The assembly of DNA barcode libraries is particularly relevant within species-rich natural communities for which accurate species identifications will enable detailed ecological forensic studies. In addition, well-resolved molecular phylogenies derived from these DNA barcode sequences have the potential to improve investigations of the mechanisms underlying community assembly and functional trait evolution. To date, no studies have effectively applied DNA barcodes sensu strictu in this manner. In this report, we demonstrate that a three-locus DNA barcode when applied to 296 species of woody trees, shrubs, and palms found within the 50-ha Forest Dynamics Plot on Barro Colorado Island (BCI), Panama, resulted in >98% correct identifications. These DNA barcode sequences are also used to reconstruct a robust community phylogeny employing a supermatrix method for 281 of the 296 plant species in the plot. The three-locus barcode data were sufficient to reliably reconstruct evolutionary relationships among the plant taxa in the plot that are congruent with the broadly accepted phylogeny of flowering plants (APG II). Earlier work on the phylogenetic structure of the BCI forest dynamics plot employing less resolved phylogenies reveals significant differences in evolutionary and ecological inferences compared with our data and suggests that unresolved community phylogenies may have increased type I and type II errors. These results illustrate how highly resolved phylogenies based on DNA barcode sequence data will enhance research focused on the interface between community ecology and evolution.T he most difficult challenge for DNA barcoding in plants is discriminating among taxa of highly speciose genera where rates of species identification by using a variety of putative barcodes rarely exceed 70% (1). In some cases of complex recently evolved species groups DNA barcoding may simply be inappropriate as an identification tool (2). This difficulty is especially acute in cases where certain life history traits have affected the rates of molecular evolution in a lineage, which in turn may affect rates of species assignment by DNA barcodes [e.g., generation times (3) and age-of-crown group diversification (4)].In the absence of a universal barcode region capable of discriminating among all species in all groups of plants, it is clear that DNA barcodes will be most effectively applied in the identification of a circumscribed set of species that occur together in a floristic region or ecological community, rather than in distinguishing among an exhaustive sample of taxonomically closely related species. In these cases only a limited number of closely related species occur in the same region, so identification to genus is all that is required.It is now generally agreed that a plant barcode will combine more than one locus (5-7) and will include a phylogenetically conservative coding locus (rbcL) with one or more rapidly evolving regions (part of the matK gene and the intergenic spacer trnH-psbA). Although more laborious than a si...

It is difficult to overstate the cultural and biological impacts that the domestication of plants and animals has had on our species. Fundamental questions regarding where, when, and how many times domestication took place have been of primary interest within a wide range of academic disciplines. Within the last two decades, the advent of new archaeological and genetic techniques has revolutionized our understanding of the pattern and process of domestication and agricultural origins that led to our modern way of life. In the spring of 2011, 25 scholars with a central interest in domestication representing the fields of genetics, archaeobotany, zooarchaeology, geoarchaeology, and archaeology met at the National Evolutionary Synthesis Center to discuss recent domestication research progress and identify challenges for the future. In this introduction to the resulting Special Feature, we present the state of the art in the field by discussing what is known about the spatial and temporal patterns of domestication, and controversies surrounding the speed, intentionality, and evolutionary aspects of the domestication process. We then highlight three key challenges for future research. We conclude by arguing that although recent progress has been impressive, the next decade will yield even more substantial insights not only into how domestication took place, but also when and where it did, and where and why it did not.The domestication of plants and animals was one of the most significant cultural and evolutionary transitions in the ∼200,000-y history of our species. Investigating when, where, and how domestication took place is therefore crucial for understanding the roots of complex societies. Domestication research is equally important to scholars from a wide range of disciplines, from evolutionary biology to sustainability science (1, 2). Research into both the process and spatiotemporal origins of domestication has accelerated significantly over the past decade through archaeological research, advances in DNA/ RNA sequencing technology, and methods used to recover and formally identify changes in interactions among plants and animals leading to domestication (2-4). In the spring of 2011, 25 scholars with a central interest in domestication and representing the fields of genetics, archaeobotany, zooarchaeology, geoarchaeology, and archaeology met at the National Evolutionary Synthesis Center to discuss recent progress in domestication research and identify challenges for the future. Our goal was to begin reconsidering plant and animal domestication within an integrated evolutionary and cultural framework that takes into account not just new genetic and archaeological data, but also ideas related to epigenetics, plasticity, geneby-environment interactions, gene-culture coevolution, and niche construction. Each of these concepts is relevant to understanding phenotypic change, heritability, and selection, and they are all fundamental components of the New Biology (5) and Expanded Modern Evolutionary Synthesis (6).

We have investigated the phylogenetic relationships among six wild and six domesticated taxa of Cucurbita using as a marker an intron region from the mitochondrial nad1 gene. Our study represents one of the first successful uses of a mtDNA gene in resolving inter-and intraspecific taxonomic relationships in Angiosperms and yields several important insights into the origins of domesticated Cucurbita. First, our data suggest at least six independent domestication events from distinct wild ancestors. Second, Cucurbita argyrosperma likely was domesticated from a wild Mexican gourd, Cucurbita sororia, probably in the same region of southwest Mexico that gave rise to maize. Third, the wild ancestor of Cucurbita moschata is still unknown, but mtDNA data combined with other sources of information suggest that it will probably be found in lowland northern South America. Fourth, Cucurbita andreana is supported as the wild progenitor of Cucurbita maxima, but humid lowland regions of Bolivia in addition to warmer temperate zones in South America from where C. andreana was originally described should possibly be considered as an area of origin for C. maxima. Fifth, our data support other molecular results that indicate two separate domestications in the Cucurbita pepo complex. The potential zone of domestication for one of the domesticated subspecies, C. pepo subsp. ovifera, includes eastern North America and should be extended to northeastern Mexico. The wild ancestor of the other domesticated subspecies, C. pepo subsp. pepo, is undiscovered but is closely related to C. pepo subsp. fraterna and possibly will be found in southern Mexico. The New World genus Cucurbita (squashes, pumpkins, and yellow-flowered gourds) is composed of 12-14 species distributed from the U.S. to Argentina (1-3). At least five different species were domesticated before the European Contact, forming important sources of food in native American economies (1-4), and some of these species were among the earliest plants taken under cultivation and domesticated in the New World (Table 1) (5). Current genetic, biogeographical, and archaeological data suggest that the crop plants are not derived from a common ancestor; each species probably represents an independent domestication event. However, geographic areas of origin are not well defined for most of the crop species, and phylogenetic relationships with sympatric free-living taxa that represent possible wild progenitors are poorly understood ( Fig. 1 A and B).The use of molecular markers and the deciphering of the genetically determined sequence of nucleotides in the DNA of domesticated plants and closely related wild taxa have significantly increased our understanding of crop plant evolution (6-9). In addition to providing the most accurate measure of relatedness between domesticated taxa and putative wild ancestors, these molecular systematic studies contribute essential information to archaeologists relating to the geography of plant domestication, and they serve as independent tests of hypotheses fo...

Abstract. To assess the historical biogeography of freshwater topminnows in the genus Poeciliopsis, we examined sequence variation in two mitochondrial genes, cytochrome b (1140 bp) and NADH subunit 2 (1047 bp). This widespread fish genus is distributed from Arizona to western Colombia, and nearly half of its 21 named species have distributions that border on the geologically active Trans-Mexican Volcanic Belt (TMVB), a region that defines the uplifted plateau (Mesa Central) of Mexico. We used the parametric bootstrap method to test the hypothesis that a single vicariant event associated with the TMVB was responsible for divergence of taxa found to the north and south of this boundary. Because the single-event hypothesis was rejected as highly unlikely, we hypothesize that at least two geological events were responsible for divergence of these species. The first (8-16 million years ago) separated ancestral populations that were distributed across the present TMVB region. A second event (2.8-6.4 million years ago) was associated with northward dispersal and subsequent vicariance of two independent southern lineages across the TMVB. The geological history of this tectonically and volcanically active region is discussed and systematic implications for the genus are outlined.

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