Permanent genetic resources added to molecular ecology resources database 1 December 2012-31 January 2013

Mass flowering and unprecedented extended pseudovivipary in seagrass (Posidonia oceanica) after a Marine Heat Wave

Seagrasses are marine flowering plants that create critical coastal ecosystems and are threatened by warming. Clonal expansion is generally the dominant strategy for meadow recovery, while sexual reproduction strongly differs among species (e.g., monoecious and diecious species, some creating seed banks, viviparous seedlings). In 2022, the Western Mediterranean underwent unprecedented warming, and, associated with it, we observed flowering (100 %) across 11 Posidonia oceanica meadows in Mallorca, Balearic Islands. Furthermore, 64 % of the sites also exhibited pseudovivipary, an extremely rare phenomenon in angiosperms whereby plantlets replace sexual reproductive structures, producing clones of the maternal plant. Our results support the notion that P. oceanica flowering and pseudovivipary (genetically confirmed) are triggered by warming, never before being pseudovivipary reported across multiple sites in a marine plant. Considering the negative impacts that warming can have on seagrasses, existence of widespread pseudovivipary is a critical aspect to consider for understanding mechanisms of resilience in seagrasses.

Colonization routes uncovered in a widely introduced Mediterranean gecko, Tarentola mauritanica

In this study, we aimed to understand the contemporary and ancient colonization routes of the Moorish gecko, Tarentola mauritanica, using simple sequence repeats. By analyzing the genetic diversity of populations in different regions, we found that Morocco is the genetic diversity hotspot for the species, followed by the Iberian Peninsula. However, historical gene flow estimates identified the Iberian Peninsula, not Morocco, as the primary contributor of colonizing individuals, along with continental Italy to a lesser extent. Currently, mainland Italy is the main source of introduced individuals, likely due to the plant nursery trade. The study suggests that human-facilitated introductions from various geographical origins, with numerous regions colonized through continental Italy during two distinct periods, are responsible for the recurrent entry of individuals belonging to the European lineage of T. mauritanica into the Mediterranean and Macaronesia. These findings can inform better monitoring surveys and conservation programs by identifying putative current colonization routes of alien species.

Signatures of positive selection in the mitochondrial genome of neotropical freshwater stingrays provide clues about the transition from saltwater to freshwater environment

Neotropical freshwater stingrays (subfamily Potamotrygoninae) are carnivorous bottom feeder batoids widely distributed in most river basins of South America. They represent the unique extant group of elasmobranchs that evolved to live exclusively in freshwater environments. These species are exploited either by commercial fisheries (e.g., for food or ornamental industry) or by indigenous communities allocated along with their natural range. Restrictive life history characteristics coupled with habitat degradation make Potamotrygoninae species highly vulnerable to human impacts and highlight the necessity of studies to inform basic biological aspects, from ecology to genetics, to guide their conservation and clarify the molecular basis of adaptation to the freshwater environment. We used available and newly assembled Potamotrygon spp. mitogenomes to perform a comparative investigation of their molecular evolution. A phylogenetic estimation using the mitogenome of Potamotrygon falkneri and other Elasmobranchii supports monophyly for Potamotrygonidae and indicates a close relationship to Dasyatidae. A synteny analysis comprising 3 Potamotrygon and other 51 batoids revealed a highly conserved mitogenomic context. We detected various amino acid sites under positive selection exclusively in Potamotrygon spp., within the sequences of ND4, ND5, ND6, and COXII genes. Positively selected mutational events in key genes of energetic metabolism may be related to the physiological adaptation of Potamotrygon spp. during the ancient incursion into freshwater. This broad comparative mitogenomic study provides novel insights into the evolutionary history of neotropical freshwater stingrays and their relatives and stands out as a valuable resource to aid in current and future research on elasmobranch molecular evolution.

Panmixia and active colonisation of the invasive palm Trachycarpus fortunei (Arecaceae) in Southern Switzerland and Northern Italy as inferred by microsatellites and SNP markers

Trachycarpus fortunei (Arecaceae: Coryphoideae) is an Asian palm that was introduced during the nineteenth century in southern Switzerland and northern Italy as an ornamental plant. In the recent decades, the palm has become an aggressive invasive species in the region. Before this study, the genetic structure and diversity of the naturalised populations were unknown. We aimed at understanding the dynamics of invasion and at comparing the results obtained with two types of markers. This genetic approach aimed at tracing back as far as possible the source of invasive populations comparing historical information found in literature and invasive genetic patterns. The genetic diversity was analysed using eight microsatellites (five were developed for that purpose) and 31′000 SNPs identified through GBS analyses. Genetic analyses were carried out for 200 naturalised individuals sampled from 21 populations in the Canton Ticino (Switzerland) and the provinces of Lombardy and Piedmont (Italy). The observed general panmixia indicates that the expansion of T. fortunei is active in its naturalised areas. The genetic pattern found for both SNPs and microsatellites appears to be related to the colonisation process, with a lack of geographic structure and bottleneck signatures occurring at the colonisation front, distantly from historical sites. This study gives a better understanding of the expansion of T. fortunei and adds new insights to its ecology.

Genetic diversity in Amazonian Jundiá (Leiarius marmoratus) stocks using heterologous primers

With the rise of world fish farming, the national scenario is favorable for using native fish for intensive farming. Among the catfish, the Amazonian Jundiá (Leiarius marmoratus) is a robust candidate, easy to grow and with good organoleptic characteristics in its flesh. For productive success in captivity, it is necessary to consider some questions about the species, such as genetic variability, which must have an acceptable level in a breeding stock, in order to maintain a good diversity; this reduces losses due to inbreeding and low diversity. Therefore, the objective of this study was to characterize the genetic variability of commercial stocks of L. marmoratus from the State of Mato Grosso through microsatellite molecular markers. We analyzed 143 individuals from three stocks. The mean heterozygosity and the inbreeding coefficients observed were 0.060; 0.084; 0.141; and 0.539; 0.562; 0.514, respectively, for the stocks of Campo Verde, Juína, and Nova Mutum. The Deviation in the Hardy-Weinberg equilibrium was observed in most of the loci in the three populations. Considering the genetic differentiation, it is concluded that the three populations are very close genetically, which requires introduction of new genetic material in the stocks to enrich them genetically for a later reproductive program.

The Moorish gecko, Tarentola mauritanica Linnaeus, 1758 (Squamata, Phyllodactylidae), in Albania

We summarised the records of Tarentola mauritanica in Albania. The first record for the country was published in 1989 from Sazan Island; however, it was never confirmed again. Another population was found recently in an urban habitat of Vlorë City near the main city port, probably of human-mediated origin.

Adaptive responses along a depth and a latitudinal gradient in the endemic seagrass Posidonia oceanica

Seagrass meadows provide important ecosystem services and are critical for the survival of the associated invertebrate community. However, they are threatened worldwide by human-driven environmental change. Understanding the seagrasses' potential for adaptation is critical to assess not only their ability to persist under future global change scenarios, but also to assess the persistence of the associated communities. Here we screened a wild population of Posidonia oceanica, an endemic long-lived seagrass in the Mediterranean Sea, for genes that may be target of environmental selection, using an outlier and a genome-wide transcriptome analysis. We identified loci where polymorphism or differential expression was associated with either a latitudinal or a bathymetric gradient, as well as with both gradients in an effort to identify loci associated with temperature and light. We found the candidate genes underlying growth and immunity to be divergent between populations adapted to different latitudes and/or depths, providing evidence for local adaptation. Furthermore, we found evidence of reduced gene flow among populations including adjacent populations. Reduced gene flow, combined with low sexual recombination, small effective population size, and long generation time of P. oceanica raises concerns for the long-term persistence of this species, especially in the face of rapid environmental change driven by human activities.

Isotropic and anisotropic processes influence fine-scale spatial genetic structure of a keystone tropical plant

Limited seed or pollen dispersal enhances spatial genetic relatedness between individuals (fine-scale spatial genetic structure, FSGS), which usually decreases as a function of physical distance. However, such isotropic pattern of FSGS may not always occur when spatially asymmetric processes, for instance, wind direction during dispersal, are considered in wind-pollinated and -dispersed plants. This study assessed the pattern of FSGS in the keystone tropical wetland plant Cyperus papyrus (papyrus) as a function of these isotropic and anisotropic processes. We tested the hypothesis that the FSGS would be influenced by predominant wind direction during pollen and seed dispersal, as well as by the physical distance between individuals. We genotyped a total of 510 adults and 407 juveniles from three papyrus swamps (Ethiopia) using 15 microsatellite markers. In addition, the contemporary directional dispersal by wind was evaluated by seed release-recapture experiments and complemented with parentage analysis. Adults and juveniles differed in the strength of isotropic FSGS ranging from 0.09 to 0.13 and 0.12 to 0.16, respectively, and this suggests variation in dispersal distance. Anisotropic FSGS was found to be a function of asymmetric wind direction during dispersal/pollination that varied between sites. Historical gene dispersal distance was astoundingly low (<4 m), possibly due to localized seed rain. According to our contemporary dispersal estimates, mean pollen dispersal distances were longer than those of seed dispersal (101 and <55 m, respectively). More than two-thirds of seeds and half of pollen grains were locally dispersed (≤80 m). The difference in historical and contemporary dispersal distance probably resulted from the asymmetric wind direction due to change in vegetation cover in the surrounding matrix. We further concluded that, in addition to wind direction, post-dispersal processes could influence gene dispersal distance inferred from the FSGS.

Clonal growth strategy, diversity and structure: A spatiotemporal response to sedimentation in tropical Cyperus papyrus swamps

Land degradation and soil erosion in the upper catchments of tropical lakes fringed by papyrus vegetation can result in a sediment load gradient from land to lakeward. Understanding the dynamics of clonal modules (ramets and genets) and growth strategies of plants on such a gradient in both space and time is critical for exploring a species adaptation and processes regulating population structure and differentiation. We assessed the spatial and temporal dynamics in clonal growth, diversity, and structure of an emergent macrophyte, Cyperus papyrus (papyrus), in response to two contrasting sedimentation regimes by combining morphological traits and genotype data using 20 microsatellite markers. A total of 636 ramets from six permanent plots (18 x 30 m) in three Ethiopian papyrus swamps, each with discrete sedimentation regimes (high vs. low) were sampled for two years. We found that ramets under the high sedimentation regime (HSR) were significantly clumped and denser than the sparse and spreading ramets under the low sedimentation regime (LSR). The HSR resulted in significantly different ramets with short culm height and girth diameter as compared to the LSR. These results indicated that C. papyrus ameliorates the effect of sedimentation by shifting clonal growth strategy from guerrilla (in LSR) to phalanx (in HSR). Clonal richness, size, dominance, and clonal subrange differed significantly between sediment regimes and studied time periods. Each swamp under HSR revealed a significantly high clonal richness (R = 0.80) as compared to the LSR (R = 0.48). Such discrepancy in clonal richness reflected the occurrence of initial and repeated seedling recruitment strategies as a response to different sedimentation regimes. Overall, our spatial and short-term temporal observations highlighted that HSR enhances clonal richness and decreases clonal subrange owing to repeated seedling recruitment and genets turnover.

Depth-specific fluctuations of gene expression and protein abundance modulate the photophysiology in the seagrass Posidonia oceanica

Here we present the results of a multiple organizational level analysis conceived to identify acclimative/adaptive strategies exhibited by the seagrass Posidonia oceanica to the daily fluctuations in the light environment, at contrasting depths. We assessed changes in photophysiological parameters, leaf respiration, pigments, and protein and mRNA expression levels. The results show that the diel oscillations of P. oceanica photophysiological and respiratory responses were related to transcripts and proteins expression of the genes involved in those processes and that there was a response asynchrony between shallow and deep plants probably caused by the strong differences in the light environment. The photochemical pathway of energy use was more effective in shallow plants due to higher light availability, but these plants needed more investment in photoprotection and photorepair, requiring higher translation and protein synthesis than deep plants. The genetic differentiation between deep and shallow stands suggests the existence of locally adapted genotypes to contrasting light environments. The depth-specific diel rhythms of photosynthetic and respiratory processes, from molecular to physiological levels, must be considered in the management and conservation of these key coastal ecosystems.

Long-term acclimation to reciprocal light conditions suggests depth-related selection in the marine foundation species Posidonia oceanica

Phenotypic differences among populations of the same species reflect selective responses to ecological gradients produced by variations in abiotic and biotic factors. Moreover, they can also originate from genetic differences among populations, due to a reduced gene flow. In this study, we examined the extent of differences in photo‐acclimative traits of Posidonia oceanica (L.) Delile clones collected above and below the summer thermocline (i.e., −5 and −25 m) in a continuous population extending along the water depth gradient. During a reciprocal light exposure and subsequent recovery in mesocosms, we assessed degree of phenotypic plasticity and local adaptation of plants collected at different depths, by measuring changes in several traits, such as gene expression of target genes, photo‐physiological features, and other fitness‐related traits (i.e., plant morphology, growth, and mortality rates). Samples were also genotyped, using microsatellite markers, in order to evaluate the genetic divergence among plants of the two depths. Measures collected during the study have shown a various degree of phenotypic changes among traits and experimental groups, the amount of phenotypic changes observed was also dependent on the type of light environments considered. Overall plants collected at different depths seem to be able to acclimate to reciprocal light conditions in the experimental time frame, through morphological changes and phenotypic buffering, supported by the plastic regulation of a reduced number of genes. Multivariate analyses indicated that plants cluster better on the base of their depth origin rather than the experimental light conditions applied. The two groups were genetically distinct, but the patterns of phenotypic divergence observed during the experiment support the hypothesis that ecological selection can play a role in the adaptive divergence of P. oceanica clones along the depth gradient.

Gene Flow Results in High Genetic Similarity between Sibiraea (Rosaceae) Species in the Qinghai-Tibetan Plateau

Studying closely related species and divergent populations provides insight into the process of speciation. Previous studies showed that the Sibiraea complex's evolutionary history on the Qinghai-Tibetan Plateau (QTP) was confusing and could not be distinguishable on the molecular level. In this study, the genetic structure and gene flow of Sibiraea laevigata and Sibiraea angustata on the QTP was examined across 45 populations using 8 microsatellite loci. Microsatellites revealed high genetic diversity in Sibiraea populations. Most of the variance was detected within populations (87.45%) rather than between species (4.39%). We found no significant correlations between genetic and geographical distances among populations. Bayesian cluster analysis grouped all individuals in the sympatric area of Sibiraea into one cluster and other individuals of S. angustata into another. Divergence history analysis based on the approximate Bayesian computation method indicated that the populations of S. angustata at the sympatric area derived from the admixture of the 2 species. The assignment test assigned all individuals to populations of their own species rather than its congeneric species. Consistently, intraspecies were detected rather than interspecies first-generation migrants. The bidirectional gene flow in long-term patterns between the 2 species was asymmetric, with more from S. angustata to S. laevigata. In conclusion, the Sibiraea complex was distinguishable on the molecular level using microsatellite loci. We found that the high genetic similarity of the complex resulted from huge bidirectional gene flow, especially on the sympatric area where population admixtures occurred. This study sheds light on speciation with gene flow in the QTP.

Contrasted patterns of genetic differentiation across eight bird species in the Lesser Antilles

Archipelagoes are considered as "natural laboratories" for studying processes that shape the distribution of diversity. The Lesser Antilles provide a favorable geographical context for divergence to occur. However, although morphological subspecies have been described across this archipelago in numerous avian species, the potential for the Lesser Antilles in driving intra-specific genetic divergence in highly mobile organisms such as birds remains understudied. Here, we assessed level of intra-specific genetic diversity and differentiation between three islands of the Lesser Antilles (Guadeloupe, Dominica and Martinique) using a multi-species approach on eight bird species. For each species, we built a set of microsatellite markers from cross-species amplifications. Significant patterns of inter-island and/or within-island genetic differentiation were detected in all species. However, levels of intra-specific genetic differentiation among the eight bird species were not always consistent with the boundaries of subspecies previously described in the sampled islands. These results suggest different histories of colonization/expansion and/or different species-specific ecological traits affecting gene flow, advocating for multi-species studies of historical and contemporary factors shaping the distribution of diversity on islands.

Genetic diversity and structure in two protected Posidonia oceanica meadows

Posidonia oceanica meadows growing along the west Mediterranean coastline are under continuous anthropogenic pressure. The way meadow health correlates with genetic and genotypic diversity in P. oceanica, is still under debate. Here we report a microsatellite analysis of two P. oceanica meadows living in protected areas of the Ligurian (Monterosso al Mare, MPA of "Cinque Terre") and central Tyrrhenian Sea (Santa Marinella, regional Site of Community Importance). Both meadows were recently classified as "disturbed", according to shoot density and other phenological parameters. Between the two meadows, Santa Marinella showed higher genetic diversity, while clear genetic substructure was present in both sites, reflecting high spatial heterogeneity. The present study suggests that genetic diversity does not match unequivocally with shoot density and leaf morphology and that small scale intra-meadow heterogeneity is an important factor to consider for establishing the relation between genetic/genotypic variability and health of natural seagrass meadows.

Seagrass radiation after Messinian salinity crisis reflected by strong genetic structuring and out-of-Africa scenario (Ruppiaceae)

Many aquatic plant and seagrass species are widespread and the origin of their continent-wide ranges might result from high gene flow levels. The response of species when extending northwards since the Last Glacial Maximum can be opposed to the structuring of their populations that survived glaciation cycles in southern regions. The peri-Mediterranean is a complex series of sea basins, coastlines, islands and river deltas with a unique history since the Messinian Crisis that potentially influenced allopatric processes of aquatic life. We tested whether vast ranges across Europe and the peri-Mediterranean of a global seagrass group (Ruppia species complexes) can be explained by either overall high levels of gene flow or vicariance through linking population genetics, phylogeography and shallow phylogenetics. A multigene approach identified haplogroup lineages of two species complexes, of ancient and recent hybrids with most of the diversity residing in the South. High levels of connectivity over long distances were only observed at recently colonized northern ranges and in recently-filled seas following the last glaciation. A strong substructure in the southern Mediterranean explained an isolation-by-distance model across Europe. The oldest lineages of the southern Mediterranean Ruppia dated back to the period between the end of the Messinian and Late Pliocene. An imprint of ancient allopatric origin was left at basin level, including basal African lineages. Thus both vicariance in the South and high levels of connectivity in the North explained vast species ranges. Our findings highlight the need for interpreting global distributions of these seagrass and euryhaline species in the context of their origin and evolutionary significant units for setting up appropriate conservation strategies.

Analysis of the black-chinned tilapia Sarotherodon melanotheron heudelotii reproducing under a wide range of salinities: from RNA-seq to candidate genes

The black-chinned tilapia Sarotherodon melanotheron heudelotii is an ecologically appealing model as it shows exceptional adaptive capacities, especially with regard to salinity. In spite of this, this species is devoid of genomic resources, which impedes the understanding of such remarkable features. De novo assembly of transcript sequences produced by next-generation sequencing technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms. It also facilitates the development of quantitative real-time PCR (qPCR) assays for analysing gene expression under different environmental conditions. Nevertheless, obtaining accurate and reliable qPCR results from such data requires a number of validations prior to interpretation. The transcriptome of S. melanotheron was sequenced to discover transcripts potentially involved in the plasticity of male reproduction in response to salinity variations. A set of 54 candidate and reference genes was selected through a digital gene expression (DGE) approach, and a de novo qPCR assay using these genes was validated for further detailed expression analyses. A user-friendly web interface was created for easy handling of the sequence data. This sequence collection represents a major transcriptomic resource for S. melanotheron and will provide a useful tool for functional genomics and genetics studies.