scholarly journals Growth rate as a modulator of tooth patterning during adaptive radiations

2021 ◽  
Author(s):  
Alexa Sadier ◽  
Neal Anthwal ◽  
Andrew L. Krause ◽  
Renaud Dessalles ◽  
Michael Lake ◽  
...  

The discovery of mechanistic rules that underlie phenotypic variation has been a longstanding goal of evolutionary biology. Developmental processes offer a potential source for such rules because they translate genomic variation into the population-scale phenotypic variation. However, our understanding of developmental rules is based on a handful of well-established model species which hindered identifying rules and investigating their evolution. Recent methodological advances, such as µCT scanning on soft tissues, two-photon imaging and modelling have facilitated the study of how developmental processes shape phenotypic variation in diverse, non-traditional model species. Here, we use the outstanding dental diversity of bats to investigate how the interplay between developmental processes can explain the morphological diversity in teeth. We find that the inhibitory cascade model, which has been used to predict the proportions of teeth and other serial organs, poorly predicts the variation in tooth number and size in bats. Instead, by tinkering with reaction/diffusion processes, we identify jaw growth as a key driver of the phenotypic evolution of tooth number and size critical to the different diets. By studying developmental processes in the context of adaptive evolution, we are able to discover a new developmental rule that explain and predict interspecific variation in serial organ number and proportion.

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kathleen M. S. A. Castro ◽  
Talita F. Amado ◽  
Miguel Á. Olalla-Tárraga ◽  
Sidney F. Gouveia ◽  
Carlos A. Navas ◽  
...  

AbstractThe origin of morphological diversity is a critical question in evolutionary biology. Interactions between the environment and developmental processes have determining roles in morphological diversity, creating patterns through space and over time. Also, the shape of organisms tends to vary with increasing size as a result of those developmental processes, known as allometry. Several studies have demonstrated that the body sizes of anurans are associated with hydric conditions in their environments and that localities with high water stress tend to select for larger individuals. However, how environmental conditions alter those patterns of covariance between size and shape is still elusive. We used 3D geometric morphometric analyses, associated with phylogenetic comparative methods, to determine if the morphological variations and allometric patterns found in Arboranae (Anura) is linked to water conservation mechanisms. We found effects of the hydric stress on the shape of Arboranae species, favouring globular shapes. Also, the allometric patterns varied in intensity according to the water stress gradient, being particularly relevant for smaller frogs, and more intense in environments with higher water deficits. Our study provides empirical evidence that more spherical body shapes, especially among smaller species, reflect an important adaptation of anurans to water conservation in water-constrained environments.


Nature Plants ◽  
2016 ◽  
Vol 2 (11) ◽  
Author(s):  
Xiangchao Gan ◽  
Angela Hay ◽  
Michiel Kwantes ◽  
Georg Haberer ◽  
Asis Hallab ◽  
...  

Abstract Finding causal relationships between genotypic and phenotypic variation is a key focus of evolutionary biology, human genetics and plant breeding. To identify genome-wide patterns underlying trait diversity, we assembled a high-quality reference genome of Cardamine hirsuta, a close relative of the model plant Arabidopsis thaliana. We combined comparative genome and transcriptome analyses with the experimental tools available in C. hirsuta to investigate gene function and phenotypic diversification. Our findings highlight the prevalent role of transcription factors and tandem gene duplications in morphological evolution. We identified a specific role for the transcriptional regulators PLETHORA5/7 in shaping leaf diversity and link tandem gene duplication with differential gene expression in the explosive seed pod of C. hirsuta. Our work highlights the value of comparative approaches in genetically tractable species to understand the genetic basis for evolutionary change.


2020 ◽  
Vol 130 (2) ◽  
pp. 239-246
Author(s):  
Rafael S Marcondes ◽  
Robb T Brumfield

Abstract Intraspecific geographic phenotypic variation is a crucial theme in evolutionary biology. Comparing its magnitude across species can provide insights into its ecological and genetic correlates. Here, we developed an index, which we dub the V index, to quantify intraspecific plumage colour variation in typical antbirds (Thamnophilidae), a family which has long interested ornithologists due to a high prevalence of intraspecific variation. The V index is based on a bivariate colour space defined by brightness and redness. Its value for each species equals the mean area occupied by each of its subspecies in that colour space, divided by the area of the species. Lower values indicate greater intraspecific geographic variation. Based on this index, Thamnophilus caerulescens (Variable Antshrike) was exceptionally geographically variable compared to other thamnophilids, as previously suggested based on qualitative evidence. In general, we found that the most variable species had disjunct distributions and deep phylogeographic structure, suggesting an effect of historical population dynamics in producing geographic variation. The V index can be adapted for use with other taxa, traits, and taxonomic levels, and we expect it will instigate novel ways of thinking about phenotypic variation in birds and other animals.


2020 ◽  
Vol 12 (6) ◽  
pp. 948-964
Author(s):  
Melissa B DeBiasse ◽  
William N Colgan ◽  
Lincoln Harris ◽  
Bradley Davidson ◽  
Joseph F Ryan

Abstract Tunicates, the closest living relatives of vertebrates, have served as a foundational model of early embryonic development for decades. Comparative studies of tunicate phylogeny and genome evolution provide a critical framework for analyzing chordate diversification and the emergence of vertebrates. Toward this goal, we sequenced the genome of Corella inflata (Ascidiacea, Phlebobranchia), so named for the capacity to brood self-fertilized embryos in a modified, “inflated” atrial chamber. Combining the new genome sequence for Co. inflata with publicly available tunicate data, we estimated a tunicate species phylogeny, reconstructed the ancestral Hox gene cluster at important nodes in the tunicate tree, and compared patterns of gene loss between Co. inflata and Ciona robusta, the prevailing tunicate model species. Our maximum-likelihood and Bayesian trees estimated from a concatenated 210-gene matrix were largely concordant and showed that Aplousobranchia was nested within a paraphyletic Phlebobranchia. We demonstrated that this relationship is not an artifact due to compositional heterogeneity, as had been suggested by previous studies. In addition, within Thaliacea, we recovered Doliolida as sister to the clade containing Salpida and Pyrosomatida. The Co. inflata genome provides increased resolution of the ancestral Hox clusters of key tunicate nodes, therefore expanding our understanding of the evolution of this cluster and its potential impact on tunicate morphological diversity. Our analyses of other gene families revealed that several cardiovascular associated genes (e.g., BMP10, SCL2A12, and PDE2a) absent from Ci. robusta, are present in Co. inflata. Taken together, our results help clarify tunicate relationships and the genomic content of key ancestral nodes within this phylogeny, providing critical insights into tunicate evolution.


2017 ◽  
Vol 284 (1860) ◽  
pp. 20171018 ◽  
Author(s):  
Yinan Hu ◽  
R. Craig Albertson

Understanding the developmental processes that underlie the production of adaptive variation (i.e. the ‘arrival of the fittest’) is a major goal of evolutionary biology. While most evo-devo studies focus on the genetic underpinnings of adaptive phenotypic variation, factors beyond changes in nucleotide sequence can also play a major role in shaping developmental outcomes. Here, we document a vigorous but enigmatic gaping behaviour during the early development of Lake Malawi cichlid larvae. The onset of the behaviour precedes the formation of bone, and we predicted that it might influence craniofacial shape by affecting the mechanical environment in which bone develops. Consistent with this, we found that both natural variation and experimental manipulation of this behaviour induced differential skeletal development that foreshadows adaptive variation in adult trophic morphology. In fact, the magnitude of difference in skeletal morphology induced by these simple shifts in behaviour was similar to those predicted to be caused by genetic factors. Finally, we demonstrate that this mechanical-load-induced shift in skeletal development is associated with differences in ptch1 expression, a gene previously implicated in mediating between-species differences in skeletal shape. Our results underscore the complexity of development, and the importance of epigenetic ( sensu Waddington) mechanisms in determining adaptive phenotypic variation.


2013 ◽  
Vol 5 (4) ◽  
pp. 661-679 ◽  
Author(s):  
Nuno A. Fonseca ◽  
Ramiro Morales-Hojas ◽  
Micael Reis ◽  
Helder Rocha ◽  
Cristina P. Vieira ◽  
...  

1998 ◽  
Vol 11 (3-4) ◽  
pp. 331-356 ◽  
Author(s):  
Evan Balaban

The ArgumentEugenics, in whatever form it may be articulated, is based on the idea that phenotypic characteristics of particular individuals can be predicted in advance. This paper argues that biology's capacity to predict many of the characteristics exhibited by an individual, especially behavioral or cognitive attributes, will always be very limited. This stems from intrinsic limitations to the methodology for relating genotypes to phenotypes, and from the nature of developmental processes which intervene between genotypes and phenotypes. While genetic studies may generate valid population predictions for conditions which impact human health, neither genetics nor developmental biology are likely to generate useful individual predictions about variation in non-disease-related human behavioral and cognitive phenotypes in the foreseeable future.


2019 ◽  
Author(s):  
Emeline Deleury ◽  
Thomas Guillemaud ◽  
Aurélie Blin ◽  
Eric Lombaert

AbstractExon capture coupled to high-throughput sequencing constitutes a cost-effective technical solution for addressing specific questions in evolutionary biology by focusing on expressed regions of the genome preferentially targeted by selection. Transcriptome-based capture, a process that can be used to capture the exons of non-model species, is use in phylogenomics. However, its use in population genomics remains rare due to the high costs of sequencing large numbers of indexed individuals across multiple populations. We evaluated the feasibility of combining transcriptome-based capture and the pooling of tissues from numerous individuals for DNA extraction as a cost-effective, generic and robust approach to estimating the variant allele frequencies of any species at the population level. We designed capture probes for ∼5 Mb of chosen de novo transcripts from the Asian ladybird Harmonia axyridis (5,717 transcripts). We called ∼300,000 bi-allelic SNPs for a pool of 36 non-indexed individuals. Capture efficiency was high, and pool-seq was as effective and accurate as individual-seq for detecting variants and estimating allele frequencies. Finally, we also evaluated an approach for simplifying bioinformatic analyses by mapping genomic reads directly to targeted transcript sequences to obtain coding variants. This approach is effective and does not affect the estimation of SNP allele frequencies, except for a small bias close to some exon ends. We demonstrate that this approach can also be used to predict the intron-exon boundaries of targeted de novo transcripts, making it possible to abolish genotyping biases near exon ends.


Author(s):  
Jana Wold ◽  
Klaus-Peter Koepfli ◽  
Stephanie Galla ◽  
Carolyn J. Hogg ◽  
David Eccles ◽  
...  

Structural variants (SVs) are large rearrangements (> 50 bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, i.e. variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While there are increasing opportunities to investigate functional genomic variation in threatened species via single nucleotide polymorphism (SNP) datasets, SVs remain understudied despite their potential influence on fitness traits of conservation interest. In this future-focused Opinion, we contend that characterizing SVs offers the conservation genomics community an exciting opportunity to complement SNP-based approaches to enhance species recovery. We also leverage the existing literature–predominantly in human health, agriculture and eco-evolutionary biology–to identify approaches for readily characterizing SVs and consider how integrating these into the conservation genomics toolbox may transform the way we manage some of the world’s most threatened species.


2017 ◽  
Author(s):  
Lu Chen ◽  
Pei Zhang ◽  
Yuan Fan ◽  
Juan Huang ◽  
Qiong Lu ◽  
...  

AbstractCircular RNAs (circRNAs) are covalently closed, single-stranded RNA molecules. Recent studies in human showed that circRNAs can arise via transcription of reverse complementary pairs of transposons. Given the prevalence of transposons in the maize genome and dramatic genomic variation driven by transposons, we hypothesize that transposons in maize may be involved in the formation of circRNAs and further modulate phenotypic variation. To test our hypothesis, we performed circRNA-Seq on B73 seedling leaves and integrate these data with 977 publicly available mRNA-Seq datasets. We uncovered 1,551 high-confidence maize circRNAs, which show distinct genomic features as compared to linear transcripts. Comprehensive analyses demonstrated that LINE1-like elements (LLE) and their Reverse Complementary Pairs (LLERCPs) are significantly enriched in the flanking regions of circRNAs. Interestingly, the accumulation of circRNA transcripts increases, while the accumulation of linear transcripts decreases as the number of LLERCPs increases. Furthermore, genes with LLERCP-mediated circRNAs are enriched among loci that are associated with phenotypic variation. These results suggest that LLERCPs can modulate phenotypic variation by the formation of circRNAs. As a proof of concept, we showed that the presence/absence variation of LLERCPs could result in expression variation of one cicrRNA, circ352, and further related to plant height through the interaction between circRNA and functional linear transcript. Our first glimpse of circRNAs uncovers a new role for transposons in the modulation of transcriptomic and phenotypic variation via the formation of circRNAs.


Sign in / Sign up

Export Citation Format

Share Document