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1,344 results for “: phylogenomics”

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dryad36/100

Delimiting the cryptic diversity and host preferences of Sycophila parasitoid wasps associated with oak galls using phylogenomic data

Cryptic species diversity is a major challenge for the species-rich community of parasitoids attacking oak gall wasps due to a high degree of sexual dimorphism, morphological plasticity, small size, and poorly known biology. As such, we know very little about the number of species present, nor the evolutionary forces responsible for generating this diversity. One hypothesis is that trait diversity in the gall wasps, including the morphology of the galls they induce, has evolved in response to selection imposed by the parasitoid community, with reciprocal selection driving diversification of the parasitoids. Using a rare, continental-scale data set of Sycophila parasitoid wasps reared from 44 species of cynipid galls from 18 species of oak across the US, we combined mitochondrial DNA barcodes, Ultraconserved Elements (UCEs), morphological, and natural history data to delimit putative species. Using these results, we generate the first large-scale assessment of ecological specialization and host association in this species-rich group, with implications for evolutionary ecology and biocontrol. We find most Sycophila target specific subsets of available cynipid host galls with similar morphologies, and generally attack larger galls. Our results suggest that parasitoid wasps such as Sycophila have adaptations allowing them to exploit particular host trait combinations, while hosts with contrasting traits are resistant to attack. These findings support the tritrophic niche concept for the structuring of plant-herbivore-parasitoid communities.

opencc-zeroJul 2023View details →

dryad36/100

Data from: Populating a continent: Phylogenomics reveal the timing of Australian frog diversification

The Australian continent's size and isolation make it an ideal place for studying the accumulation and evolution of biodiversity. Long separated from the ancient supercontinent Gondwana, most of Australia's plants and animals are unique and endemic, including the continent's frogs. Australian frogs comprise a remarkable ecological and morphological diversity categorized into a small number of distantly related radiations. We present a phylogenomic hypothesis based on an exon-capture dataset that spans the main clades of Australian myobatrachoid, pelodryadid hyloid, and microhylid frogs. Our time-calibrated phylogenomic-scale phylogeny identifies great disparity in the relative ages of these groups which vary from Gondwanan relics to recent immigrants from Asia and include arguably the continent's oldest living vertebrate radiation. This age stratification provides insight into the colonization of⁠, and diversification on, the Australian continent through deep time, during periods of dramatic climatic and community changes. Contemporary Australian frog diversity highlights the adaptive capacity of anurans, particularly in response to heat and aridity, and explains why they are one of the continent's most visible faunas.

opencc-zeroJul 2023View details →

dryad36/100

Phylogenomics reveal extensive phylogenetic discordance due to incomplete lineage sorting following the rapid radiation of alpine butterflies (Papilionidae: Parnassius)

In rapid radiation, the earliest components of evolutionary divergence are often difficult to resolve, which were always driven by the characteristics of taxa and the limitations of alternative analytical methods. The origin and radiation of the alpine butterfly Parnassius, a high-altitude mountainous insect group, can be attributed to the uplift of the Qinghai-Tibet Plateau (QTP). Despite detailed phylogenetic analyses of the genus, deep phylogenetic relationships among the major subgenera remain recalcitrant. In this study, 102 individuals from 10 representative Parnassius species were sampled to resolve the phylogenetic relationships among subgenera based on nuclear and mitochondrial genome data sets. Gene-tree/species-tree conflicts were detected by concatenation and multispecies coalescent (MSC) approaches. We recovered a well-supported species tree, despite these conflicts, and detected considerable phylogenetic discordance among genomic regions. The main explanation for the topological discordance among subgenera was extensive incomplete lineage sorting (ILS), whereas introgression events were not prominent. The origin and explosive radiation of Parnassius (i.e., rapid succession of speciation events) in the late Miocene associated with environmental events on the plateau led to short internal branches, thereby increasing ILS and topological conflicts, especially among closely related subgenera. Our results also suggested that MSC approaches (SNAPP and SVDquartets) are accurate and superior to the concatenation approach; in particular, SVDquartets can explicitly accommodate gene-tree/species-tree conflicts caused by high ILS and demonstrate strong robustness. Lastly, we explored the phylogenomic data by testing multiple sources of phylogenomic conflict to clarify the strengths and limitations of different approaches, while considering phylogenetic signal variation in mitochondrial loci. We anticipate that the phylogeny described here will be the backbone of future evolutionary studies of the genus and will provide insight into phylogenetic discordance due to rapid radiation.

opencc-zeroJul 2023View details →

dryad36/100

New insights into infrageneric relationships of Lonicera (Caprifoliaceae) as revealed by nuclear ribosomal DNA cistron data and plastid phylogenomics

The discontinuous geographic distribution pattern of plants in the north temperate zone has been a focus of biogeographic research, especially concerning the mechanisms behind the formation of such a pattern and the spatial and temporal evolution of this intermittent distribution pattern. Hypotheses of boreotropical origin, land bridge migration, and out-of-Tibet have been proposed to explain the formation of the discontinuous distribution pattern. The distribution of Lonicera shows a typical Europe-Asia-North America discontinuous distribution, which makes for a good case study to investigate the above three hypotheses. In this study, we inferred the phylogeny based on plastid genomes and a nuclear data set with broad taxon sampling, covering 83 species representing two subgenera and four sections. Both nuclear and plastid phylogenetic analyses found section Isika polyphyletic, while sections Nintooa, Isoxylosteum, and Coelxylosteum were monophyletic in subgenus Chamaecerasus. Based on the nuclear and chloroplast phylogeny, we suggest transferring L. maximowiczii and L. tangutica into section Nintooa. Reconstruction of ancestral areas suggests that Lonicera originated in the Qinghai-Tibetan Plateau (QTP) and/or Asia, and subsequently dispersed to other regions. The aridification of the Asian interior may have facilitated the rapid radiation of Lonicera in the region. At the same time, the uplifts of the Tibetan Plateau appear to have triggered the spread and recent rapid diversification of the genus on the QTP and adjacent areas. Overall, our results deepen the understanding of the evolutionary diversification history of Lonicera.

opencc-zeroAug 2023View details →

dryad36/100

Phylogenomics of mulberries (Morus, Moraceae) inferred from plastomes and single copy nuclear genes

Mulberry (genus Morus), belonging to the order Rosales, family Moraceae, is an important woody plant due to its economic value in sericulture as well as for its nutritional benefits and medicinal values. However, the taxonomy and phylogeny of Morus remain challenging due to its wide geographical distribution, morphological plasticity, and interspecific hybridization. To better understand the evolutionary history of Morus, we combined plastomes and a large-scale nuclear gene to investigate their phylogenetic relationships in the present study. We assembled the plastomes and screened 211 single-copy nuclear genes from 14 Morus species and related taxa. The plastomes of Morus species were relatively conserved in terms of genome size, gene content and order, IR boundary and codon usage. Using nuclear data, we yielded completely identical topologies based on coalescent and concatenation methods, and multiple individuals of the same species were intraspecific monophyletic. The genus Morus was supported as a monophyly, and M. notabilis was recovered as the first diverging, and the two North American Morus species, M. celtidifolia and M. rubra, were sister to the other Asian species. However, the relationships of Morus based on plastomes were strongly incongruent with those from nuclear genes, and intraspecific non-monophyly was retrieved in the plastid phylogeny. Comparisons of nuclear and plastid phylogenies, and combining with the result of network inference, hybridization/introgression was regarded as the main cause of the discordance between nuclear and plastid phylogenies in the genus Morus. Overall, the robust phylogenetic relationships of Morus described here will be useful for genetic resources development of this economically important genus and exploitation of sericulture industry.

opencc-zeroAug 2023View details →

dryad36/100

Phylogenomics improves the phylogenetic resolution and provides strong evidence of mito-nuclear discordance in two genera of a New Zealand cicada (Hemiptera: Cicadidae) species radiation

Rapid species radiations present difficulties for phylogenetic reconstruction due to lack of phylogenetic information and processes such as deep coalescence/incomplete lineage sorting and hybridization. Phylogenomic data can overcome some of these difficulties. In this study, we use Anchored Hybrid Enrichment (AHE) nuclear phylogenomic data and mitochondrial genomes recovered from AHE bycatch with several concatenated and coalescent approaches to reconstruct the poorly-resolved radiation of the New Zealand cicada species in the genera Kikihia Dugdale and Maoricicada Dugdale. Compared to previous studies using only three to five Sanger-sequenced genes, we find increased resolution across our phylogenies, but several branches remain unresolved due to topological conflict among genes. Some nodes that are strongly supported by traditional support measures like bootstraps and posterior probabilities still show significant gene and site concordance conflict. Additionally, we find strong mito-nuclear discordance; likely the result of interspecific hybridization events in the evolutionary history of Kikihia and Maoricicada.

opencc-zeroSep 2023View details →

dryad36/100

Data from: Nightmare or delight: taxonomic circumscription meets reticulate evolution in the phylogenomic era

Phylogenetic studies in the phylogenomics era have demonstrated that reticulate evolution greatly impedes the accuracy of phylogenetic inference, and consequently can obscure taxonomic treatments. However, the systematics community lacks a broadly applicable strategy for taxonomic delimitation in groups characterized by pervasive reticulate evolution. The red-fruit genus, Stranvaesia, provides an ideal model to examine the influence of reticulation on generic circumscription, particularly where hybridization and allopolyploidy dominate the evolutionary history. In this study, we conducted phylogenomic analyses integrating data from hundreds of single-copy nuclear (SCN) genes and plastomes, and interrogated nuclear paralogs to clarify the inter/intra-generic relationship of Stranvaesia and its allies in the framework of Maleae. Analyses of phylogenomic discord and phylogenetic networks showed that allopolyploidization and introgression promoted the origin and diversification of the Stranvaesia clade, a conclusion further bolstered by cytonuclear and gene tree discordance. With a well-inferred phylogenetic backbone, we propose an updated generic delimitation of Stranvaesia and introduce a new genus, Weniomeles. This new genus is distinguished by its purple-black fruits, thorns trunk and/or branches, and a distinctive fruit core anatomy characterized by multilocular separated by a layer of sclereids and a cluster of sclereids at the top of the locules. Through this study, we highlight a broadly applicable workflow that underscores the significance of reticulate evolution analyses in shaping taxonomic revisions from phylogenomic data.

opencc-zeroSep 2023View details →

zenodo36/100

Polytomous radiation revealed in phylogenomic analysis of Allium (Amaryllidaceae) plastid genomes

Alignment of 115 Allium chloroplast genomes plus three outgroups with all sites with missing data masked.

opencc-by-4.0Oct 2023View details →

dryad36/100