Progenitor-derivative Species Pair Research Articles

Genetic architecture of ecological divergence between Oryza rufipogon and Oryza nivara.

Ecological divergence due to habitat difference plays a prominent role in the formation of new species, but the genetic architecture during ecological speciation and the mechanism underlying phenotypic divergence remain less understood. Two wild ancestors of rice (Oryza rufipogon and Oryza nivara) are a progenitor-derivative species pair with ecological divergence and provide a unique system for studying ecological adaptation/speciation. Here, we constructed a high-resolution linkage map and conducted a quantitative trait locus (QTL) analysis of 19 phenotypic traits using an F2 population generated from a cross between the two Oryza species. We identified 113 QTLs associated with interspecific divergence of 16 quantitative traits, with effect sizes ranging from 1.61% to 34.1% in terms of the percentage of variation explained (PVE). The distribution of effect sizes of QTLs followed a negative exponential, suggesting that a few genes of large effect and many genes of small effect were responsible for the phenotypic divergence. We observed 18 clusters of QTLs (QTL hotspots) on 11 chromosomes, significantly more than that expected by chance, demonstrating the importance of coinheritance of loci/genes in ecological adaptation/speciation. Analysis of effect direction and v-test statistics revealed that interspecific differentiation of most traits was driven by divergent natural selection, supporting the argument that ecological adaptation/speciation would proceed rapidly under coordinated selection on multiple traits. Our findings provide new insights into the understanding of genetic architecture of ecological adaptation and speciation in plants and help effective manipulation of specific genes or gene cluster in rice breeding.

Incipient speciation in a neotropical Gesneriaceae: Columnea kucyniakii is nested within C. strigosa

Speciation is an ongoing process. Many recognized species are fully divergent from each other and their ancestors, whereas others are in earlier stages in the diversification process. Such incipient speciation may create patterns when one or a few populations are phenotypically distinct, but lack genomic level coalescence from each other or from their ancestral species. As a result, such progenitor-derivative species pairs are likely to lack reciprocal monophyly or generate paraphyletic ancestral species. Here we examine phylogenetic patterns in the Columnea strigosa (Gesneriaceae) complex to evaluate whether populations that have been named C. kucyniakii are reciprocally monophyletic with C. strigosa, its presumed ancestral species. Molecular phylogenetic results do not support reciprocal monophyly of the two species, implying that incipient speciation is occurring within the C. strigosa complex. We hereby recommend that C. kucyniakii be recognized at the specific rank despite the fact that it creates a paraphyletic C. strigosa. These findings bear importance in taxonomic decisions about paraphyletic taxa and recognizing evolutionary and morphologically distinct lineages.

Tracking the progression of speciation: variable patterns of introgression across the genome provide insights on the species delimitation between progenitor-derivative spruces (Picea mariana × P. rubens).

The genic species concept implies that while most of the genome can be exchanged somewhat freely between species through introgression, some genomic regions remain impermeable to interspecific gene flow. Hence, interspecific differences can be maintained despite ongoing gene exchange within contact zones. This study assessed the heterogeneous patterns of introgression at gene loci across the hybrid zone of an incipient progenitor-derivative species pair, Picea mariana (black spruce) and Picea rubens (red spruce). The spruce taxa likely diverged in geographic isolation during the Pleistocene and came into secondary contact during late Holocene. A total of 300 SNPs distributed across the 12 linkage groups (LG) of black spruce were genotyped for 385 individual trees from 33 populations distributed across the allopatric zone of each species and within the zone of sympatry. An integrative framework combining three population genomic approaches was used to scan the genomes, revealing heterogeneous patterns of introgression. A total of 23 SNPs scattered over 10 LG were considered impermeable to introgression and putatively under diverging selection. These loci revealed the existence of impermeable genomic regions forming the species boundary and are thus indicative of ongoing speciation between these two genetic lineages. Another 238 SNPs reflected selectively neutral diffusion across the porous species barrier. Finally, 39 highly permeable SNPs suggested ancestral polymorphism along with balancing selection. The heterogeneous patterns of introgression across the genome indicated that the speciation process between black spruce and red spruce is young and incomplete, albeit some interspecific differences are maintained, allowing ongoing species divergence even in sympatry. The approach developed in this study can be used to track the progression of ongoing speciation processes.

Genetic Evidence of a Progenitor—Derivative Species Pair in East AsianLilium

Boreal Lilium distichum and temperate L. tsingtauense are morphologically very similar, thus they have been placed in the section Martagon. Recent molecular phylogenetic analyses revealed that L. distichum and L. tsingtauense are indeed the most closely related species within that section. Lilium distichum has a wider geographic range and a broader niche than L. tsingtauense. We hypothesized that L. distichum— L. tsingtauense might be a classical “progenitor—derivative” (P–D) species pair and examined the levels of allozyme diversity in the two species in South Korea. Whereas the allelic composition of L. tsingtauense represented a subset of L. distichum, the former had significantly lower allozyme variability at both the population and the species levels than the latter. Except for the locus Fe (fluorescent esterase), allele frequencies of L. distichum were very similar to those of L. tsingtauense. Accordingly, pairwise genetic identities between populations of L. distichum and L. tsingtauense were very high, with a mean of 0.919. Our allozyme results support the hypothesis that L. tsingtauense is a derivative species of the progenitor L. distichum.

Allozyme variation within and divergence between Lemna gibba and L. disperma: Systematic and biogeographic implications

Enzyme electrophoresis was employed to assess genetic diversity within and divergence between Lemna disperma and Lemna gibba, sister species that have often been considered conspecific because of the few technical morphological characters distinguishing them. L. gibba is distributed widely except in Australia and New Zealand, where it is replaced by L. disperma. Allozyme data were employed to examine: (1) whether species recognition is supported by genetic divergence between accessions assigned to the two taxa, (2) whether the level of diversity in the two species supports the hypothesis that L. gibba– L. disperma are related as a progenitor–derivative species pair, and (3) whether estimates of divergence times obtained from allozymes are in general agreement with those from plastid sequences. Accessions of the two species are highly divergent at allozyme loci, with a genetic identity of 0.404, and the putative derivative species ( L. disperma) has only one-third the diversity of its proposed ancestor, L. gibba. Therefore, allozyme data support the continued recognition of the two species and are concordant with the hypothesis that the species are related as progenitor and derivative. The reduced morphology of L. disperma and the allozyme data indicate that this species originated via dispersal of L. gibba or of a common ancestor of the two species. Estimated divergence times from allozymes and plastid sequences vary widely, but assuming that actual divergence was within the broad range of estimates, long distance dispersal is required to explain the present distribution of the two species.

Comparisons of allozyme variation of narrow endemic and widespread species of Far East Euphorbia (Euphorbiaceae)

Genetic variation from 19 populations representing four species of Euphorbia was compared using isozyme markers. Euphorbia fauriei and E. garanbiensis are rare endemic species in Korea and Taiwan, respectively while E. pekinensis and E. jolkinii are widespread in Korea and Taiwan. A low level of genetic variation and high genetic differentiation among populations was found in E. garanbiensis, which has a restricted distribution, small population sizes, gravity-dispersed seeds, and is possibly a self-pollinator. Alternatively, E. garanbiensis may have recently evolved from a continental progenitor or may be a relictual lineage from the continental flora. The high genetic diversity found in E. fauriei is unusual and may be explained by its recent origin from a widespread continental progenitor, E. pekinensis, An alternative explanation is that E. fauriei survived in refugia during the last glaciation in the Korean peninsula. The idea of progenitor-derivative species pairs between E. pekinensis and E. fauriei is supported by the high genetic identity values between the two species and the putative derivative E. fauriei having no unique allele and lacking some rare alleles present in the putative progenitor E. pekinensis.

Evidence from sequence-tagged-site markers of a recent progenitor-derivative species pair in conifers.

Black spruce (Picea mariana [B.S.P.] Mill.) and red spruce (Picea rubens Sarg.) are two conifer species known to hybridize naturally in northeastern North America. We hypothesized that there is a progenitor-derivative relationship between these two taxa and conducted a genetic investigation by using sequence-tagged-site markers of expressed genes. Based on the 26 sequence-tagged-site loci assayed in this study, the unbiased genetic identity between the two taxa was quite high with a value of 0.920. The mean number of polymorphic loci, the mean number of alleles per polymorphic locus, and the average observed heterozygosity were lower in red spruce (P = 35%, A(P) = 2.1, H(o) = 0.069) than in black spruce (P = 54%, A(P) = 2.9, H(o) = 0.103). No unique alleles were found in red spruce, and the observed patterns of allele distribution indicated that the genetic diversity of red spruce was essentially a subset of that found in black spruce. When considered in combination with ecological evidence and simulation results, these observations clearly support the existence of a progenitor-derivative relationship and suggest that the reduced level of genetic diversity in red spruce may result from allopatric speciation through glaciation-induced isolation of a preexisting black spruce population during the Pleistocene era. Our observations signal a need for a thorough reexamination of several conifer species complexes in which natural hybridization is known to occur.

Population genetics of two rare perennials in isolated wetlands: Sagittaria isoetiformis and S. teres (Alismataceae)

We investigated genetic structure in two closely related perennial plants that occur in isolated wetlands: Sagittaria isoetiformis, restricted to the southeastern Coastal Plain of North America, and S. teres, endemic to the northeastern Coastal Plain. Using horizontal starch-gel electrophoresis, we screened 527 individuals from 11 populations of S. isoetiformis and 367 individuals from seven populations of S. teres. A high proportion of the 16 loci were polymorphic (%P(S) = 93.8% in S. isoetiformis and %P(S) = 75.0% in S. teres), with higher mean numbers of alleles per polymorphic locus and effective alleles per locus in S. isoetiformis (AP = 3.27, A(E) = 1.90) than in S. teres (AP = 2.58, A(E) = 1.30). Species- and population-level expected heterozygosities were higher in S. isoetiformis (H(ES) = 0.399, H(EP) = 0.218) than in S. teres (H(ES) = 0.177, H(EP) = 0.101). Jackknife estimates of F statistics indicated moderate levels of inbreeding in S. teres (F(IS) = 23.1%). Strong differentiation characterized these geographically isolated populations (G(ST) = 39.9% in S. isoetiformis, and G(ST) = 26.1% in S. teres). Genetic identities varied substantially within (Ī = 75%, range = 0.558-0.963 in S. isoetiformis; Ī = 89%, range = 0.776-0.963 in S. teres) and among species (Ī = 81%, range = 0.506-0.882), leading to the discrimination of four regional population clusters using nonmetric multidimensional scaling (NMDS). It appears that S. isoetiformis and S. teres are a progenitor-derivative species pair.

Isozyme Variation and Ploidy Levels within the Apomictic Ranunculus auricomus Complex: Evidence for a Sexual Progenitor Species in Southeastern Austria

Abstract: Allozyme variation of 11 enzymes in each of three populations of the diploid species Ranunculus notabilis and the tetraploid R. variabilis of the predominantly apomictic R. auricomus complex has been studied by horizontal starch gel electrophoresis. Genetic interpretation of electrophoretic patterns is supported by chromosome counts and densitometric ploidy level determination. R. notabilis is confirmed as diploid (2 n = 16), and R. variabilis as tetraploid (2 n = 32). Two triploids and one tetraploid individual were sorted out as putative hybrids. Genetic variability measures based on both allelic frequencies and genotype frequencies were calculated for 13 polymorphic loci. Allelic and genotypic variation in R. notabilis is similar to other sexual plants, and the species is shown to be an outbreeder and not a dihaploid apomict. Corresponding values in R. variabilis confirm a previously assumed clonal population structure. A higher frequency of observed heterozygotes in R. variabilis indicates its hybridogenous origin and the lack of meiosis. Putative hybrids showed combinations of morphological phenotype and electrophoretic patterns of both species. Genetic identity is high among species (0.905), but still lower than within species (R. notabilis: 0.965, R. variabilis: 0.940); corresponding distance values allow a clear separation of the two species in a dendrogram. Genetic identity and distance values between R. notabilis and R. variabilis resemble those of other progenitor‐derivative species pairs. The results favour the hypothesis that R. notabilis is an ancient sexual species of the R. auricomus complex and also one progenitor of the presumably allopolyploid R. variabilis.

Population genetics of geographically restricted and widespread species of Myrica (Myricaceae).

Allozyme variation of 11 putative loci in five populations of the rare Myrica adenophora Hance, and four populations of its widespread congeneric species, M. rubra (Lour.) Sieb. & Zucc. was studied. Among the 21 alleles studied, no unique allele was detected for M. adenophora, whereas M. rubra had 3 alleles not found in the former species. In terms of genetic diversity, populations of the rare species contained fewer alleles per locus (1.5 versus 1.7), fewer effective number of alleles per locus (1.12 versus 1.20), fewer number of alleles per polymorphic locus (2.14 versus 2.46), lower percentage of polymorphic loci (30.9 versus 40.9), and lower expected heterozygosity (0.106 versus 0.163) than populations of the widespread species. Genetic distances within species average 0.043 for M. adenophora and 0.045 for M. rubra, and between species ranged from 0.052 to 0.177, with a mean of 0.103, which agrees with the very similar gross morphologies of these two species. Intrapopulation differentiation was similar in both species: G(ST) = 0.152 for M. adenophora, and 0.146 for M. rubra, whereas estimated gene flow based on G(ST) values were moderate in these two species (Nm = 1.39 versus 1.46). We inferred that M. rubra and M. adenophora are a progenitor-derivative species pair that emerged before migrating into Taiwan during the last glacial period. We consider the Hengchun population (Chiupeng, Hsuhai, and Chufengpi) and Taitung population (Tienkuan and Lanshan) of M. adenophora which probably arose from two subsets of the genome of M. rubra. Genetic drift was inferred to be one of the forces shaping the observed genetic structure in M. adenophora and M. rubra.

Chloroplast DNA variation inCoreopsis nuecensoides andC. nuecensis (Asteraceae), a presumed progenitor-derivative species pair

Coreopsis nuecensoides andC. nuecensis are narrowly distributed endemics of southeastern Texas. While they overlap in range, they differ in chromosome number, and F1 hybrids exhibit strong sterility barriers. Previous morphological, cytogenetic, and allozyme studies suggested thatC. nuecensoides andC. nuecensis are very closely related members of a progenitor-derivative species pair. The two species differ substantially in terms of their leaf flavonoid chemistry, but the flavonoid data do not address the exact nature of the relationship between them. We have further examined the relationship between the species by analyzing genetic diversity within both species using chloroplast DNA (cpDNA) restriction site data. Sixteen restriction site changes were used to define thirteen distinct cpDNA haplotypes. The pattern of relationships among haplotypes provides some support for the presumed ancestor-descendent relationship, but other interpretations are possible. Only one cpDNA haplotype was shared by the two species; of the remaining twelve, seven were unique to one species and five to the other. This result is consistent with results of flavonoid studies, in which each species exhibited flavonoid compounds not seen in the other, but differs from the allozyme results, in which the vast majority of alleles were shared by both species and only the presumed progenitor exhibited unique alleles. Taken together, the data support a very close relationship between the species, but are equivocal with regard to a progenitor-derivative relationship.

Allozyme Variation in Coreopsis Sect. Coreopsis (Compositae)

An electrophoretic study of the nine species of Coreopsis sect. Coreopsis (C. auriculata, C. basalis, C. grandiflora, C. intermedia, C. lanceolata, C. nuecensis, C. nuecensoides, C. pubescens, and C. wrightii) revealed high genetic identities (above 0.90 for most comparisons) for all species. Uniformly high identities among all taxa made it difficult to discern patterns of relationships among the species in sect. Coreopsis. Similar levels of gene diversity were found in perennial and annual species in the section, and between geographically widespread vs. more restricted species. It is suggested that the high identities result from the recent divergence among the species in sect. Coreopsis, which is viewed as a highly evolved section within North American Coreopsis. The genus Coreopsis in North America consists of 11 sections containing a total of about 44 species. The genus is distributed throughout Mexico, California, and the eastern and southeastern United States. The sections are welldefined with regard to chromosome number, morphology, and geographic distribution (Smith 1975). Attempts to produce artificial hybrids between plants of different sections have, for the most part, failed, while there is some intercompatibility and interfertility between species within sections (Smith 1975, 1976). Section Coreopsis is the largest of the North American sections. Smith (1975) viewed it as one of the most advanced groups of North American Coreopsis. The section is native to and centered within the eastern and southeastern United States, with certain species widely distributed throughout this range while others are restricted in distribution. It consists of nine species, four of which are annuals and five are perennials. Perennial species include C. pubescens Elliott, C. auriculata L., C. intermedia Sherff, C. lanceolata L., and C. grandiflora Hogg ex Sweet. The annual species are C. basalis (Dietr.) Blake, C. wrightii (A. Gray) H. M. Parker, C. nuecensoides E. B. Smith, and C. nuecensis A. Heller. The base chromosome number for the section is n = 13. Two species, C. nuecensis and C. nuecensoides, exhibit aneuploidy (n = 6, 7, 8 and n = 9, 10, 11, respectively), and one taxon, C. grandiflora var. longipes (Hook.) Torrey & A. Gray, is hexaploid (n = 39). All species are self-incompatible and presumably strongly outcrossing (Smith 1975, 1976). Discerning evolutionary relationships within the section has proven problematical. Although the section itself is a well-defined, monophyletic group, relationships among the perennial species and origin of the annual species within the section remain unclear. However, available evidence suggests that the four annual species consist of two progenitorderivative species pairs, C. basalis-C. wrightii and C. nuecensoides-C. nuecensis, the former species in each pair representing the progenitor species (Crawford and Smith 1982a, 1982b; Smith 1974; Smith and Crawford 1981). Smith (1982) constructed a phylogenetic hypothesis for the section based largely on morphology (fig. la). He suggested that C. pubescens may represent the basal taxon within the section, and that the two progenitor-derivative annual species pairs are relatively advanced, but their origin from the perennials is obscure. His phylogeny also indicates a close relationship between C. lanceolata and C. auriculata (fig. la). The cladistic analysis of North American Coreopsis by Jansen et al. (1987) agrees in many respects with Smith's proposed phylogeny, including the separation of annuals and perennials into two distinct lines (fig. lb). Annuals are composed of two pairs, namely C. basalis-C. wrightii and C. nuecensoidesC. nuecensis, in their treatment as well. However, the cladistic study differs in that C. auriculata shows closer affinities with C. pubescens rather than with C. lanceolata as suggested by Smith (1982). Preliminary chloroplast DNA data (Crawford et al. 1988; unpubl. data) suggest that C. pubescens and C. auriculata are closely allied, and that one of these taxa (or a common ancestor) could

Molecular divergence in the Galapagos Islands?Baja California species pair,Gossypium klotzschianum andG. davidsonii (Malvaceae)

Molecular divergence betweenGossypium klotzschianum andG. davidsonii was studied. The former is endemic to five of the larger islands of the Galapagos, whileG. davidsonii is restricted to the southern half of Baja California, approximately 2 500 km distant. A substantial body of genetic and taxonomic data suggests that these two species are related as progenitor and derivative. Interspecific hybrids are fully fertile, with no evidence of F2 breakdown and normal segregation of genetic markers. Allozyme analysis of 33 populations for 41 loci indicated that the allelic composition ofG. klotzschianum represents a subset ofG. davidsonii. Although genetic diversity is relatively restricted in both species, calculated measures demonstrate higher levels of genetic variability and greater population structuring inG. davidsonii than inG. klotzschianum. The interspecific genetic identity of 0.87 is typical for progenitor-derivative species pairs. Chloroplast DNAs were surveyed for variation with 25 restriction enzymes using hybridization probes that cover the entire chloroplast genome. No intraspecific and little interspecific variation was detected among 560 cpDNA restriction sites, representing sequence information for approximately 3200 nucleotides. Only 3 mutational differences distinguished the two species, resulting in a sequence divergence estimate of 0.09%. Divergence times were estimated from both the isozyme data and the cpDNA restriction site data. Although these estimates have several sources of error, both molecular data sets were congruent in suggesting that the two lineages diverged between 250000 and 700000 years ago. Accumulated evidence suggests that dispersal was from Baja California to the Galapagos Islands rather than the reverse, and most likely was mediated by trans-oceanic drift.G. klotzschianum may be the only species of the endemic Galapagos flora to have arisen from a northern Mexican progenitor.

Flavonoids of the annual Stephanomeria (Asteraceae)

Abstract The occurrence of 11 flavonoids and two coumarins was determined for five species of annual Stephanomeria; S. exigua (four subspecies); S. paniculata, S. diegensis, S. virgata and S. malheurensis . The flavonoid profiles of these taxa are based upon glycosides of apigenin, luteolin, kaempferol, quercetin and eriodictyol. Esculetin (6, 7-dihydroxycoumarin) and its 6- O -glucoside, cichoriin, were also identified. The flavonoid and coumarin profiles of these species were very similar, as determined by examining individuals of each taxon. There was some variation in the occurrence of querecetin 3- O -rutinoside but the pattern followed no taxonomic lines. The flavonoids and coumarin profiles for S. exigua subsp, coronaria and S. malheurensis , which constitute a progenitor-derivative species pair, were identical except that one line of S. malheurensis lacked the coumarin glucoside while another had eriodictyol 7- O - glucoside as a major component. In all other specimens eriodictyol was present in much smaller amounts or was not observed.

GENETIC ORGANIZATION AND EVOLUTIONARY HISTORY IN TWO NORTH AMERICAN SPECIES OF CIRSIUM.

Relationships involving progenitor and derivative species pairs have been documented for a number of plant taxa. In this study, we used starch-gel electrophoresis to examine the probable relationship between Cirsium pitcheri, an endemic thistle restricted to the shorelines of the Great Lakes, and Cirsium canescens, a closely related species of the central Great Plains (U.S.A.). The species shared the same enzyme loci but differed greatly in levels of genetic diversity. C. pitcheri was genetically much less variable than its congener, with fewer polymorphic loci and significantly lower heterozygosity. The genetic variation in C. pitcheri represents a depauperate subset of the alleles present in C. canescens, consistent with the hypothesis that the two species represent a progenitor-derivative species pair. We suggest that C. pitcheri migrated into newly created dune habitats in the Great Lakes region near the end of the Wisconsin glaciation and that its low genetic variability results from repeated and probably prolonged population bottlenecks which accompanied its movement.