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ABSTRACT Biogeographic breaks represent crucial ecological junctures where species encounter novel environments that challenge their physiological limits and influence evolutionary trajectories. Two biogeographic breaks delineate distinct environmental regimes along the Chilean coastline on the Southeastern Pacific. In particular, the equatorward break, situated around 30° S–32° S, marks a transition from semi‐permanent upwelling to seasonal and intermittent upwelling poleward. The environmental break maintains a heterogeneous landscape for all coastal species along the region. Marine invertebrates, particularly intertidal ectothermic species such as limpets of the Scurria genus, exhibit diverse physiological responses to variation in the thermal environment. We characterized the physiological performance of five Scurria limpet species by measuring metabolic rate (oxygen consumption) and heart rate, together with buoyant weight as a proxy of shell calcification, under a standardized acclimation design under controlled laboratory conditions in individuals sourced from four locations spanning 17° of latitude, including the 30° S–32° S biogeographic break. We tested if the observed geographic variation in phenotypic traits was associated with differences in sea surface temperature, geographic location, and population genetic structure. Our findings indicate that the observed variation in metabolic traits among localities does not follow a latitudinal trend or mirror the biogeographic origin of the populations. We found no evidence supporting the role of latitudinal metabolic compensation or local adaptation in metabolism in explaining the distribution of limpets. However, significant differences in these traits among locations were observed, varying among species between sites but showing little to no correlation with the documented genetic structure. This study explores the geographic variation of different phenotypic traits in five Scurria limpet species along the Southeastern Pacific, revealing some significant trait–locality relationships but no correlation with genetic structure.

Aim To understand the origin of the most isolated endemic fish fauna of the Indo‐Pacific, Easter Island (Rapa Nui), and to infer divergence times and colonization routes of the endemic coral reef fish fauna from their closest relatives. Location Easter Island, Pacific Ocean. Methods Samples of ten species were used: six small‐range species endemic to Rapa Nui and Motu Motiro Hiva (Salas y Gómez) (i.e. small‐range endemic species) and four large‐range species endemic to the southern subtropical Pacific (i.e. large‐range endemic species). We present phylogenetic reconstruction results based on mitochondrial (1 to 5) and nuclear (1 to 6) loci to place these endemic species in their respective family phylogenies (8). Using these newly calibrated phylogenetic trees, information of species distributions and geological data, we inferred the divergence times from the closest relatives of these ten endemic fishes, compared biogeographical history estimation models to reconstruct their ancestral geographic ranges, colonization routes and underlying mechanisms of speciation. Results The divergence times (i.e. divergence times from the closest relatives) of all of the small‐range endemics studied were more recent than the age of Rapa Nui and Motu Motiro Hiva; thus, these species can be considered as neoendemics. Biogeographical history estimation models indicated that speciation following a founder‐event is the most likely scenario. In contrast, the divergence estimates of the large‐range endemic species were highly variable. This being said, the divergence times of all species were more recent than the age of the oldest islands within their distributions. Main conclusions Taken together, these results demonstrate that Rapa Nui acts as a cradle of coral reef biodiversity, being responsible for the emergence of small‐range endemic fish species, but also a route of dispersion for several large‐range endemics and as a stepping stone in the diversification of the Myripristis and Pseudolabrus genera. While no common divergence time was recovered for all of the ten endemic species studied here, the common mechanism of speciation following a founder event was recovered for most of the small‐range endemic species.

The arboreal marsupial monito del monte (genus Dromiciops, with two recognized species) is a paradigmatic mammal. It is the sole living representative of the order Microbiotheria, the ancestor lineage of Australian marsupials. Also, this marsupial is the unique frugivorous mammal in the temperate rainforest, being the main seed disperser of several endemic plants of this ecosystem, thus acting as keystone species. Dromiciops is also one of the few hibernating mammals in South America, spending half of the year in a physiological dormancy where metabolism is reduced to 10% of normal levels. This capacity to reduce energy expenditure in winter contrasts with the enormous energy turnover rate they experience in spring and summer. The unique life history strategies of this living Microbiotheria, characterized by an alternation of life in the slow and fast lanes, putatively represent ancestral traits that permitted these cold‐adapted mammals to survive in this environment. Here, we describe the ecological role of this emblematic marsupial, summarizing the ecophysiology of hibernation and sociality, updated phylogeographic relationships, reproductive cycle, trophic relationships, mutualisms, conservation, and threats. This marsupial shows high densities, despite presenting slow reproductive rates, a paradox explained by the unique characteristics of its three‐dimensional habitat. We finally suggest immediate actions to protect these species that may be threatened in the near future due to habitat destruction and climate change. We present a review summarizing the recent advances on the biology of the enigmatic monito del monte, a relict Gondwanan mammal from southern South America.

Monitoring plans using environmental DNA have the potential to offer a standardized and cost‐efficient method to survey biodiversity in aquatic ecosystems. Among these ecosystems, coastal wetlands are key elements that serve as transition zones between marine and freshwater ecosystems and are today the target of many conservation and restoration efforts. In this sense, eDNA monitoring could provide a rapid and efficient tool for studying and generating baseline biodiversity information to guide coastal wetland management programs. Here, we test an eDNA metabarcoding assay as a tool to characterize vertebrate biodiversity in one of the largest coastal wetlands of Chile, the Rio Cruces Wetland, a Ramsar designated site since 1981. We sampled surface water from 49 sites along the entire wetland. Our eDNA approach detected 91genera of vertebrates including amphibians, fishes, mammals, and birds, as well as identified several cryptic, exotic, and endangered species. Our results also indicated that the spatial distribution of eDNA from different species is spatially structured despite the complex hydrodynamics inherent in this wetland due to the influence of daily tidal regimes. For amphibians and fishes, the number of taxa detected with eDNA was higher in the periphery of the wetland, and increased with proximity to the ocean, a pattern consistent with small‐scale spatial sensitivity for some species and eDNA accumulation downstream for others. Birds and mammals showed somewhat more idiosyncratic distributions. Taken together, our results add to the growing body of evidence showing eDNA can serve as a rapid cost‐effective tool to characterize vertebrate communities in protected coastal wetlands, where visual surveys are difficult and animal collections are often prohibited. The use of multiple primer sets is also recommended as it facilitates the detection of ephemeral terrestrial organisms and resident aquatic organisms that make use of these wetlands. We test an eDNA metabarcoding assay as a tool to characterize vertebrate biodiversity in one of the largest coastal wetlands of Chile. We sampled surface water from 49 sites along the entire length of the wetland and detect 91 genera of vertebrates including amphibians, fishes, mammals, and birds. Our results also indicate that the spatial distribution of eDNA from different species is spatially structured, and varies as a function of the proximity to the ocean and distance from the shoreline of this watershed.

The two species of the microbiotheriid marsupial genus Dromiciops (Dromiciops bozinovici: “Panchos's monito del monte” and Dromiciops gliroides: “monito del monte”) exhibit a marked latitudinal genetic differentiation. Nevertheless, it is unclear whether this differentiation results from neutral processes or can be explained, to some extent, by local adaptation to different environmental conditions. Here, we used an SNP panel gathered by Rad‐seq and searched for footprints of local adaptation (putative loci under selection) by exploring genetic associations with environmental variables in the two species of Dromiciops in Chilean and Argentinean populations. We applied three methods for detecting outlier SNPs and two genotype–environment associations approaches to quantify associations between allelic frequencies and environmental variables. Both species display strong genetic structure. D. bozinovici exhibited three distinct genetic groups, marking the first report of such structuring in this species using SNPs. In contrast, D. gliroides displayed four genetic clusters, consistent with previous studies. Both species exhibited an association of their genetic structure with environmental variables. D. bozinovici exhibited significant associations of allelic frequencies with elevation, precipitation during the warmest periods, and seasonality in the thermal regime. For D. gliroides, genetic variation appeared to be associated with more variables than D. bozinovici, including precipitation and temperature‐related variables, isothermality, and elevation. All the outlier SNPs were mapped to the D. gliroides reference genome to explore if they fell within functionally known genes. These results represent a necessary first step toward identifying the genome regions that harbor genes associated with climate adaptations in Dromiciops. Notably, we identified genes involved in various functions, including carbohydrate synthesis (ALG8), muscle and neuronal regulation (MEF2D), and stress responses (PTGES3). Ultimately, this study contributes valuable insights that can inform targeted conservation strategies aimed at preserving the genetic diversity of Dromiciops in the face of environmental challenges. Local adaptation of Dromiciops marsupials.

Coral reef fish larvae are tiny, exceedingly numerous, and hard to track. They are also highly capable, equipped with swimming and sensory abilities that may influence their dispersal trajectories. Despite the importance of larval input to the dynamics of a population, we remain reliant on indirect insights to the processes influencing larval behavior and transport. Here, we used genetic data (300 independent single nucleotide polymorphisms) derived from a light trap sample of a single recruitment event of Dascyllus abudafur in the Red Sea (N = 168 settlers). We analyzed the genetic composition of the larvae and assessed whether kinship among these was significantly different from random as evidence for cohesive dispersal during the larval phase. We used Monte Carlo simulations of similar‐sized recruitment cohorts to compare the expected kinship composition relative to our empirical data. The high number of siblings within the empirical cohort strongly suggests cohesive dispersal among larvae. This work highlights the utility of kinship analysis as a means of inferring dynamics during the pelagic larval phase. Using Monte Carlo simulations and next generation sequencing, we found strong evidence of significantly high presence of siblings within a recruiting cohort of a coral dwelling damselfish, in the Red Sea. To our knowledge our study is the first to assess the significance of kinship among new settlers thus, we provide a pipeline and computational tool to encourage similar future studies. Such information is substantial for the management of marine populations.

Many coral reef fishes display remarkable genetic and phenotypic variation across their geographic ranges. Understanding how historical and contemporary processes have shaped these patterns remains a focal question in evolutionary biology since they reveal how diversity is generated and how it may respond to future environmental change. Here, we compare the population genomics and demographic histories of a commercially and ecologically important coral reef fish, the common coral grouper (Plectropomus leopardus [Lacépède 1802]), across two adjoining regions (the Great Barrier Reef; GBR, and the Coral Sea, Australia) spanning approximately 14 degrees of latitude and 9 degrees of longitude. We analysed 4548 single nucleotide polymorphism (SNP) markers across 11 sites and show that genetic connectivity between regions is low, despite their relative proximity (~100 km) and an absence of any obvious geographic barrier. Inferred demographic histories using 10,479 markers suggest that the Coral Sea population was founded by a small number of GBR individuals and that divergence occurred ~190 kya under a model of isolation with asymmetric migration. We detected population expansions in both regions, but estimates of contemporary effective population sizes were approximately 50% smaller in Coral Sea sites, which also had lower genetic diversity. Our results suggest that P. leopardus in the Coral Sea have experienced a long period of isolation that precedes the recent glacial period (~10–120 kya) and may be vulnerable to localized disturbances due to their relative reliance on local larval replenishment. While it is difficult to determine the underlying events that led to the divergence of the Coral Sea and GBR lineages, we show that even geographically proximate populations of a widely dispersed coral reef fish can have vastly different evolutionary histories.

The genetic diversity of populations is the basis for individual fitness and potential adaptability to environmental changes. The South American fur seal (Arctocephalus australis) is a pinniped species that is widely distributed along the southern cone of South America. However, two distinct populations have evolved: the Northern Pacific/Peruvian population and the Southern Pacific/Atlantic population. One of the main breeding colonies of the Southern Pacific/Atlantic population is located on Guafo Island, in southern Chilean Patagonia. This breeding colony represents the closest reproductive population to the remote Peruvian group. Therefore, our study aimed to determine whether the Guafo colony may potentially facilitate gene flow, contribute new alleles, and increase genetic variability of the Peruvian populations, thereby linking the Northern and Southern Pacific populations for the species. In this study, species‐specific microsatellite markers were developed to genetically characterize Guafo Island's South American fur seal population. Our results confirm that the Guafo colony is a panmictic population with evidence of lack of genetic structure. Further, our results indicate that most individuals are unrelated and that half‐siblings are rare, suggesting that polygyny in this species is less frequent than previously thought. Finally, based on the identification of multiple pairs of full siblings, we also present the first genetic evidence of twins in South American fur seals. These attributes suggest that the Guafo colony is a large, panmictic population, which could act as a potential genetic reservoir, and ultimately assist in linking two genetically distinct populations. Our results suggest that polygyny in South American fur seals is more relaxed than previously thought. Additionally, three full‐sibling pairs were genetically identified within the same breeding season, which is the first genetic support that describes the presence of twins for the species. These and genetic diversity attributes suggest that the colony at Guafo is a panmictic large group, and could potentially favor the connection of the entire Pacific's distribution of the species.

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. Here, we report a novel comparative population genetics study of two parapatric sister marine limpets endemic to the South Eastern Pacific and whose poleward and equatorward range edges intersect in the 30–35°S SEP biogeographic transition zone. We used RADseq to survey thousands of SNPs along with the distribution of both species, including one locality where they overlap. Our results provide evidence of hybridization between species and contrasting patterns of genetic structure between species. These species appear to 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.

Temperate mesophotic reef ecosystems (TMREs) are among the least known marine habitats. Information on their diversity and ecology is geographically and temporally scarce, especially in highly productive large upwelling ecosystems. Lack of information remains an obstacle to understanding the importance of TMREs as habitats, biodiversity reservoirs and their connections with better‐studied shallow reefs. Here, we use environmental DNA (eDNA) from water samples to characterize the community composition of TMREs on the central Chilean coast, generating the first baseline for monitoring the biodiversity of these habitats. We analyzed samples from two depths (30 and 60 m) over four seasons (spring, summer, autumn, and winter) and at two locations approximately 16 km apart. We used a panel of three metabarcodes, two that target all eukaryotes (18S rRNA and mitochondrial COI) and one specifically targeting fishes (16S rRNA). All panels combined encompassed eDNA assigned to 42 phyla, 90 classes, 237 orders, and 402 families. The highest family richness was found for the phyla Arthropoda, Bacillariophyta, and Chordata. Overall, family richness was similar between depths but decreased during summer, a pattern consistent at both locations. Our results indicate that the structure (composition) of the mesophotic communities varied predominantly with seasons. We analyzed further the better‐resolved fish assemblage and compared eDNA with other visual methods at the same locations and depths. We recovered eDNA from 19 genera of fish, six of these have also been observed on towed underwater videos, while 13 were unique to eDNA. We discuss the potential drivers of seasonal differences in community composition and richness. Our results suggest that eDNA can provide valuable insights for monitoring TMRE communities but highlight the necessity of completing reference DNA databases available for this region. Here, environmental DNA (eDNA) was used to characterize temperate mesophotic reef ecosystems (TMREs) along the central Chilean coast, shedding light on their biodiversity. Through eDNA analysis at different depths and seasons, we identified 42 phyla and 237 orders, with Arthropoda, Bacillariophyta, and Chordata being the most diverse. Notably, TMRE community composition varied seasonally, particularly in summer, emphasizing the potential of eDNA for monitoring these ecosystems and the need to enhance reference DNA databases for the region.