The deep sea is home to many different species of anglerfish, a group of animals in which females often display a dangling lure on the top of their heads. This organ shelters bacteria that make light, a partnership (known as symbiosis) that benefits both parties. The bacteria get a safe environment in which to grow, while the animal may use the light to confuse predators as well as attract prey and mates.

The genetic information of these bacteria has changed since they became associated with their host. Their genomes have become smaller and more specialized, limiting their ability to survive outside of the fish. This phenomenon is also observed in other symbiotic bacteria, but mostly in microorganisms that are directly transmitted from parent to offspring, never having to live on their own. Yet, some evidence suggests that the bacteria in the lure of anglerfish may be spending time in the water until they find a new host, crossing thousands of meters of ocean in the process.

To explore this paradox, Baker et al. looked into the type of bacteria carried by different groups of anglerfish. If each type of fish has its own kind of bacteria, this would suggest that the microorganisms are passed from one generation to the next, and are evolving with their hosts. On the other hand, if the same sort of bacteria can be found in different anglerfish species, this would imply that the bacteria pass from host to host and evolve independently from the fish.

Genetic data analysis showed that amongst six groups of anglerfishes, one species of bacteria is shared across five groups while another is specific to one type of fish. The analyses also revealed that anglerfish and their bacteria are most likely not evolving together. This means that the bacteria must make the difficult journey from host to host by persisting in the deep sea, which was confirmed by finding the genetic information of these bacteria in the water near the fish.

Anglerfish and the bacteria that light up their lure are hard to study, as they live so deep in the ocean. In fact, many symbiotic relationships are equally difficult to investigate. Examining genetic information can help to give an insight into how hosts and bacteria interact across the tree of life.

Symbiosis between animals and bacteria can enable both organisms to adapt to harsh environments or expand into new habitats, which impacts the ecology and evolution of both bacterial and host lineages (McFall-Ngai et al., 2013; Moran, 2007; Moya et al., 2008). Symbiosis with luminescent bacteria has evolved independently multiple times in diverse squid and fish species (Davis et al., 2016; Dunlap and Urbanczyk, 2013) and has been correlated with host diversification (Davis et al., 2016; Ellis and Oakley, 2016). Bioluminescence is considered an adaptive phenotype across multiple taxa and a ubiquitous function in the largest habitat on the planet, the bathypelagic biome (ocean’s midwaters below 1000 m) (Martini and Haddock, 2017). Four genera of bacteria in the family Vibrionaceae engage in luminescent symbiosis (Dunlap and Urbanczyk, 2013; Hendry et al., 2018; Schaechter, 2009), including the model species Aliivibrio fischeri, but comparatively little is known about the bioluminescent symbionts of deep-sea anglerfishes. Ceratioid anglerfishes (suborder Ceratioidei) consist of 167 species from 11 families (Froese and Pauly, 2018) and are the most speciose fish suborder in the bathypelagic zone (Pietsch, 2009). Most female ceratioid anglerfishes host extracellular luminous symbiotic bacteria in a lure-like projection (esca) above the animal’s head (Munk, 1999). The genera Cryptopsaras and Ceratias harbor bacterial symbionts in additional pouch-like symbiont-filled protuberances anterior to the dorsal fin, known as caruncles. Bioluminescent symbiosis is thought to be essential to the survival of adult anglerfishes, although the exact function has not been observed. The lure has been proposed to attract prey, confound predators, or signal mates (Pietsch, 2009). Recent research by Hendry et al. (2018) investigated symbiont genomes from two commonly collected anglerfish species, Cryptopsaras couesii and Melanocetus johnsonii, host lineages that diverged approximately 100 million years ago (Miya et al., 2010; Pietsch, 2009). Each host harbored a distinct species of bacterial symbiont: C. couesii hosts ‘Candidatus Enterovibrio luxaltus’ and M. johnsonii hosts ‘Candidatus Enterovibrio escacola,’ referred to here as E. luxaltus and E. escacola for ease (Hendry et al., 2018).

Most luminescent bacterial symbionts are facultatively symbiotic, have genome sizes typical of nonsymbiotic, free-living relatives, and are acquired by hosts from environmental populations (Bongrand et al., 2016; Bright and Bulgheresi, 2010; Dunlap et al., 2012; Dunlap and Urbanczyk, 2013; Ruby et al., 2005; Urbanczyk et al., 2011). In contrast, anglerfish symbiont genomes are reduced ~50% relative to closely related free-living bacteria, a pattern more commonly seen in intracellular, obligate symbiosis (Fisher et al., 2017; Kuwahara et al., 2007; Manzano-Marín and Latorre, 2016; Shigenobu et al., 2000). Anglerfish symbionts, which have not been successfully cultured (Haygood et al., 1984), appear to be obligately dependent on their hosts for growth, as the metabolic capacity to use carbon sources other than glucose are absent from the genome and glucose is an extremely limited resource in the deep sea (Hansell, 2013; Hendry et al., 2018). Genomic degeneration in obligate symbionts is thought to occur as a result of relaxed purifying selection on genes that are unnecessary within the host habitat (Bright and Bulgheresi, 2010; Kenyon and Sabree, 2014; Fisher et al., 2017; Sachs et al., 2011). This process may be mediated in part by relaxed regulation of transposable elements (TEs) (McCutcheon and Moran, 2011), which was observed for both E. escacola and E. luxaltus genomes (Hendry et al., 2018). Transposon expansions and pseudogenization were evident in both symbionts, with TE pseudogenes making up about 30% of each bacterial genome (Hendry et al., 2018). Phylogenetic investigation of transposon families found independent expansions within each symbiont species, suggesting that genome reduction may have occurred independently within each lineage (Hendry et al., 2018).

Although the aforementioned evolutionary patterns tend to result from physical restriction to hosts and vertical transmission between host generations (Bright and Bulgheresi, 2010; McCutcheon and Moran, 2011; Moran, 1996), several characteristics of anglerfish and their symbionts suggest that these bacteria may be environmentally acquired. The anglerfish symbiont genomes retain genes predicted to be under selection outside the host, such as genes involved in cell wall synthesis and complete motility and chemotaxis pathways. Symbionts are also capable of producing polyhydroxybutyrate (PHB), a carbon storage molecule that is hypothesized to aid in environmental persistence until colonizing suitable hosts (Haygood, 1993; Hendry et al., 2018; Hendry et al., 2016). Furthermore, anglerfish life history traits could preclude the possibility of vertical transmission. Anglerfishes reproduce through the production of an ‘egg raft’ or ‘veil’ that delivers eggs to the surface. Juvenile anglerfishes do not have lures; as anglerfishes near sexual maturity they descend to bathypelagic depths and develop their lure (Pietsch, 2009). This developmental process and the anglerfish’s poor swimming abilities, coupled with differences in surface and deep-sea currents (Etter and Bower, 2015; Pazos and Lumpkin R, 2007; Pietsch, 2009), likely result in generations separated by several kilometers of ocean, making it unlikely that juveniles acquire symbionts from their parents in the deep sea. It also appears unlikely that anglerfishes acquire symbionts from their egg raft, as juveniles have not been found with symbiotic bacteria in their developing lures (Freed et al., 2019; Munk, 1999).

An alternative hypothesis to vertical transmission is that anglerfishes acquire bacterial symbionts from persistent environmental populations despite the limited metabolic capacity of symbionts. Fishes known to harbor luminous bacteria regularly release symbionts into the environment (Haygood, 1993). In ceratioid anglerfishes, the extracellular symbiotic bacteria are likely released from the host via a small opening in the lure (Haygood et al., 1984; Munk, 1999). Environmental samples of bacteria taken concurrently with anglerfish collections in the Gulf of Mexico found 16S rDNA sequences resembling symbionts (Freed et al., 2019), which suggests that anglerfish symbionts could be environmentally acquired. Symbiont transmission between host generations via environmental populations, referred to here as environmental acquisition, is not uncommon in the deep sea; for instance, it occurs in the symbiosis of tubeworms (Feldman et al., 1997; Nussbaumer et al., 2006) and mussels (Won et al., 2008; Won et al., 2003) with their chemosynthetic bacteria. However, these bacteria have genome sizes typical of free-living relatives and lack signatures of reduction (Kleiner et al., 2012; Li et al., 2018; Ponnudurai et al., 2017). Marine symbionts with reduced genomes have been found, such as the symbionts of deep-sea clams in the genus Calyptogena (Kuwahara et al., 2007; Newton et al., 2007) or the luminous symbionts of anomalopid flashlight fishes (Hendry et al., 2016; Hendry et al., 2014). However, these symbionts are characterized as having vertical (Goffredi et al., 2003; Hurtado et al., 2003) and possibly pseudovertical transmission (Hendry and Dunlap, 2014).

Because strictly vertically transmitted symbionts will codiverge with their hosts (Bright and Bulgheresi, 2010; Clark et al., 2000; Jousselin et al., 2009; Zhang et al., 2018), we assessed the likelihood of hypothesized transmission modes of anglerfish symbionts by testing for symbiont-host codivergence. This analysis included multiple specimens of the previously studied host species C. couesii and M. johnsonii, as well as less common genera of anglerfishes, including Ceratias, Chaenophryne, Linophryne, and Oneirodes. The geographic distribution of these genera is poorly known, but based on collection data the rarest species in our study (Linophryne maderensis), has only four documented museum samples (Pietsch, 2009). These host species originate from four of the eleven families of ceratioid anglerfishes and span much of the phylogenetic diversity of the suborder Ceratioidei. We hypothesized that a high degree of congruence between host and symbiont phylogenies will indicate codivergence due to vertical transmission. Additionally, codivergence could result in diverse symbiont species associated with diverse host lineages. Alternatively, if symbiont and host phylogenies lack congruence and different host species share symbionts, this indicates likely acquisition of symbionts from environmental populations.

Within the broad phylogenetic spectrum of ceratioid anglerfishes sampled in this study we identified only two symbiont species, E. luxaltus and E. escacola. These symbiont species were previously described as the symbionts of two commonly collected anglerfish species, Cryptopsaras couesii and Melanocetus johnsonii. The fact that sampling from four additional anglerfish genera from two different ocean basins did not uncover more symbiont diversity suggests that there are a low number of luminescent symbiont species that can associate with deep-sea anglerfishes. However, it should be noted that this study was not all-inclusive, particularly since new anglerfish species are still being described (Pietsch and Sutton, 2015), and further sampling could reveal more symbiont diversity. In addition to the lack of species-level diversity, the low intra-specific diversity in each symbiont species was notable. Similar trends have been found in other obligate symbionts, such as the aphid endosymbiont Buchnera and in the obligate luminous symbionts of flashlight fishes (Hendry et al., 2014), but not in facultative luminous symbionts (Abbot and Moran, 2002; Funk et al., 2001; Hendry et al., 2014). Host population bottlenecks may lead to low genetic diversity within Buchnera (Abbot and Moran, 2002; Funk et al., 2001), but this seems unlikely to account for low diversity in obligate symbionts of fishes. It is unclear why anglerfish symbionts, even from distinct hosts and geographic locations, are so genetically similar. It is possible that although the hosts are separated by ocean basins, low mutation rates and long doubling times have resulted in a fairly stable and widespread symbiont population. Anglerfish symbionts lack many DNA repair pathways (Hendry et al., 2018), which has been implicated in increased mutation rates in obligate symbionts (Lind and Andersson, 2008), but the connection between the loss of these pathways and genomic evolution is not always clear (Tamas et al., 2002). Our finding of low genetic diversity in anglerfish symbionts supports the idea that a loss of DNA repair mechanisms does not necessarily lead to high mutation rates in bacteria. We speculate that anglerfish symbionts may instead have long doubling times, as this adaptation is common for bacteria surviving in the low-nutrient, high-hydrostatic pressure of the deep sea (Lauro and Bartlett, 2008; Wirsen and Molyneaux, 1999). Lowered metabolic rates are also common for cooperative symbionts (An et al., 2014). Collectively these factors may have led to the bacterial genomes being relatively static when free-living and resulted in the limited diversity observed in this study.

Although some obligate bacteria show low genetic diversity within a host species, obligate symbionts from different host species are often distinct due to codivergence with their hosts (Clark et al., 2000; Jousselin et al., 2009). This pattern has been found in numerous symbionts that are known to be vertically transmitted and often results in phylogenetic congruence between distinct host and symbiont taxa (Fisher et al., 2017; Sachs et al., 2011), as has been documented in the bacterial symbionts of insects (Dale and Moran, 2006; Moran et al., 2008) and deep-sea clams (Goffredi et al., 2003; Hurtado et al., 2003). Within vertically transmitted symbionts, symbiont replacements or horizontal transfers can often be observed in specific lineages where congruence breaks down (Bright and Bulgheresi, 2010), as has been observed in Wolbachia-harboring insects (Kikuchi and Fukatsu, 2003; Lefoulon et al., 2016), bacterial symbionts of marine worms (Blazejak et al., 2006), and Prochloron associated with sea-squirts (Münchhoff et al., 2007). Neither of these patterns is seen in our data. Anglerfish symbionts and their hosts lack consistently congruent phylogenies and it does not seem likely that congruence is being obscured by symbiont replacements or transfers, since very diverse host species all share low diversity symbionts. These results support the hypothesis that anglerfish symbionts are not codiverging with their host species. This conclusion is robust for E. escacola and associated hosts, but we may not have enough samples, and genetic diversity within those samples, to rule out the possibility that E. luxaltus and C. couesii could be codiverging due to vertical transmission. An alternative hypothesis is that C. couesii and E. luxaltus have a specific interaction, and that either the host or the bacterium excludes the other symbiont species (Bongrand and Ruby, 2019; Koch et al., 2014).

A lack of robust and statistically significant codivergence between hosts and symbionts contradicts the hypothesis that either symbiont species is vertically transmitted. This is consistent with previous studies of the luminous symbionts of squid and fish hosts, as they show no congruence between host and symbiont species (Dunlap et al., 2007). The most likely conclusion based on these data is that anglerfishes acquire their bacteria from an environmental symbiont pool that interacts with diverse anglerfish species. However, anglerfish symbiont genomes resemble vertically transmitted symbionts in multiple ways, including having extreme gene loss, expansion of transposable elements, and limited metabolic capacity (Hendry et al., 2018). Similar genomic patterns are seen in ‘Candidatus Photodesmus’ species, the luminous symbiont of anomalopid flashlight fishes (Hendry et al., 2016; Hendry et al., 2014). Both anglerfish and anomalopid symbionts have evaded culturing efforts and are divergent from known species of luminous bacteria in the Vibrionaceae (Haygood et al., 1992; Haygood and Distel, 1993; Hendry et al., 2018; Hendry and Dunlap, 2011). However, anglerfishes do not appear to school, nor do they exhibit diurnal cave dwelling, that is hypothesized to assist in pseudovertical transmission of Photodesmus species to flashlight fishes (Hendry et al., 2016; Hendry et al., 2014). Flashlight fishes and their symbionts lack sufficient sampling to test for codivergence, but symbiont sequencing from four fish species found high symbiont-host specificity (Hendry et al., 2014), a distinct pattern from the results presented here for E. escacola and six host species. We are not aware of other bacterial symbionts that have undergone extensive, degenerative genome reduction while maintaining environmental populations and associations with diverse and widespread hosts, as is seen with deep-sea anglerfish symbionts (For an overview of transmission modes and evolutionary patterns in symbionts, see Table 2).

Table 2

Transmission	Description	Symbiont and function	Host	Genome	References
Environmental	Acquired from free-living bacteria	Luminescence Aliivibrio fischeri Photobacterium leiognathi Photobacterium kishitanii Nutrition "Candidatus Endoriftia persephone" Various Gammaproteobacteria Burkholderia spp.	Fish and squid Fish Fish Tubeworms Mussels Insects	Comprable to free-living relatives	Dunlap and Urbanczyk, 2013; Gyllborg et al., 2012 Urbanczyk et al., 2011; Ast et al., 2007 Li et al., 2018; Kleiner et al., 2012 Ponnudurai et al., 2017 Kikuchi et al., 2005; Kikuchi et al., 2007
Proposed Environmental	Environmentally persistant cells	Luminescence "Candidatus Enterovibrio escacola" "Candidatus Enterovibrio luxaltus"	Anglerfish Anglerfish	Ongoing reduction	Hendry et al., 2018 Hendry et al., 2018
Mixed	Pseudovertical or surface transmission	Luminescence "Candidatus Photodesmus blepharus" "Candidatus Photodesmus katoptron" Nutrition Various Gammaproteobacteria “Candidatus Ishikawaella capsulata”	Flashlight fish Flashlight fish Clams Stink bug	Moderate toextreme reduction	Hendry et al., 2014; Hendry and Dunlap, 2014 Hendry et al., 2014; Hendry and Dunlap, 2014 Kuwahara et al., 2007
Inherited	Direct passage from parent to offspring on egg or sperm	Nutrition Buchnera aphidicola Carsonella ruddii Portiera aleyrodidarum Varied "Candidatus Synechococcus spongiarum"	Aphids Psyllids Whiteflies Sponges	Greatly reduced	Moran et al., 2008; Fisher et al., 2017 Moran et al., 2008; Fisher et al., 2017 Moran et al., 2008; Fisher et al., 2017 Gao et al., 2014; Burgsdorf et al., 2015

Based on catch rates and limited observation, anglerfishes are thought to be relatively solitary, and different life stages are separated by hundreds to thousands of meters of ocean (Pietsch, 2009). Anglerfishes are unlikely to encounter environmental symbionts regularly, as symbionts are unlikely to establish widespread populations due to their limited metabolic capabilities (Hendry et al., 2018). Other environmentally transmitted luminescent symbionts have much higher host densities to enrich populations in the local environment (Nealson and Hastings, 1991). Anglerfishes may have evolved mechanisms to similarly increase the concentration of symbionts in their local environment. A small pore in the lure is likely seeding the environment with symbiotic bacteria (Munk, 1999), but the caruncles on Ceratias and Cryptopsaras species are also a likely source of symbiotic bacteria. The caruncle is not externally luminescent and its function for the fish is not established (Pietsch, 2009). Although it is not connected to the esca, the caruncle does connect to the surrounding water through a small distal pore (Pietsch, 2009). The conclusion that anglerfishes must acquire their symbionts from potentially sparse environmental populations leads us to propose that the caruncle evolved as a mechanism to increase the concentration of symbiotic bacteria in the environment, thereby increasing the likelihood of symbionts being transmitted to new fish generations.

Low host densities could also drive bacterial evolution in this system. Although M. johnsonii is relatively abundant among anglerfishes, as is C. couesii, all other anglerfish genera investigated in this study are less prevalent than the most common species (Pietsch, 2009). With extremely low host densities, E. escacola may remain a viable symbiont for diverse anglerfish species due to selection against host specificity. The lack of apparent host specificity in this symbiont may increase the likelihood that these bacteria in the environment will encounter a permissive host before losing viability. In the case of E. luxaltus, this symbiont may encounter sufficient abundances of C. couesii individuals to allow for host specificity, either as a result of selection or by chance. For example, E. luxaltus and E. escacola differ in the genes present in the structural symbiosis polysaccharide (syp) pathway, the regulation of which influences host specificity in the luminous symbiont A. fischeri (Mandel et al., 2009). Both sypF and sypG are exclusive to E. luxaltus, that is neither gene is present in annotations and cannot be found in a BLAST search of any E. escacola genome. In A. fischeri, SypF is predicted to be a sensor kinase that regulates biofilm formation (Darnell et al., 2008; Thompson et al., 2018) and SypG is a response regulator that directly activates the syp locus (Hussa et al., 2008; Thompson et al., 2018; Yip et al., 2005). Although both symbionts maintain genes in the syp pathway, the loss of these regulatory genes in E. escacola could facilitate their colonization of a greater diversity of hosts.

The finding that anglerfish symbionts are likely environmentally transmitted further supports the hypothesis that the limited functional capacity of anglerfish luminous symbionts is sufficient to persist in the deep sea before contacting a new host. Motile symbionts capable of chemotaxis may be able to out-compete other non-motile deep-sea bacteria for access to the high nutrient environment of the host esca (DeLong et al., 2006). Additionally, polyhydroxybutyrate (PHB) may be a sufficient carbon source to sustain the symbiont before it arrives at a new host (Hendry et al., 2018). PHB has been estimated to sustain rhizobia for years, and may assist these microbes to survive thousands of years in a dormant state (Johnson et al., 2007; Muller and Denison, 2018); we hypothesize that PHB should function similarly for flashlight fish and anglerfish symbionts. Environmental samples of free-living bacteria collected by the DEEPEND Consortium taken concurrently with anglerfish collection found multiple samples containing 16S rDNA matching anglerfish symbionts, at various depths, and from multiple sampling efforts (Freed et al., 2019). Our characterization of symbionts using a portion of the chemotaxis protein cheA found multiple environmental samples containing either E. luxaltus or E. escacola. This result confirms previous reports that the symbiont persists in the water column (Freed et al., 2019), and further supports our conclusion that symbionts are acquired from environmental populations.

The low genetic diversity within the anglerfish symbionts made it difficult to determine if symbiont distribution was impacted by geographic origin or host identity. Using SNPs we were able to discern differences between E. luxaltus samples collected from different times at different locations, however, this result was limited to a single C. couesii individual from the North Atlantic, with esca and caruncle sampled (symbiont CCS1E and CCS2C). A subset of the E. escacola hosted by Ceratias formed a distinct clade and included two of the Northern Atlantic samples and a sample from the Gulf of Mexico. This confounding result suggests that further sampling of Ceratias may provide more insight into how location and time impact the diversity of E. escacola. Alternatively, it is possible that because the two collection sites are connected by deep-sea currents (Loop Current/Gulf Stream system), that symbionts were acquired by fishes in a similar location although they were collected hundreds of kilometers apart.

The deep sea is the earth’s largest and most understudied ecosystem, where studying symbiosis is both challenging and costly. In this study we use genomic analysis on rare samples of one of the deep sea’s most prominent symbioses to answer an outstanding question, how are deep-sea anglerfish symbionts transmitted between generations? Our findings demonstrate the value of studying relatively rare organisms in this ecosystem, as we can uncover new findings that may contrast with model systems. Bioluminescent symbiosis in anglerfishes breaks with several expectations from well-studied symbioses; symbionts that leave the host and establish environmental populations typically do not undergo genome degeneration. Yet, here we show that a luminous bacterial symbiont with an extremely reduced genome is able to traverse the low-nutrient, high-pressure environment of the deep sea to establish a symbiosis with a dispersed and relatively rare host. As samples of these fishes and symbionts become available, we may be able to address additional outstanding questions, such as the lack of diversity in anglerfish symbionts and their biogeographic population structure.

The data used to generate figures can be found in the supplementary material, denoted by "S" in text. The symbiont genomes have been submitted to the SRA database and their accessions have been listed in Table 2 and Supplementary file 1. The fish mitochondrial sequences used in this study are listed in Supplementary file 2. Mitochondrial sequences generated in this study can be found in Genbank (MK118159-MK118174). The Vibrionaceae species used to generate Figure 1 are listed in Supplementary file 3. The Vibrionaceae species used to generate the conserved single-copy protein-coding genes is listed in Supplementary file 4. The bacterial species used to generate Figure 4 can be found in Supplementary file 6. The sequences produced as a result of this study are also listed and are in Genbank (MK457129-MK457136). All methods are outlined and all statistical analysis are described in detail in the manuscript such that they can be repeated.

1. 1. Tory A Hendry
   2. Lydia J Baker

   (2018) NCBI BioProject

   ID PRJNA501852. Candidatus Enterovibrio luxaltus Genome sequencing and assembly.

   https://www.ncbi.nlm.nih.gov/bioproject/501852
2. 1. Tory A Hendry
   2. Lydia J Baker

   (2018) NCBI BioProject

   ID PRJNA501852. Diversity of anglerfish luminescent symbionts E. escacola.

   https://www.ncbi.nlm.nih.gov/bioproject/501851

1. 1. Abbot P
   2. Moran NA

   (2002) Extremely low levels of genetic polymorphism in endosymbionts (Buchnera) of aphids (Pemphigus)

   Molecular Ecology 11:2649–2660.

   https://doi.org/10.1046/j.1365-294X.2002.01646.x

   • PubMed
   • Google Scholar
2. 1. An JH
   2. Goo E
   3. Kim H
   4. Seo YS
   5. Hwang I

   (2014) Bacterial quorum sensing and metabolic slowing in a cooperative population

   PNAS 111:14912–14917.

   https://doi.org/10.1073/pnas.1412431111

   • PubMed
   • Google Scholar
3. 1. Ast JC
   2. Cleenwerck I
   3. Engelbeen K
   4. Urbanczyk H
   5. Thompson FL
   6. De Vos P
   7. Dunlap PV

   (2007) Photobacterium kishitanii sp. nov., a luminous marine bacterium symbiotic with deep-sea fishes

   International Journal of Systematic and Evolutionary Microbiology 57:2073–2078.

   https://doi.org/10.1099/ijs.0.65153-0

   • PubMed
   • Google Scholar
4. 1. Balbuena JA
   2. Míguez-Lozano R
   3. Blasco-Costa I

   (2013) PACo: a novel procrustes application to cophylogenetic analysis

   PLOS ONE 8:e61048.

   https://doi.org/10.1371/journal.pone.0061048

   • PubMed
   • Google Scholar
5. 1. Blazejak A
   2. Kuever J
   3. Erséus C
   4. Amann R
   5. Dubilier N

   (2006) Phylogeny of 16S rRNA, ribulose 1,5-bisphosphate carboxylase/oxygenase, and adenosine 5'-phosphosulfate reductase genes from gamma- and alphaproteobacterial symbionts in gutless marine worms (oligochaeta) from Bermuda and the Bahamas

   Applied and Environmental Microbiology 72:5527–5536.

   https://doi.org/10.1128/AEM.02441-05

   • PubMed
   • Google Scholar
6. 1. Bongrand C
   2. Koch EJ
   3. Moriano-Gutierrez S
   4. Cordero OX
   5. McFall-Ngai M
   6. Polz MF
   7. Ruby EG

   (2016) A genomic comparison of 13 symbiotic Vibrio fischeri isolates from the perspective of their host source and colonization behavior

   The ISME Journal 10:2907–2917.

   https://doi.org/10.1038/ismej.2016.69

   • PubMed
   • Google Scholar
7. 1. Bongrand C
   2. Ruby EG

   (2019) Achieving a multi-strain symbiosis: strain behavior and infection dynamics

   The ISME Journal 13:698–706.

   https://doi.org/10.1038/s41396-018-0305-8

   • PubMed
   • Google Scholar
8. 1. Bright M
   2. Bulgheresi S

   (2010) A complex journey: transmission of microbial symbionts

   Nature Reviews Microbiology 8:218–230.

   https://doi.org/10.1038/nrmicro2262

   • PubMed
   • Google Scholar
9. 1. Burgsdorf I
   2. Slaby BM
   3. Handley KM
   4. Haber M
   5. Blom J
   6. Marshall CW
   7. Gilbert JA
   8. Hentschel U
   9. Steindler L

   (2015) Lifestyle evolution in cyanobacterial symbionts of sponges

   mBio 6:.

   https://doi.org/10.1128/mBio.00391-15

   • PubMed
   • Google Scholar
10. 1. Bushnell B

    (2014)

    BBMap: a fast, accurate, splice-aware aligner, joint genome instritute

    LBNL Department of Energy Joint Genome Institute, Walnut Creek, CA.

    • Google Scholar
11. 1. Clark MA
    2. Moran NA
    3. Baumann P
    4. Wernegreen JJ

    (2000) Cospeciation between bacterial endosymbionts (Buchnera) and a recent radiation of aphids (Uroleucon) and pitfalls of testing for phylogenetic congruence

    Evolution 54:515–525.

    https://doi.org/10.1554/0014-3820(2000)054[0517:CBBEBA]2.0.CO;2

    • Google Scholar
12. 1. Dale C
    2. Moran NA

    (2006) Molecular interactions between bacterial symbionts and their hosts

    Cell 126:453–465.

    https://doi.org/10.1016/j.cell.2006.07.014

    • PubMed
    • Google Scholar
13. 1. Darnell CL
    2. Hussa EA
    3. Visick KL

    (2008) The putative hybrid sensor kinase SypF coordinates biofilm formation in Vibrio fischeri by acting upstream of two response regulators, SypG and VpsR

    Journal of Bacteriology 190:4941–4950.

    https://doi.org/10.1128/JB.00197-08

    • PubMed
    • Google Scholar
14. 1. Davis MP
    2. Sparks JS
    3. Smith WL

    (2016) Repeated and widespread evolution of bioluminescence in marine fishes

    PLOS ONE 11:e0155154.

    https://doi.org/10.1371/journal.pone.0155154

    • PubMed
    • Google Scholar
15. 1. DeLong EF
    2. Preston CM
    3. Mincer T
    4. Rich V
    5. Hallam SJ
    6. Frigaard NU
    7. Martinez A
    8. Sullivan MB
    9. Edwards R
    10. Brito BR
    11. Chisholm SW
    12. Karl DM

    (2006) Community genomics among stratified microbial assemblages in the ocean's interior

    Science 311:496–503.

    https://doi.org/10.1126/science.1120250

    • PubMed
    • Google Scholar
16. 1. Dunlap PV
    2. Ast JC
    3. Kimura S
    4. Fukui A
    5. Yoshino T
    6. Endo H

    (2007) Phylogenetic analysis of host–symbiont specificity and codivergence in bioluminescent symbioses

    Cladistics 23:507–532.

    https://doi.org/10.1111/j.1096-0031.2007.00157.x

    • Google Scholar
17. 1. Dunlap PV
    2. Gould AL
    3. Wittenrich ML
    4. Nakamura M

    (2012) Symbiosis initiation in the bacterially luminous sea urchin cardinalfish Siphamia versicolor

    Journal of Fish Biology 81:1340–1356.

    https://doi.org/10.1111/j.1095-8649.2012.03415.x

    • PubMed
    • Google Scholar
18. 1. Dunlap PV
    2. Urbanczyk H

    (2013)

    The Prokaryotes: Prokaryotic Physiology and Biochemistry

    495–528, Luminous bacteria, The Prokaryotes: Prokaryotic Physiology and Biochemistry, Springer, 10.1007/978-3-642-30141-4_75.

    • Google Scholar
19. 1. Easson CG
    2. Lopez JV

    (2019) Depth-Dependent environmental drivers of microbial plankton community structure in the Northern Gulf of Mexico

    Frontiers in Microbiology 9:1–13.

    https://doi.org/10.3389/fmicb.2018.03175

    • Google Scholar
20. 1. Ellis EA
    2. Oakley TH

    (2016) High rates of species accumulation in animals with bioluminescent courtship displays

    Current Biology 26:1916–1921.

    https://doi.org/10.1016/j.cub.2016.05.043

    • PubMed
    • Google Scholar
21. 1. Etter RJ
    2. Bower AS

    (2015) Dispersal and population connectivity in the deep North Atlantic estimated from physical transport processes

    Deep Sea Research Part I: Oceanographic Research Papers 104:159–172.

    https://doi.org/10.1016/j.dsr.2015.06.009

    • Google Scholar
22. 1. Feldman RA
    2. Black MB
    3. Cary CS
    4. Lutz RA
    5. Vrijenhoek RC

    (1997)

    Molecular phylogenetics of bacterial endosymbionts and their vestimentiferan hosts

    Molec Mar Biol Biotechnol 6:268–277.

    • Google Scholar
23. 1. Fisher RM
    2. Henry LM
    3. Cornwallis CK
    4. Kiers ET
    5. West SA

    (2017) The evolution of host-symbiont dependence

    Nature Communications 8:15973.

    https://doi.org/10.1038/ncomms15973

    • PubMed
    • Google Scholar
24. 1. Freed LL
    2. Easson C
    3. Baker LJ
    4. Fenolio D
    5. Sutton TT
    6. Khan Y
    7. Blackwelder P
    8. Hendry TA
    9. Lopez JV

    (2019) Characterization of the microbiome and bioluminescent symbionts across life stages of ceratioid anglerfishes of the gulf of Mexico

    FEMS Microbiology Ecology 10:.

    https://doi.org/10.1093/femsec/fiz146

    • Google Scholar
25. Website

    1. Froese R
    2. Pauly D

    (2018) FishBase

    Accessed February 1, 2018.

    https://www.fishbase.in/search.php
26. 1. Funk DJ
    2. Wernegreen JJ
    3. Moran NA

    (2001)

    Intraspecific variation in symbiont genomes: bottlenecks and the aphid-Buchnera association

    Genetics 157:477–489.

    • PubMed
    • Google Scholar
27. 1. Gao Z-M
    2. Wang Y
    3. Tian R-M
    4. Wong YH
    5. Batang ZB
    6. Al-Suwailem AM
    7. Bajic VB
    8. Qian P-Y

    (2014) Symbiotic adaptation drives genome streamlining of the cyanobacterial sponge symbiont “Candidatus Synechococcus spongiarum”

    mBio 5:.

    https://doi.org/10.1128/mBio.00079-14

    • Google Scholar
28. Preprint

    1. Garrison E
    2. Marth G

    (2012) Haplotype-based variant detection from short-read sequencing. arXiv prepr

    arXiv.

    https://arxiv.org/abs/1207.3907

    • Google Scholar
29. 1. Goffredi S
    2. Hurtado L
    3. Hallam S
    4. Vrijenhoek R

    (2003) Evolutionary relationships of deep-sea vent and cold seep clams (Mollusca: vesicomyidae) of the "pacifica/lepta" species complex

    Marine Biology 142:311–320.

    https://doi.org/10.1007/s00227-002-0941-3

    • Google Scholar
30. 1. Gyllborg MC
    2. Sahl JW
    3. Cronin DC
    4. Rasko DA
    5. Mandel MJ

    (2012) Draft genome sequence of Vibrio fischeri SR5, a strain isolated from the light organ of the Mediterranean squid Sepiola robusta

    Journal of Bacteriology 194:1639.

    https://doi.org/10.1128/JB.06825-11

    • PubMed
    • Google Scholar
31. 1. Hansell DA

    (2013) Recalcitrant dissolved organic carbon fractions

    Annual Review of Marine Science 5:421–445.

    https://doi.org/10.1146/annurev-marine-120710-100757

    • PubMed
    • Google Scholar
32. 1. Haygood MG
    2. Tebo BM
    3. Nealson KH

    (1984) Luminous bacteria of a monocentrid fish (Monocentris japonicus) and two anomalopid fishes (Photoblepharon palpebratus and Kryptophanaron alfredi): population sizes and growth within the light organs, and rates of release into the seawater

    Marine Biology 78:249–254.

    https://doi.org/10.1007/BF00393010

    • Google Scholar
33. 1. Haygood MG
    2. Distel DL
    3. Herring PJ

    (1992) Polymerase chain reaction and 16S rRNA gene sequences from the luminous bacterial symbionts of two deep-sea anglerfishes

    Journal of the Marine Biological Association of the United Kingdom 72:149–159.

    https://doi.org/10.1017/S0025315400048852

    • Google Scholar
34. 1. Haygood MG

    (1993) Light organ symbioses in fishes

    Critical Reviews in Microbiology 19:191–216.

    https://doi.org/10.3109/10408419309113529

    • PubMed
    • Google Scholar
35. 1. Haygood MG
    2. Distel DL

    (1993) Bioluminescent symbionts of flashlight fishes and deep-sea anglerfishes form unique lineages related to the genus Vibrio

    Nature 363:154–156.

    https://doi.org/10.1038/363154a0

    • PubMed
    • Google Scholar
36. 1. Hendry TA
    2. de Wet JR
    3. Dunlap PV

    (2014) Genomic signatures of obligate host dependence in the luminous bacterial symbiont of a vertebrate

    Environmental Microbiology 16:2611–2622.

    https://doi.org/10.1111/1462-2920.12302

    • PubMed
    • Google Scholar
37. 1. Hendry TA
    2. de Wet JR
    3. Dougan KE
    4. Dunlap PV

    (2016) Genome evolution in the obligate but environmentally active luminous symbionts of flashlight fish

    Genome Biology and Evolution 8:2203–2213.

    https://doi.org/10.1093/gbe/evw161

    • PubMed
    • Google Scholar
38. 1. Hendry TA
    2. Freed LL
    3. Fader D
    4. Fenolio D
    5. Sutton TT
    6. Lopez JV

    (2018) Ongoing transposon-mediated genome reduction in the luminous bacterial symbionts of deep-sea ceratioid anglerfishes

    mBio 9:e01033.

    https://doi.org/10.1128/mBio.01033-18

    • PubMed
    • Google Scholar
39. 1. Hendry TA
    2. Dunlap PV

    (2011) The uncultured luminous symbiont of Anomalops katoptron (Beryciformes: anomalopidae) represents a new bacterial genus

    Molecular Phylogenetics and Evolution 61:834–843.

    https://doi.org/10.1016/j.ympev.2011.08.006

    • PubMed
    • Google Scholar
40. 1. Hendry TA
    2. Dunlap PV

    (2014) Phylogenetic divergence between the obligate luminous symbionts of flashlight fishes demonstrates specificity of bacteria to host genera

    Environmental Microbiology Reports 6:331–338.

    https://doi.org/10.1111/1758-2229.12135

    • PubMed
    • Google Scholar
41. 1. Hurtado LA
    2. Mateos M
    3. Lutz RA
    4. Vrijenhoek RC

    (2003) Coupling of bacterial endosymbiont and host mitochondrial genomes in the hydrothermal vent clam Calyptogena magnifica

    Applied and Environmental Microbiology 69:2058–2064.

    https://doi.org/10.1128/AEM.69.4.2058-2064.2003

    • PubMed
    • Google Scholar
42. 1. Hussa EA
    2. Darnell CL
    3. Visick KL

    (2008) RscS functions upstream of SypG to control the syp locus and biofilm formation in Vibrio fischeri

    Journal of Bacteriology 190:4576–4583.

    https://doi.org/10.1128/JB.00130-08

    • PubMed
    • Google Scholar
43. 1. Johnson SS
    2. Hebsgaard MB
    3. Christensen TR
    4. Mastepanov M
    5. Nielsen R
    6. Munch K
    7. Brand T
    8. Gilbert MT
    9. Zuber MT
    10. Bunce M
    11. Rønn R
    12. Gilichinsky D
    13. Froese D
    14. Willerslev E

    (2007) Ancient bacteria show evidence of DNA repair

    PNAS 104:14401–14405.

    https://doi.org/10.1073/pnas.0706787104

    • PubMed
    • Google Scholar
44. 1. Jousselin E
    2. Desdevises Y
    3. Coeur d'acier A

    (2009) Fine-scale cospeciation between Brachycaudus and Buchnera aphidicola: bacterial genome helps define species and evolutionary relationships in aphids

    Proceedings of the Royal Society B: Biological Sciences 276:187–196.

    https://doi.org/10.1098/rspb.2008.0679

    • PubMed
    • Google Scholar
45. 1. Kalyaanamoorthy S
    2. Minh BQ
    3. Wong TKF
    4. von Haeseler A
    5. Jermiin LS

    (2017) ModelFinder: fast model selection for accurate phylogenetic estimates

    Nature Methods 14:587–589.

    https://doi.org/10.1038/nmeth.4285

    • PubMed
    • Google Scholar
46. 1. Kang DD
    2. Froula J
    3. Egan R
    4. Wang Z

    (2015) MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

    PeerJ 3:e1165.

    https://doi.org/10.7717/peerj.1165

    • PubMed
    • Google Scholar
47. 1. Katoh K
    2. Misawa K
    3. Kuma K
    4. Miyata T

    (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast fourier transform

    Nucleic Acids Research 30:3059–3066.

    https://doi.org/10.1093/nar/gkf436

    • PubMed
    • Google Scholar
48. 1. Kenyon LJ
    2. Sabree ZL

    (2014) Obligate insect endosymbionts exhibit increased ortholog length variation and loss of large accessory proteins concurrent with genome shrinkage

    Genome Biology and Evolution 6:763–775.

    https://doi.org/10.1093/gbe/evu055

    • PubMed
    • Google Scholar
49. 1. Kikuchi Y
    2. Meng XY
    3. Fukatsu T

    (2005) Gut symbiotic bacteria of the genus Burkholderia in the broad-headed bugs Riptortus clavatus and Leptocorisa chinensis (Heteroptera: alydidae)

    Applied and Environmental Microbiology 71:4035–4043.

    https://doi.org/10.1128/AEM.71.7.4035-4043.2005

    • PubMed
    • Google Scholar
50. 1. Kikuchi Y
    2. Hosokawa T
    3. Fukatsu T

    (2007) Insect-microbe mutualism without vertical transmission: a stinkbug acquires a beneficial gut symbiont from the environment every generation

    Applied and Environmental Microbiology 73:4308–4316.

    https://doi.org/10.1128/AEM.00067-07

    • PubMed
    • Google Scholar
51. 1. Kikuchi Y
    2. Fukatsu T

    (2003) Diversity of Wolbachia endosymbionts in heteropteran bugs

    Applied and Environmental Microbiology 69:6082–6090.

    https://doi.org/10.1128/AEM.69.10.6082-6090.2003

    • PubMed
    • Google Scholar
52. 1. Kleiner M
    2. Petersen JM
    3. Dubilier N

    (2012) Convergent and divergent evolution of metabolism in sulfur-oxidizing symbionts and the role of horizontal gene transfer

    Current Opinion in Microbiology 15:621–631.

    https://doi.org/10.1016/j.mib.2012.09.003

    • PubMed
    • Google Scholar
53. 1. Koch EJ
    2. Miyashiro T
    3. McFall-Ngai MJ
    4. Ruby EG

    (2014) Features governing symbiont persistence in the squid-vibrio association

    Molecular Ecology 23:1624–1634.

    https://doi.org/10.1111/mec.12474

    • PubMed
    • Google Scholar
54. 1. Konstantinidis KT
    2. Tiedje JM

    (2005) Genomic insights that advance the species definition for prokaryotes

    PNAS 102:2567–2572.

    https://doi.org/10.1073/pnas.0409727102

    • PubMed
    • Google Scholar
55. 1. Kuwahara H
    2. Yoshida T
    3. Takaki Y
    4. Shimamura S
    5. Nishi S
    6. Harada M
    7. Matsuyama K
    8. Takishita K
    9. Kawato M
    10. Uematsu K
    11. Fujiwara Y
    12. Sato T
    13. Kato C
    14. Kitagawa M
    15. Kato I
    16. Maruyama T

    (2007) Reduced genome of the thioautotrophic intracellular symbiont in a deep-sea clam, Calyptogena okutanii

    Current Biology 17:881–886.

    https://doi.org/10.1016/j.cub.2007.04.039

    • PubMed
    • Google Scholar
56. 1. Lauro FM
    2. Bartlett DH

    (2008) Prokaryotic lifestyles in deep sea habitats

    Extremophiles 12:27.

    https://doi.org/10.1007/s00792-007-0110-1

    • Google Scholar
57. 1. Lefoulon E
    2. Bain O
    3. Makepeace BL
    4. d'Haese C
    5. Uni S
    6. Martin C
    7. Gavotte L

    (2016) Breakdown of coevolution between symbiotic bacteria Wolbachia and their filarial hosts

    PeerJ 4:e1840.

    https://doi.org/10.7717/peerj.1840

    • PubMed
    • Google Scholar
58. Preprint

    1. Li H

    (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM

    arXiv.

    https://arxiv.org/abs/1303.3997

    • Google Scholar
59. 1. Li Y
    2. Liles MR
    3. Halanych KM

    (2018) Endosymbiont genomes yield clues of tubeworm success

    The ISME Journal 12:2785–2795.

    https://doi.org/10.1038/s41396-018-0220-z

    • PubMed
    • Google Scholar
60. 1. Lind PA
    2. Andersson DI

    (2008) Whole-genome mutational biases in bacteria

    PNAS 105:17878–17883.

    https://doi.org/10.1073/pnas.0804445105

    • PubMed
    • Google Scholar
61. 1. Mandel MJ
    2. Wollenberg MS
    3. Stabb EV
    4. Visick KL
    5. Ruby EG

    (2009) A single regulatory gene is sufficient to alter bacterial host range

    Nature 458:215–218.

    https://doi.org/10.1038/nature07660

    • PubMed
    • Google Scholar
62. 1. Manzano-Marín A
    2. Latorre A

    (2016) Snapshots of a shrinking partner: genome reduction in Serratia symbiotica

    Scientific Reports 6:32590.

    https://doi.org/10.1038/srep32590

    • PubMed
    • Google Scholar
63. 1. Martini S
    2. Haddock SHD

    (2017) Quantification of bioluminescence from the surface to the deep sea demonstrates its predominance as an ecological trait

    Scientific Reports 7:.

    https://doi.org/10.1038/srep45750

    • Google Scholar
64. 1. McCutcheon JP
    2. Moran NA

    (2011) Extreme genome reduction in symbiotic bacteria

    Nature Reviews Microbiology 10:13–26.

    https://doi.org/10.1038/nrmicro2670

    • PubMed
    • Google Scholar
65. 1. McFall-Ngai M
    2. Hadfield MG
    3. Bosch TC
    4. Carey HV
    5. Domazet-Lošo T
    6. Douglas AE
    7. Dubilier N
    8. Eberl G
    9. Fukami T
    10. Gilbert SF
    11. Hentschel U
    12. King N
    13. Kjelleberg S
    14. Knoll AH
    15. Kremer N
    16. Mazmanian SK
    17. Metcalf JL
    18. Nealson K
    19. Pierce NE
    20. Rawls JF
    21. Reid A
    22. Ruby EG
    23. Rumpho M
    24. Sanders JG
    25. Tautz D
    26. Wernegreen JJ

    (2013) Animals in a bacterial world, a new imperative for the life sciences

    PNAS 110:3229–3236.

    https://doi.org/10.1073/pnas.1218525110

    • PubMed
    • Google Scholar
66. 1. Miya M
    2. Pietsch TW
    3. Orr JW
    4. Arnold RJ
    5. Satoh TP
    6. Shedlock AM
    7. Ho HC
    8. Shimazaki M
    9. Yabe M
    10. Nishida M

    (2010) Evolutionary history of anglerfishes (Teleostei: lophiiformes): a mitogenomic perspective

    BMC Evolutionary Biology 10:58.

    https://doi.org/10.1186/1471-2148-10-58

    • PubMed
    • Google Scholar
67. 1. Moran NA

    (1996) Accelerated evolution and Muller's rachet in endosymbiotic bacteria

    PNAS 93:2873–2878.

    https://doi.org/10.1073/pnas.93.7.2873

    • PubMed
    • Google Scholar
68. 1. Moran NA

    (2007) Symbiosis as an adaptive process and source of phenotypic complexity

    PNAS 104 Suppl 1:8627–8633.

    https://doi.org/10.1073/pnas.0611659104

    • PubMed
    • Google Scholar
69. 1. Moran NA
    2. McCutcheon JP
    3. Nakabachi A

    (2008) Genomics and evolution of heritable bacterial symbionts

    Annual Review of Genetics 42:165–190.

    https://doi.org/10.1146/annurev.genet.41.110306.130119

    • PubMed
    • Google Scholar
70. 1. Moya A
    2. Peretó J
    3. Gil R
    4. Latorre A

    (2008) Learning how to live together: genomic insights into prokaryote-animal symbioses

    Nature Reviews Genetics 9:218–229.

    https://doi.org/10.1038/nrg2319

    • PubMed
    • Google Scholar
71. 1. Muller KE
    2. Denison RF

    (2018) Resource acquisition and allocation traits in symbiotic rhizobia with implications for life-history outside of legume hosts

    Royal Society Open Science 5:181124.

    https://doi.org/10.1098/rsos.181124

    • Google Scholar
72. 1. Münchhoff J
    2. Hirose E
    3. Maruyama T
    4. Sunairi M
    5. Burns BP
    6. Neilan BA

    (2007) Host specificity and phylogeography of the prochlorophyte Prochloron sp., an obligate symbiont in didemnid ascidians

    Environmental Microbiology 9:890–899.

    https://doi.org/10.1111/j.1462-2920.2006.01209.x

    • PubMed
    • Google Scholar
73. 1. Munk O

    (1999) The escal photophore of ceratioids (Pisces; Ceratioidei) - a review of structure and function

    Acta Zoologica 80:265–284.

    https://doi.org/10.1046/j.1463-6395.1999.00023.x

    • Google Scholar
74. 1. Nealson KH
    2. Hastings JW

    (1991)

    The Prokaryotes, a Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications

    The luminous bacteria, The Prokaryotes, a Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications, second edition, New York, Springer-Verlag.

    • Google Scholar
75. 1. Newton ILG
    2. Woyke T
    3. Auchtung TA
    4. Dilly GF
    5. Dutton RJ
    6. Fisher MC
    7. Fontanez KM
    8. Lau E
    9. Stewart FJ
    10. Richardson PM
    11. Barry KW
    12. Saunders E
    13. Detter JC
    14. Wu D
    15. Eisen JA
    16. Cavanaugh CM

    (2007) The Calyptogena magnifica chemoautotrophic symbiont genome

    Science 315:998–1000.

    https://doi.org/10.1126/science.1138438

    • Google Scholar
76. 1. Nguyen LT
    2. Schmidt HA
    3. von Haeseler A
    4. Minh BQ

    (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies

    Molecular Biology and Evolution 32:268–274.

    https://doi.org/10.1093/molbev/msu300

    • PubMed
    • Google Scholar
77. 1. Nussbaumer AD
    2. Fisher CR
    3. Bright M

    (2006) Horizontal endosymbiont transmission in hydrothermal vent tubeworms

    Nature 441:345–348.

    https://doi.org/10.1038/nature04793

    • PubMed
    • Google Scholar
78. 1. Parks DH
    2. Imelfort M
    3. Skennerton CT
    4. Hugenholtz P
    5. Tyson GW

    (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

    Genome Research 25:1043–1055.

    https://doi.org/10.1101/gr.186072.114

    • PubMed
    • Google Scholar
79. 1. Pazos RL
    2. Lumpkin R M

    (2007)

     Lagrangian Analysis and Prediction of Coastal and Ocean Dynamics

    Measuring surface currents with surface velocity program drifters: the instrument, its data, and some recent results,  Lagrangian Analysis and Prediction of Coastal and Ocean Dynamics, 67, Cambridge University Press.

    • Google Scholar
80. Book

    1. Pietsch T

    (2009)

    Oceanic Anglerfishes: Extraordinary Diversity in the Deep Sea

    University of California Press.

    • Google Scholar
81. 1. Pietsch TW
    2. Sutton TT

    (2015) A new species of the ceratioid anglerfish genus Lasiognathus regan (Lophiiformes: Oneirodidae) from the Northern Gulf of Mexico

    Copeia 103:429–432.

    https://doi.org/10.1643/CI-14-181

    • Google Scholar
82. 1. Ponnudurai R
    2. Sayavedra L
    3. Kleiner M
    4. Heiden SE
    5. Thürmer A
    6. Felbeck H
    7. Schlüter R
    8. Sievert SM
    9. Daniel R
    10. Schweder T
    11. Markert S

    (2017) Genome sequence of the sulfur-oxidizing Bathymodiolus thermophilus gill endosymbiont

    Standards in Genomic Sciences 12:.

    https://doi.org/10.1186/s40793-017-0266-y

    • PubMed
    • Google Scholar
83. Software

    1. R Development Core Team

    (2012) R: A Language and Environment for Statistical Computing, version ISBN 3-900051-07-0

    R Foundation for Statistical Computing,  Vienna, Austria.

    http://www.r-project.org/
84. 1. Ruby EG
    2. Urbanowski M
    3. Campbell J
    4. Dunn A
    5. Faini M
    6. Gunsalus R
    7. Lostroh P
    8. Lupp C
    9. McCann J
    10. Millikan D
    11. Schaefer A
    12. Stabb E
    13. Stevens A
    14. Visick K
    15. Whistler C
    16. Greenberg EP

    (2005) Complete genome sequence of Vibrio fischeri: a symbiotic bacterium with pathogenic congeners

    PNAS 102:3004–3009.

    https://doi.org/10.1073/pnas.0409900102

    • PubMed
    • Google Scholar
85. 1. Sachs JL
    2. Skophammer RG
    3. Regus JU

    (2011) Evolutionary transitions in bacterial symbiosis

    PNAS 108 Suppl 2:10800–10807.

    https://doi.org/10.1073/pnas.1100304108

    • PubMed
    • Google Scholar
86. Book

    1. Schaechter M

    (2009)

    Encyclopedia of Microbiology (Third Edition)

    Science direct.

    • Google Scholar
87. Software

    1. Seemann T

    (2015) Snippy-Rapid haploid variant calling and core SNP phylogeny

    GitHub.

    https://github.com/tseemann/snippy
88. 1. Segata N
    2. Börnigen D
    3. Morgan XC
    4. Huttenhower C

    (2013) PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

    Nature Communications 4:.

    https://doi.org/10.1038/ncomms3304

    • PubMed
    • Google Scholar
89. 1. Shigenobu S
    2. Watanabe H
    3. Hattori M
    4. Sakaki Y
    5. Ishikawa H

    (2000) Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS

    Nature 407:81–86.

    https://doi.org/10.1038/35024074

    • PubMed
    • Google Scholar
90. 1. Tamas I
    2. Klasson L
    3. Canbäck B
    4. Näslund AK
    5. Eriksson AS
    6. Wernegreen JJ
    7. Sandström JP
    8. Moran NA
    9. Andersson SG

    (2002) 50 million years of genomic stasis in endosymbiotic bacteria

    Science 296:2376–2379.

    https://doi.org/10.1126/science.1071278

    • PubMed
    • Google Scholar
91. 1. Thompson CM
    2. Marsden AE
    3. Tischler AH
    4. Koo J
    5. Visick KL

    (2018) Vibrio fischeri biofilm formation prevented by a trio of regulators

    Applied and Environmental Microbiology 84:.

    https://doi.org/10.1128/AEM.01257-18

    • PubMed
    • Google Scholar
92. 1. Urbanczyk H
    2. Ogura Y
    3. Hendry TA
    4. Gould AL
    5. Kiwaki N
    6. Atkinson JT
    7. Hayashi T
    8. Dunlap PV

    (2011) Genome sequence of Photobacterium mandapamensis strain svers.1.1, the bioluminescent symbiont of the cardinal fish Siphamia versicolor

    Journal of Bacteriology 193:3144–3145.

    https://doi.org/10.1128/JB.00370-11

    • PubMed
    • Google Scholar
93. 1. Wattam AR
    2. Abraham D
    3. Dalay O
    4. Disz TL
    5. Driscoll T
    6. Gabbard JL
    7. Gillespie JJ
    8. Gough R
    9. Hix D
    10. Kenyon R
    11. Machi D
    12. Mao C
    13. Nordberg EK
    14. Olson R
    15. Overbeek R
    16. Pusch GD
    17. Shukla M
    18. Schulman J
    19. Stevens RL
    20. Sullivan DE
    21. Vonstein V
    22. Warren A
    23. Will R
    24. Wilson MJ
    25. Yoo HS
    26. Zhang C
    27. Zhang Y
    28. Sobral BW

    (2014) PATRIC, the bacterial bioinformatics database and analysis resource

    Nucleic Acids Research 42:D581–D591.

    https://doi.org/10.1093/nar/gkt1099

    • PubMed
    • Google Scholar
94. 1. Wirsen CO
    2. Molyneaux SJ

    (1999)

    A study of deep-sea natural microbial populations and barophilic pure cultures using a high-pressure chemostat

    Applied and Environmental Microbiology 65:5314–5321.

    • PubMed
    • Google Scholar
95. 1. Won YJ
    2. Hallam SJ
    3. O'Mullan GD
    4. Pan IL
    5. Buck KR
    6. Vrijenhoek RC

    (2003) Environmental acquisition of thiotrophic endosymbionts by deep-sea mussels of the genus Bathymodiolus

    Applied and Environmental Microbiology 69:6785–6792.

    https://doi.org/10.1128/AEM.69.11.6785-6792.2003

    • PubMed
    • Google Scholar
96. 1. Won Y-J
    2. Jones WJ
    3. Vrijenhoek RC

    (2008) Absence of cospeciation between deep-sea Mytilids and their thiotrophic endosymbionts

    Journal of Shellfish Research 27:129–138.

    https://doi.org/10.2983/0730-8000(2008)27[129:AOCBDM]2.0.CO;2

    • Google Scholar
97. 1. Wright ES
    2. Yilmaz LS
    3. Noguera DR

    (2012) DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences

    Applied and Environmental Microbiology 78:717–725.

    https://doi.org/10.1128/AEM.06516-11

    • PubMed
    • Google Scholar
98. 1. Yip ES
    2. Grublesky BT
    3. Hussa EA
    4. Visick KL

    (2005) A novel, conserved cluster of genes promotes symbiotic colonization and sigma-dependent biofilm formation by Vibrio fischeri

    Molecular Microbiology 57:1485–1498.

    https://doi.org/10.1111/j.1365-2958.2005.04784.x

    • PubMed
    • Google Scholar
99. 1. Yoon SH
    2. Ha SM
    3. Lim J
    4. Kwon S
    5. Chun J

    (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity

    Antonie Van Leeuwenhoek 110:1281–1286.

    https://doi.org/10.1007/s10482-017-0844-4

    • PubMed
    • Google Scholar
100. 1. Zhang Y
     2. Su X
     3. Harris AJ
     4. Caraballo-Ortiz MA
     5. Ren Z
     6. Zhong Y

     (2018) Genetic structure of the bacterial endosymbiont Buchnera aphidicola from its host aphid Schlechtendalia chinensis and evolutionary implications

     Current Microbiology 75:309–315.

     https://doi.org/10.1007/s00284-017-1381-0

     • PubMed
     • Google Scholar

Author details

1. Lydia J Baker

   Department of Microbiology, Cornell University, New York, United States

   Contribution

   Conceptualization, Data curation, Formal analysis, Investigation, Visualization, Methodology, Writing—original draft, Writing—review and editing

   For correspondence

   lb693@cornell.edu

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-1453-421X

2. Lindsay L Freed

   Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, United States

   Contribution

   Resources, Investigation, Writing—review and editing

   Competing interests

   No competing interests declared

3. Cole G Easson

   1. Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, United States
   2. Department of Biology, Middle Tennessee State University, Murfreesboro, United States

   Contribution

   Resources, Investigation, Writing—review and editing

   Competing interests

   No competing interests declared

4. Jose V Lopez

   Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, United States

   Contribution

   Resources, Funding acquisition, Investigation, Writing—review and editing

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-1637-4125

5. Danté Fenolio

   Center for Conservation and Research, San Antonio Zoo, San Antonio, United States

   Contribution

   Resources, Investigation, Writing—review and editing

   Competing interests

   No competing interests declared

6. Tracey T Sutton

   Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, United States

   Contribution

   Resources, Investigation, Writing—review and editing

   Competing interests

   No competing interests declared

7. Spencer V Nyholm

   Department of Molecular and Cell Biology, University of Connecticut, Storrs, United States

   Contribution

   Resources, Investigation, Writing—review and editing

   Competing interests

   No competing interests declared

8. Tory A Hendry

   Department of Microbiology, Cornell University, New York, United States

   Contribution

   Conceptualization, Resources, Data curation, Supervision, Funding acquisition, Investigation, Methodology, Writing—original draft, Project administration, Writing—review and editing

   For correspondence

   th572@cornell.edu

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-8001-1783

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