Molecular diversity within the genus Laeonereis (Annelida, Nereididae) along the west Atlantic coast: paving the way for integrative taxonomy

Introduction

The genus Laeonereis Hartman, 1945 occurs over a broad geographic range and extends nearly across the entire western Atlantic Coast, from North Carolina (USA) to Canelones (Uruguay) (Jesús-Flores, Salazar-Gonzáles & Salazar-Vallejo, 2016; De León-González, Méndez & Navedo, 2018). A single species occurs from El Salvador to Costa Rica on the Pacific Coast of Central America, while another one was described occurring on the Gulf of California, Mexico (Jesús-Flores, Salazar-Gonzáles & Salazar-Vallejo, 2016; De León-González, Méndez & Navedo, 2018). The monospecificity of Laeonereis proposed by Pettibone (1971) has been questioned, resulting in the validation of six species that occur along the Atlantic and Pacific American coasts, namely Laeonereis culveri (Webster, 1879) (North America coast; Orensanz & Gianuca, 1974), L. nota (Treadwell, 1941) (Central America coast; Jesús-Flores, Salazar-Gonzáles & Salazar-Vallejo, 2016), L. acuta (Treadwell, 1923) (South America coast; Orensanz & Gianuca, 1974; Santos & Lana, 2001; Liñero-Arana & Díaz-Díaz, 2007; Pamplin, Almeida & Silva-Filho, 2007), L. pandoensis (Monro, 1937), L. watsoni De León-González, Méndez & Navedo, 2018 (Gulf of California; De León-González, Méndez & Navedo, 2018), and L. brunnea (Central America Pacific coast; Dean, 2001; Dean, Sibaja-Cordero & Cortés, 2012).

The uncertainties about the actual diversity of this genus come from scarcity of molecular data and difficult species identification (mainly by non-taxonomists), which is due to intraspecific morphological variability and subtle diagnostic characters (Jesús-Flores, Salazar-Gonzáles & Salazar-Vallejo, 2016; De León-González, Méndez & Navedo, 2018; Oliveira et al., 2010), besides a lack of updated information in reference biological and genetic databases, such as Zoobank, GenBank, and BOLD. In addition to the taxonomic issues addressed in several studies, the case of Laeonereis merits particular attention because of its relevance in biomonitoring. As a well-represented polychaete in estuarine environments from the western Atlantic Ocean (including the Gulf of Mexico and the Caribbean Sea), it has been used as a target species in population ecology and ecotoxicological studies, as well as in water and sediment quality monitoring surveys (Omena & Amaral, 2001; Rosa et al., 2005; Weis et al., 2017; Carricavur et al., 2018; Checon et al., 2018).

Estuaries constitute a prominent environment throughout the coastal region where invertebrate populations can be subject to some degree of confinement (Seixas, Paiva & Russo, 2018). However, this has not prevented many typical estuarine species from being considered cosmopolitan or at least widely distributed (Virgilio et al., 2009; Tomioka et al., 2016; Silva et al., 2017). Estuarine polychaete species have received special attention, mainly for their roles in communities and potential for biomonitoring surveys of benthic fauna (Winter, Devictor & Schweiger, 2013; Nygren, 2014; Carricavur et al., 2018). Therefore, to guarantee the success and accuracy of benthic surveys and allow their replication worldwide (Winter, Devictor & Schweiger, 2013), the correct species identification within these communities is fundamental. Moreover, estuarine Laeonereis species can occur in very high densities, which are stimulated by a small freshwater inflow from nearby streams. For example, L. culveri is one of the most common annelids in Alligator (Florida) and in the Mystic River estuary (Connecticut), where it occurs in aggregates, reaching up to 10 cm deep in fine sand and withstands variations in a salinity range of 0.5–30‰ (Mazurkiewicz, 1975). In the southwest coast of Brazil (São Paulo), high densities were found at the high intertidal areas of beaches and close to streams; in the Porto do Saco da Ribeira (Ubatuba), it reached more than 5,600 individuals/m² and a biomass wet weight above 150 g/m², which constitutes a significant contribution to the area (Amaral, 1979).

Given the sustained difficulties faced by researchers throughout decades to elucidate Laeonereis taxonomy using morphology, and considering its relevance in biomonitoring, the present study aimed to apply a molecular approach to examine the diversity of Laeonereis populations collected along the western Atlantic Ocean and investigate their geographic distribution. For this purpose, we used multi-locus sequence data generated by two mitochondrial genes, namely the 5’ end of the cytochrome c oxidase subunit I (COI) and 16S rDNA (16S), and one nuclear locus, the 28S rDNA (28S). Molecular approaches have been successfully applied to contribute and elucidate the diversity of polychaetes, particularly over the last decade (Brasier et al., 2017; Lobo et al., 2016; Nygren et al., 2018; Langeneck et al., 2020; Teixeira et al., 2020). Here, we aimed to generate the basal molecular assessment of west Atlantic Laeonereis to pave the way for future integrative taxonomy studies on this genus.

Materials and Methods

Specimen sampling

Specimens of Laeonereis were collected from 26 localities between August 2016 and December 2017, two on the east coast of the United States (USA), 22 along the coast of Brazil (BRA: Amapá State [AP]; Bahia State [BA]; Ceará State [CE]; Paraná State [PR]; Piauí State [PI]; Rio de Janeiro State [RJ]; Rio Grande do Sul State [RS]; Santa Catarina State [SC]; São Paulo State [SP]), plus one in Uruguay (URU) and one in Argentina (ARG) (Fig. 1). To this end, soft-bottom samples were taken with shovels or sediment corers in the intertidal zone during syzygy tide. All specimens were identified morphologically and confirmed as belonging to the Laeonereis genus, according to a set of morphological characters available in the literature (Hartman, 1938; 1945; Pettibone, 1971; Orensanz & Gianuca, 1974; Dean, 2001; Santos & Lana, 2001; Liñero-Arana & Díaz-Díaz, 2007; Pamplin, Almeida & Silva-Filho, 2007; Oliveira et al., 2010; Dean, Sibaja-Cordero & Cortés, 2012; Jesús-Flores, Salazar-Gonzáles & Salazar-Vallejo, 2016), as follow: sub-pyriform prostomium; pair of frontal antennae; four pairs of frontal tentacular cirri; eversible pharynx with a pair of mandibles and tufts of soft papillae within proximal and distal rings; biramous parapodia with small ventral and dorsal cirri; and pygidium with a pair of cirri. Figure S1 presents photomicrographs and illustrations of the main characters used for the genus identification.

Results

Phylogenetic inference and MOTU delimitation

Sampling sites and geographic sources of sequences retrieved from databases are illustrated and detailed in Fig. 1, in which the distribution of MOTUs along the North and South America coasts can be observed (Fig. 1). Phylogenetic inference and the four automated delimitation methods are congruent for all molecular markers (except the BIN method which is available only for COI). The phylogenetic tree of COI recovered seven reciprocally monophyletic groups, with branch support above 0.95 (BI) and 90 (ML) (Fig. 2A). MOTU 1 included specimens from the USA only; MOTUs 2 (BRA – PI), 3 (BRA – AP and PI), 4 (BRA – PA and CE), and 5 (BRA – BA) were exclusive to the North and Northeast regions of Brazil; and MOTUs 6 (BRA – RJ, SP and PR) and 7 (BRA – RJ, SP, SC, and RS; URU; and ARG) were exclusive to the Southeastern and Southern regions of Brazil; with the latter also being found in Uruguay and Argentina. MOTU 2 contained only one sequence from a specimen caught at the same site as that of MOTU 3 (PI). All different delimitation methods applied to COI resulted in the same partitioning, also separating L. culveri into seven MOTUs, except for the BIN method in which MOTU 6 was split into three different groups, resulting in nine MOTUs.

The number of specimens and localities represented in 16S (Fig. 2B) and 28S (Fig. 2C) databases are lower than those in COI, and so were the numbers of clades and MOTUs. The clade recovery in the 16S and 28S trees matches that found in the COI tree, and in all cases, node support was higher than 0.9 (BI) or 90 (ML). All delimitation methods corroborated the phylogenetic results for both markers. The 16S sequences represented MOTUs 1, 3, 6, and 7, while the 28S sequences represented MOTUs 3, 4, 6, and 7.

Haplotype network

Figure 3 displays the haplotype networks for all three markers. The COI haplotype network (Fig. 3A) showed 43 haplotypes distributed among 114 specimens. None of the MOTUs had a central position in the network. The highest number of mutations observed between two linked MOTUs was 88 (MOTU 1 – USA × MOTU 7 – Argentina, Uruguay, and South Brazil) and the lowest was 38 (MOTU 5 – BA, Northeast Brazil × MOTU 6 – PR, SP, and RJ, South and Southeastern Brazil). Besides, only two MOTUs occur in the same locations: in MOTU 6 a haplotype occured in SP and PR, while MOTU 7 occured in RJ, SP, RS, URU, and ARG (Fig. 3A). The 16S and 28S haplotype networks (Figs. 3B and 3C) corroborated the COI results. As only subsets of localities were represented, 16S and 28S presented only four MOTUs each (as mentioned in the “Phylogenetic Inference and MOTU Delimitation” section). Considering the MOTUs 6 and 7 (represented in all markers), the localities sharing haplotypes in COI were the same as observed in 16S and 28S (except RJ).

Discussion

Molecular approaches, such as DNA barcoding, have recently emerged as particularly effective tools for species identification, enabling non-taxonomists to assess diversity in a variety of scientific fields, from environmental sciences to forensics. Some authors even argue that these methods will become an essential component of taxonomic revisions and biodiversity surveys (Stein et al., 2014; DeSalle & Goldstein, 2019). During the last decade, COI barcodes have been used as reliable marker to provide diagnostic characters for species delimitation, elucidating species boundaries within several taxa (Delić et al., 2017; Teixeira et al., 2020). The molecular analysis of the genus Laeonereis performed herein confirmed the existence of a high genetic diversity within the studied populations and revealed at least seven deeply divergent lineages, six of which are distributed along the Atlantic coast of South America. These lineages may include several of the previously proposed species based on morphological characters (i.e., L. acuta, L. culveri, L. nota, L. pandoensis; Orensanz & Gianuca, 1974; Santos & Lana, 2001; Jesús-Flores, Salazar-Gonzáles & Salazar-Vallejo, 2016). However, before being inferred, the concrete matches with specific MOTUs reported here require further studies for confirmation.

The genetic distances recorded among Laeonereis MOTUs (COI: 6.8–21.9%) fit perfectly within the range reported for congeneric distances in several other studies with polychaetes. For example, comprehensive studies on the polychaete fauna of the Arctic (Carr et al., 2011) and north-eastern Atlantic (Lobo et al., 2016) reported mean COI congeneric distances (K2P) of 16.5% and 24.0%, respectively, vs the 16.9% observed here. Our findings are also consistent with pairwise comparisons among closely-related species observed both within Nereididae (e.g., Glasby, Wei & Gibb, 2013; Paiva et al., 2019) and in other polychaete families, such as Amphinomidae (Barroso et al., 2010), Capitellidae (Silva et al., 2017), Onuphidae (Rodrigues et al., 2009; Seixas et al., 2020), Sabellidae (Capa & Murray, 2015), Phyllodocidae (Ravara et al., 2017), and Syllidae (Álvarez-Campos, Giribet & Riesgo, 2017).

The high substitution rates of mitochondrial genes found here, for COI and 16S, as well as their ability to discriminate species, have already been widely reported in the literature (e.g., Brasier et al., 2017; Hupało et al., 2019; Tosuji et al., 2019; Vieira et al., 2019). On the other hand, nuclear ribosomal genes had low mutation rates and are best suited to reconstruct deep phylogenies. Thus, both COI and 16S genetic distances found herein were congruent, although the 16S sequence data had not been produced for all MOTUs. The observed distances for 28S were unexpected and, despite lower than those of the other markers, they exhibited higher distances (1.4–7.5%) than what is usually reported for other polychaetes (Tosuji et al., 2019; Teixeira et al., 2020). Thus, in our study, the 28S interspecific genetic distances for this group corroborated the species delimitation found for the COI and 16S.

Considering that Laeonereis species occurs predominantly in transitions between freshwater and marine ecosystems (e.g., estuarine, bays, coastal lagoons, and river mouths), such conditions could hypothetically promote evolutionary segregation, particularly over a broad distribution range. Moreover, the fact that L. culveri has benthic larvae that hatch from eggs fertilized inside the mucoid tube of females (Mazurkiewicz, 1975), could also contribute to limiting connectivity among populations. Although the larvae have a certain vertical locomotion/swimming capacity associated with food scavenging (Klesch, 1970, Mazurkiewicz, 1975), the time spent in the water column is short compared to species with fully planktonic larvae. All together, these features point to a comparatively low dispersal potential, as assumed by De León-González, Méndez & Navedo (2018). In these cases, strategies of larval retention or exportation, such as timing and location of egg or larval release, have great relevance for dispersal capacity (Bilton, Paula & Bishop, 2002).

The distribution of MOTUs within the genus Laeonereis is well marked by differences in oceanographic conditions. MOTU 1 is restricted to the east coast of the USA and is separated from the other MOTUs by thousands of kilometres. The MOTUs 2, 3, and 4 are associated with the northern Brazilian coast, which has a substantial contribution from river waters and terrestrial sediments (Dominguez, 2009). Hence, the salinity level of estuarine waters in the region is very close to that of freshwater. This region is also under the influence of the North Brazilian Current, which flows towards the Caribbean Sea and is marked by higher water temperatures. MOTU 5 is found in a similar region, but with slightly lower freshwater input, water temperature, and productivity. This region is influenced by the Brazilian current flowing predominantly southward. Finally, MOTUs 6 and 7 were sampled in a region influenced by upwelling events due to a mass of cold water (i.e., South Atlantic Central Water), decreasing water temperature and increasing productivity (Coelho-Souza et al., 2012; Mazzini & Barth, 2013).

To a certain extent, the geographic arrangement of the found MOTUs can be associated with the biogeographic divisions proposed by Spalding et al. (2007). Thus, MOTU 1 is restricted to the Warm Temperate Northwest Atlantic Province; MOTUs 2, 3, and 4 to the North Brazil Shelf Province; MOTU 5 to the Tropical Southwestern Atlantic Province; and MOTUs 6 and 7 to the Warm Temperate Southwestern Atlantic Province. Furthermore, phylogeographic and population genetic studies on other marine invertebrates have also matched these biogeographic divisions (corals – Peluso et al., 2018; crustaceans – Mattos, Seixas & Paiva, 2019), suggesting dominant phylogeographic discontinuities in the region pervasive across multiple and diverse taxa.

The deep genetic breaks observed among Laeonereis lineages can be explained by either dispersal followed by vicariance events or vicariance followed by dispersal events. The origin of the genus cannot be inferred from the results of this work; however, given its distribution, two scenarios are plausible: (1) origin in the North Atlantic / Caribbean followed by dispersal to South America, or (2) origin in South America followed by dispersal to North America. Both explain the initial separation of MOTU 1 from the South American MOTUs (2 to 7). Since its establishment, freshwater discharge from the Amazon River to the Atlantic Ocean (~7 mya; Hoorn et al., 2010) has been responsible for speciation between the Caribbean and Brazilian populations (Sales et al., 2017; Dias et al., 2019). Considering the South American lineages, the first splitting might have occurred between south and north populations of South America (MOTU 7 × MOTUs 2–6), perhaps ~23° S latitude, where there is currently a biogeographic break marked by a transitional area of marine fauna (Floeter & Soares-Gomes, 1999). Biogeographical processes can be chronologically categorised once the centre of origin of the Laeonereis genus was known. As the tropical regions are considered biodiversity hotspots (Bowen et al., 2013), we can suggest that the distribution limits of the ancestral lineage (MOTUs 2 to 7) might have expanded to the southern limits during favourable (interglacial) periods and subsequently retracted in unfavourable periods (glaciations).

Pleistocene glaciations caused several episodes of sea-level fluctuation, which were more severe in polar and temperate regions, such as in southern South America. For example, the Great Patagonian Glaciation between 1.78–0.78 mya resulted in sea level decreasing, higher salinity levels, and changes in sea currents (Ehlers & Gibbard, 2007). At the end of these glacial periods, postglacial marine transgression occurred, and sea levels gradually rose again. These glaciation episodes could have caused the extinction of many southern populations, which might have been restricted to a few regions (refuges). On the other hand, such glaciation events may have induced the establishment of ancestral populations in northern regions, given the more stable environmental conditions, such as temperature, salinity, and habitat availability (Ehlers & Gibbard, 2007; Tomazelli, Dillenburg & Villwock, 2017).

According to a review on the evolutionary molecular divergence for several groups of marine invertebrate species, polychaetes exhibit a K2P divergence rate ranging from 3.5 to 4.7% MY⁻¹ (Loeza-Quintana et al., 2019). Herein, the K2P distances between MOTUs ranged from 7.7 (MOTU 5 × 6) to 20.7% (MOTU 1 × 4 and 1 × 5). Thus, it is possible to infer that a probable divergence between Laeonereis species from North and South America lies within a time gap from a few to a dozen million years. Despite the high uncertainty of this estimate, it might allow us to insert the divergence of species of the Laeonereis complex into the timescale of the relevant biogeographic events cited above.

Although the Caribbean Sea was not sampled and northern Brazilian coasts under-explored in this study, the occurrence of Laeonereis species is well established in those areas. Therefore, either the nearby MOTUs (2, 3, and 4) or other yet undescribed species of the Laeonereis complex may also be present in these regions. Accordingly, the diversification of these lineages may have occurred in the Caribbean, followed by dispersal to the northern coasts of Brazil after speciation, or vice-versa. However, to reveal the complete evolutionary history of this genus, the Caribbean, Gulf of Mexico, and Pacific regions need to be investigated.

Although geographically close, MOTUs 6 and 7 showed divergence from one another. This may have occurred by population dispersal from the northeast to southeast, followed by gene flow interruption. It also explains the high genetic distance between them, whose mitochondrial and nuclear lineages are completely sorted. Thus, these MOTUs could have diverged in the distant past and currently occur in the same region due to post-speciation range expansion.

Conclusions

The most recent papers on Laeonereis species diversity have demonstrated the unlikelihood of a cosmopolitan L. culveri, recovering five species, and describing a new one, L. watsoni (Jesús-Flores, Salazar-Gonzáles & Salazar-Vallejo, 2016; De León-González, Méndez & Navedo, 2018; as summarised in WoRMS). The authors of these studies revealed a set of morphological characters capable of separating species; however, in their own words, these characters are subtle and, to some extent, difficult to be observed, which might lead to misidentification by non-taxonomists and students.

In this sense, to place our finding in a global context, we reported seven distinct lineages of Laeonereis (putative species) for the American Atlantic coast. The molecular diversity found for Laeonereis was high and suggests hidden diversity with at least two additional undescribed species. A comprehensive morphological analysis of each MOTU is still needed to reach robust conclusions on Laeonereis diversity, including a comparative analysis with the types of valid species. Our findings expand the range of the genus Laeonereis, from Connecticut—USA to Mar del Plata—Argentina.

The molecular diversity here brought to light has raised new questions about Laeonereis diversity and distribution: does each MOTU revealed herein constitute a single species? If so, how many of them can be matched with morphologically-validated species and how many are new? Could MOTUs 6 and 7 correspond to L. acuta and L. pandoensis species, respectively? Lastly, could the MOTUs detected in the northern region of Brazil match L. nota? At this moment, we are not able to confidently answer these questions without a comprehensive morphological examination. However, our molecular dataset substantially contributes to further studies in this group, paving the way for integrative approaches to clarify the taxonomy of the genus.

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