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SPOTLIGHT
29 June 2021

China’s economic approach to protecting its ecology

Ecotourism could provide an alternative income for those who risk losing their livelihoods when areas are given national-park status.

Sarah O’Meara

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Sarah O’Meara

Sarah O’Meara is a freelance journalist in London.

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Tourists take photos at a bird-observation ecotourism point in Ziyun Village, in southeast China’s Fujian province.Credit: Xinhua/Shutterstock

Later this year, China will announce the first parks to be included in its new protected-areas system. It is aiming to replace the current fragmented network of poorly managed protected areas with a national-park model similar to that in other nations.Since the idea was mooted in 2013, the Chinese government has drawn on expertise from around the world and set up ten pilot national parks to test specific conservation strategies.Yet, millions of people work in and around these areas, doing everything from farming to running hotels. And once the parks receive formal protection, there will be a much smaller window for commercial activities and these people risk losing their livelihoods, says Rose Niu, chief conservation officer at the Paulson Institute in Washington DC. For the plan to succeed, China’s National Forestry and Grassland Administration will need to achieve a balance between protecting the country’s ecological systems and its people, Niu says. Her team has been closely involved in the plan’s development: advising on policy planning, training and the sharing of information between Chinese and international experts.
Spotlight on Ecology in China
Proposed ideas to tackle the loss in earnings that local people could face include compensation schemes and the resettling of households. Jobs will also be created in park management and protection and in ecotourism to encourage residents to be employed as part of conservation efforts.Niu thinks that encouraging local people to embrace this new economy, which also includes jobs in organic farming and wildlife management, is a very ambitious goal. “People’s awareness of these ideas is, sorry to say, still not very high. So you have to develop very strict rules for planning and management, so any ecotourism doesn’t get out of control. This can happen quickly, because it’s such a lucrative area and China has a highly entrepreneurial culture.”People, protected areas and ChinaEconomic development and environmental protection have a complicated history in China, born of the competing needs of boosting rural economies and conserving their natural resources. Short-term, profit-oriented projects have often won out.For example, Jiuzhaigou, a biodiverse and famously scenic valley in Sichuan province, was designated a nature reserve in 1982 because of its endangered plants and animals, including giant pandas. Poorly managed tourism followed and the local economy boomed, but the reserve declined. A sharp rise in air and water pollution led to the removal of private transport and the closure of hotels and restaurants in the reserve at the end of 2004.However, simply suspending tourism projects to regain control over the environment has an immediate knock-on effect for local residents, says Linjing Ren, a public-policy researcher at Northwestern Polytechnical University in Xi’an, China. “Many rely on offering accommodation and catering services for tourists, and can suddenly lose their main source of income,” she says.

Wild yaks navigate the Sanjiangyuan region of northwest China’s Qinghai province. The number of wild animals in the area is on the rise.Credit: CHINE NOUVELLE/SIPA/Shutterstock

And despite government efforts, protected areas continue to be exploited for commercial use. As recently as 2016, officials from five provinces were disciplined for allowing environmental regulations to be flouted. Their misdemeanours included allowing the discharge of untreated waste water into rivers and the mining of coal.Having agricultural areas inside protected regions can also lead to conflict between people and wildlife. In the Qinling Mountains in central China, for example, the establishment of a nature reserve increased the numbers of animals such as bears and wild boar that eat and damage crops. Unfortunately, the government’s financial compensation scheme does not completely cover such losses, according to Yali Wen, a researcher at Beijing Forestry University who specializes in economics and the environment.“One thing that could be improved is more government funding for human and wildlife conflicts. Not only is this fair, but it gives communities an incentive to engage with the idea that natural resources need to be protected in the long term,” Wen says.New parks, new ecotourismThe need for a strategic approach to ensure the economic security of communities affected by the plan is urgent, given that four of the ten pilot parks are in western and central China, which contain the country’s poorest regions. The Giant Panda National Park, for instance — a 27,133-square-kilometre wildlife corridor in central China — encompasses impoverished areas in Sichuan, Shaanxi and Gansu provinces. And most of the 17,000 households who live inside the largest pilot park, 123,100-square-kilometre Sanjiangyuan in the northwest of Qinghai, make their living by yak herding. Many have collective land rights, which allow them to use the land for grazing, says Lu Zhi, a conservation biologist at Peking University in Beijing.

Bee hives, tended by local villagers, adorn cliffs in Guanba. The hives are in a community-conserved conservation area that also includes panda and otter habitats.Credit: Lu Zhi

But instead of paying compensation to local communities to convert swathes of land from grazing to parkland — an expensive exercise — the government decided to recruit one person from each household to retrain as a park ranger. According to Niu, who evaluated the retraining scheme in 2019, each community ranger is paid 20,000 yuan (US$3,100) per year to monitor wildlife and protect the local environment. This alternative livelihood makes them less dependent on the park’s natural resources, she says. “The herders said that although that salary is not a lot of money — it’s roughly the price of three yaks — they were very proud to be doing this work. The project was well designed to give them a sense of ownership.”Government statistics say that 17,211 herders have already been hired to monitor the conservation of grassland and wildlife and raise awareness of environmental laws.New ideas in actionTerry Townshend, a wildlife conservationist and biodiversity adviser to Beijing’s government, has since 2017 been training yak herders in Qinghai in the kinds of skills that ecologists hope could be a model for sustainable development since 2017. In 2016, he met the official responsible for Zaduo, a county in Qinghai Province where snow leopards roam the valleys, at a wildlife-watching festival organized by the Shan Shui Conservation Centre, a Chinese non-profit body. After mentioning that snow-leopard tours had been popular and lucrative in other countries, Townshend was invited to write an ecotourism proposal for Zaduo. Three months later, his ideas were given the green light.“There’s very little literature on doing anything like this,” says Townshend. “I think it’s the first of its kind in China. I made it up from scratch. I remember flying there, thinking, is this really going to work? Are we really going to get Tibetan herders to come to a classroom to do training?”

A-Ta, a Tibetan herder whose income largely comes from raising yaks and collecting caterpillar fungus, places debris in a bag as he leads his team of rubbish collectors in Sanjiangyuan.Credit: Ng Han Guan/AP/Shutterstock

Over 3 days, Townshend and other specialists gave 16 herders the skills they needed to host tourists and take them on tours of local wildlife spots — everything from cooking and basic first aid to animal tracking and identification. What was key to the project’s success, he says, was giving the community autonomy to make decisions. By 2019, the project had generated 1 million yuan in revenue. “They made all major calls, from pricing the tours to deciding the programme’s organizational structure, and all of the income stays with the households,” says Townshend. “The long-term advantage is that the risk of local people killing wildlife is reduced, because they now see these predators as assets. It also means that tourism is carefully managed and profits [are] divided entirely equally.”Townshend says the project was fortunate to have the three key elements he thinks are required for success: abundant wildlife, an effective community structure that can cooperatively deal with issues as they arise and the full support of local government.From working with other snow-leopard-tourism teams in Italy, India, Nepal, Sweden and Afghanistan, he has found that projects missing any one of those ingredients are likely to fail. “Often, if the project is not effectively managed, there can be a breakdown in social cohesion. Families end up competing, with some benefiting more than others, causing jealousy and negative behaviour,” he says.The need for full community buy-inIn 2018, Wen and his team at Beijing Forestry University surveyed 1,270 households inside and adjacent to the mooted pilot Giant Panda National Park. Around one-fifth had chosen to participate in local ecotourism schemes, such as running farm tours, providing catering and accommodation and selling local products to tourists. And Wen’s team found that those that did were already in a better economic and social position than were those who declined1.“The early adopters were those who could afford to take a risk. They were already financially secure, had some form of higher education and were well placed geographically to work with tourists,” says Wen, adding that successful ecotourism depends on the ability of participants to withstand the risks and difficulties common to starting a business.“In China, this means having a combination of financial and social capital: enough money to provide a safety net and strong-enough community connections to ensure that you can get support when you need it,” he says. And ultimately, the tourists need to turn up: local government has to deliver a well-considered and managed plan to encourage tourism into the area, he says.One challenge posed by bringing ecotourism into poor communities is that it has the potential to exacerbate existing social divisions. Wen’s survey participants complained that wealthy people in the area were better equipped to take advantage of the fresh economic opportunities. “They felt it resulted in a widening gap between rich and poor,” he says.Yet, despite income disparities, and complaints about how tourists can be invasive, Wen says that overall attitudes towards ecotourism were extremely positive, with most locals agreeing that the advantages entirely outweighed the disadvantages. Many of the most attractive aspects of ecotourism stem from a shift in people’s daily priorities, his research suggests. As agriculture has become more mechanized and fewer family members are needed to tend small plots, young people head to the cities for work. Creating ecotourism business models gives them an economic incentive to stay, he says. “Generations of families like the idea of being able to stay together, and the projects also increase people’s sense of pride in their home towns.” A chance for the next generationEcologists in China hope that future generations will develop and improve ecotourism projects in protected areas. Niu, who grew up in a remote area of China, says it is key that any change to a person’s way of life brought about by government policy is voluntary. “No one should be forced to move, for example. But if people who live in remote areas are willing to move to places where they can access better public services, like schooling for their children and health care for seniors, the relocation should not be criticized,” she says. “The government should also give people opportunities to take part in sustainable business such as ecotourism, so they don’t have to rely on the overuse of natural resources.”Lu has spent more than a decade developing a community conservation programme in the village of Guanba, in a part of Sichuan province that is also home to pandas. The programme includes a social enterprise that sells local honey. She says it took many years for people in China to come to appreciate these kinds of ecological products and for a market to grow around it. And it’s still in its early stages of profitability.As the programme slowly developed and overcame setbacks, the community began to think more deeply about how to protect its environment. Eventually, in 2015, it declared the forest land around Guanba a community conservation area. Now the village has three separate ventures, all owned by the community. They are run by young people who moved back to the area to be part of this work.Lu is confident that the village will benefit from the involvement of that younger generation.“We are ecologists,” she says. “We are not trained in business management. We need to train people to do both. And ensure they bring these projects to life in far less than a decade.”

doi: https://doi.org/10.1038/d41586-021-01741-1This article is part of Nature Spotlight on Ecology in China, an editorially independent supplement. Advertisers have no influence over the content.

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Genome skimming provides robust phylogenyPioneering molecular phylogenetic studies in Sepiolida that used short regions of a few mitochondrial and nuclear genes failed to resolve the relationship of major clades9,22,23. To increase the number of phylogenetically informative sites, Sanchez et al.11 sequenced and analyzed the transcriptomes of multiple species of Euprymna Steenstrup, 1887, related bobtail squids including Sepiola parva Sasaki, 1913 and Sepiola birostrata Sasaki, 1918, and several bottletail squids. They found that S. parva grouped with the Euprymna species to the exclusion of S. birostrata, and further morphological analysis led to the formal redefinition of the genus Euprymna and the reassignment of S. parva Sasaki, 1913 to Euprymna parva11. The following year, in an exhaustive study of hectocotylus structure, Bello19 proposed that Euprymna be split back into the original Euprymna Steenstrup, 1998 and a newly defined genus, Eumandya Bello 2020 that contains E. parva Sasaki, 1913 and E. pardalota Reid 2011, two taxa whose arms have two rows of suckers rather than four as in other Euprymna species. Similarly, Bello introduced a new genus, Lusepiola Bello, 2020 that has the effect of renaming Sepiola birostrata Sasaki, 1918 as Lusepiola birostrata. For clarity, we adopt the finer-grained nomenclature of Bello below, but happily note that E. parva and E. pardalota have the same abbreviations in both the notation of Sanchez et al.11 and Bello19.Sanchez et al.11 also emphasized the need for more taxon sampling, careful species assignment, and the inclusion of more informative sites when studying this group of cephalopods. However, the distribution and lifestyle of many lineages of Sepiolida makes the collection of fresh tissue for RNA sequencing very challenging. To overcome this limitation, we sequenced the genomic DNA of several Sepiolida species at shallow coverage up to 3.6× and accessed by this way several mitochondrial and nuclear loci. Most of our samples were carefully identified at the species level based on morphological characters.We recovered the mitochondrial genomes of the species targeted in this study and annotated the 13 protein-coding genes, 22 tRNAs, and two rRNAs (although only the conserved region of the large and small rRNA was obtained for Rondeletiola minor Naef, 1912).Additionally, we also downloaded the complete mitochondrial genomes of S. austrinum and Idiosepius sp., and the transcriptome of E. tasmanica available in the NCBI database. The transcriptome of E. tasmanica was used to extract its complete set of mitochondrial protein-coding genes. We could reconstruct the mitochondrial gene order for all species with complete mtDNA genomes, but we observed no re-arrangement for members of Sepiolidae, and only Sepiadarium austrinum deviated from the arrangement seen in all other Sepiadariidae (Fig. S1).To complement the mitochondrial-based evolutionary history, we also annotated several nuclear loci. As ribosomal gene clusters are present in numerous copies, they were successfully retrieved for almost all the species, except for 28S of the Sepiadariidae sp. specimen, which appeared problematic and was excluded.By mapping reads to the reference genome of E. scolopes, we obtained 3,279,410 loci shared between at least two species and further selected 5215 loci presented in most of our Sepiolidae species, but allowed some missing data in the Euprymna + Eumandya clade. This was done because the phylogenetic relationships of the Euprymna + Eumandya species were previously described in detail in Sanchez et al.11 using transcriptome data. Out of the 5215 loci, 5164 loci had a per-site coverage ranging between two and five. After trimming and removal of regions without informative sites, 577 loci remained. These ultraconserved loci had lengths ranging between 10 and 690 base pairs (bp), with an average of 65 bp. Our alignment matrix had a length of 37,512 bp and consisted of 16,495 distinct site patterns, and variable sites between 1 and 130 bp with an average value of 7 bp. We expected a low value of variable sites because these regions are highly conserved.We considered resolved nodes to be those with the ultrafast bootstrap support and posterior probability larger than 95% and 0.9, respectively. Only the very unresolved nodes were found based on the mito_nc matrix (Fig. 1). However, among the species in these nodes, Adinaefiola ligulata Naef, 1912 was well supported with amino acid sequences from mitochondrial genes (posterior probability of 1 and 94% bootstrap support) and partially by the ultraconserved loci (posterior probability of 1, but only 85% bootstrap support) as sister to the Sepiola clade (Figs. 2 and S2). Moreover, compared to the mito_nc matrix and with identical topology, mito_aa and UCEbob fully resolved the relationship of the Indo-Pacific and Mediterranean Sea Sepiolinae. The tree generated by the nuclear_rRNA produces a topology with most nodes unsupported (Fig. S3), suggesting these markers are too conserved for assessing the relationships among this group.Fig. 1: Phylogeny of Sepiolida based on nucleotide sequences from the mitochondria (mt_nc matrix).The topology of the maximum likelihood tree is shown. Numbers by the nodes indicate bootstrap support and the Bayesian posterior probabilities. Values of bootstrap support and posterior probabilities above 95% and 0.95, respectively, are not shown. (*) indicates that the node was resolved with the mito_aa and UCEbob matrices. (+) indicate that A. ligulata is sister to Sepiola using mito_aa with ultrafast bootstrap support of 94% and a posterior probability of 1. Abbreviations: IP, Indo-Pacific Ocean; MA, Mediterranean Sea, and the Atlantic Ocean.Full size imageFig. 2: Phylogenetic tree of Sepiolida based on conserved nuclear loci (UCEbob matrix).The topology of the maximum likelihood tree is shown. Numbers in by the nodes indicate the bootstrap support and the Bayesian posterior probability. Values of bootstrap support and posterior probabilities above 95% and 0.95, respectively, are not shown. IP, Indo-Pacific Ocean; MA, Mediterranean Sea, and the Atlantic Ocean.Full size imageUsing the UCEbob matrix, the topology and supported relationships of Euprymna + Eumandya species resemble those reported in Sanchez et al.11 using transcriptome sequences, proving our protocol valid when using low coverage sequencing and when a reference genome of the closest related species is available.The position of R. minor showed discordance between mitochondrial and nuclear datasets. Using the mitochondrial matrices, R. minor rendered the Sepietta Naef, 1912 clade paraphyletic, whereas using the UCEbob and rRNA_nc matrices, R. minor appeared sister to the Sepietta clade. These relationships were resolved in both mitochondrial and nuclear-based trees and require further investigation with more DNA markers and a wider population sampling.Molecular systematics of Sepiolida cladesUsing the complete mitochondrial genome, ribosomal nuclear genes, and ultraconserved loci, we recovered the monophyly of the two families of the order Sepiolida—Sepiadariidae and Sepiolidae9,24—and the monophyly of the three described subfamilies of the family Sepiolinae. However, contrary to what is proposed based on morphology in Young24, the Rossinae is not sister to all the remaining Sepiolidae but rather is sister to Heteroteuthinae, although this is unresolved in the UCE phylogeny. With the lack of systematic work on these subfamilies, our robust phylogenetic backbone in Sepiolida using new samples carefully identified by morphology and with museum vouchers, represents a notable advance to clarify the evolution of morphological traits in major clades within the family.Based on morphological characters of the hectocotylus, Bello19 recently split the polyphyletic Sepiola Leach 1817 into Lusepiola, Adinaefiola, and Boletzkyola, reserving Sepiola for the S. atlantica group sensu Naef 1923. These newly defined clades are consistent with our molecular phylogeny here and in Sanchez11, who also noted the polyphyly of Sepiola in the Indo-Pacific lineage.We find that Sepiolinae can be robustly split into two geographically distinct tribes: one that comprises species with known distribution in the Indo-Pacific region (tribe Euprymmini new tribe, defined as Sepiolinae with a closed bursa copulatrix, type genus Euprymna) and the other including all the Mediterranean and Atlantic species (tribe Sepiolini Appellof, 1989, defined here as Sepiolinae with an open bursa copulatrix, type genus Sepiola). Our molecular relationship is consistent with 13 of the 15 apomorphies used in the cladogram shown in Fig. 21 in Bello19. The other two proposed apomorphies in Bello (his apomorphic characters 4 and 6) group two IP lineages, Lusepiola and Inioteuthis, in a clade with species from the Mediterranean and Atlantic. Such relationships contradict our Euprymmini-Sepiolini sister relationship. Moreover, according to our phylogeny, apomorphy 6 of Bello, characterized by the participation of ventral and dorsal pedicels in the formation of the hectocotylus copulatory apparatus, implies that the male ancestor of Sepiolinae had a more developed hectocotylus that was simplified in the Euprymna and Eumandya clades.Among euprymins, we confirmed the monophyly of Euprymna Steenstrup 1887 as found previously by transcriptome analysis11. We also support the monophyly of Eumandya Bello, 2020 (Figs. 1 and 2), grouping the type species E. pardalota with E. parva along with the unnamed “Type 1” Ryukyuan species of Sanchez et al.11, for which only hatchlings were available. The phylogenomic grouping of Ryukyuan “Type 1” with Eumandya suggests that when its adults are found (or hatchlings are raised to maturity), its arms will carry two rows of suckers. We also found an adult of a Ryukyuan “Type 4” (extending the notation of Sanchez et al.11 in the coastal waters of Kume Island, that groups with E. scolopes from Hawaii, suggesting a divergence based on geographic isolation in the North Pacific. We also find that Lusepiola birostrata (formerly Sepiola birostrata) is grouped with Inioteuthis japonica as sister to a clade containing Euprymna, Eumandya, and an unnamed sepioline from Port Kembla, at the northeast of Martin Island in Australian waters.Among the sepiolins, we confirm the monophyly of Sepietta (only for nuclear-genome-based trees, see below). Adinaefiola, another genus erected by Bello19, with Sepiola ligulata Naef 1912 as its type species; was found sister to the Sepiola clade, but only in the tree based on amino acid mitochondrial sequences (mito_aa matrix) with a bootstrap value of 94% and a posterior probability of 1 (Fig. S2).Outside the sepiolines, members of the subfamily Heteroteuthinae are the most elusive and underrepresented in studies of cephalopod systematics due to their oceanic lifestyles. The placement of several heteroteuthin remains controversial. Lindgren et al.9, with six nuclear and four mitochondrial genes downloaded from GenBank found that Sepiolina Naef, 1912 was sister to Heteroteuthis Gray, 1849 + Rossia Owen, 1834+ Stoloteuthis Verril, 1881; rendering the subfamily Heteroteuthinae polyphyletic. In contrast, our work supports the monophyly of Heteroteuthinae by including Stoloteuthis and Heteroteuthis in this subfamily, while Rossia was placed within the Rossinae (Figs. 1, 2, S2). Members of Heteroteuthinae included in this study formed a sister group to a monophyletic Rossinae (Figs. 1, 2, S2). Semirossia, however, rendered the Rossia clade paraphyletic. Further discussion about the position of Semirossia is difficult because of the lack of information about the original source of this specimen in Kawashima et al.25.The light organ and luminescence evolutionBobtail squids are thought to use the bioluminescence of their light organ to camouflage them from predators while foraging and swimming at night through a mechanism called counter-illumination. This has been researched extensively using E. scolopes as a model system26,27,28. Unfortunately, the limited number of sequences available and the misidentification of bobtail squids in the GenBank database11,29,30 have hindered our understanding of the light organ evolution in the whole taxon.Our robust phylogeny and Bayesian reconstruction of ancestral bioluminescence clarify how the light organ and its luminescence have evolved in the family Sepiolidae. Members of Sepiolinae comprise neritic and benthic adults with bilobed light organs, except for two genera: Inioteuthis from the Indo-Pacific region, and the Sepietta species from the Mediterranean Sea and the Atlantic waters. The ancestor of the Sepiolinae very likely possessed a bilobed light organ that harbored luminescent symbiotic bacteria (Fig. 3). This character persisted until the ancestor of the euprymnins and sepiolins. Assuming that R. minor is sister to the Sepietta clade (as shown with the nuclear-based dataset, Fig. 2), it is clear that the bilobed light organ was lost once in Inioteuthis and Sepietta, and simplified to a rounded organ in R. minor. The alternative scenario, where R. minor renders the Sepietta clade paraphyletic (based on mitochondrial matrices, Fig. 1), is less plausible as it implies that the light organ was lost twice in the Sepietta group, once in S. obscura and then in the ancestor of S. neglecta and S. oweniana; or alternatively that it was lost in the ancestor of Sepietta-Rondelentiola followed by a reversion of this character in the lineage of Rondelentiola.Fig. 3: Ancestral character reconstruction (ASR).ASR of (a) the shape of the light organ and (b) the origin of luminescence in the Sepiolida. The posterior probability of each state is shown as a pie chart, mapped tree generated in BEAST (based on mito_nt matrix, see below), with the outgroups removed.Full size imageThe light organ is also present in all members of Heteroteuthinae. These bobtails are pelagic as adults, and their light organ appears as a single visceral organ rather than the bilobed form found in nektobenthic Sepiolinae. In contrast to the bacteriogenic luminescence of the light organ in E. scolopes31, previous studies in H. dispar3 failed to detect symbiotic bacteria and suggested that the luminescence has an autogenic origin. Thus, it seems plausible that the monophyly of Heteroteuthinae found in our study supports the findings in Lindgren et al.9 for convergent evolution of autogenic light organs associated with pelagic lifestyle in many squid, octopus, and Vampyroteuthis Chun, 19039,32.Divergence time of SepiolidaThe absence of fossils for this group limited our calculations of divergence time to the use of secondary calibrations. These calibrations can provide more accurate estimates depending on the type of primary calibrations that are used33. We retrieved secondary calibrations from previous estimations in Tanner et al.15, who used eleven fossil records spanning from coleoids to gastropods in transcriptome-based phylogenetic trees. Specifically, we used the time for the splits of Sepia esculenta and S. officinalis (~91 Mya), Idiosepiidae, and Sepiolida (~132 Mya) and the origin of the Decapodiformes (root age, ~174 Mya) (Fig. 4). These calibrations and our robust phylogenetic trees allow us to investigate the events that shape the divergence of some clades of the order Sepiolida (Figs. 4,  S4).Fig. 4: A chronogram of sepiolids using complete mitochondrial genes.Red dots indicate the nodes with secondary calibrations. K-Pg, refers to the Cretaceous-Paleogene boundary and MSC, to the Messinian salinity crisis.Full size imageSepiolida appeared before the Cretaceous-Paleogene extinction event34, during the middle Mesozoic around 94 Mya (95% HPD = 60.61–130.72). This time frame coincides with the rapid diversification of several oegopsida lineages15,35. Our molecular estimates also indicate that radiation of Sepiolidae and Sepidariidae occurred around the Cretaceous-Paleogene boundaries and is concurrent with the rapid diversification of modern marine percomorph fishes around the globe, after the extinction of Mesozoic fishes36,37.Among the species of Sepiolinae collected in the Mediterranean Sea for this study, only Sepiola robusta Naef, 1912, and Sepiola affinis Naef, 1912 are endemic to the Mediterranean Sea38. The distribution of the other species includes the Mediterranean Sea, North Atlantic Ocean, East Atlantic Ocean, and/or up to the Gulf of Cadiz. The confidence intervals for the split between the Mediterranean-Atlantic and Indo-Pacific lineages, and their diversification, overlap during the early Eocene to the beginning of the Oligocene (Figs. 4 and  S4). This time interval coincides with the end of the Tethys Sea, which separated the Indo-Pacific from the Mediterranean and Atlantic region through the Indian-Mediterranean Seaway39,40. This separation also influenced the divergence of loliginid clades, coinciding with the split between the Eastern Atlantic plus Mediterranean clade (Loligo, Afrololigo, Alloteuthis) and Indo-Pacific clade (Uroteuthis and Loliolus) (~55 Mya based on Fig. 2 in Anderson and Marian41).Our chronogram indicates that the ancestor of Sepiolinae arose prior to the early Eocene around 46 Mya (95% HPD = 25.16–69.49) (Fig. 4), already possessing a bilobed light organ hosting luminescent bacteria (Fig. 3). We estimate that the split between S. affinis and S. intermedia occurred around 2.62 Mya (95% HPD = 0.3–7.4) (Fig. 4) during the end of the Zanclean period, when the Atlantic Ocean refilled the Mediterranean after the Messinian salinity crisis42,43. While S. affinis is a coastal species with a narrow depth limit, S. intermedia inhabits a wider range of deeper waters. It is possible that two populations of their ancestor, each adapted to a different ecological niche and diverged sympatrically in Mediterranean waters, and, after the speciation, S. intermedia extended its distribution outside the Mediterranean to the Gulf of Cadiz44.We also estimate that the split between H. dispar Rüppell, 1844 and H. hawaiiensis (Berry, 1909) occurred around 2.4 Mya (95% HPD = 0.46–5.88), coinciding with the closure of the Isthmus of Panama around 2.8 Mya45. Surveys of these species found H. hawaiiensis in the North Pacific and H. dispar in the North Atlantic Ocean and Mediterranean Sea46. A recent speciation event might be the reason for the lack of morphological differences between the two species46. Thus, these species may be rendered as cryptic species, a phenomenon increasingly reported in oceanic cephalopods47. The sister species of this cryptic species complex, H. dagamensis Robson, 1924, appeared before, around 6 Mya, and is reported with broad distribution in the South Atlantic Ocean off South Africa, the Gulf of Mexico, North Atlantic Ocean between Ireland and Newfoundland in Canada, and the South Pacific Ocean off New Zealand48,49,50.The origin of the Heteroteuthis ancestor of H. dispar, H. hawaiiensis, and H. dagamensis can be placed in the Pacific Ocean. After the formation of the Isthmus of Panama, the northern population of Heteroteuthis might have split into H. hawaiiensis in North Pacific and H. dispar in the Atlantic Ocean (from where it also migrated to the Mediterranean Sea). Meanwhile, the formation of the equatorial currents isolated the southern population of Heteroteuthis and gave rise to H. dagamensis. Then, H. dagamensis extended its distribution from the Southern Pacific to the South Atlantic Ocean, the North Atlantic waters, and the Gulf of Mexico. Analysis of molecular species delimitation, however, suggests that H. dagamensis includes cryptic lineages among Atlantic and New Zealand populations30.While the origin of Heteroteuthis might also be in the Atlantic Ocean, the higher diversity of heteroteuthins in the Pacific (H. hawaiiensis, H. dagamensis, H. ryukyuensis Kubodera, Okutani and Kosuge, 2009, H. nordopacifica Kubodera and Okutani, 2011, and an unknown H. sp. KER (only known from molecular studies49)) than at the Atlantic (H. dispar and H. dagamensis), make its origin at the Atlantic less plausible. Moreover, the Atlantic Heteroteuthis were found nested within Heteroteuthinae species from the Pacific, supporting Pacific Ocean origin (Figs. 1, 4).By sequencing the genomic DNA of sepiolids at low coverage, we recovered complete mitochondrial genomes and nuclear ribosomal genes for most of our collections. Furthermore, mapping reads to the reference genome of E. scolopes allowed us to retrieve additional nuclear-ultraconserved regions. We demonstrate that these nuclear and mitochondrial loci are useful to reconstruct robust phylogenetic trees, especially when the transcriptomes of specimens are difficult to collect, as for sepiolids inhabiting oceanic environments. Finally, our study integrated genomic DNA sequencing with confident morphological identification, which helped to reconstruct the ancestral character of the light organ and its luminescence in sepiolids, and clarify how major lineages have evolved, establishing the existence of distinct Indo-Pacific and Mediterranean-Atlantic subfamilies of Sepiolinae. Our collections and genomically anchored phylogenies will provide a reliable foundation classification of sepiolids for future studies. More