A simulation study evaluating how population survival and genetic diversity in a newly established population can be affected by propagule size, extinction rates, and initial heterozygosity.

The introduction and establishment of invasive species in regions outside their native range, is one of the major threats for the conservation of ecosystems, affecting native organisms and the habitat where they live in, causing substantial biological and monetary losses worldwide. Due to the impact of invasive species, it is important to understand what makes some species more invasive than others. Here, by simulating populations using a forward-in-time approach combining ecological and single polymorphic nucleotides (SNPs) we evaluated the relation between propagule size (number of individuals = 2, 10, 100, and 1,000), extinction rate (with values 2%, 5%, 10%, and 20%), and initial heterozygosity (0.1, 0.3, and 0.5) on the population survival and maintenance of the heterozygosity of a simulated invasive crab species over 30 generations assuming a single introduction. Our results revealed that simulated invasive populations with initial propagule sizes of 2-1,000 individuals experiencing a high extinction rate (10-20% per generation) were able to maintain over 50% of their initial heterozygosity during the first generations and that under scenarios with lower extinction rates invasive populations with initial propagule sizes of 10-1,000 individuals can survive up to 30 generations and maintain 60-100% of their initial heterozygosity. Our results can help other researchers better understand, how species with small propagule sizes and low heterozygosities can become successful invaders.

Natural mega disturbances drive spatial and temporal changes in diversity and genetic structure on the toadfish Aphos porosus.

Natural disturbances can modify extinction-colonization dynamics, driving changes in the genetic diversity and structure of marine populations. Along Chilean coast (36°S, 73°W), a strong hypoxic-upwelling event in 2008, and a mega earthquake-tsunami in 2010 caused mass mortality within the Aphos porosus population, which is a vulnerable species with low dispersal potential. We evaluated the effects of these two major disturbances on the diversity and spatial-temporal genetic structure of Aphos porosus in two neighboring areas that were impacted on different levels (High level: Coliumo Bay; Low level: Itata Shelf). Thirteen microsatellites (from 2008 to 2015) amplified in individuals collected from both locations were used to evaluate the effects of the two disturbances. Results showed that after the strong hypoxic-upwelling event and the mega earthquake-tsunami, Aphos porosus populations exhibited lower genetic diversity and less effective population sizes (Ne < 20), as well as asymmetries in migration and spatial-temporal genetic structure. These findings suggest a rise in extinction-recolonization dynamics in local Aphos porosus populations after the disturbances, which led to a loss of local genetic diversity (mainly in Coliumo Bay area impacted the most), and to greater spatial-temporal genetic structure caused by drift and gene flow. Our results suggest that continuous genetic monitoring is needed in order to assess potential risks for Aphos porosus in light of new natural and anthropogenic disturbances.

Pleistocene expansion, anthropogenic pressure and ocean currents: Disentangling the past and ongoing evolutionary history of Patella aspera Röding, 1798 in the archipelago of Madeira.

AIMS: Rising sea-level following the Last Glacial Maximum lead to fragmentation of coastal limpet populations between islands of the Archipelago of Madeira. This fragmentation is reinforced by recent heavy exploitation reducing effective population size on Madeira Island. We use the limpet P. aspera to understand how the role of processes at different time scales (i.e. changes in the sea level and overexploitation) can influence the genetic composition of an extant species, relating these processes to reproductive phenology and seasonal shifts in ocean currents. LOCATION: Madeira Island, Porto Santo and Desertas (Archipelago of Madeira, NE Atlantic Ocean). TAXON: The limpet Patella aspera. METHODS: Twelve microsatellite genetic markers were used. A power analysis was used to evaluate the power of the microsatellite markers to detect a signal of population differentiation. Long-term past migrations were assessed using a Bayesian Markov Montecarlo approach in the software MIGRATE-n to estimate mutation-scaled migration rates (M = m/µ; m, probability of a lineage immigrating per generation; µ, mutation rate). Two scenarios were evaluated using an Approximate Bayesian Computation (ABC) in the software DIYABC 2.1 (i) Scenario 1: considered a population scenario from a reduced Ne at time t3 to a higher Ne at time t2; and (ii) Scenario 2 considering a reduction of Ne from a time t3 to a time t2. RESULTS: Colonization of the archipelago by Portuguese settlers six centuries ago probably led to an important decrease in the genetic diversity of the species (Ne). Contemporary gene flow strongly support a pattern of high asymmetric connectivity explained by the reproductive phenology of the species and spatio-temporal seasonal changes in the ocean currents. Spatio-temporal reconstructions using Bayesian methods, including coalescent and Approximate Bayesian Computation (ABC) approaches, suggest changes in the migration patterns from highly symmetric to highly asymmetric connectivity with subtle population differentiation as consequence of post-glacial maximum sea level rise during the Holocene. MAIN CONCLUSIONS: Our results suggest that anthropogenic activity could have had serious effects on the genetic diversity of heavily exploited littoral species since the end of the Pleistocene, probably accelerating in recent years.

Major ocean currents may shape the microbiome of the topshell Phorcus sauciatus in the NE Atlantic Ocean.

Studies on microbial communities are pivotal to understand the role and the evolutionary paths of the host and their associated microorganisms in the ecosystems. Meta-genomics techniques have proven to be one of the most effective tools in the identification of endosymbiotic communities of host species. The microbiome of the highly exploited topshell Phorcus sauciatus was characterized in the Northeastern Atlantic (Portugal, Madeira, Selvagens, Canaries and Azores). Alpha diversity analysis based on observed OTUs showed significant differences among regions. The Principal Coordinates Analysis of beta-diversity based on presence/absence showed three well differentiated groups, one from Azores, a second from Madeira and the third one for mainland Portugal, Selvagens and the Canaries. The microbiome results may be mainly explained by large-scale oceanographic processes of the study region, i.e., the North Atlantic Subtropical Gyre, and specifically by the Canary Current. Our results suggest the feasibility of microbiome as a model study to unravel biogeographic and evolutionary processes in marine species with high dispersive potential.

Post-Disturbance Genetic Changes: The Impact of the 2010 Mega-Earthquake and Tsunami on Chilean Sandy Beach Fauna.

Earthquake/tsunamis can have profound impacts on species and their genetic patterns. It is expected that the magnitude of this impact might depend on the species and the time since the disturbance occurs, nevertheless these assumptions remain mostly unexplored. Here we studied the genetic responses of the crustacean species Emerita analoga, Excirolana hirsuticauda, and Orchestoidea tuberculata to the 27F mega-earthquake/tsunami that occurred in Chile in February 2010. mtDNA sequence analyses revealed a lower haplotype diversity for E. analoga and E. hirsuticauda in impacted areas one month after the 27F, and the opposite for O. tuberculata. Three years after the 27F we observed a recovery in the genetic diversity of E. analoga and E. hirsuticauda and decrease in the genetic diversity in O. tuberculata in 2/3 of sampled areas. Emerita analoga displayed decrease of genetic differentiation and increase in gene flow explained by long-range population expansion. The other two species revealed slight increase in the number of genetic groups, little change in gene flow and no signal of population expansion associated to adult survival, rapid colonization, and capacity to burrow in the sand. Our results reveal that species response to a same disturbance event could be extremely diverse and depending on life-history traits and the magnitude of the effect.

Invasive species and postglacial colonization: their effects on the genetic diversity of a Patagonian fish.

The present distribution of Patagonian species is the result of a complex history involving Quaternary refugial populations, Holocene range expansions and demographic changes occurring during the Anthropocene. Invasive salmonids were introduced in Patagonia during the last century, occupying most rivers and lakes, preying on and competing with native species, including the fish Galaxias platei. Here, we used G. platei as a case study to understand how long-term (i.e. population differentiation during the Holocene) and short-term historical processes (salmonid introductions) affect genetic diversity. Using a suite of microsatellite markers, we found that the number of alleles is negatively correlated with the presence of salmonids (short-term processes), with G. platei populations from lakes with salmonids exhibiting significantly lower genetic diversity than populations from lakes without salmonids. Simulations (100 years backwards) showed that this difference in genetic diversity can be explained by a 99% reduction in population size. Allelic richness and observed heterozygosities were also negatively correlated with the presence of salmonids, but also positively correlated with long-term processes linked to Quaternary glaciations. Our results show how different genetic parameters can help identify processes taking place at different scales and their importance in terms of conservation.

Tandem Action of Natural and Chemical Stressors in Stream Ecosystems: Insights from a Population Genetic Perspective.

Agricultural and urban land use has dramatically increased over the last century and one consequence is the release of anthropogenic chemicals into aquatic ecosystems. One of the rarely studied consequences is the effect of land use change on internal concentrations of organic micropollutants (OMPs) in aquatic invertebrates and its effects on their genotype diversity. Here, we applied population genetic and internal concentrations of OMPs analyses to determine evolutionary implications of chemical pollution on Gammarus pulex populations from a natural and two agricultural streams. Along 14 consecutive months sampled, 26 different OMPs were quantified in G. pulex extracts with the highest number, concentration, and toxic pressure in the anthropogenically stressed stream ecosystems. Our results indicate distinct internal OMP profiles and changes in both genetic variation and genetic structure in streams affected by anthropogenic activity. Genetic variation was attributed to chemical pollution whereas changes in the genetic structure were attributed to environmental disturbances, such as changes in discharge in the impacted stream ecosystems, which worked both independently and in tandem. Finally, we conclude that human-impacted streams are subjected to severe alterations in their population genetic patterns compared to nonimpacted stream ecosystems.

Past, present, and future of a freshwater fish metapopulation in a threatened landscape.

It is well documented that hydropower plants can affect the dynamics of fish populations through landscape alterations and the creation of new barriers. Less emphasis has been placed on the examination of the genetic consequences for fish populations of the construction of dams. The relatively few studies that focus on genetics often do not consider colonization history and even fewer tend to use this information for conservation purposes. As a case study, we used a 3-pronged approach to study the influence of historical processes, contemporary landscape features, and potential future anthropogenic changes in landscape on the genetic diversity of a fish metapopulation. Our goal was to identify the metapopulation's main attributes, detect priority areas for conservation, and assess the consequences of the construction of hydropower plants for the persistence of the metapopulation. We used microsatellite markers and coalescent approaches to examine historical colonization processes, traditional population genetics, and simulations of future populations under alternate scenarios of population size reduction and gene flow. Historical gene flow appeared to have declined relatively recently and contemporary populations appeared highly susceptible to changes in landscape. Gene flow is critical for population persistence. We found that hydropower plants could lead to a rapid reduction in number of alleles and to population extirpation 50-80 years after their construction. More generally, our 3-pronged approach for the analyses of empirical genetic data can provide policy makers with information on the potential impacts of landscape changes and thus lead to more robust conservation efforts.

The complete mitochondrial genome of the freshwater fish Galaxias platei and a comparison with other species of the genus Galaxias (faraway, so close?).

We present the whole mitochondrial genome for Galaxias platei, a freshwater fish widely distributed throughout the Patagonian Andes, and compare it with the mitochondrial genome of three congeneric species. The position of G. platei in the phylogenetic reconstruction differs from that shown by earlier studies using multiple markers. We discuss the results in terms of the phylogenetic position of G. platei and the use of whole mitochondrial genomes versus specific regions of multiple organelles.

Anthropogenic Stressors Shape Genetic Structure: Insights from a Model Freshwater Population along a Land Use Gradient.

Environmental pollution including mutagens from wastewater effluents and discontinuity by man-made barriers are considered typical anthropogenic pressures on microevolutionary processes that are responsible for the loss of biodiversity in aquatic ecosystems. Here, we tested for the effects of wastewater treatment plants (WWTPs), weirs and other stressors on the invertebrate species Gammarus pulex at the population genetic level combining evolutionary ecotoxicology, body burden analysis and testing for exposure to mutagens. Exposure to chemical pollution alone and in combination with the presence of weirs resulted in a depression of allelic richness in native G. pulex populations. Our results suggest that the input of a mutagenic effluent from a WWTP resulted in a strong increase in private alleles over the affected populations. In addition, the presence of weirs along the river disrupted the migration across the river and thus the gene flow between G. pulex upstream and downstream. This study provides strong evidence that the assessment of genetic variation including private alleles together with the contamination of mutagenic and nonmutagenic chemical pollution offers new insights into the regulation of genetic population structure and highlights the relevance of emerging anthropogenic pressures at the genetic level.

Echoes of a distant time: effects of historical processes on contemporary genetic patterns in Galaxias platei in Patagonia.

Interpreting the genetic structure of a metapopulation as the outcome of gene flow over a variety of timescales is essential for the proper understanding of how changes in landscape affect biological connectivity. Here we contrast historical and contemporary connectivity in two metapopulations of the freshwater fish Galaxias platei in northern and southernmost Patagonia where paleolakes existed during the Holocene and Pleistocene, respectively. Contemporary gene flow was mostly high and asymmetrical in the northern system while extremely reduced in the southernmost system. Historical migration patterns were high and symmetric in the northern system and high and largely asymmetric in the southern system. Both systems showed a moderate structure with a clear pattern of isolation by distance (IBD). Effective population sizes were smaller in populations with low contemporary gene flow. An approximate Bayesian computation (ABC) approach suggests a late Holocene colonization of the lakes in the northern system and recent divergence of the populations from refugial populations from east and west of the Andes. For the southern system, the ABC approach reveals that some of the extant G. platei populations most likely derive from an ancestral population inhabiting a large Pleistocene paleolake while the rest derive from a higher-altitude lake. Our results suggest that neither historical nor contemporary processes individually fully explain the observed structure and geneflow patterns and both are necessary for a proper understanding of the factors that affect diversity and its distribution. Our study highlights the importance of a temporal perspective on connectivity to analyse the diversity of spatially complex metapopulations.

Lizards on ice: evidence for multiple refugia in Liolaemus pictus (Liolaemidae) during the last glacial maximum in the Southern Andean beech forests.

Historical climate changes and orogenesis are two important factors that have shaped intraspecific biodiversity patterns worldwide. Although southern South America has experienced such complex events, there is a paucity of studies examining the effects on intraspecific diversification in this part of the world. Liolaemus pictus is the southernmost distributed lizard in the Chilean temperate forest, whose genetic structure has likely been influenced by Pleistocene glaciations. We conducted a phylogeographic study of L. pictus in Chile and Argentina based on one mitochondrial and two nuclear genes recovering two strongly divergent groups, Northern and Southern clades. The first group is distributed from the northernmost limit of the species to the Araucanía region while the second group is distributed throughout the Andes and the Chiloé archipelago in Southern Chile. Our results suggest that L. pictus originated 751 Kya, with divergence between the two clades occurring in the late Pleistocene. Demographic reconstructions for the Northern and Southern clades indicate a decrease in effective population sizes likely associated with Pleistocene glaciations. Surprisingly, patterns of genetic variation, clades age and historical gene flow in populations distributed within the limits of the Last Glacial Maximum (LGM) are not explained by recent colonization. We propose an "intra-Andean multiple refuge" hypothesis, along with the classical refuge hypothesis previously proposed for the biota of the Chilean Coastal range and Eastern Andean Cordillera. Our hypothesis is supported by niche modelling analysis suggesting the persistence of fragments of suitable habitat for the species within the limits of the LGM ice shield. This type of refuge hypothesis is proposed for the first time for an ectothermic species.