Genome Size and Species Diversification

Theoretically, there are reasons to believe that large genome size should favour speciation. Several major factors contributing to genome size, such as duplications and transposable element activity have been proposed to facilitate the formation of new species. However, it is also possible that small genome size promotes speciation. For example, selection for genome reduction may be resolved in different ways in incipient species, leading to incompatibilities. Mutations and chromosomal rearrangements may also be more stably inherited in smaller genomes. Here I review the following lines of empirical evidence bearing on this question: (i) Correlations between genome size and species richness of taxa are often negative. (ii) Fossil evidence in lungfish shows that the accumulation of DNA in the genomes of this group coincided with a reduction in species diversity. (iii) Estimates of speciation interval in mammals correlate positively with genome size. (iv) Genome reductions are inferred at the base of particular species radiations and genome expansions at the base of others. (v) Insect clades that have been increasing in diversity up to the present have smaller genomes than clades that have remained stable or have decreased in diversity. The general pattern emerging from these observations is that higher diversification rates are generally found in small-genome taxa. Since diversification rates are the net effect of speciation and extinction, large genomes may thus either constrain speciation rate, increase extinction rate, or both. I argue that some of the cited examples are unlikely to be explained by extinction alone

Non-breeding habitat preference affects ecological speciation in migratory waders

Models of ecological speciation predict that certain types of habitat should be more conducive to species diversification than others. In this study, I test this hypothesis in waders of the sub-order Charadrii using the number of morphological sub-species per species as an index of diversity. I classified all members of this clade as spending the non-breeding season either coastally or inland and argue that these represent fundamentally different environments. Coastal mudflats are characterised by high predictability and patchy worldwide distribution, whilst inland wetlands are widespread but unpredictable. The results show that migratory species that winter coastally are sub-divided into more sub-species than those that winter inland. This was not the case for non-migratory species. I argue that coastal environments select for more rigid migratory pathways, whilst inland wetlands favour more flexible movement patterns. Population sub-division could then result from the passive segregation of breeding sites or from the active selection for assortative mating of ecomorphs

Offspring sex ratios in relation to mutual ornamentation and extra-pair paternity in the Black Swan Cygnus atratus

In sexually dichromatic birds, females may adaptively adjust the sex ratio of their offspring prior to hatching in relation to male ornamentation, for example, by producing more sons when paired to a highly attractive partner. However, to our knowledge no studies have investigated offspring sex ratio modification in species in which both sexes are ornamented, and it is unknown whether such a process would be adaptive. Here we examine variation in offspring sex ratio in the mutually ornamented Black Swan Cygnus atratus. Brood sex ratio was not related to the degree of ornament elaboration in either parent, or to extra-pair paternity. We suggest that parental attractiveness may not be inherited in a sex-linked manner, or may be largely non-heritable. Thus, females may not benefit from biasing the sex ratio of their offspring in relation to parental attractiveness

Genetic structure of Leptopilina boulardi populations from different climatic zones of Iran

<p>Abstract</p> <p>Background</p> <p>The genetic structure of populations can be influenced by geographic isolation (including physical distance) and ecology. We examined these effects in <it>Leptopilina boulardi</it>, a parasitoid of <it>Drosophila </it>of African origin and widely distributed over temperate and (sub) tropical climates.</p> <p>Results</p> <p>We sampled 11 populations of <it>L. boulardi </it>from five climatic zones in Iran and measured genetic differentiation at nuclear (Amplified Fragment Length Polymorphism; AFLP) and mitochondrial (Cytochrome Oxidase I; COI) loci. An Analysis of Molecular Variance (AMOVA) for the AFLP data revealed that 67.45% of variation resided between populations. No significant variation was observed between climatic zones. However, a significant difference was detected between populations from the central (dry) regions and those from the wetter north, which are separated by desert. A similarly clear cut genetic differentiation between populations from the central part of Iran and those from the north was observed by UPGMA cluster analysis and Principal Coordinates Analysis (PCO). Both UPGMA and PCO further separated two populations from the very humid western Caspian Sea coast (zone 3) from other northern populations from the temperate Caspian Sea coastal plain (zone 2), which are connected by forest. One population (Nour) was genetically intermediate between these two zones, indicating some gene flow between these two groups of populations. In all analyses a mountain population, Sorkhabad was found to be genetically identical to those from the nearby coastal plain (zone 2), which indicates high gene flow between these populations over a short geographical distance. One population from the Caspian coast (Astaneh) was genetically highly diverged from all other populations. A partial Mantel test showed a highly significant positive correlation between genetic and geographic distances, as well as separation by the deserts of central Iran. The COI sequences were highly conserved among all populations.</p> <p>Conclusion</p> <p>The Iranian populations of <it>L. boulardi </it>showed clear genetic structure in AFLP profiles, but not in COI sequence data. The transfer of fruits containing <it>Drosophila </it>larvae parasitized by <it>L. boulardi </it>appears to have caused some unexpected gene flow and changed the genetic composition of populations, particularly in urban areas. Nevertheless, our results suggest that climate, geographic distance and physical barriers may all have contributed to the formation of genetically distinct populations of <it>L. boulardi</it>. Inevitably, there will be overlap between the portions of variance explained by these variables. Disentangling the relative contributions of climate and geography to the genetic structure of this species will require additional sampling.</p

No Accumulation of Transposable Elements in Asexual Arthropods.

Transposable elements (TEs) and other repetitive DNA can accumulate in the absence of recombination, a process contributing to the degeneration of Y-chromosomes and other nonrecombining genome portions. A similar accumulation of repetitive DNA is expected for asexually reproducing species, given their entire genome is effectively nonrecombining. We tested this expectation by comparing the whole-genome TE loads of five asexual arthropod lineages and their sexual relatives, including asexual and sexual lineages of crustaceans (Daphnia water fleas), insects (Leptopilina wasps), and mites (Oribatida). Surprisingly, there was no evidence for increased TE load in genomes of asexual as compared to sexual lineages, neither for all classes of repetitive elements combined nor for specific TE families. Our study therefore suggests that nonrecombining genomes do not accumulate TEs like nonrecombining genomic regions of sexual lineages. Even if a slight but undetected increase of TEs were caused by asexual reproduction, it appears to be negligible compared to variance between species caused by processes unrelated to reproductive mode. It remains to be determined if molecular mechanisms underlying genome regulation in asexuals hamper TE activity. Alternatively, the differences in TE dynamics between nonrecombining genomes in asexual lineages versus nonrecombining genome portions in sexual species might stem from selection for benign TEs in asexual lineages because of the lack of genetic conflict between TEs and their hosts and/or because asexual lineages may only arise from sexual ancestors with particularly low TE loads

Candidate genes for shell colour polymorphism in [i]Cepaea nemoralis[i]

The characteristic ground colour and banding patterns on shells of the land snail Cepaea nemoralis form a classic study system for genetics and adaptation. We use RNAseq analysis to identify candidate genes underlying this polymorphism. We sequenced cDNA from the body and the mantle (the shell-producing tissue) of four individuals of two phenotypes and produced a de novo transcriptome of 147,397 contigs. Differential expression analysis identified a set of 1,961 transcripts that were upregulated in mantle tissue. Sequence variant analysis resulted in a set of 2,592 transcripts with single nucleotide polymorphisms (SNPs) that differed consistently between the phenotypes. Combining these results yielded a set of 197 candidate transcripts, of which 38 were annotated. Four of these transcripts are involved in production of the shell&apos;s nacreous layer. Comparison with morph-associated RAD-tags from a published study yielded seven transcripts that were annotated as metallothionein, a protein that is thought to inhibit the production of melanin in melanocytes. These results thus provide an excellent starting point for the elucidation of the genetic regulation of the Cepaea nemoralis shell colou

Regulatory and sequence evolution in response to selection for improved associative learning ability in Nasonia vitripennis

BACKGROUND: Selection acts on the phenotype, yet only the genotype is inherited. While both the phenotypic and genotypic response to short-term selection can be measured, the link between these is a major unsolved problem in evolutionary biology, in particular for complex behavioural phenotypes.RESULTS: Here we characterize the genomic and the transcriptomic basis of associative learning ability in the parasitic wasp Nasonia vitripennis and use gene network analysis to link the two. We artificially selected for improved associative learning ability in four independent pairs of lines and identified signatures of selection across the genome. Allele frequency diverged consistently between the selected and control lines in 118 single nucleotide polymorphisms (SNPs), clustering in 51 distinct genomic regions containing 128 genes. The majority of SNPs were found in regulatory regions, suggesting a potential role for gene expression evolution. We therefore sequenced the transcriptomes of selected and control lines and identified 36 consistently differentially expressed transcripts with large changes in expression. None of the differentially expressed genes also showed sequence divergence as a result of selection. Instead, gene network analysis showed many of the genes with consistent allele frequency differences and all of the differentially expressed genes to cluster in a single co-expression network. At a functional level, both genomic and transcriptomic analyses implicated members of gene networks known to be involved in neural plasticity and cognitive processes.CONCLUSIONS: Taken together, our results reveal how specific cognitive abilities can readily respond to selection via a complex interplay between regulatory and sequence evolution.</p

Determining the quality and complexity of next-generation sequencing data without a reference genome

Genomics, epigenetics, population genetics and bioinformatic

On distinguishing between canonical tRNA genes and tRNA gene fragments in prokaryotes

Automated genome annotation is essential for extracting biological information from sequence data. The identification and annotation of tRNA genes is frequently performed by the software package tRNAscan-SE, the output of which is listed for selected genomes in the Genomic tRNA database (GtRNAdb). Here, we highlight a pervasive error in prokaryotic tRNA gene sets on GtRNAdb: the miscategorization of partial, non-canonical tRNA genes as standard, canonical tRNA genes. Firstly, we demonstrate the issue using the tRNA gene sets of 20 organisms from the archaeal taxon Thermococcaceae. According to GtRNAdb, these organisms collectively deviate from the expected set of tRNA genes in 15 instances, including the listing of eleven putative canonical tRNA genes. However, after detailed manual annotation, only one of these eleven remains; the others are either partial, noncanonical tRNA genes resulting from the integration of genetic elements or CRISPR-Cas activity (seven instances), or attributable to ambiguities in input sequences (three instances). Secondly, we show that similar examples of the mis-categorization of predicted tRNA sequences occur throughout the prokaryotic sections of GtRNAdb. While both canonical and non-canonical prokaryotic tRNA gene sequences identified by tRNAscan-SE are biologically interesting, the challenge of reliably distinguishing between them remains. We recommend employing a combination of (i) screening input sequences for the genetic elements typically associated with non-canonical tRNA genes, and ambiguities, (ii) activating the tRNAscan-SE automated pseudogene detection function, and (iii) scrutinizing predicted tRNA genes with low isotype scores. These measures greatly reduce manual annotation efforts, and lead to improved prokaryotic tRNA gene set predictions