scholarly journals Integrating ecological genomics and eco-evo-devo reveals multiple adaptive peaks in ant populations of the Arizona Sky Islands

2016 ◽  
Author(s):  
Marie-Julie Favé ◽  
Ehab Abouheif
Keyword(s):  
Fitness Landscape ◽  
Single Species ◽  
Evolutionary Developmental Biology ◽  
High Elevation ◽  
Climatic Changes ◽  
Temperature Adaptation ◽  
Sky Islands ◽  
Ecological Genomics ◽  
Ecological Gradient ◽  
Phenotypic Differences

Uncovering the genetic basis of adaptation is a great challenge facing evolutionary biologists. We ask where is the locus of adaptation from the perspective of ecological genomics (ecogen) and evolutionary developmental biology (evodevo). Ecogen focuses on identifying loci under selection between populations in different environments by scanning genome-wide patterns of genetic divergence, while evodevo focuses on candidate developmental regulatory genes and networks underlying phenotypic differences between species and higher taxa. We attempt to reconcile these different perspectives by studying the response of ant populations to past climate change on the Arizona Sky Islands - high elevation mountain ranges that represent a replicated natural experiment. We previously used an evodevo approach to show that adaptation to climatic changes in the Arizona Sky Islands in the ant species Monomorium emersoni occurred through repeated changes within the gene network underlying the development of alternative dispersal phenotypes: winged and wingless queens. Here, using an ecogen approach we uncovered several loci under positive selection that associate with habitat temperature. These temperatureassociated loci show a repeated increase in frequency following climatic changes on each of the Sky Islands. Surprisingly, gene flow between locations within a Sky Island is restricted by temperature adaptation along the ecological gradient and not by dispersal phenotype. This finding suggests that determination of winged and wingless queens may be developmentally plastic, and this plasticity may facilitate jumps between adaptive peaks on a fitness landscape. Integration of evodevo and ecogen reveals multiple adaptive peaks and predictability at multiple biological levels within a single species.

Productivity, resource use, and competitive interactions of Fraxinus uhdei in Hawaii uplands

2001 ◽  
Vol 31 (1) ◽  
pp. 132-142 ◽  
Author(s):  
Adrián Ares ◽  
James H Fownes
Keyword(s):  
Leaf Area ◽  
Resource Use ◽  
Basal Area ◽  
Single Species ◽  
High Elevation ◽  
Mixed Stands ◽  
Canopy Development ◽  
Intrinsic Water Use Efficiency ◽  
Use Efficiency ◽  
Stand Basal Area

We examined stand growth, canopy development, and resource use of Fraxinus uhdei (Wenzig) Lingelsh, a nonindigenous tree grown in Hawaii, and its interactions with the native, N-fixing tree Acacia koa Gray. Along a gradient of decreasing rainfall with elevation, on Histosols, F. uhdei had decreased stand basal area, productivity, and canopy development. At high-elevation sites, productivity of F. uhdei was limited by N, and F. uhdei benefitted from association with A. koa, as (i) foliar N content of F. uhdei was positively related to aboveground net primary productivity (ANPP), (ii) leaf area index, biomass increment, and ANPP of F. uhdei increased in a single-species stand after N additions, but there was no response by either F. uhdei or A. koa in a mixed stand, and (iii) productivity of F. uhdei in mixed stands with A. koa at high-elevation sites was greater than in single-species stands, and F. uhdei foliage was enriched with N in proportion to the fraction of stand basal area in A. koa. Seemingly, growth of F. uhdei on Histosols was also limited by water availability, as an index of carbon isotope composition of leaves (δ13C), and, therefore, intrinsic water-use efficiency (WUE) increased with elevation. Biomass production of F. uhdei stands per unit leaf area and per unit intercepted radiation (ε) decreased with increasing elevation on Histosols. Decreased nitrogen-use efficiency and ε of F. uhdei on Histosols were both traded off against increased WUE.

scholarly journals Identifying biochemical phenotypic differences between cryptic species

2014 ◽  
Vol 10 (9) ◽  
pp. 20140615 ◽  
Author(s):  
Manuel Liebeke ◽  
Michael W. Bruford ◽  
Robert K. Donnelly ◽  
Timothy M. D. Ebbels ◽  
Jie Hao ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Molecular Genetic ◽  
Single Species ◽  
Functional Trait ◽  
Species Group ◽  
Lumbricus Rubellus ◽  
Phenotypic Differences ◽  
Functional Differences ◽  
High Concentrations ◽  
Metabolomic Approach

Molecular genetic methods can distinguish divergent evolutionary lineages in what previously appeared to be single species, but it is not always clear what functional differences exist between such cryptic species. We used a metabolomic approach to profile biochemical phenotype (metabotype) differences between two putative cryptic species of the earthworm Lumbricus rubellus . There were no straightforward metabolite biomarkers of lineage, i.e. no metabolites that were always at higher concentration in one lineage. Multivariate methods, however, identified a small number of metabolites that together helped distinguish the lineages, including uncommon metabolites such as N ε-trimethyllysine, which is not usually found at high concentrations. This approach could be useful for characterizing functional trait differences, especially as it is applicable to essentially any species group, irrespective of its genome sequencing status.

Deep Divergences within Liolaemus nigroviridis (Squamata, Liolaemidae) Lineages Associated with Sky Islands in Central Chile

Zootaxa ◽  
2013 ◽  
Vol 3619 (1) ◽  
pp. 59-69 ◽  
Author(s):  
FRANCO CIANFERONI ◽  
ROMINA P. YÁÑEZ ◽  
R. EDUARDO PALMA ◽  
CARLOS F. GARIN ◽  
FERNANDO TORRES-PÉREZ
Keyword(s):  
Genetic Divergence ◽  
Common Ancestor ◽  
High Elevation ◽  
Recent Common Ancestor ◽  
Gene Exchange ◽  
Sky Islands ◽  
Central Chile ◽  
Allopatric Populations ◽  
Most Recent Common Ancestor ◽  
Mitochondrial Cytochrome B

Evolution of montane species may be strongly influenced by climate oscillations, particularly species distributed in isolated high-elevation areas (sky islands). Chilean topography is exemplified by montane environments including the Andesand CoastalMountains. To test hypotheses related to genetic divergence associated with sky islands, we explored population genetics and phylogenetic signatures in the montane lizard Liolaemus nigroviridis Müller and Hellmich 1932. We sequenced the mitochondrial cytochrome b for samples collected from six montane areas in central Chile. We found high genetic divergence among populations, congruent with well-supported clades from phylogeny reconstructions. The most recent common ancestor of all samples of L. nigroviridis was dated around the limit of Pliocene-Pleistocene (2.7 Mya), congruent with early vicariance of Andean and coastal populations. Deep lineage divergences suggest that allopatric populations accumulated high nucleotide differences and maintained long periods without gene exchange. We discuss potential taxonomic revisions considering relative genetic divergence.

scholarly journals Multiple data revealed two new species of the Asian horned toad Megophrys Kuhl & Van Hasselt, 1822 (Anura, Megophryidae) from the eastern corner of the Himalayas

ZooKeys ◽  
2020 ◽  
Vol 977 ◽  
pp. 101-161
Author(s):  
Shengchao Shi ◽  
Meihua Zhang ◽  
Feng Xie ◽  
Jianping Jiang ◽  
Wulin Liu ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Evolutionary History ◽  
Molecular Phylogenetics ◽  
Nuclear Dna ◽  
Incomplete Lineage Sorting ◽  
High Elevation ◽  
Climatic Changes ◽  
Lineage Sorting ◽  
Multiple Data ◽  
Tibet Autonomous Region

Multiple disciplines can help to discover cryptic species and resolve taxonomic confusions. The Asian horned toad genus Megophryssensu lato as a diverse group was proposed to contain dozens of cryptic species. Based on molecular phylogenetics, morphology, osteology, and bioacoustics data, the species profiles of Megophrys toads in the eastern corner of Himalayas in Medog County, Tibet Autonomous Region, China was investigated. The results indicated that this small area harbored at least four Megophrys species, i.e., M. medogensis, M. pachyproctus, Megophrys zhouisp. nov., and Megophrys yeaesp. nov., the latter two being described in this study. Additionally, the mitochondrial DNA trees nested the low-middle-elevation and high-elevation groups of M. medogensis into a monophyletic group, being in discordance with the paraphyletic relationship between them revealed in the nuclear DNA trees. The findings highlighted the underestimated biodiversity in Himalayas, and further indicated that the Megophrys toads here have been probably experienced complicated evolutionary history, for example, introgression between clades or incomplete lineage sorting and niche divergences in microhabitats. Anyway, it is urgent for us to explore the problems because these toads are suffering from increasing threats from human activities and climatic changes.

scholarly journals Genetic studies of human–chimpanzee divergence using stem cell fusions

2021 ◽  
Vol 118 (51) ◽  
pp. e2117557118
Author(s):  
Janet H. T. Song ◽  
Rachel L. Grant ◽  
Veronica C. Behrens ◽  
Marek Kučka ◽  
Garrett A. Roberts Kingman ◽  
...  
Keyword(s):  
X Chromosome ◽  
Expression Patterns ◽  
Single Species ◽  
Regulation Of Expression ◽  
Phenotypic Differences ◽  
Chemical Treatments ◽  
Genome Wide ◽  
Induced Pluripotent ◽  
Species Specific ◽  
Nested Deletions

Complete genome sequencing has identified millions of DNA changes that differ between humans and chimpanzees. Although a subset of these changes likely underlies important phenotypic differences between humans and chimpanzees, it is currently difficult to distinguish causal from incidental changes and to map specific phenotypes to particular genome locations. To facilitate further genetic study of human–chimpanzee divergence, we have generated human and chimpanzee autotetraploids and allotetraploids by fusing induced pluripotent stem cells (iPSCs) of each species. The resulting tetraploid iPSCs can be stably maintained and retain the ability to differentiate along ectoderm, mesoderm, and endoderm lineages. RNA sequencing identifies thousands of genes whose expression differs between humans and chimpanzees when assessed in single-species diploid or autotetraploid iPSCs. Analysis of gene expression patterns in interspecific allotetraploid iPSCs shows that human–chimpanzee expression differences arise from substantial contributions of both cis-acting changes linked to the genes themselves and trans-acting changes elsewhere in the genome. To enable further genetic mapping of species differences, we tested chemical treatments for stimulating genome-wide mitotic recombination between human and chimpanzee chromosomes, and CRISPR methods for inducing species-specific changes on particular chromosomes in allotetraploid cells. We successfully generated derivative cells with nested deletions or interspecific recombination on the X chromosome. These studies confirm an important role for the X chromosome in trans regulation of expression differences between species and illustrate the potential of this system for more detailed cis and trans mapping of the molecular basis of human and chimpanzee evolution.

The effects of season, sex and habitat on the diet of the mountain pygmy-possum (Burramys parvus)

1992 ◽  
Vol 19 (6) ◽  
pp. 755 ◽  
Author(s):  
AP Smith ◽  
L Broome
Keyword(s):  
Relative Proportion ◽  
Late Summer ◽  
Single Species ◽  
High Elevation ◽  
Seasonal Migration ◽  
Seasonal Movement ◽  
Spatial And Seasonal Variation ◽  
Migration Corridors ◽  
Lower Elevation ◽  
Australian Alps

The mountain pygmy-possum (Burramys parvus) is a rare marsupial (approximately 2300 individuals) with a restricted distribution (10 km*3 confined to isolated patches of heath in the Australian Alps that are vulnerable to clearing and modification for ski-run development. In Mt Kosciusko National Park the diet of Burramys averaged 71% arthropods, 27% seeds and berries, and 2% other material. The diversity of arthropod prey was low and dominated by a single species, Agrotis infusa (the Bogong moth). The diversity of seed and berry intake was high (8 species) and dominated by the seed and fruit of Podocarpus lawrencei (8%) and fruit of Leucopogon montanus. The relative proportion of arthropod to seed and berry in the diet changed significantly with sex, age, reproductive state, body weight, season, elevation and habitat (Podocarpus lawrencei cover, boulder cover and moth abundance). Females had a higher intake of arthropod than males in all seasons and locations. This result is consistent with their higher protein requirement for reproduction and the need to ensure that young grow rapidly enough to gain sufficient weight to survive their first winter in hibernation. Patterns of spatial and seasonal variation in food availability explain the unique patterns of sexual segregation and daily and/or seasonal migration exhibited by Burramys. Nightly or seasonal movement is necessary to optimise exploitation of Bogong moths on high-elevation peaks in summer and seeds and berries in lower-elevation heaths during late summer and early autumn. These results signify the importance of protecting migration corridors along boulder screes, between low- and high-elevation habitats, from destruction or modification during ski-run development.

scholarly journals CAPRIB: a user-friendly tool to study amino acid changes and selection for the exploration of intra-genus evolution

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Juan F. Guerra Maldonado ◽  
Antony T. Vincent ◽  
Martin Chenal ◽  
Frederic J. Veyrier
Keyword(s):  
Amino Acid ◽  
Single Species ◽  
Graphical Interface ◽  
Genetic Changes ◽  
Phenotypic Differences ◽  
Phenotypic Divergence ◽  
Potential Impact ◽  
Evolutionary Paths ◽  
User Friendly ◽  
Slow Growing

Abstract Background The evolution of bacteria is shaped by different mechanisms such as mutation, gene deletion, duplication, or insertion of foreign DNA among others. These genetic changes can accumulate in the descendants as a result of natural selection. Using phylogeny and genome comparisons, evolutionary paths can be somehow retraced, with recent events being much easier to detect than older ones. For this reason, multiple tools are available to study the evolutionary events within genomes of single species, such as gene composition alterations, or subtler mutations such as SNPs. However, these tools are generally designed to compare similar genomes and require advanced skills in bioinformatics. We present CAPRIB, a unique tool developed in Java that allows to determine the amino acid changes, at the genus level, that correlate with phenotypic differences between two groups of organisms. Results CAPRIB has a user-friendly graphical interface and uses databases in SQL, making it easy to compare several genomes without the need for programming or thorough knowledge in bioinformatics. This intuitive software narrows down a list of amino acid changes that are concomitant with a given phenotypic divergence at the genus scale. Each permutation found by our software is associated with two already described statistical values that indicate its potential impact on the protein’s function, helping the user decide which promising candidates to further investigate. We show that CAPRIB is able to detect already known mutations and uncovers many more, and that this tool can be used to question molecular phylogeny. Finally, we exemplify the utility of CAPRIB by pinpointing amino acid changes that coincided with the emergence of slow-growing mycobacteria from their fast-growing counterparts. The software is freely available at https://github.com/BactSymEvol/Caprib. Conclusions CAPRIB is a new bioinformatics software aiming to make genus-scale comparisons accessible to all. With its intuitive graphical interface, this tool identifies key amino acid changes concomitant with a phenotypic divergence. By comparing fast and slow-growing mycobacteria, we shed light on evolutionary hotspots, such as the cytokinin pathway, that are interesting candidates for further experimentations.

scholarly journals Patterns of floral allocation along an elevation gradient: variation in Senecio subalpinus growing in the Tatra Mountains

Alpine Botany ◽  
2021 ◽  
Vol 131 (1) ◽  
pp. 117-124
Author(s):  
Piotr Kiełtyk
Keyword(s):  
Elevation Gradient ◽  
High Elevation ◽  
Tatra Mountains ◽  
Ecological Gradient ◽  
Elevation Gradients ◽  
Allocation Patterns ◽  
Abiotic And Biotic Factors ◽  
Elevational Shift ◽  
The Tatra Mountains ◽  
Gradient Variation

AbstractThis study examined the morphological variation in Senecio subalpinus W.D.J. Koch. (Asteraceae) along a 950-m elevation gradient in the Tatra Mountains, Central Europe, with emphasis on floral allocation patterns. Fifteen morphological traits were measured in 200 plants collected in the field from 20 sites then the findings were modelled by elevation using linear mixed-effects models. Plant aboveground biomass and height decreased steadily with increasing elevation; however, the most distinctive feature was the elevational shift in floral allocation patterns. Low-elevation plants had greater numbers of smaller flower heads with a lower overall number of flowers, while high-elevation plants had smaller numbers of bigger flower heads and a greater overall number of flowers. Accordingly, the mean individual flower mass increased significantly with increasing elevation. Interestingly, the width of the outer ligulate flowers also increased considerably with increasing elevation, increasing the fill of the overall circumference of the flower head. Results of this study confirmed that elevation is an important ecological gradient driving variation in vegetative and floral traits of S. subalpinus. Possible causes of the observed variations are subsequently discussed, including the varying effects of both abiotic and biotic factors with elevation gradients.

scholarly journals Turnover of Lecanoroid Mycobionts and Their Trebouxia Photobionts Along an Elevation Gradient in Bolivia Highlights the Role of Environment in Structuring the Lichen Symbiosis

2021 ◽  
Vol 12 ◽  
Author(s):  
Ian D. Medeiros ◽  
Edyta Mazur ◽  
Jolanta Miadlikowska ◽  
Adam Flakus ◽  
Pamela Rodriguez-Flakus ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Species Turnover ◽  
Elevation Gradient ◽  
Single Species ◽  
High Elevation ◽  
Regional Patterns ◽  
Elevation Gradients ◽  
Clade C ◽  
Community Shifts ◽  
Molecular Dataset

Shifts in climate along elevation gradients structure mycobiont–photobiont associations in lichens. We obtained mycobiont (lecanoroid Lecanoraceae) and photobiont (Trebouxia alga) DNA sequences from 89 lichen thalli collected in Bolivia from a ca. 4,700 m elevation gradient encompassing diverse natural communities and environmental conditions. The molecular dataset included six mycobiont loci (ITS, nrLSU, mtSSU, RPB1, RPB2, and MCM7) and two photobiont loci (ITS, rbcL); we designed new primers to amplify Lecanoraceae RPB1 and RPB2 with a nested PCR approach. Mycobionts belonged to Lecanora s.lat., Bryonora, Myriolecis, Protoparmeliopsis, the “Lecanora” polytropa group, and the “L.” saligna group. All of these clades except for Lecanora s.lat. occurred only at high elevation. No single species of Lecanoraceae was present along the entire elevation gradient, and individual clades were restricted to a subset of the gradient. Most Lecanoraceae samples represent species which have not previously been sequenced. Trebouxia clade C, which has not previously been recorded in association with species of Lecanoraceae, predominates at low- to mid-elevation sites. Photobionts from Trebouxia clade I occur at the upper extent of mid-elevation forest and at some open, high-elevation sites, while Trebouxia clades A and S dominate open habitats at high elevation. We did not find Trebouxia clade D. Several putative new species were found in Trebouxia clades A, C, and I. These included one putative species in clade A associated with Myriolecis species growing on limestone at high elevation and a novel lineage sister to the rest of clade C associated with Lecanora on bark in low-elevation grassland. Three different kinds of photobiont switching were observed, with certain mycobiont species associating with Trebouxia from different major clades, species within a major clade, or haplotypes within a species. Lecanoraceae mycobionts and Trebouxia photobionts exhibit species turnover along the elevation gradient, but with each partner having a different elevation threshold at which the community shifts completely. A phylogenetically defined sampling of a single diverse family of lichen-forming fungi may be sufficient to document regional patterns of Trebouxia diversity and distribution.

scholarly journals Artificial intelligence reveals environmental constraints on colour diversity in insects

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Shipher Wu ◽  
Chun-Min Chang ◽  
Guan-Shuo Mai ◽  
Dustin R. Rubenstein ◽  
Chen-Ming Yang ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Deep Learning ◽  
Structural Equation ◽  
Feature Vector ◽  
High Elevation ◽  
Image Feature ◽  
Equation Modeling ◽  
Ecological Gradient ◽  
Biogeographic Pattern ◽  
Underlying Mechanisms

Abstract Explaining colour variation among animals at broad geographic scales remains challenging. Here we demonstrate how deep learning—a form of artificial intelligence—can reveal subtle but robust patterns of colour feature variation along an ecological gradient, as well as help identify the underlying mechanisms generating this biogeographic pattern. Using over 20,000 images with precise GPS locality information belonging to nearly 2,000 moth species from Taiwan, our deep learning model generates a 2048-dimension feature vector that accurately predicts each species’ mean elevation based on colour and shape features. Using this multidimensional feature vector, we find that within-assemblage image feature variation is smaller in high elevation assemblages. Structural equation modeling suggests that this reduced image feature diversity is likely the result of colder environments selecting for darker colouration, which limits the colour diversity of assemblages at high elevations. Ultimately, with the help of deep learning, we will be able to explore the endless forms of natural morphological variation at unpreceded depths.

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