Skip to main content
NCBI home page
Molecular Biology and Evolution logoLink to Molecular Biology and Evolution
. 2025 Sep 18;42(10):msaf234. doi: 10.1093/molbev/msaf234

Chromosome-Level Genome Assembly of Eden's Whale Clarifies the Taxonomy and Speciation of Bryde's Whale Complex

Yi-Tao Lin 1, Fan Hui 2, Wentao Han 3,4,5, Yi-Xuan Li 6, Bonnie Yuen Wai Heung 7, Chun Ming How 8, Shi Wang 9,10,11, Jian-Wen Qiu 12,✉,b
Editor: Russell Corbett-Detig
PMCID: PMC12492004  PMID: 40973465

Abstract

Eden's whale (Balaenoptera edeni), a poorly understood baleen cetacean, has long been shrouded in taxonomic ambiguity due to limited genomic resources, obscuring its distinction from closely related species and its position within the cetacean Tree of Life. In this paper, we present a high-quality chromosomal-level genome of B. edeni and conduct comparative genomic analyses to address long-standing taxonomic confusion and elucidate speciation of balaenopterids. Our phylogenomic analysis and demographic reconstruction reveal that B. edeni is a distinct sister to Bryde's whale (Balaenoptera brydei), sharing a common ancestor that diverged approximately 7.84 million years ago during the late Miocene. Their genetic divergence exceeds typical intraspecific variation in whales, supporting the reinstatement of B. brydei as a valid species. Chromosomal syntenic analyses suggest that macro-fragment inversions contributed to speciation in balaenopterid whales and uncover unexpected large-scale complex genome rearrangements in Bryde's whale, offering novel insights into cetacean genome evolution. Functional enrichment analysis of inverted regions between B. edeni and Balaenoptera musculus indicates their predominant association with metabolism and biosynthesis, as well as responses to various substances, stress, and stimuli. These genomic resources for B. edeni not only lay a critical foundation for comparative genetic and evolutionary research of cetaceans but also advance our understanding of the taxonomy and evolutionary dynamics of the Bryde's whale complex, with broader implications for baleen whale conservation and biodiversity.

Keywords: Balaenoptera, cetacean, evolution, marine mammal, Mysticeti

Introduction

Cetaceans, which evolved from terrestrial ancestors, are divided into baleen and toothed whales (Mysticeti and Odontoceti, respectively), with their varied sizes and distributions reflecting adaptations to diverse marine environments (Marx and Fordyce 2015; Park et al. 2015; Perrin et al. 2018; Davis 2019; Wolf et al. 2022). Within the genus Balaenoptera, the taxonomy of the Bryde's whale complex has attracted significant attention over the past decades (Sasaki et al. 2006). Initially, Anderson (1878) described Balaenoptera edeni based on a mature specimen measuring 11.3 m, while Balaenoptera brydei was described based on individuals with sizes from 12.4 to 15.0 m, larger than B. edeni at sexual and physical maturity (Olsen 1913; Best 1977). Subsequent studies suggested that B. edeni and B. brydei were subspecies of the same species based on skeletal structures, ie Balaenoptera edeni edeni and Balaenoptera edeni brydei (Andrews 1918; Junge 1950; Kato and Perrin 2009; Kershaw et al. 2013). In this view, the smaller B. e. edeni was thought to inhabit the coasts of the Western Pacific and Indian Oceans, while B. e. brydei was considered the larger, more widely distributed form (Sasaki et al. 2006; Kato and Perrin 2009; Kershaw et al. 2013). Conversely, other morphological studies argued that Eden's and Bryde's whales should be considered distinct species due to differences in cranial structures (Soot-Ryen 1961; Wada et al. 2003; Rosel and Wilcox 2014; Rosel et al. 2021). Furthermore, the discovery of two additional species within the Bryde's whale complex, Balaenoptera omurai from the Solomon Islands and the Eastern Indian Ocean, and Balaenoptera ricei from the Gulf of Mexico, further complicated the taxonomy of this group (Wada et al. 2003; Rosel et al. 2021). Phylogenetic studies utilizing mitogenomic fragments have provided further evidence for the distinctiveness of Eden's and Bryde's whales, suggesting that B. edeni is sister to B. ricei instead of B. brydei, while B. omurai is the earliest diverging lineage within the Bryde's whale complex (Wada et al. 2003; Sasaki et al. 2006; Luksenburg et al. 2015; Rosel et al. 2021). Despite these findings, B. brydei is not yet formally recognized by the Committee on Taxonomy from the Society for Marine Mammalogy (https://marinemammalscience.org/) and is currently categorized as a synonym of B. edeni in WoRMs (https://www.marinespecies.org) due to limited genetic data (Wada et al. 2003; Rosel et al. 2021).

In contrast to other balaenopterid species like Balaenoptera acutorostrata and B. musculus, which have been extensively analyzed through genomic studies (Park et al. 2015; Attard et al. 2018; Bisconti and Carnevale 2022; Bukhman et al. 2024; Jossey et al. 2024; Wolf et al. 2025), the genomics and molecular biology of Eden's whale remain poorly explored. Only a few studies have focused on its distribution, behavior, and genetics (Ren et al. 2022; Chen et al. 2023; Sun et al. 2023; Ibrahim et al. 2024). Notably, Eden's whale is among the few species within the genus Balaenoptera that lack an assembled genome. By utilizing tissues from an Eden's whale carcass, we sequenced and assembled its genome at the chromosomal level to study the taxonomy and speciation of the family Balaenopteridae. These genomic resources enable us to examine the chromosome structure of Eden's whale and compare it with other species in the Bryde's whale complex, providing substantial evidence for the reinstatement of B. brydei as a distinct species. Accurate species delimitation will facilitate better determination of their distribution ranges, population sizes, and conservation units.

Results

High-Quality Genome Assembly and Genetic Distance

Our assembly produced a chromosomal-level genome comprising 23 chromosomes (21 autosomes and allosomes X and Y, 2n = 44), with a size of 2.2 Gb (Fig. 1a and Fig. S1, Table 1 and Tables S1 to S3). Gene prediction identified 19,476 protein-coding genes (Fig. S1, Table 1). Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment confirmed the high quality of the assembly (99.70% complete BUSCOs) and predicted gene models (97.50% complete BUSCOs). Additionally, we assembled the mitogenome of B. edeni, which is 16,409 bp in length and contains 13 protein-coding genes (Fig. 1b and Fig. S1). This mitogenome exhibits 99.98% identity with the previously published B. edeni mitogenome (GenBank accession: AB201258), further validating the taxonomic accuracy of our assembly. We estimated the Kimura 2-parameter (K2P) genetic distances using available complete cox1 sequences of cetaceans to elucidate interspecific divergence (Table S4). Our results revealed that the K2P genetic distance is 0 among the three specimens of B. edeni available for comparison and varies between 0% and 0.13% among the three specimens of B. brydei. In contrast, the cox1 genetic distance between these two species reaches 2.94% (Table S4). The cox1 K2P genetic distance between B. edeni and B. ricei is 1.81%, in stark contrast to the three Eubalaena whales (E. japonica, E. australis, and E. glacialis), which exhibit minimal interspecific distances (0.52% to 0.86%), notably lower than the divergence observed between Eden's and Bryde's whales.

Fig. 1.

Fig. 1.

Open in a new tab

Genomic structure and phylogenomic relationships of Eden's whale. a) Circus plot of 23 linkage groups (corresponding to chromosomes) showing marker distributions at 1 Mb sliding windows from outer to inner circle: gene density, GC content, and GC skew. The animal icon in the center of the circus plot was obtained from the Plazi's databases (https://plazi.org/) without copyright restriction. b) Structure of the mitogenome showing protein-coding genes and RNAs. c) Phylogenomic relationships, divergent times, and expanded and contracted gene families of cetaceans with hippo as the outgroup. The tree was constructed using 3,360 single-copy orthogroups. The bootstrap values are 100 at all nodes. The tree was fossil-calibrated at five nodes. The bar length indicated the 95% confidence interval. Sources and characteristics of the genomes are included in Table S2. The bar plot shows the number of significantly expanded and contracted gene families in each species relative to its nearest node, with a P-value < 0.05. The animal icons do not represent their real body sizes. They were obtained from the Phylopic website (https://www.phylopic.org/) without copyright restriction. d) The best putative divergence scenario of Bryde's whale complex (Scenario 1) based on the randomly sampled SNP dataset (N = 10,295). Other scenarios are shown in Fig. S3. N1, Balaenoptera ricei (BRic); N2, B. brydei (BBry); N3, B. edeni (BEde); N3b, putative mimics demographic bottleneck; t2, time point of first divergence event from the ancestor; from t2 to 0, from the ancient to present.

Table 1.

Genome assembly and annotation statistics

Item Number
Contig assembly
 Total length (Mb) 2,616.0
 No. of contigs 163
 GC content (%) 41.3
 N50 (Mb) 60.8
 Max. length (Mb) 154.1
 Min. length (kb) 29.9
 Average length (Mb) 16.0
Chromosome assembly
 Total length (Mb) 2,614.8
 No. of Chromosome 23
 No. of Scaffold 105
 GC content (%) 41.3
 N50 (Mb) 112.3
 Max. length (Mb) 188.9
 Min. length (kb) 25.0
 Average length (Mb) 20.4
 Genome coverage 43.7×
 Mapping rate 99.98%
 BUSCO cetartiodactyla_odb10 C: 99.7%; F: 0.1%; M: 0.2%
Genome annotation
 Protein-coding genes 19,476
 Average gene length 1,618
 With annotation 19,155 (98.35%)
 BUSCO cetartiodactyla_odb10 C: 97.5%; F: 0.3%; M: 2.2%
Open in a new tab

Fossil-Calibrated Phylogenomic Tree and Demographic Analyses Reveal Species Divergence History

Phylogenomic reconstruction based on 3,360 single-copy orthogroups across 25 cetaceans, along with Hippopotamus amphibius as the outgroup, revealed a topology consistent with previous phylogenomic studies of cetaceans, supported by high bootstrap values (100 for all nodes) (Fig. 1c and Fig. S1). Within Balaenopteridae, B. edeni is phylogenetically close to B. brydei, forming a clade sister to Rice's whale (B. ricei). Notably, the balaenopterid humpback whale Megaptera novaeangliae and the eschrichtiid gray whale Eschrichtius robustus are nested within the Balaenoptera clade (Fig. 1c). The clade comprising Balaenopteridae and Eschrichtiidae is sister to Balaenidae, together forming the Mysticeti clade. Calibration of the tree using fossil records indicated that the common ancestor of B. edeni and B. brydei diverged approximately 7.84 million years ago (Ma) (95% confidence interval = 5.67 to 9.94 Ma) during the late Miocene, whereas the split between their ancestral lineage and B. ricei occurred earlier, around 10.49 Ma. The species historically considered part of the Bryde's whale complex, including B. edeni, B. brydei, and B. ricei (genome of B. omurai is unavailable), diverged earlier than the divergence between harbor porpoise Phocoena phocoena and vaquita Phocoena sinus (4.47 Ma), similar to the divergence of balaenid whales Eubalaena spp. (Fig. 1c). Our results support B. edeni and B. brydei as two distinct species, with a genetic divergence comparable to or even higher than that between other congeneric sister species.

To elucidate the evolutionary history of Bryde's whale complex, we determined the most likely demographic scenario among B ricei, B. brydei, and B. edeni using genome-wide SNP data. Among six examined scenarios (Figs. S3 and S4), Scenario 1, characterized by successive divergences without subsequent population bottlenecks, received the strongest support (posterior probability = 0.9956, Fig. 1d). In this scenario, B. brydei and B. edeni shared a most common ancestor at t1 (the most recent divergence time), and this common ancestor is sister to B. ricei, which diverged from their most recent common ancestor at t2 (the most ancient divergence time among the three species). This scenario aligns with the phylogenetic topology (Fig. 1c) and suggests that the divergence history of Bryde's whale complex is well explained by clean and sequential splits without additional demographic complexity.

Chromosomal Structure Variation among Balaenopterids

Chromosomal synteny provides valuable insights into genomic evolution. Compared to the outgroup H. amphibius, which possesses 18 chromosomes (2n = 36), the genomes of the Mysticeti clade exhibit diverse structural variations, including breakages, insertions, inversions, and fusions (Fig. 2a). Despite these variations, the chromosome number in mysticetes remains largely conserved, with exceptions noted for fusions in the genomes of Eubalaena spp. (Fig. 1a to c, Table S2). All examined balaenopterid and eschrichtiid genomes consist of 21 pairs of autosomes and one pair of allosomes (2n = 44). Our microsynteny analysis of balaenopterid genomes revealed that most chromosomal structures are highly conserved within the family, particularly Chr1, Chr8, Chr10, Chr15, Chr17, Chr18, Chr19, Chr20, Chr21, and ChrX based on the chromosome numbering of B. edeni (Fig. 2a). However, several macro-fragment inversions were identified across species. Notably, each balaenopterid genome exhibits at least one inter-chromosomal macro-fragment inversion compared to its closest relatives. Specifically: (i) Chr8 of the common minke whale (B. acutorostrata) contains a significantly inverted region compared to other balaenopterid whales; (ii) Chr9, Chr10, and Chr14 of M. novaeangliae exhibit inversions relative to other balaenopterid species; (iii) in B. musculus, a small region of Chr3 is inverted compared to B. acutorostrata, while the inversions in Chr4, Chr7, and Chr8 compared to B. ricei, and Chr2, Chr5, Chr6, Chr13, and Chr16 compared to B. edeni, distinguish it from Eden's and Rice's whales; (iv) in Rice's whales, Chr2, Chr4, Chr8, and Chr13 show inversions compared to B. edeni. Unexpectedly, we found large-scale complex rearrangements in the genome of Bryde's whale (Fig. 2b and c), although we cannot rule out the possibility that these are artifacts arising from its genome misassembly. Notably, intra-chromosomal inversions and inter-chromosomal insertions frequently occur across Bryde's whale chromosomes compared to B. edeni, leading to a complex and nearly disordered syntenic relationship between Bryde's whale, other cetaceans, and the outgroup hippo (Fig. 2). In B. brydei, only chromosomes Chr4, Chr5, Chr10, Chr12, Chr20, and Chr21 maintain large syntenic blocks aligned with B. edeni, with Chr5 containing the largest syntenic block in the whole genome (Fig. 2b and c). Additionally, we used the rearrangement index (Ri) to quantify and compare the rearrangement levels among selected cetaceans. Analyses using different reference genomes, B. edeni and H. amphibius, yielded similar results. Notably, B. brydei exhibits a significantly higher chromosomal rearrangement level than other Mysticeti species, as evidenced by its largest Ri, Ci, and Si values (Fig. 2d). Moreover, in B. brydei and E. glacialis, the Ci values are larger than the Si values, indicating a predominance of intra-chromosomal rearrangements. In contrast, in M. novaeangliae, the Ci values are smaller than the Si values, indicating frequent inter-chromosomal inversions. The Ri values for these Mysticeti are similar, ranging from 0.506 to 0.591 compared to H. amphibius and from 0.058 to 0.074 compared to B. edeni, apart from E. glacialis and M. novaeangliae. This suggests that the chromosomal structures of these genomes are conserved.

Fig. 2.

Fig. 2.

Open in a new tab

Synteny relationship between Eden's whale and its relatives. a) Ribbon diagram showing the microsynteny between the chromosomes of Eden's whale and its relatives. b) Macrosynteny between Eden's, blue, and Bryde's whales, and the hippo. c) Inter-chromosomal synteny between Eden's and Bryde's whales. d) Chromosomal rearrangement index of selected genomes references Eden's whale and hippo, respectively. The animal icons were obtained from the Plazi's databases (https://plazi.org/) without copyright restriction.

Our syntenic analysis indicates that the chromosomal structure of B. edeni closely resembles that of B. musculus (Fig. 2a and b), with four macrofragment inversions identified at one end of four chromosomes (Fig. 3a). Functional enrichment analysis found that the genes located in these inversion blocks (Table S5) are primarily involved in the metabolism and biosynthesis of various substances, as well as responses to substances, stress, and stimuli (Fig. 3b, Table S6). Most of these genes are associated with cellular, primary, and organic compound metabolisms and their regulation. Additional pathways related to macromolecule, nitrogen compound, protein, lipid, acid, and hormone metabolism and biosynthesis were also identified, alongside pathways related to cellular responses to chemicals, organic compounds, carbohydrates, growth factors, toxins, oxygen, and oxidation (Fig. 3b, Table S6). Our comparison of the microsynteny between the male allosomes (ChrY) of B. edeni and B. musculus (Fig. 3c) revealed their similar length and gene count, and their nine shared genes. Most of the shared genes are arranged in the same direction, with only TSPYL1 being inverted. Furthermore, we found that most genes of B. edeni have shorter lengths and fewer introns while retaining their functional domains (Fig. 3c). For instance, the protein of the KDM6A gene contains 608 amino acids (aa) in B. edeni and 1,355 aa in B. musculus, with the transcript containing nine and 28 introns, respectively. The gene ZFX has identical amino acid counts in both genomes but contains 5 and 10 introns in B. edeni and B. musculus, respectively. The factors affecting these gene sizes and intron differences, as well as the biological implications of these structural changes, remain unknown.

Fig. 3.

Fig. 3.

Open in a new tab

Specific chromosome structures and variations between Eden's and blue whales. a) Inversion macro-fragments in four chromosomes of Eden's whale compared to those of the blue whale. b) Top 30% GO functional enrichment, based on genes within the four inversion macrofragments of Eden's whale, showing their main functions of metabolism, biosynthesis, and responses. c) Gene synteny of the Y chromosomes of Eden's and blue whales.

Discussion

Macro-Fragment Inversion Drive Speciation and Adaptation

Chromosomal rearrangements—including fusion, fission, duplication, deletion, translocation, and inversion—drive reproductive barriers and speciation. These changes either alter chromosome numbers (through fusion/fission) or modify intra-chromosomal architecture (e.g., duplications and inversions), as demonstrated across multiple systems (Feder and Nosil 2009; De Vos et al. 2020; Lucek et al. 2023). Among these, chromosomal inversions—reversals of gene order within genomic regions—can promote adaptation by suppressing recombination between alternate rearrangements. This preserves adaptive allele combinations and genetic incompatibilities, facilitating speciation (Hoffmann and Rieseberg 2008; Poikela et al. 2024). Specifically, inversions drive divergence through maintaining polymorphisms via balancing selection, shielding co-adapted gene complexes from introgressive gene flow, and accelerating reproductive isolation (Noor et al. 2001; Navarro and Barton 2003; Faria et al. 2019). Despite highly conserved karyotypes across balaenopterid whales, we detected species-specific macro-fragment inversions in every genome analyzed (Fig. 2a). These species-specific inversions between balaenopterids create recombination barriers homologous to those implicated in speciation (Faria et al. 2019). While they likely contributed to balaenopterid divergence, further genomic validation is needed to confirm their causal roles.

Chromosomal rearrangements—including inversions documented in marine mammals—can mediate environmental adaptation by altering gene function (Zhang et al. 2020), primarily through suppressing allelic recombination, disrupting reading frames, and modifying gene expression (Kirkpatrick and Barton 2006; Villoutreix et al. 2021; Wright and Schaeffer 2022). Our functional enrichment analysis of inversion regions between B. edeni and B. musculus revealed two dominant functional categories: (i) metabolism and biosynthesis pathways (macromolecules, nitrogen compounds, proteins, lipids, acids, and hormones) critical for cetacean growth, development, and body size regulation (Sun et al. 2022); and (ii) stress–response systems involving chemical/organic compounds, carbohydrates, growth factor signaling, toxin detoxification, and oxygen homeostasis (Fig. 3b and c). Both functional clusters show established links to cetacean adaptation, metabolism, and development (Bukhman et al. 2024; Charlanne et al. 2025; Zhang et al. 2025), leading us to propose that these inversions contribute to the body size divergence between B. edeni and B. musculus (Kato and Perrin 2009; Sears and Perrin 2009). However, the limited tissue types and suboptimal RNA quality of the specimen used in this study highlight the need for future transcriptomic and proteomic studies to validate the functional impacts of these inversions.

Unexpected Complex Genome Rearrangement of Bryde's Whale

Our syntenic analyses revealed unexpectedly large-scale complex rearrangements in the Bryde's whale genome, characterized by prevalent intra-chromosomal inversions and inter-chromosomal insertions, high rearrangement index values, and minimal conserved blocks (Fig. 2b to d). This substantial syntenic discrepancy with B. edeni particularly unexpected given their relatively recent divergence (7.84 Ma). Yuan et al. (2021) assembled the genome of B. brydei from Illumina short reads and Hi-C data, but they did not analyze the synteny or report chromosomal rearrangements. We examined the assembly of Bryde's whale and found that their Hi-C contact heatmap is clear (Yuan et al. 2021). The mechanistic basis for these rearrangements could be complex, potentially involving DNA recombination, translocations, or aberrant repair/replication processes (Carvalho and Lupski 2016; Berdan et al. 2024), but unlikely attributable to transposable elements given their comparably low abundance in Bryde's whale versus B. musculus and B. physalus (Fig. 1f, Fig. S1f) despite known TE-mediated rearrangement mechanisms (Jurka et al. 2011; Ip et al. 2021; Schmitz and Querques 2024). However, given the large-scale rearrangements compared to other balaenopterids and the outgroup Hippopotamus, we could not rule out the possibility that the genome was misassembled when the genomic scaffolds were anchored to the Hi-C data. Sequencing an additional Bryde's whale individual is therefore essential to exclude this artifact and confirm the biological reality of these rearrangements.

Bryde's Whale as a Distinct Species

The taxonomy of the Bryde's whale complex remains contentious. While some morphological studies have suggested that Eden's and Bryde's whales are the same species (Andrews 1918; Junge 1950; Kato and Perrin 2009; Kershaw et al. 2013), previous phylogenetic studies using mitogenomes supported their separation (Wada et al. 2003; Sasaki et al. 2006; Luksenburg et al. 2015; Rosel et al. 2021). However, B. brydei has not been formally recognized due to the limited data for genomic comparison (Wada et al. 2003; Rosel et al. 2021). Coupled with earlier morphological and phylogenetic studies, our genomic comparisons provided a compelling case for recognizing Eden's and Bryde's whales as distinct species:

  1. The genetic distance of the mitochondrial gene cox1 between Eden's and Bryde's whales is 2.94%, exceeding the threshold commonly used for species delimitation in mammals (2%) (Hebert et al. 2003; Luo et al. 2011), and substantially larger than that between B. edeni and B. ricei (1.81%), as well as among Eubalaena whales (0.52% to 0.86%).

  2. Our phylogenomic analysis, based on phylogenetic analysis using 3,360 single-copy orthogroups, indicated that the phylogenetic distance between B. edeni and B. brydei is greater than those observed among other closely related mysticete species, although we found that B. edeni is sister to B. brydei, rather than to B. ricei as proposed by prior mitogenomic studies (Wada et al. 2003; Sasaki et al. 2006; Luksenburg et al. 2015; Rosel et al. 2021).

  3. Our calibration of the multigene phylogenetic tree using fossil records indicated that the common ancestor of B. edeni and B. brydei diverged about 7.84 Ma during the late Miocene, which occurred before the divergence of Phocoena sinus and P. phocoena around 4.47 Ma.

  4. Cranial characteristics have been applied to delimit the Bryde's whale complex (Wada et al. 2003; Yamada et al. 2006, 2008; Luksenburg et al. 2015; Rosel et al. 2021). The ascending of the maxilla is slender and round in B. edeni, and broadens only slightly posteriorly in B. ricei, while it widens to become squarish in B. brydei and B. omurai. Additionally, the posterior end of the premaxilla is broad and contacts the frontal in B. edeni, whereas it is slender and also reaches the frontal in B. brydei, but it fails to reach the frontal in B. omurai. These morphological features support the recognition that B. brydei, B. edeni, B. omurai, and B. ricei are distinct species in the Bryde's whale complex. Therefore, the formal reinstatement of B. brydei as a species is warranted.

  5. The syntenic analyses revealed large-scale complex rearrangements in B. brydei compared to B. edeni, which are potentially due to the misassembly of Bryde's whale genome, which needs confirmation.

Balaenopterid Phylogeny and Evolution of Bryde's Whale Complex

The evolutionary relationships within Balaenopteridae remain debated despite extensive research. Our phylogenomic analysis using single-copy orthogroups corroborates previous genomic studies (Sasaki et al. 2006; Árnason et al. 2018; McGowen et al. 2020), confirming the paraphyletic nature of this family with gray and humpback whales (E. robustus and M. novaeangliae) nested within Balaenoptera lineages. Notably, the gray whale shows an early divergence time of 16.13 Ma preceding most Balaenoptera speciation events yet maintains close phylogenetic affinity to the major clade of Balaenopteridae, including Bryde's whale complex, humpback, fin, and blue whales. Árnason et al. (2018) suggested that gray and humpback whales originated within Balaenopteridae, advocating for their classification under Balaenoptera based on genomic data, while their unique morphological and ecological traits challenge this view, reflecting broader systematic disagreements. Moreover, the phylogenetic relationships between gray whales and other Balaenopteridae species remain disputed, with different genetic analyses offering conflicting topologies lacking strong support (Hassanin et al. 2012; Árnason et al. 2018; Wolf et al. 2022). Previous studies suggested that these conflicting topologies likely result from evolutionary complexities such as introgression and incomplete lineage sorting (Nikaido et al. 2006; Sasaki et al. 2005; Furni et al. 2024), highlighting the difficulties in resolving relationships between Balaenopteridae and Eschrichtiidae. Therefore, these findings underscore the necessity for integrative genomic and morphological analyses to resolve long-standing controversies in cetacean systematics.

Within the Bryde's whale complex, studies based on mitochondrial control region sequences have yielded conflicting topologies: some suggested B. brydei clusters with sei whales (B. borealis) as sister to B. edeni (Wada et al. 2003; Luksenburg et al. 2015), while others indicated closer B. brydei–B. edeni affinity (Sasaki et al. 2006). Recent analyses further complicated this issue with weakly supported groupings (Rosel et al. 2021). These conflicting topologies, derived from limited sequence data, have impeded understanding of evolutionary relationships within the Bryde's whale complex. Our whole-genome phylogeny definitively resolves B. brydei and B. edeni as sister lineages with robust support, revealing their clear divergence from B. ricei and providing crucial insights into this taxonomically challenging group. Additionally, our demographic reconstruction revealed a highly supported divergence history that is consistent with the phylogenomic analyses and no subsequent population bottlenecks (Fig. 1d). This scenario reflects the conserved genomic architecture between B. ricei and B. edeni (Rosel et al. 2021) but fails to explain the extensive chromosomal rearrangements observed in B. brydei relative to its congeners. Furthermore, the unavailability of genomes for B. omurai and B. borealis necessitates continued investigation into the evolutionary relationships within the Bryde's whale complex. Genomic studies of these two species will advance our understanding of the phylogenetic structure and speciation processes of the Bryde's whale complex, while also providing critical insights into cetacean evolution.

Conclusion

We assembled a high-quality chromosomal-level genome of B. edeni, achieving 99.70% complete and 0.11% fragmented BUSCOs for the assembly. The predicted gene models show 97.50% complete and 0.30% fragmented BUSCOs. Phylogenomic analysis established that B. edeni is phylogenetically most closely related to B. brydei, forming a clade that is sister to B. ricei. Calibration of the tree indicated that the common ancestor of B. edeni and B. brydei diverged approximately 7.84 Ma during the late Miocene, whereas the split between their ancestral lineage and B. ricei occurred earlier, around 10.49 Ma. Demographic reconstruction revealed a scenario indicating that B. brydei and B. edeni shared a most common ancestor at t1, and this common ancestor is sister to B. ricei, which diverged from their most common ancestor at t2. Syntenic analyses revealed that macro-fragment inversions may play a role in the speciation of balaenopterid whales and identified unexpected large-scale complex genome rearrangements in Bryde's whale compared to other balaenopterids, but we cannot rule out the possibility that the genome was misassembled. Functional enrichment analysis of the inversion regions between B. edeni and B. musculus revealed that the genes located in these inversion blocks are primarily involved in the metabolism and biosynthesis of various substances, as well as responses to substances, stress, and stimuli. Our assembly and analyses provide fundamental genomic resources for further genetic and evolutionary research on cetaceans, offering comprehensive insights into the evolution, speciation, and taxonomy of the family Balaenopteridae and the Bryde's whale complex.

Materials and Methods

Supplementary material online contains details of materials and methods. In summary, the tissues from an Eden's whale, including blubber, inner muscle, liver, outer muscle, pelvis bone, and pelvis bone fat, were collected from the carcass stranded in Port Shelter, Hong Kong, on 2023 July 31. Genomic DNA was extracted from the inner muscle for Illumina, PacBio HiFi, and Hi-C sequencing, followed by hybrid assembly using integrated bioinformatic pipelines. Total RNA isolated from all tissues was subjected to transcriptomic sequencing to support gene model prediction. The phylogenomic analysis and divergence time estimation were performed using single-copy orthologs of 25 selected cetaceans and hippo as the outgroup. Then, the analyses of divergence scenarios, chromosomal synteny, rearrangement indices, and gene family expansion/contraction were conducted to study balaenopterid taxonomy and speciation.

Supplementary Material

msaf234_Supplementary_Data
msaf234_supplementary_data.zip (1.5MB, zip)

Contributor Information

Yi-Tao Lin, Department of Biology, Hong Kong Baptist University, Hong Kong SAR 999077, China.

Fan Hui, Department of Biology, Hong Kong Baptist University, Hong Kong SAR 999077, China.

Wentao Han, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Laoshan Laboratory, Qingdao 266100, China.

Yi-Xuan Li, Department of Biology, Hong Kong Baptist University, Hong Kong SAR 999077, China.

Bonnie Yuen Wai Heung, Department of Biology, Hong Kong Baptist University, Hong Kong SAR 999077, China.

Chun Ming How, Department of Biology, Hong Kong Baptist University, Hong Kong SAR 999077, China.

Shi Wang, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Laoshan Laboratory, Qingdao 266100, China.

Jian-Wen Qiu, Department of Biology, Hong Kong Baptist University, Hong Kong SAR 999077, China.

Supplementary material

Supplementary material is available at Molecular Biology and Evolution online.

Author Contributions

J.-W.Q. conceived and designed the project. Y.-T.L. and B.Y.W.H. collected the samples. Y.-T.L. and F.H. conducted experiments. Y.-T.L., F.H., W.H., Y.-X.L., and C.M.H. performed data analyses. S.W. provided crucial comments. Y.-T.L. drafted the manuscript. All authors contributed to the article and approved the submitted version.

Funding

This study was supported by the General Research Fund (12101021, 12102222) of the University Grant Committee (UGC) and the PI Project (GML20220018) of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou). We extend our gratitude to the Director of the Agriculture, Fisheries, and Conservation Department for granting permission for sampling and to Ocean Park Hong Kong for providing the samples. We wish to acknowledge the support provided by the High-Performance Biological Supercomputing Center at the Ocean University of China for this research.

Ethical Statement

This study was supported by the Research Ethics Committee (REC) of Hong Kong Baptist University, under permission number SCI-BIOL-2023-24-008.

Data Availability

The Illumina, PacBio HiFi, and RNA sequencing data have been deposited in the National Centre for Biotechnology Information (NCBI) Sequence Read Archive under the BioProject PRJNA1110565. The genome assembly has been deposited at GenBank with accession number JBDJPH000000000. The genome annotation is available in Figshare under DOI: 10.6084/m9.figshare.25801600.

References

  1. Anderson  J. Anatomical and zoological researches: comprising an account of the zoological results of the two expeditions to western Yunnan in 1868 and 1875; and a monograph of the two cetacean genera, Platanista. Bernard Quaritch; 1878. 10.5962/bhl.title.50434. [DOI] [Google Scholar]
  2. Andrews  RC. A note on the skeletons of Balaenoptera edeni, Anderson, in the Indian Museum, Calcutta. Rec Zool Surv India. 1918:15:105–107. 10.26515/rzsi/v15/i3/1918/163553. [DOI] [Google Scholar]
  3. Árnason  Ú, Lammers  F, Kumar  V, Nilsson  MA, Janke  A. Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow. Sci Adv. 2018:4:eaap9873. 10.1126/sciadv.aap9873. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Attard  CRM  et al.  From conservation genetics to conservation genomics: a genome-wide assessment of blue whales (Balaenoptera musculus) in Australian feeding aggregations. R Soc Open Sci.  2018:5:170925. 10.1098/rsos.170925. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Berdan  EL  et al.  Structural variants and speciation: multiple processes at play. Cold Spring Harb Perspect Biol. 2024:16:a041446. 10.1101/cshperspect.a041446. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Best  PB. Two allopatric forms of Bryde's whale off South Africa. Rep Mtg Int Whal Commn. 1977:1:10–38. https://archive.iwc.int/pages/search.php?search=%21collect. [Google Scholar]
  7. Bisconti  M, Carnevale  G. Skeletal transformations and the origin of baleen whales (Mammalia, Cetacea, Mysticeti): A study on evolutionary patterns. Diversity. 2022:14:221. 10.3390/d14030221. [DOI] [Google Scholar]
  8. Bukhman  YV  et al.  A high-quality blue whale genome, segmental duplications, and historical demography. Mol Biol Evol. 2024:41:msae036. 10.1093/molbev/msae036. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Carvalho  CM, Lupski  JR. Mechanisms underlying structural variant formation in genomic disorders. Nat Rev Genet. 2016:17:224–238. 10.1038/nrg.2015.25. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Charlanne  L  et al.  Ready to dive? Early constraints help juvenile southern elephant seals (Mirounga leonina) acclimatize to aquatic life. J Exp Biol. 2025:228:jeb-249813. 10.1242/jeb.249813. [DOI] [PubMed] [Google Scholar]
  11. Chen  B  et al.  Cooperative feeding and foraging lateralization by Eden's whales off southern China. Mar Mammal Sci. 2023:39:200–219. 10.1111/mms.12974. [DOI] [Google Scholar]
  12. Davis  RW. Marine mammals: adaptations for an aquatic life. Springer International Publishing; 2019. 10.1007/978-3-319-98280-9. [DOI] [Google Scholar]
  13. De Vos  JM, Augustijnen  H, Bätscher  L, Lucek  K. Speciation through chromosomal fusion and fission in Lepidoptera. Philos Trans R Soc Lond B Biol Sci. 2020:375:20190539. 10.1098/rstb.2019.0539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Faria  R, Johannesson  K, Butlin  RK, Westram  AM. Evolving inversions. Trends Ecol Evol. 2019:34:239–248. 10.1016/j.tree.2018.12.005. [DOI] [PubMed] [Google Scholar]
  15. Feder  JL, Nosil  P. Chromosomal inversions and species differences: when are genes affecting adaptive divergence and reproductive isolation expected to reside within inversions?  Evolution. 2009:63:3061–3075. 10.1111/j.1558-5646.2009.00786.x. [DOI] [PubMed] [Google Scholar]
  16. Furni  F, et al.  Phylogenomics and pervasive genome-wide phylogenetic discordance among fin whales (Balaenoptera physalus). Syst Biol. 2024:73:873–885. 10.1093/sysbio/syae049. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Hassanin  A, et al.  Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes. C R Biol. 2012:335:32–50. 10.1016/j.crvi.2011.11.002. [DOI] [PubMed] [Google Scholar]
  18. Hebert  PDN, Cywinska  A, Ball  SL, deWaard  JR. Biological identifications through DNA barcodes. Proc R Soc Lond B Biol Sci. 2003:270:313–321. 10.1098/rspb.2002.2218. [DOI] [Google Scholar]
  19. Hoffmann  AA, Rieseberg  LH. Revisiting the impact of inversions in evolution: from population genetic markers to drivers of adaptive shifts and speciation?  Annu Rev Ecol Evol Syst. 2008:39:21–42. 10.1146/annurev.ecolsys.39.110707.173532. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Ibrahim  A, Sun  J, Lu  F, Yang  G, Chen  B. First evidence of bubble trail production in Eden's whale (Balaenoptera edeni edeni). Mar Mammal Sci. 2024:40:e13120. 10.1111/mms.13120. [DOI] [Google Scholar]
  21. Ip  JCH  et al.  Host–endosymbiont genome integration in a deep-sea chemosymbiotic clam. Mol Biol Evol. 2021:38:502–518. 10.1093/molbev/msaa241. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Jossey  S  et al.  Population structure and history of North Atlantic blue whales (Balaenoptera musculus musculus) inferred from whole genome sequence analysis. Conserv Genet. 2024:25:357–371. 10.1007/s10592-023-01584-5. [DOI] [Google Scholar]
  23. Junge  GCA. On a specimen of the rare fin whale, Balaenoptera edeni Anderson, stranded on Pulu Sugi near Singapore. Zool Verh. 1950:9:1–26. https://repository.naturalis.nl/pub/317582/ZV1950009001.pdf. [Google Scholar]
  24. Jurka  J, Bao  W, Kojima  KK. Families of transposable elements, population structure and the origin of species. Biol Direct. 2011:6:44. 10.1186/1745-6150-6-44. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Kato  H, Perrin  WF. Bryde's whales: Balaenoptera edeni/brydei. In: Perrin  WF, Würsig  B, Thewissen  JGM, editors. Encyclopedia of marine mammals. Academic Press; 2009. p. 158–163   10.1016/B978-0-12-373553-9.00042-0. [DOI] [Google Scholar]
  26. Kershaw  F  et al.  Population differentiation of 2 forms of Bryde's whales in the Indian and Pacific oceans. J Hered.  2013:104:755–764. 10.1093/jhered/est057. [DOI] [PubMed] [Google Scholar]
  27. Kirkpatrick  M, Barton  N. Chromosome inversions, local adaptation and speciation. Genetics. 2006:173:419–434. 10.1534/genetics.105.047985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Lucek  K  et al.  The impact of chromosomal rearrangements in speciation: from micro- to macroevolution. Cold Spring Harb Perspect Biol. 2023:15:a041447. 10.1101/cshperspect.a041447. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Luksenburg  JA, Henriquez  A, Sangster  G. Molecular and morphological evidence for the subspecific identity of Bryde's whales in the southern Caribbean. Mar Mammal Sci. 2015:31:1568. 10.1111/mms.12236. [DOI] [Google Scholar]
  30. Luo  A  et al.  Potential efficacy of mitochondrial genes for animal DNA barcoding: a case study using eutherian mammals. BMC Genomics. 2011:12:84. 10.1186/1471-2164-12-84. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Marx  FG, Fordyce  RE. Baleen boom and bust: a synthesis of mysticete phylogeny, diversity and disparity. R Soc Open Sci. 2015:2:140434. 10.1098/rsos.140434. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Mcgowen  MR, et al.  Phylogenomic resolution of the cetacean tree of life using target sequence capture. Syst Biol. 2020:69:479–501. 10.1093/sysbio/syz068. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Navarro  A, Barton  NH. Accumulating postzygotic isolation genes in parapatry: a new twist on chromosomal speciation. Evolution. 2003:57:447–459. 10.1111/j.0014-3820.2003.tb01537.x. [DOI] [PubMed] [Google Scholar]
  34. Nikaido  M, et al.  Baleen whale phylogeny and a past extensive radiation event revealed by SINE insertion analysis. Mol Biol Evol. 2006:23(7):1455–1455. 10.1093/molbev/msk026. [DOI] [Google Scholar]
  35. Noor  MAF, Grams  KL, Bertucci  LA, Reiland  J. Chromosomal inversions and the reproductive isolation of species. Proc Natl Acad Sci U S A.  2001:98:12084–12088. 10.1073/pnas.221274498. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Olsen  O. On the external characters and biology of Bryde's whale Balaenoptera brydei, a new rorqual from the coast of South Africa. Proc Zool Soc Lond. 1913:83:1073–1090. 10.1111/j.1096-3642.1913.tb02005.x. [DOI] [Google Scholar]
  37. Park  JY  et al.  Cetaceans evolution: insights from the genome sequences of common minke whales. BMC Genomics. 2015:16:13. 10.1186/s12864-015-1213-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Perrin  WF, Mallette  SD, Brownell  JRL. Minke whales: Balaenoptera acutorostrata and B. bonaerensis. In: Perrin  W, Wursig  B, Thewissen  JGM, editors. Encyclopedia of marine mammals. Elsevier; 2018. p. 608–613   10.1016/B978-0-12-804327-1.00175-8. [DOI] [Google Scholar]
  39. Poikela  N, Laetsch  DR, Hoikkala  V, Lohse  K, Kankare  M. Chromosomal inversions and the demography of speciation in Drosophila montana and Drosophila flavomontana. Genome Biol Evol. 2024:16:evae024. 10.1093/gbe/evae024. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Ren  X, Ma  X, Allen  E, Fang  Y, Wen  S. DNA barcoding technology used to successfully sub-classify a museum whale specimen as Balaenoptera edeni edeni. Front Ecol Evol. 2022:10:921106. 10.3389/fevo.2022.921106. [DOI] [Google Scholar]
  41. Rosel  PE, Wilcox  LA. Genetic evidence reveals a unique lineage of Bryde's whales in the northern Gulf of Mexico. Endanger Species Res. 2014:25:19–34. 10.3354/esr00606. [DOI] [Google Scholar]
  42. Rosel  PE, Wilcox  LA, Yamada  TK, Mullin  KD. A new species of baleen whale (Balaenoptera) from the Gulf of Mexico, with a review of its geographic distribution. Mar Mammal Sci. 2021:37:577–610. 10.1111/mms.12776. [DOI] [Google Scholar]
  43. Sasaki  T, et al.  Mitochondrial phylogenetics and evolution of mysticete whales. Syst Biol. 2005:54:77–90. 10.1080/10635150590905939. [DOI] [PubMed] [Google Scholar]
  44. Sasaki  T  et al.  Balaenoptera omurai is a newly discovered baleen whale that represents an ancient evolutionary lineage. Mol Phylogenet Evol. 2006:41:40–52. 10.1016/j.ympev.2006.03.032. [DOI] [PubMed] [Google Scholar]
  45. Schmitz  M, Querques  I. DNA on the move: mechanisms, functions and applications of transposable elements. FEBS Open Bio. 2024:14:13–22. 10.1002/2211-5463.13743. [DOI] [Google Scholar]
  46. Sears  R, Perrin  WF. Blue whale: Balaenoptera musculus. In: Perrin  WF, Würsig  B, Thewissen  JGM, editors. Encyclopedia of marine mammals. Elsevier; 2009. p. 120–124. 10.1016/B978-0-12-373553-9.00033-X. [DOI] [Google Scholar]
  47. Soot-Ryen  T. On a Bryde's whale stranded on Curacao. Nor Hvalfangst-Tid. 1961:50:323–332. [Google Scholar]
  48. Sun  D  et al.  Novel genomic insights into body size evolution in cetaceans and a resolution of Peto's paradox. Am Nat. 2022:199:E28–E42. 10.1086/717768. [DOI] [PubMed] [Google Scholar]
  49. Sun  J  et al.  A young Eden's whale (Balaenoptera edeni edeni) wandering in a busy international container port. Aquat Mamm. 2023:49:321. 10.1578/AM.49.4.2023.321. [DOI] [Google Scholar]
  50. Villoutreix  R  et al.  Inversion breakpoints and the evolution of supergenes. Mol Ecol. 2021:30:2738–2755. 10.1111/mec.15907. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Wada  S, Oishi  M, Yamada  TK. A newly discovered species of living baleen whale. Nature. 2003:426:278–281. 10.1038/nature02103. [DOI] [PubMed] [Google Scholar]
  52. Wolf  M, De Jong  M, Halldórsson  SD, Árnason  Ú, Janke  A. Genomic impact of whaling in north Atlantic fin whales. Mol Biol Evol. 2022:39:msac094. 10.1093/molbev/msac094. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Wolf  M, De Jong  MJ, Janke  A. Ocean-wide conservation genomics of blue whales suggest new northern hemisphere subspecies. Mol Ecol. 2025:34:e17619. 10.1111/mec.17619. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Wright  D, Schaeffer  SW. The relevance of chromatin architecture to genome rearrangements in Drosophila. Philos Trans R Soc Lond B Biol Sci. 2022:377:20210206. 10.1098/rstb.2021.0206. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Yamada  TK, et al.  Middle-sized balaenopterid whale specimens (Cetacea: Balaenopteridae) preserved at several institutions in Taiwan, Thailand, and India. Mem Natn Sci Mus Tokyo. 2006:44:1–10. https://www.kahaku.go.jp/research/publication/memoir/download/44/4401.pdf. [Google Scholar]
  56. Yamada  TK, Kakuda  T, Tajima  Y. Middle sized balaenopterid whale specimens in the Philippines and Indonesia. Mem Natn Sci Mus Tokyo. 2008:45:75–83. https://www.kahaku.go.jp/english/research/researcher/papers/18100.pdf. [Google Scholar]
  57. Yuan  Y  et al.  Comparative genomics provides insights into the aquatic adaptations of mammals. Proc Natl Acad Sci U S A.  2021:118:e2106080118. 10.1073/pnas.2106080118. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Zhang  F, et al.  Comparative genomics uncovers molecular adaptations for cetacean deep-sea diving. Mol Ecol. 2025:0:e17678. 10.1111/mec.17678. [DOI] [Google Scholar]
  59. Zhang  P  et al.  An Indo-Pacific humpback dolphin genome reveals insights into chromosome evolution and the demography of a vulnerable species. iScience. 2020:23:101640. 10.1016/j.isci.2020.101640. [DOI] [PMC free article] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

msaf234_Supplementary_Data
msaf234_supplementary_data.zip (1.5MB, zip)

Data Availability Statement

The Illumina, PacBio HiFi, and RNA sequencing data have been deposited in the National Centre for Biotechnology Information (NCBI) Sequence Read Archive under the BioProject PRJNA1110565. The genome assembly has been deposited at GenBank with accession number JBDJPH000000000. The genome annotation is available in Figshare under DOI: 10.6084/m9.figshare.25801600.

Articles from Molecular Biology and Evolution are provided here courtesy of Oxford University Press

RESOURCES