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Phenology is one of the best indicators to observe plant responses to climate change and predict future changes in plant communities. Choosing indicator species to monitor biological responses to climate change may be improved if herbarium specimens are combined with ongoing monitoring efforts to understand phenological responses over longer periods. We analyzed herbarium specimen data from Colorado’s alpine region, as alpine areas are predicted to be especially sensitive to climate change. We assessed phenological patterns in relation to temperature and precipitation for 287 species and growing degree days (GDD) for 235 species. Average low temperature, maximum GDD, and average precipitation increased over the study period. As temperature and GDD increased, phenology advanced, but as precipitation increased, phenology was delayed. Even with this variability of environmental responses, a significant trend of earlier flowering appeared when all species were analyzed together. Of the species that showed significantly earlier flowering dates, they advanced on average more than 39 days over the 61 years of the study. When assessing only specimens of species monitored in a national program (USA National Phenology Network), we found that these species showed similar trends to the entire dataset. When selecting species for ongoing monitoring efforts, herbarium specimens are an important resource to incorporate historical patterns into assessments of climate change and phenological drivers.

PREMISE OF THE STUDY This investigation establishes the first DNA-sequence-based phylogenetic hypothesis of species relationships in the coca family (Erythroxylaceae) and presents its implications for the intrageneric taxonomy and neotropical biogeography of Erythroxylum. We also identify the closest wild relatives and evolutionary relationships of the cultivated coca taxa. METHODS We focused our phylogenomic inference on the largest taxonomic section in the genus Erythroxylum (Archerythroxylum O.E.Schulz) using concatenation and gene tree reconciliation methods from hybridization-based target capture of 427 genes. KEY RESULTS We show that neotropical Erythroxylum are monophyletic within the paleotropical lineages, yet Archerythroxylum and all of the other taxonomic sections from which we sampled multiple species lack monophyly. We mapped phytogeographic states onto the tree and found some concordance between these regions and clades. The wild species E. gracilipes and E. cataractarum are most closely related to the cultivated E. coca and E. novogranatense, but relationships within this "coca" clade remain equivocal. CONCLUSIONS Our results point to the difficulty of morphology-based intrageneric classification in this clade and highlight the importance of integrative taxonomy in future systematic revisions. We can confidently identify E. gracilipes and E. cataractarum as the closest wild relatives of the coca taxa, but understanding the domestication history of this crop will require more thorough phylogeographic analysis.

High diversity and endemism in the California Floristic Province (CFP) are an alleged response to the late Cenozoic advent of Mediterranean-type climate in this region. Ceanothus comprises two divergent subgenera with centers of diversity in the CFP. We reconstruct the evolution of Ceanothus by using DNA sequence data from the nuclear gene nitrate reductase. We find that the timing of diversification events is related to geological and climatic history. In both subgenera, diversification is characterized by recent divergence of extant taxa and geographically structured phylogenetic relationships. A strong north-south divergence of subgenus Cerastes across the Transverse Ranges indicates that phylogenetic relationships may be structured by climatically divergent regions of the CFP. Divergence-time estimation suggests that the age of extant diversification in both subgenera is ∼6 Ma. This agrees with the fossil record but predates the hypothesized Quaternary (2-Ma) origin of Mediterranean-type climate in th...

Four taxa of the plant genus Erythroxylum; Erythroxylum coca var. coca (Ecc), Erythroxylum coca var. ipadu (Eci), Erythroxylum novogranatense var. novogranatense (Enn) and Erythroxylum novogranatense var. truxillense (Ent) are cultivated primarily for the illicit extraction and processing of cocaine. Despite their economic and medical importance, the evolutionary history of these species remains unknown in a modern phylogenetic framework. The aims of this study were to: (a) investigate the relationship among the cultivated and a select number of non-cultivated taxa, and (b) test Plowman’s (Journal of Psychodelic Drugs 11:103–117, 1979b) linear progression hypothesis of the cultivated Erythroxylum taxa versus Johnson’s et al. (Annals of Botany 95:601–608, 2005) hypothesis that Ec and En are sister species. AFLP phylogeny was used to compare the relationships among 36 Erythroxylum species (133 accessions) spanning the geographic distribution of the genus. A Maximum Parsimony tree revealed both geographic and taxonomic partitioning into clades representing species from Africa, Asia-Pacific and the New World (Tropical Americas). Ec and En formed distinct clades, indicating they are sister species and a cluster of non-cultivated species were the most closely related to the cultivated species. Multivariate ordination analysis was used to evaluate the relationship between cultivated and non-cultivated Erythroxylum taxa from the Tropical Americas. Our results support the hypothesis that the cultivated species are more closely related to each other than to any other species of Erythroxylum, but refute the hypothesis that Ent (and Enn) descended from Ecc. Instead our data suggest an independent, non-linear evolutionary relationship between Ec and En. Finally, the AFLP analyses identified significantly different genetic groups within Erythroxylum suggesting that the current intrageneric classification of this genus be revised.

Recent phylogenetic analyses of grammitid ferns (Polypodiaceae) have demonstrated that some genera recognized within this clade are not monophyletic. We focus on resolving the circumscriptions of some large Neotropical genera by focusing on a clade, identified in previous analyses, that includes the monophyletic genus Melpomene, plus portions of two polyphyletic genera, Lellingeria and Terpsichore. Phylogenetic analyses using chloroplast markers atpB, rbcL, and trnL-F, along with 109 morphological characters, resolve this ingroup as monophyletic and sister to a clade that includes Ceradenia, Enterosora, and Zygophlebia. We use morphological characters included in the analysis to circumscribe clades. Melpomene is clearly monophyletic, but forms a polytomy with Lellingeria s. l. in a strict consensus of MP trees. Ingroup species of Terpsichore form three well supported monophyletic groups that together are paraphyletic with respect to Melpomene plus Lellingeria. Two clades corresponding to species groups of Terpsichore will be recognized as new genera.

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Ziziphus comprises approximately 170 species native to the tropics and subtropics. Two economically important species, Z. jujuba and Z. mauritiana, are cultivated for their fruit. Given the economic importance of these two species, we undertook a reexamination of the intrageneric phylogenetic relationships to identify their closest relatives and to test two alternative intrageneric classifications. These two classifications were tested by using a simultaneous analysis of morphological characters together with nuclear (ITS and 26S rDNA) and plastid (trnL-F) genes. The Old World and New World species of Ziziphus formed two separate well-supported clades. The Old World species of Ziziphus are more closely related to Paliurus than to the New World species, thereby rendering Ziziphus paraphyletic. Sarcomphalus is placed within the New World Ziziphus clade, which supports the transfer of Sarcomphalus to Ziziphus. The earlier placement of Condaliopsis in Ziziphus was supported for one species previously placed in Condaliopsis, Z. obtusifolia, but was contradicted for the other Condaliopsis-like species, Z. celata. Ziziphus celata is more closely related to Rhamneae than it is to Paliureae.

The phylogeny of the Elaeodendron group was inferred in a simultaneous analysis of morphological characters together with nuclear (ITS and 26S rDNA) and plastid (matK, trnL-F region) genes. The circumscription of genera in this group has long been controversial, particularly with respect to Cassine and Elaeodendron. Cassine, narrowly defined so as to include three species native to southern Africa, was unambiguously supported as distinct from Elaeodendron. The widely distributed genus Elaeodendron was supported as a natural group, sister to Pleurostylia. Brexia, which has been variously assigned to the Escalloniaceae, Brexiaceae, and Grossulariaceae, was unambiguously supported as the sister group to the clade of Elaeodendron and Pleurostylia. Preliminary species sampling supported Empleuridium, which had been classified within the Rutaceae, as closely related to Mystroxylon, Pseudosalacia, and Robsonodendron. Allocassine and Lauridia were resolved as closely related to one another, supporting their previously inferred relationship. Maurocenia and Cassine were supported as closely related to one another, with evidence for Maurocenia being nested within Cassine. Lydenburgia abbottii was resolved as closely related to Lydenburgia cassinoides, supporting its transfer from Catha. Three new combinations are made: Elaeodendron bupleuroides (Guillaumin) R.H. Archer, Elaeodendron parvifolium R.H. Archer, and Elaeodendron pininsulare Hürl. subsp. poyaense (I.H. Müller) R.H. Archer.

Condaliopsis is a genus of eight thorny shrub species. Previous morphological research shed doubt on the validity of Condaliopsis as a distinct genus in Rhamnaceae. Condaliopsis species were transferred to one of two genera, Ziziphus or Condalia, but some authors continue to recognize Condaliopsis . A recent phylogenetic study did not support Condaliopsis as monophyletic and placement of Condaliopsis species in either Ziziphus or Condalia was not straightforward. To clarify the generic placement of these eight species, we conducted phylogenetic analyses based on two nuclear loci (nrITS and 26S), two chloroplast loci ( trnL-F and trnQ-rps16 ) and morphological characters. We present evidence that five of the Condaliopsis species should remain in Ziziphus , one should remain in Condalia , and two should be transferred from Ziziphus to Condalia . One of these species had an existing binomial within Condalia, Condalia parryi, and one required a new combination, Condalia celata . Condalia celata is a federally listed endangered species with a limited range in Florida.