Whether or not there exists a general relationship between ontogeny (deveopment) and phylogeny (evolution) has been a long argued issue since 19th century (e.g. Ernst Haeckel's recapitulation theory). Several models have been proposed, however, no consensus has been made to this problem (some argued that the problem is no longer a issue of "modern biology", but just a fairy story). We started tackling this issue from molecular perspective, and found that the evolutionary divergence of vertebrate embryos follow the developmental hourglass model (Originally proposed by Dr. Denis Duboule in 1994).

Remaining & Newly raised questions

- Why do animal embryos show this kind of strange divergence?
- The anatomical features found at the bottleneck is said to define the 'bodyplan' of animals.. but is it true?

- Related publications -
Development, 141:4649-4655 (2014)
Nature Genetics, 45(6):701-706, (2013)
Nature Communications, 2 : 248, (2011)
BMC Biology, 5:1, 12 January (2007)

Did you know that the back shell of turtles are composed of vertebrae and ribs? This means that their arms (especially shoulder blades) are inside of thir ribcage, which is opposite to positionings. In addition to this, turtles have strange morphological features, and thus they have once believed as early diverged (so to say,, old) reptile groups. However, based on sequences of genomic DNA, we confirmed that they are close relatives of birds, dinosaurs, and crocodiles.

What is important for us, we found that even this strange animal embryogenesis follow the rule of embryonic evolution predicted by the developmental hourglass model.
Apart from embryonic evolution, another interesting findings from the turtle genome was that we found that one of the turtle species have plenty of olphactory receptor genes, even comparable or more than dogs! However, it doesn't mean that they have highly sensitive sense of smell, but it simply imply that they may be good at sniffing out variety of ordrants.

- Related publications -
Nature Genetics, 45(6):701-706, 2013
Nature Genetics, 46, 526, 2014

Did you know that we are chimera by nature? Maternal cells that somehow migrated into our body is known to be circulating our body, no matter how old you are. Then what are they doing in our body? One possible roles of them is to help repairing our damaged tissues, and several studies actually supported this. On the other hand, some congenital disease have higher frequency of maternal cells, and some, including us, are speculating that these maternal cells could be involved in the onset or augmentation aggravation of some of these congenital disease. We still do not have strong evidences for this, but if this was the case, it means that we may have a way to alleviate the symptoms of the disease. Together with pediatric surgeons, we found that patients of biliary atresia have much higher maternal microchimeric cells in liver, and they had higher immunological compatibility to their mothers.

- Related publications -
Journal of Pediatric Gastroenterology & Nutrition, Volume 49, Issue 4, 488-492, 2009
Pediatrics, 121 (3), Mar 1, 2008

Which reptiles evolved the most? Actually, current biology cannot make a consensual answer to that question. Let's say we are comparing Lizards, turtles, crocodilians, and birds. All of them experienced exactly the same geological time since the split from their common ancester, however, some (e.g., crocodilians) retain relatively similar morphological features to their common ancestor, and some (e.g., birds) show highly derived features. One assumption for this is that crocodilians spent less biological time (perhaps due to longer generation time etc.), but is it ture? To tackle this question, we have sequenced genomes of three crocodilian species, and compared them to those of other animals such as mammals and brids. We found that crocodilians do have relatively slowly evolving genomic sequence. It is clear that crocodilians have spent the same geological time compared to other sister groups, however, biological time (in terms of changes in genomic information) they have spent may be different from the others.


- Related publications / documents -
Science, 346, 6215 (2017)

How did birds evolve from dinosaurs? Especially, what kind of genetic changes were made to avian genomic program during the evolution? By analyzing 48 avian genomes, we found that most (> 99%) of avian specific DNA sequences are non-coding sequences with potential gene regulatory functions. Actually, one of these sequences had enhancer activity to drive certain gene (Sim1) at tissues that later develop flight feather. Considering that birds did not obtain new coding genes during the evolution, it can be said that macroevolutionary transition from dinosaur to birds were achieved mostly by rewiring of gene regulatory network.

- Related publications -
Nature Communications, 114229, (2017)

Phenotypic evolution is not completely free in diversification. It seems phenotypes (traits) in eadch lineage are somehow limited to some extent. Animals for example, species in the same phylum (kind of group) share the same basic anatomical architecture (bodyplan), and bodyplans have not been changed since the cambrian explotion (> 550 million years ago). In chordates (phylum chordata), while they (we) have diversified into variety of niches including sea, fresh water, land and sky, the bodyplan remain the same. Phylotype hypothesis predicted that this is due to conserved organogenesis stage during development, however, the reason why this developmental phase is conserved still remain unclear. By identifying and analyzing gene expression profiles of 8 chordate species, we (EXPANDE internaltional collaborative group) have tackled this problem. Based on our study, we found that intensively re-used genes (pleiotropic genes) were suggested to be imposing constraint on the diversification of organogenesis stages in vertebrates, and this may have led to the conservation of vertebrates' basic anatomical architecture. Re-use (or recruitment) of genes into different biological process has been known to accelerate the acquisition of evolutionary novelty (diversification), however, our findings suggest that gene recruitment could also limit the diversification of traits, implyling double-edged feature of gene recruitment in evolution.
(Press release document [English] [Japanese])


- Related publications / documents -
Nature Ecology & Evolution, (2017)
Behind the paper (Nature EcoEvo blog)


- Related research project -
Constrained & Directional Evolution

Echinoderms, such as feather star (top left in the figure) appears like as if they are plant, or something else. However, they belong to "bilaterians" like us, a group which show bilaterally symmetrical body (bilateral during embryo, but become basically pentameral as an adult). But how?　One possibility is that the echinoderm's genomes (especially the Hox cluster genes) have been so heavily mutated and modified, and that enabled them to become pentameral bodyplan. To test this hypothesis, we started an international collaboration project, and sequenced the genomes of echinoderms, including sea urchin and feather star, and further analyzed gene expression profiles during the development of three echinoderm species by adding a sea cucumber. Surprisingly, the echinoderm's genome was not as strange as we expected. Gene sets were comparable to chordates, and what is important, the Hox cluster genes showed somewhat similar in composition to their sister lineage, the hemichordates. The results indicate that echinoderms evolved pentameral bodyplan without introducing dramatic change in genetic information. As is the case in many other organisms, change in the use of existing genes that are widely conserved aomong animals may have contributed their pentameral bodyplan evolution. On the other hand, we found a sign of exception during their development. As with other animal groups, the middle stage of development was the most conserved phase (as in the developmental hourglass model), however, the phase did not match with the establishment of bodyplan (i.e., the development of pentameral bodyplan). This implies the need for revisiting the one of the predictions of hourglass model (the phylotype hypothesis), or the definition of bodyplan in echinoderms (pentameral symmetry). Our results contain enourmous amount of genomic, and transcriptomic information, and we expect these data to be utilized to elucidate the mystery of bodyplan evolution in animals.


- Related publications / documents -
Communications Biology, (2020)
Press release documents [in Japanese]

Offsprings of placental mammals inherit variety of information from their mother, including maternal cells. These cells, so called maternal microchimeric cells, migrate not only when we were embryos, but also during breast feeding, and remain in our body throughout our life. But what for? What kind of cells they are? By applying single cell RNAseq technology to mice embryos, we, for the first time, clarified major cell types of the maternal cells. While majority of cells were immune related cells, stem cells, and even terminally differentiated cells were detected. We further found that neonatal immune cells get activated when maternal cells were removed, suggesting that maternal cells may be involved in repressing over-activatino of neonatal immune system. 　　What was surprising was that although transfer of maternal cells occur in all pregnant cases, their frequency and cell types vary greatly from child to child, even among children born to the same parents. This interindividual variation may potentially explain the fact that mother-derived cells contribute not only to avoid immunological conflicts between mother and child, but also to seemingly conflicting phenomena, such as their alleged role in certain congenital abnormalities.

- Related publications -
Scientific Reports,volume 12, Article number: 18313 (2022)
Biology Open, Biol Open (2022) 11 (11): bio059334.
PLOS ONE (2021) 16(12): e0261357