Using transcriptomics to investigate the Circadian clock

Circadian clocks provide a mechanism that allows organisms to anticipate environmental rhythms, like light-dark cycles. Nematostella vectensis, an estuarine sea anemone, has a surprising degree of overlap in genomic complexity with vertebrates, including circadian clock genes. These genes are predicted to serve a similar role in driving circadian patterns in sea anemones, but we have not worked out the exact mechanism they use.

Photo courtesy of Whitney Leach

In this study, we utilize next-generation sequencing to investigate the time-course transcriptional profiles of animals over 3 days, to dissociate true circadian gene expression vs. photo-responsiveness, by exposing animals to regular light-dark cycles for one month, then abruptly removing the light cue. Hypothesized ‘clock’ genes were rhythmic in the presence of light-dark cycles; however, several of these genes lost their characteristic oscillation after 1 or 2 days in the dark, suggesting lack of endogenous circadian regulation. One would expect a truly circadian gene to continue to cycle in the absence of light, however our results indicate either: 1) the hypothesized ‘clock’ genes simply respond directly to light cues, which implies they are not circadian, or 2) a circadian regulator resides in specific cell types, and the expression signal is too dampened when measuring in the whole animal.

Whitney Leach, Doctoral Candidate, The Reitzel Laboratory, University of North Carolina at Charlotte

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Finding the diamonds in the rough: using genomics and climate data to re-explore crop collections

Global crop collections carry a wealth of native genes and alleles of immense potential value for farmers and consumers. Equally, within their DNA lies variation of negative value. The challenge is finding the diamonds in the rough – this is such a difficult task that the vast majority of collections remains underutilized and under-explored. As genotyping methods have evolved to generate larger densities of data for lower costs, comprehensive genotypic fingerprinting of collections is now within reach.

Photo courtesy of CIMMYT’s Flickr account

Phenotypic data (field, greenhouse and chemical analysis data), the stalwart of plant breeding, and counterpart data used to determine the value of genes for breeding is now more expensive and complex to obtain than genotypic data. In our study, we used climate data from the sites of origin of the maize collections studied – a cheap proxy for phenotypic data related to constraint such as acid soils and high temperatures. Applying innovative analyses to fingerprinting and climatic data we identified genes, genomic regions and maize of potential value for breeding. This approach highlights an opportunity to use genomics and climate data to re-explore crop collections, excluding large numbers of irrelevant materials and identifying the potential gems that will contribute to feeding and nourishing future generations.       

Sarah Hearne and HuiHui Li (International Maize and Wheat Improvement Center)

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Summary from the authors: Detection of environmental and morphological adaptation despite high landscape genetic connectivity in a pest grasshopper

Male and female Phaulacridium vittatum. Photo credit: Sonu Yadav.

The Australian native grasshopper, Phaulacridium vittatum, known as the wingless grasshopper, is a common pest of pastures and crops in Australia, with outbreaks recorded every four or five years. With climate change and the expansion of agricultural land use, there is concern that grasshopper outbreaks could increase in frequency and severity. We used both neutral analysis of landscape genetic resistance combined with detection of selection using Environmental Association Analysis (EAA) to investigate common and disparate environmental drivers of  genetic dispersal and local adaptation in this grasshopper pest. With SNP data collected across a 900km gradient, we found that gene flow was best predicted by temperature, with only urban areas and water bodies limiting genetic dispersal. Although there was considerable admixture across the study area, local adaptation was evident and similarly driven by temperature, with additional evidence of morphological adaptation (body size and stripe polymorphism). Gene annotations revealed functions linked to UV shielding, and detoxification processes. Our study indicates that P. vittatum has high potential to adapt to heterogenous environments under high gene flow, and that temperature is the primary driver of both neutral and adaptive genetic structure. Thus, P. vittatum may become a more serious pest in the future as temperatures become warmer, and agricultural land use expands. 

Yadav S, Stow AJ, Dudaniec RY. Detection of environmental and morphological adaptation despite high landscape genetic connectivity in a pest grasshopper (Phaulacridium vittatum). Mol Ecol. 2019;28:3395–3412.

Summary from the authors: Dispersal limitations and historical factors determine the biogeography of specialized terrestrial protists

The diversity and geographical distribution of plants and animals are well documented and this information was essential to understand the factors that generate biodiversity, the most famous example being Darwin and Wallace’s theory of evolution. However, we know much less about microbial diversity and distribution, and hence it is unclear if the same factors drive the diversity of large and small organisms.

Hyalosphenia papilio from Le Cachot Bog, Swiss Jura Mountains. Picture by Prof. Daniel Lahr.

Using molecular tools, we studied the distribution and diversity of a species complex of the testate (shell-producing) amoeba species Hyalosphenia papilio, a microorganism restricted to Sphagnum peatland of Eurasia and North America. H. papilio is a complex of 14 distinct molecular lineages. Based on the DNA sequences, we inferred how, where and when this diversity evolved.

Our results suggest that H. papilio evolved in western North America and subsequently colonized other regions of Eurasia and North America during interglacial periods. Colonization of Eurasia occurred most recently, possibly after the last glaciation.

The patterns we observed for H. papilio are consistent with those commonly observed for macroscopic plants and animals. This in turn suggests that microbial diversity may be much higher than currently thought and may include “relict” taxa with restricted distributions, as commonly found among macroscopic plants and animals.

Read the full article: Singer D, Mitchell EAD, Payne RJ, etal. Dispersal limitations and historical factors determine thebiogeography of specialized terrestrial protists. Mol Ecol. 2019;28:3089–3100.

Summary from the authors: Genome‐scale sampling suggests cryptic epigenetic structuring and insular divergence in Canada lynx

Wild populations are often genetically structured in complex ways due to migration, selection, and drift. In highly mobile species such as the Canada lynx (Lynx canadensis), these complexities are exacerbated due to high levels of gene flow, which can make population delimitation challenging. Previously, Canada lynx populations appeared largely undifferentiated across continental North America at neutral genetic markers, with only small fine-scale differences across the landscape being correlated with climatic gradients. This climatic structuring aroused our interest in potential epigenetic differences between Canada lynx across their range, as environmentally-induced modifications to DNA could explain geographical or morphological differences that are not apparent in neutral DNA.

A lynx stalks its prey in the Northern forests of the Canadian Yukon, bordering Alaska. Photo credit to Dr. Melanie Boudreau.

To test this hypothesis, we examined neutral genetic differences and patterns of DNA methylation between 95 Canada lynx across 4 geographical regions (Alaska, Manitoba, Québec, and an insular population on Newfoundland). We found that Newfoundland lynx were the most distinct at both genetic and epigenetic markers, consistent with what we would expect for an island population. However, despite low neutral genetic differentiation between all mainland populations, we detected stark epigenetic differences between Alaska lynx and the remaining mainland lynx. Further analyses indicated that these differences might correlate with increased energetic demands, consistent with Alaskan lynx being the morphologically largest of all in their range. Our study exemplifies the utility of epigenetic markers for assessing population structure, even in non-model systems characterized by extreme levels of gene flow. 

Summary of neutral genetic structure with SNPs (left) and patterns of DNA methylation (right) between Canada lynx, where each circle represents an individual lynx colored by geographic region. Alaskan lynx (purple) are largely undifferentiated at neutral genetic markers compared to other mainland lynx, in contrast to their epigenetic profiles. 

Read the full article: Meröndun J, Murray DL, Shafer ABA. Genome-scale sampling suggests cryptic epigenetic structuring and insular divergence in Canada lynx. Mol Ecol. 2019;28:3186–3196.

Summary from the authors: Geography best explains global patterns of genetic diversity and post-glacial co-expansion in marine turtles

A hawksbill turtle (Eretmochelys imbricata). Photo Credit: Banco de Imagens Projeto Tamar.

Marine turtle species exhibit differences in characteristics that could affect their sensitivity to climate change, such as size, generation time, diet, and thermal preferences. Research on nesting turtles has also shown that there are often multiple maternal lineages within a species, some spanning whole ocean basins and others much more restricted. These geographic differences could also have influenced past responses to climate change. We compiled data from 23 marine turtle lineages and compared the observed data to many simulated datasets to determine whether lineages were stable, expanding, or contracting over time. We then looked at which factors best predicted past population history and genetic diversity. We found evidence for population expansion in 60% of the lineages, with the remaining lineages stable over time. A co-expansion model showed that the lineages that expanded did so in a highly synchronous manner after the last Ice Age. Geographic factors (ocean basin and range extent) were much better predictors of population history and genetic diversity than species traits. So, where you were mattered more than who you were in determining response to global warming. This can inform conservation planning for these species and other marine organisms in the face of climate change.

For the full article: Reid BN, Naro‐Maciel E, Hahn AT, FitzSimmons NN, Gehara M. Geography best explains global patterns of genetic diversity and postglacial co‐expansion in marine turtles. Mol Ecol. 2019;28:3358–3370.

Summary from the authors: The rise and fall of differentiated sex chromosomes in geckos

Link to the paper:

The Madagascar ground gecko (Paroedura picta) is a member of one of the few vertebrate lineages suspicious of the loss of highly differentiated sex chromosomes. Photo credit: Petr Jan Juračka.

Differentiated sex chromosomes such as XX/XY chromosomes of viviparous mammals and ZZ/ZW sex chromosomes of birds with highly degenerated Y and W, respectively, evolved in animals multiple times. Their noteworthy convergent characteristic is the evolutionary stability, documented among amniotes for dozens of millions of years in mammals, birds, and some lineages of lizards, snakes and turtles. The differentiation of sex chromosomes stemming from the cessation of recombination between them is assumed to be largely a one-way process. We found that the differentiated ZZ/ZW sex chromosomes with highly degenerated W of the Madagascan geckos of the genus Paroedura were likely present in the common ancestor of the genus. However, the subclade of the genus seems to reverse the for a considerable evolutionary time highly differentiated ZZ/ZW sex chromosomes back to poorly differentiated state and thus represents a rare case of the loss of once highly differentiated sex chromosomes. Notably, the differentiated ZZ/ZW sex chromosomes of these geckos share genes with the XX/XY sex chromosomes of viviparous mammals and the ZZ/ZW sex chromosomes of lacertid lizards, as well as with the XX/XY sex chromosomes of iguanas and ZZ/ZW sex chromosomes of softshell turtles. Along with other analogous cases which we summarize in our contribution, this finding reinforces the observation that particular chromosomes are repeatedly co -opted for the function of sex chromosomes in amniotes.

The reconstruction of the evolutionary history of sex chromosomes in the gecko genus Paroedura as revealed by the distribution of the sexual differences in copy numbers of genes linked to differentiated ancestral Z chromosome of the genus. Note that these genes were originally likely autosomal, i.e. they had the same number of copies in males and females (yellow). In the common ancestor of the genus, these genes had twice as many copies in males (ZZ) than in females (ZW) as a consequence of their loss from the degenerated W (violet). Still later in a subclade of the genus, the same genes turned back to the same copy numbers in both sexes (light blue) suggesting a reversal of the ancestral differentiated sex chromosomes back to poorly differentiated state.