GENETIC STRUCTURE OF POPULATIONS OF GEOGRAPHICALLY RESTRICTED AND WIDESPREAD SPECIES OF ASTRAGALUS (FABACEAE)

Evolutionary theory predicts that species with small ranges and few individuals will exhibit low levels of genetic polymorphism. We investigated the population genetic structure of two locally endemic and two geographically widespread species of Astragalus. To facilitate direct comparisons among these congeners, three populations of each species were sampled in a consistent manner and scored for allozyme polymorphisms at 12 loci. Genetic polymorphism was lower in restricted A. linifolius and A. osterhouti than in widespread A. pectinatus. However, the restricted species do exhibit a moderate level of isozyme variation, comparable to that of widespread A. pattersoni and higher than has been detected in several other rare plant taxa. As measured by Wright's F statistics, there were no consistent differences between the restricted and widespread taxa with respect to the organization of genetic variation. F_ST values were low in all taxa, indicating little heterogeneity among populations.     

Genetic differentiation within and among island populations of the endangered plant Aster miyagii (Asteraceae), an endemic to the Ryukyu Islands

Genetic diversity was examined at 17 putative allozyme loci in 18 populations of the insular endemic plant Aster miyagii (Asteraceae). This species is geographically restricted to only three islands of the Ryukyu Islands and is on the federal list of threatened plants. Genetic differentiation within an island is small, suggesting that gene flow among populations on the same island is sufficiently large to prevent divergence. By contrast, genetic differentiation among islands is large, especially between Amamioshima Island and the other two islands, suggesting that gene flow between the islands is highly restricted. Two unique alleles are nearly fixed in populations on Amamioshima Island, which is the southernmost island of the three. Comparatively, genetic diversity is the smallest on Amamioshima Island. This genetic paucity on Amamioshima Island is probably a result of a population bottleneck at colonization or the small effective population size on this island. Genetic diversity at the species level of A. miyagii is larger than those of the species with a similar life history and of the congeneric widespread species, suggesting that the species has an old origin as an insular endemic species.     

Genetic diversity within and divergence between rare and geographically widespread taxa of the Acacia acuminata Benth. (Mimosaceae) complex

The Acacia acuminata complex is a group of woody shrubs and small trees comprised of three formally described taxa (A. oldfieldii, A. acuminata ssp. acuminata and ssp. burkittii) and two informal taxa ("small seed" and "narrow phyllode") with contrasting geographical distributions within the south-west of Western Australia. In addition, a series of variant populations of possible hybrid origin exist. Population genetic structure was investigated in 25 populations representing the taxa and variants using 16 polymorphic allozyme loci. All taxa and variants exhibited relatively high levels of genetic variation compared with other woody angiosperms with similar geographic distributions. Levels of genetic diversity in the widely distributed ssp. burkittii and "narrow phyllode" taxon were considerably higher (H(e), 0.311 and 0.319, respectively) than expected for widespread woody shrubs. In contrast, the rare and highly restricted A. oldfieldii exhibited significantly lower levels of genetic diversity (H(e), 0.173) compared with the other taxa in the complex, but higher than other rare woody shrubs. Although morphologically close, associations based on genetic distance showed A. oldfieldii was highly divergent from the other taxa (D = 0.85) while including variant populations confused systematic alliances. The unusual placement of some of these populations and high degree of population differentiation (G(ST), 12.7%) supports the suggestion that these may represent a series of hybridisation events between the various taxa.     

The evolution of the Streptanthus glandulosus complex (Cruciferae): genetic divergence and gene flow in serpentine endemics

An analysis of the levels and distribution of allozyme variation in the Streptanthus glandulosus species complex was undertaken to test paradigms of speciation processes in the context of serpentine endemism. Electrophoretic analysis of 21 putative enzyme loci in 1,224 individuals representing 56 populations revealed extensive intrapopulational variation and interpopulational divergence. Estimates of gene flow among populations within taxa are typically lower than is theoretically needed to counteract the effects of genetic drift (i.e., Nm values are below 0.5), suggesting that drift may play a significant role in the evolution of the complex. A cluster analysis of genetic identities between populations using UPGMA demonstrates geographically structured groupings, some of which include neighboring populations of different taxa. Moreover, the genetic identity between two populations is correlated with the distance by which they are separated. The results are consistent with a hypothesis of a paleoendemic origin of the complex. The ancestor of the complex (perhaps S. glandulosus ssp. glandulosus) probably was formerly distributed more continuously across serpentine and nonserpentine habitat throughout its range. Elimination of the nonserpentine populations allowed regional and population-level divergence, following a model of geographic speciation.     

Genetic diversity in Mediterranean diploid and tetraploid Bromus L. (section Bromus Sm.) populations.

The levels of genetic diversity assessed from allozyme data were investigated in 25 populations of Mediterranean Bromus intermedius, B. squarrosus, B. lanceolatus, and B. hordeaceus from Algeria. The geographically restricted diploids B. intermedius and B. squarrosus displayed less genetic diversity (the mean population gene diversity of Nei (Hu) ranged from 0.03 to 0.12) than the widespread tetraploid colonizers B. lanceolatus and B. hordeaceus (Hu = 0.07-0.27). Deviations from Hardy-Weinberg expectations in diploid populations of B. intermedius and B. squarrosus were observed owing to heterozygote excess at several loci and suggested that these self-fertilizing species may have substantial amounts of allogamy. Tetraploid populations of B. lanceolatus and B. hordeaceus were largely homozygous at homologous loci and frequently exhibited intergenomic fixed heterozygosity in accordance with their alloploid origin. Genetic variation at the infraspecific level was mostly distributed within populations in the four species, B. hordeaceus showing the lowest level of interpopulation differentiation (Gst = 0.06) and the highest level of gene flow (Nm = 3.75). Consistent gene flows are in agreement with the strongest intercontinental invasive behaviour of B. hordeaceus. Less differentiation was reported in the literature among later introduced B. hordeaceus populations from England and Australia, indicating reduced differentiation under the process of colonization. Moderate divergence occured among the four taxa, with interspecific genetic identities ranging from 0.87 to 0.93. In spite of substantial genetic similarity, species were clearly differentiated, with each tetraploid being more closely related to a diploid: B. hordeaceus to B. squarrosus and B. lanceolatus to B. intermedius.     

Does genetic variation and gene flow vary with rarity in obligate seeding Persoonia species (Proteaceae)?

Theory predicts that genetic variation is a determinant of persistence, and that the abundance and distribution of variation is strongly dependent on genetic drift and gene flow. Small, isolated populations are expected to be less diverse and more differentiated than large, inter-connected populations. Thus rare species may be more at risk of extinction. We used 389 putative AFLP loci to compare genetic variation and structuring in two pairs of closely-related common (large populations geographically widespread) and rare (small populations spatially restricted) Persoonia species. We genotyped 15–22 adult plants, from four populations, covering the geographic range of each species. Although genetic diversity was low for all four species (for long-lived outcrossing perennials), we found significantly more diversity within populations of the rare species than within those of the common species. AMOVA revealed significant levels of structure both among species (21%) and populations (15%). The proportion of inter-population variation within species did not vary consistently with rarity (Pair 1 rare 21.1% versus common 16.5%; Pair 2 rare 15.8% versus common 20.6%). However populations of the rare species were more differentiated than common species with similar geographic separation, suggesting greater gene flow between populations of the common species. Therefore, even relatively small genetically isolated populations of rare Persoonia species were more diverse than large populations of common Persoonia species. We hypothesise that common Persoonia species have undergone a rapid range expansion from a narrow gene pool, while genetic diversity is maintained in the soil seed-bank of rare remnants.     

The distribution of Quercus suber chloroplast haplotypes matches the palaeogeographical history of the western Mediterranean

Combining molecular analyses with geological and palaeontological data may reveal timing and modes for the divergence of lineages within species. The Mediterranean Basin is particularly appropriate for this kind of multidisciplinary studies, because of its complex geological history and biological diversity. Here, we investigated chloroplast DNA of Quercus suber populations in order to detect possible relationships between their geographical distribution and the palaeogeographical history of the western Mediterranean domain. We analysed 110 cork oak populations, covering the whole distribution range of the species, by 14 chloroplast microsatellite markers, among which eight displayed variation among populations. We identified five haplotypes whose distribution is clearly geographically structured. Results demonstrated that cork oak populations have undergone a genetic drift geographically consistent with the Oligocene and Miocene break-up events of the European-Iberian continental margin and suggested that they have persisted in a number of separate microplates, currently found in Tunisia, Sardinia, Corsica, and Provence, without detectable chloroplast DNA modifications for a time span of over 15 million years. A similar distribution pattern of mitochondrial DNA of Pinus pinaster supports the hypothesis of such long-term persistence, in spite of Quaternary climate oscillations and of isolation due to insularity, and suggests that part of the modern geographical structure of Mediterranean populations may be traced back to the Tertiary history of taxa.     

Genetic diversity and spatial correlation patterns unravel the biogeographical history of the European sweet vernal grasses (Anthoxanthum L., Poaceae)

Different processes have contributed to shaping the present distribution of the European biotas. Up to three different tertiary- to quaternary-time-scale evolutionary scenarios have been proposed to interpret the divergence and genetic structuring of plant species in Europe. In the present study, the Amplified Fragment Length Polymorphisms technique has been used to unravel the species and regional phylogeography of the European sweet vernal grasses (Anthoxanthum L. Poaceae). Forty-six populations belonging to all seven European species of Anthoxanthum and covering a broad geographical and ecological range were selected. Different phylogeography and population genetics diversity and structure estimates indicated a clear divergence of old Messinian Mediterranean lineages, followed by a pre-Pliocene split between Mediterranean annuals and Eurosiberian perennials and a more recent Pleistocene differentiation of Arctic-Alpine, Atlantic and Submediterranean diploid to polyploid landraces. Regional and population correlation tests between geographical and genetic distances allowed to postulate distinct pre- and post-glacial colonization pathways across Europe for the taxa of this widespread genus.     

Allozyme Variation and Genetic Relationships among Species of Cimicifuga (Ranunculaceae) from Korea

Allozyme investigation of the five Cimicifuga taxa in Korea was conducted to assess genetic and clonal diversity within populations and genetic divergence among populations and taxa. Levels of allozyme variation maintained in Korean Cimicifuga taxa were comparable to those for most herbaceous perennials. In general, samples excluding copies of the same multilocus genotype maintained higher levels of genetic diversity than the total samples within populations. Copies of homozygous genotypes at several loci resulting from clonal spread lead to decreased levels of genetic diversity within populations, indicating that clonal reproduction found in Cimicifuga affects population genetic structure. In general, more widely distributed species such as C. dahurica and C. japonica harbored higher levels of allozyme diversity than the other taxa examined. Although two varieties of C. heracleifolia are geographically and reproductively isolated, the genetic and clonal structure of var. bifida seems to resemble var. heracleifolia, indicating that the two varieties may have had a similar evolutionary history. However, the allozyme data strongly indicate that the two morphological types (Groups I and II) of C. simplex should be treated as separate species.     

GENETIC LEAKAGE AFTER ADAPTIVE AND NONADAPTIVE DIVERGENCE IN THE ENSATINA ESCHSCHOLTZII RING SPECIES

The salamander Ensatina eschscholtzii is an example of a ring species in which extant intermediate stages of terminal forms have a nearly continuous range, offering replicated interactions at several stages of divergence. We employ a greatly expanded allozyme database and individual-based analyses to separate the effects of divergence time and gene flow to evaluate how gradual divergence of populations around the ring contributes to the development of reproductive isolation. Despite the high degree of genetic ( D ≤ 0.39) and ecomorphological divergence observed in secondary contacts around the ring, reproductive isolation or rare hybridization is observed only at the terminus of the ring. Instead, in the secondary contacts sampled around the ring, hybrids are common and reproductively successful, enabling genetic leakage between parental genomes and the potential for genetic merger. Nevertheless, genetic admixture is geographically broad (<100 km) only in contacts between ecomorphologically similar populations (within subspecies). When divergence is accompanied by alternative patterns of adaptive divergence (between subspecies), zones of intergradation are narrower and affect populations only locally (>8 km). Diversification and consequent genetic interactions in Ensatina reveal a continuum between populations, ecological races, and species, where polytypic traits and high genetic differentiation are maintained without reproductive isolation.     

Evolutionary history of lamprey paired species Lampetra fluviatilis (L.) and Lampetra planeri (Bloch) as inferred from mitochondrial DNA variation

A remarkable trend in the evolution of lampreys is the occurrence in most genera of 'paired species', in which the parasitic anadromous lampreys are believed to have given rise to nonparasitic freshwater resident populations. The present work examines the phylogeography of the European paired species Lampetra fluviatilis and Lampetra planeri, in an attempt to elucidate species pair evolutionary history. We studied sequence variation in cytochrome b and ATPase 6, 8 mitochondrial genes in 63 individuals from 21 localities of the paired species throughout their distribution range. Results from the phylogenetic and nested clade analyses were largely consistent, suggesting the existence of three major evolutionary lineages: lineage I and possibly lineage II are widespread throughout Europe, while the most ancestral lineage III is apparently restricted to the Iberian Peninsula. The high genetic diversity observed in the Iberian Peninsula is probably the result of refugial persistence and subsequent accumulation of variation over several ice ages, whereas the low levels of genetic diversity observed in central and northern Europe should reflect a rapid postglacial colonization. Results suggest that L. planeri originated within at least two distinct evolutionary lineages, rejecting the single origin hypothesis. The observed lack of taxa monophyly within lineage I may be the result of ongoing gene flow if the two taxa are alternate life-history forms of a single species. However, structure within lineage I is also consistent with the hypothesis of divergence of taxa after postglacial dispersion (around 2000 generations ago) with incomplete lineage sorting. Further testing of the alternative hypotheses is warranted.     

Allozyme Variation within and between Populations of Coreopsis intermedia (Asteraceae)

Abstract Enzyme electrophoresis was used to measure genetic diversity in two populations of Coreopsis intermedia of section Coreopsis , a rare species endemic to a small area of Texas and Louisiana. Genetic diversity is higher in C. intermedia than has been reported for many other geographically restricted species. C. intermedia contains levels of genetic variation comparable to those of other species in section Coreopsis , and a greater amount of diversity than either the rare congener, C. latifolia (section Silphidium ), or the Florida endemic, C. leavenworthii (section Calliopsis ). The two populations, although greatly different in size, exhibited similar levels of genetic diversity.     

Diverse historical processes shape deep phylogeographical divergence in the pollinating seed parasite Greya politella

Understanding the historical framework in which species interactions have diversified across landscapes may help to partition the effects of vicariance and geographically variable selection in shaping the geographical mosaic of coevolving species. We used phylogeographical analyses of the pollinating seed parasite Greya politella (Lepidoptera: Prodoxidae) to define the historical processes that may have structured interactions of this species with its host plants across major biogeographical breaks in western North America. Using 648 bp of cytochrome oxidase I and amplified fragment length polymorphisims, we identified deep genetic breaks among some populations consistent with some definitions of cryptic species. A combination of phylogenetic and population genetic approaches indicates that different historical processes may have structured G. politella genetic diversity in four regions: northern Pacific Northwest, southern Oregon, southern Sierra Nevada, and the remainder of California. The northern Pacific Northwest had high genetic diversity likely due to glacial refugia and subsequent spatial expansion, concordant with some other taxa. Populations in southern Oregon possessed unique, closely related haplotypes with restricted gene flow, possibly indicating a long-standing set of populations in this endemic-rich region. Analyses of California populations showed evidence of restricted gene flow and spatial expansion with many closely related haplotypes that occupy a broad geographical range. Southern Sierra Nevada populations were genetically distinct and highly diverse, possibly due to a localized glacial refugium. Together, these results suggest that vicariance and population expansion, possibly in combination with geographically variable selection, have shaped the diversification of G. politella and its interactions with its host plants.     

Population genetic diversity and structure of a naturally isolated plant species, Rhodiola dumulosa (Crassulaceae)

AIMS: Rhodiola dumulosa (Crassulaceae) is a perennial diploid species found in high-montane areas. It is distributed in fragmented populations across northern, central and northwestern China. In this study, we aimed to (i) measure the genetic diversity of this species and that of its populations; (ii) describe the genetic structure of these populations across the entire distribution range in China; and (iii) evaluate the extent of gene flow among the naturally fragmented populations. METHODS: Samples from 1089 individuals within 35 populations of R. dumulosa were collected, covering as much of the entire distribution range of this species within China as possible. Population genetic diversity and structure were analyzed using AFLP molecular markers. Gene flow among populations was estimated according to the level of population differentiation. IMPORTANT FINDINGS: The total genetic diversity of R. dumulosa was high but decreased with increasing altitude. Population-structure analysis indicated that the most closely related populations were geographically restricted and occurred in close proximity to each other. A significant isolation-by-distance pattern, caused by the naturally fragmented population distribution, was observed. At least two distinct gene pools were found in the 35 sampled populations, one composed of populations in northern China and the other composed of populations in central and northwestern China. The calculation of Nei's gene diversity index revealed that the genetic diversity in the northern China pool (0.1972) was lower than that in the central and northwestern China pool (0.2216). The populations were significantly isolated, and gene flow was restricted throughout the entire distribution. However, gene flow among populations on the same mountain appears to be unrestricted, as indicated by the weak genetic isolation among these populations.     

Pan-European phylogeography of the aquatic snail Theodoxus fluviatilis (Gastropoda: Neritidae)

Investigating the geographical distribution of genetic lineages within species is critical to our understanding of how species evolve. As many species inhabit large and complex ranges, it is important that phylogeographical research take into account the entire range of widespread species to clarify how myriad extrinsic variables have affected their evolutionary history. Using phylogenetic, nested clade, and mismatch distribution analyses on a portion of the mitochondrial COI gene, I demonstrate that the wide-ranging freshwater snail Theodoxus fluviatilis possesses in parallel many of the phylogeographical patterns seen in less widespread freshwater species of Europe. Fragmentary forces play a major part in structuring the range of this species, with 12 of 14 geographically structured nested clades displaying a distribution consistent with fragmentation or restricted dispersal. Certain regions of southern Europe harbour the majority of genetic diversity (total haplotype diversity, H = 0.87), particularly Italy (H = 0.87) and areas surrounding the Black Sea (H = 0.81). Post-Pleistocene range expansion is pronounced, with the majority of northern European populations (95% of sample sites) having arisen from northern Italian individuals that initially colonized northern Germany. Additionally, two highly divergent haplotype lineages present in northern Germany imply that there were at least two postglacial recolonization routes. Estuaries may also provide a means of dispersal given that no genetic differentiation was found between estuarine populations and neighbouring freshwater populations. Taken together, these data reveal a species with a complex genetic history resulting from the fragmentary effects of European geology as well as continuous and discrete range expansion related to their aquatic biology.     

GENETIC RELATIONSHIPS AND PATTERNS OF ALLOZYMIC DIVERGENCE IN THE IPOMOPSIS AGGREGATA COMPLEX AND RELATED SPECIES (POLEMONIACEAE)

The Ipomopsis aggregata complex consists of diploid, outcrossing, perennial herbs. The group is highly variable morphologically and is treated as three species: I. aggregata, I. tenuituba, and I. arizonica. Geographic races of I. aggregata and I. tenuituba are recognized as subspecies. Enzyme electrophoresis was used to examine genetic relationships among populations and taxa in the Ipomopsis aggregata complex and some related species. Genetic data for 23 allozyme loci from 60 populations were also used to determine how genetic variation is distributed geographically. Populations in the southwestern United States were more variable than those in the northwest: the center of genetic diversity corresponded to the center of species diversity. Allozymic data provided no evidence of loss of genetic variability associated with recent and rapid divergence. Genetic relationships based on Nei's genetic identity did not correspond to taxonomic relationships. For example, populations of both I. arizonica and I. tenuituba clustered within I. aggregata. Despite relatively high levels of genetic diversity among populations, diversity among taxa was low. Results indicated that floral divergence and concomitant speciation have occurred recently in the Ipomopsis aggregata complex. Allozymic patterns also reflected convergent evolution for floral morphology and possible introgression. Despite morphological differences among species, insufficient evolutionary time has elapsed for allelic fixation at neutral or near-neutral allozyme loci.     

Genetic diversity enhanced by ancient introgression and secondary contact in East Pacific black mangroves

Regional distribution of genetic diversity in widespread species may be influenced by hybridization with locally restricted, closely related species. Previous studies have shown that Central American East Pacific populations of the wide-ranged Avicennia germinans , the black mangrove, harbour higher genetic diversity than the rest of its range. Genetic diversity in this region might be enhanced by introgression with the locally restricted Avicennia bicolor . We tested the hypotheses of ancient hybridization using phylogenetic analysis of the internal transcribed spacer region (ITS) of the nuclear ribosomal DNA and intergenic chloroplast DNA; we also tested for current hybridization by population level analysis of nuclear microsatellites. Our results unveiled ancient ITS introgression between a northern Pacific Central American A. germinans lineage and A. bicolor . However, microsatellite data revealed contemporary isolation between the two species. Polymorphic ITS sequences from Costa Rica and Panama are consistent with a zone of admixture between the introgressant ITS A. germinans lineage and a southern Central American lineage of A. germinans . Interspecific introgression influenced lineage diversity and divergence at the nuclear ribosomal DNA; intraspecific population differentiation and secondary contact are more likely to have enhanced regional genetic diversity in Pacific Central American populations of the widespread A. germinans .     

Genetic variation in a geographically restricted and two widespread species of South American Nothofagus

The amount and distribution of genetic variation is compared using starch gel electrophoresis among populations of the three evergreen species of South American Nothofagus : the geographically restricted Nothofagus nitida (Phil.) Krasser and the widespread Nothofagus betuloides (Mirb.) Oerst. and Nothofagus dombeyi (Mirb.) Oerst. Ten enzyme systems were resolved coding for fifteen putative genetic loci. N. betuloides and N. dombeyi were more genetically variable than N. nitida ; they had higher total number of alleles, mean number of alleles per locus, percent of polymorphic loci, mean expected heterozygosity, and mean total genetic diversity. These results are in agreement with the hypothesis that widespread species are often associated with historically large and more continuously distributed populations which in turn can maintain higher levels of genetic variation. Conversely, the genetic structure of N. nitida including its low genetic identity with the other two species and the presence of four unique alleles support the hypothesis that N. nitida has been isolated from the other two species for a considerable period of time. Genetic data in concert with the fossil record indicate that these taxa may be members of a pre-Pleistocene flora and consequently their genetic structures reflect a more ancient evolutionary history than previously hypothesized.     

Phylogeographically concordant chloroplast DNA divergence in sympatric Nothofagus s.s. How deep can it be?

? Here, we performed phylogenetic analyses and estimated the divergence times on mostly sympatric populations of five species within subgenus Nothofagus. We aimed to investigate whether phylogenetic relationships by nuclear internal transcribed spacer (ITS) and phylogeographic patterns by chloroplast DNA (cpDNA) mirror an ancient evolutionary history that was not erased by glacial eras. Extant species are restricted to Patagonia and share a pollen type that was formerly widespread in all southern land masses. Weak reproductive barriers exist among them. ? Fifteen cpDNA haplotypes resulted from the analysis of three noncoding regions on 330 individuals with a total alignment of 1794 bp. Nuclear ITS data consisted of 822 bp. We found a deep cpDNA divergence dated 32 Ma at mid-latitudes of Patagonia that predates the phylogenetic divergence of extant taxa. Other more recent breaks by cpDNA occurred towards the north. ? Complex paleogeographic features explain the genetic discontinuities. Long-lasting paleobasins and marine ingressions have impeded transoceanic dispersal during range expansion towards lower latitudes under cooler trends since the Oligocene. ? Cycles of hybridization-introgression among extant and extinct taxa have resulted in widespread chloroplast capture events. Our data suggest that Nothofagus biogeography will be resolved only if thorough phylogeographic analyses and molecular dating methods are applied using distinct genetic markers.