacial maximum.