Symposium proposal | |
Organizer: | The 2nd AsiaEvo Conference Organizing Committee |
The topic of this symposium is omnibus. |
OS3-1
Kleptoprotein Bioluminescence: Protein uptake in a fish from luminous crustacean.
Manabu Bessho-Uehara1, Naoyuki Yamamoto1, Shuji Jigenobu2, Keiko Kuwata1, Yuichi Oba3
1Nagoya University, Japan
2National Institute for Basic Biology, Japan
3Chubu University, Japan
2National Institute for Basic Biology, Japan
3Chubu University, Japan
Animals obtain some materials to express convergent function in ingested prey items, which is often seen in the cases of toxins or pigments or less in subcellular units such as a chloroplast (kleptoplastid) or stinging cell (kleptocnidid). However, uptake of ingested protein and the use of that function s never been reported. Here, we report that Parapriacanthus ransonneti, a bioluminescent fish, obtains its luciferase protein from bioluminescent ostracod prey. The protein purified from the fish’s light organs was identical to the luciferase of Cypridina noctiluca, a bioluminescent crustacean that they feed upon. Experiments where fish were fed with a related ostracod, Vargula hilgendorfii, demonstrated the specific uptake of the luciferase to the fish’s light organs. This “kleptoprotein” system allows an organism to use novel functional proteins that are not encoded in its genome and provides an evolutionary alternative to DNA-based molecular evolution.
OS3-2
Rapid Molecular Evolution of NRK for Acquiring Function of Regulating Placental Cell Proliferation
Beni Lestari1, Satomi Naito1, Akinori Endo2, Hidenori Nishihara1, Akira Kato1, Erika Watanabe1, Kimitoshi Denda1, Masayuki Komada1,2, Toshiaki Fukushima1,2
1School of Life Science and Technology, Tokyo Institute of Technology, Japan
2Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
2Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
The placenta is a defining organ of eutherians (placental mammals). We previously reported that murine NIK-related kinase (mNRK) plays a role in preventing hyperplasia of the placenta. Here, we investigated molecular mechanisms underlying inhibition of placental cell proliferation by mNRK and its molecular evolution to acquire this function.
Expression of mNRK is restricted to the placenta, whereas the chicken ortholog (cNRK) is expressed in various tissues. We compared the functions of mNRK and cNRK. Both share a C-terminal citron homology (CNH) domain. Our biochemical analyses revealed that 1) a specific region in mNRK interacted with casein kinase 2 (CK2) and inhibited the kinase activity of the latter, and 2) the CNH domain of mNRK interacted with phospholipids. In contrast, cNRK interacted with neither CK2 nor phospholipids.
Our cell culture experiments suggested that mNRK was localized in the plasma membrane via its CNH domain. Further, mNRK inhibited the activity of CK2, thereby preventing CK2-mediated inhibition of PTEN, which led to suppression of AKT signaling and cell proliferation. We also confirmed the function of mNRK in regulating AKT signaling in the placenta. In contrast, cNRK suppressed neither AKT signaling nor cell proliferation.
Phylogenetic analysis of vertebrate NRK-encoding genes suggested that, during early evolution of mammals, the length of the amino acid sequence of NRK was increased owing to certain base insertions. In addition, NRK underwent many amino acid substitutions, leading to acquisition of the CK2-interacting region and lipid-binding CNH domain, two functional regions essential for regulating cell proliferation. Furthermore, the two regions have been conserved by negative selection in placental mammals.
In conclusion, our study provides evidence for the rapid molecular evolution of NRK during which it acquired the function of regulating placental development.
OS3-3
Developmental canalization may contribute to macro-scale morphological evolution.
Yui Uchida1, Naoki Irie2
1RIKEN Center for Biosystems Dynamics Research
2The University of Tokyo
2The University of Tokyo
Animal morphology and their developmental processes exhibit distinct levels of evolutionary variability, with the vertebrate body plan being a representative example of remarkable conservation. Interestingly, the body plan establishing period during embryogenesis has also been highly conserved in vertebrates, but developmental features leading to the conservation of this period are still under debate. In this study, we tested whether strong canalization on body plan establishing period during embryogenesis could contribute to the evolutionary conservation of the period. To quantify canalization as developmental dynamics clearly distinguishing from evolutionary dynamics, we assessed phenotypic variation in the absence of genetic diversity (i.e., evolutionary tracks).
Using inbred twin embryos of medaka (Oryzias latipes), phenotypic variation was quantified at different developmental stages with minimum genetic diversity, environmental variation, and experimental technique error. We found that phenotypic variation was significantly smaller during the body plan establishment period. Gene-by-gene analysis further demonstrated that genes with less expression variation during embryogenesis tended to be more conserved in their expression levels in micro- and macro-evolution. Although gene regulatory mechanisms underlying developmental canalization and evolutionary conservation remain unclear, our data indicated a potential contribution of the number of tissues and developmental stages for a gene expressed, namely pleiotropy of gene expression.
Our results suggest that developmental canalization may bias phenotypic evolution even on a scale of hundreds of millions of years. In addition, comparisons of developmental canalization among traits and phylogenies may open up an avenue to tackle the origin of differences in evolvability and the evolution of evolvability.
OS3-4
Heterosis, Phenotypic Variance and Dominance in Diploid Gene Regulatory Network
Kenji Okubo1, Kunihiko Kaneko1,2
1Department of Basic Science, University of Tokyo
2Universal Biology Institute, University of Tokyo
2Universal Biology Institute, University of Tokyo
Heterosis refers to the phenomenon of enhanced hybrid performance. Heterosis has long been associated with the degree of dominance, such as dominance, overdominance, and quasi-dominance. Concerning the heterosis, however, many genes are involved in quantitative traits and determination of the cause of heterosis remains hard by using only molecular biological methods.
As heterosis is a consequence of the dynamics of complex gene regulatory networks (GRN), here we introduced a gene-expression dynamics model for a diploid gene regulatory network (Okubo,Kaneko 2021). Here, by noting the previous experimental reports (Phelan 1994), we studied the phenotoypic variance by noise, and uncovered that it is reduced in the heterozogotes compared with the homozygotes. This decrease in the phenotypic variance of the heterozygotes is consistent with the experimental observations, and suggests that the phenotypic robustness is enhanced in the heterozogote. Further, we defined dominance and overdominance for diploid GRNs and tested which of the two is more responsible for the heterosis of the robustness to noise. Our results demonstrate the tight connection among heterosis, henotypic robustness in heterozygotes, and dominance in gene expression patterns that goes beyond the traditional Mendelain dominance.
OS3-5
Speciation continuum in marine free-spawning invertebrates in Asia
Shotaro Hirase1, Yo Y. Yamasaki2, Masashi Sekino3, Masato Nishisako4, Minoru Ikeda4, Motoyuki Hara5, Juha Merilä6,7, Kiyoshi Kikuchi1
1Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo
2Ecological Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics
3Bioinformatics and Biosciences Division, Fisheries Resources Institute, Japan Fisheries Research and Education Agency
4Laboratory of Integrative Aquatic Biology, Graduate School of Agricultural Sciences, Tohoku University
5Tohoku Ecosystem-Associated Marine Sciences, Tohoku University
6Research Division of Ecology and Biodiversity, Faculty of Sciences, The University of Hong Kong
7Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki
2Ecological Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics
3Bioinformatics and Biosciences Division, Fisheries Resources Institute, Japan Fisheries Research and Education Agency
4Laboratory of Integrative Aquatic Biology, Graduate School of Agricultural Sciences, Tohoku University
5Tohoku Ecosystem-Associated Marine Sciences, Tohoku University
6Research Division of Ecology and Biodiversity, Faculty of Sciences, The University of Hong Kong
7Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki
How early stages of speciation in free-spawning marine invertebrate proceeds is poorly understood. An example demonstrating such process is the coevolution of interacting fertilization proteins, Lysin in sperm and VERL in egg, in the North American abalones. Many nonsynonymous substitutions among abalones in their coding genes have been suggested to prevent interspecies fertilization and cause reproductive isolation in absence of physical barriers to gene flow. In contrast, the Western Pacific abalones, Hatiois discus, H. madaka, and H. gigantea, have diverged recently and occur in sympatry with shared breeding season and are capable of producing viable F1 hybrids in spite of being ecologically differentiated, suggesting that these abalones occupy the early stages speciation continuum. Population genomic analyses revealed that although the three species are genetically distinct, there is evidence for historical and ongoing gene flow among these species. Evidence from demographic modeling suggests that reproductive isolation among the three species started to build in allopatry and have proceeded with gene flow, possibly driven by ecological selection. We identified differentiation islands between the closely related H. discus and H. madaka characterized by high FST and dA, but not high dXY values, as well as high genetic diversity in one H. madaka population. These genomic signatures suggest differentiation driven by recent ecological divergent selection in presence of gene flow outside of the genomic islands of differentiation. The differentiation islands showed low polymorphism in H. gigantea, and both high FST, dXY, and dA values between H. discus and H. gigantea, as well as between H. madaka and H. gigantea. Collectively, the differentiation islands associated with ecological divergence among the abalones do not appear to have acted as barrier loci to gene flow in the younger divergences but appear to do so in older divergences.
OS3-6
Genome-Wide Association Study of the Noni-toxin Tolerance in Drosophila melanogaster
Chau-T Ting1, Sheng-Yu Chang1, Shu Fang1
1Institute of Ecology and Evolutionary Biology, National Taiwan University, Taiwan
2Research Center for Biodiversity, Academia Sinica, Taiwan
3Department of Life Science, National Taiwan University, Taiwan
2Research Center for Biodiversity, Academia Sinica, Taiwan
3Department of Life Science, National Taiwan University, Taiwan
Diet adaptation is an important cause of host-associated differentiation. Many studies have focused on the species in which host specialization has driven speciation or population differentiation. In Drosophila, noni fruit is toxic to most species except very few species such as D. sechellia, and multiple mechanisms have evolved in this noni specialization. Some D. melanogaster lines have shown noni-toxin tolerance. However, whether the underlying genetic changes of this toxin tolerance in D. melanogaster is similar to that in D. sechellia is still unknown. To understand the genetic change in this pre-adaptation for a potential niche expansion in the future, we chose D. melanogaster that exhibits some tolerance variation to noni fruit. We performed a genome-wide association study (GWAS) to reveal the genetic basis of noni-toxin tolerance in D. melanogaster using Drosophila Genetic Reference Panel (DGRP) lines. We found considerable sexual and strain variation of noni-toxin tolerance. Among the ~4 million variants detected in the DGRP lines, 116 candidate variants shared between the two sexes were associated with the noni-toxin tolerance. These candidate variants were mainly located in non-coding regions of the genome. The genetic basis of toxin tolerance in D. melanogaster is different from that in D. sechellia because most candidate variants were derived alleles, which were not present in the closely related species including D. sechellia. These candidate variants were mainly from standing variation, which also exists in ancestral African populations. A low correlation was found between the observed noni-fruit tolerance in the two African DPGP2 populations and the predicted tolerance based on the candidate variants identified from the American DGRP population, suggesting that the underlying genetic bases of tolerance are different. These findings advance our understanding on the evolutionary genetics of diet adaptation.
OS3-7
Genomic analysis reveals the demographic history and genetic cost of chicken domestication
Ming-Shan Wang1
1Howard Hughes Medical Institute, University of California, Santa Cruz, CA 95064, 20 USA
Domestication is generally characterized by exploiting high-impact mutations through processes involving complex shifting demographics of domesticated species. These include inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks and post-divergence gene flow and introgression. Although domestication potentially affects the occurrence of both desired and undesired mutations, the way wild relatives of domesticated species evolve and how expensive the genetic cost underlying domestication is, remain poorly understood. Our recent study demonstrated that domestic chickens, the most numerous domestic animals, were initially derived from the RJF subspecies G.g.spadiceus whose present-day distribution is predominantly in southwestern China, northern Thailand, and Myanmar. Here, we investigated the ancestral demographic trajectory changes and the genetic load of chicken domestication by analyzing a dataset comprised of over 800 whole genomes from both indigenous chickens and wild jungle fowls. We show that despite having a higher genetic diversity than their wild counterparts, the red jungle fowls, the present-day domestic chickens experienced a dramatic population size decline during their early domestication. Our analyses suggest that the concomitant bottleneck induced the accumulation of deleterious mutations across chicken genomes, supporting the " cost of domestication " hypothesis. Particularly, we find that deleterious SNPs are largely maintained in heterozygous states and masked as recessive alleles in domestic chickens, challenging the power of modern breeding programs to effectively eliminate these genetic loads. Finally, we indicate that positive selection decreases the incidence but increases the frequency of deleterious SNPs in domestic chicken genomes. This study depicts a new landscape of genomic changes associated with domestication and aviculture, and provides an understanding of the evolutionary genomic profiles of domesticated animals managed under modern human selection.
OS3-8
Reconstructing the evolution of amniote karyotypes and nuclear architectures
Jing Liu1, Qi Zhou2
1Dept. Neurosciences and Developmental Biology, University of Vienna, Vienna 1090, Austria
2MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, HangZhou 310058, China
2MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, HangZhou 310058, China
Amniotes exhibit a great interspecific diversity of chromosome number and syntenic order. Previous efforts of reconstructing the ancestral karyotypes to infer the amniote chromosome evolution process suffered from using mostly scaffold-level fragmented genomes or the lack of key species at certain nodes. We recently produced a chromosome-level genome of platypus which allows us to reconstruct the 32 ancestral linkage groups (ALGs) of mammals, and the 42 and 43 ALGs of reptiles and amniotes with other 13 chromosome-level genomes. Comparison of the reconstructed ancestral genomes to the extant species uncovered that birds and turtles have a karyotype best approximating that of the amniote ancestor, with much fewer lineage-specific changes than other species during their 310 million years’ evolution. The chromosomal changes reveal a general pattern of the fission of macrochromosomes and the fusion of microchromosomes. Although the mammalian ancestor probably had a similar karyotype to that of reptile or amniote ancestor, subsequent translocations of ancestral macrochromosome and microchromosome fragments have dramatically rearranged the interchromosomal syntenic order in mammals compared to other amniotes. We uncovered that this may be mediated by the spatial interactions of the expanded mammalian transposable elements, namely SINE_Alu and LINE_L1. As a result, reptiles and birds have maintained a similar nuclear organization to that of the amniote ancestor, while mammals have undergone reorganized chromosomal distribution in the 3D nuclear space. Our results provide novel insights into the evolution of amniote chromosomes and nuclear architecture.