Genetic analyses of marine population structure often find only slight geo- graphic differentiation in species with high dispersal potential. Interpreting the significance of this slight genetic signal has been difficult because even mild genetic structure implies very limited demographic exchange between populations, but slight differentiation could also be due to sampling error. Examination of genetic isolation by distance, in which close populations are more similar than distant ones, has the potential to increase confidence in the significance of slight genetic differentiation. Simulations of one-dimensional stepping stone populations with particular larval dispersal regimes shows that isolation by distance is most obvious when comparing populations separated by 2-5 times the mean larval dispersal distance. Available data on fish and invertebrates can be calibrated with this simulation approach and suggest mean dispersal distances of 25-150 km. Design of marine reserve systems requires an understanding of larval transport in and out of reserves, whether reserves will be self-seeding, whether they will accumulate recruits from surrounding exploited areas, and whether reserve networks can exchange recruits. Direct measurements of mean larval dispersal are needed to understand connectivity in a reserve system, but such measurements are extremely difficult. Genetic patterns of isolation by distance have the potential to add to direct measurement of larval dispersal distance and can help set the appropriate geographic scales on which marine reserve systems will function well.

https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1890/1051-0761%282003%29013%5B0146%3APGDCAT%5D2.0.CO%3B2

Population genetics, demographic connectivity, and the design of marine reserves

https://appliedecology.cals.ncsu.edu/absci/wp-content/uploads/Gilman-et-al2008.pdf

Threats to mangroves from climate change and adaptation options: A review

Larvae have been difficult to study because their small size limits our ability to understand their behavior and the conditions they experience. Questions about larval transport focus largely on (a) where they go [dispersal] and (b) where they come from [connectivity]. Mechanisms of transport have been intensively studied in recent decades. As our ability to identify larval sources develops, the consequences of connectivity are garnering more consideration. Attention to transport and connectivity issues has increased dramatically in the past decade, fueled by changing motivations that now include management of fisheries resources, understanding of the spread of invasive species, conservation through the design of marine reserves, and prediction of climate-change effects. Current progress involves both technological advances and the integration of disciplines and approaches. This review focuses on insights gained from physical modeling, chemical tracking, and genetic approaches. I consider how new findings are motivating paradigm shifts concerning (1) life-history consequences; (2) the openness of marine populations, self-recruitment, and population connectivity; (3) the role of behavior; and (4) the significance of variability in space and time. A challenge for the future will be to integrate methods that address dispersal on short (intragenerational) timescales such as elemental fingerprinting and numerical simulations with those that reflect longer timescales such as gene flow estimates and demographic modeling. Recognition and treatment of the continuum between ecological and evolutionary timescales will be necessary to advance the mechanistic understanding of larval and population dynamics.

/pdf/recent-progress-in-understanding-larval-dispersal-new-4h408zxe1g.pdf

Recent progress in understanding larval dispersal: new directions and digressions

Background Aberrant crypt foci of the colon are possible precursors of adenoma and cancer, but these lesions have been studied mainly in surgical specimens from patients who already had colon cancer. Methods Using magnifying endoscopy, we studied the prevalence, number, size, and dysplastic features of aberrant crypt foci and their distribution according to age in 171 normal subjects, 131 patients with adenoma, and 48 patients with colorectal cancer. We also prospectively examined the prevalence of aberrant crypt foci in 11 subjects (4 normal subjects, 6 with adenoma, and 1 with cancer) before and after the administration of 100 mg of sulindac three times a day for 8 to 12 months and compared the results with those in 9 untreated subjects (4 normal subjects and 5 with adenoma). All 20 subjects had aberrant crypt foci at base line. Results We identified 3155 aberrant crypt foci, 161 of which were dysplastic; the prevalence and number increased with age. There were significant (P<0.001) correlations between...

https://www.nejm.org/doi/pdf/10.1056/NEJM199810293391803

Aberrant Crypt Foci of the Colon as Precursors of Adenoma and Cancer

The tools of molecular genetics have enormous potential for clarifying the nature and age of species boundaries in marine organisms. Below I summarize the genetic implications of various species concepts, and review the results of recent molecular genetic analyses of species boundaries in marine microbes, plants, invertebrates and vertebrates. Excessive lumping, rather than excessive splitting, characterizes the current systematic situation in many groups. Morphologically similar species are often quite distinct genetically, suggesting that conservative systematic traditions or morphological stasis may be involved. Some reproductively isolated taxa exhibit only small levels of genetic differentiation, however. In these cases, large population sizes, slow rates of molecular evolution, and relatively recent origins may contribute to the difficulty in finding fixed genetic markers associated with barriers to gene exchange. The extent to which hybridization blurs species boundaries of marine organisms remains a subject of real disagreement in some groups (e.g. corals). The ages of recently diverged species are largely unknown; many appear to be older than 3 million years, but snails and fishes provide several examples of more recent divergences. Increasingly sophisticated genetic analyses make it easier to distinguish allopatric taxa, but criteria for recognition at the species level are highly inconsistent across studies. Future molecular genetic analyses should help to resolve many of these issues, particularly if coupled with other biological and paleontological approaches.

Molecular genetic analyses of species boundaries in the sea

Unlike populations of many terrestrial species, marine populations often are not separated by obvious, permanent barriers to gene flow. When species have high dispersal potential and few barriers to gene flow, allopatric divergence is slow. Nevertheless, many marine species are of recent origin, even in taxa with high dispersal potential. To understand the relationship between genetic structure and recent species formation in high dispersal taxa, we examined population genetic structure among four species of sea urchins in the tropical Indo-West Pacific that have speciated within the past one to three million years. Despite high potential for gene flow, mtDNA sequence variation among 200 individuals of four species in the urchin genus Echinometra shows a signal of strong geographic effects. These effects include (1) substantial population heterogeneity; (2) lower genetic variation in peripheral populations; and (3) isolation by distance. These geographic patterns are especially strong across scales of 5000-10,000 km, and are weaker over scales of 2500-5000 km. As a result, strong geographic patterns would not have been readily visible except over the wide expanse of the tropical Pacific. Surface currents in the Pacific do not explain patterns of gene flow any better than do patterns of simple spatial proximity. Finally, populations of each species tend to group into large mtDNA regions with similar mtDNA haplotypes, but these regional boundaries are not concordant in different species. These results show that all four species have accumulated mtDNA differences over similar spatial and temporal scales but that the precise geographic pattern of genetic differentiation varies for each species. These geographic patterns appear much less deterministic than in other well-known coastal marine systems and may be driven by chance and historical accident.

https://www.jstor.org/stable/pdfplus/2411203.pdf

Speciation and population genetic structure in tropical pacific sea urchins.

Mechanisms of the antimutagenic action of chlorophyllin (CHL) towards benzo[a]pyrene (BP) were studied in vitro. In the Salmonella assay, CHL inhibited the mutagenic activity of BP in the presence of an S9 activation system and was particularly effective against the direct-acting ultimate carcinogen, benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (BPDE). Spectral studies indicated that the time-dependent hydrolysis of BPDE to tetrols was augmented in the presence of CHL concentrations on the order of 5 μM. Dose-related inhibition of several cytochrome P450-dependent enzyme activities was observed upon addition of CHL to in vitro incubations. Spectral changes for the interaction between CHL and cytochrome P450 indicated that CHL does not bind to the active site of the enzyme, but exerts its inhibitory effect indirectly. This was achieved by inhibiting NADPH-cytochrome P450 reductase (Ki ∼ 120 μM with cytochrome c as substrate), and did not involve lowering of the effective substrate concentration by complex formation with the procarcinogen. It is concluded that the in vitro antimutagenic activity of CHL towards BP involves accelerated degradation of the ultimate carcinogen, with inhibition of carcinogen activation occurring only at high CHL concentrations. The latter mechanism is unlikely to occur in vivo following p.o. administration due to the limited uptake of CHL from the gut, but tissue concentrations may be sufficiently high to cause degradation of BPDE.

Mechanisms of the in vitro antimutagenic action of chlorophyllin against benzo[a]pyrene: Studies of enzyme inhibition, molecular complex formation and degradation of the ultimate carcinogen

Aberrant crypt foci (ACF) are putative peneoplastic lesions that develop after treatment of animals with colon carcinogens, including cooked-meat heterocyclic amines such as 2-amino-3-methylimidazo[4,5-f]quinoline (IQ). Male F344 rats given IQ by gavage on alternating days for 2 wk (130 mg/kg body weight) and killed 12 wk after the final carcinogen dose had an average of 4.4 ACF/colon and an average of 3.2 crypts/focus. The DNA from these ACF was amplified by the polymerase chain reaction and analyzed by 3′-primer mismatch and direct sequencing methods for mutations in the Ki-ras proto-oncogene. Of the 37 IQ-induced ACF screened, three contained a GGT→GAT mutation in codon 12 and one contained a GGC→GCC mutation in codon 13. The approximately 11% frequency of mutation in IQ-induced ACF is within the range of previous ACF studies of azoxymethane, which reported a 7–37% incidence of Ki-ras mutaion. These findings suggest that for both compounds, ras mutations occur during early stages of colorectal tumorigenesis. However, while ras mutations can be detected with increasing frequency in azoxymethane-induced adenomas and carcinomas, they are reportedly absent in IQ-induced colon tumors. Thus, for IQ and related compounds additional factors (possibly increased cell proliferation) may be important in the later stages of colorectal tumorigenesis. © 1995 Wiley-Liss Inc.

Evidence for ras gene mutation in 2-amino-3-methylimidazo[4,5-f]quinoline-induced colonic aberrant crypts in the rat.

Intron sequences from the elongation factor-1α (EF1α) gene from the marine shrimp Penaeus vannamei reveal extensive variation even among inbred populations of hatchery-raised shrimp. Among 44 individuals analyzed, we found 13 alleles varying by up to 7.5% sequence differences, and including several allele-diagnostic insertions and deletions. High heterozygosity contrasts with low genetic variation at allozyme loci, but we observed up to four alleles per individual, suggesting that we have identified two separate, polymorphic loci. We partitioned the observed alleles into two groups representing hypothetical duplicated loci. However, the alleles are so similar to one another that a phylogenetic analysis does not cluster them into monophyletic groupings. A possible explanation is that concerted evolution is acting to homogenize genetic variation among these two putative loci.

Nicholas Tachino

Papers

Speciation and population genetic structure in tropical pacific sea urchins.

Mechanisms of the in vitro antimutagenic action of chlorophyllin against benzo[a]pyrene: Studies of enzyme inhibition, molecular complex formation and degradation of the ultimate carcinogen

Evidence for ras gene mutation in 2-amino-3-methylimidazo[4,5-f]quinoline-induced colonic aberrant crypts in the rat.

Intraspecific Genetic Diversity in the Marine Shrimp Penaeus vannamei: Multiple Polymorphic Elongation Factor-1α Loci Revealed by Intron Sequencing