International Journal of Marine Science, 2025, Vol.15, No.1, 35-44 http://www.aquapublisher.com/index.php/ijms 42 Figure 2 Relationships between genome size and categorical forms of social organization (A) and the eusociality index (B). In A, shapes represent raw values, closed circles and error bars represent posterior means and 95% CI. In B, solid line and gray shade represents the predicted linear relationship and 95% CI. The models control for the effect of egg and body size. In A, letters indicate significant differences in the posterior means in pair-wise comparisons between the three forms of social organization observed in Synalpheus snapping shrimps (a and b) and planned comparisons between eusocial and noneusocial species (pair-living and communal species combined) (A and B) (pMCMC < 0.05). Symbols represent pair-living ( ○), communal breeding ( △), and eusocial species (■) (Adopted from Chak et al., 2021) 7.3 Phylogeny and diversification of the family Pulmonidae The family of lobsters is actually quite complex. Not only are there many species, but also their lifestyles are very varied. It is difficult to clarify their relationships based on morphology alone. Therefore, the comparative genomic method comes in handy. By measuring the genomes or transcriptomes of various lobsters, researchers are drawing a more detailed molecular phylogenetic tree and trying to superimpose some key evolutionary events, such as genome expansion and the time nodes of the emergence of sociality. Current evidence shows that true sociality has evolved independently in the family of lobsters many times, and it occurred relatively late. Each emergence of sociality is almost accompanied by similar genomic changes - mainly the accumulation of transposons. This phenomenon of parallel evolution is equivalent to nature doing an evolutionary experiment itself, which is very rare. In terms of taxonomy, genomic data also exposes many problems. For example, some geographically separated pistol shrimp populations have surprisingly large genomic differences, which may actually be hidden new species, and subsequent re-evaluation needs to be combined with morphological and molecular data. 8 Future Directions of Comparative Genomics of Decapod Shrimps 8.1 Expanding the scope of genome sampling Currently, the sequenced shrimp genomes are mainly concentrated in economically cultivated species and very few deep-sea species, and many taxa are still blank. For example, only a few Penaeidae species of the suborder Cladobranchia have genomes, and the genomes of the infraorder Gammaridae and some special ecological niches (such as polar cold-water shrimp) have not yet been explored. In the future, a diverse layout of genome projects should be carried out, especially for sequencing key node species on the phylogenetic tree (such as primitive true shrimps, unexplored freshwater crayfish, etc.). With the reduction of sequencing costs and the improvement of technology, this goal is technically feasible. A wider range of species genomes will build a more comprehensive shrimp comparative genome framework, avoid the limitations of inference caused by sampling bias, and thus more accurately reconstruct the evolutionary history of shrimp. 8.2 In-depth analysis of genomic functional elements Past comparative studies have focused on the gains and losses of coding genes and sequence variations, but a large number of non-coding regions in the genome (such as regulatory elements and repetitive sequences) also play an important role in evolution. In the future, multi-omics methods should be used to integrate transcriptome and
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