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 tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis

https://www2.clarku.edu/faculty/dhibbett/Reprints%20PDFs/Taylor%20et%20al%202000%20FGB.pdf

Phylogenetic Species Recognition and Species Concepts in Fungi

Because of the correlation expected between the phylogenetic relatedness of two taxa and their net ecological similarity, a measure of the overall phylogenetic relatedness of a community of interacting organisms can be used to investigate the contemporary ecological processes that structure community composition. I describe two indices that use the number of nodes that separate taxa on a phylogeny as a measure of their phylogenetic relatedness. As an example of the use of these indices in community analysis, I compared the mean observed net relatedness of trees (≥10 cm diameter at breast height) in each of 28 plots (each 0.16 ha) in a Bornean rain forest with the net relatedness expected if species were drawn randomly from the species pool (of the 324 species in the 28 plots), using a supertree that I assembled from published sources. I found that the species in plots were more phylogenetically related than expected by chance, a result that was insensitive to various modifications to the basic m...

/pdf/exploring-the-phylogenetic-structure-of-ecological-1i7tf95d9h.pdf

Exploring the Phylogenetic Structure of Ecological Communities: An Example for Rain Forest Trees

Polyploidy and genome evolution in plants.

Evolution of secondary metabolites from an ecological and molecular phylogenetic perspective.

Phylogenetic analysis of the chloroplast-encoded rbcL gene in Leguminosae are consistent with previous hypotheses in suggesting that the family as a whole is monophyletic, but that only two of its three subfamilies are natural. The earliest dichotomies in the family appear to have involved tribes Cercideae or Cassieae (subtribe Dialiinae), followed by Detarieae/ Macrolobieae, all of which are members of subfamily Caesalpinioideae. The remainder of the family is divided into two clades: (1) Mimosoideae and the caesalpinioid tribes Caeasalpinieae and Cassieae (subtribes Ceratoniinae and Cassiinae); (2) Papilionoideae. Basal groups within Papilionoideae are, as expected, elements of the grade tribes Sophoreae and Swartzieae. Major clades within Papilionoideae include: (1) a Genistoid Alliance comprising Genisteae, Crotalarieae, Podalyrieae, Thermopsideae, Euchresteae, and also some Sophoreae; (2) a clade marked by the absence of one copy of the chloroplast inverted repeat, with which are associated Robinieae. Loteae, and some Sophoreae; (3) Phaseoleae, Desmodieae. Psoraleeae, and most Millettieae, a group also marked by presence of pseudoracemose inflorescences; and (4) a well-supported clade comprising Aeschynomeneae, Adesmieae, and some Dalbergieae. Nodulation is most parsimoniously optimized on the rbcL strict consensus tree as three parallel gains, occurring in Papilionoideae, the caesalpioioid ancestors of Mimosoideae, and in the genus Chamaecrista (Caesalpinieae: Cassieae).

A phylogeny of the chloroplast gene rbcL in the Leguminosae: taxonomic correlations and insights into the evolution of nodulation

The respiratory gene cox2, normally present in the mitochondrion, was previously shown to have been functionally transferred to the nucleus during flowering plant evolution, possibly during the diversification of legumes. To search for novel intermediate stages in the process of intracellular gene transfer and to assess the evolutionary timing and frequency of cox2 transfer, activation, and inactivation, we examined nuclear and mitochondrial (mt) cox2 presence and expression in over 25 legume genera and mt cox2 presence in 392 genera. Transfer and activation of cox2 appear to have occurred during recent legume evolution, more recently than previously inferred. Many intermediate stages of the gene transfer process are represented by cox2 genes in the studied legumes. Nine legumes contain intact copies of both nuclear and mt cox2, although transcripts could not be detected for some of these genes. Both cox2 genes are transcribed in seven legumes that are phylogenetically interspersed with species displaying only nuclear or mt cox2 expression. Inactivation of cox2 in each genome has taken place multiple times and in a variety of ways, including loss of detectable transcripts or transcript editing and partial to complete gene loss. Phylogenetic evidence shows about the same number (3–5) of separate inactivations of nuclear and mt cox2, suggesting that there is no selective advantage for a mt vs. nuclear location of cox2 in plants. The current distribution of cox2 presence and expression between the nucleus and mitochondrion in the studied legumes is probably the result of chance mutations silencing either cox2 gene.

Intracellular gene transfer in action: dual transcription and multiple silencings of nuclear and mitochondrial cox2 genes in legumes.

Summary
The perennial soybeans (Glycine subgenus Glycine), are the sister group of the annual cultivated soybean (G. max). Among the approximately 20 species are diploids and polyploids, the former confined to Australia and neighboring islands and the latter more widespread. Although most subgenus Glycine species reproduce predominantly by selfing in cleistogamous flowers, phylogenetic evidence exists for reticulate evolution throughout the history of the subgenus. The entire genus is a paleopolyploid, and could possibly be allopolyploid, though there is as yet no evidence for a hybrid origin. Incongruence among the major nuclear genome groups in nuclear and chloroplast gene trees can be explained by several ancient introgressions. Within the B-genome group there is substantial incongruence between chloroplast and nuclear single copy gene trees that is explained better by introgressive hybridization than by stochastic sorting of ancestral lineages. Several allopolyploids originated by hybridization among a subset of genome groups to form a single large interconnected polyploid complex. A number of allopolyploid combinations have arisen recurrently, some bidirectionally. Some recurrent polyploids show evidence of lineage recombination, indicating that their populations comprise a single biological species. Neopolyploidy has involved hybridization among a subset of subgenus Glycine genome groups, and appears to have occurred recently, whereas hybridization at the diploid level has occurred throughout the history of the group.

Diploid and polyploid reticulate evolution throughout the history of the perennial soybeans (Glycine subgenus Glycine)

The Distribution and Phylogenetic Significance of a 50-kb Chloroplast DNA Inversion in the Flowering Plant Family Leguminosae

The losses of genes or introns from the chloroplast genome are of potential utility as phylogenetic characters. Previous broad surveys of angiosperms, along with sequencing studies in Pisum sativum, uncovered several instances of variation for such characters within the Legumi- nosae. Using a slot blot hybridization method that did not require high molecular weight DNA, probes for six genes and three introns typically found in angiosperm chloroplast genomes were used to screen 392 legume genera, representing all three subfamilies and 50 out of 51 tribes, and 48 genera from 26 other families of dicots. Few cases of chloroplast gene or intron loss from chloroplast genomes were observed among nonlegumes or within the legume subfamilies Mimo- soideae and Caesalpinioideae, but numerous apparent losses were observed in the large subfamily Papilionoideae. Certain cases of suspected losses were tested by polymerase chain reaction. The genes rpl2 and rbcL appear to be present in all taxa surveyed, and virtually all possess accD. In contrast, ORF184 and rpsl6 each appear to have been lost multiple, independent times within Leguminosae, while all members of the family appear to lack rp122. The intron of rpl2 has likely been lost at least four times within the family, and its absence is a synapomorphy for a core group of the papilionoid tribe Desmodieae. No convincing evidence of loss was observed among legumes for the introns of trnI and rpll6. These results indicate that gene or intron loss characters may often be homoplastic. Intron losses are a more reliable and valuable class of phylogenetic characters than are gene losses.

Jane L. Doyle

Papers

A phylogeny of the chloroplast gene rbcL in the Leguminosae: taxonomic correlations and insights into the evolution of nodulation

Intracellular gene transfer in action: dual transcription and multiple silencings of nuclear and mitochondrial cox2 genes in legumes.

Diploid and polyploid reticulate evolution throughout the history of the perennial soybeans (Glycine subgenus Glycine)

The Distribution and Phylogenetic Significance of a 50-kb Chloroplast DNA Inversion in the Flowering Plant Family Leguminosae

Multiple Independent Losses of Two Genes and One Intron from Legume Chloroplast Genomes