An integrated system to assess marine extinctions.

More than 20 global marine extinctions and over 700 local extinctions have reportedly occurred during the past 500 years. However, available methods to determine how many of these species can be confidently declared true disappearances tend to be data-demanding, time-consuming, and not applicable to all taxonomic groups or scales of marine extinctions (global [G] and local [L]). We developed an integrated system to assess marine extinctions (ISAME) that can be applied to any taxonomic group at any geographic scale. We applied the ISAME method to 10 case studies to illustrate the possible ways in which the extinction status of marine species can be categorized as unverified, possibly extinct, or extinct. Of the 10 case studies we assessed, the ISAME method concludes that 6 should be categorized as unverified extinctions due to problems with species' identity and lack of reliable evidence supporting their disappearance (periwinkle-Littoraria flammea [G], houting-Coregonus oxyrinchus [G], long-spined urchin-Diadema antillarum [L], smalltooth sawfish-Pristis pectinata [L], and largetooth sawfish-P. pristis [L]). In contrast, ISAME classified the Guadalupe storm-petrel (Oceanodroma macrodactyla [G]) and the lost shark (Carcharhinus obsolerus [G]) as possibly extinct because the available evidence indicates that their extinction is plausible-while the largetooth sawfish [L] and Steller's sea cow (Hydrodamalis gigas [G]) were confirmed to be extinct. Determining whether a marine population or species is actually extinct or still extant is needed to guide conservation efforts and prevent further biodiversity losses.

Multidecadal fluctuations in green turtle hatchling production related to climate variability.

The state of Campeche, Mexico, harbors one of the largest green turtle (Chelonia mydas) rookeries of the Wider Caribbean Region. Since the 1970s, harvesting of this population was common practice, but it has since ceased, and the population is rebounding as a consequence. In this rookery, during the past 37 years (1984-2020), the positive relationship between the annual number of nesting females and the number of hatchlings they produce has revealed a long-term population signal that we postulate could be related to environmental factors. To investigate this relationship more deeply, we adopt a stock-recruitment (SR) approach, which is commonly used in fisheries. Regression analysis methods for the SR relationship, including a dynamic version of the model that incorporates the effect of sea surface temperature, show that the number of recruits produced and the number of hatchlings per unit nester were significantly and inversely correlated with a 26-year cycle of the Atlantic Multidecadal Oscillation (AMO) with a three year lag. A possible explanation for this finding is that environmental conditions during warming periods of the 26-year AMO cycle may negatively affect hatchling production by altering the nest moisture content during the incubation period, and increasing embryonic mortality, while the annual female abundance at nesting beaches may decrease due to trophic effects. The time series of abundance corresponding to other population units of green turtles as well as other species of sea turtles in the Gulf of Mexico present a similar behavior to that evaluated here, suggesting a basin-wide environmental effect.

Complex genetic patterns and distribution limits mediated by native congeners of the worldwide invasive red-eared slider turtle.

Non-native (invasive) species offer a unique opportunity to study the geographical distribution and range limits of species, wherein the evolutionary change driven by interspecific interactions between native and non-native closely related species is a key component. The red-eared slider turtle, Trachemys scripta elegans (TSE), has been introduced and successfully established worldwide. It can coexist with its native congeners T. cataspila, T. venusta and T. taylori in Mexico. We performed comprehensive fieldwork, executed a battery of genetic analyses and applied a novel species distribution modelling approach to evaluate their historical lineage relationships and contemporary population genetic patterns. Our findings support the historical common ancestry between native TSE and non-native (TSEalien ), while also highlighting the genetic differentiation of the exotic lineage. Genetic patterns are associated with their range size/endemism gradient; the microendemic T. taylori showed significant reduced genetic diversity and high differentiation, whereas TSEalien showed the highest diversity and signals of population size expansion. Counter to our expectations, lower naturally occurring distribution overlap and little admixture patterns were found between TSE and its congeners, exhibiting reduced gene flow and clear genetic separation across neighbouring species despite having zones of contact. We demonstrate that these native Trachemys species have distinct climatic niche suitability, probably preventing establishment of and displacement by the TSEalien . Moreover, we found major niche overlap between TSEalien and native species worldwide, supporting our prediction that sites with closer ecological optima to the invasive species have higher establishment risk than those that are closer to the niche-centre of the native species.

Environmental heterogeneity explains coarse-scale ß-diversity of terrestrial vertebrates in Mexico.

We explored the hypothesis that high ß-diversity of terrestrial vertebrates of Mexico is associated with a high environmental heterogeneity (HEH) and identify the drivers of ß-diversity at different spatial scales. We used distribution range maps of 2,513 species of amphibians, reptiles, mammals, and birds occurring in Mexico. We estimated ß-diversity for each taxon at four spatial scales (grid cells of 2°, 1°, 0.5° and 0.25°) using the multiplicative formula of Whittaker ßw. For each spatial scale, we derived 10 variables of environmental heterogeneity among cells based on raw data of temperature, precipitation, elevation, vegetation and soil. We applied conditional autoregressive models (CAR) to identify the drivers of ß-diversity for each taxon at each spatial scale. CARs increased in explanatory power from fine-to-coarse spatial scales in amphibians, reptiles and mammals. The heterogeneity in precipitation including both, coefficient of variation (CV) and range of values (ROV), resulted in the most important drivers of ß-diversity of amphibians; the heterogeneity in temperature (CV) and elevation (ROV) were the most important drivers of ß-diversity for reptiles; the heterogeneity in temperature (ROV) resulted in the most important driver in ß-diversity for mammals. For birds, CARs resulted significant at fine scales (grid cells of 0.5° and 0.25°), and the precipitation (ROV and CV), temperature (ROV), and vegetation (H) and soil (H) were heterogeneity variables retained in the model. We found support for the hypothesis of environmental heterogeneity (HEH) for terrestrial vertebrates at coarse scales (grid cell of 2°). Different variables of heterogeneity, mainly abiotic, were significant for each taxon, reflecting physiological differences among terrestrial vertebrate groups. Our study revealed the importance of mountain areas in the geographic patterns of ß-diversity of terrestrial vertebrates in Mexico. At a coarse scale, specific variables of heterogeneity can be used as a proxy of ß-diversity for amphibians and reptiles.

Would behavioral thermoregulation enable pregnant viviparous tropical lizards to cope with a warmer world?

Sceloporus lizards depend on external heat to achieve their preferred temperature (Tsel ) for performing physiological processes. Evidence both in the field and laboratory indicates that pregnant females of this Genus select body temperatures (Tb ) lower than 34 °C as higher temperatures may be lethal to embryos. Therefore, thermoregulation is crucial for successful embryo development. Given the increase in global air temperature, it is expected that the first compensatory response of species that inhabit tropical climates will be behavioral thermoregulation. We tested whether viviparous Sceloporus formosus group lizards in the wild exhibited differences in thermoregulatory behavior to achieve the known Tsel for developing embryos regardless of local thermal conditions. We quantified field active body temperature, thermoregulatory behavior mechanisms (time of sighting, microhabitat used and basking time) and available microhabitat thermal conditions (i.e. operative temperature) for 10 lizard species during gestation, distributed along an altitudinal gradient. We applied both conventional and phylogenic analyses to explore whether Tb or behavioral thermoregulation could be regulated in response to different thermal conditions. These species showed no significant differences in field Tb during gestation regardless of local thermal conditions. In contrast, they exhibited significant differences in their behavioral thermoregulation associated with local environmental conditions. Based on these observations, the differences in thermoregulatory behavior identified are interpreted as compensatory adjustments to local thermal conditions. We conclude that these species may deal with higher temperatures predicted for the tropics by modulating their thermoregulatory behavior.

Macro-Scale Patterns in Upwelling/Downwelling Activity at North American West Coast.

The seasonal and interannual variability of vertical transport (upwelling/downwelling) has been relatively well studied, mainly for the California Current System, including low-frequency changes and latitudinal heterogeneity. The aim of this work was to identify potentially predictable patterns in upwelling/downwelling activity along the North American west coast and discuss their plausible mechanisms. To this purpose we applied the min/max Autocorrelation Factor technique and time series analysis. We found that spatial co-variation of seawater vertical movements present three dominant low-frequency signals in the range of 33, 19 and 11 years, resembling periodicities of: atmospheric circulation, nodal moon tides and solar activity. Those periodicities might be related to the variability of vertical transport through their influence on dominant wind patterns, the position/intensity of pressure centers and the strength of atmospheric circulation cells (wind stress). The low-frequency signals identified in upwelling/downwelling are coherent with temporal patterns previously reported at the study region: sea surface temperature along the Pacific coast of North America, catch fluctuations of anchovy Engraulis mordax and sardine Sardinops sagax, the Pacific Decadal Oscillation, changes in abundance and distribution of salmon populations, and variations in the position and intensity of the Aleutian low. Since the vertical transport is an oceanographic process with strong biological relevance, the recognition of their spatio-temporal patterns might allow for some reasonable forecasting capacity, potentially useful for marine resources management of the region.

Statistical inference for extinction rates based on last sightings.

Rates of extinction can be estimated from sighting records and are assumed to be implicitly constant by many data analysis methods. However, historical sightings are scarce. Frequently, the only information available for inferring extinction is the date of the last sighting. In this study, we developed a probabilistic model and a corresponding statistical inference procedure based on last sightings. We applied this procedure to data on recent marine extirpations and extinctions, seeking to test the null hypothesis of a constant extinction rate. We found that over the past 500 years extirpations in the ocean have been increasing but at an uncertain rate, whereas a constant rate of global marine extinctions is statistically plausible. The small sample sizes of marine extinction records generate such high uncertainty that different combinations of model inputs can yield different outputs that fit the observed data equally well. Thus, current marine extinction trends may be idiosyncratic.

A prospective cohort study to evaluate peridomestic infection as a determinant of dengue transmission: protocol.

BACKGROUND: Vector control programs, which have focused mainly on the patient house and peridomestic areas around dengue cases, have not produced the expected impact on transmission. This project will evaluate the assumption that the endemic/epidemic transmission of dengue begins around peridomestic vicinities of the primary cases. Its objective is to assess the relationship between symptomatic dengue case exposure and peridomestic infection incidence. METHODS/DESIGN: A prospective cohort study will be conducted (in Tepalcingo and Axochiapan, in the state of Morelos, Mexico), using the state surveillance system for the detection of incident cases. Paired blood specimens will be collected from both the individuals who live with the incident cases and a sample of subjects residing within a 25-meter radius of such cases (exposed cohort), in order to measure dengue-specific antibodies. Other subjects will be selected from areas which have not presented any incident cases within 200 meters, during the two months preceding the sampling (non-exposed cohort). Symptomatic/asymptomatic incident infection will be considered as the dependent variable, exposure to confirmed dengue cases, as the principal variable, and the socio-demographic, environmental and socio-cultural conditions of the subjects, as additional explanatory variables. DISCUSSION: Results indicating a high infection rate among the exposed subjects would justify the application of peridomestic control measures and call for an evaluation of alternate causes for insufficient program impact. On the other hand, a low incidence of peridomestic-infected subjects would support the hypothesis that infection occurs outside the domicile, and would thus explain why the vector control measures applied in the past have exerted such a limited impact on cases incidence rates. The results of the present study may therefore serve to reassess site selection for interventions of this type.

Niches and distributional areas: concepts, methods, and assumptions.

Estimating actual and potential areas of distribution of species via ecological niche modeling has become a very active field of research, yet important conceptual issues in this field remain confused. We argue that conceptual clarity is enhanced by adopting restricted definitions of "niche" that enable operational definitions of basic concepts like fundamental, potential, and realized niches and potential and actual distributional areas. We apply these definitions to the question of niche conservatism, addressing what it is that is conserved and showing with a quantitative example how niche change can be measured. In this example, we display the extremely irregular structure of niche space, arguing that it is an important factor in understanding niche evolution. Many cases of apparently successful models of distributions ignore biotic factors: we suggest explanations to account for this paradox. Finally, relating the probability of observing a species to ecological factors, we address the issue of what objects are actually calculated by different niche modeling algorithms and stress the fact that methods that use only presence data calculate very different quantities than methods that use absence data. We conclude that the results of niche modeling exercises can be interpreted much better if the ecological and mathematical assumptions of the modeling process are made explicit.

Use of approximate inference in an index of completeness of biological inventories.

To assess the completeness of a floristic or faunal inventory, one may use the ratio of the observed number of species to the "true number" of species (C). If the inventory is complete, C =1. The estimate of the true number can be obtained from accumulation curves, nonparametric methods, or other techniques. We devised a simple method for computing confidence intervals (CI) for C and for evaluating the null hypothesis that the inventory is complete. The method is based on the assumptions that an estimate of the variance of the true number of species is known and that the distribution of the estimator of the true number of species is approximately normal. We applied our method to bird inventories in the Balsas Basin of Mexico. The completeness index for subtransects were lower (84.0, 85.4, and 89.9%) than for the whole transect (91.6%) (all significantly different from 100%). Thus, these particular inventories were incomplete at 2 spatial resolutions. Our method of estimating CI for C can be used to estimate species richness obtained from databases of different sites or to test the null hypothesis that an inventory derived from a database is complete.

Measles in Mexico, 1941-2001: interruption of endemic transmission and lessons learned.

In Mexico, measles occurred in a cyclical endemic-epidemic pattern until the early 1970s. Beginning in 1973, routine vaccination augmented by mass vaccination campaigns led to a decrease in the incidence of measles until the 1989-1990 regional pandemic, when the measles attack rate rose to 80 cases per 100000, resulting in 5899 deaths. Since the pandemic, measles elimination efforts in Mexico have resulted in increasing coverage to >95% among children aged 1-6 years with 2 doses of either measles or measles-mumps-rubella vaccine since 1996 and in coverage of 97.6% among children aged 6-10 since 1999. Surveillance data suggest that the transmission of indigenous measles virus was interrupted in 1997. After almost 4 years without measles cases, in April 2000, measles virus was reintroduced into Mexico and 30 laboratory-confirmed cases were reported. Detection of relatively few cases in nonprogrammatic age groups affirms the high immunization coverage and the sensitivity of measles surveillance in Mexico. We conclude that the specific strategies adopted for measles elimination have enabled Mexico to eliminate the endemic transmission of measles.