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A comparison of levels of genetic polymorphism and self-compatibility in geographically restricted and widespread plant congeners
Abstract
Evolutionary theory predicts low levels of genetic polymorphism and high levels of self-compatibility in plant species with small ranges and few individuals. To test these predictions, I compared published data on electrophoretically detectable genetic variation and breeding systems for geographically restricted and widespread congeners in eleven genera. The restricted species exhibit significantly fewer polymorphic loci and alleles per polymorphic locus than do their widespread congeners. Although some rare species are genetically impoverished, others are nearly as polymorphic as their widespread congeners. The restricted species and their widespread congeners do not differ consistently with respect to breeding systems.
... Although the correlation between genetic diversity and geographic distribution is generally accepted, comparison of rare species and more widespread congeners can be used to examine relationships between geographical range and genetic diversity [2,3]. Comparison of rare and widespread congeners has indicated that genetic diversity within populations is significantly lower in rare species, although the levels of diversity are highly heterogeneous among genera [3]. ...
... The limited number of samples and populations of Q. glauca likely led to an underestimation of the species-wide genetic diversity such that this value can be expected to be larger with a greater number of samples. The lower genetic diversity of Q. hondae is consistent with previous studies indicating that geographically restricted species exhibit lower levels of genetic diversity compared to more common congeneric species [2,3,37]. The average within-population heterozygosity was 0.402 in Q. hondae, which was 41% lower than in Q. glauca (H s = 0.676). ...
... number of samples; N a , number of alleles; N e , effective number of alleles; H o , observed heterozygosity; uH e , unbiased expected heterozygosity; F is (FSTAT), inbreeding coefficient; F is (INEST), inbreeding coefficient correcting for null alleles; *, p < 0.05.1 The Wilcoxon one-tail probabilities of heterozygosity excess under the infinite allele model (IAM), two-phase model (TPM) and the stepwise mutation model (SMM).2 The allelic distribution modes expected from mutation-drift equilibrium (Normal L-shaped), or from recent bottleneck event (Shifted mode).3 ...
Conservation of rare species is essential for maintaining ecosystem function. Quercus hondae is a rare evergreen oak species (Cyclobalanopsis) endemic to Japan. This species is found in several locations in Southwestern Japan; small populations remain in the tutelary forests of the Japanese shrine. To evaluate the genetic diversity and phylogeographic structure of this rare species, 11 microsatellite loci and chloroplast DNA sequences are analyzed for 12 populations of Q. hondae and 8 populations of the more widespread congeneric species, Q. glauca. It is found that heterozygosity at both the population and species level is substantially lower in Q. hondae than in Q. glauca. Genetic differentiation among populations of Q. hondae was high, in contrast to Q. glauca, in which populations exhibit largely insignificant differentiation. STRUCTURE analysis shows that at K = 7, the clusters largely corresponded to major predefined populations. This study suggests that there is little gene flow among extant Q. hondae populations and that Q. hondae is genetically differentiated due to the greater effect of genetic drift in small populations. This pattern is in sharp contrast to that of a more common congeneric species, which will be an important consideration in the conservation of Q. hondae.
... A comparison such as Hamrick's (1983) survey is rather coarse grained: the geographic categories are somewhat arbitrary and unrelated species with totally different life histories are compared. To resolve these problems, Karron (1987) compared levels of genetic variation in species with restricted distributions with genetic variability in their more widespread congeners. He defined a restricted species as an "extremely localized endemic that occurs in 20 or fewer populations; in many cases, taxa have fewer than 20,000 individuals." ...
... Using the Wilcoxon two-sample test, both measures of gc:netic variation are statistically significantly lower (P < 0.05) in the endemics than in the widespread species. This agrees with Karron's (1987) results for restricted and widespread congeners in 11 genera. ...
... The results obtained in this study raise the need for conservation policies for some species of the R. decipiens group, especially the narrow endemics. Narrow endemics are inherently vulnerable due to their limited geographic ranges and often have small and isolated populations, which usually translates into low levels of genetic diversity (Ellstrand & Elam 1993, Gitzendanner & Soltis 2000 that can be further reduced by their low competitive ability (Lavergne et al. 2004) and high habitat specificity (Babbel & Selander 1974, Karron 1987. Because of this they are commonly included in conservation priority assessments (e.g., Wulff et al. 2013). ...
Oceanic islands have been recognized as natural laboratories in which to study a great variety of evolutionary processes. One such process is evolutionary radiations, the diversification of a single ancestor into a number of species that inhabit different environments and differ in the traits that allow them to exploit those environments. The factors that drive evolutionary radiations have been studied for decades in charismatic organisms such as birds or lizards, but are lacking in lichen-forming fungi, despite recent reports of some lineages showing diversification patterns congruent with radiation. Here we propose the Ramalina decipiens group as a model system in which to carry out such studies. This group is currently thought to be comprised of five saxicolous species, all of them endemic to the Macaronesian region (the Azores, Madeira, Selvagens, Canary and Cape Verde islands). Three species are single-island endemics (a rare geographic distribution pattern in lichens), whereas two are widespread and show extreme morphological variation. The latter are suspected to harbor unrecognized species-level lineages. In order to use the Ramalina decipiens group as a model system it is necessary to resolve the group's phylogeny and to clarify its species boundaries. In this study we attempt to do so following an integrative taxonomy approach. We constructed a phylogenetic tree based on six molecular markers, four of which are newly developed and generated competing species hypotheses based on molecular (species discovery strategies based on both single locus and multilocus datasets) and phenotypic data (unsupervised clustering algorithms based on morphology, secondary chemistry and geographic origin). We found that taxonomic diversity in the Ramalina decipiens group has been highly underestimated in previous studies. In consequence, we describe six new species, most of them single-island endemics and provide a key to the group. Phylogenetic relationships among species have been reconstructed with almost full support which, coupled with the endemic character of the group, makes it an excellent system for the study of island radiations in lichen-forming fungi.
... Among the fifteen populations, the AN population displayed the highest genetic diversity (Hd = 0.7; π = 0.00019), followed by the BY population (Hd = 0.4; π = 0.00057) ( Table 1). Previous studies have suggested that geographical distribution is a factor influencing the genetic diversity of plant species, with species covering a broader range that typically exhibits higher levels of genetic diversity [22]. However, our present study has revealed that both mainland and island populations of Korean and Japanese A. spathulifolius have notably low genetic diversity levels. ...
Aster spathulifolius, an ecologically significant plant species native to the coastal regions of Korea and Japan, remains understudied in terms of its genetic structure and evolutionary history. In this study, we employed four chloroplast markers and the nuclear ITS region from 15 populations of A. spathulifolius from both Korea and Japan, including their islands, to unravel the spatial genetic structure, differentiation, gene flow, phylogenetic, and biogeographical relationships. Analysis based on multiple methods identified a low level of genetic diversity, genetic differentiation and gene flow among A. spathulifolius populations. Network analysis and principal coordinates analysis showed that 15 populations could be divided into two groups: mainland and island. Furthermore, UPGMA, neighbor-net, maximum-likelihood and Bayesian inference-based phylogenetic tree confirmed that these populations formed two distinct clades. Therefore, the island populations might be treated as A. spathulifolius populations rather than A. oharai populations. Divergence time analysis estimated the divergence of A. spathulifolius lineages approximately 23.09 million years ago, while ancestral area reconstruction analysis suggested Korea as the potential origin, conflicting with alternative scenarios. These findings contribute to a comprehensive understanding of the evolutionary history, genetic structure, and adaptive strategies of A. spathulifolius in coastal environments. Our study challenges previous assumptions and underscores the necessity for further population studies to elucidate the intricate dynamics of this distinctive plant species.
... The capacity of species to adapt to environmental change depends on their genetic diversity (Frankham, 2005;Futuyma, 2010), but theory suggests that rare species suffer from low genetic variability due to the effects of genetic drift (Wright, 1931) and persistent directional natural selection in rare habitats (Van Valen, 1965). Indeed, rare species often exhibit reduced population genetic variation (Karron, 1987;Gitzendanner & Soltis, 2000;Cole, 2003). However, genetic differences between rare and common species can be minimal. ...
Species differ dramatically in their prevalence in the natural world, with many species characterized as rare due to restricted geographic distribution, low local abundance and/or habitat specialization.
We investigated the ecoevolutionary causes and consequences of rarity with phylogenetically controlled metaanalyses of population genetic diversity, fitness and functional traits in rare and common congeneric plant species. Our syntheses included 252 rare species and 267 common congeners reported in 153 peer‐reviewed articles published from 1978 to 2020 and one manuscript in press.
Rare species have reduced population genetic diversity, depressed fitness and smaller reproductive structures than common congeners. Rare species also could suffer from inbreeding depression and reduced fertilization efficiency.
By limiting their capacity to adapt and migrate, these characteristics could influence contemporary patterns of rarity and increase the susceptibility of rare species to rapid environmental change. We recommend that future studies present more nuanced data on the extent of rarity in focal species, expose rare and common species to ecologically relevant treatments, including reciprocal transplants, and conduct quantitative genetic and population genomic analyses across a greater array of systems. This research could elucidate the processes that contribute to rarity and generate robust predictions of extinction risks under global change.
... The shared life-history traits commonly associated with the woody growth form found in Mauritian species (i.e., dioecy and long lifespan) may be important in buffering against large changes in levels of genetic diversity, despite recent shifts in population size. Our results correspond to those from previous studies that found no relationship between rarity and genetic variation, with rare species frequently displaying levels of genetic diversity comparable to those of widespread congeners (Karron 1987;Gitzendanner and Soltis 2000) or even greater genetic diversity (Lanes et al. 2018). But other studies have found a positive correlation between genetic diversity (AFLP allelic richness) and range size (Rivers et al. 2014), and have found that common species had higher levels of genetic diversity than rare species (Hamrick et al. 1992;Hamrick and Godt 1996;Edwards et al. 2014). ...
Many factors shape the genetic diversity of island-endemic trees, with important implications for conservation. Oceanic island-endemic lineages undergo an initial founding bottleneck during the colonization process and subsequently accumulate diversity following colonization. Moreover, many island endemics occur in small populations and are further threatened by anthropogenic factors that cause population declines, making them susceptible to losses in genetic diversity through genetic drift, inbreeding, and bottlenecks. However, life-history traits commonly found in trees, such as outcrossing mechanisms, long lifespans, and a propensity for interspecific hybridization, may help buffer against losses of genetic variation. To assess the relative importance of colonization history, rarity, and distribution in shaping genetic diversity of island-endemic trees, we conducted a comparative population genomic analysis of 13 species of Diospyros (Ebenaceae) endemic to the Mascarene Islands that differ in island colonization history, distribution, population size, and IUCN threat status. We genotyped 328 individuals across the islands using 2b-RADseq, compared genetic diversity both among and within species, and assessed patterns of genetic structure. Genetic diversity did not vary significantly by IUCN status, but we found that species that co-occur with others on the same intermediate-aged island (Mauritius) had much greater genetic diversity than those that occur solitarily on an island (Réunion and Rodrigues), likely because of greater interspecific hybridization among species with overlapping distributions and processes related to time since island colonization. Results presented here were used to determine priority localities for in situ and ex situ conservation efforts to maximize the genetic diversity of each Mascarene Diospyros species.
... Higher genetic diversity was observed in the most northern sites, such as Semera, compared to the most southern, such as Godey. Lower genetic diversity can be a signature of a more recent population produced through range expansions or introduction [41][42][43]. Often, introductions start with a small population with a relatively small amount of genetic diversity, and variation is acquired over time through spontaneous mutation or gene flow. In this study, the observation of higher diversity in the northern sites and lower diversity in the southern sites may indicate that An. stephensi in the south represent a more recent population relative to the population in the north. ...
Background
The recent detection of the South Asian malaria vector Anopheles stephensi in the Horn of Africa (HOA) raises concerns about the impact of this mosquito on malaria transmission in the region. Analysis of An. stephensi genetic diversity and population structure can provide insight into the history of the mosquito in the HOA to improve predictions of future spread. We investigated the genetic diversity of An. stephensi in eastern Ethiopia, where detection suggests a range expansion into this region, in order to understand the history of this invasive population.
Methods
We sequenced the cytochrome oxidase subunit I ( COI ) and cytochrome B gene ( CytB ) in 187 An. stephensi collected from 10 sites in Ethiopia in 2018. Population genetic, phylogenetic, and minimum spanning network analyses were conducted for Ethiopian sequences. Molecular identification of blood meal sources was also performed using universal vertebrate CytB sequencing.
Results
Six An. stephensi COI-CytB haplotypes were observed, with the highest number of haplotypes in the northeastern sites (Semera, Bati, and Gewana towns) relative to the southeastern sites (Kebridehar, Godey, and Degehabur) in eastern Ethiopia. We observed population differentiation, with the highest differentiation between the northeastern sites compared to central sites (Erer Gota, Dire Dawa, and Awash Sebat Kilo) and the southeastern sites. Phylogenetic and network analysis revealed that the HOA An. stephensi are more genetically similar to An. stephensi from southern Asia than from the Arabian Peninsula. Finally, molecular blood meal analysis revealed evidence of feeding on cows, goats, dogs, and humans, as well as evidence of multiple (mixed) blood meals.
Conclusion
We show that An. stephensi is genetically diverse in Ethiopia and with evidence of geographical structure. Variation in the level of diversity supports the hypothesis for a more recent introduction of An. stephensi into southeastern Ethiopia relative to the northeastern region. We also find evidence that supports the hypothesis that HOA An. stephensi populations originate from South Asia rather than the Arabian Peninsula. The evidence of both zoophagic and anthropophagic feeding support the need for additional investigation into the potential for livestock movement to play a role in vector spread in this region.
Graphical Abstract
... We used a sequence-based approach based on the CytB B gene and a universal vertebrate specific primer set to first: 1) confirm whether there was detectable vertebrate DNA present in the sample and 2) identify the vertebrate host based on querying NCBI nucleotide sequence database. This primer set can be used to distinguish a broad range of vertebrate species including human, cow, and [41][42][43] . In this study, the observation of higher diversity in the northern sites and lower diversity in the southern sites suggests that An. stephensi in the south represent a more recent introduction relative to the population in the north. ...
The recent detection of the South Asian malaria vector Anopheles stephensi in the Horn of Africa (HOA) raises concerns about the impact of this mosquito on malaria transmission in the region. The mode and history of introduction is important for predicting the likelihood of continued introduction and future spread. Analysis of An. stephensi genetic diversity and population structure can provide insight into the history of the mosquito in the HOA. We investigated genetic diversity of An. stephensi in eastern Ethiopia where detection suggests a range expansion to this region to understand the history of this invasive population. We sequenced the cytochrome oxidase subunit I (COI) and cytochrome B gene (CytB) in 187 An. stephensi collected from 10 sites in Ethiopia in 2018. Phylogenetic analyses using a maximum-likelihood approach and minimum spanning network were conducted for Ethiopian sequences. Molecular identification of bloodmeal sources was also performed using universal vertebrate CytB sequencing. Six COI-CytB haplotypes were observed based on five segregating sites, with the highest number of haplotypes in the northeastern sites (Semera, Bati, and Gewana towns) relative to the southeastern sites (Kebridehar, Godey, and Degehabur) in eastern Ethiopia. In the phylogenetic and network analysis, we observed population differentiation based on the distribution of the haplotypes across the northeastern and central sites (Erer Gota, Dire Dawa, and Awash Sebat Kilo) compared to the southeastern sites and evidence of a South Asian origin of the HOA An. stephensi lineages. The presence of the putative South Asian haplotype of origin at sites closest to Ethiopia's northeastern borders support route of introductions into Ethiopia from the northeast. Finally, molecular bloodmeal analysis revealed evidence of feeding on bovines, goats, dogs, and humans, as well as evidence of multiple (mixed) blood meals. In conclusion, we find support for the hypothesis for the recent expansion of An. stephensi into southeastern Ethiopia with multiple introductions. We also find evidence that supports the hypothesis that HOA An. stephensi populations originate from South Asia rather than the Arabian Peninsula. The evidence of both zoophagic and anthropophagic feeding support the potential for livestock movement to play a role in vector spread in this region.
Population‐scale genome resequencing of endangered animals may contribute to gaining an understanding of how genomes vary as population sizes become smaller, as well as the functional implications of such variation. In this study, we analysed structural variations and gene presence and absence variations in the genomes of population of the endangered crocodile lizards. We found that the frequencies of some genes showed significant differences between crocodile lizards in different regions, indicating the influence of environmental selection, as well as potential contributions from demography and isolation, in shaping gene presence and absence variations. The haplotype diversity of major histocompatibility complex (MHC) genes was also found to differ among crocodile lizards inhabiting different regions. These findings indicate that well‐designed interbreeding of crocodile lizards from different regions may facilitate the exchange of genes between different lizard populations and increase the haplotype diversity of MHC genes, which may be beneficial for the survival of these lizards. Our findings in this study, based on differences in gene structural variation, provide new insights into genomic variation and may contribute to the conservation of endangered animals.
Astragalus is the largest genus of seed plants; however, information on its reproductive biology and life history is widely scattered in the literature. About 96% of the species are perennials and 4% annuals; many are rare endemics. Astragalus species are obligate or facultative outcrossers, and inbreeding depression is higher in self-compatible (SC) than in self-incompatible (SI) species. The most frequent pollinators are Bombus, Osmia and Anthophora. On average, 48% of ovules produce seeds, and 40% of flowers produce fruits. Seed/ovule and fruit/flower ratios are lower in SC than in SI species. Predispersal insect seed predation ranges from 0 to 93%, and major predators are Acanthoscelides, Bruchophagus and Tychius. Seeds have physical dormancy and typically form a seed bank. C3 is the only photosynthetic pathway in the genus. Population growth may be cyclic or noncyclic, and genetic diversity of a taxon may or may not be related to size of geographic range.
Evidence is presented that a geographically peripheral population of the annual Stephanomcria exigua ssp. coronaria (Compositae), a widespread and ecologically diverse species, has recently given rise by a process of sympatric speciation to a diploid species presently designated “Malheurensis.” The new species comprises less than 250 individuals and is found only at a single locality in eastern Oregon where it grows interspersed with its parental population. Stephanomeria exigua ssp. coronaria is an obligate outcrosser and “Malheurensis” is highly self-pollinating. Reproductive isolation is maintained by differences in breeding system, a crossability barrier that reduces seed set following cross-pollination between them, and reduction in hybrid fertility caused by chromosomal structural differences. They are very similar morphologically. Electrophoretic analyses of seven enzyme systems demonstrate that all the alleles but one at the controlling 13 gene loci in “Malheurensis” are identical to alleles in ssp. coronaria. The new species displays certain maladapted features including loss of the specific requirements for seed germination characteristic of the progenitor population of ssp. coronaria. The origin of “Malheurensis” appears to be an exception to the theory of geographical speciation because spatial isolation is not necessary at any time for the origin or establishment of its reproductive isolating barriers. The nature of these barriers plus the genetic homogeneity of the species are compatible with the hypothesis that it derives from a single progenitor individual. Very little genetic change is involved initially in this mode of speciation.
Electrophoretic variability was examined in six species of Layia (Compositae), native to California, which have previously been studied by Clausen, Keck, and Hiesey, and are regarded as a classic example of geographic speciation in plants. The study was carried out to test the hypothesis that the extent of divergence in structural genes coding enzymes is concordant with divergence in morphological characteristics, ecological traits, and reproductive isolation. Eleven enzymes specified by 17 loci were analyzed. The genetic identity values were consistent with those expected on the model that the species diverged gradually as they adapted to geographically separate habitats. Thus, the values between the three species complexes proposed by Clausen, Keck, and Hiesey (L. chrysanthemoides/L. fremontii; L. jonesii/L. leucopappa/L. munzii; L. platyglossa) were substantially lower than the values between species within the complexes. The results provide an important contrast to the very high genetic identities between species which originated rapidly from their progenitors. The electrophoretic results also provided evidence that the cytosolic isozyme of phosphoglucomutase and the cytosolic NADP-dependent isocitrate dehydrogenase in the six species are coded by duplicate genes.