SummaryChloroplast biogenesis is a complex process that requires close co-ordination between two genomes. Many of the proteins that accumulate in the chloroplast are encoded by the nuclear genome, and the developmental transition from proplastid to chloroplast is regulated by nuclear genes. Here we show that a pair of Golden 2-like (GLK) genes regulates chloroplast development in Arabidopsis. The GLK proteins are members of the GARP superfamily of transcription factors, and phylogenetic analysis demonstrates that the maize, rice and Arabidopsis GLK gene pairs comprise a distinct group within the GARP superfamily. Further phylogenetic analysis suggests that the gene pairs arose through separate duplication events in the monocot and dicot lineages. As in rice, AtGLK1 and AtGLK2 are expressed in partially overlapping domains in photosynthetic tissue. Insertion mutants demonstrate that this expression pattern re¯ects a degree of functional redundancy as single mutants display normal phenotypes in most photosynthetic tissues. However, double mutants are pale green in all photosynthetic tissues and chloroplasts exhibit a reduction in granal thylakoids. Products of several genes involved in light harvesting also accumulate at reduced levels in double mutant chloroplasts. GLK genes therefore regulate chloroplast development in diverse plant species.

In this article we explore the paradox of why morphological data are currently utilized less for phylogeny reconstruction than are DNA sequence data, whereas most of what we know about phylogeny stems from classifications founded on morphological data. The crucial difference between the two data sources relates to the number of potentially unambiguous characters available, their ease and speed of discovery, and their suitability for analysis using transformational models. We consider that the increased use of DNA sequence data, relative to morphology, for phylogeny reconstruction is inevitable and well founded, but that a crucial issue remains concerning the role of morphology in phylogeny reconstruction. We present the view that rigorous and critical anatomical studies of fewer morphological characters, in the context of molecular phylogenies, is a more fruitful approach to integrating the strengths of morphological data with those of sequence data. This approach is preferable to compiling larger data matrices of increasingly ambiguous and problematic morphological characters.We argue below that a main constraint of morphologybased phylogenetic inference concerns the limited number of unambiguous characters available for analysis in a transformational framework. This problem of a limited number of unambiguous characters is further compounded by obstacles to accurate homology assessment and character coding, which further reduce the number of characters available for analysis. We discuss and disagree with the view that more morphological data should be used in phylogeny reconstruction. Furthermore, we consider the claim that the greatest strength of morphological data-increased taxon sampling-to be mistaken. In the discussion that follows we use "phylogeny reconstruction" to refer to the computer-based algorithmic analyses routinely conducted in systematics today. NUMBERS OF CHARACTERS Accuracy and SupportHillis (1987) cited the increased number of characters as the greatest advantage of molecular data. Increased numbers of characters have been shown to be crucial in relation to issues of accuracy (Hillis, 1987(Hillis, , 1996(Hillis, , 1998Huelsenbeck and Hillis, 1993;Hillis et al., 1994aHillis et al., , 1994bLamboy, 1994;Cummings et al., 1995;Givnish and Sytsma, 1997b;Rosenberg and Kumar, 2001) and support (Felsenstein, 1985;Sanderson, 1995;Bremer et al., 1999) (Figs. 1a, 1b). Although the number of characters needed for accurate phylogeny reconstruction is difficult to estimate, the number of characters needed in simulation studies to recover accurate trees is an order of magnitude greater than that available from morphology

Vascular plants evolved in the Middle to Late Silurian period, about 420 million years ago. The fossil record indicates that these primitive plants had branched stems with sporangia but no leaves. Leaf-like lateral outgrowths subsequently evolved on at least two independent occasions. In extant plants, these events are represented by microphyllous leaves in lycophytes (clubmosses, spikemosses and quillworts) and megaphyllous leaves in euphyllophytes (ferns, gymnosperms and angiosperms). Our current understanding of how leaves develop is restricted to processes that operate during megaphyll formation. Because microphylls and megaphylls evolved independently, different mechanisms might be required for leaf formation. Here we show that this is not so. Gene expression data from a microphyllous lycophyte, phylogenetic analyses, and a cross-species complementation experiment all show that a common developmental mechanism can underpin both microphyll and megaphyll formation. We propose that this mechanism might have operated originally in the context of primitive plant apices to facilitate bifurcation. Recruitment of this pathway to form leaves occurred independently and in parallel in different plant lineages.

Despite the importance of species discovery, the processes including collecting, recognizing, and describing new species are poorly understood. Data are presented for flowering plants, measuring quantitatively the lag between the date a specimen of a new species was collected for the first time and when it was subsequently described and published. The data from our sample of new species published between 1970 and 2010 show that only 16% were described within five years of being collected for the first time. The description of the remaining 84% involved much older specimens, with nearly one-quarter of new species descriptions involving specimens >50 y old. Extrapolation of these results suggest that, of the estimated 70,000 species still to be described, more than half already have been collected and are stored in herbaria. Effort, funding, and research focus should, therefore, be directed as much to examining extant herbarium material as collecting new material in the field.herbarium specimen | monograph | taxonomy A ccurate species recognition underpins our knowledge of global biodiversity (1-3). In recent years, the lack of taxono mic activity has led to increased political (4) and scientific calls (3) to invest in the science of taxonomy, which is fundamental for what we know about species-level diversity. The assumptions behind these demands are that increased resources would necessarily lead to increased taxonomic productivity and accuracy. Given finite resources, it is essential that scientifically sound criteria regarding where funds should most usefully be targeted are used to determine priorities for taxonomic research. It is therefore surprising that the processes of collecting, recognizing, and describing species are poorly understood and only rarely discussed (5-7) and that there is little research focused on the processes that result in the recognition of new species. Many groups of organisms are so poorly known that measuring any aspect of the discovery process suffers from lack of data. In terms of completing the species-level "inventory of life," the flowering plants are viewed as an attainable priority research target because they are already relatively well known and the final inventory is estimated to be only 10-20% from completion (8). Furthermore, plants are pivotal organisms for monitoring and measuring global biodiversity because they comprise a species-rich component of almost all habitats on earth (9). An enhanced scientific understanding of the discovery process for flowering plants could help define specific priorities for funding agencies and facilitate the meeting of global biodiversity targets. Here, we focus on the temporal dynamics of the lag between the collection of flowering plant specimens and their subsequent recognition and description as new species (7). For a representative dataset, the discovery time (I) between the date of the earliest specimen collected (C) and date the description was published (D) was calculated for each species (Fig. 1). ResultsDiscovery I ranged fro...

A common approach to estimating the total number of extant species in a taxonomic group is to extrapolate from the temporal pattern of known species descriptions. A formal statistical approach to this problem is provided. The approach is applied to a number of global datasets for birds, ants, mosses, lycophytes, monilophytes (ferns and horsetails), gymnosperms and also to New World grasses and UK flowering plants. Overall, our results suggest that unless the inventory of a group is nearly complete, estimating the total number of species is associated with very large margins of error. The strong influence of unpredictable variations in the discovery process on species accumulation curves makes these data unreliable in estimating total species numbers.

Specimens of plants and animals preserved in museums are the primary source of verifiable data on the geographical and temporal distribution of organisms. Museum datasets are increasingly being uploaded to aggregated regional and global databases (e.g. the Global Biodiversity Information Facility; GBIF) for use in a wide range of analyses. Thus, digitisation of natural history collections is providing unprecedented information to facilitate the study of the natural world on a global scale. The digitisation of this information utilises information provided on specimen labels, and assumes they are correctly identified. Here we evaluate the accuracy of names associated with 4,500 specimens of African gingers from 40 herbaria in 21 countries. Our data show that at least 58% of the specimens had the wrong name prior to a recent taxonomic study. A similar pattern of wrongly named specimens is also shown for Dipterocarps and Ipomoea (morning glory). We also examine the number of available plant specimens worldwide. Our data demonstrate that, while the world's collections have more than doubled since 1970, more than 50% of tropical specimens, on average, are likely to be incorrectly named. This finding has serious implications for the uncritical use of specimen data from natural history collections.

The sweet potato is one of the world's most widely consumed crops, yet its evolutionary history is poorly understood. In this paper, we present a comprehensive phylogenetic study of all species closely related to the sweet potato and address several questions pertaining to the sweet potato that remained unanswered. Our research combined genome skimming and target DNA capture to sequence whole chloroplasts and 605 single-copy nuclear regions from 199 specimens representing the sweet potato and all of its crop wild relatives (CWRs). We present strongly supported nuclear and chloroplast phylogenies demonstrating that the sweet potato had an autopolyploid origin and that Ipomoea trifida is its closest relative, confirming that no other extant species were involved in its origin. Phylogenetic analysis of nuclear and chloroplast genomes shows conflicting topologies regarding the monophyly of the sweet potato. The process of chloroplast capture explains these conflicting patterns, showing that I. trifida had a dual role in the origin of the sweet potato, first as its progenitor and second as the species with which the sweet potato introgressed so one of its lineages could capture an I. trifida chloroplast. In addition, we provide evidence that the sweet potato was present in Polynesia in pre-human times. This, together with several other examples of long-distance dispersal in Ipomoea, negates the need to invoke ancient human-mediated transport as an explanation for its presence in Polynesia. These results have important implications for understanding the origin and evolution of a major global food crop and question the existence of pre-Columbian contacts between Polynesia and the American continent.

AimPhylogenetic trees provide a framework for understanding the evolution of features (properties, characters or traits) of species, where closely related species share many common or similar features. This property of phylogenetic trees has practical use in applications such as bio‐prospecting, where an optimal strategy exploits phylogenetic information to target closely related species to search for shared features of interest. The implicit corollary of this is that distantly related species share few features in common. This property of phylogenetic trees is thought to be useful for conservation evaluation in choosing sets of species that maximize the present utilitarian benefits of extant feature diversity (such as biologically active compounds or source systems for genetic engineering) as well as maximizing the range of evolutionary trajectories into the future.LocationGlobal.MethodsHere, we investigate the relationship between phylogenetic trees and biological features through both simulation and meta‐analysis of 223 publicly available feature matrices.ResultsWe demonstrate that phylogenetic tree distance, both in real and simulated datasets, is correlated with feature similarity only for a short relative distance along the tree, such that there is no relationship for the majority of the length of most phylogenetic trees. In other words, close relatives share more features than distant relatives but beyond a certain threshold increasingly more distant relatives are not more divergent in phenotype.Main conclusionsMeasures of phylogenetic diversity based upon maximizing phylogenetic distance may not maximize feature diversity.