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Conservation of rare species with island‐like distributions: A case study of Lasthenia conjugens (Asteraceae) using population genetic structure and the distribution of rare markers
Abstract
Californian vernal pools, a patchy, island-like habitat, are endangered as a result of habitat destruction. Conservation of the remaining vernal pool habitat is essential for the persistence of several endangered species. We present the first study examining DNA-level genetic diversity within and among populations of a vernal pool plant species. We investigated genetic variation across eight populations of the US federally endangered vernal pool endemic Lasthenia conjugens (Asteraceae) using intersimple sequence repeat (ISSR) markers. Genetic diversity within the species was high (Nei's gene diversity estimate was 0.37), with moderate differentiation among populations (Bayesian FST analog of 0.124). Using an amova analysis, we found that the majority of the genetic variation (84%) was distributed within populations. There is a significant relationship between geographical distance and pairwise genetic differentiation as measured by the Bayesian estimate θB. The alternative hypotheses of historic geological processes within the Central Valley and contemporary gene flow are discussed as explanations of the data. Because of the vulnerability of the populations, we calculated a probability of loss for rare alleles (fragments) in the populations. Calculations show that sampling only one of the eight populations for ex-situ conservation or restoration will capture approximately 54% of the sampled rare fragments. We believe that one of the sampled populations has become extinct since it was sampled. When removing this population from the above-mentioned calculations, sampling one population will capture only 41.3% of the sampled rare fragments. We recommend sampling strategies for future conservation and restoration efforts of L. conjugens.
... Most rare and endemic plants with small populations are maintained by low levels of genetic variation, which are heavily impacted by changes within the genetic structure, whether it be genetic drift, the founder effect or inbreeding depression (Hamrick and Godt, 1989;Ellstrand and Elam, 1993;Neale et al., 2008). The lack of genetic variability within such species can lead to population extinctions. ...
... However, some rare species have been reported to have a high genetic variation compared to widespread congeners, and it can be difficult to establish that species with a limited geographic range have low genetic diversity (Gitzendanner and Soltis, 2000;Park, 2004;Neale et al., 2008). The high genetic diversity of some rare species can usually be explained by the unique histories, which may include recent origin from a widespread ancestor, multiple or refugia origins, or a high contemporary gene flow (Park, 2004;Neale et al., 2008). ...
... However, some rare species have been reported to have a high genetic variation compared to widespread congeners, and it can be difficult to establish that species with a limited geographic range have low genetic diversity (Gitzendanner and Soltis, 2000;Park, 2004;Neale et al., 2008). The high genetic diversity of some rare species can usually be explained by the unique histories, which may include recent origin from a widespread ancestor, multiple or refugia origins, or a high contemporary gene flow (Park, 2004;Neale et al., 2008). ...
The genetic variation in populations of Eranthis byunsanensis, an endemic and rare species of Korea, was studied using starch gel electrophoresis. All five known populations were sampled for allozyme electrophoresis of nine enzymes coded by 10 loci. The overall genetic variation of E. byunsanensis population was shown to be considerably high within the populations (A
... L. glaberrima). While obligatory outcrossing may hinder genetic divergence among populations, gravity-mediated dispersal (Emery 2006;Neale et al. 2008), highly localized pollinator behavior (Emery 2009), and differences in flowering time within and among pools (Emery 2009) may restrict gene flow and facilitate genetic differentiation and local adaptation. ...
... Ornduff (1976) observed interpopulation variation in the responses of both L. conjugens and L. fremontii to the presence of competitors in artificial pools, and speculated that these patterns were driven by intraspecific differentiation in competitive abilities within each species. Recent studies have examined genetic patterns of population structure using neutral molecular markers in the two endangered Lasthenia species, L. conjugens (Ramp et al. 2006;Neale et al. 2008) and L. burkei (Sloop and Ayres In press). These studies, and prior work in the L. conjugens/fremontii/burkei complex using isozymes (Crawford and Ornduff 1989), have found evidence for genetic differences among populations across the ranges of these species (Crawford and Ornduff 1989;Neale et al. 2008;Sloop and Ayres In press). ...
... Recent studies have examined genetic patterns of population structure using neutral molecular markers in the two endangered Lasthenia species, L. conjugens (Ramp et al. 2006;Neale et al. 2008) and L. burkei (Sloop and Ayres In press). These studies, and prior work in the L. conjugens/fremontii/burkei complex using isozymes (Crawford and Ornduff 1989), have found evidence for genetic differences among populations across the ranges of these species (Crawford and Ornduff 1989;Neale et al. 2008;Sloop and Ayres In press). Ramp et al. (2006) found low but statistically significant differentiation among naturallyoccurring L. conjugens populations occupying closely spaced pools at Travis Air Force Base (5.44% of total variation; Θ ST = 0.0569), indicating that gene flow is somewhat restricted among pools even at this local scale. ...
... These patterns, however, are built on evolutionary dynamics over long periods of time and may not adequately reflect the genetic consequences of more contemporary processes, such as habitat reduction, fragmentation, altered natural disturbances, inbreeding depression, and exotic species. For example, small populations with restrictive connectivity (gene flow) across the modern landscape may have reduced genetic diversity due to genetic drift, inbreeding depression, or population growth and maintenance primarily through clonal growth (Frankel and Soule 1981;Frankham 2005;Ramp Neale, Ranker, and Collinge 2008;Gustafson, Guinta, and Echt 2013). In a literature review of rare southeastern plant allozyme studies, Godt and Hamrick (2001) found that rare species were genetically depauperate relative to more widespread congers, although this pattern was not universal. ...
... In a literature review of rare southeastern plant allozyme studies, Godt and Hamrick (2001) found that rare species were genetically depauperate relative to more widespread congers, although this pattern was not universal. Quantifying the geographic patterns of genetic variation and understanding the processes shaping intraspecific variation are essential for effective conservation management (Fleishman et al. 2001, Ramp Neale et al. 2008, Laikre et al. 2010. Furthermore, Reed and Frankham (2003) found a significant correlation between measures of genetic diversity at the population level and fitness across 34 plant data sets, with diversity explaining 19% of variation in fitness. ...
Single nucleotide polymorphic (SNP) markers were used to characterize the genetic structure of Symphyotrichum georgianum (Alexander) G.L. Nesom, known more commonly as the Georgia aster, from 26 populations across the species' range. This species is considered vulnerable (G3) and was a candidate for listing under the Endangered Species Act. We sampled large (> 500 stems) and small (< 100 stems) populations from across the entire range for the species. Next generation sequencing was used to assess 36 SNP markers for pooled population samples, consisting of equal amounts of genomic DNA from 30 individual stems sampled across each population. Most of the genetic variation was partitioned within and less among populations, which is consistent with perennial outcrossing species. There was a significant (r = 0.506, P < 0.001) positive association between geographic distance and genetic distance among populations, indicating increasing genetic distance (genetic dissimilarity) with increasing geographic distances between populations. There was no statistically significant difference in genetic diversity between large and small populations, but trends were observed. The Georgia and North Carolina large populations were more genetically diverse than the small populations, while the small populations were more genetically diverse than the large populations in Alabama and South Carolina. Symphyotrichum georgianum is an outcrossing perennial aster with a rhizomatous growth habit. Extensive clonal growth could account for the low genetic diversity estimates from large populations; however, quantifying the extent of clonal growth within sites is beyond the scope of the current study. There was no association between genetic diversity measures and seed fill or germination rates. Additional fine scale genetic structure studies are underway to address the extent of clonal growth in these remnant populations and how that may affect viable seed production.
... Although rare species often exhibit lower genetic diversity than more widespread species, there are no differences in how rare and widespread species partition genetic variation among populations , Gitzendanner and Soltis 2000, Cole 2003). Thus, quantifying geographic patterns of genetic variation in rare species and understanding historical and contemporary evolutionary processes shaping intraspecific variation are important first steps in designing effective conservation management plans (Fleishman et al. 2001, Ramp Neale et al. 2008, Laikre et al. 2009). ...
... To maintain genetic variation in a species, more populations must be protected when levels of population divergence are high relative to when levels of divergence are low (Godt and Hamrick 2001). Because isolated populations could retain unique genetic variants that warrant consideration in conservation planning (Petit et al. 1998, Ramp Neale et al. 2008, decisions should be based on both overall genetic variability, as well as population divergence. ...
Theory predicts that edaphic endemics should exhibit high levels of population differentiation due to restricted gene flow among patchily distributed habitats. Here, we tested this prediction with the federally threatened annual Geocarpon minimum, an edaphic endemic restricted to sandstone outcrops and slick spots associated with saline prairies in the Southeastern United States. We used AFLP data to quantify population genetic variation and structure in 13 G. minimum populations using a bulked sampling scheme. Modest but significant components of genetic variance are partitioned among populations (16%) and among regions (north, south; 3%). The maintenance of private bands within most G. minimum populations suggests limited gene flow among geographically isolated populations. However, a Mantel test failed to detect a pattern of isolation by distance. Estimates of within population variation in G. minimum are relatively low compared to other edaphic endemics with similar life-histories. Results suggest conservation efforts should focus on protecting genetically unique populations and ensuring that genetic variability is adequately
captured in ex situ collections.
... Typically, species with restricted distributions have less genetic diversity than more widespread congeners owing to greater effects of drift and isolation in the former (Karron 1987;Hamrick & Godt 1989;Gitzendanner & Soltis 2000). Thus, our study contributes to the growing body of evidence that narrow endemics may maintain as much genetic variation as their common congeners (Linhart & Premoli 1993;Lewis & Crawford 1995;Godt & Hamrick 1998;Ge et al. 1999;Neale et al. 2008). Relatively high genetic diversity in rare plant species has been explained by several factors. ...
... Relatively high genetic diversity in rare plant species has been explained by several factors. Hybridization, recent speciation from a widespread species, multiple origins, comparatively recent bottlenecks and maintenance of genetic diversity within refugial populations recently severed from continuous distributions have all been suggested as causes of relatively high genetic diversity in rare plant species (Lewis & Crawford 1995;Neale et al. 2008). Recent historical events related to these factors could be determining the high genetic diversity of S. carbonensis. ...
We tested the hypothesis that South Andean populations of the highly polymorphic and mostly Northern Hemisphere perennial forb Cerastium arvense L. show ecotypic variation along distinct habitats. We compared differences in morphology and flowering phenology among six natural populations occurring in different environments. Genetic differences were analyzed by a common-garden experiment and isozyme electrophoresis. Several of the morphological differences observed in the field were maintained after more than a year of cultivation in the common garden (e.g., plant height and leaf width). Mean tests and multivariate analyses on morphological traits generally distinguished high-elevation populations from the rest, and a similar grouping of populations was obtained from isozyme data at 10 loci. Cerastium arvense had genetic polymorphism levels of >50% in all populations and an average genetic diversity (HT = 0.254) of which approximately 20% was distributed among populations. These marked genetic differences are probably maintained by restricted gene flow due to variation in flowering time. Morphological and genetic differences suggest ecotypic variation in C. arvense in the southern Andes, which seems to have originated by disruptive selective pressures in different environments and the effect of genetic drift in response to the extreme climatic changes occurring during the Pleistocene.Key words: common-garden experiment, ecotypic variation, elevation and precipitation, genetic diversity, Patagonian Andes, phenology.
... Typically, species with restricted distributions have less genetic diversity than more widespread congeners owing to greater effects of drift and isolation in the former (Karron 1987;Hamrick & Godt 1989;Gitzendanner & Soltis 2000). Thus, our study contributes to the growing body of evidence that narrow endemics may maintain as much genetic variation as their common congeners (Linhart & Premoli 1993;Lewis & Crawford 1995;Godt & Hamrick 1998;Ge et al. 1999;Neale et al. 2008). Relatively high genetic diversity in rare plant species has been explained by several factors. ...
... Relatively high genetic diversity in rare plant species has been explained by several factors. Hybridization, recent speciation from a widespread species, multiple origins, comparatively recent bottlenecks and maintenance of genetic diversity within refugial populations recently severed from continuous distributions have all been suggested as causes of relatively high genetic diversity in rare plant species (Lewis & Crawford 1995;Neale et al. 2008). Recent historical events related to these factors could be determining the high genetic diversity of S. carbonensis. ...
We studied morphological variation, reproductive biology and genetic structure of Senecio carbonensis, a narrow endemic from high elevations of the southern Andes, and compared it to Senecio peteroanus, a closely related widespread congeneric species. Using ANOVAs and discriminant analysis we showed that populations of S. carbonensis were more similar to each other in their morphology, had comparatively limited reproductive capacity and presented lower plant density and more reduced plant cover than populations of S. peteroanus. Similar high genetic variation was found at the population and species level in both species, based on isozyme variation at 14 and 11 putative gene loci that were resolved in S. carbonensis and S. peteroanus, respectively. The two species were genetically distinct. However, the small genetic distance between populations of each species suggests that either they were recently founded and that genetic drift did not have time to promote divergence, or that its effects are masked by significant current gene flow. These results show that ecological and reproductive characteristics of S. carbonensis may limit its extension and abundance. In contrast, high genetic variation at the population level is probably favored by self-incompatibility. Despite the restricted geographical distribution and low plant density of S. carbonensis populations, genetic characteristics do not seem to be limiting their long-term persistence. This information suggests that populations of S. carbonensis are not at risk of extinction as a result of genetic factors, although it is important to study and monitor population dynamics to further assess the degree of recruitment through time.
... Collection-based botanical gardens exhibit plant species and thus have a special connection with nature (Miller et al., 2004). Citizen science projects at botanical gardens include studies on demographics (Wagenuis et al., 2007), reproduction (Donaldson et al., 2002;Wagenuis, 2006), and ecological and genetic responses to habitat fragmentation (Neale et al., 2008). According to a recent study on the interactions between climate change and the functions of botanical gardens, environmental education or citizen science can affect the knowledge, attitudes, and beliefs of the people involved (Sellmann, 2014). ...
Plant diversity is currently being lost at an unprecedented rate, resulting in an associated decrease in ecosystem services. About a third of the world's vascular plant species face the threat of extinction due to a variety of devastating activities, including, over-harvesting and over exploitation, destructive agricultural and forestry practices, urbanization, environmental pollution, land-use changes, exotic invasive species, global climate change, and more. We therefore need to increase our efforts to develop integrative conservation approaches for plant species conservation. Botanical gardens devote their resources to the study and conservation of plants, as well as making the world's plant species diversity known to the public. These gardens also play a central role in meeting human needs and providing well-being. In this minireview, a framework for the integrated missions of botanical gardens, including scientific research, in/ex situ conservation, plant resource utilization, and citizen science are cataloged. By reviewing the history of the development of Kunming Botanical Garden, we illustrate successful species conservation approaches (among others, projects involving Camellia, Rhododendron, Magnolia, Begonia, Allium, Nepenthes, medicinal plants, ornamental plants, and Plant Species with Extreme Small Populations), as well as citizen science, and scientific research at Kunming Botanical Garden over the past 80 years. We emphasize that Kunming Botanical Garden focuses largely on the ex situ conservation of plants from Southwest China, especially those endangered, endemic, and economically important plant species native to the Yunnan Plateau and the southern Hengduan Mountains. We also discuss the future challenges and responsibilities of botanical gardens in a changing world, including: the negative effects of outbreeding and/or inbreeding depression; promoting awareness, study, and conservation of plant species diversity; accelerating global access to information about plant diversity; increasing capacity building and training activities. We hope this minireview can promote understanding of the role of botanical gardens. © 2018 Kunming Institute of Botany, Chinese Academy of Sciences
... Overall, our results demonstrate that the RADseq approach provided an effective method for obtaining SNP markers in L. fremontii, which has an uncharacterized and potentially large (C3.5 GB) genome if it is similar to other Asteraceae (Lai et al. 2012;Harter et al. 2004). The availability of SNP markers, which are co-dominant and highly variable, provides a substantial advance over the markers that were previously available for this species and its closest relatives, including two Lasthenia species that are listed as endangered by California and federal standards (e.g., allozymes, SSRs, and sequence-based markers like nuclear ribosomal and chloroplast DNA; Crawford and Ornduff 1989;Chan et al. 2001;Ramp et al. 2006;Ramp Neale et al. 2008;Sloop et al. 2012). SNPs can be compared among species and genomes, and thus these resources can contribute generally to further ecological and evolutionary studies in this genus. ...
California vernal pool (VP) ecosystems support a diverse community of endemic plants that are threatened by multiple anthropogenic pressures, generating a need for molecular tools to quantify the extent and distribution of genetic variation in native populations. Here, we used RADseq to discover single nucleotide polymorphisms (SNPs) for a widespread VP endemic plant species, Lasthenia fremontii. We discovered nuclear-based SNPs using a RAD-tag library of 12 individuals from different VP complexes using SbfI, a restriction enzyme that does not cleave the chloroplast genome in Lasthenia. A total of 316,106 catalog loci were obtained across all twelve individuals in the library. Of these, 713 loci were polymorphic, yielding 3918 candidate SNPs. Next, we genotyped an additional 285 additional plants to validate and characterize 71 of the candidate SNPs. Of these, 44 were polymorphic among VP complexes. A preliminary analysis of the distribution of genetic variation using these loci revealed significant isolation-by-distance across the species’ geographic range. Weaker, but in some cases significant, genetic differentiation was detected among subpopulations from different pools within a single VP complex. Thus, in this study, RADseq allowed the discovery of SNP markers that can characterize patterns of genetic variation at multiple spatial scales in L. fremontii, which can be used to inform the conservation and mitigation of VP populations.
... The number of ISSR loci scored is not unusual, and is comparable with other studies using ISSRs (e.g. Culley et al. 2007;Fant et al. 2008;Ramp Neale et al. 2008). ...
... Goldfields follow a common vernal pool development pattern of germination at the onset of winter rains, remaining in an immature seedling state during months of inundation and bolting with flowers during the rapid spring dry down (Linhart 1974, Collinge and Ray 2009, Emery 2009, Faist et al. 2013). As has been found with other vernal pool species, Goldfields are not able to self-pollinate, which increases gene flow (Ornduff 1969, Ramp 2004, Ramp Neale et al. 2008) and the flowers are often pollinated by specialist solitary bees (Thorp 1990, Thorp and Leong 1998, Emery et al. 2009). This plant-pollinator relationship coupled with habitat loss has prompted a need for conservation areas protecting the limited available habitat and has fueled restoration projects aimed at restoring degraded habitat. ...
The role of plant-pollinator interactions in influencing the success of ecological restoration projects is important and often overlooked. In our study, we examined floral visitation in an endangered vernal pool plant species, Contra Costa Goldfields (Lasthenia conjugens; Asteraceae). We observed Goldfields abundance and floral visitation in the early and late stages of an ecological vernal pool restoration project located in the Central Valley of California. After an initially high abundance at our study site in the early stages of restoration, we noted a sharp decline of this endangered species ten years later. Our floral visitor observations demonstrated that the abundance of gnats (Sciaridae) was high in the restored pools across the ten years, but was very low to nonexistent in the nearby naturally occurring pools. Solitary bee abundance was the inverse of that observed for gnats, with a very low instance of solitary bee pollinators in the restored pools, yet a higher abundance in the naturally occurring pools. With this difference in floral visitors between pool types, we found significantly more mature potentially viable seeds in the restored pools, but a general overall decline over the three observation years. The higher number of mature, potentially viable seeds in the restored pools leads us to believe that the gnats are filling the role of the solitary bees and have maintained this function over the duration of the ten-year observation period. We conclude that gnats may be acting as surrogate pollinators for Goldfields in restored pools.
... The number of ISSR loci scored is not unusual, and is comparable with other studies using ISSRs (e.g. Culley et al. 2007;Fant et al. 2008;Ramp Neale et al. 2008). ...
Sourcing plant species of local provenance (eco-sourcing) has become standard practice in plantcommunity restoration projects. Along with established ecological restoration practices, knowledge of genetic variation in existing and restored forest fragments is important for ensuring the maintenance of natural levels of genetic variation and connectivity (gene flow) among populations. The application of restoration genetics often employs anonymous ‘fingerprinting’ markers in combination with limited sample sizes due to financial constraints. Here, we used two such marker systems, AFLPs (amplified fragment length polymorphism) and ISSRs (inter-simple sequence repeats), to estimate population-level genetic variation of a frequently used species in restoration projects in New Zealand, mahoe (Melicytus ramiflorus, Violaceae). We examined two rural and two urban forest fragments, as potential local source populations, to determine whether the māhoe population at the recently (re)constructed ecosystem at Waiwhakareke Natural Heritage Park, Hamilton, New Zealand, reflects the genetic variation observed in these four potential source populations. Both marker systems produced similar results and indicated that, even with small population sizes, levels of genetic variation at the heritage park were comparable with in situ populations. However, the AFLPs did provide finer resolution of the population genetic structure than ISSRs. ISSRs, which are less expensive and technically less demanding to generate than AFLPs, may be sufficient for restoration projects where only a broad level of genotypic resolution is required. We recommend the use of AFLPs when species with a high conservation status are being used, due to the greater resolution of this technique.
... In fact, the efficient design of conservation strategies for endangered species largely depends on knowledge of the levels of genetic diversity of the target species (e.g. Ramp Neale et al., 2008). Ranunculus cabrerensis subsp. ...
... A larger percentage of genetic variance can be better explained by the differences between populations belonging to the same biogeographical group rather than by the differences between groups (even in the case of group WB, which could show greater differentiation with respect to the others). This result is coincidental with those of O. echioides, Abies zinuayensis and Lasthenia conjugens (Mengoni et al. 2006;Tang et al. 2008;Ramp Neale et al. 2008), plant species with an " island-like " distribution, and is similar to the values found for an alpine plant, Papaver alpinum (Kropf et al. 2006). Most of the populations showed high levels of intrapopulational diversity. ...
Background and aims Jurinea pinnata is an Iberian vascular plant which only grows on gypsum and dolo-mite, two types of rocks associated with their exclusive endemic floras. In addition, the plant has an island-like distribution which could affect the differentiation and the genetic variability of wild populations. Thus, the species provides a unique opportunity for comparing (bio)geographical and ecological (edaphic) differenti-ation by means of molecular markers. Methods For our investigation we took 24 soil samples paired with a similar number of foliar samples for nutritional analyses. Our molecular-marker approach (AFLPs) involved 16 populations. Results The edaphic parameters revealed significant dissimilarities between dolomitic and gypsum soils. These differences are also found in the mineral com-position of the leaves. However, molecular data re-vealed that the differentiation between populations correlates better with geographical isolation than with the substrate character. Conclusions The populations showing the greatest ge-netic diversity are those of the East Baetic territory where the species grow on both substrates and its populations are closer together. The plant tolerance to gypsum and dolomite can be explained either as a result of common adaptive mechanisms or of a more general adaptation to arid environments.
... The vast distribution of vernal pools, historically a signature feature of California grasslands , has been severely reduced in the last century with only 10 % of historic habitat remaining (Holland 1978; Griggs and Jain 1983; Keeler-Wolf et al. 1998). This has resulted in population extirpation, reduction, fragmentation , and increased isolation of many vernal pool specialists , including many naturally rare and endemic plant species, with serious implications for population and species persistence (Gordon et al. 2012; Sloop et al. 2011; Sloop and Ayres 2011; Neale et al. 2008; Ramp et al. 2006; Gilpin and Soulé 1986). This trend applies in particular to vernal pool specialists with highly restricted geographic ranges found near expanding urban centers or intensive agriculture (Sloop and Ayres 2011; Sloop et al. 2011; CH2MHILL 1995). ...
Many California vernal pool plants are endangered requiring information on genetic diversity and structure to inform conservation efforts. We determined the temporal, and range-wide population genetic status of the outcrossing endangered vernal pool forb Limnanthes vinculans, endemic to Sonoma and Napa Counties with 10 microsatellite markers. Allelic diversity was threefold higher than in an endangered self-pollinating congener. Most populations showed heterozygote deficiency indicating past bottlenecks, inbreeding or genetic drift. Analysis of molecular variance and Bayesian ordination revealed genetic distinction at the county scale (F
CT = 0.158); within Sonoma County, population genetic distinctions were lower (F
SC = 0.043). Eight gene flow barriers demarcated most natural populations (F
ST > 0.05). We found temporal genetic structure among six natural populations (F
ST = 0.07). We conclude that breeding system and natural, anthropogenic, and temporal seed inputs combined to influence the patterns of genetic variation we found in natural and created populations informing conservation of the species.
... To do this, managers need information about genetic diversity and structure of vernal pool ecosystems. However, data on genetic patterns within vernal pool species are limited to a small number of taxa (Solomeshch et al. 2007; Ramp et al. 2006; Ramp Neal et al. 2008; Sloop and Ayres in press; Sloop et al. 2011). A meta-analysis of datasets examining a correlation between fitness and heterozygosity by Reed and Frankham (2003) confirmed that loss of heterozygosity has a deleterious effect on population fitness, a conclusion that supports the IUCN (International Union for the Conservation of Nature) designation of genetic diversity as worthy of conservation. ...
Vernal pool ecosystems are declining throughout California, with only 10% of historic habitat remaining. This has endangered many specialist endemic plant species, leaving extant populations fragmented, isolated, and threatened or endangered. Recovery plans for the increasing number of endangered vernal pool species require information on their genetic and ecological status to guide conservation and restoration efforts. Federally threatened Neostapfia colusana (Colusa grass) and federally endangered Tuctoria greenei (Greene’s tuctoria) are two endemic vernal pool grasses of high conservation concern in central California. Remaining populations are highly fragmented due to range-wide habitat destruction. Using five polymorphic microsatellite markers for each species, we performed genetic surveys of 240 individuals from eight vernal pools for N. colusana, and 317 individuals from 13 vernal pools for T. greenei. We detected high within-population genetic diversity for both species, with average allelic diversities of 24 alleles/locus (mean Hobs = 0.68, mean Hexp = 0.71) for N. colusana, and 19 alleles/locus (mean Hobs = 0.77, and mean Hexp = 0.79) for T. greenei. Bayesian clustering and AMOVA indicated two genetically distinct population groups for N. colusana (Fst = 0.268, P < 0.0001), and three for T. greenei (Fst = 0.11, P < 0.0001). We found very slight temporal genetic structure at one N. colusana (Fst = 0.013, P < 0.05) and two T. greenei (Fst = 0.015, Fst = 0.018, P < 0.05) pools. These estimates of population genetic diversity and structure are critical measures for both species that will help inform recovery management actions.
... see Godwin, Aitken & Smith, 1997). ISSR analysis produces large numbers of dominant multilocus markers from the nuclear genome that have been shown to be highly reproducible (Wolfe & Liston, 1998;Qian, Ge & Hong, 2001;Ramp, Collinge & Ranker, 2006;Ramp Neale, Ranker & Collinge, 2008) and to estimate genetic diversity more accurately than some other commonly used population genetic markers (Esselman et al., 1999). This is the first time the ISSR technique has been applied to the study of Metrosideros, although it has been used in other studies involving tree species (Aga, Bekele & Bryngelsson, 2005;Sheng et al., 2005). ...
The Hawaiian endemic Metrosideros polymorpha is known for its high levels of morphological diversity and localized adaptation to a range of habitats. At the ecotone between bogs and forests, individuals exhibiting morphological extremes can be found within a few metres of each other. The objective of this study was to examine the genetic diversity and structure of morphologically distinct neighbouring populations of M. polymorpha, growing in bogs and adjacent forests across multiple islands. We explored these relationships using the molecular technique of inter-simple sequence repeats (ISSRs). The majority (90.79%) of genetic variation was found within populations, 8.53% of the differentiation among populations can be attributed to differences between microhabitat types within islands and very little of the genetic differentiation is explained by the differences among islands (0.68%). These high levels of genetic homogeneity across populations could be the result of extensive gene flow and/or recent isolation of populations. We introduce a nearest genetic neighbour (NGN) analysis to examine detailed relationships of dispersal within and among populations by habitat and island. Using this approach, we provide evidence for habitat fidelity within bog populations and a positive correlation between island age and the proportion of same-island NGNs. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 162, 558–571.
... Thus P. apennina belongs to the subset of herbaceous endemics, possessing high levels of genetic variability, as revealed by ISSR markers, like P. interjacens (H sp 0.462) (Xue et al. 2004), Monarda fistulosa var. brevis (H sp 0.194) (Kimball et al. 2001), Lasthenia conjugens (H sp 0.390) (Ramp Neale et al. 2008), Gentiana atuntsiensis (H sp 0.391) and G. striolata (H sp 0.324)Table 4Analysis of molecular variance among and within six populations of P. apennina based on ISSR data Source of variation(Zhang et al. 2007). These levels are comparable to those obtained for more widespread species of the same genus: P. sikkimensis (H sp 0.558) (Wang et al. 2008), P. obconica (H pop 0.035–0.309) ...
Primula apennina Widmer is endemic to the North Apennines (Italy). ISSR were used to detect the genetic diversity within and among six populations
representative of the species distribution range. High levels of genetic diversity were revealed both at population percentage
of polymorphic band (PPB=75.92%, H
S=0.204, H
pop=0.319) and at species level (PPB=96.95%, H
T=0.242, H
sp=0.381). Nei gene diversity statistics (15.7%), Shannon diversity index (16.3%) and AMOVA (14%) detected a moderate level
of interpopulation diversity. Principal coordinate and Bayesian analyses clustered the populations in three major groups along
a geographic gradient. The correlation between genetic and geographic distances was positive (Mantel test, r=0.232). All together, these analyses revealed a weak but significant spatial genetic structure in P. apennina, with gene flow acting as a homogenizing force that prevents a stronger differentiation of populations. Conservation measures
are suggested based on the observed pattern of genetic variability.
... Limited pollen mediated gene flow may be caused by an absence or decline of pollinators due to habitat fragmentation, restricting pollinator movement, and loss or degradation of upland habitat that supports pollinators, as has been documented throughout California (Davis 1998;Leong 1994;Thorp andLeong 1995, 1998). In other species of vernal pool Limnanthes, solitary bees are important pollinators, and they usually have a close co-evolutionary relationship with the species they pollinate (Thorp 1990; Thorp and Leong 1998;Ramp Neale et al. 2008). Yet, to what degree L. floccosa ssp. ...
The endangered annual plant Limnanthes floccosa ssp. californica Arroyo is restricted to vernal pools in Butte County, California. To identify populations with unique genetic resources, guide reintroduction efforts, and design seed collection scenarios for long-term ex situ seed storage we determined extant genetic diversity and structure by surveying 457 individuals from 21 distinct populations using nine polymorphic microsatellite markers. We found low within population genetic diversity: low allelic diversity (1.9 [0.06 SE] alleles/locus); low heterozygosity (H
obs = 0.10 ± 0.018, H
exp = 0.19 ± 0.015), and a high fixation index (0.556 ± 0.044). The number of polymorphic loci ranged between 11 and 89%. Bayesian ordination determined 20 distinct populations and we found high genetic structure among these (F
st = 0.65, P < 0.0001). We identified notable gene flow barriers across populations, confirming regional structuring between three previously defined population density centers and two outlying populations (F
st = 0.21, P < 0.0001). Population size estimates ranged between ~50 and >5,000 extant plants per site. Our study confirms previous isozyme-based results and suggests that the loss of any population would represent a significant loss in the species’ genetic diversity. Recovery requires active restoration of existing populations and permanent habitat protection. We recommend close comparison of microhabitats of declining populations with genetically similar populations, to determine the potential for human assisted gene flow via seed movement to recover declining populations.
The Earth is rich in biodiversity, rich in valuable flora and fauna. Even so, many destructions are happening through time. Plants, for example, despite their valuable services to mankind, are being ruthlessly destroyed due to development projects and increased dependence. Although many species are threatened by anthropogenic pressure, many are threatened by invasive alien species and climate changes. Thus, many plants are threatened with extinction and are included in the RET group by IUCN. Before taking scientific measures to ensure their conservation and cultivation, it is essential to study their natural distribution and their demographic status. There are a number of strategies adopted by the government and various organizations to protect them. The ex situ and in situ formulas are mostly applicable for RET plant conservation. But there are so many limitations to each of them, and the strategies are specific to plants including in the threatened category. Botanical gardens and seed banks have a major role in this conservation.
Keywords: RET plants- Conservation strategies- Ex situ -In situ-Challenges-GSPC-BRAHMS
Castrilanthemum debeauxii is a critically endangered annual plant narrowly distributed in mountains of SE Iberia. It occurs in spiny scrublands on limestone soils dominated by Erinacea anthyllis at medium altitudes. Phylogenetic results indicate that the monotypic Castrilanthemum constitutes a paleoendemic lineage that diverged from its closest extant relatives in the Miocene. To achieve a better understanding of its recent evolution and conservation status, we performed an analysis of genetic variation and structure of four subpopulations using plastid haplotypes and AFLPs. We also investigated additional characteristics (ecological requirements, reproductive biology, pre-dispersal seed predation) that are relevant to evaluate the conservation status of the species. Castrilanthemum was found to be a facultative selfer with no major germination limitations. We detected moderate levels of genetic diversity based on AFLPs and plastid DNA sequences. The low genetic structure found for both nuclear and plastid markers, together with species distribution modeling results, pointed to high gene flow, which might counteract processes of genetic erosion caused by the low number of individuals. We found significant levels of pre-dispersal seed predation by the burrowing larvae of a tephritid fly, which may have contributed to the decline of the populations. Based on our results, we suggest directions for the management of Castrilanthemum. In particular, we recommend seeding and collection of seeds for banks, and discuss the possibilities of population reinforcement and reintroduction in localities where the species is currently extinct.
Centaurea wiedemanniana is an endemic plant species native to Turkey. The plant is known to have a narrow distribution in two abutting counties, Bilecik and Eskisehir. Genetic variability within and among 6 known natural populations of this plant was assessed by using RAPD markers. High levels of genetic diversity were detected both at population (PPB = 62.83%, I = 0.301, H-S = 0.196) and species level (PPB = 94.65%, I = 0.429, H-T = 0.278). Analyses of molecular variance showed that among and within-population genetic variation accounted for 71.70% and 28.30% of the total genetic variation, respectively. A high degree of genetic differentiation was also found among populations (G(ST) = 0.223). The genetic structure of C. wiedemanniana has probably been shaped by its breeding characteristics, habitat preference and short distance seed and pollen dispersal. The observed genetic variations suggest that as many populations as possible should be considered in any planned in situ or ex situ conservation programs for this vulnerable endemic species.
In this study, we examined the genetic diversity in three populations of the critically endangered annual, Bidens cernua, in Japan by using inter-simple sequence repeat markers and compared our data with those from two common congeners: Bidens radiata var. pinnatifida and Bidens tripartita. In contrast to our expectations, the degree of genetic diversity at the species level was higher in B. cernua than in B. radiata var. pinnatifida or B. tripartita. At the population level, the degree of genetic diversity was highest in B. cernua. These results may be ascribed to the mating system and method of seedbank formation in B. cernua. An analysis of molecular variance revealed relatively high genetic differentiation among the populations of all three species. We concluded that the distribution width could not be an index of genetic variability in Bidens examined in this study.
Primula apennina Widmer is endemic to the North Apennines (Italy). ISSR were used to detect the genetic diversity within and among six populations representative of the species distribution range. High levels of genetic diversity were revealed both at population (PPB = 75.92%, HS = 0.204, Hpop = 0.319) and at species level (PPB = 96.95%, HT = 0.242, Hsp = 0.381). Nei gene diversity statistics (15.7%), Shannon diversity index (16.3%) and AMOVA (14%) detected a moderate level of interpopulation diversity. Principal coordinate and bayesian analyses clustered the populations in three major groups along a geographic gradient. The correlation between genetic and geographic distances was positive (Mantel test, r = 0.232). All together, these analyses revealed a weak but significant spatial genetic structure in P. apennina, with gene flow acting as a homogenizing force that prevents a stronger differentiation of populations. Conservation measures are suggested based on the observed pattern of genetic variability.
P. apennina belongs to Primula subsect. Euauricula which includes 15 species distributed on the whole Alps and Apennines. A phylogenetic analysis was carried out using AFLP markers in order both to clarify the relationships among the species of subsection Euauricula that remained unresolved in previous works and to make some hypoteses on their evolutive dynamics. NJ, PCO and BAPS analyses strongly confirmed the monophyly of P. subsect. Euauricula and all the species form strongly supported clades. NJ tree topology suggested a simultaneous fragmentations of ancestral species in a large number of isolated populations that survived in refugia along the unglaciated margins of the Alps in response to the Pleistocene climatic oscillations.
The contributions of botanic gardens to conservation biology and global-change research need to be understood within the context of the traditional strengths of such gardens in herbarium collections, living collections and interactions with the public. Here, I propose that research in conservation planning, modelling species responses to climate change, conservation of threatened species and experimental tests of global change build on the core strengths of botanic gardens. However, there are limits to what can be achieved through traditional gardens-based programs, and some botanic gardens have adapted their research to include studies of threatening processes and to monitor and verify global-change impacts. There is an opportunity for botanic gardens to use their living collections more effectively in global-change research and for them to have a role in linking biodiversity conservation with benefits derived from ecosystem services.
Strategies for the sampling of genetic resources should rest on a clear statement of the purposes for which the material is to be used. For ex situ collections of rare and endangered species, various purposes have been proposed (e.g., Given 1987). The major actual or potential roles for such collections are to provide material (1) to cultivate for study and display in botanic gardens; (2) to exploit commercially in horticulture, plantations, or forestry, and thereby replace commercial harvesting from natural populations; (3) to reestablish or enrich wild populations; (4) to be a source of single genes or characters for future transfer to domesticated species; and (5) to act as a refuge of last resort against extinction.
A comprehensive, but simple-to-use software package for executing a range of standard numerical analysis and operations used in quantitative paleontology has been developed. The program, called PAST (PAleontological STatistics), runs on standard Windows computers and is available free of charge. PAST integrates spreadsheettype data entry with univariate and multivariate statistics, curve fitting, time-series analysis, data plotting, and simple phylogenetic analysis. Many of the functions are specific to paleontology and ecology, and these functions are not found in standard, more extensive, statistical packages. PAST also includes fourteen case studies (data files and exercises) illustrating use of the program for paleontological problems, making it a complete educational package for courses in quantitative methods.
Although the potential genetic risks associated with rare or endangered plants and small populations have been discussed previously, the practical role of population genetics in plant conservation remains unclear. Using theory and the available data, we examine the effects of genetic drift, inbreeding, and gene flow on genetic diversity and fitness in rare plants and small populations. We identify those circumstances that are likely to put these plant species and populations at genetic risk. Warning signs that populations may be vulnerable include changes in factors such as population size, degree of isolation, and fitness. When possible, we suggest potential management strategies.
Rare species are frequently genetically depauperate compared with widespread species, but the degree to which low genetic variation affects short-term viability is still unresolved. We examined the relationship between population-level genetic variation and fitness in small, experimental populations of Brassica rapa (a Eurasian annual) in a stable, mild environment. We used allozyme and morphological markers to create populations with either high or low levels of genetic variation. We then grew three high-variation and three low-variation populations for six generations under benign growing conditions, with consistent levels of light, nutrients, and water. We measured fitness components and genetic variation throughout the experiment. All populations were maintained at equal sizes (n = 100 seeds to start each generation), and plants were mass-pollinated to avoid differential inbreeding. Under mild conditions, high-variation plants did not have consistently higher fitness than low-variation plants. In generation three, plants in low-variation populations outperformed high-variation plants. In generation four, however, which was subjected to unplanned heat stress, high-variation plants had higher values for many of the fitness components measured, suggesting that, under stress, genetic variation may be associated with a fitness advantage. No differences in multiplicative fitness were found in any generation, indicating that high- and low-variation populations did not differ significantly in overall population viability. Our results indicate that when degree of inbreeding and population size are held constant, genetic variation per se does not increase fitness under benign conditions. As theory predicts, the role of population-level genetic variation may instead be in enhancing the ability of small populations to remain viable under fluctuating, stressful, or novel conditions.
One goal of conservation biology is to preserve the evolutionary potential of species by maintaining natural levels of genetic diversity. Knowledge of the levels and distribution of genetic variation thus becomes a prerequisite for the establishment of effective and efficient conservation practices (Beardmore 1983; Frankel 1983; Allendorf and Leary 1986). Without such knowledge, the efforts of conservation biologists, no matter how well meaning, may not be effective (Asins and Carbonell 1987). For conservation purposes, information can best be obtained by empirically determining the level and distribution of genetic variation for morphometric and physiological traits, allozyme loci, and DNA sequences. However, since few endangered species have been studied, and since the resources for such studies are frequently limited, we must often rely on previously accumulated knowledge to make educated guesses pertaining to the genetic diversity of these species.
The biological diversity of our planet is being depleted due to the direct and indirect consequences of human activity. As the size of animal and plant populations decrease, loss of genetic diversity reduces their ability to adapt to changes in the environment, with inbreeding depression an inevitable consequence for many species. This textbook provides a clear and comprehensive introduction to the importance of genetic studies in conservation. The text is presented in an easy-to-follow format with main points and terms clearly highlighted. Each chapter concludes with a concise summary, which, together with worked examples and problems and answers, emphasise the key principles covered. Text boxes containing interesting case studies and other additional information enrich the content throughout, and over 100 beautiful pen and ink portraits of endangered species help bring the material to life.
Enzyme electrophoresis was employed to examine genetic variation at 20 loci in 16 populations of Lasthenia minor and 18 populations of its presumed derivative species L. maritima. The purposes of the study were to ascertain levels of genetic variation in each species, to assess how the variation at enzyme-coding genes is apportioned within and among populations of each species, and to determine the level of divergence between the two species. The two species are both diploid annuals, similar morphologically, and produce fertile F1 hybrids when crossed. Lasthenia minor is self-incompatible and restricted to mainland California, whereas L. maritima is self-compatible and probably largely autogamous; it occurs on seabird rocks from central California to British Columbia. Mean genetic identities for pair-wise comparisons of populations of the two species are similar to values for populations of the same species, indicating they have not diverged at the 20 genes coding for soluble enzymes. Despite its more extensive geographical range, L. maritima exhibits only 50% of the genetic diversity of L. minor. The latter species apportions a greater amount of its diversity within populations, whereas the former harbors more diversity among populations than within them. This is probably a reflection of the different breeding systems of the two species. Six unique alleles were detected in L. minor, whereas only one novel allele was found in a single individual of L. maritima. The electrophoretic data are concordant with the suggestion that L. maritima is relatively recently derived from L. minor. The switch from outcrossing to selfing and selection of genotypes adapted to the chemically and physically unusual substrate on the seabird rocks are considered the critical steps in the evolution of L. maritima.
Enzyme electrophoresis was used to examine variation at 18 gene loci in Lasthenia burkei, L. conjugens, and L. femontii. The species consist of diploid annuals restricted to vernal pools in California; a variety of data has indicated that they are closely related. Populations of the three species are similar at isozyme loci; L. conjugens and L. fremontii are most similar with a genetic identity of 0.965. Lasthenia conjugens and L. burkei are next most similar (0.934), while L. burkei and L. fremontii have an identity of 0.909. Lasthenia burkei and L. femontii each contain a different subset of the alleles found in L. conjugens. Electrophoretic data are concordant with the view that these three species are closely related, but do not support the hypothesis that L. burkei is a stabilized hybrid derivative of L. conjugens and L. fremontii because alleles unique to each of the latter two species are not combined in the former. Rather, distribution of alleles among the three species suggests two possible alternative hypotheses of evolutionary relationships. One hypothesis considers Lasthenia conjugens a hybrid derivative of L. burkei and L. fremontii while the alternative explanation views the latter two species as independent derivatives of the former. Neither of these hypotheses appears to be concordant with morphological data.
We established replicated experimental populations of the annual plant Clarkia pulchella to evaluate the existence of a causal relationship between loss of genetic variation and population survival probability. Two treatments differing in the relatedness of the founders, and thus in the genetic effective population size (Ne ), were maintained as isolated populations in a natural environment. After three generations, the low Ne treatment had significantly lower germination and survival rates than did the high Ne treatment. These lower germination and survival rates led to decreased mean fitness in the low Ne populations: estimated mean fitness in the low Ne populations was only 21% of the estimated mean fitness in the high Ne populations. This inbreeding depression led to a reduction in population survival: at the conclusion of the experiment, 75% of the high Ne populations were still extant, whereas only 31% of the low Ne populations had survived. Decreased genetic effective population size, which leads to both inbreeding and the loss of alleles by genetic drift, increased the probability of population extinction over that expected from demographic and environmental stochasticity alone. This demonstrates that the genetic effective population size can strongly affect the probability of population persistence.
We present theory clarifying the general behavior of FST -based and GST -based estimators of gene flow, and confirm these predictions with simulations. In particular, we use the correlation of genes within groups within populations to define an estimator. The theoretical value of the correlation doe not depend on the number of groups in a population, and properties of the estimated correlation do not depend on the number of groups sampled or the number of individuals sampled per group. This invariance is in contrast to properties of GST . For a complete census of a population, bias and variance considerations would suggest the use of the GST -based estimator of gene flow, but lack of knowledge of population size or group number in practice suggests preference be given to the correlation-based estimator. We acknowledge that these estimators require that several conditions of a population-genetic model be met, since they do not make use of direct observations on the flow of genes. Our results differ from some of those based on simulation in a series of recent papers by M. Slatkin.
Molecular markers derived from PCR amplification of genomic DNA are an important part of the toolkit of evolutionary geneticists. RAPDs, AFLPs, and ISSR polymorphisms allow analysis of species for which prior DNA sequence information is lacking, but dominance makes it impossible to apply standard techniques to calculate F-statistics. We describe a Bayesian method that allows direct estimates of Fst from dominant markers. In contrast to existing alternatives, we do not assume prior knowledge of the degree of within-population inbreeding. In particular, we do not assume that genotypes within populations are in Hardy-Winberg proportions. Our estimate of Fst incorporates uncertainty about the magnitude of within-population inbreeding. Simulations show that samples from even a relatively small number of loci and populations produce reliable estimates of Fst. Moreover, some information about the degree of within population inbreeding (Fis) is available from data sets with a large number of loci and populations. We illustrate the method with reanalysis of RAPD data from 14 populations of a North American orchid, Platanthera leucophaea.
A method is presented by which the gene diversity (heterozygosity) of a subdivided population can be analyzed into its components, i.e., the gene diversities within and between subpopulations. This method is applicable to any population without regard to the number of alleles per locus, the pattern of evolutionary forces such as mutation, selection, and migration, and the reproductive method of the organism used. Measures of the absolute and relative magnitudes of gene differentiation among subpopulations are also proposed.
It has always been obvious that organisms vary, even to those pre-Darwinian idealists who saw most individual variation as distorted shadows of an ideal. It has been equally apparent, even to those post-Darwinians for whom variation between individuals is the central fact of evolutionary dynamics, that variation is nodal, that individuals fall in clusters in the space of phenotypic description, and that those clusters, which we call demes, or races, or species, are the outcome of an evolutionary process acting on the individual variation. What has changed during the evolution of scientific thought, and is still changing, is our perception of the relative importance and extent of intragroup as opposed to intergroup variation. These changes have been in part a reflection of the uncovering of new biological facts, but only in part. They have also reflected general sociopolitical biases derived from human social experience and carried over into “scientific” realms. I have discussed elsewhere (Lewontin, 1968) long-term trends in evolutionary doctrine as a reflection of long-term changes in socioeconomic relations, but even in the present era of Darwinism there is considerable diversity of opinion about the amount or importance of intragroup variation as opposed to the variation between races and species. Muller, for example (1950), maintained that for sexually reproducing species, man in particular, there was very little genetic variation within populations and that most men were homozygous for wild-type genes at virtually all their loci.
Two populations of Veronica peregrina growing in temporary pools in the Central Valley of California were studied. Each population grew in great density at the center of a pool and decreased in density to become very sparse in the bare areas and among the grasses surrounding the periphery. The amount of moisture present is greater and more predictable at the center of a pool than at the periphery. Consequently, plants in the central zone and plants in the peripheral zone of any given population are subjected to very different regimes of competition, moisture availability, and environmental predictability. Plants from the center and periphery produced progeny which differed in many characteristics when grown under uniform greenhouse conditions. A number of these characteristics, when considered concurrently with environmental conditions, can be interpreted in adaptive terms. To vernal pool species, the central portion of a pool is a relatively predictable environment, but intra-specific competition is very intense. Veronica growing in such areas produce fewer but heavier seeds and the seeds germinate rapidly and over a short span of time. These features can be advantageous under intra-specific competition. Conversely, the pool periphery is a more erratically patchy environment, and a large amount of mortality may be related to this greater variability in time and space. Veronica from peripheral areas produced more but lighter seeds. This may be advantageous because: 1) smaller seeds have better dispersability, 2) larger numbers of seeds increase the probability of successful survival, and 3) a greater variety of offspring genotypes increases the amount of variability put forth to 'test' the environment. Around the periphery, there can be interspecific competition from tall grasses. Veronica from this area can grow to a larger size which may enable them to compete against the tall grasses. Thus, differentiation of adaptive significance appears to have occurred in these populations, and is maintained, perhaps by disruptive selection. In the populations studied, the distance separating the center from the periphery is only two to five meters, and gene flow by pollen and seed undoubtedly goes on. The differentiation observed suggests that the disruptive effects of selection overcome the homogenizing effects of gene flow. However, when seed mixing is very extensive, as it appears to be in the population from a cultivated field, the differentiation is relatively slight.
We established replicated experimental populations of the annual plant Clarkia pulchella to evaluate the existence of a causal relationship between loss of genetic variation and population survival probability. Two treatments differing in the relatedness of the founders, and thus in the genetic effective population size (Ne), were maintained as isolated populations in a natural environment. After three generations, the low Ne treatment had significantly lower germination and survival rates than did the high Ne treatment. These lower germination and survival rates led to decreased mean fitness in the low Ne populations: estimated mean fitness in the low Ne populations was only 21% of the estimated mean fitness in the high Ne populations. This inbreeding depression led to a reduction in population survival: at the conclusion of the experiment, 75% of the high Ne populations were still extant, whereas only 31% of the low Ne populations had survived. Decreased genetic effective population size, which leads to both inbreeding and the loss of alleles by genetic drift, increased the probability of population extinction over that expected from demographic and environmental stochasticity alone. This demonstrates that the genetic effective population size can strongly affect the probability of population persistence.
One goal of population genetics is to quantify and explain genetic structure within and among populations. Factors such as genetic drift, inbreeding, gene flow and selection are expected to influence levels and distribution of genetic variation. I review available data on genetic structure of vernal pool plant species with respect to these factors. Where relevant data are lacking, as is often the case for vernal pool plants, I examine how these factors are expected to influence vernal pool population genetic structure. I also consider whether the available population genetic data and theory can help provide approximate predictions of the genetic structure of unstudied vernal pool plant species and suggest reasonable approaches to conservation and management.
Genetic variation and clonal diversity of seven Psammochloa villosa(Poaceae) populations from northwest China were investigated using inter simple sequence repeat (ISSR) markers. Of the 84 primers screened, 12 produced highly reproducible ISSR bands. Using these primers, 173 discernible DNA fragments were generated with 122 (70.5%) being polymorphic, indicating considerable genetic variation at the species level. In contrast, there were relatively low levels of polymorphism at the population level with the percentage of polymorphic bands (PPB) ranging from 6.1 to 26.8. Analysis of molecular variance (AMOVA) showed that a large proportion of genetic variation (87.46%) resided among populations, while only 12.54% resided among individuals within populations. Clonal diversity was also high with 98 genets being detected from among 157 individuals using 12 ISSR primers. The evenness of distribution of genotypes in P. villosa populations varied greatly, with all of the genotypes being local ones. No significant differences in genetic or clonal diversity were found between populations in mobile or fixed dunes. The main factor responsible for the high level of differentiation among populations and the low level of diversity within populations is probably the clonal nature of this species, although selfing may also affect the population genetic structure to some extent. The efficiency of ISSRs in identifying genetic individuals was much higher than that of allozymes. An approximately asymptotic correlation was found between the number of genets detected and the number of polymorphic loci used, suggesting that use of a high number of polymorphic bands is critical in genet identification.
Data are concordant with the suggestion that L. maritima is relatively recently derived from L. minor. The switch from outcrossing to selfing and selecting of genotypes adapted to the chemically and physically unusual substrate on the seabird rocks are considered the critical steps in the evolution of L. maritima. - from Authors
A computer simulation program was used to examine interacting effects of genetic drift, mutation, immigration from outside populations, directional and balancing selection, and population subdivision on the loss of genetic variability from small, managed populations. Stochastic ewnts were simulated with a pseudo‐random number generator, and the genetic variation (expected heterozygosity) witbin and between populations was monitored in 25 populations for 100 generations.
Genetic drift was the overriding factor controling the loss of genetic variation Mutation has no noticeable effect on populations of the size typically managed in zoos and nature preserves Immigration from a large source population can strikingly slow, halt, or even reverse the loss of genetic variation, even with only one or a few migrants per generation. Unless selection is stronger than commonly observed in natural populations, it is inefficient in countering drift when population sizes are on the order of 100 or fewer. Subdivided populations rapidly lose variability from within each sub‐population but retain variation across the subpopulations better than does a panmictic population.
These results suggest that population managers should be concerned with the variation‐depleting effects of genetic drift, perhaps almost to the exclusion of consideration of selection and mutation Drift can be countered by the introduction of vety occasional immigrants or, less effectively, by division of the managed population into smaller breeding groups that interchange enough migrants to prevent unacceptably deleterious inbreeding within each subpopulation
The Butte County meadowfoam (Limnanthes floccosa subsp. californica), an endangered annual endemic to vernal pools in Butte County, California, is of agronomic interest as a sperm whale oil substitute. Because it is threatened by rapid development of the community of Chico, a field and genetic survey was required to guide a conservation program. Eight new populations were discovered, bringing the total known to eleven Population sizes varied from 220 to 45,689 plants, mean seed set per flower, a bioassay of site quality, ranged from 0.82 to 2.56 among populations. The array of associated taxa, an indicator of appropriate habitat, was fairly uniform across populations. Based on allozyme and morphometric data, no introgression between L. floccosa subsp. californica and L. alba subsp. alba at sympatric sites was found. Populations were remarkably monomorphic, probably due to past population bottlenecks in conjunction with high selfing rates. Electrophoretic analysis of 28 isozyme loci revealed that 96% of total genetic diversity was distributed among populations. The migration rate, Nm, calculated from the mean frequency of private alleles, (-p(1)BAR), and from the proportion of genetic variation distributed between populations, Gst, estimated exchange between local populations of one diploid individual every 50 to 100 generations, respectively. Mean genetic identity among populations was 0.91 +/- 0.068. Grouping of populations on the basis of genetic distance identified two distinct populations and three clusters of populations that deserve high priority for preservation because they are likely to have high frequencies of locally adapted alleles. The low migration rates and substantial differentiation among populations suggest a conservation plan that emphasizes preservation of as many populations as possible, at possible expense of numbers of individuals.
We present theory clarifying the general behavior of F(ST)-based and G(ST)-based estimators of gene flow, and confirm these predictions with simulations. In particular, we use the correlation of genes within groups within populations to define an estimator. The theoretical value of the correlation doe not depend on the number of groups in a population, and properties of the estimated correlation do not depend on the number of groups sampled or the number of individuals sampled per group. This invariance is in contrast to properties of G(ST). For a complete census of a population, bias and variance considerations would suggest the use of the G(ST)-based estimator of gene flow, but lack of knowledge of population size or group number in practice suggests preference be given to the correlation-based estimator. We acknowledge that these estimators require that several conditions of a population-genetic model be met, since they do not make use of direct observations on the flow of genes. Our results differ from some of those based on simulation in a series of recent papers by M. Slatkin.
RAPDs were generated from plants of six populations of Isotoma petraea F. Muell. The species occurs on rock outcrops in southern and western Australia, with populations exhibiting different breeding systems, including complete autogamy, varying levels of outbreeding and complex hybridity. Non-metric multidimensional scaling (nMDS) analysis of the random amplified polymorphic DNA (RAPD) data set clearly resolved all populations. The Pigeon Rock population, which is home to both complex hybrid and structural homozygote plants, was divided into those two groups by the nMDS analysis. There was little diversity in highly autogamous populations, but levels were higher in the outbred Yackeyackine population. All complex hybrid populations and plants possessed numerous genetic system-specific RAPDs, some of which were shown to be held in fixed heterozygosity. Estimating GST using RAPDs has been problematical due to their dominance, and analytical methods usually rely on knowledge of the selfing rate or assume Hardy–Weinberg equilibrium. This assumption does not hold when populations exhibit fixed heterozygosity, and an alternative method, Shannon's Index, was used to partition genetic diversity. The distribution of genetic diversity fit expectations for an inbreeding species, with most of the variation (87.5%) occurring between populations. This compares to an average RAPD-based GST of 59.6% for inbreeding species generally and 15.5% for outbreeding species.
Tilted Cenozoic strata in the eastern Great Valley, California, record progressive late Cenozoic uplift of the Sierra Nevada. The magnitude of tilting is combined with other geologic data, using a technique pioneered by Grant and others, to infer the rate and timing of post-late Miocene uplift between the Kings River and the Feather River. Previously published tilt data from the San Joaquin Valley combined with new work in the eastern Sacramento valley indicate that the rate of post-late Miocene tilting has been approximately uniform in the east-central Great Valley. Early to middle Pleistocene units typically dip 0.5°-0.7° southwest; middle Pleistocene units dip 0.2°-0.4°; middle to late Pleistocene units dip 0.1°-0.15°; late Pleistocene units dip 0.05°-0.1°. Post-late Miocene tilting of the Sierra Nevada is temporally associated with late Cenozoic uplift of the northern Basin and Range, uplift of the Cascades, uplift of the Colorado Plateau, and uplift of the southern Rocky Mountains, supporting the contention that tilting of the Sierra Nevada may have occurred as part of a Cordillera-wide uplift event. -from Author
While tens of millions of dollars have been spent on land acquisition and planning for current and future floodplain and wetland restoration in the Sacramento-San Joaquin Delta, knowledge of the historical processes and landscape heterogeneity that are helpful in guiding the environmental restoration are often scarce. This study used palaeoenvironmental reconstruction to increase the historical perspective, with the aim of improving environmental management. Twelve sediment cores collected from the McCormack-Williamson Tract (MWT) leveed farmland and the juxtaposed Delta Meadows (DM) tidal wetland were sampled for a suite of environmental proxies. MWT was a non-tidal flood plain during much of the late-Holocene, with a mosaic of other habitats including dry uplands, riparian forests, and freshwater wetlands persisting nearby. Comparison with the regional sea-level history suggests that the upper delta gradually came under tidal influence 3000–800 calendar years before present (cal BP). Despite this, floodplain landforms and habitats prevailed at DM from 3650–330 cal BP, after which wetlands expanded, suggesting that a flood-based disturbance regime typified the upper delta for most of the late-Holocene. Recently, the upper deltaic plain has been profoundly disturbed by agriculture and other activities, rendering significant loss of habitat. It is believed that a flood-based disturbance regime will recur at MWT if the levees surrounding the tract are intentionally breached as planned for restoration, culminating in a variety of habitats similar to pre-agricultural conditions. Concentrations of Hg, Pb, As, and P pollutants elevated several-fold in surficial sediments are of particular concern, potentially becoming problematic after restoration.
In three investigations of the common outbreeding grass Festuca ovina The geographic variation of alleles was studied. The aim was to determine the role this variability has on the probability that an allele is lost from a particular sample, (i) In the investigation of Skane, where 35 populations were studied for 12 independent alleles, it was found that the probability of loss as a function of an allele's overall frequency was increased compared to the null-hypothesis of its frequency being the same in all populations. This implies that genes in a particular sample are only partly informative about the genetic composition of the area as a whole. A method is described how to calculate this degree of representativity, R. In the investigation of Skåne, with an average of 33 analysed genes per sample, the estimated value for R was 0.68. This value can be taken as an upper estimate of R for other herbaceous plants, since the investigated system was chosen to be as homogeneous and have as high an R value as possible, (ii) From a study of 16 samples from the whole of Fennoscandia could be concluded that sampling populations with different post-glacial histories is an effective way of increasing the number of recorded alleles. (iii) A study of seeds from seven selected plants in a local population at Vomb in Skåne, showed that the allele frequencies vary significantly between the pollen clouds that fertilize different individual plants. Thus, in a plant as outbreeding as Festuca ovina, genetic variability is pronounced at the smallest and the largest geographic scales, but is weak at the intermediary scale.
Allozyme electrophoresis was used to examine genetic diversity within live-bearing Peripatopsid Onychophora from the North Island of New Zealand. Specimens of two previously described morpho-species that differ in leg number (Peripatoides suteri and P. novaezealandiae) were found to be genetically diverse. P. suteri showed little intraspecific genetic variation but were very distinct from specimens assignable to P. novaezealandiae. Within P. novaezealandiae five genetically differentiated species were identified although none showed any consistent morphological differentiation, thus P. novaezealandiae (Hutton) is a species complex. All of these species occur in sympatry or parapatry (in one instance) with other cryptic species of the P. novaezealandiae group or with P. suteri. Four new species are described on the basis of this genetic evidence, they are P. morgani, P. aurorbis, P. kawekaensis and P. sympatrica. Other genotypes encountered indicate further cryptic species remain unrecognized. Among the North Island species, P. suteri and P. aurorbis sp. nov. are both more closely related to undescribed species from the South Island than to others examined from the North Island. P. sympatrica sp. nov. exists in sympatry with at least three other species in different parts of its range. The complexity of relationships and distributions probably arose through the interaction of low vagility in peripatus and the active geophysical history of the region. How these cryptic species persist in sympatry is not known but may be linked to differences in ecology not evident in their morphology, and/or may indicate recent dispersal from allopatry.
Genetic diversity is one of the three forms of biodiversity recognized by the World Conservation Union (IUCN) as deserving conservation. The need to conserve genetic diversity within populations is based on two arguments: the necessity of genetic diversity for evolution to occur, and the expected relation-ship between heterozygosity and population fitness. Because loss of genetic diversity is related to inbreed-ing, and inbreeding reduces reproductive fitness, a correlation is expected between heterozygosity and pop-ulation fitness. Long-term effective population size, which determines rates of inbreeding, should also be correlated with fitness. However, other theoretical considerations and empirical observations suggest that the correlation between fitness and heterozygosity may be weak or nonexistent. We used all the data sets we could locate (34) to perform a meta-analysis and resolve the issue. Data sets were included in the study, provided that fitness, or a component of fitness, was measured for three or more populations along with heterozygosity, heritability, and/or population size. The mean weighted correlation between measures of genetic diversity, at the population level, and population fitness was 0.4323. The correlation was highly sig-nificant and explained 19% of the variation in fitness. Our study strengthens concerns that the loss of het-erozygosity has a deleterious effect on population fitness and supports the IUCN designation of genetic di-versity as worthy of conservation. Correlación entre Adaptabilidad y Diversidad Genética Resumen: La diversidad genética es una de las tres formas de biodiversidad reconocidas por la Unión de Conservación Mundial (IUCN) que merecen ser conservadas.