Distinctness, phylogenetic relations and biogeography of intertidal mussels (Brachidontes, Mytilidae) from the south-western Atlantic

Rocky shore intertidal communities along the cold- and warm-temperate coasts of the south-western Atlantic are dominated by small mussels of the genus Brachidontes s.l. (Mytilidae), yet the status of species occurring in the region remains unresolved. Taxonomic studies have been based on shell morphology, but high phenotypic variability has led to much confusion. Based on mitochondrial and nuclear genes (COI, 28S rDNA and ITS1) from nine localities in Uruguay and Argentina we confirmed the occurrence of three species in the south-western Atlantic: Brachidontes darwinianus and B. rodriguezii in the warmtemperate and B. purpuratus in the cold-temperate sector. The latter two species coexist in the same beds along the transition zone (41?438S). The phylogeny based on mitochondrial and nuclear genes, indicate an early divergence of B. purpuratus. At the intra-specific level, low genetic differentiation and absence of fossil record for B. purpuratus from the earlier Quaternary marine terraces of Patagonia likely result from a relatively recent (post-LGM) colonization originated from populations in the southeastern Pacific. In the case of B. rodriguezii, by contrast, genetic intraspecific differentiation, a fossil record of phenotypically-related forms going back to the Late Miocene, and phylogenetic position in the COI-based phylogeny, prompts the hypothesis that this species is derived from a local stock with a long history of occurrence in the warm-temperate region of the south-western Atlantic. While intertidal mussel beds from the south-western Atlantic are ecologically similar in appearance, their assembly involves components clearly differentiated in terms of historical biogeography and phylogeny.Fil: Trovant, Berenice. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; ArgentinaFil: Ruzzante, Daniel E.. Dalhousie University Halifax. Department Of Biology. Marine Conservation Genetics; CanadáFil: Basso, Nestor Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; ArgentinaFil: Orensanz, Jose Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentin

Surviving historical Patagonian landscapes and climate: molecular insights from Galaxias maculatus

<p>Abstract</p> <p>Background</p> <p>The dynamic geological and climatic histories of temperate South America have played important roles in shaping the contemporary distributions and genetic diversity of endemic freshwater species. We use mitochondria and nuclear sequence variation to investigate the consequences of mountain barriers and Quaternary glacial cycles for patterns of genetic diversity in the diadromous fish <it>Galaxias maculatus </it>in Patagonia (~300 individuals from 36 locations).</p> <p>Results</p> <p>Contemporary populations of <it>G. maculatus</it>, east and west of the Andes in Patagonia, represent a single monophyletic lineage comprising several well supported groups. Mantel tests using control region data revealed a strong positive relationship when geographic distance was modeled according to a scenario of marine dispersal. (<it>r </it>= 0.69, <it>P = 0.055</it>). By contrast, direct distance between regions was poorly correlated with genetic distance (<it>r </it>= -0.05, <it>P </it>= 0.463). Hierarchical AMOVAs using mtDNA revealed that pooling samples according to historical (pre-LGM) oceanic drainage (Pacific vs. Atlantic) explained approximately four times more variance than pooling them into present-day drainage (15.6% vs. 3.7%). Further <it>post-hoc </it>AMOVA tests revealed additional genetic structure between populations east and west of the Chilean Coastal Cordillera (coastal vs. interior). Overall female effective population size appears to have remained relatively constant until roughly 0.5 Ma when population size rapidly increased several orders of magnitude [100× (60×-190×)] to reach contemporary levels. Maximum likelihood analysis of nuclear alleles revealed a poorly supported gene tree which was paraphyletic with respect to mitochondrial-defined haplogroups.</p> <p>Conclusions</p> <p>First diversifying in the central/north-west region of Patagonia, <it>G. maculatus </it>extended its range into Argentina via the southern coastal regions that join the Pacific and Atlantic oceans. More recent gene flow between northern populations involved the most ancient and most derived lineages, and was likely facilitated by drainage reversal(s) during one or more cooling events of the late Pleistocene. Overall female effective population size represents the end result of a widespread and several hundred-fold increase over approximately 0.5 Ma, spanning several climatic fluctuations of the Pleistocene. The minor influence of glacial cycles on the genetic structure and diversity of <it>G. maculatus </it>likely reflects the access to marine refugia during repeated bouts of global cooling. Evidence of genetic structure that was detected on a finer scale between lakes/rivers is most likely the result of both biological attributes (i.e., resident non-migratory behavior and/or landlocking and natal homing in diadromous populations), and the Coastal Cordillera as a dispersal barrier.</p

Understanding and Estimating Effective Population Size for Practical Application in Marine Species Management

Effective population size (Ne) determines the strength of genetic drift in a population and has long been recognized as an important parameter for evaluating conservation status and threats to genetic health of populations. Specifically, an estimate of Ne is crucial to management because it integrates genetic effects with the life history of the species, allowing for predictions of a population’s current and future viability. Nevertheless, compared with ecological and demographic parameters, Ne has had limited influence on species management, beyond its application in very small populations. Recent developments have substantially improved Ne estimation; however, some obstacles remain for the practical application of Ne estimates. For example, the need to define the spatial and temporal scale of measurement makes the concept complex and sometimes difficult to interpret. We reviewed approaches to estimation of Ne over both long-term and contemporary time frames, clarifying their interpretations with respect to local populations and the global metapopulation. We describe multiple experimental factors affecting robustness of contemporary Ne estimates and suggest that different sampling designs can be combined to compare largely independent measures of Ne for improved confidence in the result. Large populations with moderate gene flow pose the greatest challenges to robust estimation of contemporary Ne and require careful consideration of sampling and analysis to minimize estimator bias. We emphasize the practical utility of estimating Ne by highlighting its relevance to the adaptive potential of a population and describing applications in management of marine populations, where the focus is not always on critically endangered populations. Two cases discussed include the mechanisms generating Ne estimates many orders of magnitude lower than census N in harvested marine fishes and the predicted reduction in Ne from hatchery-based population supplementation

Understanding and Estimating Effective Population Size for Practical Application in Marine Species Management

Effective population size (Ne) determines the strength of genetic drift in a population and has long been recognized as an important parameter for evaluating conservation status and threats to genetic health of populations. Specifically, an estimate of Ne is crucial to management because it integrates genetic effects with the life history of the species, allowing for predictions of a population’s current and future viability. Nevertheless, compared with ecological and demographic parameters, Ne has had limited influence on species management, beyond its application in very small populations. Recent developments have substantially improved Ne estimation; however, some obstacles remain for the practical application of Ne estimates. For example, the need to define the spatial and temporal scale of measurement makes the concept complex and sometimes difficult to interpret. We reviewed approaches to estimation of Ne over both long-term and contemporary time frames, clarifying their interpretations with respect to local populations and the global metapopulation. We describe multiple experimental factors affecting robustness of contemporary Ne estimates and suggest that different sampling designs can be combined to compare largely independent measures of Ne for improved confidence in the result. Large populations with moderate gene flow pose the greatest challenges to robust estimation of contemporary Ne and require careful consideration of sampling and analysis to minimize estimator bias. We emphasize the practical utility of estimating Ne by highlighting its relevance to the adaptive potential of a population and describing applications in management of marine populations, where the focus is not always on critically endangered populations. Two cases discussed include the mechanisms generating Ne estimates many orders of magnitude lower than census N in harvested marine fishes and the predicted reduction in Ne from hatchery-based population supplementation

Validation of close‐kin mark–recapture (CKMR) methods for estimating population abundance

Under embargo until: 2020-06-181. Knowing how many individuals there are in a population is a fundamental problem in the management and conservation of freshwater and marine fish. We compare abundance estimates (census size, Nc) in seven brook trout Salvelinus fontinalis populations using standard mark–recapture (MR) and the close‐kin mark–recapture (CKMR) method. Our purpose is to validate CKMR as a method for estimating population size. 2. Close‐kin mark–recapture is based on the principle that an individual's genotype can be considered a “recapture” of the genotypes of each of its parents. Assuming offspring and parents are sampled independently, the number of parent–offspring pairs (POPs) genetically identified in these samples can be used to estimate abundance. We genotyped (33 microsatellites) and aged c. 2,400 brook trout individuals collected over 5 consecutive years (2014–2018). 3. We provide an alternative interpretation of CKMR in terms of the Lincoln– Petersen estimator in which the parents are considered as tagging the offspring rather than the offspring “recapturing” the parents. 4. Despite various sources of uncertainty, we find close agreement between standard MR abundance estimates obtained through double‐pass electrofishing and CKMR estimates, which require information on age‐specific fecundity, and population‐ and age‐specific survival rates. Population sizes (N) are estimated to range between 300 and 6,000 adult individuals. Our study constitutes the first in situ validation of CKMR and establishes it as a useful method for estimating population size in aquatic systems where assumptions of random sampling and thorough mixing of individuals can be met.acceptedVersio

Geography, environment, and colonization history interact with morph type to shape genomic variation in an Arctic fish

Funding Information: Thanks go to our editor and three anonymous reviewers whose suggestions greatly improved this study. We thank S. Avery, J. Callahan, S. Duffy, S. Hann, L. Pike, R. Solomon, A. Walsh, for assistance with sample collection and fieldwork. We are grateful to X. Dallaire and J.S. Moore for providing samples from Ungava, Bay (HAB) and to L. Bernatchez for his valuable comments on an earlier version of this manuscript. Thanks to Parks Canada for allowing us access to the Torngat Mountains National Park and the Nunatsiavut government for allowing us to collect samples from their lands. Thanks to A. Belay at Mount Sinai Hospital for her help with sequencing, A. Mesmer for help with genotyping, and S. Lehnert for insightful data analysis suggestions. We also thank the Institute for Biodiversity, Ecosystem Science, and Sustainability of the Department of Environment and Conservation of the Government of Labrador and Newfoundland for funding for this project; NSERC for the Strategic Grant STPGP 430198 and Discovery Grant awarded to DER, for the CGS‐D awarded to SJS; the Killam Trust for the Level 2 Izaak awarded to SJS; and the Government of Nova Scotia for the Graduate Scholarship awarded to SJS. Publisher Copyright: © 2023 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.Peer reviewedPublisher PD

Landscape, colonization and life history : their effects on genetic diversity in four sympatric species inhabiting a dendritic system

Funding: Marine Alliance for Science and Technology for Scotland (MASTS), which is funded by the Scottish Funding Council (grant reference HR09011) (O.E.G.).To what degree are patterns of genetic structure in fragmented systems the result of contemporary landscape vs. history? We examined the distribution of genetic diversity as a function of colonization history and contemporary landscape in four fish species inhabiting a hierarchically fragmented, unaltered system, the Kogaluk drainage (Labrador): lake trout, longnose sucker, round whitefish, and lake chub. The footprint of colonization history was still observable in the three species where this issue was examined regardless of the generations since their arrival. ABC analyses suggest colonization took place from the southwest. The species exhibit similar diversity patterns despite different Nes and generation intervals. Contemporary gene flow was largely negligible except for gene flow from a centrally located lake. These results suggest landscape has driven colonization history, which still has influence on genetic structuring. The species are widespread. Understanding how they behave in the pristine Kogaluk provides a baseline against which to evaluate how other anthropogenically perturbed systems are performing. Improved understanding of historical and contemporary processes is required to fully explain diversity patterns in complex metapopulationsPostprintPeer reviewe

Genomic evidence of past and future climate-linked loss in a migratory Arctic fish

Acknowledgements We thank staff of the Newfoundland DFO Salmonids section, Parks Canada, the Nunatsiavut Government, the NunatuKavut Community Council, the Sivunivut Inuit Community Corporation, the Innu Nation, the Labrador Hunting and Fishing Association and fishers for their support, participation and tissue collections and the staff of the Aquatic Biotechnology Lab at the Bedford Institute of Oceanography for DNA extractions. This study was supported by the Ocean Frontier Institute, a Genomics Research and Development Initiative (GRDI) Grant, a Natural Sciences and Engineering Research Council (NSERC) Discovery Grant and Strategic Project Grant to I.R.B., the Weston Family Award for research at the Torngat Mountains Base Camp and an Atlantic Canada Opportunities Agency and Department of Tourism, Culture, Industry and Innovation grant allocated to the Labrador Institute. Author Correction: Layton, K.K.S., Snelgrove, P.V.R., Dempson, J.B. et al. Author Correction: Genomic evidence of past and future climate-linked loss in a migratory Arctic fish. Nat. Clim. Chang. 11, 551 (2021). https://doi.org/10.1038/s41558-021-01023-8Peer reviewedPostprin

Resolving fine-scale population structure and fishery exploitation using sequenced microsatellites in a northern fish

Funding Information Natural Sciences and Engineering Research Council of Canada (NSERC) Strategic Project Atlantic Canada Opportunities Agency and Department of Tourism, Culture, Industry and Innovation grants allocated to the Labrador Institute (MC) Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Genomics Research and Development Initiative (GRDI) Weston Family AwardPeer reviewedPublisher PD