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Figures 22-25 from: Doorenweerd C, Ekayanti A, Rubinoff D (2020) The Dacini fruit fly fauna of Sulawesi fits Lydekker's line but also supports Wallacea as a biogeographic region (Diptera, Tephritidae). ZooKeys 973: 103-122. https://doi.org/10.3897/zookeys.973.55327
Figures 22-25 The two specimens of Bactrocera carambolae that represent the first records for Sulawesi, photographed in ethanol (wings were removed) 22 dorsal view of specimen ms08439 23 lateral view of specimens ms08439 24 dorsal view of specimen ms10710 25 lateral view of specimen ms10710. Both specimens have the typical rectangular black mark on the lateral sides of the fourth abdominal segment, but lack the black mark on the fore femur, which can further help to distinguish B. carambolae from B. dorsalis.
Figures 14- 15 from: Doorenweerd C, Ekayanti A, Rubinoff D (2020) The Dacini fruit fly fauna of Sulawesi fits Lydekker's line but also supports Wallacea as a biogeographic region (Diptera, Tephritidae). ZooKeys 973: 103-122. https://doi.org/10.3897/zookeys.973.55327
Figures 14- 15 Maximum Likelihood trees based on COI (14) and EF1-alpha (15) DNA sequence data for Dacus longicornis, with D. pullescens Munro and D. vertebratus Bezzi as outgroups. Branch support values are rapid bootstrap values and approximate-likelihood ratio test values, scale bar indicates substitutions per site. Full details on the samples can be found in BOLD dataset DOI: http://dx.doi.org/10.5883/DS-DACSU.
Figures 20- 21 from: Doorenweerd C, Ekayanti A, Rubinoff D (2020) The Dacini fruit fly fauna of Sulawesi fits Lydekker's line but also supports Wallacea as a biogeographic region (Diptera, Tephritidae). ZooKeys 973: 103-122. https://doi.org/10.3897/zookeys.973.55327
Figures 20- 21 Maximum Likelihood trees based on COI (20) and EF1-alpha (21) DNA sequence data for Bactrocera melastomatos and allied species, using B. lombokensis Drew & Hancock and B. digressa Radhakrishnan as outgroup. Branch support values are rapid bootstrap values and approximate-likelihood ratio test values, scale bar indicates substitutions per site. Full details on the samples can be found in BOLD dataset DOI: http://dx.doi.org/10.5883/DS-DACSU.
Figure 1 from: Doorenweerd C, Ekayanti A, Rubinoff D (2020) The Dacini fruit fly fauna of Sulawesi fits Lydekker's line but also supports Wallacea as a biogeographic region (Diptera, Tephritidae). ZooKeys 973: 103-122. https://doi.org/10.3897/zookeys.973.55327
Figure 1 Map of Sulawesi and neighboring areas showing the four sampling localities with orange spots; the three localities in South Sulawesi were in close proximity to each other. Two typical biogeographical boundaries are indicated with dotted lines: Wallace's line and Lydekker's line. Land masses west of Wallace's line were connected during ice ages as Sunda, east of Lydekker's line land masses were connected as Sahul. Islands in between the two biogeographical boundaries were never connected by land and are jointly known as Wallacea.
Figures 16-19 from: Doorenweerd C, Ekayanti A, Rubinoff D (2020) The Dacini fruit fly fauna of Sulawesi fits Lydekker's line but also supports Wallacea as a biogeographic region (Diptera, Tephritidae). ZooKeys 973: 103-122. https://doi.org/10.3897/zookeys.973.55327
Figures 16-19 Sulawesi Bactrocera melastomatos resemble sympatric Bactrocera usitata16 specimen ms09144 B. usitata, dorsal view 17 close up of abdomen of ms09144 18 specimen ms08838 B. melastomatos, dorsal view 19 close up of abdomen of ms08838.
Figures 8-13 from: Doorenweerd C, Ekayanti A, Rubinoff D (2020) The Dacini fruit fly fauna of Sulawesi fits Lydekker's line but also supports Wallacea as a biogeographic region (Diptera, Tephritidae). ZooKeys 973: 103-122. https://doi.org/10.3897/zookeys.973.55327
Figures 8-13 Two forms of Dacus longicornis8D. longicornis collected in Bangladesh, Pabna district, 30-ix-3-x-2013 Leg. M. A. Hossain 9D. longicornis collected in Bangladesh, Maulvi Bazar Rainforest resort, Leg. L. Leblanc & M. A. Hossain 10 specimen ms08424, collected in Sulawesi, with a faint medial postsutural yellow vitta 11 specimen ms08432, collected in Sulawesi 12 specimen ms08428, collected in Sulawesi 13 specimen ms08421, collected in Sulawesi.
Figures 2-7 from: Doorenweerd C, Ekayanti A, Rubinoff D (2020) The Dacini fruit fly fauna of Sulawesi fits Lydekker's line but also supports Wallacea as a biogeographic region (Diptera, Tephritidae). ZooKeys 973: 103-122. https://doi.org/10.3897/zookeys.973.55327
Figures 2-7 Bactrocera (Bactrocera) niogreta sp. nov. Holotype, ms09121 2 dorsal view 3 frontal view of the face 4 lateral view 5 posterior view of the abdomen showing the ceromatae 6 dissected wing 7 lateral close-up of the genitalia.
Seminal fluid-mediated fitness effects in the simultaneously hermaphroditic flatworm Macrostomum lignano
<p>As a class, seminal fluid proteins are expected to exert strong effects on mating partners due to the selection pressures of sperm competition and sexual conflict. But because of the complexity of this secretion, linking specific proteins to downstream effects on own fitness – via manipulating the reproductive behavior, physiology and ultimately the sperm utilization of mating partners – is not straightforward. Here we adopted a systematic gene knockdown approach to screen for seminal fluid-mediated fitness effects in the simultaneously hermaphroditic flatworm <i>Macrostomum lignano</i>. We focused on 18 transcripts in <i>M. lignano</i> seminal fluid, testing how their RNA interference-induced knockdown impacted on three aspects of donor (male) reproductive success: (i) fertility (offspring production of the partner); (ii) defensive sperm competitive ability, <i>P</i><sub>1</sub>; and (iii) offensive sperm competitive ability, <i>P</i><sub>2</sub>. In general, the knockdown of most individual transcripts appeared to have only a minor impact on male reproductive success, though we found evidence that the knockdown of up to five different transcripts impacted on fertility; the knockdown of two other transcripts resulted in reduced <i>P</i><sub>2</sub>, and knockdown of a further transcript actually increased <i>P</i><sub>2</sub>. We thus identify a number of candidate seminal fluid transcripts that appear to modulate offspring production and sperm competitiveness in <i>M. lignano</i>. That only a minority of transcripts exhibit such a pattern likely reflects both the difficulty of accurately estimating sperm competitiveness and the functional redundancy of seminal fluid.</p>
Data from: Canalisation in the wild: effects of developmental conditions on physiological traits are inversely linked to their association with fitness
Ecological conditions affect fitness, but mechanisms causing such effects are not well known, while evolved responses to environmental variation may depend on the underlying mechanisms. Consequences of environmental conditions vary strongly between traits, but a framework to interpret such variation is lacking. We propose that variation in trait response may be explained by differential canalisation, with traits with larger fitness effects showing weaker responses to environmental perturbations due to preferential resource allocation to such traits. We tested the canalisation hypothesis using brood size manipulation in wild jackdaw nestlings in which we measured eight physiological traits (mainly oxidative stress markers), and two feather traits. For each trait, we estimated manipulation response and association with fitness (over-winter survival). As predicted, a strong negative correlation emerged between manipulation response and association with fitness (r=-0.76). We discuss the consequences of differential trait canalization for the study of mechanisms mediating environmental effects on fitness.
Data from: The genetic architecture of fitness drives population viability during rapid environmental change
<p>The rapid global loss of biodiversity calls for improved predictions of how populations will evolve and respond demographically to ongoing environmental change. The heritability (<i>h</i><sup>2</sup>) of selected traits has long been known to affect evolutionary and demographic responses to environmental change. However, effects of the genetic architecture underlying the <i>h</i><sup>2</sup> of a selected trait on population responses to selection are less well understood. We use deterministic models and stochastic simulations to show that the genetic architecture underlying <i>h</i><sup>2</sup> can dramatically affect population viability during environmental change. Polygenic trait architectures (many loci, each with a small phenotypic effect) conferred higher population viability than genetic architectures with the same initial <i>h</i><sup>2</sup> and large-effect loci under a wide range of scenarios. Population viability also depended strongly on the initial frequency of large-effect beneficial alleles, with moderately low initial allele frequencies conferring higher viability than rare or already-frequent large-effect alleles. Greater population viability associated with polygenic architectures appears to be due to higher short term evolutionary potential compared to architectures with large-effect loci. These results suggest that integrating information on the trait genetic architecture into quantitiative genetic analysis will substantially improve our understanding and prediction of evolutionary and demographic responses to environmental change.</p>
Influence of genetic compatibility on offspring fitness in the red-backed toadlet
<p>Presented are data from a manipulative study investigating the influence of parental genetic compatibility on offspring viability in the red backed toadlet (<em>Pseudophryne coriacea</em>). The study used artificial fertilisation techniques combined with a cross-classified breeding design (North Carolina type II) to control parentage and partition sources of genetic and phenotypic variance in offspring fitness. The study also tested the influence of parental genetic similarity on offspring viability. Quantitative genetic analysis of the data revealed no significant additive genetic effects (sire effects), but highly significant non-additive genetic effects (sire x dam interaction effects), on fertilisation success, survival during embryonic development, and hatching success. Analysis also revealled significant associations between parental genetic similarity and offspring survival (whereby survival was higher when parents were more related), and significant positive relationships between fertilisation success and embryo survival through to hatching.</p>
Data for: Immigration counter-acts local micro-evolution of a major fitness component: migration-selection balance in free-living song sparrows
<p>Ongoing adaptive evolution, and resulting 'evolutionary rescue' of declining populations, requires additive genetic variation in fitness. Such variation can be increased by gene flow resulting from immigration, potentially facilitating evolution. But, gene flow could in fact constrain rather than facilitate local adaptive evolution if immigrants have low additive genetic values for local fitness. Local migration-selection balance and micro-evolutionary stasis could then result. However, key quantitative genetic effects of natural immigration, comprising the degrees to which gene flow increases the total local additive genetic variance yet counter-acts local adaptive evolutionary change, have not been explicitly quantified in wild populations. Key implications of gene flow for population and evolutionary dynamics consequently remain unclear. Our quantitative genetic analyses of long-term data from free-living song sparrows (<i>Melospiza melodia</i>) show that mean breeding value for local juvenile survival to adulthood, a major component of fitness, increased across cohorts more than expected solely due to drift. Such micro-evolutionary change should be expected given non-zero additive genetic variance and consistent directional selection. However, this evolutionary increase was counter-acted by negative additive genetic effects of recent immigrants, which increased total additive genetic variance but prevented a net directional evolutionary increase in total additive genetic value. These analyses imply an approximate quantitative genetic migration-selection balance in a major fitness component, and hence demonstrate a key mechanism by which substantial additive genetic variation can be maintained yet decoupled from local adaptive evolutionary change.</p>
Context-dependent reproductive isolation: host plant variability drives fitness of hybrid herbivores
<p><span>The role of divergent selection between alternative environments is well-recognized to promote reproductive isolation (RI) between lineages. However, most studies view each divergent environment as homogenous, thereby overlooking the potential role of within environment variation on RI between differentiating lineages. Here we test the importance of microenvironmental variation on RI using individual trees of two host plants each harboring locally adapted populations of the cynipid wasp, <i>Belonocnema treatae</i>. We compared the fitness surrogate (survival) of offspring from hybrid crosses with residents across individuals of each host plant <i>Quercus virginiana</i> and <i>Q. geminata</i>. We found evidence of weak hybrid inviability between host-associated lineages of <i>B. treatae</i> despite strong genomic differentiation. However, averaging across environments, masked great variation in hybrid fitness on individual trees, where hybrids performed worse than, equal to, or better than residents. Considering the environmental context of hybridization is thus critical to improving the predictability of divergence under variable selection.</span></p>
Data from: Evaluating the role of inbreeding depression in heterozygosity-fitness correlations: how useful are tests for identity disequilibrium?
Heterozygosity-fitness correlations (HFCs) have been observed for several decades, but their causes are often elusive. Tests for identity disequilibrium (ID, correlated heterozygosity between loci) are commonly used to determine if inbreeding depression is a possible cause of HFCs. We used computer simulations to determine how often ID is detected when HFCs are caused by inbreeding depression. We also used ID in conjunction with HFCs to estimate the proportion of variation (r2) in fitness explained by the individual inbreeding coefficient (F). ID was not detected in a large proportion of populations with statistically significant HFCs (sample size = 120 individuals) unless the variance of F was high (σ2(F) ≥ 0.005) or many loci were used (100 microsatellites or 1000 SNPs). For example, with 25 microsatellites, ID was not detected in 49% of populations when HFCs were caused by six lethal equivalents and σ2(F) was typical of vertebrate populations (σ2(F) ≈ 0.002). Estimates of r2 between survival and F based on ID and HFCs were imprecise unless ID was strong and highly statistically significant (P ≈ 0.01). These results suggest that failing to detect ID in HFC studies should not be taken as evidence that inbreeding depression is absent. The number of markers necessary to simultaneously detect HFC and ID depends strongly on σ2(F). Thus the mating system and demography of populations, which influence σ2(F), should be considered when designing HFC studies. ID should be used in conjunction with HFCs to estimate the correlation between fitness and F, because HFCs alone reveal little about the strength of inbreeding depression.
Data from: Sex-specific heterogeneity in fixed morphological traits influences individual fitness in a monogamous bird population
Theoretical work has emphasized the important role of individual traits on population dynamics, but empirical models are often based on average or stage-dependent demographic rates. In this study on a monogamous bird, the Eurasian hoopoe (Upupa epops), we show how the interactions between male and female fixed and dynamic heterogeneity influence demographic rates and population dynamics. We built an integral projection model including individual sex, age, condition (reflecting dynamic heterogeneity) and fixed morphology (reflecting fixed heterogeneity). Fixed morphology was derived from a principal component analysis of six morphological traits. Our results revealed that reproductive success and survival were linked to fixed heterogeneity whereas dynamic heterogeneity influenced mainly the timing of reproduction. Fixed heterogeneity had major consequences for the population growth rate, but interestingly, its effect on population dynamics differed between the sexes. Female fixed morphology was directly linked to annual reproductive success whereas male fixed morphology influenced also annual survival, being twice higher in large than in small males. Even in a monogamous bird with shared parental care, large males can reach 10\% higher fitness than females. Including the dynamics of male and female individual traits in population models refines our understanding of the individual mechanisms that influence demographic rates and population dynamics and can help identifying differences in sex-specific strategies.
Data from: The fitness costs of antibiotic resistance mutations
Antibiotic resistance is increasing in pathogenic microbial populations and is thus a major threat to public health. The fate of a resistance mutation in pathogen populations is determined in part by its fitness. Mutations that suffer little or no fitness cost are more likely to persist in the absence of antibiotic treatment. In this review, we performed a meta-analysis to investigate the fitness costs associated with single mutational events that confer resistance. Generally, these mutations were costly, although several drug classes and species of bacteria on average did not show a cost. Further investigations into the rate and fitness values of compensatory mutations that alleviate the costs of resistance will help us to better understand both the emergence and management of antibiotic resistance in clinical settings.
Data from: Fitness consequences of female alternative reproductive tactics in house mice (Mus musculus domesticus)
Alternative reproductive tactics are defined as discrete differences in morphological, physiological and/or behavioral traits associated with reproduction, which occur within the same sex and population. House mice provide a rare example for alternative reproductive tactics in females, which can either rear their young solitarily, or together with one or several other females in a communal nest. We assessed the fitness consequences of communal and solitary breeding in a wild population to understand how the two tactics can be evolutionarily stable. Females switched between the two tactics (with more than 50% of all females having two or more litters using both tactics), pointing towards communal and solitary breeding being two tactics within a single strategy and not two genetically determined strategies. Communal breeding resulted in reduced pup survival and negatively impacted female reproductive success. Older and likely heavier females more often reared their litters solitarily, indicating that females use a condition dependent strategy. Solitary breeding seems the more successful tactic and only younger and likely less competitive females might opt for communal nursing, even at the cost of increased pup mortality. This study emphasizes the importance of analyzing phenotypic plasticity and its role in cooperation in the context of female ARTs.
Data from: No fitness benefits of early molt in a fairy-wren: relaxed sexual selection under genetic monogamy?
The evolution of male ornamentation has long been the focus of sexual selection studies. However, evidence is accumulating that sexually selected traits can also be lost, although the process is ill-understood. In male fairy-wrens (Malurus spp.), early molt into the seasonal breeding plumage is critical for obtaining extra-pair paternity (EPP), which reaches very high levels in these socially monogamous songbirds. A notable exception is the purple-crowned fairy-wren, Malurus coronatus, which, like its congeners, breeds cooperatively, but where EPP is very rare. Nevertheless, males develop a conspicuous seasonal breeding plumage at highly variable times. Based on 6 years of molt data collected for 137 individuals, we investigated the adaptive significance of pre-breeding molt timing as a sexual signal under (near) genetic monogamy. Molt timing varied between and within individuals with age and climate: molt was completed earlier in older males and after wetter years. Despite its potential to act as a sexual signal of male quality, fitness benefits and costs of early molt appear limited: molt timing did not correlate with 1) the likelihood of gaining a breeding position; 2) female mate preference (EPP/cuckoldry, divorce); 3) female reproductive investment (breeding timing, clutch size, number of clutches); 4) breeding performance (hatching success, fledging success, fledgling survival, annual reproductive success); and 5) male survival. However, although molt timing did not predict which subordinates would become breeders, breeders molted earlier than subordinates. The lack of EPP in this species might imply relaxed sexual selection on early molt with potential to lead to trait disappearance.
Data from: Long-term evaluation of fitness and demographic effects of a Chinook salmon supplementation program
While the goal of supplementation programs is to provide positive, population-level effects for species of conservation concern, these programs can also present an inherent fitness risk when captive-born individuals are fully integrated into the natural population. In order to evaluate the long-term effects of a supplementation program and estimate the demographic and phenotypic factors influencing the fitness of a threatened population of Chinook salmon (Oncorhynchus tshawytscha), we genotyped tissue samples spanning a 19-year period (1998-2016) to generate pedigrees from adult fish returning to Johnson Creek, Idaho USA. We expanded upon previous estimates of relative reproductive success (RRS) to include two full generations and used generalized linear models to determine if origin (hatchery or natural) or phenotypic traits (timing of arrival to spawning grounds, body length, and age) significantly predicted reproductive success (RS) across multiple years. Our results provide evidence that this supplementation program with 100% natural-origin broodstock provided a long-term demographic boost to the population (mean of 4.56 times in the 1st generation and mean of 2.52 times in the 2nd generation). Overall when spawning in nature, hatchery-origin fish demonstrated a trend towards lower RS compared to natural-origin fish (p<0.05). However, when hatchery-origin fish successfully spawned with natural-origin fish, they had similar RS compared to natural by natural crosses (1st generation mean hatchery by natural cross RRS = 1.11 females, 1.13 males; 2nd generation mean hatchery by natural cross RRS = 1.03 females, 1.08 males). While origin, return year, and body length were significant predictors of fitness for both males and females (p<0.05), return day was significant for males but not females (p>0.05). These results indicate that supplementation programs that reduce the potential for genetic adaptation to captivity can be effective at increasing population abundance while limiting long-term fitness effects on wild populations.
Data from: Sexual selection has minimal impact on effective population sizes in species with high rates of random offspring mortality: an empirical demonstration using fitness distributions
The effective population size (Ne) is a fundamental parameter in population genetics that influences the rate of loss of genetic diversity. Sexual selection has the potential to reduce Ne by causing the sex-specific distributions of individuals that successfully reproduce to diverge. To empirically estimate the effect of sexual selection on Ne, we obtained fitness distributions for males and females from an outbred, laboratory-adapted population of Drosophila melanogaster. We observed strong sexual selection in this population (the variance in male reproductive success was ∼14 times higher than that for females), but found that sexual selection had only a modest effect on Ne, which was 75% of the census size. This occurs because the substantial random offspring mortality in this population diminishes the effects of sexual selection on Ne, a result that necessarily applies to other high fecundity species. The inclusion of this random offspring mortality creates a scaling effect that reduces the variance/mean ratios for male and female reproductive success and causes them to converge. Our results demonstrate that measuring reproductive success without considering offspring mortality can underestimate Ne and overestimate the genetic consequences of sexual selection. Similarly, comparing genetic diversity among different genomic components may fail to detect strong sexual selection.
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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.