Genetic variation in low elevation Douglas-fir of British Columbia and its relevance to gene conservation

Patterns of variation were studied at 20 isozyme loci in 49 coastal, low-elevation Douglas-fir populations in SW British Columbia and NW Washington State. Several components of variation were estimated for each population including the number of alleles per locus N _a, number of alleles per polymorphic locus N _a(95), inbreeding F, heterozygosity H, and population divergence D. F was near zero indicating nearly complete outcrossing within populations. H was quite high (16%) and in aecord with previous studies of Douglas-fir. D values were low (equivalent to Wrights F _ST of 0.08) indicating levels of gene flow sufficient to largely homogenize populations. The parameters of diversity N _a, N _a(95), H, and D showed little intercorrelation across populations. A homogenous pattern of genetic relationship among populations was shown by the clustering of populations based on their inferred relationship, and by the principal components of the matrix of inferred genetic relationship. Because of the complex nature of gene diversity and the continuous nature of population differentiation in Douglas-fir, it is difficult with isozyme markers to identify specific populations of value for genetic conservation in this species.This paper is dedicated to J.C. Heaman on the occasion of his retirement.     

Genetic variation across species' geographical ranges: the central-marginal hypothesis and beyond

There is growing interest in quantifying genetic population structure across the geographical ranges of species to understand why species might exhibit stable range limits and to assess the conservation value of peripheral populations. However, many assertions regarding peripheral populations rest on the long-standing but poorly tested supposition that peripheral populations exhibit low genetic diversity and greater genetic differentiation as a consequence of smaller effective population size and greater geographical isolation relative to geographically central populations. We reviewed 134 studies representing 115 species that tested for declines in within-population genetic diversity and/or increases in among-population differentiation towards range margins using nuclear molecular genetic markers. On average, 64.2% of studies detected the expected decline in diversity, 70.2% of those that tested for it showed increased differentiation and there was a positive association between these trends. In most cases, however, the difference in genetic diversity between central and peripheral population was not large. Although these results were consistent across plants and animals, strong taxonomic and biogeographical biases in the available studies call for a cautious generalization of these results. Despite the large number of studies testing these simple predictions, very few attempted to test possible mechanisms causing reduced peripheral diversity or increased differentiation. Almost no study incorporated a phylogeographical framework to evaluate historical influences on contemporary genetic patterns. Finally, there has been little effort to test whether these geographical trends in putatively neutral variation at marker loci are reflected by quantitative genetic trait variation, which is likely to influence the adaptive potential of populations across the geographical range.     

Genetic structure and differentiation of the Japanese extremely long-tailed chicken breed (Onagadori), associated with plumage colour variation: suggestions for its management and conservation

The Onagadori is a distinguished chicken breed that is characterized by an extremely long tail in the male. In this breed, three different plumage colour varieties have been developed (black-breasted white, black-breasted red and white) in which the black-breasted white is believed to be the original colour of the Onagadori, based on historical records. To establish a conservation strategy, 176 birds were genotyped for autosomal microsatellites. Significant genetic distinctness was found between the original (black-breasted white) and two derivative varieties ( F _ST = 0.091 and 0.093). At the same time, a Bayesian model-based clustering revealed that the majority of individuals belonging to the black-breasted red and white varieties had an extremely low proportion of the genome shared with the original type (black-breasted white). This suggests that derivative varieties were created by crossing with other breeds, with low introgression of the original-type genome. We propose that the three plumage colour varieties should be treated as separate genetic units in a conservation programme.     

Genetic variation in populations of the endangered fish Ladigesocypris ghigii and its implications for conservation

1. The genetic variation of the endangered freshwater fish Ladigesocypris ghigii, endemic to the island of Rhodes (Greece), was investigated for nine populations, originating from seven different stream systems and a reservoir, both at the mtDNA and nuclear level, in order to suggest conservation actions. 2. Both restriction fragment length polymorphism analysis of five segments of mitochondrial DNA (ND‐5/6, COI and 12S‐16S rRNA) amplified by polymerase chain reaction, and random amplified polymorphic DNA analysis, revealed extremely low levels of intra‐population polymorphism. It is highly likely that the low intra‐population variability is the result of successive bottleneck events evident in shrinkage and expansion of the populations year after year, which may have led to a complete loss of several genotypes and haplotypes, and an increased degree of inbreeding. 3. Inter‐population genetic structuring was high, with fixation of haplotypes within six of the nine populations and fixation of alleles within populations originating from different waterbodies. It is probable that all haplotypes and/or alleles found were initially represented in all populations. However, because of the long time of isolation coupled with successive bottleneck and subsequent genetic drift, common mtDNA haplotypes and alleles among the populations may have become rare or extinct through stochastic lineage loss. 4. Although nucleotide divergence among haplotypes was very shallow, half of the haplotypes recorded (three of six), resulted from nucleotide changes on the 12S–16S rRNA segments, which are the most conserved part of the mitochondrial genome. This fact may indicate that the observed genetic variation did not necessarily result only from the retention of ancestral polymorphism, but may have arisen through mutation and complete lineage sorting over a relatively small number of generations, once the populations had become isolated from one another. 5. Our data suggest that two of the L. ghigii populations may be on independent evolutionary trajectories. Considering that each population appears so far well adapted within each site, all populations should be managed and conserved separately.     

Genetic variation, its assessment and implications to the conservation of seagrasses

In a study of the widespread Australian endemic seagrass Posidonia australis , allozyme analysis identified a wide range in population genetic structure assessed using the multilocus genotype diversity statistic ( D _G). Values of D _G between zero and one were obtained; however, RAPD analysis generally detected higher levels of diversity, where D _G values were all greater than 0.5 ( D _G = 0.67 – 1). Some populations were allozymically monomorphic using allozyme analysis yet were highly polymorphic using RAPD analysis. The differences observed between methods, particularly among allozymically uniform populations, demonstrate the importance of choosing an appropriate method when assessing genotypic diversity. Different methods may reflect different historical aspects of population processes where allozymes reflect broader-scale gene flow and population establishment and DNA fingerprinting methods such as RAPDs may reflect fine-scale local recruitment events and shorter-term population processes. Using either method alone, particularly in genotypically depauperate organisms such as seagrasses and other clonal organisms, will be problematic in assessing their population genetic potential, a parameter being used by conservation managers to decide upon management strategies in rare and endangered organisms. It is recommended that the impact of disturbance assessed using genotypic diversity measures requires more than one technique to provide the most appropriate information for designing subsequent conservation strategies.     

Genetic variation in Holocene bowhead whales from Svalbard

Bowhead whales (Balaena mysticetus) are distributed in the Arctic in five putative stocks. All stocks have been heavily depleted due to centuries of exploitation. In the present study, nucleotide sequence variation of the mitochondrial control region was determined from bone remains of 99 bowhead whales. The bones, 14C dated from recent to more than 50,000 bp, were collected on Svalbard (Spitsbergen) and are expected to relate to ancestors of the today nearly extinct Spitsbergen stock. Fifty-eight haplotypes were found, a few being frequent but many only found in one individual. The most abundant haplotypes of the Spitsbergen stock are the same as those most abundant in the extant Bering-Chukchi-Beaufort (BCB) Seas stock of bowhead whales. Although F(ST) indicates a slight but statistically significant genetic differentiation between the Spitsbergen and the BCB stocks this was not considered informative due to the very high levels of genetic diversity of mitochondrial DNA haplotypes in both bowhead whale stocks. Other measures such as K(ST) also indicated very low genetic differentiation between the two populations. Nucleotide diversity and haplotype diversity showed only minor differences between the Spitsbergen and BCB stocks. The data suggest that the historic Spitsbergen stock--before the severe bottleneck caused by whaling--did not have substantially more genetic variation than the extant BCB stock. The similar haplotypes of the Holocene Svalbard samples and the current BCB stock indicate significant migration between these two stocks and question the current designation of five distinct stocks of bowhead whales in the Arctic.     

Genetic variation and relationships among eight Indian riverine buffalo breeds

Twenty-seven microsatellite loci were used to define genetic variation and relationships among eight Indian riverine buffalo breeds. The total number of alleles ranged from 166 in the Toda breed to 194 each in the Mehsana and the Murrah. Significant departures from the Hardy-Weinberg equilibrium were observed for 26 locus-breed combinations due to heterozygote deficiency. Breed differentiation was analysed by estimation of F(ST) index (values ranging from 0.75% to 6.00%) for various breed combinations. The neighbour-joining tree constructed from chord distances, multidimensional scaling (MDS) display of F(ST) values and Bayesian clustering approach consistently identified the Toda, Jaffarabadi, and Pandharpuri breeds as one lineage each, and the Bhadawari, Nagpuri, Surati, Mehsana and Murrah breeds as admixture. Analysis of molecular variance refuted the earlier classification of these breeds proposed on the basis of morphological and geographical parameters. The Toda buffaloes, reared by a tribe of the same name, represent an endangered breed from the Nilgiri hills in South India. Divergence time of the Toda buffaloes from the other main breeds, calculated from Nei's standard genetic distances based on genotyping data on seven breeds and 20 microsatellite loci, suggested separation of this breed approximately 1800-2700 years ago. The results of the present study will be useful for development of rational breeding and conservation strategies for Indian buffaloes.     

Genetic structure among populations in the endemic Hawaiian Plantago lineage: insights from microsatellite variation

Endemic Hawaiian species in the genus Plantago show considerable morphological and ecological diversity. Despite their variation, a recent phylogenetic analysis based on DNA sequence data showed that the group is monophyletic and that sequence variation among species and morphotypes is low. This lack of sequence polymorphisms resulted in an inability to resolve species and population affinities within the most recently derived clade of this lineage. To assess species boundaries, population genetic structure and interpopulation connectivity among the morphologically and ecologically distinct populations within this clade, genetic variation was examined using eight microsatellite loci. Within‐population genetic diversity was found to be lowest in the Maunaiu, Hawai'i population of the endangered P. hawaiensis, and highest in the large P. pachyphylla population from 'Eke, West Maui. Isolation by distance across the range of populations was detected and indicated restricted dispersal. This result is likely to be attributable to few interisland dispersal events in the evolutionary history of this lineage. Genetic differentiation within islands tended to be higher among populations occurring in contrasting bog and woodland habitats, suggesting ecological barriers to gene flow and the potential role of ecological divergence in population diversification. Overall, these results are consistent with findings from phylogenetic analysis of the entire lineage. Our data bring new insights regarding patterns of dispersal and population genetic structure to this endemic and endangered group of island taxa. As island environments become increasingly fragmented, information of this type has important implications for the successful management of these fragile populations and habitats.     

Genetic variation,population structure and cryptic species within the black mudfish,Neochanna diversus,an endemic galaxiid from New Zealand

To investigate the phylogenetic relationships and geographical structure among landlocked populations of the black mudfish, Neochanna diversus, mitochondrial DNA nucleotide sequence data were sampled from seven populations from the Waikato and Northland regions of New Zealand. The complete D-loop region was sequenced from 70 individuals, with 913 bp from the tRNA-pro end used in population and phylogenetic analysis. A tandem repeat array, which ranged in size up to 200 bp, was found in most populations at the 3′ end of the D-loop that was not able to be aligned for analysis. Of the seven sites sampled, two from Northland exhibited significant sequence divergence from all other sites. There was also a clear distinction among remaining Northland sites and those from the Waikato. An additional 518 bp segment of the 16S region was sequenced from all sites and compared with the other New Zealand mudfish species, N. apoda, N. burrowsius and the Tasmanian mudfish Galaxias (Neochanna) cleaveri using Galaxias maculatus as an outgroup. Both D-loop and 16S sequence data provided strong evidence for a cryptic species of mudfish present in Northland. The significant genetic structure apparent in the black mudfish appears most probably to be attributed to geological conditions during the Pliocene, where peat wetlands became apparent in the Waikato while Northland consisted of disjunct ‘islands’. Conservation and management of these populations must take into account the historical processes that have shaped these patterns of genetic diversity.     

Rapid microsatellite marker development for African mahogany (Khaya senegalensis, Meliaceae) using next-generation sequencing and assessment of its intra-specific genetic diversity

Khaya senegalensis (African mahogany or dry-zone mahogany) is a high-value hardwood timber species with great potential for forest plantations in northern Australia. The species is distributed across the sub-Saharan belt from Senegal to Sudan and Uganda. Because of heavy exploitation and constraints on natural regeneration and sustainable planting, it is now classified as a vulnerable species. Here, we describe the development of microsatellite markers for K. senegalensis using next-generation sequencing to assess its intra-specific diversity across its natural range, which is a key for successful breeding programs and effective conservation management of the species. Next-generation sequencing yielded 93,943 sequences with an average read length of 234 bp. The assembled sequences contained 1030 simple sequence repeats, with primers designed for 522 microsatellite loci. Twenty-one microsatellite loci were tested with 11 showing reliable amplification and polymorphism in K. senegalensis. The 11 novel microsatellites, together with one previously published, were used to assess 73 accessions belonging to the Australian K. senegalensis domestication program, sampled from across the natural range of the species. STRUCTURE analysis shows two major clusters, one comprising mainly accessions from west Africa (Senegal to Benin) and the second based in the far eastern limits of the range in Sudan and Uganda. Higher levels of genetic diversity were found in material from western Africa. This suggests that new seed collections from this region may yield more diverse genotypes than those originating from Sudan and Uganda in eastern Africa.     

Genetic variation in host susceptibility to attack by the mahogany shoot borer, Hypsipyla grandella (Zeller)

1 Attack by shoot borers (Hypsipyla grandella Zeller) is the main factor limiting the cultivation of Cedrela odorata and Swietenia macrophylla, two economically important members of the mahogany family. No viable methods of pest control are currently available. To assess for genetic variation in susceptibility to pest attack, a combined progeny/provenance test of C. odorata and a provenance test of S. macrophylla were established separately at CATIE, Turrialba, Costa Rica, and assessed intensively over an 84-week period. 2 Variation in height growth between provenances was highly significant in both species, provenance means varying by a factor of 2.7 and 1.2 in C. odorata and S. macrophylla, respectively. Cedrela odorata also displayed provenance variation in foliar phenology, as 94.7% of the trees from a ‘wet zone’ provenance remained foliated, whereas > 35% of trees from three ‘dry zone’ provenances abscised their leaves during the dry season. 3 Both species displayed significant genetic variation in susceptibility to shoot borer attack. At the peak of attack during the second year of growth, the effect of provenance was highly significant in both species, the mean number of attacks per tree varying between 0.8–2.4 and 0.6–1.3 in different provenances of C. odorata and S. macrophylla, respectively. A provenance of C. odorata from San Carlos, Costa Rica, displayed consistently lower susceptibility to pest attack, being subjected to fewer attacks during the first year and demonstrating a higher mean height to first point of damage. 4 The nitrogen, total tannin and proanthocyanidin concentration of foliage varied significantly between C. odorata provenances: nitrogen concentration was significantly lower and tannin and proanthocyanidin contents were significantly higher in trees from the San Carlos provenance, Costa Rica. This study therefore suggests that proanthocyanidins may reduce susceptibility of C. odorata to H. grandella, at least during the early period of growth. 5 These results provide support for the development of plant resistance as a strategy for managing shoot borers. In particular, there may be scope for selecting for high foliar proanthocyanidin content and the ability to tolerate attack by vigorous apical growth.     

Genetic variation in Australian Merino sheep

Variation at 22 gene loci was investigated in a flock of Australian Merino sheep using restriction fragment length polymorphism (RFLP) analysis. Polymorphism was observed at 20 loci, including loci for wool keratin, hormone and immunoglobulin light chain genes. Eleven loci yielded unambiguous genotypes suitable for population data analysis. Average heterozygosity, determined from these and two monomorphic loci, was estimated as 0.107 (SE = 0.024). Average heterozygosity excluding all monomorphic data was estimated as 0–377 (SE = 0.031), which is comparable with human RFLP heterozygosities for loci chosen in the same way that we selected sheep loci.     

Genetic variation in Costa Rican populations of the tropical timber species Cedrela odorata L., assessed using RAPDs

Cedrela odorata L. (Spanish cedar), an economically important timber species native to the American tropics, is the focus of increasing conservation concern due to high rates of deforestation within its native range. To assess the extent of the genetic diversity within and between populations of this species, samples were obtained from 10 widely dispersed populations within Costa Rica and analysed for random amplified polymorphic DNA (RAPD) variation. Fourteen 10-mer primers were used to generate 97 polymorphic RAPD bands. Presence/absence data for all bands were subjected to a pairwise genetic distance analysis, according to Jaccard's coefficient, then neighbour-joining cluster analysis was performed on these distances, as was an analysis of molecular variance ( AMOVA ), to assess levels of differentiation between populations and regions, and Shannon's Diversity Index was used to quantify levels of diversity within and between populations. Results indicated highly significant genetic differentiation ( P < 0.004, AMOVA ) between populations originating from the North Pacific and Atlantic/South Pacific regions of Costa Rica, with 35.3% of the total variation attributable to a difference between these areas. Little differentiation was recorded between populations from within the same region ( P = 0.757, AMOVA ), and 65.1% of the total variance was attributable to variation within populations. Estimated values for within-population diversity, calculated as H _pop/ H _sp by means of Shannon's Diversity Index, were found to vary greatly between primers, but the overall within-population component of genetic diversity was 0.45. Possible reasons for the high degree of intraspecific genetic variation within this species are discussed and the implications of these results for the conservation and use of its genetic resources are described.     

Reproductive Strategies Explain Genetic Diversity in Atlantic Salmon, Salmo salar

Synopsis We investigated the relationship between conservation status and genetic variability in European and North American Atlantic salmon, Salmo salar, populations, many of which have suffered severe bottlenecks. A negative north--south cline exists for the status of population conservation in this species. A literature review of genetic variability and demographic parameters of wild Atlantic salmon populations resulted in no statistical associations between population conservation status and genetic variation at enzyme or VNTR loci. We found however, a negative relationship between male parr maturation rates and geographical latitude for both American and European populations. The increase in effective population size due to participation by mature male parr and the increased proportions of these males in smaller (southern) populations could explain the lack of expected relationship between genetic variation and conservation status.     

Genetic variation in five Mediterranean populations of Juniperus phoenicea as revealed by inter-simple sequence repeat (ISSR) markers

BACKGROUND AND AIMS: The assessment of the genetic variability and the identification of isolated populations within a given species represent important information to plan conservation strategies on a genetic basis. In this work, the genetic variability in five natural populations of Juniperus phoenicea, three from Sardinia, one from Cyprus and the last one in the Maritime Alps was analysed by means of ISSRs, on the hypothesis that the latter could have been a refugial one during the last glaciation. METHODS: ISSRs were chosen because of their ability to detect variation without any prior sequence information. The use of three primers yielded 45 reproducible, polymorphic bands, which were utilized to estimate the basic parameters of genetic variability and diversity. KEY RESULTS: All of the populations analysed harboured an adequate amount of genetic variability, with H(S) = 0.1299. The proportion of genetic diversity between populations has been estimated by G(ST) = 0.12. The three Sardinian populations are separated, as tested by AMOVA, from the Cyprus and the continental ones. CONCLUSIONS: The results indicate that geographical isolation has represented a major barrier to gene flow in Juniperus phoenicea. This work represents a first step towards a full genetic characterization of a conifer from the Mediterranean, a world biodiversity hotspot confronted with climate change, and thus contributes towards the planning of genetics-informed conservation strategies.     

Genetic variation and social structure: a case-study from Africa

Understanding the relations between social and biological factors in determining the evolution of human populations is one of the principal aims of bio-anthropological research. The recent introduction of unilinearly transmitted polymorphisms of mitochondrial DNA and Y-chromosome has disclosed new possibilities for the study of bio-cultural evolutionary processes. In this communication, I present a study on the relationships between social structure and genetic variation in sub-Saharan Africa based on published and unpublished mitochondrial and Y-chromosomal data relative to a total of 40 populations. The results obtained reveal a striking difference in the genetic structure of farming (Bantu speakers) and hunting-gathering (Pygmies and Bushmen) populations. To explain this difference, I propose that asymmetric gene flow, polyginy and patrilocality, and hence the socio-cultural factors underlying them, have had an important role in determining and differentiating the genetic structure of sub-Saharan populations. The limits and the implications of this study are discussed.     

Genetic variation at the Me-2 locus in the Atlantic salmon within and between rivers: evidence for its selective maintenance

Spatial variation at the diallelic Me-2 locus in the Atlantic salmon, Salmo salar L., was analysed using data from 95 river basins. Gene diversity was apportioned as follows: 63% within samples, 20% between North America and Europe, 14% between regions within continents and 3% within and among rivers within regions. On both continents the variation between rivers was clinal with latitude and highly correlated with summer temperatures. The correlation was detectable within and between rivers. These correlations strongly suggest that variation at the locus is subject to the direct or indirect effects of natural selection, and that caution is required when interpreting between-location differentiation at the locus as evidence for distinct stocks.     

Microsatellite DNA variation in Bornean orangutans (Pongo pygmaeus)

Orangutans (Pongo pygmaeus) on the islands of Borneo and Sumatra are considered two separate subspecies. However, the genetic relationships between isolated populations on Borneo are not clear. This study determined the extent of variation within the Bornean subspecies of orangutan, using microsatellite DNA analysis. Blood samples were collected from 96 individuals of known origin from East, West and Central Kalimantan. Human microsatellite primer pairs located at human map position D2S141, D4S431, D 11S925, D16S420 and D17S791 were suitable for use in primates. D4S431 appeared monomorphic for all orangutans. In three cases (D2S141 East and West and D16S420 West), a highly significant excess of homozygous allele frequencies was detected, but with other primer pairs no significant difference in allele frequencies occurred. We conclude that the divergence between the different populations on Borneo is less than the variation within the populations. There was also evidence that inbreeding occurred within the populations.     

Genetic variation in a tropical tree species influences the associated epiphytic plant and invertebrate communities in a complex forest ecosystem

Genetic differences among tree species, their hybrids and within tree species are known to influence associated ecological communities and ecosystem processes in areas of limited species diversity. The extent to which this same phenomenon occurs based on genetic variation within a single tree species, in a diverse complex ecosystem such as a tropical forest, is unknown. The level of biodiversity and complexity of the ecosystem may reduce the impact of a single tree species on associated communities. We assessed the influence of within-species genetic variation in the tree Brosimum alicastrum (Moraceae) on associated epiphytic and invertebrate communities in a neotropical rainforest. We found a significant positive association between genetic distance of trees and community difference of the epiphytic plants growing on the tree, the invertebrates living among the leaf litter around the base of the tree, and the invertebrates found on the tree trunk. This means that the more genetically similar trees are host to more similar epiphyte and invertebrate communities. Our work has implications for whole ecosystem conservation management, since maintaining sufficient genetic diversity at the primary producer level will enhance species diversity of other plants and animals.