Single-copy Nuclear Genes Research Articles

Malus includes Docynia (Maleae, Rosaceae): evidence from phylogenomics and morphology.

Docynia has been treated as a separate genus or merged into Cydonia or Docyniopsis. Our phylogenomic evidence from 797 single-copy nuclear genes and plastomes confirmed the sister relationship between Docynia and Docyniopsis. By integrating the phylogenomic and morphological evidence, we propose to accept a broad generic concept of Malus and merge Docynia into Malus. Three new combinations are also made here: Malusdelavayi (Franch.) B.B.Liu, M.indica (Wall.) B.B.Liu and M.longiunguis (Q.Luo & J.L.Liu) B.B.Liu.

Transcriptome-Based Study on the Phylogeny and Hybridization of Marattialean Ferns (Marattiaceae).

Marattiaceae is a phylogenetically isolated family of tropical eusporangiate ferns including six genera with more than one-hundred species. In Marattiaceae, monophyly of genera has been well-supported phylogenetically. However, the phylogenetic relationships among them were elusive and controversial. Here, a dataset of 26 transcriptomes (including 11 newly generated) were used to assess single-copy nuclear genes and to obtain the organelle gene sequences. Through phylotranscriptomic analysis, the phylogeny and hybridization events of Marattiaceae were explored and a robust phylogenomic framework for the evolution of Marattiaceae was provided. Using both concatenation- and coalescent-based phylogenies, the gene-tree discordance, incomplete lineage sorting (ILS) simulations, and network inference were examined. Except the low support with mitochondrial genes of Marattiaceae, nuclear genes and chloroplast genes strongly supported a sister relationship between Marattiaceae and leptosporangiate ferns. At the genus level, all phylogenetic analysis based on nuclear genes datasets recovered five genera in Marattiaceae as monophyletic with strong support. Danaea and Ptisana were the first two diverged clades in turn. Christensenia was a sister clade to the clade Marattia + Angiopteris s.l. In Angiopteris s.l., three clades (Angiopteris s.s., the Archangiopteris group, and An. sparsisora) were well identified with maximum support. The Archangiopteris group was derived from Angiopteris s.s. at ca. 18 Ma. The putative hybrid species An. sparsisora between Angiopteris s.s. and the Archangiopteris group was verified by the species network analyses and the maternal plastid genes. This study will improve our understanding for using the phylotranscriptomic method to explore phylogeny and investigate hybridization events for difficult taxa in ferns.

Phylogenomics reveals widespread hybridization and polyploidization in Henckelia (Gesneriaceae).

Hybridization has long been recognized as an important process for plant evolution and is often accompanied by polyploidization, another prominent force in generating biodiversity. Despite its pivotal importance in evolution, the actual prevalence and distribution of hybridization across the tree of life remain unclear. We used whole-genome shotgun (WGS) sequencing and cytological data to investigate the evolutionary history of Henckelia, a large genus in the family Gesneriaceae with a high frequency of suspected hybridization and polyploidization events. We generated WGS sequencing data at about 10× coverage for 26 Chinese Henckelia species plus one Sri Lankan species. To untangle the hybridization history, we separately extracted whole plastomes and thousands of single-copy nuclear genes from the sequencing data, and reconstructed phylogenies based on both nuclear and plastid data. We also explored sources of both genealogical and cytonuclear conflicts and identified signals of hybridization and introgression within our phylogenomic dataset using several statistical methods. Additionally, to test the polyploidization history, we evaluated chromosome counts for 45 populations of the 27 Henckelia species studied. We obtained well-supported phylogenetic relationships using both concatenation- and coalescent-based methods. However, the nuclear phylogenies were highly inconsistent with the plastid phylogeny, and we observed intensive discordance among nuclear gene trees. Further analyses suggested that both incomplete lineage sorting and gene flow contributed to the observed cytonuclear and genealogical discordance. Our analyses of introgression and phylogenetic networks revealed a complex history of hybridization within the genus Henckelia. In addition, based on chromosome counts for 27 Henckelia species, we found independent polyploidization events occurred within Henckelia after different hybridization events. Our findings demonstrated that hybridization and polyploidization are common in Henckelia. Furthermore, our results revealed that H. oblongifolia is not a member of the redefined Henckelia and they suggested several other taxonomic treatments in this genus.

CRISPR/Cas12a-mediated Enzymatic recombinase amplification for rapid visual quantitative authentication of halal food

Economically motivated adulteration (EMA) has become a concern in food safety. We propose a CRISPR/Cas12a Mediated Enzymatic Recombinase Amplification detection system (CAMERA) that integrates Enzymatic Recombinase Amplification (ERA) and Cas12a cleavage to detect halal food adulteration. We designed and screened crRNA targeting CLEC, a porcine-specific nuclear single-copy gene, and optimized the reagent concentrations and incubation times for the ERA and Cas12a cleavage steps. CAMERA was highly specific for pork ingredients detection. The DNA concentration and fluorescence signal intensity relationship was linear at DNA concentrations of 20–0.032 ng/μL. CAMERA detected as few as two CLEC copies and quantified samples with porcine DNA content as low as 5% within 25 min. The system could be operated in a miniaturized working mode that requires no technical expertise or professional equipment, making CAMERA a valuable tool in resource-limited areas for the qualitative and quantitative detection of pork ingredients in halal food.

Revalidation of Phalangomyia Dyar & Knab as a subgenus of Culex L. (Diptera: Culicidae) based on morphological and molecular evidence

Culex apicinus Philippi, 1865 and its synonyms, Phalangomyia debilis Dyar & Knab, 1914, Cx. escomeli Brèthes, 1920 and Cx. alticola Martini, 1931, were re-examined employing molecular and morphological phylogenetic methods. Archival and fresh specimens were used for morphological diagnosis and to generate fragments of two single-copy nuclear genes (CAD, HB) and one mitochondrial gene (COI). Additional sequences of Cx. apicinus and species of the subgenus Culex of Culex Linnaeus, 1758 and other subgenera of the genus were obtained from GenBank for molecular analysis. Diagnostic morphological characteristics of Cx. apicinus and other species of the subgenus Culex were contrasted. Phylogenetic relationships were generated using DNA sequences of protein coding genes under both Maximum Likelihood and Bayesian approaches. Culex apicinus showed unique morphological traits that allow its classification in a separate subgenus. The subspecific status is supported by its recovery as a monophyletic clade within the genus Culex based on morphological and molecular characters. The synonymous Phalangomyia debilis provides an available subgeneric name. Consequently, Phalangomyia Dyar & Knab, 1914 is resurrected from synonymy with Culex Linnaeus, 1758 as a monobasic subgenus of Culex.

Disentangling Crocus Series Verni and Its Polyploids.

Spring crocuses, the eleven species within Crocus series Verni (Iridaceae), consist of di- and tetraploid cytotypes. Among them is a group of polyploids from southeastern Europe with yet-unclear taxonomic affiliation. Crocuses are generally characterized by complex dysploid chromosome number changes, preventing a clear correlation between these numbers and ploidy levels. To reconstruct the evolutionary history of series Verni and particularly its polyploid lineages associated with C. heuffelianus, we used an approach combining phylogenetic analyses of two chloroplast regions, 14 nuclear single-copy genes plus rDNA spacers, genome-wide genotyping-by-sequencing (GBS) data, and morphometry with ploidy estimations through genome size measurements, analysis of genomic heterozygosity frequencies and co-ancestry, and chromosome number counts. Chromosome numbers varied widely in diploids with 2n = 8, 10, 12, 14, 16, and 28 and tetraploid species or cytotypes with 2n = 16, 18, 20, and 22 chromosomes. Crocus longiflorus, the diploid with the highest chromosome number, possesses the smallest genome (2C = 3.21 pg), while the largest diploid genomes are in a range of 2C = 7-8 pg. Tetraploid genomes have 2C values between 10.88 pg and 12.84 pg. Heterozygosity distribution correlates strongly with genome size classes and allows discernment of di- and tetraploid cytotypes. Our phylogenetic analyses showed that polyploids in the C. heuffelianus group are allotetraploids derived from multiple and partly reciprocal crosses involving different genotypes of diploid C. heuffelianus (2n = 10) and C. vernus (2n = 8). Dysploid karyotype changes after polyploidization resulted in the tetraploid cytotypes with 20 and 22 chromosomes. The multi-data approach we used here for series Verni, combining evidence from nuclear and chloroplast phylogenies, genome sizes, chromosome numbers, and genomic heterozygosity for ploidy estimations, provides a way to disentangle the evolution of plant taxa with complex karyotype changes that can be used for the analysis of other groups within Crocus and beyond. Comparing these results with morphometric analysis results in characters that can discern the different taxa currently subsumed under C. heuffelianus.

An updated phylogeny, biogeography, and PhyloCode-based classification of Cornaceae based on three sets of genomic data.

A major goal of systematic biology is to uncover the evolutionary history of organisms and translate that knowledge into stable classification systems. Here, we integrate three sets of genome-wide data to resolve phylogenetic relationships in Cornaceae (containing only Cornus s. l.), reconstruct the biogeographic history of the clade, and provide a revised classification using the PhyloCode to stabilize names for this taxonomically controversial group. We conducted phylogenetic analyses using 312 single-copy nuclear genes and 70 plastid genes from Angiosperms353 Hyb-Seq, plus numerous loci from RAD-Seq. We integrated fossils using morphological data and produced a dated phylogeny for biogeographical analysis. A well-resolved, strongly supported, comprehensive phylogeny was obtained. Biogeographic analyses support an origin and rapid diversification of Cornus into four morphologically distinct major clades in the Northern Hemisphere (with an eastern Asian ancestor) during the late Cretaceous. Dispersal into Africa from eastern Asia likely occurred along the Tethys Seaway during the Paleogene while dispersal into South America likely occurred during the Neogene. Diversification within the Northern Hemisphere likely involved repeated independent colonization of new areas during the Paleogene and Neogene along the Bering Land Bridge, the North Atlantic Land Bridge, and the Tethys Seaway. Thirteen strongly supported clades were named following the PhyloCode. Our study provides an example of integrating genomic and morphological data to produce a robust, explicit species phylogeny that includes fossil taxa, which we translate into an updated classification scheme using the PhyloCode to stabilize names. This article is protected by copyright. All rights reserved.

Phylotranscriptomics Shed Light on Intrageneric Relationships and Historical Biogeography of Ceratozamia (Cycadales).

Ceratozamia Brongn. is one of the species-rich genera of Cycadales comprising 38 species that are mainly distributed in Mexico, with a few species reported from neighboring regions. Phylogenetic relationships within the genus need detailed investigation based on extensive datasets and reliable systematic approaches. Therefore, we used 30 of the known 38 species to reconstruct the phylogeny based on transcriptome data of 3954 single-copy nuclear genes (SCGs) via coalescent and concatenated approaches and three comparative datasets (nt/nt12/aa). Based on all these methods, Ceratozamia is divided into six phylogenetic subclades within three major clades. There were a few discrepancies regarding phylogenetic position of some species within these subclades. Using these phylogenetic trees, biogeographic history and morphological diversity of the genus are explored. Ceratozamia originated from ancestors in southern Mexico since the mid-Miocene. There is a distinct distribution pattern of species through the Trans-Mexican Volcanic Belt (TMVB), that act as a barrier for the species dispersal at TMVB and its southern and northern part. Limited dispersal events occurred during the late Miocene, and maximum diversification happened during the Pliocene epoch. Our study provides a new insight into phylogenetic relationships, the origin and dispersal routes, and morphological diversity of the genus Ceratozamia. We also explain how past climatic changes affected the diversification of this Mesoamerica-native genus.

Draft genome assembly for the colombian freshwater bocachico fish, Prochilodus magdalenae.

We report the first draft genome assembly for Prochilodus magdalenae, the leading representative species of the Prochilodontidae family in Colombia. This 1.2-Gb assembly, with a GC content of 42.0% and a repetitive content of around 31.0%, is in the range of previously reported characid species genomes. Annotation identified 34,725 nuclear genes, and BUSCO completeness value was 94.9%. Gene ontology and primary metabolic pathway annotations indicate similar gene profiles for P. magdalenae and the closest species with annotated genomes: blind cave fish (Astyanax mexicanus) and red piranha (Pygocentrus nattereri). A comparative analysis showed similar genome traits to other characid species. The fully sequenced and annotated mitochondrial genome reproduces the taxonomic classification of P. magdalenae and confirms the low mitochondrial genetic divergence inside the Prochilodus genus. Phylogenomic analysis, using nuclear single-copy orthologous genes, also confirmed the evolutionary position of the species. This genome assembly provides a high-resolution genetic resource for sustainable P. magdalenae management in Colombia and, as the first genome assembly for the Prochilodontidae family, will contribute to fish genomics throughout South America.

Comparative transcriptome analyses of three Gentiana species provides signals for the molecular footprints of selection effects and the phylogenetic relationships.

Species in Gentiana section Cruciata are important alpine plants with a center of diversity and speciation in Qinghai-Tibet Plateau (QTP), and some of these species are sympatrically distributed in northeastern QTP. Studies on genome features and natural selection signatures of sympatric species in section Crucata have been impeded by a lack of genomic resources. Here, we showed transcript characterizations and molecular footprints of selection effects on G. straminea, G. dahurica and G. officinalis based on the comparative transcriptome. A total of 62.97Gb clean reads were obtained with unigene numbers per species ranging from 141,819 to 236,408 after assembly. We found that these three species had similar distribution of functional categories in different databases, and key enzyme-encoding genes involved in the iridoids biosynthesis were also obtained. The selective pressure analyses indicated that most paired orthologs between these three species were subject to negative selection, and only a low proportion of the orthologs that underwent positive selection were detected. We found that some positive selected genes were involved in "catalytic activity", "metabolic process", "response to stimulus" and "response to stress". Besides, large numbers of SSR primer pairs with transferabilities were successfully designed based on the available transcriptome datasets of three Gentiana species. The phylogenetic relationships reconstructed based on 352 single-copy nuclear genes provided a rough phylogenetic framework for this genus and confirmed the monophyly of section Cruciata. Our study not only provides insights for the natural selection effects on sympatric Gentiana species, but also enhances future genetic breeding or evolutionary studies on Qinjiao species.

Phylogenetic relationships among Australian native citrus species based upon complete chloroplast genomes and single copy nuclear genes

Phylogenetic relationships among Australian native citrus species based upon complete chloroplast genomes and single copy nuclear genes

Population bottleneck associated with but likely preceded the recent evolution of self-fertilization in a coastal dune plant.

Evolution of self-fertilization may be initiated by a historical population bottleneck, which should diagnostically reduce lineage-wide genetic variation. However, selfing can also strongly reduce genetic variation after it evolves. Distinguishing process from pattern is less problematic if mating system divergence is recent and geographically simple. Dramatically reduced diversity is associated with the transition from outcrossing to selfing in the Pacific coastal endemic Abronia umbellata that includes large-flowered, self-incompatible populations (var. umbellata) south of San Francisco Bay and small-flowered, autogamous populations (var. breviflora) to the north. Compared to umbellata, synonymous nucleotide diversity across 10 single-copy nuclear genes was reduced by 94% within individual populations and 90% across the whole selfing breviflora lineage, which contained no unique polymorphisms. The geographic pattern of genetic variation is consistent with a single origin of selfing that occurred recently (7-28 kya). These results are best explained by a historical bottleneck, but the two most northerly umbellata populations also contained little variation and clustered with selfing populations, suggesting that substantial diversity loss preceded the origin of selfing. A bottleneck may have set the stage for the eventual evolution of selfing by purging genetic load that prevents the spread of selfing.

Eriobotryacrassifolia (Rosaceae), a new species from Yunnan Province, China.

The new species Eriobotryacrassifolia, collected from Yunnan Province, China, is characterised and illustrated. A phylogeny based on chloroplast genomes supported its closest affinity with E.tengyuehensis, while a phylogeny based on 197 single-copy nuclear genes supported its closest affinity with E.fragrans and E.deflexa. Morphologically, however, it resembles E.angustissima. Nevertheless, it can be easily distinguished from E.angustissima by its abaxially retroflexed and sharply serrate leaf margins, densely rusty tomentose inflorescences, and oblong or elliptic leaves.

Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes.

We assess relationships among 192 species in all 12 monocot orders and 72 of 77 families, using 602 conserved single-copy (CSC) genes and 1375 benchmarking single-copy ortholog (BUSCO) genes extracted from genomic and transcriptomic datasets. Phylogenomic inferences based on these data, using both coalescent-based and supermatrix analyses, are largely congruent with the most comprehensive plastome-based analysis, and nuclear-gene phylogenomic analyses with less comprehensive taxon sampling. The strongest discordance between the plastome and nuclear gene analyses is the monophyly of a clade comprising Asparagales and Liliales in our nuclear gene analyses, versus the placement of Asparagales and Liliales as successive sister clades to the commelinids in the plastome tree. Within orders, around six of 72 families shifted positions relative to the recent plastome analysis, but four of these involve poorly supported inferred relationships in the plastome-based tree. In Poales, the nuclear data place a clade comprising Ecdeiocoleaceae+Joinvilleaceae as sister to the grasses (Poaceae); Typhaceae, (rather than Bromeliaceae) are resolved as sister to all other Poales. In Commelinales, nuclear data place Philydraceae sister to all other families rather than to a clade comprising Haemodoraceae+Pontederiaceae as seen in the plastome tree. In Liliales, nuclear data place Liliaceae sister to Smilacaceae, and Melanthiaceae are placed sister to all other Liliales except Campynemataceae. Finally, in Alismatales, nuclear data strongly place Tofieldiaceae, rather than Araceae, as sister to all the other families, providing an alternative resolution of what has been the most problematic node to resolve using plastid data, outside of those involving achlorophyllous mycoheterotrophs. As seen in numerous prior studies, the placement of orders Acorales and Alismatales as successive sister lineages to all other extant monocots. Only 21.2% of BUSCO genes were demonstrably single-copy, yet phylogenomic inferences based on BUSCO and CSC genes did not differ, and overall functional annotations of the two sets were very similar. Our analyses also reveal significant gene tree-species tree discordance despite high support values, as expected given incomplete lineage sorting (ILS) related to rapid diversification. Our study advances understanding of monocot relationships and the robustness of phylogenetic inferences based on large numbers of nuclear single-copy genes that can be obtained from transcriptomes and genomes.

Genome-partitioning strategy, plastid and nuclear phylogenomic discordance, and its evolutionary implications of Clematis (Ranunculaceae).

Clematis is one of the largest genera of Ranunculaceae with many phylogenetic problems left to be resolved. Clematis species have considerable genome size of more than 7 Gbp, and there was no whole-genome reference sequence published in this genus. This raises difficulties in acquiring nuclear genome data for its phylogenetic analysis. Previous studies based on Sanger sequencing data, plastid genome data, and nrDNA sequences did not well resolve the phylogeny of Clematis. In this study, we used genome skimming and transcriptome data to assemble the plastid genome sequences, nuclear single nucleotide polymorphisms (SNPs) datasets, and single-copy nuclear orthologous genes (SCOGs) to reconstruct the phylogenetic backbone of Clematis, and test effectiveness of these genome partitioning methods. We also further analyzed the discordance among nuclear gene trees and between plastid and nuclear phylogenies. The results showed that the SCOGs datasets, assembled from transcriptome method, well resolved the phylogenetic backbone of Clematis. The nuclear SNPs datasets from genome skimming method can also produce similar results with the SCOGs data. In contrast to the plastid phylogeny, the phylogeny resolved by nuclear genome data is more robust and better corresponds to morphological characters. Our results suggested that rapid species radiation may have generated high level of incomplete lineage sorting, which was the major cause of nuclear gene discordance. Our simulation also showed that there may have been frequent interspecific hybridization events, which led to some of the cyto-nuclear discordances in Clematis. This study not only provides the first robust phylogenetic backbone of Clematis based on nuclear genome data, but also provides suggestions of genome partitioning strategies for the phylogenomic study of other plant taxa.

A Droplet Digital PCR Based Approach for Identification and Quantification of Porcine and Chicken Derivatives in Beef.

Adulteration of high-value beef with lower-priced alternatives is a world-wide problem resulting in consumers’ distrust and market chaos. Therefore, effective methods for the identification and quantification of adulterated beef products are urgently needed. In this study, we developed a reliable droplet digital PCR (ddPCR) method targeting the single-copy nuclear genes for qualitative and quantitative detection of the presence of porcine and chicken derivatives in beef. A fixed constant (transfer coefficient) was introduced to directly transform the ratio of DNA copy number to the mass proportion of targeted meats. Results revealed that the linearity range of quantification for pork and chicken were both from 1% (w/w) to 90% (w/w). The limit of detection (LOD) and limit of quantification (LOQ) of the developed ddPCR method were the same for pork and chicken in beef, with LOD 0.1% (w/w) and LOQ 1% (w/w). The accuracy and applicability of the method was tested and verified using mixed samples with the known proportions and commercially available beef products. We conclude that our developed ddPCR method was accurate and reliable in identifying and quantifying porcine and chicken derivatives in beef and therefore has great potential to be applied in routine analyses and quality control of beef products.

Phylotranscriptomics reveal the spatio-temporal distribution and morphological evolution of Macrozamia, an Australian endemic genus of Cycadales.

Cycads are regarded as an ancient lineage of living seed plants, and hold important clues to understand the early evolutionary trends of seed plants. The molecular phylogeny and spatio-temporal diversification of one of the species-rich genera of cycads, Macrozamia, have not been well reconstructed. We analysed a transcriptome dataset of 4740 single-copy nuclear genes (SCGs) of 39 Macrozamia species and two outgroup taxa. Based on concatenated (maximum parsimony, maximum likelihood) and multispecies coalescent analyses, we first establish a well-resolved phylogenetic tree of Macrozamia. To identify cyto-nuclear incongruence, the plastid protein coding genes (PCGs) from transcriptome data are extracted using the software HybPiper. Furthermore, we explore the biogeographical history of the genus and shed light on the pattern of floristic exchange between three distinct areas of Australia. Six key diagnostic characters are traced on the phylogenetic framework using two comparative methods, and infra-generic classification is investigated. The tree topologies of concatenated and multi-species coalescent analyses of SCGs are mostly congruent with a few conflicting nodes, while those from plastid PCGs show poorly supported relationships. The genus contains three major clades that correspond to their distinct distributional areas in Australia. The crown group of Macrozamia is estimated to around 11.80 Ma, with a major expansion in the last 5-6 Myr. Six morphological characters show homoplasy, and the traditional phenetic sectional division of the genus is inconsistent with this current phylogeny. This first detailed phylogenetic investigation of Macrozamia demonstrates promising prospects of SCGs in resolving phylogenetic relationships within cycads. Our study suggests that Macrozamia, once widely distributed in Australia, underwent major extinctions because of fluctuating climatic conditions such as cooling and mesic biome disappearance in the past. The current close placement of morphologically distinct species in the phylogenetic tree may be related to neotenic events that occurred in the genus.

Establishment of an allotetraploid fern species, Lepisorus yamaokae Seriz., between two highly niche-differentiated parental species.

The successful establishment of polyploid species is hypothesized to be promoted by niche differentiation from the parental species or by range shifts during climate oscillations. However, few studies have considered both of these factors simultaneously. We resolved the origin of a tetraploid fern, Lepisorus yamaokae, and explored a pattern of niche differentiation among the allotetraploid and parental species in past and current climates. We reconstructed phylogenetic trees based on plastid marker and single-copy nuclear genes to resolve the allopolyploid origin of L. yamaokae. We also evaluated climatic niche differentiation among L. yamaokae and its two parental species using species distribution models in geographic space and principal component analysis. We infer that L. yamaokae had a single allotetraploid origin from L. annuifrons and L. uchiyamae. Climatic niche analyses show that the parental species currently occupy different niche spaces. The predicted distribution of the parental species at the Last Glacial Maximum (LGM) suggests more opportunities for hybridization during the LGM or during other recent temporary range shifts. Lepisorus yamaokae has a narrower niche than the additive niche of the parental species. We also observed niche conservatism in L. yamaokae. Range shifts of the parental species during climatic oscillations in the Quaternary likely facilitated the formation and establishment of L. yamaokae. Further, the genetic intermediacy of L. yamaokae may have enabled a niche shift in its microenvironment, resulting in its successful establishment without a macroclimatic niche shift in L. yamaokae.

Identification of Putative Parental Species of Yuzu (Citrus junos Sieb. Ex Tanaka) by Comparative Analyses of Variations in Chloroplast Genomes and Nuclear Single-copy Genes of Citrus

Identification of Putative Parental Species of Yuzu (Citrus junos Sieb. Ex Tanaka) by Comparative Analyses of Variations in Chloroplast Genomes and Nuclear Single-copy Genes of Citrus

Dilemmas in generic delimitation of Senegalia and allies (Caesalpinioideae, mimosoid clade): how to reconcile phylogenomic evidence with morphology and taxonomy?

Senegalia comprises 219 species distributed in tropical and subtropical regions of North and South America, Africa, Asia and Australia. Two sections are currently recognised within Senegalia and these are most readily distinguished by the differences in disposition of their cauline prickles, i.e. sect. Senegalia with prickles at or near leaf nodes and sect. Monacanthea with mostly internodal prickles. Previous phylogenetic studies, based primarily on small numbers of plastid DNA loci, found Senegalia to be monophyletic with two large subclades corresponding to the sections. Here, we present new phylogenomic evidence from 997 single-copy nuclear gene sequences for a small, but representative set of species. These new analyses show that Senegalia is non-monophyletic, but instead, forms a grade that is paraphyletic with respect to the remainder of the ingoid clade (i.e. Ingeae + Acacia s.s. + Acaciella), comprising two well-supported subclades most likely representing the same clades as found in previous phylogenetic studies of the genus and, interspersed between these, a third, moderately supported clade, comprising the genera Mariosousa, Pseudosenegalia and Parasenegalia. In marked contrast to the nuclear phylogeny, the two Senegalia clades are sister groups in the plastid phylogeny, based on analyses of 72 chloroplast genes, rendering the genus monophyletic, based on plastid data alone. We discuss this new evidence that Senegalia is non-monophyletic in relation to the marked cytonuclear discordance, high gene tree conflict and lack of resolution across this senegalioid grade and review the consistency of the key morphological characters distinguishing the two sections of Senegalia. We conclude that it is likely that Senegalia will need to be split into two (or possibly more) genera: a re-circumscribed Senegalia s.s. that corresponds to the existing Senegaliasect.Senegalia plus the S.ataxacantha group (Senegaliasect.Monacanthea s.s.; future studies may show that this group warrants generic status) and a new genus corresponding to the remainder of sect. Monacanthea (here designated as Senegaliasect.Monacanthea p.p.). However, re-delimiting Senegalia now would be premature given that the key morphological characters are not fully congruent with the two sections and pending denser phylogenetic sampling of taxa. A judiciously selected list of critical taxa is presented to facilitate future phylogenomic studies. Finally, we discuss the identity of Albizialeonardii, which is also placed in this senegalioid grade in these new phylogenomic analyses and place it in synonymy with Parasenegaliavogeliana.