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.

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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.

pic
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

Genome-wide signatures of convergent evolution in Echo locating mammals

by Daniel Considine

 

Most people understand that evolution, for the most part, works in a divergent way. This concept is fairly easy to grasp. When some form of reproductive barrier is introduced to a population, drift and many other factors will take over. When given enough time this will result in the two separated populations diverging to the point where they are now two completely different species, this is the fundamental process of divergence. What is not so intuitive is when two completely distinct species both independently evolve similar features. This is referred to as convergent evolution, and there are some notable examples. The most commonly cited example is how birds and bats both evolved the ability of flight. This is known as an analogous trait, where in two unrelated species face similar environmental challenges and both arrive at the same solution. Analysis of the anatomy of these species makes it clear that their wings are related in no way besides function.

Until recently, researchers were unsure of how convergent evolution worked, if at all, at the molecular level. One major breakthrough was in the analysis of amino acid substitutions at the active site of protease enzymes of different species. A recent paper in Nature (Parker et al, 2013) demonstrated how the nucleic sequence of completely unrelated species show convergent evolution at the site of functionally similar genes. Evidence suggests that echolocation has arisen at three independent times; once in whales and twice in bats. What is truly remarkable about these findings is that in all three instances, there are far more convergent amino acid substitutions to genes involved in hearing than would be expected by chance.

Researchers took 4 distinct bat species, consisting of both echo locating and non-echo locating species, and sequenced their genomes. To align these sequences, they took a further 18 mammal genomes from databases, one of which was the echo locating bottlenose dolphin, to make comparisons. Analysis of this data showed that genes involved with hearing, and in particular those which are important for echolocation, showed similarities with a very high likelihood of convergent evolution. To compound this finding, analysis was also carried out on the genes involved in vision, as bats and dolphins have both undergone adaptation for low-light environments. Again researchers found that the amount of similarities across these sequences strongly supported the hypothesis that convergent evolution was taking place. Finally, analysis of the nature of nucleic sequence substitutions was carried out. This analysis showed that these loci were under strong selection, which adds to the evidence of a convergent theory. One criticism of this methodology however, is their lack of comparison to a non-echolocating species of Cetacean.

So why is this research of importance? For a start it gives biologists new insight into how phenotypic traits can have great similarities, yet still be from completely unrelated species. This research can potentially explain some of the problems evolutionary biologists face. For example when analysing the genome sequences of different species for relatedness, and finding unexpected similarities, which until now would have suggested homology. This research could be taken one step further by measuring tissue-specific gene expression levels, which would not only improve our understanding of how protein-coding genes may converge, but also our overall ability to identify and understand gene regulation at the molecular level.

 

Reference: Parker et al, 2013 Nature

The Origin of the Tasmanian Devil Clonally Transmissible Cancer

by Elena Shanti Franchina

 

The transmissible cancer known as devil facial tumor disease (DFTD) has endangered the devil population in Tasmania, causing its number to collapse since 1996, date when it was first observed in northeastern Tasmania.

An international team of scientists led by Elizabeth Murchison, an investigator at Cold Spring Harbor Laboratory (CSHL), have discovered that the deadly facial tumors decimating Australia’s Tasmanian devil (Sarcophilus harrisii) probably originated in Schwann cells, a type of tissue that insulates and protects nerve fibers. The discovery comes from the effort of the team to carry out a genetic analysis of tumor cells. Based on these data, scientists have identified a genetic marker to accurately diagnose the DFTD.

The DFTD is a unique type of cancer: it is derived from neuroectoderm and is composed of undifferentiated round to spindle-shaped cells with few defining ultrastructural features. The genotype of all DFTD-tumors is similar across all loci, regardless of location, sex or age of the devil. One of the features that make this tumor nothing like previously described devil cancers is the fact that cancer cells are transmitted horizontally from animal to animal through biting. Biting is a normal part of the devil’s behaviour, involved in simple play and reproduction, this is the reason why the disease is highly spread among the population. This mechanism resemble that involved in canine transmissible venereal tumor (CTVT) and a transmissible sarcoma affecting Syrian hamsters, still this type of cancer remain unique in some of its features.

The tumor affects the face and mouth primarily, and lead to death by starvation or due to metastasis to internal organ. So far, no diagnostic tests or vaccines are present for DFTD, and models predict the disappearance of the Tasmanian devils within 25-35 years, due to this disease. “Our discovery is a major step forward in the race to save the Tasmanian devil from extinction,” notes Dr. Murchison, who points out that this research has provided a method to distinguish the DFTD from other cancers that affect the marsupial, allowing easy identification and isolation of affected animals.

The analysis presented in this study, propose that DFTD likely originated in the Schwann cells of a single devil. Schwann cells are found in the peripheral nervous system and produce myelin and other proteins essential for the functions of nerve cells in the tissue.  25 tumors were sampled in the process and they were all found to be genetically identical. Using miRNA deep sequencing and transcriptomes, a match was found for Schwann cells, revealing high activity in many of the genes coding for myelin basic protein production. Moreover several marker were identified, that may enable a more accurate discrimination of DFTD from other types of cancer and may eventually help identify a genetic pathway that can be targeted to treat it.

The researches also compiled a catalog of genes that may influence the pathology and transmission of the tumor, and can help develop a DFTD preclinical test and vaccine. Also further compared analysis of the DFTD and the canine clonally transmissible cancer, could lead to deeper insights in their occurrence, evolution and biology, potentially helping saving the devil from extinction.

 

 

Journal Reference: Science, DOI: 10.1126/science.1180616.

Comparative population genomics in animals uncovers the determinants of genetic diversity

Countless research has provided evidence of genetic diversity being a central component to many conservation challenges. Being able to predict species diversity is therefore a very beneficial strategy which is what this paper aims to investigate. So far the main focus of conservation has been directed on large sized vertebrates. However these popular animals have been shown to represent a very small subset. This study aims to investigate nucleotide diversity of a larger representation of all species which includes the invertebrates. From this we can uncover whether we can predict genetic diversity of a species.

The gap for molecular data across invertebrates still needs to be filled and the first distribution of genome wide polymorphism levels across metazoan trees of life have been presented, 31 Families of animals spread across 8 animal phyla. For 10 individuals in each family high coverage transcriptomic data was produced and a very weak relationship between nucleotide diversity and any of the geographic variables studied were found. Conversely the body size of the stage that an offspring leaves its parents is by far the most predictive variables. Overall the analysis of the paper indicates that species diversity can be predicted by the number of offspring and longevity of a species. The paper also shows that long lived species with a high brooding ability were shown to be less genetically diverse than short lived species.

The study acknowledges the central population genetic theory that a higher effective population size gives rise to higher genetic diversity and shows how empirical evidence gathered from RNA seq data does not support this. A weakness of the study is that it does not mention the impact of crowdedness of ecological niche on reproduction strategy.

Often organisms do not fall neatly into the strict categories of either producing few offspring and being short lived or producing more offspring and being shorter lived, we feel that ecological life histories could be viewed more as falling along a spectrum.

Species that produce small numbers of offspring and have high longevity have lower genetic diversity which could put them at risk. However the strategy of having many offspring has more risks associated with it, as their “quality” is not equal to the offspring of the lower fecundity strategists. The low fecundity strategists have the advantage of being well selected for their environment and thought to be more resistant to changes within it.

Presently, species conservation often prioritises the rare species ,whether endangered or endemic, and focuses on areas deemed as having a high level of biodiversity (large numbers of different species per unit area). This study encourages us to look beyond the species that are already defined as being endangered and to ones that could become wiped out very quickly due to lack of genetic diversity within the species population. Genetic diversity provides populations with resistance to changing environments and  diseases. The ecological strategy of a species could now become a factor in prioritising species for conservation, where DNA data is not available.

The study used extensive evidence and used a variety of  non-model organisms. In future studies more organisms could be included. From having a clear pre-understanding of the future diversification of species, extinction can possibly be avoided.

References:

Romiguier, J, Gayral, P, Ballenghein, M, Bernard, A, Cahais, V, Chenuil, A, Chiari, A, Dernat, R, Duret, L, Faivre, N, Loire, E, Lourencho, J.M, Nabholz, B, Roux C, Tsagokogeorga, G, Weber, A.A-T, Weinert, L.A, Belkhir, K, Bierne, N, Gelemin, and Galtier, N 2014 ‘Comparative population genomics in animals uncovers the determinants of genetic diversity’ Nature doi:10.1038/nature13685

Genome chronicles – The Giant Panda’s (hi)story

by Luca Dellisanti & Megan Saul

The Giant Panda, native to China and its surrounding South-Eastern countries, is at great risk of going extinct. An interesting study led by S. Zhao from the Chinese Academy of Science in Bejing has given a deep insight on the evolution of the species from 8 million years ago to the present day. The first of its kind, this study looks at the genetic makeup of 2% of the total world population of living wild Giant Pandas, a much larger study than any previously attempted. The size of this study has made it possible to identify three distinct populations for the first time.  It highlights something quite remarkable. This study helps us understand how the populations were formed through a variety of bottlenecks, expansions and divergences as a consequence of climate change and human activity. In the last 3000 years humans might have had more of a detrimental impact than 8 million years of climate change.

The fossil record of China and its surroundings provides evidence for three ancestral species of panda living in the area in the past. Their struggle for survival has been great and the species evolved a bigger body size, better suited to cold climates. They also switched their dietary preferences. Previously carnivores, pandas became more reliant on bamboo as a staple. Whole-genome sequencing has been used to look at the past history of the species and revealed two major events of dangerous population decline. Very interestingly, the timings of the two declines, respectively 200 and 20 thousand years ago have been found to correspond to periods of cold and dry climate, poor conditions for bamboo (see Fig. 1).

Fig 1. Demographic history from the panda's origin to 10,000 years ago, showing two expansions followed by two bottlenecks (blue and red lines). Change in climatic conditions is shown with the thin borwn line. High values represent cold and dry conditions, low values indicate warm and wet conditions. The approximate chronological ranges of three fossil panda species or subspecies (primal, pygmy and baconi panda) are shaded in pink, orange and blue, respectively.
Fig 1. Demographic history from the panda’s origin to 10,000 years ago, showing two expansions followed by two bottlenecks (blue and red lines). Change in climatic conditions is shown with the thin brown line. High values represent cold and dry conditions, low values indicate warm and wet conditions. The approximate chronological ranges of three fossil panda species or subspecies (primal, pygmy and baconi panda) are shaded in pink, orange and blue, respectively.

A variety of techniques and programmes were used to infer past information about the panda genome. After the initial whole genome sequencing of several living individuals the patterns of occurrence of SNPs (point substitutions of nucleotides in the DNA) from each individual were compared and genetic relationships highlighted. This along with further analysis helped separate out 3 populations: Qinling (QIN), Minshan (MIN) and Qionglai-Daxiangling-Xiaoxiangling-Liangshan (QXL).

Positive selection was found to have acted on functional genes related to bitter taste in the QIN population. These pandas eat more bamboo leaves, known to be bitter. Many olfactory receptor genes are also shown to be under balancing and directional selection. This is particularly relevant as pandas use these senses to locate others in the forest so is important for panda reproduction and survival. MIN and QXL compared to QIN and non-QIN populations were found to have less variation.

The study has helped us gain a better understanding of the living panda population which could be crucial in conservation efforts. The writers suggested re-introducing captive pandas into the wild to boost population numbers but they may struggle to survive in the wild and constant monitoring would be necessary. We are now aware of strong impact humans have had in the recent years on population decline and of the role we have played in dividing current populations into smaller, more at risk groups. We can no longer solely blame climate change for the decline in populations. If we are to make a marked attempt to conserve the giant panda more needs to be done to study the populations at a local level and people living in these areas need to be aware of the effect they are having on the giant pandas.

Figure and content from Zhao et al, Nature 2013