dcyphr | The tuatara genome reveals ancient features of amniote evolution


The tuatara is a reptile species living only in New Zealand. The tuatara are a species that connect the extinct dinosaurs and modern reptiles evolutionarily. Researchers often study the tuatara to understand amniote evolution and development. Amniotes are vertebrates that lay eggs, including reptiles, birds, and some mammals. In this paper, the researchers analyzed the tuatara genome, which is one of the largest vertebrate genomes. They looked at proteins and non-coding RNA, and sequences that are repeated multiple times in the DNA. From the genome, the tuatara has a combination of reptile and mammal characteristics. The study provides insight into tuatara and genome sequencing in general.


The researchers aim to share findings and implications from sequencing the tuatara genome.


The tuatara are so important because they are the last surviving species in the order Rhynchocephalia. Rhynchocephalia is an ancient order of reptiles. The most recent common ancestor of today’s reptiles and the tuatara lived 250 million years ago. 


The tuatara have other unique characteristics. The Māori tribe treasure the tuatara and consider it to be a guardian. The tuatara has features that resemble lizards, birds, and turtles. So, its taxonomy was uncertain for many years. This endangered species is not like other reptiles. Temperature plays a role in determining the sex of a tuatara. They have low metabolism rates, and they live long.


The Māori tribe protects the tuatara. The researchers obtained permission from the Māori tribe to conduct this genome project. From the genome, the tuatara has both features of ancestors and new characteristics.


The tuatara has a similar number of transposable elements as other reptiles. Still, they have repeats that more closely resemble mammals than reptiles. The repeats show a greater amount of diversity. The genome included long interspersed elements, which is a family of transposons. The type of transposons that is most abundant is L2. 


Tuatara also have short interspersed elements (SINEs), which are another type of transposons. They also share many SINEs with other amniotes called CORE-SINEs. Tuataras also have SINEs that are found in mammals called mammalian-wide interspersed repeats (MIRs). This amount of SINE diversity is the most in any amniote (Figure 2)


Tuataras have many retroviral transposons, including spumaretroviruses, which are some of the oldest retroviruses. Other features of the genome include non-coding regions and duplications. The high number of transposons and combination of mammal and reptile features is evolutionarily unique. 


The tuatara genome is highly methylated compared to other amniotes. 81%% of the CpG sites are methylated. The researchers think that the methylation may inactivate the many repeats in the genome. The researchers also found the ND5, tRNAThr, and tRNAHis mitochondrial genes. Other papers had previously reported that these genes do not exist. The genome also has non-coding regions, which are named NC1, NC2, and NC3, that only exist in the tuatara.


Genomic Innovations

The tuatara has genes for the major histocompatibility complex (MHC), which is important for the immune system. The tuatara is able to see in locations with little light. However, the genes indicate that ancestors have genes that could sense light. Tuataras also have strong color vision. Furthermore, tuataras have receptors for smelling and identifying prey. They contain more genes for these receptors than other sauropsids, which are similar reptiles.


The tuatara also has genes that regulate temperature called transient receptor potential ion channels (TRP) genes. They have unique TRP genes, such as an extra TRPV-like gene, which allows high sensitivity to heat. It seems like these genes for thermoregulation were positively regulated during evolution. The tuatara often live past 100 years. Their genes for selenoproteins provide protection against reactive oxidative species, resulting in longevity. Tuataras have genes, such as CIRBP24, which help determine the sex based on temperature. If the temperature of the egg has a higher temperature, the offspring will me male.


Phylogeny and evolutionary rates

Based on its genome, the tuatara evolves relatively slowly. This is consistent due to the lack of diversity. They seem to follow punctuated evolution like other amniotes. Punctuated evolution is when a species only evolves suddenly and then becomes stable for a time.


Population Genomics

The main reasons why the tuatara population is declining are pests and habitat loss. Climate change will likely cause population decline due to their temperature-dependent sex determination. 


Different parts of New Zealand have different tuataras genetically. From the genomes, the researchers found that the tuatara population drastically increased and decreased at different points in time. Population increase may be due more land and habitats. Population decrease is probably due to cooling, which destroyed habitats.


The tuatara lacks genetic diversity. The North Brother Island tuatara specifically has a lot of inbreeding. This is likely due to a bottleneck effect. However, the North Brother Island tuatara has a lot of unique alleles not found in other tuatara populations.


A Cultural Dimension

The researchers made an agreement with Ngātiwai iwi to conduct research on the tuataras. They explained how the research may benefit the conservation and knowledge about tuataras. They made sure to protect the rights of the Indeginous communities. They urge that researchers in science be inclusive.


The tuatara has many mammalian and reptile characteristics. Their genome is highly methylated. The evolution of the tuatara is punctuated and slow. The tuatara genome can also explain many unique characteristics, such as immunity and longevity. Population genomics also give insight into differences in tuatara populations. This genome analysis will guide future research on tuataras.


The researchers conducted genome sequencing with Illumina to understand tuatara genomes. They conducted phylogenetic analyses. They did low-coverage bisulfite sequencing to determine the methylation pattern of the tuatara genes.