Firmiana danxiaensis is a critically endangered and ecologically important tree currently only found in four locations in Danxia or Karst habitats in northern Guangdong Province, China. The ...specialized habitat preference makes it an ideal model species for study of adaptive evolution. Meanwhile, the phylogenetic relationships of F. danxiaensis in four locations under two landforms are unclear. Therefore, we sequenced its complete chloroplast (cp.) genomes and conducted comprehensive interspecific and intrageneric plastome studies.
The F. danxiaensis plastomes in four locations showed a typical quadripartite and circular structure that ranged from 160,832 to 161,206 bp in size, with 112 unique genes encoded. Comparative genomics showed that the plastomes of F. danxiaensis were relatively conserved with high similarity of genome organization, gene number, GC content and SSRs. While the genomes revealed higher biased codon preferences in Karst habitat than those in Danxia habitats. Eighteen and 11 divergent hotpots were identified at interspecific and intrageneric levels for species identification and further phylogenetic studies. Seven genes (clpP, accD, ccsA, ndhH, rpl20, rpoC2, and rps4) were under positive selection and may be related to adaptation. Phylogenetic analysis revealed that F. danxiaensis is sister to F. major and F. simplex. However, the interspecific relationships are not consistent with the habitat types.
The characteristics and interspecific relationship of F. danxiaensis plastomes provide new insights into further integration of geographical factors, environmental factors, and genetic variations on the genomic study of F. danxiaensis. Together, our study will contribute to the study of species identification, population genetics, and conservation biology of F. danxiaensis.
PREMISE OF THE STUDY: Land-plant plastid genomes have only rarely undergone significant changes in gene content and order. Thus, discovery of additional examples adds power to tests for causes of ...such genome-scale structural changes. METHODS: Using next-generation sequence data, we assembled the plastid genome of saguaro cactus and probed the nuclear genome for transferred plastid genes and functionally related nuclear genes. We combined these results with available data across Cactaceae and seed plants more broadly to infer the history of gene loss and to assess the strength of phylogenetic association between gene loss and loss of the inverted repeat (IR). KEY RESULTS: The saguaro plastid genome is the smallest known for an obligately photosynthetic angiosperm (~113 kb), having lost the IR and plastid ndh genes. This loss supports a statistically strong association across seed plants between the loss of ndh genes and the loss of the IR. Many nonplastid copies of plastid ndh genes were found in the nuclear genome, but none had intact reading frames; nor did three related nuclear-encoded subunits. However, nuclear pgr5, which functions in a partially redundant pathway, was intact. CONCLUSIONS: The existence of an alternative pathway redundant with the function of the plastid NADH dehydrogenase-like complex (NDH) compex may permit loss of the plastid ndh gene suite in photoautotrophs like saguaro. Loss of these genes may be a recurring mechanism for overall plastid genome size reduction, especially in combination with loss of the IR.
Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this ...phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus (Carnegiea gigantea) of the Sonoran Desert. We assembled a high-coverage draft genome for saguaro and lower coverage genomes for three other genera of tribe Pachycereeae (Pachycereus, Lophocereus, and Stenocereus) and a more distant outgroup cactus, Pereskia. We used these to construct 4,436 orthologous gene alignments. Species tree inference consistently returned the same phylogeny, but gene tree discordance was high: 37% of gene trees having at least 90% bootstrap support conflicted with the species tree. Evidently, discordance is a product of long generation times and moderately large effective population sizes, leading to extensive incomplete lineage sorting (ILS). In the best supported gene trees, 58% of apparent homoplasy at amino sites in the species tree is due to gene tree-species tree discordance rather than parallel substitutions in the gene trees themselves, a phenomenon termed “hemiplasy.” The high rate of genomic hemiplasy may contribute to apparent parallelisms in phenotypic traits, which could confound understanding of species relationships and character evolution in cacti.
Premise
Astragalus (Fabaceae), with more than 3000 species, represents a globally successful radiation of morphologically highly similar species predominant across the northern hemisphere. It has ...attracted attention from systematists and biogeographers, who have asked what factors might be behind the extraordinary diversity of this important arid‐adapted clade and what sets it apart from close relatives with far less species richness.
Methods
Here, for the first time using extensive phylogenetic sampling, we asked whether (1) Astragalus is uniquely characterized by bursts of radiation or whether diversification instead is uniform and no different from closely related taxa. Then we tested whether the species diversity of Astragalus is attributable specifically to its predilection for (2) cold and arid habitats, (3) particular soils, or to (4) chromosome evolution. Finally, we tested (5) whether Astragalus originated in central Asia as proposed and (6) whether niche evolutionary shifts were subsequently associated with the colonization of other continents.
Results
Our results point to the importance of heterogeneity in the diversification of Astragalus, with upshifts associated with the earliest divergences but not strongly tied to any abiotic factor or biogeographic regionalization tested here. The only potential correlate with diversification we identified was chromosome number. Biogeographic shifts have a strong association with the abiotic environment and highlight the importance of central Asia as a biogeographic gateway.
Conclusions
Our investigation shows the importance of phylogenetic and evolutionary studies of logistically challenging “mega‐radiations.” Our findings reject any simple key innovation behind high diversity and underline the often nuanced, multifactorial processes leading to species‐rich clades.
Herbivorous insects are extraordinarily diverse, yet are found in only one-third of insect orders. This skew may result from barriers to plant colonization, coupled with phylogenetic constraint on ...plant-colonizing adaptations. The plant-penetrating ovipositor, however, is one trait that surmounts host plant physical defences and may be evolutionarily labile. Ovipositors densely lined with hard bristles have evolved repeatedly in herbivorous lineages, including within the Drosophilidae. However, the evolution and genetic basis of this innovation has not been well studied. Here, we focused on the evolution of this trait in
, a genus sister to Hawaiian
, that contains a herbivorous clade. Our phylogenetic approach revealed that ovipositor bristle number increased as herbivory evolved in the
lineage. Through a genome-wide association study, we then dissected the genomic architecture of variation in ovipositor bristle number within
. Top-associated variants were enriched for transcriptional repressors, and the strongest associations included genes contributing to peripheral nervous system development. Individual genotyping supported the association at a variant upstream of
, a neural development gene, contributing to a gain of 0.58 bristles/major allele. These results suggest that regulatory variation involving conserved developmental genes contributes to this key morphological trait involved in plant colonization.
Abstract
The plastid genomes of photosynthetic green plants have largely maintained conserved gene content and order as well as structure over hundreds of millions of years of evolution. Several ...plant lineages, however, have departed from this conservation and contain many plastome structural rearrangements, which have been associated with an abundance of repeated sequences both overall and near rearrangement endpoints. We sequenced the plastomes of 25 taxa of Astragalus L. (Fabaceae), a large genus in the inverted repeat-lacking clade of legumes, to gain a greater understanding of the connection between repeats and plastome inversions. We found plastome repeat structure has a strong phylogenetic signal among these closely related taxa mostly in the New World clade of Astragalus called Neo-Astragalus. Taxa without inversions also do not differ substantially in their overall repeat structure from four taxa each with one large-scale inversion. For two taxa with inversion endpoints between the same pairs of genes, differences in their exact endpoints indicate the inversions occurred independently. Our proposed mechanism for inversion formation suggests the short inverted repeats now found near the endpoints of the four inversions may be there as a result of these inversions rather than their cause. The longer inverted repeats now near endpoints may have allowed the inversions first mediated by shorter microhomologous sequences to propagate, something that should be considered in explaining how any plastome rearrangement becomes fixed regardless of the mechanism of initial formation.
Abstract
Herbivorous insects are exceptionally diverse, accounting for a quarter of all known eukaryotic species, but the genomic basis of adaptations that enabled this dietary transition remains ...poorly understood. Many studies have suggested that expansions and contractions of chemosensory and detoxification gene families—genes directly mediating interactions with plant chemical defenses—underlie successful plant colonization. However, this hypothesis has been challenging to test because the origins of herbivory in many insect lineages are ancient (>150 million years ago (mya)), obscuring genomic evolutionary patterns. Here, we characterized chemosensory and detoxification gene family evolution across Scaptomyza, a genus nested within Drosophila that includes a recently derived (<15 mya) herbivore lineage of mustard (Brassicales) specialists and carnation (Caryophyllaceae) specialists, and several nonherbivorous species. Comparative genomic analyses revealed that herbivorous Scaptomyza has among the smallest chemosensory and detoxification gene repertoires across 12 drosophilid species surveyed. Rates of gene turnover averaged across the herbivore clade were significantly higher than background rates in over half of the surveyed gene families. However, gene turnover was more limited along the ancestral herbivore branch, with only gustatory receptors and odorant-binding proteins experiencing strong losses. The genes most significantly impacted by gene loss, duplication, or changes in selective constraint were those involved in detecting compounds associated with feeding on living plants (bitter or electrophilic phytotoxins) or their ancestral diet (fermenting plant volatiles). These results provide insight into the molecular and evolutionary mechanisms of plant-feeding adaptations and highlight gene candidates that have also been linked to other dietary transitions in Drosophila.
The evolution of species radiations has involved two processes: diversification, or the formation of many species, as well as disparification, the differentiation of species in traits associated with ...differing ecological niches. Extremes of disparification are a hallmark of classic examples of adaptive radiations, which have also often proceeded with comparable rates of diversification. While disparification is thought to be limited in nonadaptive radiations, the focus of studies on large groups of grossly ecologically similar species has often been on rates of diversification rather than on levels of ecological and associated morphological or physiological differentiation. Disparification in nonadaptive radiations may very well have occurred but involved cryptic or difficult to observe, yet ecologically important traits. Disparity in cryptic traits may also involve convergent evolution or homoplasy, which may be difficult to document without well-resolved phylogenies that have often remained elusive in large groups of recently radiated species. The radiation of the Neo-Astragalus clade of Astragalus L. (Fabaceae), a group of nearly 500 species of largely temperate, perennial herbaceous plants in North and South America, is estimated to have occurred only in the last ca. 4.4 Ma. I estimate greatly improved phylogenies of Neo-Astragalus to examine the evolution of multiple types of characters and shed light on cryptic differentiation and homoplasy within this large clade.While not as disparate in climatic niche or growth form as classic examples of plant adaptive radiations, Neo-Astragalus species do display key differences in cryptic but ecologically important traits such as specialization on specific geological substrates and the production of different kinds of toxins, as well as in morphological characters (especially of the fruit) and characters of genomic organization. In Chapter 1, I examine the structure of Neo-Astragalus plastomes with regard to the abundance and placement of repeated sequences and the locations of endpoints of large inversions found in several Neo-Astragalus species. Specific repeated sequences near inversion endpoints shed light on the potential mechanisms of inversion formation and retention and also reveal inversions in two species with endpoints between the same sets of loci to be homoplastic. In Chapter 2, I estimate improved phylogenies of Neo-Astragalus from a broad taxonomic sampling of species using both plastome and nuclear ribosomal DNA (nrDNA) sequences. These phylogenies resolve relationships within Neo-Astragalus to a much greater extent than ever before but also reveal rampant homoplasy in morphological characters used to form the taxonomic system of Astragalus in North America. In Chapter 3, I characterize the trait of selenium hyperaccumulation with chemical assays of individuals from 26 Neo-Astragalus species either previously documented as or assumed to be accumulators of the element. Reconstructing the evolutionary history of this trait reveals there were multiple independent origins of selenium hyperaccumulation in the Neo-Astragalus clade, although the exact number and placement of these origins are less certain.Homoplasy, which I document in plastome inversions, morphological characters, and through multiple independent origins of selenium hyperaccumulation, is a striking feature of character evolution in Neo-Astragalus. This homoplasy, especially in selenium hyperaccumulation, may be indicative of even greater disparification that accompanied the evolution of Neo-Astragalus in cryptic but ecologically relevant traits, including substrate specialization and the production of toxic compounds.
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