Hagfish, until now the only vertebrate that hadn't had its genome sequenced.
Image credit: Juan Pascual Anaya
One of the mysteries of vertebrate evolution is from where did all the genetic information come, but a recently completed sequencing of the hagfish genome has solved that mystery.
Creationists traditionally parrot the claim that information can't increase without magic because of some half-baked notion that it is like energy, so is subject to the third law of thermodynamics, which states that energy can neither be created nor destroyed.
But it only takes a moment's thought to realise that every time a cell replicates, the amount of genetic information normally doubles, without the help of magic, because it is simply a controlled organisation of existing matter. Similarly, if the genome gets doubled, or lengths of DNA get accidentally duplicated, this is simply the incorporation of existing matter into the resulting genome. No new matter is created yet the amount of information in the genome increases.
The other source of creationist confusion stems from them not understanding the difference between information and meaning. Meaning is information in the context of the environment. I'll illustrate this with a simple analogy:
Take the character strings 'INFORMATION' and 'TEAVE'. Which of these has the most information? To an English-speaker, the first is perfectly clear but the second is meaningless, yet they both contain the same information, as anyone bilingual in Latvian and English will tell you. They both mean the same thing - 'information'. The information is given meaning by the context of the language it's read in.
So, when a gene gets duplicated in the genome, the original copy is still working normally but the duplicate is free to mutate. Most of these mutations will be meaningless of course and will simply add to the junk DNA in the genome, but what if a mutation changed an enzyme into a more efficient enzyme, or an enzyme that did something the organism couldn't do before?
Let's extend the 'INFORMATION/TEAVE' analogy a bit more, with local languages representing the local environment giving meaning to the information in character strings:
Suppose 'INFORMATION' became 'REFORMATION' or, even better, 'TEAVE' became 'LEAVE' or 'GRAVE', it would then lose any meaning in Latvian but would gain meaning in English. In the context of a biological organism, the new genome might enable it to occupy a new niche in which 'LEAVE' or 'GRAVE' meant something. In the case of 'INFORMATION' mutating into 'REFORMATION', the organism's genome would now have new information in its original context.
Let's apply that now to a situation where a pathological bacterium's genome mutates in such a way that it can live and replicate in the presence of an antibiotic. In an environment in which that antibiotic is used to kill it, that mutation has hugely important new meaning for the bacterium, but in the context of an environment in which there are no antibiotics, the mutation would be entirely meaningless - just noise in the bacterial genome.
To press home that point: suppose a bacterium developed a mutation that means it could now make an enzyme for digesting plastic. That bacterium could now thrive in the oceans where microplastics are ubiquitous; before plastics were invented, that same new information in its genome would be meaningless junk. And this is exactly what the bacterium Ideonella sakaiensis has done.
What's that got to do with hagfish and their genome? First a little about hagfish:
Tell me all about hagfish and their place in the vertebrate family tree, please. Hagfish are primitive, jawless fish that belong to the class Myxini within the subphylum Vertebrata. They are unique and intriguing creatures with some distinctive characteristics. Here are some key points about hagfish and their place in the vertebrate family tree:It has been accepted for some time that there was a gene duplication at some point in the evolutionary history of vertebrates, but there was disagreement about exactly when this occurred.In summary, hagfish occupy a unique and primitive position in the vertebrate family tree. Their jawless nature, slime production, and ancient lineage make them important subjects for researchers studying the early evolution of vertebrates. Hagfish provide valuable insights into the transition from invertebrates to the more complex vertebrate forms seen in modern animals.
- Physical Characteristics:
- No Jaws: Hagfish are jawless fish, distinguishing them from more advanced vertebrates like lampreys and jawed fish.
- Slime Production: One of the most distinctive features of hagfish is their ability to produce copious amounts of slime as a defense mechanism. When threatened, they can release a gelatinous substance that expands rapidly in water, creating a slimy barrier.
- Taxonomy:
- Class Myxini: Hagfish are classified under the class Myxini within the subphylum Vertebrata. They are considered the most primitive living vertebrates.
- Lack of Vertebrae: Despite being vertebrates, hagfish lack true vertebrae. Instead, they have a cartilaginous notochord, which serves as a primitive axial support structure.
- Evolutionary Significance:
- Ancient Lineage: Hagfish are often regarded as living fossils due to their ancient lineage, dating back hundreds of millions of years. They provide valuable insights into the early evolution of vertebrates.
- Transition from Invertebrates to Vertebrates: The study of hagfish is crucial for understanding the evolutionary transition from invertebrates to vertebrates, particularly regarding the development of vertebrate characteristics.
- Habitat and Behavior:
- Deep-sea Dwellers: Hagfish are primarily found in deep-sea environments, although some species inhabit shallower waters. They are often associated with muddy or sandy substrates.
- Scavengers: Hagfish are scavengers, feeding on the soft tissues of dead or dying marine animals. They use their tooth-like structures to rasp away at the flesh of their prey.
- Relationship to Lampreys:
- Similarities and Differences: Hagfish share some similarities with lampreys, another group of jawless fish. However, there are key differences in their anatomy, behavior, and life history.
- Separate Evolutionary Paths: While hagfish and lampreys both represent ancient vertebrate lineages, they have followed separate evolutionary paths, leading to distinct adaptations and characteristics.
The newly sequenced hagfish genome has revealed that it happened deep in the evolutionary history of the vertebrates, when this doubling of the genome created lots of new genetic information to mutate and create new meaning.
The decade-long study was carried out by a large international team co-led by Philip C. J. Donoghue of the Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK, with more than 30 institutions from Spain, the United Kingdom, Japan, China, Italy, Norway, and the United States, including the University of Tokyo, the Japan RIKEN research institute, the Chinese Academy of Sciences, and the Center for Genomic Regulation in Barcelona, among others. Their findings are published open access in Nature Ecology & Evolution and explained in a Bristol University press release:
The findings, published today in the journal Nature Ecology & Evolution, have helped unravel the evolutionary history of genomic duplications that occurred in the ancestors of vertebrates, including humans. It is now known that the common ancestor of all vertebrates derived from a species that completely duplicated its genome once.Technical detail, including the background to the research, is in the team's publication in Nature Ecology & Evolution:
There has been considerable debate among evolutionary researchers as to when these genome duplications occurred in the history of vertebrates, and without information from the hagfish, which separates from the other vertebrates very early in the group’s history, it was difficult to place them.
Hagfish, also known as 'sea hags' or 'slime eels,' are deep-sea dwellers. They are recognised for the amount of mucus they release when threatened and their role as an ecological link in the ocean depths—acting as scavengers, responsible for removing, among other things, whale carcasses that end up on the seafloor after death. Until now, their genome had not been sequenced due to its complexity, composed of a large number of microchromosomes, which, in turn, consist of repetitive sequences. Microchromosomes are also lost during the animal's development, which means only the reproductive organs retain a complete genome.
The lineages that led to modern jawed and jawless vertebrates diverged, and each of these independently multiplied its genome: while the former, including humans, duplicated it, jawless vertebrates tripled the size of their genome. Genome doubling in jawed vertebrates might explain why hagfishes and lampreys are such simple organisms, while jawed vertebrates like sharks and humans are so much more complex.This study has significant implications in the evolutionary and molecular fields, as it helps us understand the genome changes that accompanied the origin of vertebrates and their most unique structures, such as the complex brain, jaw, and limbs. This is important because it allows us to compare, for example, the gene order between this and other vertebrates, including sharks and humans. This has resolved one of the most important open debates in genomic evolution: the number of genomic duplications and when these occurred during the origin of different vertebrate lineages.
Juan Pascual Anaya, lead author University of Málaga (UMA)For this research, the genome of Eptatretus burgeri, inhabiting the Pacific coast of East Asia, was sequenced in collaboration with the Chinese Academy of Sciences. Data produced for this study were up to 400 times the size of its genome, using advanced techniques like Hi-C for chromosomal proximity and successfully assembling it at the chromosome level.Genome duplication in jawed vertebrates was different, resulting from interbreeding between separate species of ancestral vertebrates. This would have disrupted the genome much more severely than genome duplication with species, providing the spur for evolutionary innovations such as vertebrate sensory organs, neural crest cells, a boney skeleton and paired fins, alongside the corresponding increase in regulatory complexity: the number of switches that turn genes on or off.
Philip Donoghue, corresponding author
School of Biological Sciences
University of Bristol, Bristol, UK
An analysis of genome functionality, based on extremely rare hagfish embryo samples from the prestigious laboratory of Professor Shigeru Kuratani at RIKEN; and a study on the potential impact of genomic duplications in each vertebrate, developed in collaboration with Professor Philip Donoghue of the University of Bristol, completes this multidisciplinary research crucial for understanding the evolutionary history of vertebrates.
AbstractLots of things for creationists to ignore here. Firstly, there is the evidence of gene duplication showing how new information arises in a genome without the help of magic. Secondly, there is the evidence of common ancestry of the vertebrates, including humans, and thirdly there is the researchers' dependence on the theory of evolution to explain the observations with no hint that it should be replaced by one involving magic and unproven supernatural entities that are a mere figment of the imagination. The TOE is so firmly embedded in modern biology that none of it would make sense without it.
Polyploidy or whole-genome duplication (WGD) is a major event that drastically reshapes genome architecture and is often assumed to be causally associated with organismal innovations and radiations. The 2R hypothesis suggests that two WGD events (1R and 2R) occurred during early vertebrate evolution. However, the timing of the 2R event relative to the divergence of gnathostomes (jawed vertebrates) and cyclostomes (jawless hagfishes and lampreys) is unresolved and whether these WGD events underlie vertebrate phenotypic diversification remains elusive. Here we present the genome of the inshore hagfish, Eptatretus burgeri. Through comparative analysis with lamprey and gnathostome genomes, we reconstruct the early events in cyclostome genome evolution, leveraging insights into the ancestral vertebrate genome. Genome-wide synteny and phylogenetic analyses support a scenario in which 1R occurred in the vertebrate stem-lineage during the early Cambrian, and 2R occurred in the gnathostome stem-lineage, maximally in the late Cambrian–earliest Ordovician, after its divergence from cyclostomes. We find that the genome of stem-cyclostomes experienced an additional independent genome triplication. Functional genomic and morphospace analyses demonstrate that WGD events generally contribute to developmental evolution with similar changes in the regulatory genome of both vertebrate groups. However, appreciable morphological diversification occurred only in the gnathostome but not in the cyclostome lineage, calling into question the general expectation that WGDs lead to leaps of bodyplan complexity.
Main
Polyploidy or whole-genome duplication (WGD) is a dramatic genomic event commonly invoked causally in organismal evolution1. The generally accepted ‘2R hypothesis’2,3 suggests that two rounds of WGD occurred during early vertebrate evolution (referred to as 1R and 2R); however, their timing and macroevolutionary consequences remain unclear4,5,6. Most studies agree that 1R occurred before the divergence of living vertebrates, but debate centres on whether 2R predated7,8 or postdated9,10,11,12 the divergence between cyclostomes and gnathostomes (Fig. 1c). Reconstruction of the ancestral vertebrate karyotype is fundamental to unravel the timing of 2R8,12,13,14,15, but this goal has been stymied by a dearth of cyclostome genomes. The recently described genome of the sea lamprey (Petromyzon marinus) has been interpreted to support 2R occurring before8 or after12 the gnathostome–cyclostome split, or not at all (with the karyotype diversity explained as the result of large-scale segmental duplications16,17). Analysis of the Arctic lamprey (Lethenteron camtschaticum) genome has suggested that 2R occurred in the gnathostome lineage while independent WGD event(s) might have occurred in the lamprey lineage11,18, perhaps shared with the hagfish11,19 (Fig. 1c). However, the lack of a hagfish genome assembly, the only major vertebrate group without a reference genome, has challenged attempts to constrain the number and phylogenetic timing of ploidy events in early vertebrate evolution. Here we describe the outcome of sequencing and comparative analysis of the genome of the inshore hagfish, Eptatretus burgeri (Fig. 1a,b).
a, Dorsal view of a young adult of the inshore hagfish E. burgeri, with the head to the top right. The teeth apparatus (and not a jaw) can be observed in a magnification of the head region of a fixed adult individual (a’). b, Fertilized egg of E. burgeri with a developing embryo at stage Dean 53 (ref. 48). Blood vessels can be observed from the exterior. c, Two competing hypotheses of vertebrate phylogeny. WGD events corresponding to the 2R hypothesis (lilac), to an alternative vertebrate 2R hypothesis (orange) and to those recently proposed in the lamprey lineage (light blue) are marked. Whether the lamprey-specific events actually occurred in a stem cyclostome remains elusive. d, Hi-C contact heatmap of the corrected hagfish genome assembly ordered by cluster (chromosome) length. Dashed boxes indicate the cluster boundaries. e, Completeness assessment of the genome assembly of the inshore hagfish E. burgeri genome (red), three lamprey species (blue) and two jawed vertebrates (green). Number of conserved metazoan orthologues (metazoa_odb10 dataset, containing 954 BUSCOs) is indicated for each case. F. E., Far Eastern. f, Correspondence analysis (CoA) on RSCU values was performed using the nucleotide sequences of all predicted genes concatenated for individual species. The percentage of variance is indicated for each axis. g, CoA of amino acid composition, with the percentage of variance indicated for each axis. In f and g: red, hagfish; blue, lamprey; green, jawed vertebrates; black, invertebrates.
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