A Comparative Statistical Analysis of Genetic Distances. II–Confidence Intervals and Tests of Comparison

We present methods for constructing the confidence intervals of the estimations of absolute genetic distance and Nei's minimum and standard genetic distances. Two different estimators of the standard distance are considered: jack-knife and corrected. A Monte-Carlo simulation analysis permitted to choose the best adapted confidence interval type for each distance estimator and for each size of the samples of loci and of gametes, taking into account the magnitude of the estimation value. Simulated true confidence levels showed that the best results are obtained using abolute genetic distance. We also give rules for testing the significance of the difference of two distance estimations. Monte-Carlo simulations were performed in order to obtain the distributions of the difference of two distance estimations under the null hypothesis and consequently the true type I errors of tests. Test powers, obtained by simulation under the alternative hypothesis, also showed the superiority of absolute genetic distance.     

A Comparative Statistical Analysis of Genetic Distances. I - Estimation of Distances and of their Variances: Distribution of the Estimators

We present a Monte-Carlo simulation analysis of the statistical properties of absolute genetic distance and of Nei's minimum and standard genetic distances. The estimation of distances (bias) and of their variances is analysed as well as the distributions of distance and variance estimators, taking into account both gamete and locus samplings. Both of Nei's statistics are non-linear when distances are small and consequently the distributions of their estimators are extremely asymmetrical. It is difficult to find theoretical laws that fit such asymmetrical distributions. Absolute genetic distance is linear and its distributions are better fit by a normal distribution. When distances are medium or large, minimum distance and absolute distance distributions are close to a normal distribution, but those of the standard distance can never be considered as normal. For large distances the jack-knife estimator of the standard distance variance is bad; another standard distance estimator is suggested. Absolute distance, which has the best mathematical properties, is particularly interesting for small distances if the gamete sample size is large, even when the number of loci is small. When both distance and gamete sample size are small, this statistic is biased.     

Nonmetric cranial variation and biological distances between samples of six nontribal populations of India

Sixty-nine nonmetrical morphological variants of the cranium have been studied in six samples of non-tribal, state populations in India, and their incidence reported. Using C.A.B. Smith’s angular transformation of frequencies, the multivariate Thetasquare distances and their respective standard deviations have been presented. On the basis of nonmetrical cranial variation, it is clear that the samples from Uttar Pradesh, Andhra Pradesh and Bihar are closer to each other but distant from Madhya Pradesh, Karnataka and Maharashtra. On the other hand, Karnataka and Maharashtra samples are quite close to each other and both, in turn, are comparatively closer to Madhya Pradesh than to Uttar Pradesh, Andhra Pradesh and Bihar. Madhya Pradesh sample emerges as the most divergent group among the six population samples studied. This, in general, is in conformity with the picture that emerges from various analysis of morphometric and other biological data on various populations of India.     

A preliminary investigation of allozyme genetic variation and population geographical structure in Aphanius fasciatus from Italian brackish-water habitats

A total of 150 individuals from Aphanius fasciatus from coastal brackish-water habitats was analysed by allozyme electrophoresis to collect data on its genetic variation. From 22 enzymes, 43 putative enzyme-coding loci were resolved, 12 of which were polymorphic at P_0·99 level. Only one of the 31 probability tests showed a significant departure from the Hardy-Weinberg equilibrium. Aphanius fasciatus showed low levels of genetic polymorphism, with expected heterozygosity values ranging from 0·027 (S.E.=0·013) to 0·064 ( s.e. =0·023). Nei's genetic distances between populations ranged from 0·002 to 0·042. Weir & Cockerham F -statistics showed high levels of genetic heterogeneity among populations (jackknifed θ=0·302, s.e. =0·045) and estimates of N _m were < 1, indicating restricted gene flow. Significant positive correlation between genetic distance and geographical distance matrices, detected by Mantel's test ( g =1·941; P 0·001), is consistent with the prediction that the species is genetically structured by isolation-by-distance.     

Genetic variation and recent population history of the tropical gar Atractosteus tropicus Gill (Pisces: Lepisosteidae)

The tropical gar Atractosteus tropicus belongs to one of the few extant lineages of early bony fishes. The genetic variation detected both within and among 11 natural populations of A. tropicus in Mesoamerica along with the implications for their recent history are presented. Sequences from cytochrome b (307 bp) and cytochrome oxidase subunit II (607 bp) were used as data sources. Apparently, the populations of this fish have decreased in size because of anthropogenic pressures, such as habitat degradation and destruction. The observed values for nucleotide diversity (0·0016 ± 0·0018) and haplotype diversity (0·477 ± 0·302) suggest low levels of genetic variation. Nonetheless, most of the populations studied are currently in a period of genetic stasis. Recent isolation by distance, reduced gene flow and translocation were inferred as the processes maintaining this stasis. Phylogenetic analyses showed reciprocal monophyly between the haplotypes from Guatemala and the other populations. This, together with the observed genetic variation, suggests that the Guatemalan haplotypes might represent a new species. The haplotypes, other than those from Guatemala, exhibited a geographic pattern consistent with two main reproductive populations, one from the Pacific and the other from the Gulf of Mexico–Caribbean slope of Mesoamerica. Pleistocene glacial and interglacial periods might be responsible for moulding the heterogeneity in the genetic structure observed during this study.     

Mitochondrial DNA variation and genetic population structure of chum salmon Oncorhynchus keta around the Pacific Rim

A survey of mtDNA variation among populations of chum salmon Oncorhynchus keta around the Pacific Rim revealed four large population groups: Rim of the Sea of Japan, the Rim of the Okhotsk Sea and West Bering Sea, North‐west Alaska and Gulf of Alaska. The observed population structure appears to reflect isolation by distance with limited gene flow between regions and larger amounts of gene flow between populations within these four regions.     

Genetic variation in the life‐history traits of Epiphyas postvittana: population structure and local adaptation

The light brown apple moth, Epiphyas postvittana (Walker) shows high intraspecific variability in morphological, physiological, demographic and behavioural characters. To gain insight into the extent of adaptation and evolutionary changes in response to environmental heterogeneity in this species, quantitative genetic analyses of life‐history variation were conducted for two natural populations under two thermal conditions (23°C and 28°C). Paternal half‐sib heritability and genetic correlation in six life‐history traits (i.e. development time, adult body weight, adult lifespan, age at first reproduction, the number of eggs laid during the first 5 days after emergence, and total fecundity) were compared. Significant heritabilities were shown consistently in development time; this is also true for adult body weight, except for the Canberra population at 23°C. However, neither population differences nor the effect of temperature were statistically detectable for any of these heritabilities, confirming the genetically determined flexibility. Positive genetic correlations between development time and adult body weight, and negative genetic correlations between the number of eggs laid during the first 5 days and adult lifespan were present for these populations at both temperatures, indicating the presence of genetic constraints. Pairwise comparisons of genetic correlations revealed the heterogeneity of the two populations and across temperatures. These results suggest that the structure of genetic covariance might have changed significantly during the divergence of natural populations and in response to the alteration of environmental conditions in E. postvittana.     

Mitochondrial DNA-inferred population structure and demographic history of the mitten crab (Eriocheir sensu stricto) found along the coast of mainland China

The mitten crab, Eriocheir sensu stricto , is economically important in East Asia, although it is an invasive species in Europe and North America. Little is known about its population structure and historical demography in its native range, especially along the Pacific coast of China. We collected mitochondrial cytochrome oxidase subunit II and cytochrome  b sequences from 154 individuals distributed in the rivers along the Chinese coast and 15 individuals from Japan. Phylogenetic analysis resulted in three major monophyletic groups: northern China, southern China and Japan. Negligible migration was detected among those groups by coalescent analysis. Hence, we support the recognition of three species: Eriocheir hepuensis in southern China, Eriocheir sinensis in northern China and Eriocheir japonica in Japan. The populations in the middle (the Oujiang and Minjiang Rivers) possess a mixture of haplotypes similar to either the northern or the southern haplotypes. We believe that secondary intergradation as the most likely cause of the clinal variation based on examining the genetic variation in the latitudinal space. The estimated divergence time between E. sinensis and E. hepuensis is 2.24 million years ago (Ma), while the divergence time between E. japonica and E. sinensis is 1.83 Ma. Both are in the late Pliocene, suggesting that land bridges associated with low sea level during that time might have severed as vicariant barriers for speciation. The divergence of the northern population and the 'northern haplotypes' in the middle population was estimated at 0.12 Ma, while the time separating the southern population and the 'southern haplotypes' in the middle populations was estimated as 0.16 Ma, implicating possible secondary contact in the late Pleistocene.     

The effects of selection,drift and genetic variation on life‐history trait divergence among insular populations of natterjack toad,Bufo calamita

Although loss of genetic variation is frequently assumed to be associated with loss of adaptive potential, only few studies have examined adaptation in populations with little genetic variation. On the Swedish west coast, the northern fringe populations of the natterjack toad Bufo calamita inhabit an atypical habitat consisting of offshore rock islands. There are strong among‐population differences in the amount of neutral genetic variation, making this system suitable for studies on mechanisms of trait divergence along a gradient of within‐population genetic variation. In this study, we examined the mechanisms of population divergence using Q_ST–F_ST comparisons and correlations between quantitative and neutral genetic variation. Our results suggest drift or weak stabilizing selection across the six populations included in this study, as indicated by low Q_ST–F_ST values, lack of significant population × temperature interactions and lack of significant differences among the islands in breeding pond size. The six populations included in this study differed in both neutral and quantitative genetic variation. Also, the correlations between neutral and quantitative genetic variation tended to be positive, however, the relatively small number of populations prevents any strong conclusions based on these correlations. Contrary to the majority of Q_ST–F_ST comparisons, our results suggest drift or weak stabilizing selection across the examined populations. Furthermore, the low heritability of fitness‐related traits may limit evolutionary responses in some of the populations.     

Within‐population variation in social strategies characterize the social and mating system of an Australian lizard,Egernia whitii

The lizard genus Egernia has been suggested as an excellent model system for examining the evolution of sociality as it exhibits considerable diversity in social organization both between and within species. To date the majority of work examining the factors responsible for the evolution of sociality within Egernia has advocated a broad scale approach; identifying the social structure of specific species or populations and comparing the degree of sociality between them. However, we argue that significant advancements could also be gained by examining variation in social strategies within populations. Here we integrate a detailed, 3‐year, field‐based examination of social spacing and juvenile dispersal with molecular analyses of paternity to determine the social and mating system of a Tasmanian population of White's skink (Egernia whitii). We show that E. whitii live in small stable family groups consisting of an adult male, his female partner(s), as well as juvenile or sub‐adults individuals. In addition, while the mating system is characterized by considerable genetic monogamy, extra‐pair fertilizations are relatively common, with 34% of litters containing offspring sired by males from outside the social group. We also show that traits related to social organization (social group composition, group size, stability and the level of extra‐pair paternity) vary both between and within individuals. We suggest that ecological factors, such as habitat saturation, quality and availability, play a key role in maintaining between individual variation in social strategies, and that examining these individual level processes will allow us to more clearly understand variation in sociality among species.     

Development and characterization of microsatellite markers to study population genetic diversity of Przewalski's naked carp Gymnocypris przewalskii in China

Two populations of Przewalski's naked carp Gymnocypris przewalskii, 30 individuals per population, were screened for 10 microsatellite loci. Moderate allele variation was found in these loci with two to eight alleles per locus. The expected and observed heterozygosity ranged from 0·019 to 0·805 and from 0·160 to 0·575, respectively.     

Spatial population genetic structure in Trillium grandiflorum: the roles of dispersal, mating, history, and selection

The roles of the various potential ecological and evolutionary causes of spatial population genetic structure (SPGS) cannot in general be inferred from the extant structure alone. However, a stage-specific analysis can provide clues as to the causes of SPGS. We conducted a stage-specific SPGS analysis of a mapped population of about 2000 Trillium grandiflorum (Liliaceae), a long-lived perennial herb. We compared SPGS for juvenile (J), nonreproductive (NR), and reproductive (R) stages. Fisher's exact test showed that genotypes had Hardy-Weinberg frequencies at all loci and stage classes. Allele frequencies did not differ between stages. Bootstrapped 99% confidence intervals (99%CI) indicate that F-statistic values are indistinguishable from zero, (except for a slightly negative FIT for the R stage). Spatial autocorrelation was used to calculate f the average kinship coefficient between individuals within distance intervals. Null hypothesis 99%CIs for f were constructed by repeatedly randomizing genotypic locations. Significant positive fine-scale genetic structure was detected in the R and NR stages, but not in the J stage. This structure was most pronounced in the R stage, and declined by about half in each remaining stage: near-neighbor f = 0.122, 0.065, 0.027, for R, NR, and J, respectively. For R and NR, the near-neighbor f lies outside the null hypothesis 99%CI, indicating kinship at approximately the level of half-sibs and first cousins, respectively. We also simulated the expected SPGS of juveniles post dispersal, based on measured R-stage SPGS, the mating system, and measured pollen and seed dispersal properties. This provides a null hypothesis expectation (as a 99%CI) for the J-stage correlogram, against which to test the likelihood that post-dispersal events have influenced J-stage SPGS. The actual J correlogram lies within the null hypothesis 99%CI for the shortest distance interval and nearly all other distance intervals indicating that the observed low recruitment, random mating and seed dispersal patterns are sufficient to account for the disappearance of SPSG between the R and the J stages. The observed increase in SPGS between J and R stages has two potential explanations: history and local selection. The observed low total allelic diversity is consistent with a past bottleneck: a possible historical explanation. Only a longitudinal stage-specific study of SPGS structure can distinguish between historical events and local selection as causes of increased structure with increasing life history stage.     

Spatial and temporal population genetic variation and structure of Nothotsuga longibracteata (Pinaceae), a relic conifer species endemic to subtropical China

Nothotsuga longibracteata, a relic and endangered conifer species endemic to subtropical China, was studied for examining the spatial-temporal population genetic variation and structure to understand the historical biogeographical processes underlying the present geographical distribution. Ten populations were sampled over the entire natural range of the species for spatial analysis, while three key populations with large population sizes and varied age structure were selected for temporal analyses using both nuclear microsatellites (nSSR) and chloroplast microsatellites (cpSSR). A recent bottleneck was detected in the natural populations of N. longibracteata. The spatial genetic analysis showed significant population genetic differentiation across its total geographical range. Notwithstanding, the temporal genetic analysis revealed that the level of genetic diversity between different age class subpopulations remained constant over time. Eleven refugia of the Last Glacial Maximum were identified, which deserve particular attention for conservation management.     

Insights from life history traits of Risso's dolphins (Grampus griseus) in Taiwanese waters: Shorter body length characterizes northwest Pacific population

Risso's dolphins (Grampus griseus) are widely distributed throughout temperate to tropical pelagic waters of the world and are one of the most frequently encountered cetaceans in eastern Taiwanese coastal waters. Because their life history is poorly known, the goal of this study was to investigate the relationship between age, body length, and sexual maturity of Risso's dolphins in Taiwanese waters. Ninety‐two carcasses of dead‐stranded or fisheries bycaught dolphins (1994–2008) were measured and dissected (total body length, TBL 125–290 cm); sexual maturity was assessed in 33 dolphins; and age was estimated by counting dentinal growth layer groups in routine histologically prepared tooth sections of 28 dolphins. Sexual dimorphism in TBL was not detected. The onset of sexual maturity occurred at 240–255 cm in females and 253–265 cm in males, which was at about 10 yr of age for both sexes. Our stranding, bycatch, and previous boat survey records suggest that Risso's dolphins occur year‐round and likely have a summer‐fall calving season in Taiwanese waters. The similar life history parameters and calving season in dolphins from Taiwanese and Japanese waters suggest a common population in the northwest Pacific, which has a noticeably shorter body length than in other regions.     

Y chromosome haplotype distribution of brown bears (Ursus arctos) in Northern Europe provides insight into population history and recovery

High‐resolution, male‐inherited Y‐chromosomal markers are a useful tool for population genetic analyses of wildlife species, but to date have only been applied in this context to relatively few species besides humans. Using nine Y‐chromosomal STRs and three Y‐chromosomal single nucleotide polymorphism markers (Y‐SNPs), we studied whether male gene flow was important for the recent recovery of the brown bear (Ursus arctos) in Northern Europe, where the species declined dramatically in numbers and geographical distribution during the last centuries but is expanding now. We found 36 haplotypes in 443 male extant brown bears from Sweden, Norway, Finland and northwestern Russia. In 14 individuals from southern Norway from 1780 to 1920, we found two Y chromosome haplotypes present in the extant population as well as four Y chromosome haplotypes not present among the modern samples. Our results suggested major differences in genetic connectivity, diversity and structure between the eastern and the western populations in Northern Europe. In the west, our results indicated that the recovered population originated from only four male lineages, displaying pronounced spatial structuring suggestive of large‐scale population size increase under limited male gene flow within the western subpopulation. In the east, we found a contrasting pattern, with high haplotype diversity and admixture. This first population genetic analysis of male brown bears shows conclusively that male gene flow was not the main force of population recovery.     

Barcoding,population structure,and demographic history of Prodiplosis longifila associated with the Andes

Prodiplosis longifila Gagné (Diptera: Cecidomyiidae) is an insect pest that attacks various types of crops, including tomato, Solanum lycopersicum L. (Solanaceae), a vegetable with substantial economic significance worldwide. Prodiplosis longifila is a widely distributed pest in Colombia, Ecuador, and Peru, countries characterized by the presence of significant geographic barriers like the Andes Mountains. It has been reported that geographic barriers affect the dynamics and genetic differentiation of insect populations. Therefore, the aim of this study was to assess the diversity, genetic structure, and demographic history of P. longifila through the analysis of sequences within the mitochondrial region of cytochrome oxidase I (COI) and rDNA‐ITS2 in 27 populations located in Colombia and Ecuador. Analyses were performed on populations distributed in three geographic groups separated by the presence of the Andes Mountains. A total of 11 haplotypes were identified with the COI gene and only one haplotype in the rDNA‐ITS2 was found. Analyses of population structure and demographic history revealed that there is a structure associated with the Andes, which is reflected in an uneven distribution of the haplotype frequencies between regions, but even so, gene flow between populations was detected which produces low genetic differentiation. Because P. longifila has a short‐range dispersion that determines its territorial nature, it would be expected that other factors are producing the genetic exchange between populations. We suggest that the anthropogenic effect produced by farming practices, such as the use of seedlings as seed, which may carry P. longifila larvae, cause passive dispersal of pest throughout the Andes, particularly in Colombia.     

Forecasting species ranges by statistical estimation of ecological niches and spatial population dynamics

Aim The study and prediction of species–environment relationships is currently mainly based on species distribution models. These purely correlative models neglect spatial population dynamics and assume that species distributions are in equilibrium with their environment. This causes biased estimates of species niches and handicaps forecasts of range dynamics under environmental change. Here we aim to develop an approach that statistically estimates process‐based models of range dynamics from data on species distributions and permits a more comprehensive quantification of forecast uncertainties. Innovation We present an approach for the statistical estimation of process‐based dynamic range models (DRMs) that integrate Hutchinson's niche concept with spatial population dynamics. In a hierarchical Bayesian framework the environmental response of demographic rates, local population dynamics and dispersal are estimated conditional upon each other while accounting for various sources of uncertainty. The method thus: (1) jointly infers species niches and spatiotemporal population dynamics from occurrence and abundance data, and (2) provides fully probabilistic forecasts of future range dynamics under environmental change. In a simulation study, we investigate the performance of DRMs for a variety of scenarios that differ in both ecological dynamics and the data used for model estimation. Main conclusions Our results demonstrate the importance of considering dynamic aspects in the collection and analysis of biodiversity data. In combination with informative data, the presented framework has the potential to markedly improve the quantification of ecological niches, the process‐based understanding of range dynamics and the forecasting of species responses to environmental change. It thereby strengthens links between biogeography, population biology and theoretical and applied ecology.