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Most plant nuclear-encoded genes exist in gene families of various sizes. We present a characterization of the structure and evolution of the alcohol dehydrogenase {Adh) gene family in diploid and tetraploid members of the cotton genus {Gossypium). A PCR-based approach was employed to isolate and sequence multiple Adh gene family members. We used Southern hybridization analyses to docimient variation in gene copy number in three diploids which represent the primary centers of Gossypium diversity (Australia — G. robinsonii, Africa — G. herbaceum. New World — G. raimondii), as well as one of the five allotetraploid species (G. hirsutum). The diploid species of Gossypium contain at least seven Adh loci in two primary gene lineages. One of these lineages contains two loci that are the result of a local duplication; the other lineage contains at least five loci. Sequence analysis reveals extensive variation in intron lengths between loci, and one locus has lost two introns usually found in other plant Adh genes. Evolutionary rate estimates differ between loci and in some cases between organismal lineages at the same locus. Finally, the Adh gene family appears relatively active in that multiple examples of apparent gene duplication events were found and at least one case of pseudogenization and one case of gene elimination were also found. Key Words; Adh, cotton, genetic mapping, molecular evolution, gene family, polj^loidy

 Premise of the study: The role of hybridization in plant evolution remains a source of intense debate. Potential consequences range from genetic dead-ends to species fusion or hybrid speciation. While much has been learned from model systems such as Populus , Iris , and Helianthus , many questions remain. Consisting of 11 species that are all capable of hybridizing, Sarracenia presents an excellent system in which to study hybridization.  Methods: Using microsatellites, we examined a single fi eld site consisting of three species: S. leucophylla , S. alata , and S. rubra subsp. wherryi. We determined the level of genetic admixture and compared it with allopatric sites of the same taxa.  Key results: In contrast to the well-defi ned clusters formed when we examined the allopatric sites, the sympatric fi eld site exhibited a wide range of admixture. Additionally, when the relative genetic makeup of “pure” species at the site was compared with the makeup of hybrids, we found that Sarracenia alata contributed disproportionately to the hybrid genomes.  Conclusions: Our study provides further evidence that hybridization is contributing to interspecifi c gene fl ow in the genus and that all species do not contribute equally to hybridization. Implications for conservation are discussed.

Distinguishing between hybrid zones formed by secondary contact versus parapatric divergence-with-gene-flow is an important challenge for understanding the interplay of geographic isolation and local adaptation in the origin of species. Similarly, distinguishing between natural hybrid zones and those that formed as a consequence of recent human activities has important conservation implications. Recent work has demonstrated the existence of a narrow hybrid zone between the plains gartersnake (Thamnophis radix) and Butler’s gartersnake (T. butleri) in the Great Lakes region of North America, raising questions about the history and conservation value of genetically admixed populations. Both taxa are of conservation concern, and it is not clear whether to regard hybridization as a threat or a natural interaction. Here we use phylogeographic and population genetic methods to assess the timescales of divergence and hybridization, and test for evidence that the hybrid zone is of recent origin. We assayed AFLP markers and ND2 mitochondrial DNA (mtDNA) sequences from T. radix, T. butleri, and the closely related short-headed gartersnake (T. brachystoma) throughout their North American ranges. We find shallow mtDNA divergence overall and high levels of variation within the contact zone. These patterns are inconsistent with recent contact of long-diverged taxa. It is not possible to distinguish true divergence-with-gene-flow from a long-term secondary contact zone, but we infer that the hybrid zone is a long-standing, natural interaction.

Comparative analyses were made of agamospermous populations of Eupatorium sessilifolium, which have previously been documented to be polyploid, to determine whether they are alloploid or autoploid in origin and to assess the possibility that they have arisen more than once. There was no variability in ITS sequences among seven agamospermous and eight sexual diploid populations of E. sessilifolium, which is consistent with morphological observations in suggesting that the agamospermous populations were autoploids. The ITS sequence characteristic of E. sessilifolium differs from all other North American species by a minimum of 15 changes, and heterogeneity or polymorphism would be expected if the agamospermous populations were alloploids. Analysis of the chloroplast-based trnC-psbM spacer region showed variability among both sexual diploid and agamospermous populations of E. sessilifolium, which suggested that the agamospermous populations stem from multiple origins. Analysis of ISSR data revealed considerable intraspecific variability within E. sessilifolium, and the distribution of variability, with agamospermous populations showing variability from one another, added further evidence for multiple origins of agamospermous populations. The results in conjunction with distributional evidence that the sexual diploid populations of E. sessilifolium are geographically restricted and uncommon suggest that monitoring of populations might be warranted to evaluate whether measures are needed to enhance their continued survival.

Within the past decade, Scrophulariaceae sensu lato has been shown to be polyphyletic and, as a result, is currently undergoing major systematic revision. The traditionally recognized family is now generally considered to comprise several smaller families including the newly expanded Plantaginaceae, a family of 12 tribes, 92 genera, and approximately 2000 species. Recent evidence from molecular phylogenetics supports the inclusion of the tribe Gratioleae within the Plantaginaceae. Gratioleae includes 16–40 genera, depending on generic circumscription, many of which have yet to be assessed phylogenetically. Amphianthus is a monotypic genus whose systematic affinities have long been poorly known. We included Amphianthus, 10 additional Gratioleae genera, and several outgroup genera from Plantaginaceae in a phylogenetic investigation to examine the relationships of Amphianthus. We present the most complete phylogeny of the Gratioleae to date and provide evidence from chloroplast DNA sequences of the ...

Prunus subg. Prunus sect. Prunocerasus (Rosaceae) is a North American taxon with 17 commonly recognized taxa. To test the hypothesis of monophyly for the section we sequenced the trnG and rpL16 introns and the trnH-psbA and trnS-trnG intergenic spacers for at least two representatives of each of the five subgenera in Prunus. Additionally we sampled heavily among Prunus subg. Prunus sections Prunus and Armeniaca and Prunus subg. Amygdalus because these groups are putatively most closely related to Prunocerasus. Once monophyly of sect. Prunocerasus was shown we added the sequences of trnL and rpS16 introns and the trnL-trnF spacer in an attempt to increase resolution within the section. The species of sect. Prunocerasus showed an initial split with P. subcordata, the only species from western North America, sister to the rest of the group. The remaining species fell into three primary clades. Within each of the three primary clades there was little phylogenetic resolution. Lastly, we present evidence that P. texana, previously classified in subg. Amygdalus, may be a plum or at least contain a Prunocerasus chloroplast. This is the first phylogenetic hypothesis presented for sect. Prunocerasus, and the clades recovered contrast sharply with previously defined groups based on morphological characters.

Hibiscus section Muenchhusia is a North American taxon with five species as recognized in the most recent taxonomic revision: H. coccineus, H. dasycalyx, H. grandiflorus, H. laevis, and H. moscheutos. To investigate the monophyly of Hibiscus section Muenchhusia, its relationship to other Hibiscus species, and the phylogenetic relationships among its species, DNA sequence data were obtained. To investigate the placement of section Muenchhusia within Hibiscus, chloroplast ndhF gene and rpL16 intron sequences were generated and added to a recently published dataset. To investigate relationships within section Muenchhusia three DNA sequence data sets were generated: a non-coding region of the chloroplast genome (rpL16 intron), nuclear ribosomal ITS, and a nuclear gene encoding granule-bound starch synthase (GBSSI). Analyses of ndhF + rpL16 data indicated that section Muenchhusia is indeed monophyletic and is embedded in a clade that includes representatives of Hibiscus section Trionum sensu lato plus...

The Mexican cotton Gossypium gossypioides is a perplexing entity, with conflicting morphological, cytogenetic, and molecular evidence of its phylogenetic affinity to other American cottons. We reevaluated the evolutionary history of this enigmatic species using 16.4 kb of DNA sequence. Phylogenetic analyses show that chloroplast DNA (7.3 kb), nuclear ribosomal internal transcribed spacers (ITS; 0.69 kb), and unique nuclear genes (8.4 kb) yield conflicting resolutions for G. gossypioides. Eight low-copy nuclear genes provide a nearly unanimous resolution of G. gossypioides as the basalmost American diploid cotton, whereas cpDNA sequences resolve G. gossypioides deeply nested within the American diploid clade sister to Peruvian G. raimondii, and ITS places G. gossypioides in an African (rather than an American) clade. These data, in conjunction with previous evidence from the repetitive fraction of the genome, implicate a complex history for G. gossypioides possibly involving temporally separated introgression events from genetically divergent cottons that are presently restricted to different hemispheres. Based on repetitive nuclear DNA, it appears that G. gossypioides experienced nuclear introgression from an African species shortly after divergence from the remainder of the American assemblage. More recently, hybridization with a Mexican species may have resulted in cpDNA introgression, and possibly a second round of cryptic nuclear introgression. Gossypium gossypioides provides a striking example of the previously unsuspected chimeric nature of some plant genomes and the resulting phylogenetic complexity produced by multiple historical reticulation events.

It has long been known that genomes vary over a remarkable range of sizes in both plants (Bennett, Cox, and Leitch 1997) and animals (Gregory 2001). It also has become evident that across the broad phylogenetic sweep, genome size may be correlated with intron size (Deutsch and Long 1999; Vinogradov 1999; McLysaght et al. 2000), suggesting that some component of genome size evolution takes place within genes. Examples include humans and pufferfish (Fugu), where comparisons of 199 introns in 22 orthologous genes showed that introns in Fugu were on average eight times as small as those in humans, consistent with their ratio of genome sizes (McLysaght et al. 2000). Similarly, Deutsch and Long (1999) tabulated intron sizes across a broad phylogenetic spectrum of eukaryotes and noted a general but weak correlation with genome size, with humans having the most and longest introns (mean of 3.4 kbp) among the 10 taxa studied. Intron size is also correlated with genome size in Drosophila (Moriyama, Petrov, and Hartl 1998), showing that the correlation may extend to more recent divergences. At present there is little information on the correlation between genome and intron sizes in plants, although there are suggestions that plants with small genomes have smaller introns (Deutsch and Long 1999; Vinogradov 1999). Whereas broad comparisons across widely divergent taxa are now possible given completed draft sequences for the rice (Goff et al. 2002; Yu et al. 2002) and Arabidopsis (Arabidopsis Genome Initiative 2000) genomes, the divergence time between Poaceae and Brassicaceae is so large that the influence of genome size on intron size may be confounded by numerous other, unstudied covariables. It seems likely that more informative studies will involve closely related taxa that vary significantly in genome size but which share recent evolutionary history and a broad suite of life-history features. An additional advantage of comparing close relatives is that orthology among genes, and hence introns, may be more readily established. This latter point may be especially important, given the relative lability of copy-number for many gene families (Small and Wendel 2000). To exemplify this approach, we studied the relationship between intron size and genome size for or

The 13 “D-genome”cotton species are a monophyletic assemblage of morphologically diverse diploids that inhabit arid to semiarid regions in Mexico, with 1 disjunct species each in Peru and the Galapagos Islands and 1 species whose range extends northward into Arizona. While these species lack commercially significant fiber (i.e., cotton), they are important in that they represent one of the parental genomes of the cultivated tetraploid cottons. To assess phylogenetic relationships among these species, we sequenced and analyzed a region of a nuclear-encoded alcohol dehydrogenase gene (AdhA). Phylogenetic analysis resulted in a topology that is generally consistent with current taxonomic alignment of the species, although the phylogeny based on AdhA sequences conflicts with those inferred from cpDNA and ITS data sets, most notably in the position of the anomalous species Gossypium gossypioides. In one lineage, we detected both gene duplication and sequence polymorphisms that transcend species boundaries; sequences in this lineage formed a monophyletic clade, yet no taxon within the clade contained a monophyletic collection of sequences. Potential explanations for this latter phenomenon, including gene duplication, gene flow, and lineage sorting, are discussed.

Phylogenetic resolution is often low within groups of recently diverged taxa due to a paucity of phylogenetically informative characters. We tested the relative utility of seven noncoding cpDNA regions and a pair of homoeologous nuclear genes for resolving recent divergences, using tetraploid cottons ( Gossypium) as a model system. The five tetraploid species of Gossypium are a monophyletic assemblage derived from an allopolyploidization event that probably occurred within the last 0.5‐2 million years. Previous analysis of cpDNA restriction site data provided only partial resolution within this clade despite a large number of enzymes employed. We sequenced three cpDNA introns (rpl16, rpoC1, ndhA) and four cpDNA spacers (accD-psaI, trnL-trnF, trnT-trnL, atpB-rbcL) for a total of over 7 kb of sequence per taxon, yet obtained only four informative nucleotide substitutions (0.05%) resulting in incomplete phylogenetic resolution. In addition, we sequenced a 1.65-kb region of a homoeologous pair of nuclear-encoded alcohol dehydrogenase (Adh) genes. In contrast with the cpDNA sequence data, the Adh homoeologues yielded 25 informative characters (0.76%) and provided a robust and completely resolved topology that is concordant with previous cladistic and phenetic analyses. The enhanced resolution obtained using the nuclear genes reflects an approximately three- to sixfold increase in nucleotide substitution rate relative to the plastome spacers and introns.

The phylogeny of baobab trees was analyzed using four data sets: chloroplast DNA restriction sites, sequences of the chloroplast rpl16 intron, sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA, and morphology. We sampled each of the eight species of Adansonia plus three outgroup taxa from tribe Adansonieae. These data were analyzed singly and in combination using parsimony. ITS and morphology provided the greatest resolution and were largely concordant. The two chloroplast data sets showed concordance with one another but showed significant conflict with ITS and morphology. A possible explanation for the conflict is genealogical discordance within the Malagasy Longitubae, perhaps due to introgression events. A maximum-likelihood analysis of branching times shows that the dispersal between Africa and Australia occurred well after the fragmentation of Gondwana and therefore involved overwater dispersal. The phylogeny does not permit unambiguous reconstruction of floral evolution but suggests the plausible hypothesis that hawkmoth pollination was ancestral in Adansonia and that there were two parallel switches to pollination by mammals in the genus.

 Premise of the study: Narrow-ranging, rare species often exhibit levels of genetic diversity lower than more common or widespread congeners. These taxa are at increased risk of extinction due to threats associated with natural as well as anthropogenic events. We assessed genetic variation in three federally endangered Sarracenia species. We discuss maintenance of genetic diversity and evolutionary implications of rarity.  Methods: We analyzed three noncoding chloroplast regions and nine microsatellite loci in populations spanning the geographic ranges of S. oreophila , S. alabamensis , and S. jonesii . The same microsatellite loci were used to examine a single fi eld site of three more widespread species ( S. alata , S. leucophylla , and S. rubra subsp. wherryi ).  Key results: All three endangered species have experienced reductions in population size and numbers. All show considerably less variation than more widespread members of the genus. Sarracenia alabamensis maintains the greatest microsatellite variation but has the fewest remaining populations and may be under the greatest threat. More widespread S. oreophila maintains surprising chloroplast diversity, yet exhibits little microsatellite diversity. Sarracenia jonesii lacks chloroplast diversity, yet maintains greater microsatellite diversity than S. oreophila .  Conclusions: The three endangered species differ in levels and structure of diversity, yet not in predictable ways, emphasizing that unique demographic and ecological histories, rather than current distribution and population size, best explain present patterns of genetic variation. Maintenance of remaining genetic variation is important, but preventing further habitat loss and degradation is critical.

Previous molecular phylogenetic studies have failed to resolve the branching order among the major cotton (Gossypium) lineages, and it has been unclear whether this reflects actual history (rapid radiation) or sampling properties of the genes evaluated. In this paper, we reconsider the phylogenetic relationships of diploid cotton genome groups using DNA sequences from 11 single-copy nuclear loci (10 293 base pairs [bp]), nuclear ribosomal DNA (695 bp), and four chloroplast loci (7370 bp). Results from individual loci and combined nuclear and chloroplast DNA partitions reveal that the cotton genome groups radiated in rapid succession following the formation of the genus. Maximum likelihood analysis of nuclear synonymous sites shows that this radiation occurred within a time span equivalent to 17% of the time since the separation of Gossypium from its nearest extant relatives in the genera Kokia and Gossypioides. Chloroplast and nuclear phylogenies differ significantly with respect to resolution of the basal divergence in the genus and to interrelationships among African cottons. This incongruence is due to limited character evolution in cpDNA and either previously unsuspected hybridization or unreliable phylogenetic performance of the cpDNA characters. This study highlights the necessity of using multiple, independent data sets for resolving phylogenetic relationships of rapidly diverged lineages.

Chloroplast DNA sequences are a primary source of data for plant molecular systematic studies. A few key papers have provided the molecular systematics community with universal primer pairs for noncoding regions that have dominated the field, namely trnL-trnF and trnK/matK. These two regions have provided adequate information to resolve species relationships in some taxa, but often provide little resolution at low taxonomic levels. To obtain better phylogenetic resolution, sequence data from these regions are often coupled with other sequence data. Choosing an appropriate cpDNA region for phylogenetic investigation is difficult because of the scarcity of information about the tempo of evolutionary rates among different noncoding cpDNA regions. The focus of this investigation was to determine whether there is any predictable rate heterogeneity among 21 noncoding cpDNA regions identified as phylogenetically useful at low levels. To test for rate heterogeneity among the different cpDNA regions, we used three species from each of 10 groups representing eight major phylogenetic lineages of phanerogams. The results of this study clearly show that a survey using as few as three representative taxa can be predictive of the amount of phylogenetic information offered by a cpDNA region and that rate heterogeneity exists among noncoding cpDNA regions.

The North American plums are a closely related group that are not easily circumscribed, have overlapping morphologies, and are known to hybridize. We previously showed that the North American plums are a closely related, monophyletic group of taxa with little to no cpDNA sequence divergence between taxa. In that study, we came to the unanticipated conclusion that relationships inferred among the taxa contrast sharply with previously defined groups based on morphological characters. Here the aim was to determine if the primary cpDNA haplotypes identified in our earlier study are confined to the taxa in which they were initially observed. The cpDNA rpL16 intron was sequenced for 207 accessions of the 17 North American plum taxa plus Prunus texana. The results show that many taxa contain more than one of the three primary cpDNA haplotypes. Aside from the results found in sect. Prunocerasus, this study has broader implications for phylogenetics in general. The common practice of choosing a single exemplar to represent a taxon can be profoundly misleading in closely related groups. In hindsight, the possibility existed in our earlier study that we could have chosen a different combination of exemplars, which could have resulted in a different inferred phylogeny.

Although the chloroplast genome contains many noncoding regions, relatively few have been exploited for interspecific phylogenetic and intraspecific phylogeographic studies. In our recent evaluation of the phylogenetic utility of 21 noncoding chloroplast regions, we found the most widely used noncoding regions are among the least variable, but the more variable regions have rarely been employed. That study led us to conclude that there may be unexplored regions of the chloroplast genome that have even higher relative levels of variability. To explore the potential variability of previously unexplored regions, we compared three pairs of single-copy chloroplast genome sequences in three disparate angiosperm lineages: Atropa vs. Nicotiana (asterids); Lotus vs. Medicago (rosids); and Saccharum vs. Oryza (monocots). These three separate sequence alignments highlighted 13 mutational hotspots that may be more variable than the best regions of our former study. These 13 regions were then selected for a more detailed analysis. Here we show that nine of these newly explored regions (rpl32-trnL((UAG)), trnQ((UUG))-5'rps16, 3'trnV((UAC))-ndhC, ndhF-rpl32, psbD-trnT((GGU)), psbJ-petA, 3'rps16-5'trnK((UUU)), atpI-atpH, and petL-psbE) offer levels of variation better than the best regions identified in our earlier study and are therefore likely to be the best choices for molecular studies at low taxonomic levels.

While multiple phylogenetic markers have been used in the culture-independent study of microcystin-producing cyanobacteria, in only a few instances have multiple markers been studied within individual cells, and in all cases these studies have been conducted with cultured isolates. Here, we isolate and evaluate large DNA fragments (>6 kb) encompassing two genes involved in microcystin biosynthesis ( mcyA2 and mcyB1 ) and use them to identify the source of gene fragments found in water samples. Further investigation of these gene loci from individual cyanobacterial cells allowed for improved analysis of the genetic diversity within microcystin producers as well as a method to predict microcystin variants for individuals. These efforts have also identified the source of the novel mcyA genotype previously termed Microcystis -like that is pervasive in the Laurentian Great Lakes and they predict the microcystin variant(s) that it produces.

Knowledge of patterns of organellar inheritance are crucial for analyses of organellar genetics and population or phylogenetic analyses based on organellar genes. While it has previously been shown that chloroplast DNA is maternally inherited in cotton (Gossypium L.), no, studies have assessed the mitochondrial genome complement of the allotetraploid species of cotton or addressed inheritance of mitochondrial DNA. In this article we report Southern hybridization analyses that indicate that the AD-genome allotetraploid species have an A-genome-like mitochondrial genome and provide evidence that mitochondrial genomes are also maternally inherited in cotton.

Pleistocene events played an important role in the differentiation of North American vertebrate populations. Michigan, in particular, and the Great Lakes region, in general, were greatly influenced by the last glaciation. While several hypotheses regarding the recolonization of this region have been advanced, none have been strongly supported. We generated 148 complete ND2 mitochondrial DNA (mtDNA) sequences from common gartersnake (Thamnophis sirtalis) populations throughout the Great Lakes region to evaluate phylogeographic patterns and population structure and to determine whether the distribution of haplotypic variants is related to the post-Pleistocene retreat of the Wisconsinan glacier. The common gartersnake was utilized, as it is believed to have been one of the primary vertebrate invaders of the Great Lakes region following the most recent period of glacial retreat and because it has been a model species for a variety of evolutionary, ecological, behavioral, and physiological studies. Several genetically distinct evolutionary lineages were supported by both genealogical and molecular population genetic analyses, although to different degrees. The geographic distribution of the majority of these lineages is interpreted as reflecting post-glacial recolonization dynamics during the late Pleistocene. These findings generally support previous hypotheses of range expansion in this region.

Intra- and interspecific relationships of 12 out of 13 described species as well as a potential new species in the spider genus Agelenopsis (Araneae: Agelenidae) were analyzed using sequence data from two mitochondrial genes, cytochrome oxidase I (COI) and 16S ribosomal RNA. Approximately half of the species examined formed well-supported monophyletic groups, whereas the rest of the species were part of well-supported monophyletic species groups. Rather than viewing cases where species were not identified as being monophyletic as poor taxonomy, these cases more likely represent recent speciation and offer insights into the process of speciation. The clade with the lowest levels of interspecific sequence divergence was found in eastern North America, whereas western species displayed much higher levels of interspecific divergence. These patterns appear to extend below the species level as well, with southwestern species exhibiting the highest levels of intraspecific sequence divergence and geographic structuring. The relationship between Agelenopsis and Barronopsis, a genus once considered a sub-genus of Agelenopsis, was also examined. The two genera are reciprocally monophyletic but more generic level sampling is needed to confirm an apparent sister relationship between the two.

Noncoding DNA sequences from numerous regions of the chloroplast genome have provided a significant source of characters for phylogenetic studies in seed plants. In lycophytes and monilophytes (leptosporangiate ferns, eusporangiate ferns, Psilotaceae, and Equisetaceae), on the other hand, relatively few noncoding chloroplast DNA regions have been explored. We screened 30 lycophyte and monilophyte species to determine the potential utility of PCR amplification primers for 18 noncoding chloroplast DNA regions that have previously been used in seed plant studies. Of these primer sets eight appear to be nearly universally capable of amplifying lycophyte and monilophyte DNAs, and an additional six are useful in at least some groups. To further explore the application of noncoding chloroplast DNA, we analyzed the relative phylogenetic utility of five cpDNA regions for resolving relationships in Botrychium s.l. (Ophioglossaceae). Previous studies have evaluated both the gene rbcL and the trnL(UAA)-trnF(GAA) intergenic spacer in this group. To these published data we added sequences of the trnS(GCU)-trnG(UUC) intergenic spacer + the trnG(UUC) intron region, the trnS(GGA)-rpS4 intergenic spacer+rpS4 gene, and the rpL16 intron. Both the trnS(GCU)-trnG(UUC) and rpL16 regions are highly variable in angiosperms and the trnS(GGA)-rpS4 region has been widely used in monilophyte phylogenetic studies. Phylogenetic resolution was equivalent across regions, but the strength of support for the phylogenies varied among regions. Of the five sampled regions the trnS(GCU)-trnG(UUC) spacer+trnG(UUC) intron region provided the strongest support for the inferred phylogeny.

Levels and patterns of nucleotide diversity vary widely among lineages. Because allopolyploid species contain duplicated (homoeologous) genes, studies of nucleotide diversity at homoeologous loci may facilitate insight into the evolutionary dynamics of duplicated loci. In this study, we describe patterns of sequence diversity from an alcohol dehydrogenase homoeologous locus pair (AdhC) in allotetraploid cotton (Gossypium, Malvaceae). These data are compared with equivalent information from another homoeologous alcohol dehydrogenase gene pair (AdhA, Small, Ryburn, and Wendel 1999. Mol. Biol. Evol. 16:491-501) which has an overall slower evolutionary rate than AdhC. As expected from the predicted correlation between nucleotide diversity and evolutionary rate, nucleotide diversity was higher for AdhC than for AdhA. In addition, nucleotide diversity is higher in the D-subgenome of allotetraploid cotton for AdhC, confirming earlier observations for AdhA. These observations indicate that for these two pairs of Adh loci, the null hypothesis of equivalent evolutionary dynamics for duplicated genes in allotetraploid cotton is rejected.

Nuclear-encoded genes exist in families of various sizes. To further our understanding of the evolutionary dynamics of nuclear gene families we present a characterization of the structure and evolution of the alcohol dehydrogenase (Adh) gene family in diploid and tetraploid members of the cotton genus (Gossypium, Malvaceae). A PCR-based approach was employed to isolate and sequence multiple Adh gene family members, and Southern hybridization analyses were used to document variation in gene copy number. Adh gene copy number varies among Gossypium species, with diploids containing at least seven Adh loci in two primary gene lineages. Allotetraploid Gossypium species are inferred to contain at least 14 loci. Intron lengths vary markedly between loci, and one locus has lost two introns usually found in other plant Adh genes. Multiple examples of apparent gene duplication events were observed and at least one case of pseudogenization and one case of gene elimination were also found. Thus, Adh gene family structure is dynamic within this single plant genus. Evolutionary rate estimates differ between loci and in some cases between organismal lineages at the same locus. We suggest that dynamic fluctuation in copy number will prove common for nuclear genes, and we discuss the implications of this perspective for inferences of orthology and functional evolution.

Of the many processes that generate gene duplications, polyploidy is unique in that entire genomes are duplicated. This process has been important in the evolution of many eukaryotic groups, and it occurs with high frequency in plants. Recent evidence suggests that polyploidization may be accompanied by rapid genomic changes, but the evolutionary fate of discrete loci recently doubled by polyploidy (homoeologues) has not been studied. Here we use locus-specific isolation techniques with comparative mapping to characterize the evolution of homoeologous loci in allopolyploid cotton ( Gossypium hirsutum ) and in species representing its diploid progenitors. We isolated and sequenced 16 loci from both genomes of the allopolyploid, from both progenitor diploid genomes and appropriate outgroups. Phylogenetic analysis of the resulting 73.5 kb of sequence data demonstrated that for all 16 loci (14.7 kb/genome), the topology expected from organismal history was recovered. In contrast to observations involving repetitive DNAs in cotton, there was no evidence of interaction among duplicated genes in the allopolyploid. Polyploidy was not accompanied by an obvious increase in mutations indicative of pseudogene formation. Additionally, differences in rates of divergence among homoeologues in polyploids and orthologues in diploids were indistinguishable across loci, with significant rate deviation restricted to two putative pseudogenes. Our results indicate that most duplicated genes in allopolyploid cotton evolve independently of each other and at the same rate as those of their diploid progenitors. These indications of genic stasis accompanying polyploidization provide a sharp contrast to recent examples of rapid genomic evolution in allopolyploids.

Morphological distinctions between sugar maples and black maples are not consistently evident, and molecular assessment of genetic diversity is lacking for these taxa. We examined restriction-site polymorphisms in the ndhA intron of the chloroplast DNA (cpDNA) in populations of sugar maples and black maples representing their zones of allopatry and sympatry in eastern North America. Restriction-site analysis of the ndhA intron after digestion with HinfI and Sau3AI yielded no polymorphisms. Restriction digestion of the ndhA intron with TaqI revealed two cpDNA haplotypes that were neither geographically localized nor taxon specific. Although testing additional accessions of sugar maples and black maples for cpDNA variation will further elucidate patterns of genetic variation, our initial results suggest that the taxa are either exchanging genes or share an ancestral cpDNA polymorphism.