A whale apart: further evidence for genetic isolation of Arabian Sea humpback whales from other recognised subspecies

Abstract

Genetic studies have differentiated three subspecies of humpback whales: Megaptera novaeangliae novaeangliae in the North Atlantic, M. n. australis in the Southern Hemisphere and M. n. kuzira in the North Pacific. However, these analyses did not include samples from the Arabian Sea humpback whale population (ASHW). Historic, behavioural, and previously published genetic data suggested that ASHWs are a discrete, isolated and resident population. This study provides further evidence of genetic uniqueness of the ASHWs by comparing samples collected in Oman with the three existing humpback whale subspecies. The morphological and genetic data obtained in this study confirmed the identification of the type specimen for Megaptera indica from Iraq as a humpback whale, closely related to contemporary ASHWs. Genetic differentiation between ASHWs and other subspecies were found (Fst values 0.1213-0.2441 and φ_ST values 0.0831-0.6470). Together with the multiple lines of evidence for reproductive and behavioural isolation of this unique humpback whale population that does not undertake seasonal latitudinal migrations as do all other populations, this genetic data support the recognition of a fourth subspecies, which would be named for the type specimen from Iraq: Megaptera novaeangliae indica. Anthropogenic threats to ASHWs and their habitat are severe and escalating and there is a risk of extirpation. Population abundance is low with no evidence of increasing over the past two decades. The genetic differentiation of ASHWs may have been driven by a range of interdependent biogeographical and ecological factors coupled with behavioural adaptations over a period of ~43,000-113,000 years. Regionally coordinated conservation action is urgently needed to preserve this population’s unique genetic diversity.

Introduction

Understanding and identifying different evolutionary trajectories within species and among population groups is of paramount importance for effective conservation planning and management. Central to this is determining whether populations are demographically or genetically isolated. Population differentiation can reflect long-term isolation, local adaptation, and restricted gene flow, which are factors that often warrant taxonomic reassessment and may influence conservation priorities (Crandall et al., 2000; Moritz, 1994).

Among cetaceans, several species with broad geographic distributions comprise subpopulations that have followed partially independent evolutionary trajectories and are therefore recognized as subspecies. The harbor porpoise, Phocoena phocoena, has been divided into three formally recognized subspecies corresponding to the North Atlantic (P. p. Phocoena), North Pacific (P. p. vomerina) and the Black Sea relict population (P. p. relicta) (Celemín et al., 2025; Perrin et al., 2009; Viaud-Martinez et al., 2007). Killer whales (Orcinus orca) are structured into multiple, behaviorally and genetically distinct ecotypes, with recent genomic studies arguing that some eastern North Pacific ecotypes merit species-level recognition (Morin et al., 2024). Minke whales (Balaenoptera acutorostrata) are likewise divided into divided into three sub-species: the North Atlantic (B.a. acutorostrata), the North Pacific (B. a. scammoni), and the dwarf common minke whale (B. a. unnamed sub-species), which is thought to be restricted to the Southern hemisphere, revealing hemisphere-scale and regional units that reflect ecological segregation and limited gene flow (Quintela et al., 2014).

Humpback whales, Megaptera novaeangliae, are a globally distributed species with a broad range structured into multiple defined breeding stocks (e.g. IWC, 2006) and three recognised subspecies (M. n. novaeangliae in the North Atlantic, M. n. australis in the Southern Hemisphere and M. n. kuzira in the North Pacific) (Jackson et al., 2014). The Arabian Sea humpback whale population is unique among studied humpback whale populations as it exhibits clear behavioural, genetic, physiological, and ecological traits that suggest a long history of isolation from other humpback whale populations (Pomilla et al., 2014; Minton et al., 2011).

Humpback whales living in the Arabian Sea are unique among all other studied populations of humpback whales because they do not undertake long seasonal latitudinal migrations between polar or temperate feeding grounds and tropical breeding grounds (e.g. Reeves et al., 1991; Mikhalev, 1997; Minton et al., 2011). Various studies have shown that they adhere to a northern hemisphere breeding cycle despite having no feasible migration routes to northern feeding grounds (Mikhalev, 1997), are present year-round off the coast of Oman (e.g. Minton et al., 2011), are genetically distinct from neighboring Indian Ocean populations (Pomilla et al., 2014), and have a vocal repertoire that differs from other humpback whale populations (Cerchio et al., 2018). Strong seasonal upwelling driven by the southwest monsoon creates hyper-productive conditions more typical of temperate climates, allowing the whales to feed at tropical latitudes normally associated only with humpback whale breeding activities (Reeves et al., 1991; Mikhalev, 1997). The population is recognized by the International Whaling Commission (IWC) as a discrete breeding and feeding population, and has been recommended for an IWC Conservation Management Plan (IWC, 2018). It is recognized under the US Endangered Species Act as an Endangered humpback whale Distinct Population Segment (Bettridge et al., 2015), and has been assessed as an Endangered subpopulation on the IUCN Red List of Threatened Species (Minton et al., 2008).

Gervais (1883) formally described a new species of humpback whale, Megaptera indica, based on a baleen whale that had stranded in the western Persian/Arabian Gulf at Basora Bay, within the Shatt al-Arab River Delta near present-day Basra (30°30’54”N, 47°48’36”E), Iraq. This skeleton was deposited in the Paris Natural History Museum (Muséum National d’Histoire Naturelle, MNHN-ZM-AC-1883-2255). The new species was quickly considered another synonym in an already long list of nominal humpback whale species given to various specimens collected around the world. Megaptera indica was noted when Robineau (1989) published a list of cetacean holotypes in the MNHN. Interest in the species identification and the taxonomic status of the holotype was renewed following the completion of genetic work suggesting the Arabian Sea humpback whales were different from other humpback populations (Pomilla et al., 2014) and following a morphological re-examination of the holotype in May 2019 (Van Waerebeek et al., 2025) which confirmed the identification as Megaptera novaeangliae.

The aims of this study are: i) to confirm the taxonomic identity of the holotype of Megaptera indica (Gervais, 1883) using morphology and by sequencing the mitochondrial DNA control region; ii) investigate if the type specimen for Megaptera indica is genetically closely related to contemporary humpback whale samples from the Arabian Sea; and iii) further clarify the taxonomic status of the contemporary Arabian Sea humpback whale (ASHW) population.

Materials and methods

Morphological data

The cranial characteristics of M. indica holotype (n° 1883-2255) were examined by KVW and RB, at the MNHN museum (Van Waerebeek et al., 2025), and a sample of cranial bone was obtained for genetic analysis. The cranial sample used came from appropriate permissions for bone sample extraction, and export and import of the more than 100-year-old specimen were obtained from the museum and CITES. The skull is incomplete, and the whereabouts of postcranial bones collected with the specimen is unknown. The specimen was cranially mature. A protocol of 50 standard cranial measurements was prepared on the skull, following mostly Omura (1975). However, only about half of the craniometrics could be measured or estimated given the incomplete condition of the skull.

Genetic data

Ancient DNA extraction, sequencing and mapping

DNA extraction from the M. indica holotype was performed in a lab dedicated to ancient biomolecules with a workflow that minimized risk of contamination from modern DNA. A sterilized Dremel drill was used to sub-sample the bone, from which bone dust was collected. We followed the extraction protocol of Dabney and Meyer (2019). Briefly, we incubated 50mg of pulverized bone sample at 37 °C overnight (~18 hours) in the extraction buffer. We then added the binding buffer to the sample and used a MinElute (Qiagen) tube with an attached Zymo reservoir to centrifuge the lysate through the MinElute filter. We then performed two washes with PE Buffer (Qiagen). We eluted in 50 μL of an elution buffer consisting of 1979 parts water, 20 parts Tris-HCl (1M, pH 8.0) and 1 part Tween20. Single-stranded ancient DNA libraries were prepared by Arbor Biosciences. Libraries were subsequently sequenced on an Illumina NovaSeq X Plus platform.

We used the Paleomix pipeline (Schubert et al., 2014) to trim reads and map them to the M. novaeangliae mitochondrial genome (GenBank ID: AP006467.1). Overlapping paired-end reads were collapsed and all resulting paired, single, or collapsed reads were mapped to the reference mitogenome using bwa mem (Li, 2013). Only reads with a mapping quality greater than 20 were kept, and PCR duplicates were removed. MapDamage 2.0 (Jónsson et al., 2013) was used to characterize DNA damage patterns and rescale base quality scores. A consensus sequence for the M. indica holotype mitogenome was generated from the resulting BAM file using ANGSD -doFasta 2 (Korneliussen et al., 2014), using the most common base pair at each position. Sites with less than 5X read depth were marked as missing (‘N’).

Genetic identity

The genetic identity of the holotype specimen for M. indica was verified by aligning the obtained sequence with a complete humpback whale mitochondrial genome as reference (GenBank Accession Number AP006467.1), by performing a BLAST search (https://blast.ncbi.nlm.nih.gov/Blast.cgi), and by phylogenetic inference as described below.

Sequence sampling

Sequences of the mtDNA control region were compiled from the North Pacific (n = 195), South Pacific (n = 897), South Indian Ocean (n = 909), Arabian Sea (n = 47)¹, South Atlantic (n = 213) and North Atlantic (n = 23) (GenBank Accession Numbers in Supplementary Table S1) comprising the three described humpback whale subspecies. For the phylogenetic reconstructions, a fin whale (Balaenoptera physalus) sequence was used (GenBank Accession Number OQ924505). In total, 2285 humpback whale mtDNA control region sequences were analyzed including the holotype specimen for M. indica. Sequences were aligned using Geneious Prime (Geneious Prime 2025.0.3, https://www.geneious.com).

Genetic diversity and population genetics

Genetic diversity, measured as haplotypic (h) and nucleotide (π) diversities, were estimated in Arlequin 3.5.2.2 (Excoffier and Lischer, 2010). Genetic differentiation between the different oceanographic regions was estimated as Pairwise F- and Φ- statistics in Arlequin using 50–000 matrix permutations. Φ-st was adjusted to the Kimura 2-parameter model as estimated by IQ-TREE (see below), to correct for multiple substitutions. The net nucleotide divergence, d_A, was also estimated in DNAsp 6.12.03 (Rozas et al., 2017). All pairwise comparisons were adjusted using Bonferroni correction.

Hierarchical AMOVA tests were conducted in Arlequin 3.5.2.2 (Excoffier and Lischer, 2010) to test for different population differentiation scenarios: 1) Four oceanographic regions corresponding to the three subspecies proposed by Jackson et al., 2014 and the Arabian Sea (North Pacific, North Atlantic, Southern Hemisphere and Arabian Sea); 2) Six main oceanographic regions with further levels of differentiation per ocean basin and hemisphere (North Atlantic, South Atlantic, Arabian Sea, South Indian Ocean, North Pacific and South Pacific).

Phylogenetic analyses

For phylogenetic reconstructions, haplotypes from the whole dataset were obtained using DNAsp 6.12.03 (Rozas et al., 2017). A maximum-likelihood tree was estimated in IQ-TREE 2 (Minh et al., 2020) with branch supports obtained with the ultrafast bootstrap (Hoang et al., 2018). Default settings, as suggested by the authors, were used. The best fitting substitution model for the dataset was estimated as part of the algorithm. The resulting phylogenetic tree was visualized in FigTree 1.4.4 (Rambaut, 2018).

To further investigate phylogenetic relationships and to estimate divergence times among humpback whale groups from different oceanographic regions, BEAST 10.5.0 (Suchard et al., 2018) was used with a smaller dataset of 265 humpback whale mtDNA control region sequences. These were selected randomly for each one of the oceanographic regions considered. Analyses were run for 25 million generations with a strict molecular clock using a rate of 3.94% bp^-1 Myr^-1 for the humpback control region as determined by phylogenetic approaches (Jackson et al., 2009). Three coalescent models were tested for best fit: constant, expansion and logistic size population. The program TRACER 1.7.2 (Rambaut et al., 2018) was used to assess mixing and convergence of the posterior distribution and parameter estimates by examining estimated sample size (ESS) values and to determine the best-fitting parameters.

Results

Morphologic and genetic identity of the M. indica type specimen

The museum holotype specimen for M. indica was confirmed to be a humpback whale based on both morphological and genetic evidence. Detailed morphological study of the skull (Van Waerebeek et al., 2025) identified several key features diagnostic of M. novaeangliae: (i) The supraorbital processes of the frontal bone in Megaptera are most prominent. (ii) Humpback whales have the largest breadth of skull relative to rostrum width at base among balaenopterids. However, M. indica positioned intermediate between M. novaeangliae and other balaenopterids. In fact, M. indica overlaps with the lower range for Atlantic humpback whales and amply exceeds the ratio in other balaenopterid species. (iii) In M. novaeangliae, the imaginary line that unites the external borders of the orbital processes of the maxillae lies behind the nasals. (iv) Among large balaenopterids, M. novaeangliae has the maximum zygomatic process width index (relative to condylobasal length), somewhat higher than M. indica. So here again, M. indica scores in between M. novaeangliae and other balaenopterids, suggesting a taxonomic significance. (v) The naso-frontal process of the maxillae widens posteriad in all balaenopterids, except in M. novaeangliae and M. indica. (vi) Gervais (1883) reported the M. indica scapula without a coracoid process and that the acromion was a mere rudimentary tubercle. This feature is uniquely diagnostic for M. novaeangliae. Gervais also mentioned black baleen and long flippers, equally consistent with humpback whale. (vii) As observed in M. indica, the anterior margin of the squamosal is rounded or U-shaped in M. novaeangliae, versus pointed or V-shaped in Balaenoptera spp. In addition, the squamosal bones in M. indica are heavily built. Indicative also for Megaptera is the lack of a distinct fold or “squamosal crease”. In conclusion, the M. indica holotype clearly differs morphologically from Balaenoptera spp. and shows all diagnostic characters of M. novaeangliae. Nonetheless, two cranial indices in M. indica expose some level of differentiation with M. novaeangliae specimens from the North Atlantic, suggested at subspecific level.

The genetic analyses independently corroborate the morphological identification. Mitochondrial DNA from the holotype specimen aligned with the M. novaeangliae mitochondrial genome used as a reference. Subsequent BLAST search results (99%) and phylogenetic reconstruction confirmed this identification (GenBank Accession Number PX526867).

Genetic diversity and differentiation

A consensus region of 462 bp of the mtDNA control region was assembled from 2285 humpback whale individuals sampled throughout the species’ distribution and included the holotype specimen for M. indica. A total of 254 haplotypes (Supplementary Table S2) were detected from 98 polymorphic sites. Total worldwide haplotypic diversity (h) was 0.9850 and nucleotide diversity (π) was 2%, values that are within the diversity measures that have been previously described for the species (Jackson et al., 2014). Within each ocean basin, the Arabian Sea population showed the lowest levels of haplotypic (0.667) and nucleotide diversity (1.1%), followed by the North Pacific (h = 0.775 and π=1.2%) (Table 1).

Estimates of pairwise F_ST and Φ_ST showed high levels of differentiation for the ASHW in all comparisons (Tables 2, 3). The highest divergence was with the North Pacific (F_ST=0.2441 and Φ_ST=0.6470), and with North Atlantic (F_ST=0.2049 and Φ_ST=0.2345), (Table 2). When Southern Ocean populations were considered separated by ocean basin, comparisons with the Arabian Sea population showed the lowest values with the South Indian Ocean (F_ST=0.1123 and Φ_ST=0.0682), with a differentiation gradient related to geographic distance (Table 3). Overall, differentiation was greatest between the North Pacific, North Atlantic and the Arabian Sea and lowest in all comparisons with Southern Ocean regions (Table 3).

For F_ST estimates, values of differentiation for the Arabian Sea were higher than those for the comparison between North Pacific and North Atlantic; but for φ_ST estimates, the highest differentiation value was observed for the North Pacific. Nei’s measure of net nucleotide divergence (d_A) ranged from 0.0019 and 0.0174 (Table 4). The highest values were found for the North Pacific while the lowest value was found for the comparison between Southern Ocean and Arabian Sea humpback whales.

The hierarchical AMOVA showed strong differentiation among ocean basins and the Arabian Sea. Greater differentiation was found between the four main regions considered (31% and 10% of total molecular and haplotypic genetic variation, respectively) than between the six oceanographic regions considered (13% and 4% of total molecular and haplotypic genetic variation, respectively) (Table 5).

The maximum likelihood phylogenetic tree obtained for the 254 haplotypes revealed four major clades previously identified in humpback whale studies (Figure 1) (Olavarria et al., 2007; Baker et al., 1993; Jackson et al., 2014). These are: 1) clade ‘AE’, more basal and clearly separated from all others, including most of the North Pacific haplotypes, but also five Southern Ocean haplotypes; 2) clade “IJ” (97 bootstrap support), which, though the majority of the haplotypes are from the Southern Ocean, also includes most of the North Atlantic (seven) and Arabian Sea (five) haplotypes; 3) clade ‘CD’ (100 bootstrap support), the largest clade including Southern Ocean haplotypes, but also three Arabian Sea haplotypes (including the holotype specimen for M. indica), two North Atlantic haplotypes and two North Pacific haplotypes; 4) clade ‘SH’ (99 bootstrap support) including Southern Ocean haplotypes only.

Figure 1

Baker et al., 1993 and Olavarria et al., 2007. North Pacific haplotypes are colored in red, North Atlantic haplotypes in blue, Arabian Sea haplotypes in green and Southern Hemisphere haplotypes in black. Bootstrap support values are shown in each clade. * denotes the museum voucher specimen M. indica.

The Bayesian coalescent approach implemented in BEAST for a subset of the samples resulted in a phylogenetic tree with a similar topology to the maximum-likelihood tree described above (Figure 2). The main difference is that most Arabian Sea individuals are placed in the Southern Hemisphere ‘CD’ clade, forming two polyphyletic groups (including the holotype specimen for M. indica). Two additional smaller polyphyletic groups are observed within the ‘IJ’ clade (Figure 2).

Figure 2

Baker et al., 1993 and Olavarria et al., 2007. North Pacific clades are colored in red, North Atlantic clades in blue, Arabian Sea clades in green and Southern Hemisphere in black. Numbers represent the divergence time estimates in ka. * denotes the museum voucher specimen M. indica.

After examining the posterior distributions of ESS, where relevant parameters reached ESS values well above the recommended threshold (>200), indicating that the analyses converged and that parameter estimates are reliable, the constant size model was selected. The median root age of the tree was 522ka (95%HPD 394-691ka), separating the Southern Hemisphere ‘CD’ clade from the North Pacifc ‘AE’ clade and the ‘IJ’ clade. The North Pacific clade diverged from the ‘IJ’ clade 346ka (95%HPD 224–466 ka). The earliest divergence within the ‘CD’ clade was 439ka (95%HPD 347-574ka). The Arabian Sea clade that included the museum holotype for M. indica, which is also the largest, diverged 78ka (95%HPD 34-128ka) and the other smaller clade diverged 43ka (95%HPD 11-98ka). Within the ‘IJ’ clade, the largest Arabian Sea clade diverged 113ka (95%HPD 48-182ka).

Discussion

The morphological and genetic data obtained in this study confirmed that the type specimen for M. indica from Iraq is Megaptera novaeangliae, and the genetic data confirmed that it is closely related to contemporary ASHW. This suggests that contemporary humpback whales encountered in the Persian/Arabian Gulf (Dakhteh et al., 2017) likely belong to the ASHW population.

Previous worldwide analysis of humpback whale mtDNA diversity found significant genetic structure between the North Atlantic, North Pacific and the Southern Hemisphere, and suggested that whales occurring in these regions be considered separate subspecies (Jackson et al., 2014). The authors based their argument on the existence of two types of evidence supporting an independent evolutionary trajectory for humpback whales in the three ocean basins: i) differentiation and divergence of mtDNA and ii) multiple nuclear loci, reflecting reproductive isolation (Jackson et al., 2014). Subsequently, these subspecies designations were formally adopted by the Society for Marine Mammalogy’s Committee on Taxonomy (Society for Marine Mammalogy, Committee on Taxonomy, 2026). Jackson et al. (2014), however, did not include humpback whales from the Arabian Sea, a population which has been previously shown to be highly differentiated from all others (Pomilla et al., 2014). In the present study, individuals from all four ocean basins were analyzed, building upon what has been previously published.

The high levels of genetic differentiation between ASHW and the subspecies occurring in the North Pacific, North Atlantic and the Southern Hemisphere suggest very limited gene flow. Obtained levels of F_ST and Φ_ST were relatively high (0.11-0.24 and 0.08-0.64, respectively) compared to those obtained in other balaenopterids (Quintela et al., 2014; Archer et al., 2019). These results also support the existence of an equatorial barrier to gene flow in humpback whales. This pattern of divergence between hemispheres has been well established for cetacean species (Davies, 1963), as seen for example in fin whales, where very limited gene flow occurs between North Pacific, North Atlantic and the Southern Oceans (Archer et al., 2019). However, for humpback whales there is also a apparent barrier to gene flow in the Indian Ocean, separating humpback whales in the Arabian Sea from others further south. As with humpback whale and fin whale populations in other ocean basins the main barrier to gene flow for ASHW and Southern Indian Ocean humpback whales is likely the asynchronous breeding cycle in which ASHW adhere to a northern hemisphere breeding cycle six months out of phase with Southern Hemisphere counterparts (Mikhalev, 1997).

Phylogenetic analyses show that ASHW do not group monophyletically, with individuals from this region distributed in separate clades, with different divergence time estimates ranging from 113ka to 43 ka. This suggests there could have been several radiation events, likely from the Southern Hemisphere. The estimated divergence times fall within the Late Pleistocene, a period characterised by pronounced glacial–interglacial climatic oscillations that substantially altered sea level, ocean circulation, and productivity in the Indian Ocean, potentially facilitating episodic isolation and dispersal (Lisiecki and Raymo, 2005; Lambeck et al., 2014; Clemens and Prell, 1991).

A lack of monophyly is also seen in humpback whales from the North Pacific, North Atlantic and the Southern hemisphere. These patterns can arise through incomplete lineage sorting, particularly in recently diverged lineages where ancestral genetic variation has not yet sorted into regionally exclusive clades (Maddison and Knowles, 2006) and is documented in several cetacean species (Amaral et al., 2012).

Criteria for subspecies delimitation in cetacean species have been proposed by Reeves (2004), and more recently by Taylor et al. (2017), who state that: A subspecies is a population, or collection of populations, that appears to be a separately evolving lineage with discontinuities resulting from geography, ecological specialization, or other forces that restrict gene flow to the point that the population or collection of populations is diagnosably distinct.” The data presented here provide further evidence that ASHW are likely to meet the criteria for a distinct subspecies Megaptera novaeangliae indica (Gervais 1883) based on the multiple lines of evidence provided below.

Genetic differentiation

ASHW show high levels of genetic differentiation in mtDNA (as shown above), with the highest F_ST comparisons of any humpback whale population, but also in microsatellites (see Pomilla et al., 2014).

Ecological and behavioral differentiation

Multiple studies have confirmed the year-round residency of ASHW at tropical and subtropical latitudes (e.g. Minton et al., 2011), which have led to multiple forms of the ‘ecological specialization, or other forces that restrict gene flow’ cited as a condition for subspecies recognition by Taylor et al. (2017). These specializations include: 1) adherence to a Northern Hemisphere breeding and feeding cycle (Mikhalev, 1997; Minton et al., 2011; Cerchio et al., 2016). This almost certainly prevents interbreeding with Southern hemisphere humpback whale populations, that would only have an opportunity for contact when they are in neighbouring tropical latitudes (e.g. Maldives, Tanzania, Sri Lanka) during the Boreal summer months, when ASHW are engaged in feeding activity and not singing, which is associated with reproduction (Minton et al., 2011; Cerchio et al., 2018; Anderson et al., 2022). 2) The evolution of a distinct song, shared between Oman and India, but not with Southern Indian Ocean populations (Cerchio et al., 2018; Cerchio et al., 2023a) which would render the Arabian Sea population culturally and behaviorally distinct.

Analysis of stomach contents of ASHW also demonstrated differences in prey between ASHW and Southern Hemisphere populations, with ASHW relying more heavily on sardines (particularly off the coast of Oman) than krill (Mikhalev, 2000).

Morphological differentiation

ASHW are currently not easily distinguishable from other subspecies of M. novaeangliae by diagnostic morphological characters. However, they are larger than other described subspecies. The total lengths of 238 whales examined in the Arabian Sea in the 1960s were 13.31 m and 12.78 m for females and males respectively (Mikhalev, 2000). The average size of both sexes combined was 13.05 m (Mikhalev, 2000). This is larger than the combined average size of 12.47 m for whales taken in the Southern Hemisphere (Tomilin, 1957). The largest ASHW female was 15.2 m (Mikhalev, 1997). Mikhalev (2000) attributes the larger size of the Arabian Sea whales to a lack of previous exploitation, while selection of larger individuals for hunting drove average sizes down in other populations. Mikhalev (1997) and Minton et al. (2011) described differences in the proportions of ventral pigmentation types (dark to light) in ASHW and Southern Hemisphere populations, as well as a total lack of cookie-cutter scarring on ASHW, something which is typical of Southern Hemisphere humpback whales. Both Mikhalev (1997) and Minton et al. (2023) also describe a much lower rate of barnacle scarring on ASHW than Southern Hemisphere populations.

Evidence for subspeciation

Collectively, these data clearly show that ASHW are on an independent evolutionary trajectory, despite lack of clear monophyly or fixed, diagnostic characters present in mtDNA. This pattern is not uncommon for cetacean subspecies (Rosel et al., 2017). In a speciation continuum, recent diverged taxa can reveal a lack of monophyly, likely due to incomplete lineage sorting and the fact that gene trees do not always adequately model species trees (Knowles and Carstens, 2007; Amaral et al., 2012). A threshold of Nei’s D_A higher than 0.004 has been suggested as a proxy to infer subspecies in cetaceans (Taylor et al., 2017). ASHW and Southern Ocean humpbacks show a value lower than 0.004. However, caution should be applied when establishing genetic thresholds, since these do not explicitly take into account how the timing of speciation influences patterns of genetic differentiation (Knowles and Carstens, 2007). For ASHW, other lines of evidence, as stated above, strongly support the distinction into a separate subspecies.

Conservation implications

The results of the current genetic and morphological analyses further emphasize the discrete and evolutionary distinctiveness of this population. Such isolation results in vulnerability to extirpation, which is exacerbated by a range of both direct and indirect anthropogenic threats. Minton et al. (2022) found that over two thirds of examined ASHW from the coast of Oman bore signs of scarring consistent with entanglement in fishing gear, and Farinelli et al. (2024) calculated high bycatch risk within core habitat identified in the Gulf of Masirah, Oman. Oman, Iran and Pakistan all have large tuna fishing fleets that almost exclusively use large mesh gillnets, known to entangle cetaceans generally (Perrin et al., 1994) and humpback whales specifically (Lien, 1994; Johnson et al., 2005). Use of long gillnets from artisanal and multi-day vessels is prevalent in ASHW range states, particularly from illegal unreported fishing (Willson, 2021; Trygg Mat Tracking and Global Fishing Watch, 2020). The region hosts a growing number of ports and increasing levels of commercial and military vessel traffic. Container vessel traffic in the northern Indian Ocean increased by 5% per year between 2009 and 2018 (Willson, 2021). Globally, the humpback whale ranks the second-highest in total documented whale fatalities from vessel strikes (Van Waerebeek and Leaper, 2008). Willson et al. (2023) documented high ship strike risk in core ASHW habitats off the coast of Oman and the wider Arabian Sea. Offshore oil and gas exploration and production is present in AHSW habitat (Baldwin et al., 2015), and together with shipping, fishing, infrastructure development and military activity introduce unquantified and indirect threats from underwater noise and pollution.

Climate change, which is affecting the strength and predictability of monsoons and related upwelling (Goes et al., 2020; Kiefer et al. 2006; Watanabe et al., 2021) may also affect prey availability. Sardines are a key prey item for ASHW (Mikhalev, 1997), and fluctuations of sardine landings off the coast of Oman have been reported as a basin-scale decline (Piontkovski et al., 2014). Prey depletion may in turn negatively impact body condition and reproductive fitness and/or susceptibility to disease (Van Bressem et al., 2014; Minton et al., 2022; Pirotta et al., 2025). These changes may already be affecting humpback whale reproductive rates, distribution and feeding patterns, with marked fluctuations in encounter rates recorded during vessel-based and acoustic surveys in core areas of habitat off the coast of Oman in recent years (Cerchio et al., 2023b; Minton et al., 2023).

While these threats are evident throughout the Arabian Sea and Sea of Oman, they may be even more extreme in the waters of the Persian/Arabian Gulf, where even higher levels of human activity occur and include chemical and organic (eutrophication) pollution and oil spills (e.g. Robineau and Fiquet, 1994; Preen, 2004; Shokat et al., 2010). Although the holotype of M. indica was collected in the Gulf, recent sightings remain few and far between, with only seven confirmed records of the species between 1883 and 2017 (Dakhteh et al., 2017), despite increasing research and citizen science efforts in the region (e.g. Natoli et al., 2022).

As the only known humpback whale population in which the entire population both feeds and breeds in the same geographic area, ASHW are genetically, demographically, ecologically and culturally unique. Their extirpation would lead to an irreversible and permanent loss of a suite of distinctive traits that could provide valuable insights into how baleen whale populations adapt to environmental changes. Moreover, the biogeographical, ecological, temporal, and behavioral factors that have shaped the genetic isolation and divergence of the ASHW population are likely influencing similar patterns of evolution and endemism in other marine species throughout the Arabian Sea. Avoiding the loss of this distinct population requires urgent dedicated allocation of appropriate resources and effort for the effective mitigation of major threats.

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