Extremely low genetic diversity and extensive genetic admixture at the northern range margins of Bombax ceiba

Understanding the evolutionary processes in species at the margins of their range is of great significance, because marginal populations may harbor local adaptations and will initiate further expansion in response to changes in the environment. Here we examined genetic variation in two nuclear genes and one chloroplast intergenic spacer in 13 northern marginal populations and one geographically central population of Bombax ceiba, a tree distributed mainly in tropical regions. Our results revealed an extremely low level of genetic diversity in each population at the northern margin of its range and strong genetic differentiation between southern China and South Asia. Cultivated and natural populations showed no significant differences in genetic variability. Genetic admixture in a nuclear gene was detected in 10 of the 13 populations at the northern margin of their range. The founder effect, in which a small number of individuals colonize the northern margins of its range, may explain the extremely low genetic diversity. During the establishment of new populations, different source populations may mix and undergo further genetic drift and differentiation. This study indicates that patterns of genetic diversity in tropical species at the margin of their range may also be severely influenced by founder effects.     

Evidence of two genetic clusters of manatees with low genetic diversity in Mexico and implications for their conservation

The Antillean manatee (Trichechus manatus manatus) occupies the tropical coastal waters of the Greater Antilles and Caribbean, extending from Mexico along Central and South America to Brazil. Historically, manatees were abundant in Mexico, but hunting during the pre-Columbian period, the Spanish colonization and throughout the history of Mexico, has resulted in the significantly reduced population occupying Mexico today. The genetic structure, using microsatellites, shows the presence of two populations in Mexico: the Gulf of Mexico (GMx) and Chetumal Bay (ChB) on the Caribbean coast, with a zone of admixture in between. Both populations show low genetic diversity (GMx: N_A = 2.69; H_E = 0.41 and ChB: N_A = 3.0; H_E = 0.46). The lower genetic diversity found in the GMx, the largest manatee population in Mexico, is probably due to a combination of a founder effect, as this is the northern range of the sub-species of T. m. manatus, and a bottleneck event. The greater genetic diversity observed along the Caribbean coast, which also has the smallest estimated number of individuals, is possibly due to manatees that come from the GMx and Belize. There is evidence to support limited or unidirectional gene flow between these two important areas. The analyses presented here also suggest minimal evidence of a handful of individual migrants possibly between Florida and Mexico. To address management issues we suggest considering two distinct genetic populations in Mexico, one along the Caribbean coast and one in the riverine systems connected to the GMx.     

High genetic diversity in a small population: the case of Chilean blue whales

It is generally assumed that species with low population sizes have lower genetic diversities than larger populations and vice versa. However, this would not be the case for long‐lived species with long generation times, and which populations have declined due to anthropogenic effects, such as the blue whale (Balaenoptera musculus). This species was intensively decimated globally to near extinction during the 20th century. Along the Chilean coast, it is estimated that at least 4288 blue whales were hunted from an apparently pre‐exploitation population size (k) of a maximum of 6200 individuals (Southeastern Pacific). Thus, here, we describe the mtDNA (control region) and nDNA (microsatellites) diversities of the Chilean blue whale aggregation site in order to verify the expectation of low genetic diversity in small populations. We then compare our findings with other blue whale aggregations in the Southern Hemisphere. Interestingly, although the estimated population size is small compared with the pre‐whaling era, there is still considerable genetic diversity, even after the population crash, both in mitochondrial (N = 46) and nuclear (N = 52) markers (H_d = 0.890 and H_o = 0.692, respectively). Our results suggest that this diversity could be a consequence of the long generation times and the relatively short period of time elapsed since the end of whaling, which has been observed in other heavily‐exploited whale populations. The genetic variability of blue whales on their southern Chile feeding grounds was similar to that found in other Southern Hemisphere blue whale feeding grounds. Our phylogenetic analysis of mtDNA haplotypes does not show extensive differentiation of populations among Southern Hemisphere blue whale feeding grounds. The present study suggests that although levels of genetic diversity are frequently used as estimators of population health, these parameters depend on the biology of the species and should be taken into account in a monitoring framework study to obtain a more complete picture of the conservation status of a population.     

Long-term survival despite low genetic diversity in the critically endangered Madagascar fish-eagle

The critically endangered Madagascar fish-eagle ( Haliaeetus vociferoides ) is considered to be one of the rarest birds of prey globally and at significant risk of extinction. In the most recent census, only 222 adult individuals were recorded with an estimated total breeding population of no more than 100–120 pairs. Here, levels of Madagascar fish-eagle population genetic diversity based on 47 microsatellite loci were compared with its sister species, the African fish-eagle ( Haliaeetus vocifer ), and 16 of these loci were also characterized in the white-tailed eagle ( Haliaeetus albicilla ) and the bald eagle ( Haliaeetus leucocephalus ). Overall, extremely low genetic diversity was observed in the Madagascar fish-eagle compared to other surveyed Haliaeetus species. Determining whether this low diversity is the result of a recent bottleneck or a more historic event has important implications for their conservation. Using a Bayesian coalescent-based method, we show that Madagascar fish-eagles have maintained a small effective population size for hundreds to thousands of years and that its low level of neutral genetic diversity is not the result of a recent bottleneck. Therefore, efforts made to prevent Madagascar fish-eagle extinction should place high priority on maintenance of habitat requirements and reducing direct and indirect human persecution. Given the current rate of deforestation in Madagascar, we further recommend that the population be expanded to occupy a larger geographical distribution. This will help the population persist when exposed to stochastic factors (e.g. climate and disease) that may threaten a species consisting of only 200 adult individuals while inhabiting a rapidly changing landscape.     

High genetic diversity and low differentiation reflect the ecological versatility of the African leopard

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Molecular genetic diversity in populations of the stingless bee Plebeia remota: A case study

Genetic diversity is a major component of the biological diversity of an ecosystem. The survival of a population may be seriously threatened if its genetic diversity values are low. In this work, we measured the genetic diversity of the stingless bee Plebeia remota based on molecular data obtained by analyzing 15 microsatellite loci and sequencing two mitochondrial genes. Population structure and genetic diversity differed depending on the molecular marker analyzed: microsatellites showed low population structure and moderate to high genetic diversity, while mitochondrial DNA (mtDNA) showed high population structure and low diversity in three populations. Queen philopatry and male dispersal behavior are discussed as the main reasons for these findings.     

Ecology: linking species diversity and genetic diversity

Although there is a great deal of interest in the biological diversity of species and of genes, it is only recently that researchers have begun to investigate the processes that exert parallel influences on these different levels of diversity.     

Piecing together the global population puzzle of wandering albatrosses: genetic analysis of the Amsterdam albatross Diomedea amsterdamensis

Wandering albatrosses have been subjected to numerous taxonomic revisions due to discoveries of new species, analyses of morphological data and, more recently, the inclusion of genetic data. The small population of albatrosses (170 individuals including 26 pairs breeding annually) on Amsterdam Island in the Indian Ocean, Diomedea amsterdamensis, has been given species status based on plumage and morphometrics, but genetic data published to date provide weak support and its specific status remains controversial for some authors. We used mitochondrial control region sequence data to elucidate the relationship of the Amsterdam albatross within the wandering albatross complex (Diomedea amsterdamensis, D. antipodensis, D. dabbenena and D. exulans). Three novel haplotypes were present in 35 individuals from Amsterdam Island, and were highly divergent (3.6–7.3%) from haplotypes found in the other three members of the wandering albatross complex. Low levels of genetic variation in Amsterdam albatross likely resulted, at least in part, from a population bottleneck. Geographic isolation in the wandering albatross complex is maintained by high natal philopatry. As Amsterdam Island is the only breeding ground for this critically endangered species, we strongly urge conservation efforts in the area, especially in relation to long line fisheries and other threats such as disease and introduced predators, and it be listed as a distinct species.     

Microsatellite analysis reveals high genetic diversity but low genetic structure in Ethiopian indigenous cattle populations

Ethiopian cattle are under threat from uncontrolled mating practices and are at high risk of becoming genetically homogeneous. Therefore, to evaluate genetic diversity, population structure and degree of admixture, 30 microsatellite markers were genotyped using 351 DNA samples from 10 Ethiopian cattle populations and the Holstein breed. The mean number of alleles per cattle population ranged from 6.93 ± 2.12 in Sheko to 7.50 ± 2.35 in Adwa. The mean observed and expected heterozygosities were 0.674 ± 0.015 and 0.726 ± 0.019 respectively. Ethiopian cattle populations have maintained a high level of within-population genetic differentiation (98.7%), the remainder being accounted for by differentiation among populations (1.3%). A highly significant deficiency in heterozygotes was detected within populations ( F _IS = 0.071; P  <   0.001) and total inbreeding ( F _IT = 0.083; P  <   0.001). The study populations were highly admixed but distinct from pure Bos taurus and Bos indicus breeds. The various levels of admixture and high genetic diversity make Ethiopian cattle populations suitable for future genetic improvement and utilization under a wide range of agro-ecologies in Ethiopia.     

Multilocus genotypic data reveal high genetic diversity and low population genetic structure of Iranian indigenous sheep

Iranian livestock diversity is still largely unexplored, in spite of the interest in the populations historically reared in this country located near the Fertile Crescent, a major livestock domestication centre. In this investigation, the genetic diversity and differentiation of 10 Iranian indigenous fat‐tailed sheep breeds were investigated using 18 microsatellite markers. Iranian breeds were found to host a high level of diversity. This conclusion is substantiated by the large number of alleles observed across loci (average 13.83, range 7–22) and by the high within‐breed expected heterozygosity (average 0.75, range 0.72–0.76). Iranian sheep have a low level of genetic differentiation, as indicated by the analysis of molecular variance, which allocated a very small proportion (1.67%) of total variation to the between‐population component, and by the small fixation index (F_ST = 0.02). Both Bayesian clustering and principal coordinates analysis revealed the absence of a detectable genetic structure. Also, no isolation by distance was observed through comparison of genetic and geographical distances. In spite of high within‐breed variation, signatures of inbreeding were detected by the F_IS indices, which were positive in all and statistically significant in three breeds. Possible factors explaining the patterns observed, such as considerable gene flow and inbreeding probably due to anthropogenic activities in the light of population management and conservation programmes, are discussed.     

Assessing genetic diversity for conservation management: a case study of a threatened reptile

The consequences of inbreeding in small isolated populations are well documented, yet populations are often managed in isolation to avoid irreversibly mixing genetic lineages and to maintain the historic integrity of each population. Three remaining populations of Whitaker's skink ( Cyclodina whitakeri ) in New Zealand, remnants of a once wider distribution, illustrate the conflict between this genetic goal (separate management of populations) with the more tangible and immediate threats of small population size and inbreeding. Middle and Castle Islands harbour populations of C. whitakeri and have been separated from each other and from the mainland for ∼10 000 years. The single mainland population at Pukerua Bay is extremely small, declining and deemed a high priority for management. We sequenced a 550 bp region of mitochondrial DNA (mtDNA,ND2) and genotyped animals from all three populations at 13 microsatellite loci. The population of C. whitakeri at Pukerua Bay showed marked differences from the island populations at both mtDNA (unique, fixed haplotype) and microsatellite loci ( F _ST∼0.20), and private alleles were detected at a high frequency (24% of all alleles). However, we attribute this pattern to an historic genetic gradient coupled with rapid genetic drift. Further, animals in captivity show genetic signatures of both Pukerua Bay and island populations, despite the goal to maintain a pure Pukerua Bay stock. The mixed genetic stock in captivity provides an opportunity for the addition of skinks from Middle Island to evaluate the risks of further population hybridization, including the disruption of potential local adaptation, while mitigating the risks of inbreeding.     

Diet breadth and its relationship with genetic diversity and differentiation: the case of southern beech aphids (Hemiptera: Aphididae)

Herbivorous insect species with narrow diet breadth are expected to be more prone to genetic differentiation than insect species with a wider diet breadth. However, a generalist can behave as a local specialist if a single host-plant species is locally available, while a specialist can eventually behave as a generalist if its preferred host is not available. These problems can be addressed by comparing closely related species differing in diet breadth with overlapping distributions of insect and host populations. In this work, diet breadth, genetic diversity and population differentiation of congeneric aphid species from southern beech forests in Chile were compared. While at the species level no major differences in genetic diversity were found, a general trend towards higher genetic diversity as diet breadth increased was apparent. The aphid species with wider diet breadth, Neuquenaphis edwardsi (Laing), showed the highest genetic diversity, while the specialist Neuquenaphis staryi Quednau & Remaudière showed the lowest. These differences were less distinct when the comparisons were made in the same locality and over the same host. Comparison of allopatric populations indicates that genetic differentiation was higher for the specialists, Neuquenaphis similis Hille Ris Lambers and N. staryi, than for the generalist N. edwardsi. Over the same host at different locations, genetic differentiation among populations of N. edwardsi was higher than among populations of N. similis. The results support the assumption that specialists should show more pronounced genetic structuring than generalists, although the geographical distribution of host plants may be playing an important role.     

Extremely low genetic diversity in the endangered Hawaiian monk seal (Monachus schauinslandi)

Hunted to near extinction in the late 19th century, the endangered and endemic Hawaiian monk seal (Monachus schauinslandi) exhibits low variation at all molecular markers tested to date. Here we confirm extreme paucity of genetic diversity, finding polymorphisms at only 8 of 154 microsatellite loci tested (143 novel species-specific loci, 10 loci from Antarctic seals, and 1 previously characterized locus). This screening revealed unprecedentedly low levels of allelic diversity and heterozygosity (A = 1.1, H(e) = 0.026). Subsequent analyses of 2409 Hawaiian monk seals at the 8 polymorphic loci provide evidence for a bottleneck (P = 0.002), but simulations indicate low genetic diversity (H(e) < 0.09) prior to recorded human influence. There is little indication of contemporary inbreeding (F(IS) = 0.018) or population structure (K = 1 population). Minimal genetic variation did not prevent partial recovery by the late 1950s and may not be driving the current population decline to approximately 1200 seals. Nonetheless, genotyping nearly every individual living during the past 25 years sets a new benchmark for low genetic diversity in an endangered species.     

Human genetic diversity: Lewontin's fallacy

In popular articles that play down the genetical differences among human populations, it is often stated that about 85% of the total genetical variation is due to individual differences within populations and only 15% to differences between populations or ethnic groups. It has therefore been proposed that the division of Homo sapiens into these groups is not justified by the genetic data. This conclusion, due to R.C. Lewontin in 1972, is unwarranted because the argument ignores the fact that most of the information that distinguishes populations is hidden in the correlation structure of the data and not simply in the variation of the individual factors. The underlying logic, which was discussed in the early years of the last century, is here discussed using a simple genetical example.     

smogd: software for the measurement of genetic diversity

Software for the measurement of genetic diversity (SMOGD) is a web-based application for the calculation of the recently proposed genetic diversity indices G'(ST) and D(est) . SMOGD includes bootstrapping functionality for estimating the variance, standard error and confidence intervals of estimated parameters, and SMOGD also generates genetic distance matrices from pairwise comparisons between populations. SMOGD accepts standard, multilocus Genepop and Arlequin formatted input files and produces HTML and tab-delimited output. This allows easy data submission, quick visualization, and rapid import of results into spreadsheet or database programs.     

High genetic diversity with low connectivity among Mauritia flexuosa (Arecaceae) stands from Ecuadorean Amazonia

Mauritia flexuosa dominated palm swamps are an important forest resource covering over 30,000 km² across the Amazon basin. In Ecuadorean Amazonia, Mauritia flexuosa, a dioecious and arborescent palm species, forms small and isolated populations or large and dense stands on poorly drained soils. How these populations are genetically interconnected and how genetic diversity varies between cohorts of different ages remains little studied although they are important for conservation of these ecosystems. The genetic structure of Mauritia flexuosa was studied in five natural stands using eight microsatellite loci and two cohorts (seedling and adults). In addition, age structure and sex ratio within the stands were assessed using transects. The age structure of the studied Mauritia flexuosa stands is represented by a high number of seedlings (mean = 1,153.6/ha) and adults (mean = 563.2/ha), with a sex ratio favoring female individuals (1.42:1). These stands are also characterized by a fine‐scale genetic structure, high observed heterozygosity (mean: H_{O seedlings}=0.52; H_{O adults}=0.52), high inbreeding (mean: F_{IS seedlings} = 0.26; F_{IS adults} = 0.26), low number of migrants (N_m=0.29), strong genetic differentiation (mean: pairwise R_ST/ D‐values _seedlings = 0.08/ 0.74; mean R_ST/D‐values _adults = 0.17/ 0.76), and an average effective population size (N_e) of 191.42 individuals. No intergenerational genetic variation was detected between seedlings and adults. We suggest that the high genetic diversity and inbreeding as well as the strong differentiation among stands of these populations could be explained, at least partially, by a low genetic connectivity among populations. Destructive harvesting of its fruits and defaunation will be major threats to Mauritia flexuosa populations in the future. Abstract in Spanish is available with online material     

Strong founder effects and low genetic diversity in introduced populations of Coqui frogs

The success of non-native species may depend on the genetic resources maintained through the invasion process. The Coqui ( Eleutherodactylus coqui ), a frog endemic to Puerto Rico, was introduced to Hawaii in the late 1980s via the horticulture trade, and has become an aggressive invader. To explore whether genetic diversity and population structure changed with the introduction, we assessed individuals from 15 populations across the Hawaiian Islands and 13 populations across Puerto Rico using six to nine polymorphic microsatellite loci and five dorsolateral colour patterns. Allelic richness ( R _T) and gene diversity were significantly higher in Puerto Rico than in Hawaii populations. Hawaii also had fewer colour patterns (two versus three to five per population) than Puerto Rico. We found no isolation by distance in the introduced range, even though it exists in the native range. Results suggest extensive mixing among frog populations across Hawaii, and that their spread has been facilitated by humans. Like previous research, our results suggest that Hawaiian Coquis were founded by individuals from sites around San Juan, but unlike previous research the colour pattern and molecular genetic data (nuclear and mtDNA) support two separate introductions, one on the island of Hawaii and one on Maui. Coquis are successful invaders in Hawaii despite the loss of genetic variation. Future introductions may increase genetic variation and potentially its range.     

Chick growth in albatrosses: curve fitting with a twist

We present a new type of equation to describe the growth patterns of procellariiform seabirds and other species whose chicks characteristically lose mass towards the end of the rearing period. Our equation is based on the Gompertz curve; our principles are also applicable to logistic and von Bertalanffy curves. From our model, five coefficients can be derived to characterise the patterns of growth. These are: growth rate, peak mass and age at which it is attained, loss rate and an index describing the overall shape of the curve. We illustrate the use of this new equation with data collected, using automated weighing platforms, on six years of chick growth of Black-browed Diomedea melanophris and Grey-headed D. chrysostoma albatrosses at Bird Island, South Georgia. In comparison with Grey-headed Albatross, Black-browed Albatross chicks grow at a faster rate and to a higher peak mass; they also reach their peak mass at an earlier age, and lose mass at a faster rate in the mass recession period. However, in both species, chicks reached peak mass when 72% of the rearing period had elapsed; within species, only this did not vary between years. This new equation not only enables the period of mass recession to be incorporated into growth analysis, but, because it does not require assumptions about asymptotic mass, greatly facilitates inter-species comparisons.