Comparative phylogeography of the ocean planet Bowen, Brian W.; Gaither, Michelle R.; DiBattista, Joseph D. ...
Proceedings of the National Academy of Sciences - PNAS,
07/2016, Volume:
113, Issue:
29
Journal Article
Peer reviewed
Open access
Understanding how geography, oceanography, and climate have ultimately shaped marine biodiversity requires aligning the distributions of genetic diversity across multiple taxa. Here, we examine ...phylogeographic partitions in the sea against a backdrop of biogeographic provinces defined by taxonomy, endemism, and species composition. The taxonomic identities used to define biogeographic provinces are routinely accompanied by diagnostic genetic differences between sister species, indicating interspecific concordance between biogeography and phylogeography. In cases where individual species are distributed across two or more biogeographic provinces, shifts in genotype frequencies often align with biogeographic boundaries, providing intraspecific concordance between biogeography and phylogeography. Here, we provide examples of comparative phylogeography from (i) tropical seas that host the highest marine biodiversity, (ii) temperate seas with high productivity but volatile coastlines, (iii) migratory marine fauna, and (iv) plankton that are the most abundant eukaryotes on earth. Tropical and temperate zones both show impacts of glacial cycles, the former primarily through changing sea levels, and the latter through coastal habitat disruption. The general concordance between biogeography and phylogeography indicates that the population-level genetic divergences observed between provinces are a starting point for macroevolutionary divergences between species. However, isolation between provinces does not account for all marine biodiversity; the remainder arises through alternative pathways, such as ecological speciation and parapatric (semiisolated) divergences within provinces and biodiversity hotspots.
The origins of agriculture date to about 9000 years, but commercial culture and supplementation of marine populations reach back only a few centuries. Hence, wild populations still play a major role ...in seafood production. Closed culture, stock restorations, sea ranching and stock enhancements of marine fishes and invertebrates have been implemented with various outcomes. A review of the literature indicates that considerable effort has been directed toward culture technologies to maximize production, but scant attention has been given to genetic risks to wild populations. Genetic risks from stock enhancements can be substantial, because of inattention to brood-stock sizes, and because hybridization between hatchery-reared and wild individuals can lower the fitness or lead to the extinction of a natural population. In many cases, small brood-stock sizes have led to the loss of genetic diversity. In some cases, hatchery-reared individuals appear to have replaced, rather than supplemented, wild populations. Here, we outline a responsible approach to managing genetic resources that includes six steps: (1) assess the costs and benefits of a stock restoration or enhancement, (2) set goals and genetic benchmarks, (3) use appropriate brood stock and limit domestication, (4) design release strategies that maximize the effectiveness of supplementation efforts, (5) track individuals after release and (6) minimize genetic impacts on wild populations. Stock supplementation is often viewed as an immediate solution to a stock decline, but should be undertaken as a last resort because of the high cost of implementation and the substantial ecological and genetic risks to wild populations.
The average sizes of Pacific salmon have declined in some areas in the Northeast Pacific over the past few decades, but the extent and geographic distribution of these declines in Alaska is ...uncertain. Here, we used regression analyses to quantify decadal trends in length and age at maturity in ten datasets from commercial harvests, weirs, and spawner abundance surveys of Chinook salmon Oncorhynchus tshawytscha throughout Alaska. We found that on average these fish have become smaller over the past 30 years (~6 generations), because of a decline in the predominant age at maturity and because of a decrease in age-specific length. The proportion of older and larger 4-ocean age fish in the population declined significantly (P < 0.05) in all stocks examined by return year or brood year. Our analyses also indicated that the age-specific lengths of 4-ocean fish (9 of 10 stocks) and of 3-ocean fish (5 of 10 stocks) have declined significantly (P < 0.05). Size-selective harvest may be driving earlier maturation and declines in size, but the evidence is not conclusive, and additional factors, such as ocean conditions or competitive interactions with other species of salmon, may also be responsible. Regardless of the cause, these wide-spread phenotypic shifts influence fecundity and population abundance, and ultimately may put populations and associated fisheries at risk of decline.
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► Critique of Bayesian skyline plots to time population events. ► Signatures of population growth are mis-timed by phylogenetic substitution rate. ► Historical signals are erased by ...population declines during the Last Glacial Maximum. ► Evaluation of the Pacific herring biogeographic hypotheses of J.-X. Liu et al. (2011).
A previous analysis of Pacific herring mitochondrial (mt) DNA with Bayesian skyline plots (BSPs) was interpreted to reflect population growth in the late Pleistocene that was preceded by population stability over several hundred thousand years. Here we use an independent set of mtDNA control region (CR) sequences and simulations to test these hypotheses. The CR haplotype genealogy shows three deeply divided lineages, A, B and C, with divergences ranging from d=1.6% to 1.9% and with similar genetic diversities (h=0.95, 0.96, 0.94; Θπ=0.011, 0.012, 0.014, respectively). Lineage A occurs almost exclusively in the NW Pacific and Bering Sea, but lineages B and C are co-distributed in the Northeastern Pacific. This distribution points to a historical allopatric separation between A and B-C across the North Pacific during Pleistocene glaciations. The origins of B and C are uncertain. One hypothesis invokes long-term isolation of lineage C in the Sea of Cortez, but the present-day lack of geographical segregation from lineage B argues for lineage sorting to explain the deep divergence between B and C. BSPs depict rapid population growth in each lineage, but the timing of this growth is uncertain, because of questions about an appropriate molecular clock calibration. We simulated historical demographies under a Pleistocene climate model using observed genetic parameters. BSPs for these sequences showed rapid population growth after the Last Glacial Maximum (LGM) 18–20kyears ago and a flat population history during previous climate fluctuations. Population declines during the LGM appear to have erased signals of previous population fluctuations.
Systems genetics has begun to tackle the complexity of insulin resistance by capitalising on computational advances to study high-diversity populations. 'Diversity Outbred in Australia (DOz)' is a ...population of genetically unique mice with profound metabolic heterogeneity. We leveraged this variance to explore skeletal muscle's contribution to whole-body insulin action through metabolic phenotyping and skeletal muscle proteomics of 215 DOz mice. Linear modelling identified 553 proteins that associated with whole-body insulin sensitivity (Matsuda Index) including regulators of endocytosis and muscle proteostasis. To enrich for causality, we refined this network by focusing on negatively associated, genetically regulated proteins, resulting in a 76-protein fingerprint of insulin resistance. We sought to perturb this network and restore insulin action with small molecules by integrating the Broad Institute Connectivity Map platform and in vitro assays of insulin action using the Prestwick chemical library. These complementary approaches identified the antibiotic thiostrepton as an insulin resistance reversal agent. Subsequent validation in ex vivo insulin-resistant mouse muscle and palmitate-induced insulin-resistant myotubes demonstrated potent insulin action restoration, potentially via upregulation of glycolysis. This work demonstrates the value of a drug-centric framework to validate systems-level analysis by identifying potential therapeutics for insulin resistance.
Abstract
I had the privilege of being a part of fishery genetics from its start in the 1970s, when protein electrophoresis was first used to identify stocks of commercially important fishes and ...shellfishes. Research questions in fishery genetics have evolved tremendously over the past few decades, as new molecular techniques changed the nature of the questions that could be posed. The development of new DNA methods spurred the development of new theoretical models, new statistical methods and an unending stream of computer programs. These developments have led to conceptual shifts in the understanding of natural populations and how to manage them. Twists and turns in the history of fishery genetics parallel the story of the Red Queen in Lewis Carroll's Through the Looking Glass. I have had to “run in place” during my career to learn new techniques and ideas that, in turn, have been replaced with yet newer ones. However, my personal challenge throughout my career has been to develop “scientific intuition” to find underlying causes in datasets. Even though we now have the ability to sequence entire genomes, it is premature to announce the “end of history” for technical and conceptual advances in fishery genetics.
Abstract
The extent that Pleistocene climate variability promoted speciation has been much debated. Here, we surveyed genetic markers in winged kelp Alaria in the Gulf of Alaska, Northeast Pacific ...Ocean to understand how paleoclimates may have influenced diversity in this kelp. The study included wide geographic sampling over 2800 km and large sample sizes compared to previous studies of this kelp. Mitochondrial 5′-COI (664 bp), plastid rbcL-3′ (740 bp) and 8 microsatellite markers in 16 populations resolved 5 well-defined lineages. COI-rbcL haplotypes were distributed chaotically among populations around the Gulf of Alaska. Principal Coordinates Analysis of microsatellite genotypes grouped plants largely by organellar lineage instead of geography, indicating reproductive isolation among lineages. However, microsatellite markers detected hybrids at 3 sites where lineages co-occurred. Local adaptation on various time scales may be responsible for some genetic differences between populations located along wave-energy and salinity gradients, but the chaotic pattern of variability over hundreds of kilometers is likely due to isolations in northern refugia during Pleistocene ice ages. The range of divergences between populations indicates that episodic glaciations led to the creation of new lineages, but population turnover (local extinctions and recolonizations) limited the formation of new species in the Northeastern Pacific Ocean.
Graphical Abstract
Pacific herring show an abrupt genetic discontinuity in the central North Pacific that represents secondary contact between refuge populations previously isolated during Pleistocene glaciations. ...Paradoxically, high levels of gene flow produce genetic homogeneity among ocean-type populations within each group. Here, we surveyed variability in mtDNA control-region sequences (463 bp) and nine microsatellite loci in Pacific herring from sites across the North Pacific to further explore the nature of the genetic discontinuity around the Alaska Peninsula. Consistent with previous studies, little divergence (Φ(ST) = 0.011) was detected between ocean-type populations of Pacific herring in the North West Pacific, except for a population in the Yellow Sea (Φ(ST) = 0.065). A moderate reduction in genetic diversity for both mtDNA and microsatellites in the Yellow Sea likely reflects founder effects during the last colonization of this sea. Reciprocal monophyly between divergent mtDNA lineages (Φ(ST) = 0.391) across the Alaska Peninsula defines the discontinuity across the North Pacific. However, microsatellites did not show a strong break, as eastern Bering Sea (EBS) herring were more closely related to NE Pacific than to NW Pacific herring. This discordance between mtDNA and microsatellites may be due to microsatellite allelic convergence or to sex-biased dispersal across the secondary contact zone. The sharp discontinuity between Pacific herring populations may be maintained by high-density blocking, competitive exclusion or hybrid inferiority.
To assess the effect of a primary care-based community-links practitioner (CLP) intervention on patients' quality of life and well-being.
Quasi-experimental cluster-randomized controlled trial in ...socioeconomically deprived areas of Glasgow, Scotland. Adult patients (aged 18 years or older) referred to CLPs in 7 intervention practices were compared with a random sample of adult patients from 8 comparison practices at baseline and 9 months.
health-related quality of life (EQ-5D-5L, a standardized measure of self-reported health-related quality of life that assesses 5 dimensions at 5 levels of severity).
well-being (Investigating Choice Experiments for the Preferences of Older People Capability Measure for Adults ICECAP-A), depression (Hospital Anxiety and Depression Scale, Depression HADS-D), anxiety (Hospital Anxiety and Depression Scale, Anxiety HADS-A), and self-reported exercise. Multilevel, multiregression analyses adjusted for baseline differences. Patients were not blinded to the intervention, but outcome analysis was masked.
Data were collected on 288 and 214 (74.3%) patients in the intervention practices at baseline and follow-up, respectively, and on 612 and 561 (92%) patients in the comparison practices. Intention-to-treat analysis found no differences between the 2 groups for any outcome. In subgroup analyses, patients who saw the CLP on 3 or more occasions (45% of those referred) had significant improvements in EQ-5D-5L, HADS-D, HADS-A, and exercise levels. There was a high positive correlation between CLP consultation rates and patient uptake of suggested community resources.
We were unable to prove the effectiveness of referral to CLPs based in primary care in deprived areas for improving patient outcomes. Future efforts to boost uptake and engagement could improve overall outcomes, although the apparent improvements in those who regularly saw the CLPs may be due to reverse causality. Further research is needed before wide-scale deployment of this approach.
Geographic surveys of allozymes, microsatellites, nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) have detected several genetic subdivisions among European anchovy populations. However, these ...studies have been limited in their power to detect some aspects of population structure by the use of a single or a few molecular markers, or by limited geographic sampling. We use a multi-marker approach, 47 nDNA and 15 mtDNA single nucleotide polymorphisms (SNPs), to analyze 626 European anchovies from the whole range of the species to resolve shallow and deep levels of population structure. Nuclear SNPs define 10 genetic entities within two larger genetically distinctive groups associated with oceanic variables and different life-history traits. MtDNA SNPs define two deep phylogroups that reflect ancient dispersals and colonizations. These markers define two ecological groups. One major group of Iberian-Atlantic populations is associated with upwelling areas on narrow continental shelves and includes populations spawning and overwintering in coastal areas. A second major group includes northern populations in the North East (NE) Atlantic (including the Bay of Biscay) and the Mediterranean and is associated with wide continental shelves with local larval retention currents. This group tends to spawn and overwinter in oceanic areas. These two groups encompass ten populations that differ from previously defined management stocks in the Alboran Sea, Iberian-Atlantic and Bay of Biscay regions. In addition, a new North Sea-English Channel stock is defined. SNPs indicate that some populations in the Bay of Biscay are genetically closer to North Western (NW) Mediterranean populations than to other populations in the NE Atlantic, likely due to colonizations of the Bay of Biscay and NW Mediterranean by migrants from a common ancestral population. Northern NE Atlantic populations were subsequently established by migrants from the Bay of Biscay. Populations along the Iberian-Atlantic coast appear to have been founded by secondary waves of migrants from a southern refuge.
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