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35 results for “ecological constraints”
Supporting Data from Ecological Opportunities and Constraints in the Evolution of Diatoms
<p>2016-02-01<br /> Teofil Nakov</p> <p>Data and code for Nakov, Ruck, Alverson: Ecological opportunities and constraints in the evolution of diatom</p> <p>This packet contains the following files:</p> <p>1. Sequence alignment for 540 diatoms and 2 Bolidomonas: Nakov-etal-542-taxon-alignment-clean.fasta<br /> 2. The constraint topology used in tree searches: Nakov-etal-constraint-small-clades.phylip<br /> 3. Alignment partition file: Nakov-etal-tiger-partitions-rax<br /> 4. Character data for 540 diatoms and 2 Bolidomonas: Nakov-etal-542-taxon-discrete-characters.csv<br /> 5. The best tree from 420 RAxML optimizations: Nakov-etal-RAxML_bestTree.opt_89<br /> 6. 99 additional trees used in the analyses: Nakov-etal-99-randomly-sampled-unique-trees.newick<br /> 7. All 100 trees converted into chronograms: Nakov-etal-100-chronograms-smooth-1000.newick<br /> 8. Script with random seeds for RAxML optimizations: Nakov-etal-RAxML-calls-for-420-optimizations<br /> 9. R scripts with random seeds: Nakov-etal-R-scripts.zip (three scripts: equal-rates, independent, and coordinated + paint regimes models)<br /> 10. TreePL control file: Nakov-etal-TreePL-control-file.txt</p>
Universal metabolic constraints shape the evolutionary ecology of diving in animals
<p>Diving as a lifestyle has evolved on multiple occasions when air-breathing terrestrial animals invaded the aquatic realm, and diving performance shapes the ecology and behaviour of all air-breathing aquatic taxa, from small insects to great whales. Using the largest dataset yet assembled, we show that maximum dive duration increases predictably with body mass in both ectotherms and endotherms. Compared to endotherms, ectotherms can remain submerged for longer, but the mass scaling relationship for dive duration is much steeper in endotherms than in ectotherms. These differences in diving allometry can be fully explained by inherent differences between the two groups in their metabolic rate and how metabolism scales with body mass and temperature. Therefore, we suggest that similar constraints on oxygen storage and usage have shaped the evolutionary ecology of diving in all air-breathing animals, irrespective of their evolutionary history and metabolic mode. The steeper scaling relationship between body mass and dive duration in endotherms not only helps explain why the largest extant vertebrate divers are endothermic rather than ectothermic, but also fits well with the emerging consensus that large extinct tetrapod divers (e.g. plesiosaurs, ichthyosaurs and mosasaurs) were endothermic.</p>
Olfactory receptor alignments for: Ecological constraints on highly evolvable olfactory receptor genes and morphology in neotropical bats
<p>While evolvability of genes and traits may promote specialization during species diversification, how ecology subsequently restricts such variation remains unclear. Chemosensation requires animals to decipher a complex chemical background to locate fitness-related resources, and thus the underlying genomic architecture and morphology must cope with constant exposure to a changing odorant landscape; detecting adaptation amidst extensive chemosensory diversity is an open challenge. In phyllostomid bats, an ecologically diverse clade that evolved plant-visiting from an insectivorous ancestor, the evolution of novel food detection mechanisms is suggested to be a key innovation, as plant-visiting species rely strongly on olfaction, supplementarily using echolocation. If this is true, exceptional variation in underlying olfactory genes and phenotypes may have preceded dietary diversification. We compared olfactory receptor (OR) genes sequenced from olfactory epithelium transcriptomes and olfactory epithelium surface area of bats with differing diets. Surprisingly, although OR evolution rates were quite variable and generally high, they are largely independent of diet. Olfactory epithelial surface area, however, is relatively larger in plant-visiting bats and there is an inverse relationship between OR evolution rates and surface area. Relatively larger surface areas suggest greater reliance on olfactory detection and stronger constraint on maintaining an already diverse OR repertoire. Instead of the typical case in which specialization and elaboration are coupled with rapid diversification of associated genes, here the relevant genes are already evolving so quickly that increased reliance on smell has led to stabilizing selection, presumably to maintain the ability to consistently discriminate among specific odorants — a potential ecological constraint on sensory evolution.</p>
Olfactory receptor alignments for: Ecological constraints on highly evolvable olfactory receptor genes and morphology in neotropical bats
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Universal metabolic constraints shape the evolutionary ecology of diving in animals
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Data from: Evolutionary constraint on low elevation range expansion: defense-abiotic stress tolerance tradeoff in crosses of the ecological model Boechera stricta
Most transplant experiments across species geographic range boundaries indicate that adaptation to stressful environments outside the range is often constrained. However, the mechanisms of these constraints remain poorly understood. We used extended generation crosses from diverged high and low elevation populations. In experiments across low elevation range boundaries, there was selection on the parental lines for abiotic stress tolerance and resistance to herbivores. However, in support of a defense-tolerance tradeoff, extended generation crosses showed non-independent segregation of these traits in the lab across a drought-stress gradient and in the field across the low elevation range boundary. Genotypic variation in a marker from a region of the genome containing a candidate gene (MYC2) was associated with change in the genetic tradeoff. Thus, using crosses and forward genetics, we found experimental genetic and molecular evidence for a pleiotropic tradeoff that could constrain the evolution of range expansion.
Data from: Quantifying the effects of ecological constraints on trait expression using novel trait-gradient analysis parameters
1. Complex processes related to biotic and abiotic forces can impose limitations to assembly and composition of plant communities. Quantifying the effects of these constraints on plant functional traits across environmental gradients, and among communities, remains challenging. We define ecological constraint (Ci) as the combined, limiting effect of biotic interactions and environmental filtering on trait expression (i.e., the mean value and range of functional traits). 2. Here we propose a set of novel parameters to quantify this constraint by extending the trait-gradient analysis (TGA) methodology. The key parameter is ecological constraint, which is dimensionless and can be measured at various scales, e.g., on population and community levels. It facilitates comparing the effects of ecological constraints on trait expressions across environmental gradients, as well as within and among communities. 3. We illustrate the implementation of the proposed parameters using the bark thickness of 14 woody species along an aridity gradient on granite outcrops in southwestern Australia. We found a positive correlation between increasing environmental stress and strength of ecological constraint on bark thickness expression. Also, plants from more stressful habitats (shrublands on shallow soils and in sun-exposed locations) displayed higher ecological constraint for bark thickness than plants in more benign habitats (woodlands on deep soils and in sheltered locations). 4. The relative ease of calculation and dimensionless nature of Ci allow it to be readily implemented at various scales and make it widely applicable. It therefore has the potential to advance the mechanistic understanding of the ecological processes shaping trait expression. Some future applications of the new parameters could be investigating the patterns of ecological constraints i) among communities from different regions, ii) on different traits across similar environmental gradients, and iii) for the same trait across different gradient-types.
Data from: Acoustic identification of Mexican bats based on taxonomic and ecological constraints on call design
Monitoring global biodiversity is critical for understanding responses to anthropogenic change, but biodiversity monitoring is often biased away from tropical, megadiverse areas that are experiencing more rapid environmental change. Acoustic surveys are increasingly used to monitor biodiversity change, especially for bats as they are important indicator species and most use sound to detect, localise and classify objects. However, using bat acoustic surveys for monitoring poses several challenges, particularly in megadiverse regions. Many species lack reference recordings, some species have high call similarity or differ in call detectability, and quantitative classification tools, such as machine learning algorithms, have rarely been applied to data from these areas. Here, we collate a reference call library for bat species that occur in a megadiverse country, Mexico. We use 4685 search-phase calls from 1378 individual sequences of 59 bat species to create automatic species identification tools generated by machine learning algorithms (Random Forest). We evaluate the improvement in species-level classification rates gained by using hierarchical classifications, reflecting either taxonomic or ecological constraints (guilds) on call design, and examine how classification rate accuracy changes at different hierarchical levels (family, genus and guild). Species-level classification of calls had a mean accuracy of 66%, and the use of hierarchies improved mean species-level classification accuracy by up to 6% (species within families 72%, species within genera 71·2% and species within guilds 69·1%). Classification accuracy to family, genus and guild-level was 91·7%, 77·8% and 82·5%, respectively. The bioacoustic identification tools we have developed are accurate for rapid biodiversity assessments in a megadiverse region and can also be used effectively to classify species at broader taxonomic or ecological levels. This flexibility increases their usefulness when there are incomplete species reference recordings and also offers the opportunity to characterise and track changes in bat community structure. Our results show that bat bioacoustic surveys in megadiverse countries have more potential than previously thought to monitor biodiversity changes and can be used to direct further developments of bioacoustic monitoring programs in Mexico.
Data from: Causes and consequences of failed adaptation to biological invasions: the role of ecological constraints
Biological invasions are a major challenge to native communities and have the potential to exert strong selection on native populations. As a result, native taxa may adapt to the presence of invaders through increased competitive ability, increased antipredator defences or altered morphologies that may limit encounters with toxic prey. Yet, in some cases, species may fail to adapt to biological invasions. Many challenges to adaptation arise because biological invasions occur in complex species-rich communities in spatially and temporally variable environments. Here, we review these 'ecological' constraints on adaptation, focusing on the complications that arise from the need to simultaneously adapt to multiple biotic agents and from temporal and spatial variation in both selection and demography. Throughout, we illustrate cases where these constraints might be especially important in native populations faced with biological invasions. Our goal was to highlight additional complexities empiricists should consider when studying adaptation to biological invasions and to begin to identify conditions when adaptation may fail to be an effective response to invasion.
Data from: The evolution of life cycle complexity in aphids: ecological optimization, or historical constraint?
For decades, biologists have debated why many parasites have obligate multi-host life cycles. Here, we use comparative phylogenetic analyses of aphids to evaluate the roles of ecological optimization and historical constraint in the evolution of life cycle complexity. If life cycle complexity is adaptive, it should be evolutionarily labile, i.e., change in response to selection. We provide evidence that this is true in some aphids (aphidines), but not others (non-aphidines) – groups that differ in the intensity of their relationships with primary hosts. Next, we test specific mechanisms by which life cycle complexity could be adaptive or a constraint. We find that among aphidines there is a strong association between complex life cycles and polyphagy but only a weak correlation between life cycle complexity and reproductive mode. In contrast, among non-aphidines the relationship between life cycle complexity and host breadth is weak but the association between complex life cycles and sexual reproduction is strong. Thus, although the adaptiveness of life cycle complexity appears to be lineage specific, across aphids, life cycle evolution appears to be tightly linked with the evolution of other important natural history traits.
The functional diversity of marsupial limbs is influenced by both ecology and developmental constraint
<p>Extant marsupials are less ecologically diverse than placentals, and this is reflected by placentals exhibiting a greater diversity of locomotor modes, including powered flight and fully aquatic swimming. One proposed explanation for this discrepancy is that the development of more disparate marsupial forelimbs is prevented by the neonate's crawl to the pouch, which requires precocious forelimb development for climbing adaptations. To test predictions of this Developmental Constraint Hypothesis, we pursue a comparative morphometric study on osteological traits of mammalian limbs, with an emphasis on functional differentiation of marsupial limbs among locomotor modes. We apply multivariate analyses to a large dataset of limb metrics and a diverse sample of mammals, with the placental sample limited to taxa whose locomotor modes are exhibited in marsupials. Overall, we do not find consistent evidence in support of the Developmental Constraint Hypothesis. Diprotodontia serves as an exception, with comparisons of their forelimbs to hind limbs supporting the Developmental Constraint Hypothesis. Our results suggest that developmental constraints on marsupial forelimbs may have limited marsupial diversity to some degree. Despite this, the marsupial locomotor groups show unexpectedly high levels of morphological differentiation relative to placentals of the same locomotor modes, indicating that ecological functions may overcome developmental constraints on a macroevolutionary scale.</p>
Dataset for the manuscript: Phylogenetic and functional constraints of plant facilitation rewiring. ECOLOGY
<p>The following directory contains the data necessary to replicate the results obtained in the manuscript entitled: <strong>Phylogenetic and functional constraints of plant facilitation rewiring</strong></p> <p>We provided two spreadsheets containing the data "Adult species data" and "Interactions data.xlsx". Each archive contains a readme textbox with detailed information on the variables included in the archives</p>
How long is 3 kilometres for a butterfly? Ecological constraints and functional traits explain high mitochondrial genetic diversity between Sicily and the Italian Peninsula
<p>1. Populations inhabiting Mediterranean islands often show contrasting genetic lineages, even on islands that were connected to the mainland during glacial maxima. This pattern is generated by forces acting in historical and contemporary times. Understanding these phenomena requires comparative studies relating genetic structure, functional traits and dispersal constraints.</p> <p>2. Using as a model the butterfly species living across the Messina strait separating Sicily from the Italian Peninsula (3 km wide), we aimed to unravel the mechanisms limiting the dispersal of matrilines across a narrow sea strait and producing genetic differentiation. </p> <p>3. We analysed the mitochondrial COI gene of 84 butterfly species out of 90 documented in Sicily and compared them with populations from the neighbouring southern Italian Peninsula (1398 sequences) and from the entire Palearctic region (8093 sequences). For each species, we regressed 13 functional traits and two ecological constraints to dispersal (winds experienced at the strait and climatic suitability) against genetic differentiation between Sicily and Italian Peninsula to understand the factors limiting dispersal.</p> <p>4. More than a third of the species showed different haplogroups across the strait and most of them also represented endemic haplogroups for this island. One fifth of Sicilian populations (and 32.3% of endemic lineages) had their closest relatives in distant areas, instead of the neighbouring Italian Peninsula, which suggests high relictuality. Haplotype diversity was significantly explained by length of the flight period, an intrinsic phenology trait, while genetic differentiation was explained by both intrinsic traits (wingspan and degree of generalism) and contemporary local constraints (winds experienced at the strait and climatic suitability).</p> <p>5. A relatively narrow sea strait can produce considerable differentiation among butterfly matrilines and this phenomenon showed a largely deterministic fingerprint. Because of unfavourable winds, populations of the less dispersive Sicilian butterflies tended to differentiate into endemic variants or to maintain relict populations. Understanding these phenomena required the integration of DNA sequences, species traits and physical constraints for a large taxon at continental scale. Future studies may reveal if the patterns here shown for mitochondrial DNA are also reflected in the nuclear genome or, alternatively, are the product of limited female dispersal.</p>
Data from: Parentage analysis of Ansell's mole-rat family groups indicates a high reproductive skew despite relatively relaxed ecological constraints on dispersal
To better understand evolutionary pathways leading to eusociality, interspecific comparisons are needed, which would use a common axis, such as that of reproductive skew, to array species. African mole-rats (Bathyergidae, Rodentia) provide an outstanding model of social evolution because of a wide range of social organizations within a single family; however, their reproductive skew is difficult to estimate, due to their cryptic lifestyle. A maximum skew could theoretically be reached in groups where reproduction is monopolized by a stable breeding pair, but the value could be decreased by breeding-male and breeding-female turnover, shared reproduction and extra-group mating. The frequency of such events should be higher in species or populations inhabiting mesic environments with relaxed ecological constraints on dispersal. To test this prediction, we studied patterns of parentage and relatedness within 16 groups of Ansell's mole-rat (Fukomys anselli) in mesic miombo woodland. Contrary to expectation, there was no shared reproduction (more than one breeder of a particular sex) within the studied groups, and proportion of immigrants and offspring not assigned to current breeding males was low. The within-group parentage and relatedness patterns observed resemble arid populations of 'eusocial' Fukomys damarensis, rather than a mesic population of 'social' Cryptomys hottentotus. As a possible explanation, we propose that the extent ecological conditions affect reproductive skew may be markedly affected by life history and natural history traits of the particular species and genera.
Data from: Quantifying the effects of ecological constraints on trait expression using novel trait-gradient analysis parameters
Open the record for dataset details and reuse information.
Data from: The evolution of life cycle complexity in aphids: ecological optimization, or historical constraint?
Open the record for dataset details and reuse information.
Data from: Parentage analysis of Ansell's mole-rat family groups indicates a high reproductive skew despite relatively relaxed ecological constraints on dispersal
Open the record for dataset details and reuse information.
How long is 3 kilometres for a butterfly? Ecological constraints and functional traits explain high mitochondrial genetic diversity between Sicily and the Italian Peninsula
Open the record for dataset details and reuse information.
Data from: Acoustic identification of Mexican bats based on taxonomic and ecological constraints on call design
Open the record for dataset details and reuse information.
The functional diversity of marsupial limbs is influenced by both ecology and developmental constraint
Open the record for dataset details and reuse information.
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