Antarctic and sub-Antarctic Nacella limpets reveal novel evolutionary characteristics of mitochondrial genomes in Patellogastropoda.

Mitochondrial genomes (mitogenomes) provide valuable phylogenetic information and genome-level characters that are useful in resolving evolutionary relationships within major lineages of gastropods. However, for more than one decade, these relationships and the phylogenetic position of Patellogastropoda have been inferred based on the genomic architecture as well as the nucleotide and protein sequences of a single representative, the limpet Lottia digitalis. This mitogenome exhibits extensive rearrangements and several repetitive units that may not represent universal features for Patellogastropoda. Here, we sequenced the complete mitogenomes of three Nacella limpets, providing new insights into the dynamics of gene order and phylogenetic relationships of Patellogastropoda. Comparative analyses revealed novel gene rearrangements in Gastropoda, characterised by two main translocations that affect the KARNI and the MYCWQ clusters in Nacella limpets. Our phylogenetic reconstructions using combined sequence datasets of 13 mitochondrial protein-coding genes and two rRNAs, recovered Patellogastropoda, and Gastropoda in general, as non-monophyletic. These findings could be related to the long-branch attraction tendency of these groups, and/or taxon sampling bias. In our novel mitogenome-based phylogenetic hypothesis, L. digitalis is placed in a sister position to Bivalvia and Heterobranchia, whereas Nacella limpets are placed sister to a clade containing Caenogastropoda + Neritimorpha and Vetigastropoda + Neomphalina.

Filling phylogenetic gaps and the biogeographic relationships of the Octodontidae (Mammalia: Hystricognathi).

Endemic to South America, octodontid rodents are remarkable by being the only mammal taxa where allotetraploidy has been documented. The taxon's extensive morpho-physiological radiation associated to niche shifts has allowed testing phylogeographic hypotheses. Using maximum likelihood and Bayesian inference analyses, applied to all nominal species of octodontids, phylogenetic reconstructions based on sequences of 12S rRNA and growth hormone receptor gene are presented. Species boundaries were determined by coalescent analyses and divergence times among taxa were estimated based on mutation rates. Two main clades associated to the Andean orogenesis were recognized. The essentially western clade comprises genera Aconaemys, Octodon, Spalacopus, and Octodontomys whereas the eastern one included genera Octomys, Pipanacoctomys, Salinoctomys, and Tympanoctomys. Genetic relationships, coalescent analyses, and genetic distance supported the specific status given to Octodon pacificus and that given to Pipanacoctomys aureus as a species of Tympanoctomys. However, these analyses failed to recognize Salinoctomys loschalchalerosorum as a valid taxon considering its position within the diversity of Tympanoctomys barrerae. Although the origin of genome duplication remains contentious, the coincidence of the basal clade split with distinctive modes of karyotypic evolution across the Andes emphasizes the role of physiographic barriers and westerlies in shaping different edaphological conditions, selective grounds, and concomitantly distinct adaptations within the octodontids.

Towards a model of postglacial biogeography in shallow marine species along the Patagonian Province: lessons from the limpet Nacella magellanica (Gmelin, 1791).

BACKGROUND: Patagonia extends for more than 84,000 km of irregular coasts is an area especially apt to evaluate how historic and contemporary processes influence the distribution and connectivity of shallow marine benthic organisms. The true limpet Nacella magellanica has a wide distribution in this province and represents a suitable model to infer the Quaternary glacial legacy on marine benthic organisms. This species inhabits ice-free rocky ecosystems, has a narrow bathymetric range and consequently should have been severely affected by recurrent glacial cycles during the Quaternary. We performed phylogeographic and demographic analyses of N. magellanica from 14 localities along its distribution in Pacific Patagonia, Atlantic Patagonia, and the Falkland/Malvinas Islands. RESULTS: Mitochondrial (COI) DNA analyses of 357 individuals of N. magellanica revealed an absence of genetic differentiation in the species with a single genetic unit along Pacific Patagonia. However, we detected significant genetic differences among three main groups named Pacific Patagonia, Atlantic Patagonia and Falkland/Malvinas Islands. Migration rate estimations indicated asymmetrical gene flow, primarily from Pacific Patagonia to Atlantic Patagonia (Nem=2.21) and the Falkland/Malvinas Islands (Nem=16.6). Demographic reconstruction in Pacific Patagonia suggests a recent recolonization process (< 10 ka) supported by neutrality tests, mismatch distribution and the median-joining haplotype genealogy. CONCLUSIONS: Absence of genetic structure, a single dominant haplotype, lack of correlation between geographic and genetic distance, high estimated migration rates and the signal of recent demographic growth represent a large body of evidence supporting the hypothesis of rapid postglacial expansion in this species in Pacific Patagonia. This expansion could have been sustained by larval dispersal following the main current system in this area. Lower levels of genetic diversity in inland sea areas suggest that fjords and channels represent the areas most recently colonized by the species. Hence recolonization seems to follow a west to east direction to areas that were progressively deglaciated. Significant genetic differences among Pacific, Atlantic and Falkland/Malvinas Islands populations may be also explained through disparities in their respective glaciological and geological histories. The Falkland/Malvinas Islands, more than representing a glacial refugium for the species, seems to constitute a sink area considering the strong asymmetric gene flow detected from Pacific to Atlantic sectors. These results suggest that historical and contemporary processes represent the main factors shaping the modern biogeography of most shallow marine benthic invertebrates inhabiting the Patagonian Province.

Contrasting Patterns of Genetic Diversity and Divergence Between Landlocked and Migratory Populations of Fish Galaxias maculatus, Evaluated Through Mitochondrial DNA Sequencing and Nuclear DNA Microsatellites.

Galaxias species are interesting biogeographic models due to their distribution and different types of life cycles, with migratory and landlocked populations. To obtain a better understanding of the genetic consequences of the Quaternary glacial cycles in Galaxias maculatus, in this work we compared landlocked and migratory populations collected in areas that were differentially affected by ice advances and retreats. We included nine populations of G. maculatus, four collected from lakes (landlocked) and five from their associated estuaries/rivers (migratory) in three estuary-lake systems across southern Chile. Genetic analyses were performed using the mitochondrial control region and nine microsatellite loci. Genetic diversity measured with both markers was significantly higher in migratory than in landlocked populations across the study area. The levels of genetic differentiation showed higher differentiation among lakes than estuaries. Genetic diversity was higher in migratory populations located in areas that were less impacted by ice during Quaternary glacial processes. These results may be the consequence of recent recolonization of small freshwater bodies following the Last Glacial Maximum (LGM). Finally, the greatest differentiation was observed in populations that were exposed to continental ice advances and retreats during the LGM. Thus, in the present work we corroborate a pattern of differentiation between lakes and estuaries, using mtDNA sequences and microsatellite nuclear markers. This pattern may be due to a combination of biological factors, i.e., resident non-migratory behaviour or landlocking and natal homing-in, as well as geological factors, i.e., Expansion-Contraction Quaternary glacial biogeographic processes.

Molecular phylogeny and historical biogeography of Nacella (Patellogastropoda: Nacellidae) in the Southern Ocean.

The evolution and the historical biogeography of the Southern Ocean marine benthic fauna are closely related to major tectonic and climatic changes that occurred in this region during the last 55 million years (Ma). Several families, genera and even species of marine organisms are shared between distant biogeographic provinces in this region. This pattern of distribution in marine benthic invertebrates has been commonly explained by vicariant speciation due to plate tectonics. However, recent molecular studies have provided new evidence for long-distance dispersion as a plausible explanation of biogeographical patterns in the Southern Ocean. True limpets of the genus Nacella are currently distributed in different biogeographic regions of the Southern Ocean such as Antarctica, Kerguelen Province, southern New Zealand Antipodean Province, North-Central Chile and South American Magellanic Province. Here, we present phylogenetic reconstructions using two mitochondrial DNA markers (Cytochrome Oxidase I and Cytochrome b) to look into the relationships among Nacella species and to determine the origin and diversification of the genus. Phylogenies were reconstructed using two methods, Maximum Parsimony and Bayesian Inference, while divergence time among Nacella species was estimated following a relaxed Bayesian approach. For this purpose, we collected inter- and subtidal species belonging to four biogeographic regions in the Southern Ocean: Antarctica, Kerguelen Province, Central Chile, and Magellanic Province. Our molecular results agree with previous morphological and molecular studies supporting the monophyly of Nacella and its sister relationship with Cellana. Two rounds of diversification are recognized in the evolution of Nacella. The first one occurred at the end of the Miocene and gave rise to the main lineages, currently distributed in Antarctica, South America or Kerguelen Province. Large genetic divergence was detected among Nacella species from these distant biogeographic provinces emphasizing the significance of trans-oceanic discontinuities and suggesting long-distance dispersal was relatively unimportant. The second diversification round consisted of a more recent Pleistocene radiation in the Magellanic region. In this province, different morphological species of Nacella exhibit extreme low levels of genetic divergence with absence of reciprocal monophyly among them. According to our time estimation, the origin and diversification of Nacella in the Southern Ocean is more recent (<15 MY) than the expected under the hypothesis of vicariant speciation due to plate tectonics. The evolution of this genus seems to be closely related to drastic climatic and oceanographic changes in the Southern Ocean during the middle-Miocene climatic transition. In spite of the high number of species described for the Magellanic Province, molecular results indicate that these species are the most derived ones in the evolution of the genus and therefore that the Magellanic region does not need to correspond to the origin center of Nacella. The absence of genetic divergence among these species supports a very recent radiation process accompanied by rapid morphological and ecological diversification.

Signatures of local adaptation in the spatial genetic structure of the ascidian Pyura chilensis along the southeast Pacific coast.

The highly heterogeneous Humboldt Current System (HCS) and the 30°S transition zone on the southeast Pacific coast, represent an ideal scenario to test the influence of the environment on the spatial genomic structure in marine near-shore benthic organisms. In this study, we used seascape genomic tools to evaluate the genetic structure of the commercially important ascidian Pyura chilensis, a species that exhibits a low larval transport potential but high anthropogenic dispersal. A recent study in this species recorded significant genetic differentiation across a transition zone around 30°S in putatively adaptive SNPs, but not in neutral ones, suggesting an important role of environmental heterogeneity in driving genetic structure. Here, we aim to understand genomic-oceanographic associations in P. chilensis along the Southeastern Pacific coast using two combined seascape genomic approaches. Using 149 individuals from five locations along the HCS, a total of 2,902 SNPs were obtained by Genotyping-By-Sequencing, of which 29-585 were putatively adaptive loci, depending on the method used for detection. In adaptive loci, spatial genetic structure was better correlated with environmental differences along the study area (mainly to Sea Surface Temperature, upwelling-associated variables and productivity) than to the geographic distance between sites. Additionally, results consistently showed the presence of two groups, located north and south of 30°S, which suggest that local adaptation processes seem to allow the maintenance of genomic differentiation and the spatial genomic structure of the species across the 30°S biogeographic transition zone of the Humboldt Current System, overriding the homogenizing effects of gene flow.

Biogeography in Cellana (Patellogastropoda, Nacellidae) with Special Emphasis on the Relationships of Southern Hemisphere Oceanic Island Species.

Oceanic islands lacking connections to other land are extremely isolated from sources of potential colonists and have acquired their biota mainly through dispersal from geographically distant areas. Hence, isolated island biota constitutes interesting models to infer biogeographical mechanisms of dispersal, colonization, differentiation, and speciation. Limpets of the genus Cellana (Nacellidae: Patellogastropoda) show limited dispersal capacity but are broadly distributed across the Indo-Pacific including many endemic species in isolated oceanic islands. Here, we examined main distributional patterns and geographic boundaries among Cellana lineages with special emphasis in the relationships of Southern Hemisphere oceanic islands species. Phylogenetic reconstructions based on mtDNA (COI) recognized three main clades in Cellana including taxa from different provinces of the Indo-Pacific. Clear genetic discontinuities characterize the biogeography of Cellana and several lineages are associated to particular areas of the Indo-Pacific supporting the low dispersal capacity of the genus across recognized biogeographical barriers in the region. However, evolutionary relationships within Cellana suggest that long-distance dispersal processes have been common in the history of the genus and probably associated to the origin of the species in Hawaii and Juan Fernández Archipelago. Therefore, the presence of Cellana species in geographically distant Southern Hemisphere oceanic islands, such as the Juan Fernández Archipelago, suggests that long-distance dispersal mediated by rafting may have played an important role in the biogeography of the genus.

Genetics, Gene Flow, and Glaciation: The Case of the South American Limpet Nacella mytilina.

Glacial episodes of the Quaternary, and particularly the Last Glacial Maximum (LGM) drastically altered the distribution of the Southern-Hemisphere biota, principally at higher latitudes. The irregular coastline of Patagonia expanding for more than 84.000 km constitutes a remarkable area to evaluate the effect of Quaternary landscape and seascape shifts over the demography of near-shore marine benthic organisms. Few studies describing the biogeographic responses of marine species to the LGM have been conducted in Patagonia, but existing data from coastal marine species have demonstrated marked genetic signatures of post-LGM recolonization and expansion. The kelp-dweller limpet Nacella mytilina is broadly distributed along the southern tip of South America and at the Falkland/Malvinas Islands. Considering its distribution, abundance, and narrow bathymetry, N. mytilina represents an appropriate model to infer how historical and contemporary processes affected the distribution of intraspecific genetic diversity and structure along the southern tip of South America. At the same time, it will be possible to determine how life history traits and the ecology of the species are responsible for the current pattern of gene flow and connectivity across the study area. We conducted phylogeographic and demographic inference analyses in N. mytilina from 12 localities along Pacific Patagonia (PP) and one population from the Falkland/Malvinas Islands (FI). Analyses of the mitochondrial gene COI in 300 individuals of N. mytilina revealed low levels of genetic polymorphism and the absence of genetic differentiation along PP. In contrast, FI showed a strong and significant differentiation from Pacific Patagonian populations. Higher levels of genetic diversity were also recorded in the FI population, together with a more expanded genealogy supporting the hypothesis of glacial persistence of the species in these islands. Haplotype genealogy, and mismatch analyses in the FI population recognized an older and more complex demographic history than in PP. Demographic reconstructions along PP suggest a post-LGM expansion process (7.5 ka), also supported by neutrality tests, mismatch distribution and maximum parsimony haplotype genealogies. Migration rate estimations showed evidence of asymmetrical gene flow from PP to FI. The absence of genetic differentiation, the presence of a single dominant haplotype, high estimated migration rates, and marked signal of recent demographic growth, support the hypothesis of rapid post-glacial expansion in N. mytilina along PP. This expansion could have been sustained by larval and rafting-mediated dispersal of adults from northernmost populations following the Cape Horn Current System. Marked genetic differentiation between PP and FI could be explained through differences in their respective glacial histories. During the LGM, Pacific Patagonia (PP) was almost fully covered by the Patagonian Ice Sheet, while sheet coverage in the FI ice was restricted to small cirques and valleys. As previously recorded in the sister-species N. magellanica, the FI rather than represent a classical glacial refugium for N. mytilina, seems to represent a sink area and/or a secondary contact zone. Accordingly, historical and contemporary processes, contrasting glacial histories between the analyzed sectors, as well as life history traits constitute the main factors explaining the current biogeographical patterns of most shallow Patagonian marine benthic organisms.

Isolation Driven Divergence in Osmoregulation in Galaxias maculatus (Jenyns, 1848) (Actinopterygii: Osmeriformes).

BACKGROUND: Marine species have colonized extreme environments during evolution such as freshwater habitats. The amphidromous teleost fish, Galaxias maculatus is found mainly migrating between estuaries and rivers, but some landlocked populations have been described in lakes formed during the last deglaciation process in the Andes. In the present study we use mtDNA sequences to reconstruct the historical scenario of colonization of such a lake and evaluated the osmoregulatory shift associated to changes in habitat and life cycle between amphidromous and landlocked populations. RESULTS: Standard diversity indices including the average number of nucleotide differences (Π) and the haplotype diversity index (H) indicated that both populations were, as expected, genetically distinctive, being the landlocked population less diverse than the diadromous one. Similarly, pairwise GST and NST comparison detected statistically significant differences between both populations, while genealogy of haplotypes evidenced a recent founder effect from the diadromous stock, followed by an expansion process in the lake. To test for physiological differences, individuals of both populations were challenged with a range of salinities from 0 to 30 ppt for 8 days following a period of progressive acclimation. The results showed that the landlocked population had a surprisingly wider tolerance to salinity, as landlocked fish survival was 100% from 0 to 20 ppt, whereas diadromous fish survival was 100% only from 10 to 15 ppt. The activity of ATPase enzymes, including Na+/K+-ATPase (NKA), and H+-ATPase (HA) was measured in gills and intestine. Activity differences were detected between the populations at the lowest salinities, including differences in ATPases other than NKA and HA. Population differences in mortality are not reflected in enzyme activity differences, suggesting divergence in other processes. CONCLUSIONS: These results clearly demonstrate the striking adaptive changes of G. maculatus osmoregulatory system, especially at hyposmotic environments, associated to a drastic shift in habitat and life cycle at a scale of a few thousand years.

Phylogeography in Galaxias maculatus (Jenyns, 1848) along Two Biogeographical Provinces in the Chilean Coast.

Major geologic and climatic changes during the Quaternary exerted a major role in shaping past and contemporary distribution of genetic diversity and structure of aquatic organisms in southern South America. In fact, the northern glacial limit along the Pacific coast, an area of major environmental changes in terms of topography, currents, and water salinity, represents a major biogeographic transition for marine and freshwater species. We used mitochondrial DNA sequences (D-loop) to investigate the consequences of Quaternary glacial cycles over the pattern of genetic diversity and structure of G. maculatus (Pisces: Galaxiidae) along two biogeographical provinces in the Chilean coast. Extreme levels of genetic diversity and strong phylogeographic structure characterize the species suggesting a low amount of influence of the last glacial cycle over its demography. However, we recognized contrasting patterns of genetic diversity and structure between main biogeographical areas here analyzed. Along the Intermediate Area (38°-41° S) each estuarine population constitutes a different unit. In contrast, Magellanic populations (43°-53° S) exhibited low levels of genetic differentiation. Contrasting patterns of genetic diversity and structure recorded in the species between the analyzed biogeographic areas are consistent with the marked differences in abiotic factors (i.e., different coastal configurations, Quaternary glacial histories, and oceanographic regimes) and to inherent characteristics of the species (i.e., salt-tolerance, physiology, and reproductive behavior).