Morphological and Molecular Identification of Ulva spp. (Ulvophyceae; Chlorophyta) from Algarrobo Bay, Chile: Understanding the Composition of Green Tides.

Green algae blooms of the genus Ulva are occurring globally and are primarily attributed to anthropogenic factors. At Los Tubos beach in Algarrobo Bay along the central Chilean coast, there have been blooms of these algae that persist almost year-round over the past 20 years, leading to environmental, economic, and social issues that affect the local government and communities. The objective of this study was to characterize the species that form these green tides based on a combination of ecological, morpho-anatomical, and molecular information. For this purpose, seasonal surveys of beached algal fronds were conducted between 2021 and 2022. Subsequently, the sampled algae were analyzed morphologically and phylogenetically using the molecular markers ITS1 and tufA, allowing for the identification of at least five taxa. Of these five taxa, three (U. stenophylloides, U. uncialis, U. australis) have laminar, foliose, and distromatic morphology, while the other two (U. compressa, U. aragoensis) have tubular, filamentous, and monostromatic fronds. Intertidal surveys showed that U. stenophylloides showed the highest relative coverage throughout the seasons and all intertidal levels, followed by U. uncialis. Therefore, we can establish that the green tides on the coast of Algarrobo in Chile are multispecific, with differences in relative abundance during different seasons and across the intertidal zone, opening opportunities for diverse future studies, ranging from ecology to algal biotechnology.

Combining population genomics and biophysical modelling to assess connectivity patterns in an Antarctic fish.

Connectivity is a fundamental process of population dynamics in marine ecosystems. In the last decade, with the emergence of new methods, combining different approaches to understand the patterns of connectivity among populations and their regulation has become increasingly feasible. The Western Antarctic Peninsula (WAP) is characterized by complex oceanographic dynamics, where local conditions could act as barriers to population connectivity. Here, the notothenioid fish Harpagifer antarcticus, a demersal species with a complex life cycle (adults with poor swim capabilities and pelagic larvae), was used to assess connectivity along the WAP by combining biophysical modelling and population genomics methods. Both approaches showed congruent patterns. Areas of larvae retention and low potential connectivity, observed in the biophysical model output, coincide with four genetic groups within the WAP: (1) South Shetland Islands, (2) Bransfield Strait, (3) the central and (4) the southern area of WAP (Marguerite Bay). These genetic groups exhibited limited gene flow between them, consistent with local oceanographic conditions, which would represent barriers to larval dispersal. The joint effect of geographic distance and larval dispersal by ocean currents had a greater influence on the observed population structure than each variable evaluated separately. The combined effect of geographic distance and a complex oceanographic dynamic would be generating limited levels of population connectivity in the fish H. antarcticus along the WAP. Based on this, population connectivity estimations and priority areas for conservation were discussed, considering the marine protected area proposed for this threatened region of the Southern Ocean.

Shedding light on variation in reproductive success through studies of population genetic structure in a Southeast Pacific Coast mussel.

Phylogeography often focuses on the spatial dimension of genetic diversity, rarely including the temporal dynamics occurring interannually among local populations, which can provide insight into past variations in reproductive success. Currently, there is an intense aquaculture industry of Mytilus spp. on the Southeast Pacific Coast which depends entirely on the spat released by natural populations forming a relevant and sensitive social-ecological system. Temporal and spatial spat variability from natural mussel beds could be related to interannual reproductive dynamics with variable reproductive success and recruitment, which leave genetic signatures. Temporal and spatial genetic structure was evaluated in six natural beds in the Southeast Pacific (from 39°25'S to 43°07'S) on the most abundant and widespread Mytilus lineage detected, Mytilus cf. chilensis, in 4 consecutive years. Analyses included data from >180 individuals per year, with a total of 751 (mitochondrial COI) and 747 (nuclear H1) individuals, respectively. Overall, both markers showed high haplotype diversity and low spatial and temporal genetic differentiation. Likely, the high dispersal capacity of Mytilus cf. chilensis maintains population homogeneity and prevents diversity erosion. The slight differences in genetic variance of COI were better explained by differences among sites (space), and conversely, the H1 genetic variance was better explained by interannual (temporal) comparisons, which could explain temporal variability in spat availability. This study highlights the important insights achieved with the evaluation of both temporal and spatial population genetic structures in marine species with high reproductive output, which can condition the success and sustainability of the relevant social-ecological system.

Population genomic analyses reveal hybridization and marked differences in genetic structure of Scurria limpet sister species with parapatric distributions across the South Eastern Pacific.

The study of sister species that occur in parapatry around biogeographic transition zones can help understand the evolutionary processes that underlie the changes in species composition across biogeographic transition zones. The South Eastern Pacific (SEP) coast is a highly productive coastal system that exhibits a broad biogeographic transition zone around 30-35°S. Here, we present a comparative genome-wide analysis of the sister species Scurria viridula and Scurria zebrina, that occur in parapatry and whose poleward and equatorward range edges intersect in the 30-35°S SEP biogeographic transition zone. We sampled 118 specimens sourced from nine sites from Tocopilla (22°S) to Chiloé (41°S) including one site where both species overlap and analyzed over 8000 biallelic single nucleotide polymorphisms. We found evidence of hybridization between these species in the contact zone and found significant but contrasting population structures for both species. Our results indicate that the genetic structure in S. viridula, which is currently expanding its range poleward, follows a simple isolation by distance model with no traces of natural selection (no evidence of outlier loci). In contrast, S. zebrina, which has  its equatorward range edge at the transition zone, displayed a pronounced genetic break approximately at 32-34°S, along a region of marked environmental heterogeneity in association with a semi-permanent coastal upwelling regime. For S. zebrina we also found 43 outlier loci associated with this genetic break, with a significant proportion of them clustering in a single linkage group. This marked difference in the presence of outlier loci between species suggests that they could be responding differently to local environmental challenges found at their overlapping geographic range edges, thus providing important new insights about genomic changes around biogeographic transition zones in sister species and the forces that shape genetic diversity in intertidal marine species.

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.

Genetic and morphological divergence at a biogeographic break in the beach-dwelling brooder Excirolana hirsuticauda Menzies (Crustacea, Peracarida).

BACKGROUND: There is a biogeographic break located at 30°S in the southeast Pacific, in a coastal area of strong environmental discontinuities. Several marine benthic taxa with restricted dispersal have a coincident phylogeographic break at 30°S, indicating that genetic structure is moulded by life history traits that limit gene flow and thereby promote divergence and speciation. In order to evaluate intraspecific divergence at this biogeographic break, we investigated the genetic and morphological variation of the directly developing beach isopod Excirolana hirsuticauda along 1900 km of the southeast Pacific coast, across 30°S. RESULTS: The COI sequences and microsatellite data both identified a strong discontinuity between populations of E. hirsuticauda to the north and south of 30°S, and a second weaker phylogeographic break at approximately 35°S. The three genetic groups were evidenced by different past demographic and genetic diversity signatures, and were also clearly distinguished with microsatellite data clustering. The COI sequences established that the genetic divergence of E. hirsuticauda at 30°S started earlier than divergence at 35°. Additionally, the three groups have different past demographic signatures, with probable demographic expansion occurring earlier in the southern group (south of 35°S), associated with Pleistocene interglacial periods. Interestingly, body length, multivariate morphometric analyses, and the morphology of a fertilization-related morphological character in males, the appendix masculina, reinforced the three genetic groups detected with genetic data. CONCLUSIONS: The degree of divergence of COI sequences, microsatellite data, and morphology was concordant and showed two geographic areas in which divergence was promoted at differing historical periods. Variation in the appendix masculina of males has probably promoted reproductive isolation. This variation together with gene flow restrictions promoted by life history traits, small body size, oceanographic discontinuities and sandy-beach habitat continuity, likely influenced species divergence at 30°S in the southeast Pacific coast. The degree of genetic and morphological differentiation of populations to the north and south of 30°S suggests that E. hirsuticauda harbours intraspecific divergence consistent with reproductive isolation and an advanced stage of speciation. The speciation process within E. hirsuticauda has been shaped by both restrictions to gene flow and a prezygotic reproductive barrier.

Hemilamprops chilensis sp. nov. (Crustacea: Cumacea: Lampropidae) from the coast of Chile, with a key to the Chilean Lampropidae and remarks on the status of H. ultimaespei Zimmer, 1921 and H. lotusae Bacescu, 1969.

A new species is described, Hemilamprops chilensis, from Chile. The new species was collected at several localities, from Bahia Herradura in the central part of the country, to Ancud on the island of Chiloe in the south. The depth of collection ranged from 0-30 m. The species with the closest affinity to H. chilensis is the South African species, H. glabrus Day, 1978. The new species is distinguished from all other Hemilamprops by the combination of a short lateral ridge anteriorly on the carapace, maxilliped 3 with the basis much longer than the remainder of the appendage, and the telson bearing 3 terminal setae and 2 pairs of small lateral setae. The identities of H. ultimaespei and H. lotusae are fixed by lectotype and neotype designation, respectively. The lectotype of H. ultimaespei is selected as the neotype of H. lotusae, making H. lotusae a junior objective synonym of H. ultimaespei.

Lineage divergence, local adaptation across a biogeographic break, and artificial transport, shape the genetic structure in the ascidian Pyura chilensis.

Marine benthic organisms inhabit a heterogeneous environment in which connectivity between populations occurs mainly through dispersive larval stages, while local selective pressures acting on early life history stages lead to non-random mortality, shaping adaptive genetic structure. In order to test the influence of local adaptation and neutral processes in a marine benthic species with low dispersal, in this study we used Genotyping by Sequencing technology to compare the neutral and putatively selected signals (neutral and outlier loci, respectively) in SNPs scattered throughout the genome in six local populations of the commercially exploited ascidian Pyura chilensis along the southeast Pacific coast (24°-42°S). This species is sessile as an adult, has a short-lived larval stage, and may also be dispersed by artificial transport as biofouling. We found that the main signal in neutral loci was a highly divergent lineage present at 39°S, and a subjacent signal that indicated a separation at 30°S (north/south), widely reported in the area. North/south separation was the main signal in outlier loci, and the linage divergence at 39°S was subjacent. We conclude that the geographic structure of the genetic diversity of outlier and neutral loci was established by different strengths of environmental, historical and anthropogenic factors.

Multiple transisthmian divergences, extensive cryptic diversity, occasional long-distance dispersal, and biogeographic patterns in a marine coastal isopod with an amphi-American distribution.

Excirolana braziliensis is a coastal intertidal isopod with a broad distribution spanning the Atlantic and Pacific tropical and temperate coasts of the American continent. Two separate regional studies (one in Panama and one in Chile) revealed the presence of highly genetically divergent lineages, implying that this taxon constitutes a cryptic species complex. The relationships among the lineages found in these two different regions and in the rest of the distribution, however, remain unknown. To better understand the phylogeographic patterns of E. braziliensis, we conducted phylogenetic analyses of specimens from much of its entire range. We obtained DNA sequences for fragments of four mitochondrial genes (16S rDNA, 12S rDNA, COI, and Cytb) and also used publicly available sequences. We conducted maximum likelihood and Bayesian phylogenetic reconstruction methods. Phylogeographic patterns revealed the following: (1) new highly divergent lineages of E. braziliensis; (2) three instances of Atlantic-Pacific divergences, some of which appear to predate the closure of the Isthmus of Panama; (3) the distributional limit of highly divergent lineages found in Brazil coincides with the boundary between two major marine coastal provinces; (4) evidence of recent long-distance dispersal in the Caribbean; and (5) populations in the Gulf of California have closer affinities with lineages further south in the Pacific, which contrasts with the closer affinity with the Caribbean reported for other intertidal organisms. The high levels of cryptic diversity detected also bring about challenges for the conservation of this isopod and its fragile environment, the sandy shores. Our findings underscore the importance of comprehensive geographic sampling for phylogeographic and taxonomical studies of broadly distributed putative species harboring extensive cryptic diversity.

Transcriptome characterization of the ascidian Pyura chilensis using 454-pyrosequencing data from two distant localities on the southeast Pacific.

This study describes the results from transcriptomes sequenced by 454-pyrosequencing from two populations separated by 10° of latitude of the endemic tunicate Pyura chilensis. Most transcripts were assembled in 43,972 contigs with an average length of 842 nucleotides. De novo assembly revealed that less than 30% of the contigs were annotated to Gene Ontology terms. A total of 71,662 single nucleotide polymorphisms (SNPs) were detected in 14,712 contigs. In silico differential expression of contigs annotated for SNPs revealed several genes differentially expressed in individuals collected from both populations. The present genomic resource will provide the basis to perform functional genomics on the species via the localization of genomic markers that can aid in determining levels of local adaptation, overall genetic structure and the genetic assessment of restocking programs for this species.

Phylogeographic structure in benthic marine invertebrates of the southeast Pacific coast of Chile with differing dispersal potential.

The role of dispersal potential on phylogeographic structure, evidenced by the degree of genetic structure and the presence of coincident genetic and biogeographic breaks, was evaluated in a macrogeographic comparative approach along the north-central coast of Chile, across the biogeographic transition zone at 30°S. Using 2,217 partial sequences of the mitochondrial Cytochrome Oxidase I gene of eight benthic invertebrate species along ca. 2,600 km of coast, we contrasted dispersal potential with genetic structure and determined the concordance between genetic divergence between biogeographic regions and the biogeographic transition zone at 30°S. Genetic diversity and differentiation highly differed between species with high and low dispersal potential. Dispersal potential, sometimes together with biogeographic region, was the factor that best explained the genetic structure of the eight species. The three low dispersal species, and one species assigned to the high dispersal category, had a phylogeographic discontinuity coincident with the biogeographic transition zone at 30°S. Furthermore, coalescent analyses based on the isolation-with-migration model validate that the split between biogeographic regions north and south of 30°S has a historic origin. The signatures of the historic break in high dispersers is parsimoniously explained by the homogenizing effects of gene flow that have erased the genetic signatures, if ever existed, in high dispersers. Of the four species with structure across the break, only two had significant albeit very low levels of asymmetric migration across the transition zone. Historic processes have led to the current biogeographic and phylogeographic structure of marine species with limited dispersal along the north-central coast of Chile, with a strong lasting impact in their genetic structure.

Isolation with differentiation followed by expansion with admixture in the tunicate Pyura chilensis.

BACKGROUND: Pyura chilensis, a tunicate commercially exploited as food resource in Chile, is subject to management strategies, including restocking. The goal of this study was to examine the genetic structure of P. chilensis using information from a mitochondrial gene (Cytochrome Oxidase I, COI) and a nuclear gene (Elongation 1 alpha, EF1a), to characterize the geographic distribution of genetic diversity and differentiation, and to identify the main processes that have shaped it. We analyzed 268 and 208 sequences of COI and EF1a, respectively, from samples of eight local populations covering ca. 1800 km. RESULTS: For Pyura chilensis, partial sequences of the gene COI revealed three highly supported haplogroups that diverged 260000 to 470000 years ago. Two haplogroups currently are widely distributed and sympatric, while one is dominant only in Los Molinos (LM, 39°50'S). The two widespread COI haplogroups underwent a geographic expansion during an interglacial period of the Late Pleistocene ca. 100000 years ago. The nuclear gene was less divergent and did not resolve the COI haplogroups. Bayesian clustering of the nuclear gene's SNPs revealed that individuals from the two widespread COI haplogroups were mostly assigned to two of the three detected clusters and had a marked degree of admixture. The third cluster predominated in LM and showed low admixture. Haplotypic diversity of both genes was very high, there was no isolation by distance, and most localities were genetically undifferentiated; only LM was consistently differentiated with both genes analyzed. CONCLUSIONS: Pyura chilensis has less genetic structure than expected given its life history, which could be a consequence of dispersal on ship hulls. The only differentiated local population analyzed was LM. Coincidentally, it is the one furthest away from main maritime routes along the coast of Chile.The use of mitochondrial and nuclear markers allowed detection of divergent mitochondrial haplogroups in P. chilensis, two of which revealed nuclear admixture. The genetic structure of P. chilensis has likely been shaped by Pleistocene's climatic effect on sea level leading to population contraction with isolation, followed by geographic range expansions with concomitant secondary contact and admixture.

Species replacement along a linear coastal habitat: phylogeography and speciation in the red alga Mazzaella laminarioides along the south east Pacific.

BACKGROUND: The Chilean shoreline, a nearly strait line of coast expanding across 35 latitudinal degrees, represents an interesting region to assess historical processes using phylogeographic analyses. Stretching along the temperate section of the East Pacific margin, the region is characterized by intense geologic activity and has experienced drastic geomorphological transformations linked to eustatic and isostatic changes during the Quaternary. In this study, we used two molecular markers to evaluate the existence of phylogeographic discontinuities and detect the genetic footprints of Pleistocene glaciations among Patagonian populations of Mazzaella laminarioides, a low-dispersal benthic intertidal red seaweed that inhabits along ~3,700 km of the Chilean coastal rocky shore. RESULTS: Three main genetic lineages were found within M. laminarioides. They are distributed along the Chilean coast in strict parapatry. The deep divergence among lineages suggests that they could be considered putative genetic sibling species. Unexpectedly, genetic breaks were not strictly concordant with the biogeographic breaks described in the region. A Northern lineage was restricted to a broad transition zone located between 30°S and 33°S and showed signals of a recent bottleneck. The reduction of population size could be related to warm events linked to El Niño Southern Oscillation, which is known to cause massive seaweed mortality in this region. To the south, we propose that transient habitat discontinuities driven by episodic tectonic uplifting of the shoreline around the Arauco region (37°S-38°S); one of the most active forearc-basins in the South East Pacific; could be at the origin of the Central/South genetic break. The large beaches, located around 38°S, are likely to contribute to the lineages' integrity by limiting present gene flow. Finally, the Southern lineage, occupies an area affected by ice-cover during the last glaciations. Phylogeny suggested it is a derived clade and demographic analyses showed the lineage has a typical signature of postglacial recolonization from a northern glacial refugium area. CONCLUSIONS: Even if environmental adaptation could have strengthened divergence among lineages in M. laminarioides, low dispersal capacity and small population size are sufficient to generate phylogeographic discontinuities determined by genetic drift alone. Interestingly, our results confirm that seaweed population connectivity over large geographic scales does not rely only on dispersal capacity but also seem to depend highly on substratum availability and population density of the receiving locality.

Heterochronic phenotypic plasticity with lack of genetic differentiation in the southeastern Pacific squat lobster Pleuroncodes monodon.

Two forms of the squat lobster Pleuroncodes monodon can be found along the Pacific coast of South America: a smaller pelagic and a larger benthic form that live respectively in the northern and southern areas of the geographic distribution of the species. The morphological and life history differences between the pelagic and benthic forms could be explained either by genetic differentiation or phenotypic plasticity. In the latter case it would correspond to a heterochronic phenotypic plasticity that is fixed in different environments (phenotype fixation). The aim of this study was to evaluate whether the two forms are genetically differentiated or not; and thus to infer the underlying basis-heritable or plastic-of the existence of the two forms. Based on barcoding data of mitochondrial DNA (the COI gene), we show that haplotypes from individuals of the pelagic and benthic forms comprise a single genetic unit without genetic differentiation. Moreover, the data suggest that all studied individuals share a common demographic history of recent and sudden population expansion. These results strongly suggest that the differences between the two forms are due to phenotypic plasticity.

Molecular insights into Cumacean family relationships (Crustacea, Cumacea).

Cumaceans are a diverse order of small, benthic marine crustaceans. Phylogenetic hypotheses for the eight currently recognized cumacean families have not been formally proposed. However, based on external morphological traits and Linnean classification, a few conflicting hypotheses of relatedness have been proposed. Family definitions rely on morphological characters that often overlap and diagnoses are based on a combination of non-unique characters. Morphological analysis does not provide a well-resolved phylogeny. In the present study, we use amino acid sequences from the mitochondrial cytochrome oxidase I gene to produce a molecular phylogenetic hypothesis for the families of Cumacea. Phylogenetic analyses at the amino acid level were performed under Bayesian, likelihood, and parsimony methods. Results strongly suggest that families lacking an articulated telson form a monophyletic group. This pleotelson clade, composed of the families Bodotriidae, Leuconidae, and Nannastacidae, is the most derived within the Cumacea. Within this group, the Bodotriidae resolve paraphyletically, with Leuconidae and Nannastacidae embedded within it. Comparison of the molecular phylogeny with that based on morphology suggests that many "diagnostic" characters are homoplasious.

Molecular systematics of the Acoela (Acoelomorpha, Platyhelminthes) and its concordance with morphology.

The phylogenetic relationships of the lower worm group Acoela were investigated using newly obtained nuclear 18S rDNA sequences from 16 acoels in combination with 16 acoel sequences available on GenBank from other laboratories. Parsimony and maximum likelihood analyses of the molecular data supported the concept that the Acoela is monophyletic; however, the gene tree produced by these analyses conflicts with the current taxonomic system for the Acoela in several family-level groupings. Most notable is the apparent polyphyly of the largest family of acoels, the Convolutidae. DNA analysis grouped together species of small-bodied convolutids in one clade, while large-bodied convolutids grouped in a separate clade with other large-bodied acoels. Despite such conflicts, the branching pattern in the gene tree is well supported by morphological characters of sperm and body-wall musculature.