Molecular phylogeny and historical biogeography of marine palaemonid shrimps (Palaemonidae: Palaemonella–Cuapetes group)
Phylogenetic relationships inside the family Palaemonidae remain unresolved, despite being frequently discussed in recent publications9,10. Nevertheless, the last published study5 presented the main lineages of the family as well supported. Among those, the studied Pon-I group of predominantly free-living taxa is basal-positioned to the remaining genera of the former subfamily Pontoniinae, usually more specialised and associated with a wide range of hosts. The basal separation of the symbiotic genera led some authors to consider the assemblage, following Bruce22, to be a primitive group, or descendants of such7,23. Additionally, Gan et al.8 suggested that the taxa of the Pon-I group might be direct descendants of the ancestors of the former subfamily Pontoniinae, sharing the main plesiomorphies appearing frequently in former palaemonine taxa, e.g., the genera Brachycarpus, Leptocarpus, Macrobrachium, or Palaemon. The median process on the fourth thoracic sternite can be considered a plesiomorphic feature; indeed, it is a common symplesiomorphy of all Pon-I taxa, including Ischnopontonia and Anapontonia, for which the process was formerly reported as missing24 (its presence was confirmed in present examined specimens). In addition to that, the mandibular palp occurring in the genera Exoclimenella, Eupontonia, Palaemonella, and Vir25, or the presence of two arthrobranchs on the third maxilliped in Exoclimenella26, can also be considered plesiomorphic features.The Pon-I group’s internal relations have been unclear until now due to lower generic and species coverage in previous studies4,5,8. The present analysis based on a six-marker molecular dataset allows a deeper insight into the phylogenetic relationships of the study group involving all 11 currently recognised genera, and represented by 52 species, i.e. about 60% of the overall known species diversity of the group. The results provide a strong support for the monophyly and/or taxonomic validity of the current genera Exoclimenella, Anapontonia, Ischnopontonia, and suggest the monophyly of genera Harpilius and Philarius. Moreover, the results reveal non-monophyly of the most speciose genera Palaemonella and Cuapetes, as well as the species-poor Eupontonia. The genus Palaemonella was found to be paraphyletic owing to the nested species of the genera Eupontonia and Vir, which all share a common synapomorphy, the presence of the mandibular palp (mentioned above). Such conclusion was expressed also in the study of Chow et al.5.The present phylogenetic analysis confirmed that the genus Cuapetes is not monophyletic, as found to a lesser extent, in a few previous molecular studies 4,5,23. In this study, the genus Cuapetes was recovered in four separate genetic lineages. The type species C. nilandensis is nested in the Clade 1 along with C. johnsoni and C. seychellensis. This phylogenetic finding is in line with the study of Marin and Sinelnikov27, who indicated morphological differences between two of the above-mentioned species and most of the remaining species of the genus (respective of the present Clade 5, also covering C. grandis, the type species of the ex-genus Kemponia), and questioned the validity of the two latter generic names. The further genetic lineage is shown by the position of C. americanus nested in the eastern Pacific—Atlantic branch of the genus Palaemonella (Clade 3). This result is also supported by recent phylogenetic studies suggesting the different systematic positions of this species4,5,10. Due to the lack of the mandibular palp, the species had been properly, but evidently incorrectly, assigned to the genus Cuapetes. The fourth genetic lineage is shown by a separate position of C. darwiniensis in the Clade 4 as the sister species of Madangella altirostris.The remaining majority of the Cuapetes species (Clade 5) are heterogeneous due to comprising also representatives of the genus Periclimenella. Ďuriš and Bruce26 hypothesised, based on morphological traits (mainly the unique shape of the first pereiopod chelae and the distinctly asymmetrical and specific second pereiopods), that the genera Exoclimenella and Periclimenella are closely related. Nevertheless, the present study revealed Periclimenella as a part of the genus Cuapetes. This result was previously supported in the molecular study by Horká et al.4 and weakly supported by Kou et al.23.Fossil records of palaemonid shrimps are rare due to their aquatic habit and poorly calcified exoskeletons. Only a few palaemonid representatives are known compared to many extant taxa; the oldest fossil records contain only genera from the previous subfamily Palaemoninae from the Lower Cretaceous (middle Albian, 100 Myr)28. For this reason, we used the known mutation rate of mitochondrial gene (16S rRNA) for dating rather than fossil records.The present inferred phylogeny and ancestral analysis indicate multiple formations of primary symbioses within the clades dominated by free-living relatives, as shown by previous molecular analyses4,5. Our results revealed eight independent lineages within the Pon-I group that evolved from free-living ancestors (Fig. 3). Free-living palaemonids (Exoclimenella, Palaemonella, Cuapetes; Fig. 2) are characterised by an elongate body shape with a dentate rostrum, slender, long, a/symmetrical chelipeds and slender ambulatory pereiopods with simple dactyli. Their carapace might bear the full complement of teeth (i.e., supraorbital, antennal, hepatic, epigastric)25. Primary symbiotic forms do not fundamentally differ morphologically from free-living ancestors. Their adaptations to the host affiliation have mainly manifested by changes in body shape, colouration, and the reduction of carapace ornamentation. Their hosts belong to different invertebrate phyla, including Cnidaria (mainly Scleractinia and Antipatharia22) and Echinodermata (Crinoidea29) in ectosymbiotic forms, but also to spoon worms (Echiura), burrowing Crustacea (alpheid shrimps), and/or gobiid fishes15, in inquilinistic forms.While scleractinian corals were hypothesised as the primary hosts of palaemonid shrimp commensalism7, our results revealed the antipatharian association as possibly the earlier one among the Pon-I shrimps. That association was established via a single speciation act at approximately 43 Myr (Eocene), specifically with the ancestor of the recent Cuapetes nilandensis (Clade 1). Except a small body size, this species does not show specific morphological adaptations to antipatharian association. The possibly oldest lineage associated with the scleractinian corals forms a common multigeneric composition of Anapontonia, Ischnopontonia, Harpilius and Philarius (Clade 4), which was established at approximately 38.2 Myr (Eocene). The genera share some homoplasic adaptations with ectosymbioses, such as strongly hooked dactyli of the ambulatory pereiopods adapted to climbing on coral colonies. An extremely compressed body and similar tail fan structure of the genera Ischnopontonia (Fig. 1H) and Anapontonia (Fig. 1D) are adaptations to life in narrow spaces amongst corallites of the oculinid coral Galaxea24,30; the intercorallite channels might be temporarily fully covered by tentacles of exposed polyps. This lifestyle was thus termed ‘semi-endosymbiosis’ by Horká et al.4, as potential evolutionary precursors of the true endosymbioses. In contrast, the genera Philarius and Harpilius have depressed bodies and associate exclusively as regular ectosymbionts with scleractinian corals, mainly of the genera Acropora and Pocillopora22.A further multispecies symbiotic lineage is represented by the genus Vir (Clade 3), whose origin is dated to approximately 21.1 Myr (Miocene). All species of this genus live in associations mainly with the acroporid, pocilloporid and euphylliid genera of scleractinian corals31,32. The adaptation to their symbiotic lifestyle is expressed in the loss of the hepatic tooth, partial or full reduction of ambulatory propodal spines, and cryptic colouration, including transparency of the body and appendages31,33 (Fig. 1J). Subsequent scleractinian-associated lineages are represented by separate species that appeared in the Miocene (21.9–10.1 Myr), namely: Eupontonia oahu, Cuapetes amymone, and C. kororensis, which live in association with Pocillopora, Acropora, and Heliofungia, and show only minor adaptations to their symbiotic habits, e.g. loss of the hepatic tooth, dense distal setae on the walking propodi, or extremely slender chelae and a specific cryptic colouration, respectively22,34,35.A single crinoid-associated species, Palaemonella pottsi (Clade 3), represents the only case of the switch from a free-living lifestyle to the association with echinoderms in the present study group; it originated at approximately 10.4 Myr (Miocene). Retaining the body shape typical for Palaemonella12, the species also does not show any noticeable morphological adaptation to such a host; its affiliation with the symbiotic life is, however, clearly observed in the deep-red to black cryptic colouration36.In Palaemonella aliska (Fig. 1E) and Eupontonia nudirostris (Clade 3), a pair of sister-positioned species in the present analyses (Figs. 2, 3), the ability to co-habit with burrowing animals (e.g., alpheids, gobiid fish, or echiurids) had developed. Their type of symbiosis, inquilinism, formed at approximately 14.8 Myr (Miocene). The reduction of the rostrum length, depressed body, stout main chelae in both, and full lack of the epigastric and hepatic teeth in the latter species15,25, were evidently due to that mode of life. Inquilinism is best known in the family Alpheidae, in which multiple genera associate with a variety of burrowing animals37. In the family Palaemonidae, inquilinism developed only in the Pon-I group, including Palaemonella shirakawai (not analysed here)14.As evident from the present and previously published reports4,5,7,8,10, the life history of the Pon-I group was largely shaped by coevolution with coral reefs. The coral reefs were deeply impacted by the K–T mass extinction at the end of the Cretaceous, which was one of the most destructive events in the Phanerozoic38. However, coral reefs recovered and became increasingly abundant in the Eocene39. This also matches the time of either the origin of host associations, or a wider species radiation of the Pon-I group. The first fossil records of the main coral hosts of the present shrimps are dated after the K-T extinction during the Paleogene (e.g., Euphyllia 66.0–61.6 Myr, Acropora 59.2–56.0 Myr, Galaxea and Pocillopora 56–33.9 Myr40).The biogeographic history suggested by S-DIVA analysis points to some dispersal and vicariant events shaping the current pattern of the Pon-I group’s distribution. This reconstruction (Fig. 4) estimates the present-day IWP region within the former Paleo-Tethys Ocean as the most likely ancestral area of the present study group, which originated ~ 91.6 Myr (Late to Early Cretaceous). The present shrimp group had radiated across the entire IWP region and subsequently expanded into the Atlantic Ocean. We assume that the spread of the group took place in the following sequence of events: (1) dispersal of Palaemonella spp. from the IWP into the eastern Pacific in the Paleocene (∼ 55.2 Myr; P. asymmetrica and P. holmesi); (2) dispersal into the western Atlantic (2 spp., complex of “Cuapetes” americanus) via the eastern Pacific and vicariance event separating the IWP at Eocene (∼ 46.2 Myr). It was the time after the formation of the Eastern Pacific Barrier (EPB), which was considered the largest extension of the open ocean (ca. 5000 km), that separated the IWP area from the eastern Pacific17; (3) the another vicariance event, separating the western Atlantic populations from those of the eastern Pacific in the Oligocene (∼ 30.9 Myr), i.e., before the closure of the Isthmus of Panama, followed by a dispersion of P. atlantica into the eastern Atlantic in the Miocene (∼ 21.6 Myr). The exact time of the formation of the Isthmus of Panama, which separated the Atlantic from the eastern Pacific and remained isolated from the central Pacific by the EPB, still remains questionable. Bacon et al.18 assume that the initial land bridge formed at approximately 23 Myr, and the final closure of the Isthmus of Panama formed between 10 and 6 Myr. Montes et al.19 presupposed the earlier formation of the barrier at ∼ 14 Myr, whereas O’Dea et al.20 concluded that the potential gene flow continued between the Pacific and Atlantic subpopulations of marine organisms until at least ∼ 2.8 Myr.The eastern Pacific Cuapetes canariensis closely related to IWP Cuapetes spp., has been recently described by Fransen et al.41, from the Canary Islands. This could indicate alternative dispersal pathways into the Atlantic, as suggested by recent studies17,42. The Tethys seaway allowed natural dispersion between the Atlantic and Indian Oceans across the region of the Mediterranean Sea. The closure of this interoceanic seaway at approximately 14 Myr (18–12 Myr) was caused by intense tectonic activity in the Near East17. Since the closure of that seaway, remaining possible dispersal to the Atlantic has been limited to the warm-water corridor around the southern tip of Africa, however curtailed by the cold Benguela Current upwelling from the Late Pliocene43. More
