Whale shark Rhincodon typus strandings in the Gulf of California,Mexico

The present study analyses whale shark Rhincodon typus stranding in the Gulf of California, Mexico, reported by the public, scientists, authorities and artisanal fishermen. A total of 14 strandings were documented during the period 2001–2018. The total length of R. typus ranged from 350–1,102 cm, with a sex ratio of 3.5:1 (males: females). This study highlights potential stranding areas, the need for better stranding protocols to assist R. typus recovery and the importance of samples from dead animals for scientific research.     

Genetic Variation at Exon 2 of the MHC Class II DQB Locus in Blue Whale (Balaenoptera musculus) from the Gulf of California

The genes of the Major Histocompatibility Complex (MHC) play an important role in the vertebrate immune response and are among the most polymorphic genes known in vertebrates. In some marine mammals, MHC genes have been shown to be characterized by low levels of polymorphism compared to terrestrial taxa; this reduction in variation is often explained as a result of lower pathogen pressures in marine habitats. To determine if this same reduction in variation applies to the migratory population of blue whales (Balaenoptera musculus) that occurs in the Gulf of California, we genotyped a 172 bp fragment of exon 2 of the MHC Class II DQB locus for 80 members of this population. Twenty-two putatively functional DQB allotypes were identified, all of which were homologous with DQB sequences from other cetacean species. Up to 5 putative alleles per individual were identified, suggesting that gene duplication has occurred at this locus. Rates of non-synonymous to synonymous substitutions (ω) and maximum likelihood analyses of models of nucleotide variation provided potential evidence of ongoing positive selection at this exon. Phylogenetic analyses of DQB alleles from B. musculus and 16 other species of cetaceans revealed trans-specific conservation of MHC variants, suggesting that selection has acted on this locus over prolonged periods of time. Collectively our findings reveal that immunogenic variation in blue whales is comparable to that in terrestrial mammals, thereby providing no evidence that marine taxa are subject to reduced pathogen-induced selective pressures.     

Horizontal Movements,Migration Patterns,and Population Structure of Whale Sharks in the Gulf of Mexico and Northwestern Caribbean Sea

Whale sharks, Rhincodon typus, aggregate by the hundreds in a summer feeding area off the northeastern Yucatan Peninsula, Mexico, where the Gulf of Mexico meets the Caribbean Sea. The aggregation remains in the nutrient-rich waters off Isla Holbox, Isla Contoy and Isla Mujeres, Quintana Roo for several months in the summer and then dissipates between August and October. Little has been known about where these sharks come from or migrate to after they disperse. From 2003–2012, we used conventional visual tags, photo-identification, and satellite tags to characterize the basic population structure and large-scale horizontal movements of whale sharks that come to this feeding area off Mexico. The aggregation comprised sharks ranging 2.5–10.0 m in total length and included juveniles, subadults, and adults of both sexes, with a male-biased sex ratio (72%). Individual sharks remained in the area for an estimated mean duration of 24–33 days with maximum residency up to about 6 months as determined by photo-identification. After leaving the feeding area the sharks showed horizontal movements in multiple directions throughout the Gulf of Mexico basin, the northwestern Caribbean Sea, and the Straits of Florida. Returns of individual sharks to the Quintana Roo feeding area in subsequent years were common, with some animals returning for six consecutive years. One female shark with an estimated total length of 7.5 m moved at least 7,213 km in 150 days, traveling through the northern Caribbean Sea and across the equator to the South Atlantic Ocean where her satellite tag popped up near the Mid-Atlantic Ridge. We hypothesize this journey to the open waters of the Mid-Atlantic was for reproductive purposes but alternative explanations are considered. The broad movements of whale sharks across multiple political boundaries corroborates genetics data supporting gene flow between geographically distinct areas and underscores the need for management and conservation strategies for this species on a global scale.     

Population Structure of Tundra Swans Wintering in Eastern North America

ABSTRACT Our objective was to determine whether there were subpopulations within the eastern population of tundra swans (Cygnus columbianus columbianus) wintering along the mid-Atlantic coast. Movement rates between regions were substantial enough to result in continual mixing of wintering birds. Thus, we were unable to identify distinct subpopulations based on exclusive use of specific wintering areas. These birds should therefore be monitored, and their harvest managed, as if they were one population.     

Genome-wide Insights into the Patterns and Determinants of Fine-Scale Population Structure in Humans

Studying genomic patterns of human population structure provides important insights into human evolutionary history and the relationship among populations, and it has significant practical implications for disease-gene mapping. Here we describe a principal component (PC)-based approach to studying intracontinental population structure in humans, identify the underlying markers mediating the observed patterns of fine-scale population structure, and infer the predominating evolutionary forces shaping local population structure. We applied this methodology to a data set of 650K SNPs genotyped in 944 unrelated individuals from 52 populations and demonstrate that, although typical PC analyses focus on the top axes of variation, substantial information about population structure is contained in lower-ranked PCs. We identified 18 significant PCs, some of which distinguish individual populations. In addition to visually representing sample clusters in PC biplots, we estimated the set of all SNPs significantly correlated with each of the most informative axes of variation. These polymorphisms, unlike ancestry-informative markers (AIMs), constitute a much larger set of loci that drive genomic signatures of population structure. The genome-wide distribution of these significantly correlated markers can largely be accounted for by the stochastic effects of genetic drift, although significant clustering does occur in genomic regions that have been previously implicated as targets of recent adaptive evolution.     

Fine-Scale Spatial Genetic Structure in Emmer Wheat and the Role of Population Range Position

The extent of spatial genetic structure (SGS) within plant populations depends on seed and pollen dispersal distance, breeding type, level of self-fertilization and effective plant density. Self-fertilizing species with gravity-dispersed seeds are expected to have both small effective population sizes and low pollen movement leading to high genetic structure. Higher SGS can be expected in more patchy and peripheral populations because of lower plant density and population sizes, and lower intensity of gene flow. We tested these predictions analyzing SGS in two core and two peripheral populations of predominantly self-fertilizing emmer wheat. Analysis of SGS with 11 nuclear microsatellites revealed (1) a negative linear relationship between kinship coefficients, calculated for pairs of individuals, and the logarithm of geographical distance between members of the pairs, in all studied populations; and (2) a significant autocorrelation for a distance up to 5 m (core populations) or 20 m (peripheral populations). Pollen flow, estimated from comparison of nuclear and chloroplast variation, was spatially limited, as was seed dispersal. Our results support a hypothesized relationship between SGS intensity and breeding system, the mode of seed dispersal and the population range position (core vs. periphery).     

Structure and Dynamics of Minke Whale Surfacing Patterns in the Gulf of St. Lawrence,Canada

Animal behavioral patterns can help us understand physiological and ecological constraints on animals and its influence on fitness. The surfacing patterns of aquatic air-breathing mammals constitute a behavioral pattern that has evolved as a trade-off between the need to replenish oxygen stores at the surface and the need to conduct other activities underwater. This study aims to better understand the surfacing pattern of a marine top predator, the minke whale (Balaenoptera acutorostrata), by investigating how their dive duration and surfacing pattern changes across their activity range. Activities were classified into resting, traveling, surface feeding and foraging at depth. For each activity, we classified dives into short and long dives and then estimated the temporal dependence between dive types. We found that minke whales modified their surfacing pattern in an activity-specific manner, both by changing the expression of their dives (i.e. density distribution) and the temporal dependence (transition probability) between dive types. As the depth of the prey layer increased between activities, the surfacing pattern of foraging whales became increasingly structured, going from a pattern dominated by long dives, when feeding at the surface, to a pattern where isolated long dives were followed by an increasing number of breaths (i.e. short dives), when the whale was foraging at depth. A similar shift in surfacing pattern occurred when prey handling time (inferred from surface corralling maneuvers) increased for surface feeding whales. The surfacing pattern also differed between feeding and non-feeding whales. Resting whales did not structure their surfacing pattern, while traveling whales did, possibly as a way to minimize cost of transport. Our results also suggest that minke whales might balance their oxygen level over multiple, rather than single, dive cycles.     

Population genetic structure of the round stingray Urobatis halleri (Elasmobranchii: Rajiformes) in southern California and the Gulf of California

The round stingray, Urobatis halleri, is a viviparous elasmobranch that inhabits inshore, benthic habitats ranging from the western U.S.A. to Panama. The population genetic structure of this species was inferred with seven polymorphic microsatellite loci in samples collected at three sites in coastal southern California, one near Santa Catalina Island, California and one in the eastern Gulf of California. Urobatis halleri is relatively common, but little is known of its movement patterns or population structure. Small F_ST values (?0·0017 to 0·0005) suggested little structure among coastal populations of southern and Baja California. The population sampled at Santa Catalina Island, which is separated by a deep‐water channel from the coastal sites, however, was significantly divergent (large F_ST, 0·0251) from the other populations, suggesting low connectivity with coastal populations. The Santa Catalina Island population also had the lowest allele richness and lowest average heterozygosity, suggesting recent population bottlenecks in size.     

Recent Demographic History and Present Fine-Scale Structure in the Northwest Atlantic Leatherback (Dermochelys coriacea) Turtle Population

The leatherback turtle Dermochelys coriacea is the most widely distributed sea turtle species in the world. It exhibits complex life traits: female homing and migration, migrations of juveniles and males that remain poorly known, and a strong climatic influence on resources, breeding success and sex-ratio. It is consequently challenging to understand population dynamics. Leatherbacks are critically endangered, yet the group from the Northwest Atlantic is currently considered to be under lower risk than other populations while hosting some of the largest rookeries. Here, we investigated the genetic diversity and the demographic history of contrasted rookeries from this group, namely two large nesting populations in French Guiana, and a smaller one in the French West Indies. We used 10 microsatellite loci, of which four are newly isolated, and mitochondrial DNA sequences of the control region and cytochrome b. Both mitochondrial and nuclear markers revealed that the Northwest Atlantic stock of leatherbacks derives from a single ancestral origin, but show current genetic structuration at the scale of nesting sites, with the maintenance of migrants amongst rookeries. Low nuclear genetic diversities are related to founder effects that followed consequent bottlenecks during the late Pleistocene/Holocene. Most probably in response to climatic oscillations, with a possible influence of early human hunting, female effective population sizes collapsed from 2 million to 200. Evidence of founder effects and high numbers of migrants make it possible to reconsider the population dynamics of the species, formerly considered as a metapopulation model: we propose a more relaxed island model, which we expect to be a key element in the currently observed recovering of populations. Although these Northwest Atlantic rookeries should be considered as a single evolutionary unit, we stress that local conservation efforts remain necessary since each nesting site hosts part of the genetic diversity and species history.     

鄱阳湖越冬水鸟种群变化动态

鄱阳湖是东亚-澳大利西亚候鸟迁徙路线上重要的越冬地,开展鄱阳湖越冬水鸟种群变化动态研究,对指导鄱阳湖湿地生境管理,尤其是水位管控具有重要意义。2005～2007年的越冬季节,我们对鄱阳湖国家级自然保护区内3个重要湖泊(大湖池、沙湖和梅西湖)的越冬水鸟种群变化动态进行了调查,调查时间为每年10月至次年4月。3年共记录到水鸟53种,隶属于7目13科。3个越冬季节中单个调查日种类的最低值为9种,最高为31种。鄱阳湖越冬水鸟从10月上旬开始出现,在11月份鸟类数量急剧增加,在12月上旬和中旬达到数量峰值,然后开始缓慢减少,至4月初仅有少于1%的鸟类还停留在监测区域。在鄱阳湖要继续深入开展越冬候鸟空间分布动态变化的研究,分析水文节律变化对越冬鸟类生境的潜在影响,并深入研究气候因子与鄱阳湖越冬水鸟迁徙的关系。     

贺兰山岩羊种群结构的季节性变化

2001年3月至2002年2月,每月定期在固定的样线上,采用样线法对贺兰山3929只岩羊种群结构进行调查。小群体是贺兰山岩羊种群的基本特征,全年群平均数为5．5只,独羊全年存在,以雄性成体为主,在雌性群中,母仔群全年稳定,占雌性群的44．0％。岩羊雌性群群体大小平均3．5只,雄性群群体平均4．5只,混合群群体平均8．0只;全年雌性多于雄性,雌性群小于雄性群。群体表现为雌性群群体小,群体数量多;混合群体大,群体数量少。混合群群体大小范围离散,雄性群次之,雌性群群体范围变化最小。全年雌幼比为100：48。雌雄性比全年100：71,其中,2～6月份,雌雄性比为100：130～155;7—12月份,雌雄性比为100：43．68。另外,中还指出3．5～8．5龄雄羊占63．9％,1．5～3．5龄和超过8．5龄老年雄性岩羊所占的百分率明显较少。     

Fine-Scale Spatial Organization Reflects Genetic Structure in Sheep

Preferential spatial associations between related animals have been reported in several species, but whether these relationships extend to fine resolution is largely unknown. Using a novel approach that combined pedigrees and precise geographic locations, we tested the relationship between extremely fine-scale (<3 m) spatial structure and relatedness within a captive flock of domestic female Dorset sheep ( Ovis aries ). Using GPS, we recorded the spatial distribution of individuals while foraging on summer pasture; we compared this to pair-wise coefficients of relatedness (r) and assessed significance of the patterns using Mantel and partial Mantel tests. Population organization was discernible even at this fine spatial resolution. Closely related ewes, especially full- and half-siblings (r ≥ 0.25), formed closer spatial associations than lesser-related and unrelated pairs. The genetic structuring of the flock provides a potential platform for kin selection and suggests that random population organization may not exist even at the finest spatial scales.     

Fine-Scale Ecological and Genetic Population Structure of Two Whitefish (Coregoninae) Species in the Vicinity of Industrial Thermal Emissions

Thermal pollution from industrial processes can have negative impacts on the spawning and development of cold-water fish. Point sources of thermal effluent may need to be managed to avoid affecting discrete populations. Correspondingly, we examined fine-scale ecological and genetic population structure of two whitefish species (Coregonus clupeaformis and Prosopium cylindraceum) on Lake Huron, Canada, in the immediate vicinity of thermal effluent from nuclear power generation. Niche metrics using δ¹³C and δ¹⁵N stable isotopes showed high levels of overlap (48.6 to 94.5%) in resource use by adult fish captured in areas affected by thermal effluent compared to nearby reference locations. Isotopic niche size, a metric of resource use diversity, was 1.3- to 2.8-fold higher than reference values in some thermally affected areas, indicative of fish mixing. Microsatellite analyses of genetic population structure (F_st, STRUCTURE and DAPC) indicated that fish captured at all locations in the vicinity of the power plant were part of a larger population extending beyond the study area. In concert, ecological and genetic markers do not support the presence of an evolutionarily significant unit in the vicinity of the power plant. Thus, future research should focus on the potential impacts of thermal emissions on development and recruitment.     

Fish larvae assemblages in the Gulf of California

The distributional diversity and assemblages of fish larvae in the Gulf of California indicated two main seasonal stages and two transitional periods: in winter, the tropical water mass is confined to the south‐east portion of the mouth of the Gulf and larval fish assemblages are dominated by subtropical and temperate‐subarctic species; in summer; tropical water invades the Gulf and assemblages are dominated by tropical species. Both seasonal stages are separated by transitional periods coinciding with strong latitudinal temperature gradients. During the autumn and spring transitional periods, the Gulf of California splits into three regions: a northern region where temperate and subarctic species spawn from autumn to spring, a southern region dominated by tropical and subtropical species year round and a central region where tropical and temperate assemblages merge. Seasonal changes in the location of the regions, as well as the borders between them, show expansion and contraction of the northern and southern faunas related to the general oceanic circulation patterns during the year.     

甘肃东大山自然保护区夏季岩羊种群的初步调查

2004年7月和8月,通过样线调查、野外直接跟踪观察和瞬间取样的方法,首次对东大山自然保护区的岩羊种群进行了初步调查。东大山自然保护区夏季岩羊以小群为主,在观察到的720只岩羊中,719只组成了50个群,最大群82只,最小群2只,平均为14.38只,2～10只群占总群数的66%;雌性群占30%,雄性群占26%,混合群占44%,整个东大山的岩羊密度为34.8±19.2只/km2;岩羊的雌雄性比为1∶0.63,成年雌体、亚成体和幼体之比是1∶0.4∶0.24。研究结果表明,东大山近几年的狩猎对岩羊的种群并未造成大的影响。     

Fine-Scale Genetic Structure in the United Arab Emirates Reflects Endogamous and Consanguineous Culture,Population History,and Geography

The indigenous population of the United Arab Emirates (UAE) has a unique demographic and cultural history. Its tradition of endogamy and consanguinity is expected to produce genetic homogeneity and partitioning of gene pools while population movements and intercontinental trade are likely to have contributed to genetic diversity. Emiratis and neighboring populations of the Middle East have been underrepresented in the population genetics literature with few studies covering the broader genetic history of the Arabian Peninsula. Here, we genotyped 1,198 individuals from the seven Emirates using 1.7 million markers and by employing haplotype-based algorithms and admixture analyses, we reveal the fine-scale genetic structure of the Emirati population. Shared ancestry and gene flow with neighboring populations display their unique geographic position while increased intra- versus inter-Emirati kinship and sharing of uniparental haplogroups, reflect the endogamous and consanguineous cultural traditions of the Emirates and their tribes.     

Fine-Scale Patterns of Population Stratification Confound Rare Variant Association Tests

Advances in next-generation sequencing technology have enabled systematic exploration of the contribution of rare variation to Mendelian and complex diseases. Although it is well known that population stratification can generate spurious associations with common alleles, its impact on rare variant association methods remains poorly understood. Here, we performed exhaustive coalescent simulations with demographic parameters calibrated from exome sequence data to evaluate the performance of nine rare variant association methods in the presence of fine-scale population structure. We find that all methods have an inflated spurious association rate for parameter values that are consistent with levels of differentiation typical of European populations. For example, at a nominal significance level of 5%, some test statistics have a spurious association rate as high as 40%. Finally, we empirically assess the impact of population stratification in a large data set of 4,298 European American exomes. Our results have important implications for the design, analysis, and interpretation of rare variant genome-wide association studies.     

Seasonal and Geographic Variation of Southern Blue Whale Subspecies in the Indian Ocean

Understanding the seasonal movements and distribution patterns of migratory species over ocean basin scales is vital for appropriate conservation and management measures. However, assessing populations over remote regions is challenging, particularly if they are rare. Blue whales (Balaenoptera musculus spp) are an endangered species found in the Southern and Indian Oceans. Here two recognized subspecies of blue whales and, based on passive acoustic monitoring, four “acoustic populations” occur. Three of these are pygmy blue whale (B.m. brevicauda) populations while the fourth is the Antarctic blue whale (B.m. intermedia). Past whaling catches have dramatically reduced their numbers but recent acoustic recordings show that these oceans are still important habitat for blue whales. Presently little is known about the seasonal movements and degree of overlap of these four populations, particularly in the central Indian Ocean. We examined the geographic and seasonal occurrence of different blue whale acoustic populations using one year of passive acoustic recording from three sites located at different latitudes in the Indian Ocean. The vocalizations of the different blue whale subspecies and acoustic populations were recorded seasonally in different regions. For some call types and locations, there was spatial and temporal overlap, particularly between Antarctic and different pygmy blue whale acoustic populations. Except on the southernmost hydrophone, all three pygmy blue whale acoustic populations were found at different sites or during different seasons, which further suggests that these populations are generally geographically distinct. This unusual blue whale diversity in sub-Antarctic and sub-tropical waters indicates the importance of the area for blue whales in these former whaling grounds.     

Wintering Habitat Model for the North Atlantic Right Whale (Eubalaena glacialis) in the Southeastern United States

The coastal waters off the southeastern United States (SEUS) are a primary wintering ground for the endangered North Atlantic right whale (Eubalaena glacialis), used by calving females along with other adult and juvenile whales. Management actions implemented in this area for the recovery of the right whale population rely on accurate habitat characterization and the ability to predict whale distribution over time. We developed a temporally dynamic habitat model to predict wintering right whale distribution in the SEUS using a generalized additive model framework and aerial survey data from 2003/2004 through 2012/2013. We built upon previous habitat models for right whales in the SEUS and include data from new aerial surveys that extend the spatial coverage of the analysis, particularly in the northern portion of this wintering ground. We summarized whale sightings, survey effort corrected for probability of whale detection, and environmental data at a semimonthly resolution. Consistent with previous studies, sea surface temperature (SST), water depth, and survey year were significant predictors of right whale relative abundance. Additionally, distance to shore, distance to the 22°C SST isotherm, and an interaction between time of year and latitude (to account for the latitudinal migration of whales) were also selected in the analysis presented here. Predictions from the model revealed that the location of preferred habitat differs within and between years in correspondence with variation in environmental conditions. Although cow-calf pairs were rarely sighted in the company of other whales, there was minimal evidence that the preferred habitat of cow-calf pairs was different than that of whale groups without calves at the scale of this study. The results of this updated habitat model can be used to inform management decisions for a migratory species in a dynamic oceanic environment.