Fragmentation and genetic differentiation among subpopulations of the endangered Hawaiian mint Haplostachys haplostachya (Lamiaceae)

Haplostachys haplostachya was at one time a prevalent species in the mid-elevation (1650–1800 m) xerophytic shrubland between Mauna Loa and Mauna Kea on Hawaii. Grazing pressure by feral ungulates, destruction of habitat from military activity, and conversion of forest to pastures have fragmented its range to small subpopulations restricted to several cinder cones and portions of the remaining shrubland. Some subpopulations are still extensive, while others are reduced to 20 or fewer individuals. Genetic analyses using random amplified polymorphic DNA (RAPD) markers demonstrate that plants in subpopulations with a large number of individuals maintain levels of genetic variation similar to the entire population, whereas plants in a small subpopulation at Pu'u Leilani (14 individuals remaining) have reduced levels of variation. Of the 122 loci identified, 54 (44%) were polymorphic. Two large populations showed variation at 45 and 49 loci, but the Pu'u Leilani plants showed variation at only 37 loci. The mean expected heterozygosity ( H ) in this subpopulation was also lower (0.137 vs. 0.163 and 0.154) and genetic differentiation ( G _ST) was higher (0.167 vs. 0.018 and 0.052) than in other subpopulations. An examination of variation indicates that although plants of the three subpopulations are genetically similar, there is evidence of genetic restructuring among the subpopulations. The impact of these results towards conservation efforts of this and other endangered species is discussed.     

Molecular genetic variation following a population crash in the endangered Mauna Kea silversword, Argyroxiphium sandwicense ssp. sandwicense (Asteraceae)

The endangered Mauna Kea silversword, Argyroxiphium sandwicense ssp. sandwicense (Asteraceae), has experienced a severe decline in distribution and abundance because of predation by alien ungulates. The small remnant natural population on the Mauna Kea volcano contains only 46 individuals. By contrast, the Haleakala silversword, A. sandwicense ssp. macrocephalum, consists of a large, vigorous population exceeding 60 000 individuals. Molecular genetic variation in the two populations was assessed using random amplified polymorphic DNA (RAPD) loci. Despite its severe crash in size, the Mauna Kea population did not differ significantly from the Haleakala population in the number of detectably polymorphic loci or in heterozygosity. The lack of substantial reduction in genetic variation, at least as measured with RAPD loci, suggests that the Mauna Kea population may not yet have gone through multiple generations at very small size.     

Microsatellite analysis of a population crash and bottleneck in the Mauna Kea silversword, Argyroxiphium sandwicense ssp. sandwicense (Asteraceae), and its implications for reintroduction

The Mauna Kea silversword, Argyroxiphium sandwicense ssp. sandwicense, has experienced both a severe population crash associated with an increase in alien ungulate populations on Mauna Kea, and a population bottleneck associated with reintroduction. In this paper, we address the genetic consequences of both demographic events using eight microsatellite loci. The population crash was not accompanied by a significant reduction in number of alleles or heterozygosity. However, the population bottleneck was accompanied by significant reductions in observed number of alleles, effective number of alleles, and expected heterozygosity, though not in observed heterozygosity. The effective size of the population bottleneck was calculated using both observed heterozygosities and allele frequency variances. Both methods corroborated the historical census size of the population bottleneck of at most three individuals. The results suggest that: (i) small populations, even those that result from severe reductions in historical population size and extent, are not necessarily genetically depauperate; and (ii) species reintroduction plans need to be conceived and implemented carefully, with due consideration to the genetic impact of sampling for reintroduction.     

Genetic variation in parthenogenetic Caucasian rock lizards of the genus Lacerta (L. dahli, L. armeniaca, L. unisexualis) analyzed by DNA fingerprinting

Multilocus DNA fingerprinting has been used to study the variability of some mini- and microsatellite sequences in parthenogenetic species of Caucasian rock lizards of the genus Lacerta (L. dahli, L. armeniaca and L. unisexualis). We demonstrate that these clonally reproducing lizards possess species-specific DNA fingerprints with a low degree of intra- and interpopulation variation. Mean indices of similarity obtained using M13 DNA, (GACA)4 and (TCC)50 as probes were 0.962 and 0.966 in L. dahli and L. armeniaca, respectively. The mean index of similarity obtained using M 13 and GATA probes in L. unisexualis was estimated to be 0.95. However, despite the high degree of band-sharing, variable DNA fragments were revealed in all populations with the microsatellite probes. An particularly high level of variability was observed for (TCC)n microsatellites in populations of L. unisexualis. In fact TCC-derived DNA fingerprints were close to being individual-specific, with a mean index of similarity of 0.824. Fingerprint analysis of parthenogenetic families of L. armeniaca showed that all maternal fragments were inherited together by the progeny, and no differences in fingerprint patterns were observed. On the other hand, while identical DNA fingerprints were obtained from L. unisexualis families with M13 and (GATA)4 probes, use of the (TCC)50 probe revealed remarkable intrafamily variation in this species. It is assumed that the genetic heterogeneity observed in parthenogenetic populations may be explained, at least in part, by the existence of genetically unstable microsatellite loci. Our data serve to illustrate processes of spontaneous mutagenesis and the initial stages of clonal differentiation in natural populations of the lizard species studied.     

Population estimates of the Endangered Hawaiʻi ʻĀkepa (Loxops coccineus) in different habitats on windward Mauna Loa

Endangered Hawai‘i ?ākepas (Loxops coccineus) are endemic to Hawai‘i island, where they occur in five spatially distinct populations. Data concerning the status and population trends of these unique Hawaiian honeycreepers are crucial for assessing the effectiveness of recovery and management actions. In 2016, we used point‐transect distance sampling to estimate the abundance of Hawai‘i ?ākepas in portions of Hawai‘i Volcanoes National Park (HAVO) and the Ka?ū Forest Reserve (KFR) on Mauna Loa volcano. We then compiled the survey data from four other populations to provide a global population estimate. In our HAVO and KFR study area, we mapped habitat classes to determine the population densities in each habitat. Densities were highest (1.03 birds/ha) in open‐canopy montane ?ōhi?a (Metrosideros polymorpha) woodland. In contrast, densities of the largest ?ākepa population on Mauna Kea volcano were highest in closed‐canopy ?ōhi?a and koa (Acacia koa) forest where the species is dependent on nest cavities in tall (> 15 m), large (> 50‐cm diameter at breast height) trees. We surveyed potential nesting habitat in HAVO and KFR and found only one cavity in the short‐stature montane ?ōhi?a woodland and five cavities in the tall‐stature forest. Differences in densities between the Mauna Kea and Mauna Loa populations suggest that Hawai‘i ?ākepas may exhibit different foraging and nesting behaviors in the two habitats. The estimated overall population density in the HAVO and KFR study area was 0.52 birds/ha, which equates to 3663 (95% CI 1725–6961) birds in their 11,377‐ha population range. We calculated a global population of 16,428 (95% CI 10,065–25,198) birds, which is similar to an estimate of 13,892 (95% CI 10,315–17,469) birds made in 1986. Our results suggest that populations are stable to increasing in the two largest populations, but the three other populations are smaller (range = 77–1443 birds) and trends for those populations are unknown.     

Genetic variability among root voles (Microtus oeconomus) from different geographic regions: populations can be distinguished by DNA fingerprinting

Genetic variability among root voles (Microtus oeconomus [Pallas, 1776]) originating from two distantly separate regions of Norway (Valdres and Finnmark) was studied by DNA fingerprinting using the probes 33.15, 33.6 and M13. All three probes revealed polymorphic, although relatively simple, patterns. DNA fingerprint banding patterns were clearly diagnostic of the animals' region of origin. Notably, Valdres animals display a high molecular-weight cluster of bands not found in Finnmark, reflective of the isolation, and possibly an indication of separate colonization events, of the two groups. On the local level in Finnmark, bands associating with a specific trap site were observed in trappings on consecutive years. Comparisons of Finnmark animals taken at three trap sites at approximately 10 km intervals show a gradient of genetic similarity. Captive bred siblings were also compared, yielding average values significantly higher than those seen from same-site comparisons. We suggest that the sensitivity provided by DNA fingerprinting with multi-locus minisatellite probes is appropriate for population genetic studies in M. oeconomus. Also, because band-sharing correlates to spacing in M. oeconomus, we propose that DNA fingerprinting may be used to study dispersal, recruitment and other population processes in this and possibly other rodent species.     

Estimation of heterozygosity for single-probe multilocus DNA fingerprints

In spite of the increasing application of DNA fingerprinting to natural populations and to the genetic identification of humans, explicit methods for estimation of basic population genetic parameters from DNA fingerprinting data have not been developed. Contributing to this omission is the inability to determine, for multilocus fingerprinting probes, relatively important genetic information, such as the number of loci, the number of alleles, and the distribution of these alleles into specific loci. One of the most useful genetic parameters that could be derived from such data would be the average heterozygosity, which has traditionally been employed to measure the level of genetic variation within populations and to compare genetic variation among different loci. We derive here explicit formulas for both the estimation of average heterozygosity at multiple hypervariable loci and a maximum value for this estimate. These estimates are based upon the DNA restriction-pattern matrices that are typical for fingerprinting studies of humans and natural populations. For several empirical data sets from our laboratory, estimates of average and maximal heterozygosity are shown to be relatively close to each other. Furthermore, variances of these statistics based on simulation studies are relatively small. These observations, as well as consideration of the effect of missing alleles and alternate numbers of loci, suggest that the average heterozygosity can be accurately estimated using phenotypic DNA fingerprint patterns, because this parameter is relatively insensitive to the lack of certain genetic information.      

DNA fingerprinting: a tool for determining genetic distances between strains of poultry

Summary DNA fingerprinting, a technique based on the detection of hypervariable minisatellite regions in DNA restriction fragments, was tested for its applicability to conduct population genetics in poultry. Using MspI digestion and phage M13 DNA as a probe, between 25 and 35 minisatellite-containing DNA fragments were observed per bird. Comparison of the banding pattern of offspring with their parents revealed that the bands were inherited as stable genetic traits. The variability of the DNA fingerprinting pattern was reduced in inbred strains. DNA fingerprints of chickens from five well-defined populations of known genetic relationships were analyzed and indices of genetic distances were computed. They correctly reflected the history of these strains, indicating that DNA fingerprinting may be a powerful tool to characterize genetic relationships between different breeding populations of the same species.     

Intra- and Interpopulation Genome Variation In Meloidogyne arenaria

The genetic heterogeneity of two M. arenaria race 2 populations (designated Pelion and Govan) was examined using RFLP analysis of 12 clonal lines established from single egg masses (six distinct clonal lines from each population). These populations are essentially identical by traditional biochemical and race identification schemes; however, the Govan population is more aggressive than the Pelion population, producing larger galls and exhibiting greater reproductive capabilities on many soybean cultivars and experimental accessions. Variation at the genomic DNA level was examined using probes representative of expressed DNA sequences present in the eukaryotic genome. Ribosomal DNA, interspersed repeated sequences, and cDNA probes were tested for detection of polymorphism within and between single egg mass lines of each population. Cloned cDNAs and ribosomal intergenic spacer sequences detect polymorphism both within and between populations, demonstrating the usefulness of these sequence classes for molecular genetic analysis of population structure and genome evolution.     

Use of DNA fingerprinting to determine parentage in muskrats (Ondatra zibethicus).

The detection of high levels of genetic variability by DNA fingerprinting probes has allowed researchers to accurately assess relatedness. Multiple-mating strategies are characteristic of the mating systems of small mammals. As such, techniques that provide an accurate indication of how individuals are related genetically is of great importance to assess the mating system of a species. In this study, we applied the DNA fingerprinting technique to captive and wild muskrats (Ondatra zibethicus) to determine its usefulness for parentage analysis in wild populations. We found that DNA digested with the restriction enzyme Hae III and probed with Jeffrey's minisatellite 33. 15 identified a large amount of polymorphism in both groups of muskrats. The DNA fingerprinting technique correctly assessed parentage within the captive group. In the wild population, paternity was assigned between two adult males based on diagnostic fragments and similarity of banding patterns. The likelihood that paternity could be misassigned to a full sibling was high in this free-ranging population. However, because natal dispersal in muskrats is male biased, it is unlikely that two brothers would associate with the same female.     

A landscape perspective of the Hawaiian rain forest dieback

Abstract. Throughout the 1960s and 1970s there was a rapid decline and canopy dieback in the Metrosideros polymorpha dominated rain forest of Hawai'i. An analysis of air photo sets from 1954, 1965, and 1972, covering the windward slopes of Mauna Kea and Mauna Loa, gave support for an alien disease hypothesis. A total demise of the native forest was predicted for the early 1990s. This prediction as well as the disease hypothesis proved to be wrong. Various searches for a single climatic cause also failed to explain the dieback. The spatial dynamics of the dieback phenomenon were newly analyzed with an additional air photo set from 1977 and by using GIS with spatial statistics. Two juxtaposed and climatically similar landscape matrix samples of ca. 200 km², one each on Mauna Loa and Mauna Kea, were subjected to an analysis of landform heterogeneity and superimposed dieback patterns. The Mauna Loa matrix displays up to 15 000 yr old lava flows, while the Mauna Kea matrix displays up to 250 000 yr old substrates. Initiation of dieback occurred simultaneously on both mountains and was highly correlated with poorly-drained sites. The progression of dieback, however, followed a gradient of decreasing soil moisture, which often terminated at clearly recognizable substrate boundaries in the Mauna Loa matrix and moved over well-drained hill sites in the Mauna Kea matrix. Metrosideros dieback spread across the entire spectrum of volcanic substrates and habitat moisture regimes and developed from a smaller into a larger patch mosaic. By 1977, ca. 50 % of the forest area in both sample matrices had gone into dieback. Thereafter, the dieback came to a halt. The domino-type collapse, which frequently came to a halt at volcanic substrate boundaries, indicates that stands in better drained sites were also predisposed to die. Stands on adjoining substrates often survived. Substrates with dieback stands displayed no other obvious vigor-reducing stresses. The canopy trees on such substrates may have a common history, such as a major disturbance (including dieback) that synchronized stand development in the past. Subsequent weather disturbances and other abiotic/endogenous stresses associated with stand maturation, such as nutrient limitations and stand-level senescence, may reinforce a rhythmic synchrony over several generations of canopy cohorts.     

Genetic and morphological differentiation between remnant populations of an endangered species: the case of the Seychelles White-eye

The Seychelles White-eye Zosterops modestus is a critically endangered species that survives in two remnant populations on the islands of Mahé and Conception. Multilocus minisatellite DNA fingerprinting and morphometric measurements were used to assess the levels of variation between these populations. Mahé White-eyes are on average significantly larger than Conception birds, as are males compared to females. The mean level of bandsharing ( c.  60%) indicates low levels of genetic variability within both populations. Bandsharing is significantly lower between populations (32%), suggesting that the two populations are genetically isolated from each other, and that one is not a subsample from the other. Both populations should therefore be considered as equally important genetic reservoirs that deserve to be safeguarded. Although each population appears locally adapted to its particular island environment, such limited differentiation is not considered of major taxonomic significance. Recombining genetic variation by mixing individuals from both populations may be beneficial for the species in view of future island transfers. This illustrates the importance of investigating differentiation between remnant populations of a threatened species to orientate future conservation and management measures.     

DNA fingerprinting and the problems of paternity determination in an inbred captive population of guinea baboons (Papio hamadryas papio)

Multilocus DNA fingerprinting was carried out on 65 individuals from a captive colony of guinea baboons (Papio hamadryas papio) at Brookfield Zoo, in order to determine the allocation of reproductive success among 7 active males. DNA fingerprinting was found to reveal very low levels of genetic variability in the study population, rendering discrimination of different levels of relatedness, and hence paternity, impossible. A method was therefore developed for emphasizing the region of the fingerprint pattern which revealed the greatest level of band variability, and the effect of this experimental modification on band sharing statistics was tested. Band sharing coefficients among unrelated individuals were significantly lower using the modified system, which was then applied to paternity testing in the whole population. However even when using the modified system, of the 33 offspring analyzed only 4 could be assigned solely to 1 male, 14 offspring were assigned to 1 of 2 males, 7 offspring had 3 potential fathers, and the remainder had 4 or more possible fathers. The implications of the limitations of these data for behavioural studies and genetic management of captive populations are discussed.     

中国东部栗疫病菌群体的遗传分化*

本实验采用RFLP技术,对中国东部栗疫病菌(Cryphonectria parasitica)进行了群体遗传结构的研究。313个参试菌株来自10个省(市)的16个群体(子群体),样本分布在北纬24°N—41°N。各菌株的DNA分别用限制性内切酶Pst Ⅰ和EcoR Ⅰ酶切,先后以10个低拷贝DNA探针和1个DNA指纹图谱探针进行了杂交和检测。结果表明,两个探针(pCB29和pMS29.1)的杂交图谱呈单态性;探针pCB19的杂交图谱显示,菌株DNA以PstⅠ酶切的为单态性,以EcoR Ⅰ酶切的则呈多态性;其他7个低拷贝探针的杂交图谱都呈多态性(Pst Ⅰ酶切)、指纹图谱探针的检测结果显示,辽宁凤城群体的菌株与中国东部其他群体的菌株相比,具有更多的限制性杂交片段,菌株间的遗传变异性也更大。     

Genotypic diversity revealed by allozymes and oligonucleotide DNA fingerprinting in French populations of the aquatic macrophyte Sparganium erectum

The vast majority of perennial plants reproduce sexually and vegetatively at the same time. This may lead to important variation among clonal plant populations in their amount of genotypic diversity. In order to verify this assumption, we compare the clonal diversity of 10 natural populations of the aquatic clonal macrophyte Sparganium erectum in France. Diversity was quantified by DNA fingerprinting and allozyme electrophoresis for a sample of 10 shoots per population. Two DNA probes (CA)₈ and (TAA)₆ TA, were selected among 10 synthetic oligonucleotide probes containing simple repeat motifs. Both allozymes and DNA fingerprints revealed different amounts of diversity among populations. Five populations consist of a single genotype, whereas two populations were genetically highly diverse. In four of the monomorphic populations, absence of fingerprints diversity was combined with uniformly heterozygous allozyme loci, suggesting that each population was composed of a single clone. In the highly diverse populations, the level of clonal diversity combined with the allele segregation of the two allozyme loci Lap and Est suggests frequent seedling recruitment. The origin of new genotypes remains unclear but the absence of widespread genotypes together with the discrete distribution of Sparganium erectum populations implies that new genotypes are locally produced through sexual reproduction.     

Genetic variation between strains of the Mediterranean fruit fly, Ceratitis capitata, detected by DNA fingerprinting.

DNA fingerprinting has been used to detect genetic variation in the Mediterranean fruit fly, Ceratitis capitata. Three different probes have been identified that can be used to detect DNA restriction fragment length polymorphisms between strains of this species. The strains used in this study differ only in terms of their geographic origin or genetic background. One of the probes used is the bacteriophage vector M13, and the other two are repetitive sequences derived from the medfly genome based on a weak homology to M13. Within a strain, each probe produces a consistent restriction fragment profile that is not affected by the method or timing of DNA extraction. Between strains, when M13 is used as a probe, an average of 10% of the observable bands are polymorphic. Use of the medfly genomic sequences as a probe increases the proportion of polymorphic bands between strains up to 30%. The fact that genetic differences between even such closely related strains can be reliably detected by this method holds great promise for studies of insect pests including the ability to monitor the movements of pest species, determining the extent of genetic variation in pest populations, and in making identifications from otherwise unidentifiable material.     

Genetic differentiation in a captive population of the endangered Siberian crane (Grus leucogeranus Pall.)

DNA fingerprinting, followed by multivariate analysis of data, was used to characterize genetic heterogeneity in captive populations of the endangered Siberian and sandhill cranes. The genetic structure revealed reflected the natural population and species distributions. The relevant groups differed not only from each other, but also from interspecies and inter-population hybrids bred in captivity. In this study we have tested an approach to the analysis of population structure based on individual genotypes. Interpretation of fingerprinting data by means of the analytical system applied here is a useful and reliable procedure for the estimation of genetic relationships between individuals.     

Genetic differentiation in a captive population of the endangered Siberian crane (Grus leucogeranus Pall.)

DNA fingerprinting, followed by multivariate analysis of data, was used to characterize genetic heterogeneity in captive populations of the endangered Siberian and sandhill cranes. The genetic structure revealed reflected the natural population and species distributions. The relevant groups differed not only from each other, but also from interspecies and inter-population hybrids bred in captivity. In this study we have tested an approach to the analysis of population structure based on individual genotypes. Interpretation of fingerprinting data by means of the analytical system applied here is a useful and reliable procedure for the estimation of genetic relationships between individuals.     

DNA fingerprinting and genetic diversity of the European bison (Bison bonasus), American bison (Bison bison), and gray Ukrainian cattle (Bos taurus)

To describe genetic variability and population diversity in domesticated populations of American bison (Bison bison), aurochs (Bison bonasus), and gray Ukrainian cattle (Bos taurus) different variants of DNA fingerprinting technique (utilizing the M13 phage DNA, (TTAGGG)4 synthetic oligonucleotide, and three arbitrary primers as hybridization probes) were used. Several parameters characterizing polymorphism and genetic diversity levels in each population (species) were evaluated on the basis of the profiles obtained. Dendrograms reflecting similarities between individual animals were constructed. Genetic variability of minisatellite and telomeric markers observed in the gray Ukrainian cattle flock was higher than that in aurochs and bisons. Comparison of the intrapopulation similarity (S) and gene diversity (H) indices along with the analysis of clusters in the dendrograms showed that the relatedness between the aurochs individuals was much higher than between the individual animals in the bison and gray Ukrainian cattle flocks. Furthermore, the gray Ukrainian cattle flock was represented by more distant relatives than the bison flock. It is suggested that reduced genetic variability and the appearance of deviant genotype observed in the two bison lines under selection, resulted from close inbreeding and the founder effect. The diagnostic value and efficacy of utilization of different molecular markers for estimation of genetic diversity and relatedness in domesticated animal populations is discussed.     

Study on DNA Diversity of Liaodong Oak Population at Dongling Mountain Region,Beijing

Random amplified polymorphic DNA(RAPD) and DNA amplification fingerprinting (DAF) markers were used in detecting genetic structure and DNA diversity of two Liaodong oak ( Quercus liaotungensis Koidz. ) populations at Dongling mountain region, a suburb of Beijing City. Shannon's index of phenotypic diversity was used to partition diversity into components within and between populations. Two hundred and five bands from twelve primers were analyzed. The results showed very high genetic variability within the Liaodong oak populations. The diversity in the central population was higher than that of the marginal one. 95 % of total genetic diversity occurred within populations and the coefficient of gene differentiation was 0.05. Significant difference of gene frequency has been detected in a few loci between populations. The study of different age groups of the oak trees implied that deforestation exerted certain impacts on the genetic structure of the Liaodong oak.