Surfing among species, populations and morphotypes: Inferring boundaries between two species of new world silversides (Atherinopsidae)

Differential expression analyses and detection of SNP loci associated with environmental variables: Are salinity and temperature factors involved in population differentiation and speciation in Odontesthes?

Environmental factors play a key role in individual adaptation to different local conditions. Because of this, studies about the physiological and genetic responses of individuals exposed to different natural environments offer clues about mechanisms involved in population differentiation, and as a subsequent result, speciation. Marine environments are especially suited to survey this kind of phenomena because they commonly harbor species adapted to different local conditions along a geographic continuum. Silversides belonging to Odontesthes are commonly distributed in tropical and temperate regions of South America and exhibit noticeable phenotypic plasticity, which allows them to adapt to contrasting environments. In this study, the genetic expression of O. argentinensis sampled along the Uruguayan Atlantic coast and estuarine adjacent areas was investigated. In addition, the correlation between individual genotypes and environmental variables was also analysed in O. argentinensis and O. bonariensis. Results obtained suggest a differential expression pattern of low magnitude among individuals from the different areas sampled and a correlation between several SNP loci and environmental variables. The analyses carried out did not show a clear differentiation among individuals sampled along different salinity regimens, but enriched GOTerms seem to be driven by water oxygen content. On the other hand, a total of 46 SNPs analysed in O. argentinensis and O. bonariensis showed a correlation with salinity and temperature. Although none of the correlated SNPs and corresponding genes from our both analyses were directly associated with hypoxia, genes related to the cardiovascular system and muscle cell differentiation were found. All these genes are interesting candidates for future studies since they are closely related to the differentially expressed genes. Although salinity was also mentioned as an important parameter limiting introgression between O. argentinensis and O. bonariensis, it was found that salinity does not drive differential expression in O. argentinensis, but rather oxygen levels. Moreover, salinity does not directly affect the structure and genetic divergence of the populations, they appear to be structured based on their degree of isolation and geographical distance between them. Further studies, like genome-wide analyses, could help to elucidate additional genes adapted to the different environments in these silverside species.

Hybridization is strongly constrained by salinity during secondary contact between silverside fishes (Odontesthes, Atheriniformes)

This study investigates a contact zone between two silverside fish species (marine Odontesthes argentinensis and freshwater O. bonariensis) in the estuarine Mar Chiquita lagoon along the Atlantic coast in Argentina (MChL), in which intermediate morphs had been reported. It has been suggested that admixture and introgression occur in MChL between these two species, but direct genetic evidence is lacking. Leveraging samples collected over several years (n = 676), we document the spatial distribution of both species and intermediate morphs within this habitat and collect landmark-based morphometric and multilocus genetic data (9876 loci for n = 110 individuals) to test the hypothesis of hybridization. Our analysis unambiguously characterizes intermediate morphs as F1 or F2 hybrids. We show that the low frequency of hybrid individuals in MChL may be explained by uneven abundance of parental species, which in turn are strongly affected by water salinity, limiting the size of the contact zone. Although hybrids seem to be fertile, their fitness may be reduced by external and intrinsic factors that may limit their success and suggest that this is an unstable hybrid zone. Genetic distinctiveness of both parental species is strongly supported by genome-wide data, explaining a known pattern of mitonuclear discordance as a consequence of hybridization followed by mitochondrial introgression. A clear signature of population genetic structure was detected in O. argentinensis, distinguishing MChL residents from marine populations of this species, that also was supported by distinctive morphometric features among these groups. Previous hypotheses of speciation in these fishes are discussed in the light of the new findings.

A new species of Hoplias malabaricus species complex (Characiformes: Erythrinidae) from the Crepori River, Amazon basin, Brazil

A new species belonging to the Hoplias malabaricus complex from the Amazon basin, Brazil, is described. The new species is characterized by 15-16 predorsal scales, 37-39 lateral-line scales, 5 scales from dorsal fin to lateral line, 38-39 vertebrae, iii-iv, 7-8 anal-fin rays, ii-iv, 12-15 caudal-fin rays, last vertical series of scales on the base of caudal-fin rays forming a straight line, 6-7 dark bands in anal fin and no distinctive dark bands or blotches on flanks. The new species is also distinguished from other congeners of the H. malabaricus species-group by means of landmark-based morphometrics and DNA Barcoding (Cytochrome c Oxidase I gene). An identification key to species of the H. malabaricus species complex is provided.

Mitochondrial genome architecture and phylogenetic relationships of Odontesthes argentinensis within Atherinomorpha

Silversides are a widely distributed group across South America, with several species occupying marine, freshwater and estuarine environments. Several authors suggest main transitions among these environments took place during Pleistocene, and were accompanied with rapid speciation events. This scenario produced very limited genetic and morphological differentiation among the species. However, most of these surveys have an incomplete coverage of the intraspecific genetic diversity of the taxa studied. In this work, we reconstructed six mitochondrial genomes of O. argentinensis using transcriptomic data, and used them-in combination with several nuclear markers retrieved from the same transcriptomes-to explore the effect of additional coverage of intraspecific diversity of this species in phylogenetic reconstructions. Unlike previous works, phylogenetic analyses failed to identify O. argentinensis as a monophyletic group in relation with closely related taxa. Our results suggest that several species of the genus, especially those related to O. argentinensis, need further taxonomic revision.

Evidence of a landlocked reproducing population of the marine pejerrey Odontesthes argentinensis (Actinopterygii; Atherinopsidae)

In South America, the order Atheriniformes includes the monophyletic genus Odontesthes with 20 species that inhabit freshwater, estuarine and coastal environments. Pejerrey Odontesthes argentinensis is widely distributed in coastal and estuarine areas of the Atlantic Ocean and is known to foray into estuaries of river systems, particularly in conditions of elevated salinity. However, to our knowledge, a landlocked self-sustaining population has never been recorded. In this study, we examined the pejerrey population of Salada de Pedro Luro Lake (south-east of Buenos Aires Province, Argentina) to clarify its taxonomic identity. An integrative taxonomic analysis based on traditional meristic, landmark-based morphometrics and genetic techniques suggests that the Salada de Pedro Luro pejerrey population represents a novel case of physiological and morphological adaptation of a marine pejerrey species to a landlocked environment and emphasises the environmental plasticity of this group of fishes.

Inferring boundaries among fish species of the new world silversides (Atherinopsidae; genus Odontesthes): new evidences of incipient speciation between marine and brackish populations of Odontesthes argentinensis

Species of new world silversides (Actinopterygii; Atherinopsidae; genus Odontesthes) possess economic relevance, biological interest and ecological importance. In the present paper we: (A) investigate the molecular diversity in marine species of Odontesthes from the South West Atlantic Ocean (SWAO), and analyse their interspecific relationships and divergence by means of DNA Barcoding, including its freshwater congeners, as well. (B) Explore the suitability of DNA Barcoding to analyse the diversity and distribution of haplotypes in Odontesthes argentinensis, the only well documented marine species from the SWAO that exhibit putative estuarine and marine populations. Molecular analysis revealed 100% of agreement between morphological identification and molecular identity. Odontesthes argentinensis, Odontesthes platensis, Odontesthes smitti, Odontesthes nigricans and Odontesthes incisa were assigned to five different barcode index numbers (BINs). Maximum-likelihood analysis showed that all marine species of Odontesthes clustered separately in a unique monophyletic phylogroup, comprising five well defined haplogroups, with genetic divergence between groups ranging from 2.75 to 7.11%. The genetic analysis including freshwater congeners showed that O. incisa clustered alone occupying a basal position. The F_st pairwise comparisons within O. argentinensis support the existence of three population groups: one conformed by Mar Chiquita Lagoon (MCh) specimens, and the others by Mar del Plata/Mar Chiquita coast and San Blas Bay coastal specimens, respectively. The AMOVA showed significant overall differentiation (F_st = 0.238; p = 0.00001) for the entire data set. The previous/present evidence is discussed, and strongly suggests that incipient speciation is occurring in O. argentinensis argentinean populations, and specimens from MCh would be considered at present as the leading candidate of a marine to freshwater incipient speciation event.

Almost a century of oblivion: Integrative taxonomy allows the resurrection of the longnose skate Zearaja brevicaudata (Marini, 1933) (Rajiformes; Rajidae)

Zearaja chilensis has been reported from Southern Brazil in the Southwest Atlantic (SWA) to northern Chile in the Southeast Pacific (SEP), and it was listed as vulnerable by the IUCN. Recent molecular studies have called into question the conspecificity between specimens from these opposite coasts of South America, which can have implications for the conservation status of the species. To verify the identity of specimens identified as Z. chilensis, 47 individuals from SWA and 22 from SEP were examined. By comparing external morphology, spinulation pattern, clasper, egg cases, and mitochondrial cytochrome c oxidase I (COI) sequence data, differences between groups were found. Adults from SWA presented longer snout length and shorter tail than those from SEP. Dermal denticles were restricted to the rostral area in SWA skates, whereas in SEP skates most of the dorsal surface was covered with denticles. Marked differences in the morphology of several components of clasper were noticeable. Egg cases of SWA skates had thinner lateral keels than those of SEP. Molecular analysis revealed two well-defined cohesive clusters, corresponding to SWA and SEP specimens, respectively. Average K2P distance between groups was 3.4%, higher than expected for intraspecific differences, and sequences were assigned to different BINs. These integrative approaches strongly support that specimens from SWA known as Z. chilensis correspond to a different nominal species than those from SEP. Herein, Z. brevicaudata (Marini 1933) is resurrected from synonymy with Z. chilensis.

Transcriptomic differentiation underlying marine-to-freshwater transitions in the South American silversides Odontesthes argentinensis and O. bonariensis (Atheriniformes)

Salinity gradients are critical habitat determinants for freshwater organisms. Silverside fishes in the genus Odontesthes have recently and repeatedly transitioned from marine to freshwater habitats, overcoming a strong ecological barrier. Genomic and transcriptomic changes involved in this kind of transition are only known for a few model species. We present new data and analyses of gene expression and microbiome composition in the gills of two closely related silverside species, marine O. argentinensis and freshwater O. bonariensis and find more than three thousand transcripts differentially expressed, with osmoregulatory/ion transport genes and immune genes showing very different expression patterns across species. Interspecific differences also involve more than one thousand transcripts with nonsynonymous SNPs in the coding sequences, most of which were not differentially expressed. In addition to characterizing gill transcriptomes from wild‐caught marine and freshwater fishes, we test experimentally the response to salinity increases by O. bonariensis collected from freshwater habitats. Patterns of expression in gill transcriptomes of O. bonariensis exposed to high salinity do not resemble O. argentinensis mRNA expression, suggesting lack of plasticity for adaptation to marine conditions in this species. The diversity of functions associated with both the differentially expressed set of transcripts and those with sequence divergence plus marked microbiome differences suggest that multiple abiotic and biotic factors in marine and freshwater habitats are driving transcriptomic differences between these species.