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The short-finned pilot whale (SFPW), Globicephala macrorhynchus, has a pan-tropical and -temperate distribution. The existence of two morphologically and genetically distinct forms (Naisa and Shiho) suggests a complex speciation process, which remains to be deciphered. Here, we used whole genome data of 56 individuals from three poorly surveyed regions (Macaronesian islands - Eastern central Atlantic, China and Brazil) to assess the patterns of population structure and genetic diversity of the SFPW. We inferred population structure from admixture and principal component analyses. Additionally, we determined patterns of differentiation of the maternally-inherited mitogenomes. We estimated changes in population size through time using the Pairwise Sequentially Markovian Coalescent (PSMC) analysis. Finally, we searched for genomic regions of high differentiation in each assigned population using the population branch statistics and performed a windows-based analysis to uncover the top outliers of genetic differentiation, corresponding to regions that are potentially under selection. Our results provide evidence for three main genetic clusters of SPFW populations across the analysed individuals, emphasizing the genomic distinctiveness of Atlantic individuals compared with other individuals belonging to the Naisa form – known to be present in the western/central Pacific and Indian Oceans. The exception to this pattern is a Naisa mitochondrial and nuclear genotype found in one individual from Brazil. Moreover, PSMC suggests a shared recent evolutionary history in all three assigned populations. Our study provides a significant contribution to the overall understanding of the demographic history and spatial patterns of genetic diversity in SPFW, by complementing data previously described

Cetaceans (dolphins, whales, and porpoises) have large and anatomically sophisticated brains. To expand our understanding of the cellular makeup of cetacean brains and the similarities and divergence between the brains of cetaceans and terrestrial mammals, we report a short-finned pilot whale (Globicephala macrorhynchus) single-nucleus transcriptome atlas. To achieve this goal, we assembled a chromosome-scale reference genome spanning 2.25 Gb on 22 chromosomes and profiled the gene expression of five major anatomical cortical regions of the short-finned pilot whale by single-nucleus RNA-sequencing (snRNA-seq). We identified six major cell lineages in the cerebral cortex (excitatory neurons, inhibitory neurons, oligodendrocytes, oligodendrocyte precursor cells, astrocytes, and endothelial cells), eight molecularly distinct subclusters of excitatory neurons, and four subclusters of inhibitory neurons. Finally, a comparison of snRNA-seq data from the short-finned pilot whale, human, and rhesus macaque revealed a broadly conserved cellular makeup of brain cell types. Our study provides genomic resources and molecular insights into cetacean brain evolution., Cetaceans (dolphins, whales, and porpoises) have large and anatomically sophisticated brains. To expand our understanding of the cellular makeup of cetacean brains and the similarities and divergence between the brains of cetaceans and terrestrial mammals, we report a short-finned pilot whale (Globicephala macrorhynchus) single-nucleus transcriptome atlas. To achieve this goal, we assembled a chromosome-scale reference genome spanning 2.25 Gb on 22 chromosomes and profiled the gene expression of five major anatomical cortical regions of the short-finned pilot whale by single-nucleus RNA-sequencing (snRNA-seq). We identified six major cell lineages in the cerebral cortex (excitatory neurons, inhibitory neurons, oligodendrocytes, oligodendrocyte precursor cells, astrocytes, and endothelial cells), eight molecularly distinct subclusters of excitatory neurons, and four subclusters of inhibitory neurons. Finally, a comparison of snRNA-seq data from the short-finned pilot whale, human, and rhesus macaque revealed a broadly conserved cellular makeup of brain cell types. Our study provides genomic resources and molecular insights into cetacean brain evolution.

Observer-based counts and photo-identification are two well-established methods with an extensive use in cetacean studies. Using these two methods, group size has been widely reported, especially for small dolphins. Both methods may come with potential errors in estimating the group size, yet there is still a lack of comparison between both methods over a broad range of group size. Particularly, biogeographical variances in group size estimates were often mixed with methodological variances, making it difficult to compare estimates from different geographic regions. Here, group size estimates of a small, shallow-water, and near-shore delphinid species, Indo-Pacific humpback dolphins (Sousa chinensis), were simultaneously sampled using observer-based counts and photo-identification at three regions in the northern South China Sea. Data showed that dolphin group size from two methods were highly variable and associated with sampling regions. Generalized linear mixed models (GLMMs) indicated that dolphin group size significantly differed among regions. Statistical examinations further demonstrated dolphin group size could be affected by a complex combination of methodological and biogeographical variances. A common hurdle to examine potential factors influencing the estimation process is the inability to know the true group size at each sample. Therefore, other methods that could generate comparable estimates to represent true group size are warranted in future studies. To conclude, our findings present a better understanding of methodological and biogeographical variances in group size estimates of humpback dolphins, and help yield more robust abundance and density estimation for these vulnerable animals.

Group size is a key social trait influencing population dynamics of group-living animals. The Indo-Pacific humpback dolphins (IPHDs), Sousa chinensis, a shallow water delphinid species, display a fission-fusion social system. Yet little is known about how social organization of this species vary with temporal scales and behavioral state. In this study, we sampled group size estimates from the world's second largest population of humpback dolphins (Sousa spp.), which inhabit the eastern waters of Zhanjiang, China. IPHD group sizes changed seasonally and inter-annually, but not with tidal phases. Group sizes also changed with behavioral state of IPHD groups and with number of mother-calf pairs present. IPHDs formed larger groups in the autumn than in other seasons, which might be related to seasonal changes in food availability and reproductive cycle. Of the groups observed, we recorded the presence of mother calf pair in 85 groups (i.e., nursery groups: 47 ones with one pair, 25 ones with two pairs, and others with three pairs). Notably, nursery groups were about 2-4 times larger than non-nursery groups. In addition, group sizes greatly increased with the number of mother-calf pairs. Living in relatively large groups, more protection, food, and resources might be available for IPHD mothers and calves, and such social strategy provide higher reproduction efficiency and survival success for this species. During our observations, feeding (45.5%) and traveling (25.2%) represented the majority of IPHD's behavioral budget, while socializing (8.4%) and resting/milling (6.8%) were not frequently observed. Resting/milling groups were approximately 50% smaller than feeding, traveling, or socializing groups, while the latter three types had a similar mean group size. Large groups when IPHDs foraged, traveled, or socialized, might provide more added group benefits. For the first time, our findings clearly revealed intra-population variability in IPHD group sizes ac

Humpback dolphins (Sousa spp.) are obligate shallow-water and resident species, and they typically live in fission-fusion societies composed of small-sized groups with changeable membership. However, we have scant knowledge of their behavioural ecology, starting with potential factors influencing inter-population variability of their group sizes. Here, we compiled a new global dataset of humpback dolphin group sizes based on 150 published records. Our data indicated an inter-specific consistency of group-living strategy among the four species in the Sousa genus, as these species preferred living in small-sized groups with a mean size of mostly no more than 10, a minimum size of single individual or small pairs, and a maximum size of several tens or ∼100. In addition, we clearly showed the geographic variations in group sizes of humpback dolphins at a global scale. We found that the geographic variations in humpback dolphin group sizes were primarily associated with the latitude, sea surface temperature, and abundance. To conclude, our findings provide insights into social dynamics and socioecological trade-offs of humpback dolphins, and helps better understand how these resident animals adapted to their shallow-water habitats from the perspectives of biogeography and socioecology.