Category Archives: Genome Dynamics

Sex, does everyone need it? Apparently not, the bdelliod rotifer Adineta vaga doesn’t

by Tayara Favarao and Stuart Brown

The loss of sexual reproduction in metazoans (animals) is widely believed to be an evolutionary dead end and would lead to the extinction of most metazoans. There is of course an exception, the bdelloid rotifers Adineta vaga (see figure 1).

Figure 1: The bdelloid rotifers Adineta vaga
Figure 1: The bdelloid rotifer Adineta vaga

These strange, weird and wonderful creatures seriously challenge this view that sexual reproduction is necessary for long-term evolutionary success. Rotifers of the Bdelloidea Class are a common group of asexual freshwater invertebrates that have persisted for millions of years. Never have we yet observed the existence of male sex organs or even meiosis in these bizarre animals. Their only recorded method of reproduction is via mitotically produced eggs with no reduction in chromosome number or any form of chromosome pairing. However, it is also thought that the bdelliod rotifers could have sex on exceedingly rare occasions and in a cryptic way yet to be defined.

Recent research by Flot et al (2013) looked at the genetic landscape of the bdelloid rotifer Adineta vaga, and they interpret their findings as evidence for bdelloids having evolved ameiotically. Shotgun sequencing on 454 and Illumina platforms were used for the genetic analyses. The chromosomes of the rotifers have a strange structure that means that it is impossible for the genome to split into haploid sets required for meiotic division. To combat their lack of recombination and keep the amount of deleterious mutations low, A. vaga have frequent events of gene conversion, which is when one allele of the same gene replaces another allele, these events promotes repair of mutations that arise (see figure 2). The rotifers also have expanded genomic regions that prevent transposons, jumping genes that often arise by duplication or cut themselves from one part of the genome and paste themselves into another part. Rotifer transposons comprise only 3% of the rotifers 244 Mb (Megabase) genome size, in humans transposons make up 44% of our 3300 Mb genome size. Rotifers have over twice the amount of genes (~49300) than humans (~21000) where over 8% of the rotifer genes are from non-metazoan origin, harking at a prokaryotic-like lifestyle involving horizontal gene transfer.

Figure 2: In sexual organisms, meiotic recombination can generate offspring with fewer or more deleterious mutations (hence increasing or decreasing fitness) than the previous generation. The same outcome is expected in ameiotic organisms that experience gene conversion: a deleterious allele may be overwritten by a beneficial or neutral one, resulting in an increase in fitness, or may overwrite it, resulting in decreased fitness.
Figure 2: In sexual organisms, meiotic recombination can generate offspring with fewer or more deleterious mutations (hence increasing or decreasing fitness) than the previous generation. The same outcome is expected in ameiotic organisms that experience gene conversion: a deleterious allele may be overwritten by a beneficial or neutral one, resulting in an increase in fitness, or may overwrite it, resulting in decreased fitness.

Flot and his colleagues found in the A. vaga   genome, evidence of genomic palindrome, which is when the DNA sequence has a complement sequence that when reversed shows the original sequence of nucleotide-by-nucleotide, such as: ACCTAGGTIS (original sequence),SITGGATCCA (complement sequence) and ACCTAGGTIS (complement sequence reverted). After analysing palindromic regions they found that there was colinearlity and divergence signatures of allelic regions and that there were no other allelic duplicates in the assembly. Suggesting that they arose by inter-allelic rearrangements rather than local duplication. They also found three direct repeats that present the signatures of allelic blocks found on the same chromosome, which cannot segregate during meiosis. A. vaga genome structure suggests that they have a mitotic lineage.

The frequent cycles of desiccation and rehydration that A. vaga undergo causes breaks in their DNA double-strand, facilitating the integration of the horizontally transferred genetic material and promotes gene conversion when repaired. These processes are believed to replace the role of sex in gene homogeneity and diversity.

This paper showed a new insight of how some species might be able to maintain health genes and viable lineages without the use of sexual reproduction. Hence providing a new possibilities perspective on asexual reproduction.

Origins and functional evolution of Y chromosomes across mammals

By Olivia Niblock and Aikaterini Liarelli

When determining sex, you must take into account the sex chromosomes.  In most mammalian cases, the females are XX and the males XY, i.e. it is the masculine genes on the ‘Y’ chromosome which determine the gender of the offspring. However, sex determination does not have to follow the exact pattern of defining the males with a different chromosome, or indeed by a genetic element at all. For example, there is a variant of the XX/XY system where females have two copies of the X chromosome, as in humans, but males have only one (X0), and sex is expressed depending on the dosage of hormones on the chromosomes. Additionally, there is the ZW sex-determination system which determines femininity, not masculinity. In these cases, females have two types kinds of chromosomes, ZW, whereas the males are homozygous (that is, have two copies of the same chromosome) for Z. The ZW system is found in birds, reptiles and some insects.

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Figure 1: Y or W protein coding repertoires and their origins: Strata are divided from S1 to S5. Genes are ordered within strata, differentiated sex chromosome genes are in the ‘Added’ section, and independently recruited genes are indicated in red.

In this 2014 study, a Mexican scientist Juan Cortez and his team, traced the evolution of the Y chromosome across 10 mammals and 5 birds (15 species in all). Since the Y chromosome underlies sex determination, its evolutionary path is worth exploring and many evolutionary studies have dealt with it in the past.  By using high-throughput genome and transcriptome sequencing, Cortez et al. produced a phylogenetic tree, with an attached table showing individual genes which are classed as ‘Y’ specific – or only in males (Figure 1). Interestingly enough, their goal was to explore the evolution of the Y chromosome across mammals, but they decided to use 5 birds for comparison (the birds in question being chicken, turkey, finch and ostrich).

The results showed three sex chromosome originations: the Y chromosome found in Eutherians and Marsupials such as giraffes and kangaroos respectively, the Y 1-5 in the Monotremes, which include animals like the dark-billed platypus, and finally the W chromosome in birds.

In Eutherians and Marsupials, SRY gene played a role in sex determination. This is a sex determining gene and it is considered the decision-maker in sex determination. Individuals with the gene become males, whereas individuals without the gene become females instead. The SRY gene was traced back to its original ancestor, approximately 180 million years ago whilst the Y chromosomes found in monotremes arose independently. Later on, approximately 140 million years ago, the W chromosome arose in birds, as shown in Figure 1.

The most interesting part of this study was that even though Y/W chromosomes arose millions of years ago, Y/W genes conserve a lot of their initial expression patterns, despite undergoing selection and expression decreases. Cortez and his team concluded that dosage constrains were the case; one gene is not overexpressed in relation to the others, and thus the individual can turn up with “testis-specificities through differential regulatory decay”, which affects the level of protein of an individual.

It is important to study the Y chromosome and trace back its evolutionary history, as it is thought that sex was determined non-chromosomally initially (i.e. sex was determined by temperature, perhaps, as it is in turtle species) and only took on a chromosomal form fairly recently in evolutionary history . Not so many years ago, people thought that Y chromosome’s function was to only determine sex, but it has other properties which have only recently been discovered. It is thought to be an X chromosome that has decayed across the ages of evolutionary time, and it is well known that the X chromosome does indeed carry genes not specific to sex determination (like colour-vision capabilities, for example). The Y chromosome is not only important in sex determination, but is involved in male disease susceptibility, and most importantly, phenotypic differences between the two sexes in health and disease. It would be interesting to see the scope of this research broadened to include many other species, as opposed to simply 15 subjects as in this study, as the results would be very useful to future studies.

The Origin of the Honeybee – A Worldwide Survey of Honeybee Genomes Reveals their Evolutionary History

by Thomaz Pinotti and Fay Morland

A large group of international researchers have united to try to answer one of the most lasting questions in the biology regarding one of the most economically important animals mankind has domesticated: where does the honeybee come from?

The honeybee, scientifically named Apis mellifera, is humanity’s most important pollinator, currently valued at more than $200 billion for agriculture worldwide. The fact that populations of bees are mysteriously decreasing is, therefore, quite the cause for alarm. In search for a better understanding, a team of scientists, led by the Sweden-based Dr. Andreas Wallberg, performed a large-scale genome sequencing of honeybees. They sampled from 14 different populations from across the world, including extremely important domesticated strains. The research hoped to reveal the evolutionary history of the honeybee, including the species’ adaptions to different climates and resistance to disease. What did they find? • The honeybee was previously believed to originate in Africa, however this study contradicted this, finding evidence that the honeybee may originate in East Asia, where all other bee species are believed to originate. • Genes related to immunity are unexpectedly very different between European and African strains, explaining the difference in disease resistance. Further studies of these genes may be very important in protecting the honeybee from disease and further population decline. • Genes related to sperm motility and maturation have undergone especially strong selection, suggesting that they may be a major driver of honeybee evolution. The study also revealed facts about the evolutionary history of honeybees. The results show that honeybees split into 4 groups (fig 1) 1 million years ago: A. Africa M. West and North Europe C. East and South Europe O. Middle East and Asia So what? Parasites, such as mites, that are restricted to Africa have resulted in the difference in immunity genes between African and European honeybees. The exportation of bees from Africa spreads the parasites to populations of bees without immunity, causing colonies to decline. Additionally, they found that African populations peaked at glacial maximums, whereas all other populations peaked during interglacial periods. Since the last glacial maximum, 20,000 years ago, African populations have been declining, whereas other populations have been slowly increasing. These results suggest that honeybee populations are affected by climate, and in particular that the African subspecies thrives in cold climates. Is this paper perfect? Although these results are interesting, there may be some problems with how they were obtained. Samples from each population were only 10 bees in size. Additionally, Africa and West and North Europe groups contained more samples than East and South Europe and Asia . A skew in sampling and small sample sizes can lead to an erroneous representation of populations and a lack of statistical significance. This and issues with methodology means that these results are not universally accepted by the scientific community, but they are a large step forward in understanding the genomics of the honeybees and the reasons behind colony decline. What’s all the buzz about? This study has provided innovative insights into the evolution and genetic adaption of the honeybee. This key pollinator is of critical importance to human society and the natural world and an understanding of genes relating to immunity may open doors to future studies into disease prevention. Additionally, understanding how subspecies respond to changes in climate sheds light on how populations may respond to current climate change.     References: Walberg et al., Nature 2014

A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera

by Dylan Wood and Jashan Abraham

 

Apis mellifera is among the most important species globally and is of huge economic and ecological importance. The species is a key pollinator responsible for agricultural services estimated at >$200 billion which directly impacts over 30% of our food production. Humans have been taking advantage of these services for over 7000 years. However, today there are a growing number of concerns regarding this fundamental specimen. Unexplained colony loss and global genomic variation are threatening this honeybee.

Wallberg et al. published this year on their findings into genome sequence variation in A. mellifera. The study took 140 workers bees from 14 separate populations spread worldwide and obtained an impressively stringent genome data set displaying 8.3 single-nucleotide polymorphisms (SNPs). Over a million of the SNP’s were found to be polymorphic in nature within the 4 tested groups of A. mellifera. A high degree of allele sharing was also shown across the tested populations. They found that large levels of global gene flow and random mating have led to this high level of genome variation They also state that population sizes have varied greatly in the past, most likely due to climatic changes. Analysis of the 140 worker bees showed no signs that this species originated in Africa, but that a more likely relationship is with the Asian Apis species.

The results implicate sperm competition as a major driver in honeybee evolution as a whole. Other genes identified showed that worker bee traits are often involved in adaptation, supporting a case for kin selection. Specific mutations were identified for adaptations to variations in climate, exposure to different pathogens, morphology and behaviour. The study also displays a number of differences between European and African A. mellifera, including disease resistance and the reproductive advantages in the Africanised form. These findings contrast with the previous ideology that, as suggested by molecular dating, the diverging populations of A. mellifera split around a million years ago. Indeed, further evaluation of the results of the study by Walberg et al indicate human transportation of colonies and selective breeding for desired traits played a huge role in the development of variation within A. mellifera. Finally, climactic influences upon the habitats of wild A. mellifera colonies likely played a greater role in their diversification and development than previously thought.

The results of the study provide a solid framework for further work to be undertaken on the genes outlined here. Research can now become more streamlined and focused upon protecting these bees against pathogens, rewriting management strategies and evaluating current conservation and farming methods. The invested interest in this species is clear from its aforementioned price tag of >$200bn which clearly defines the importance of studies such as this. A need for the recognition and identification of the biological mechanisms behind disease resistance is apparent here. Protecting this species and its obvious benefits must take into account the high genetic variability of populations, the threat to disease and the genetic barriers behind them and the risks of climate change to Apis mellifera; all of which are well studied in this paper.

References:

 

Walberg, A., Han, F., Wellhagen, G., Dahle, B., Kawata, M., Haddad, N., Simoes, Z.L.P., Allsopp, M.H., Kandemir, I., Dea la Rua, P., Pirk, C.W., Webster, M.T. “A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis melliferaNature 24.08.2014