Nuclear Phylogenies Research Articles

Phylogeny of the Dipus sagitta Species Complex by Nuclear Gene Sequences.

The northern three-toed jerboa Dipus sagitta had long been considered to be a single polytypic species. High genetic diversity of D. sagitta was earlier revealed on the basis of several mitochondrial and nuclear genes, and several separate species were hypothesized to occur within the taxon. However, the relationships between phylogenetic lineages have not been established because of the small sample size of nuclear genes. In the present work, a far larger set of nuclear DNA loci was used, and thus, a higher resolution of the phylogenetic tree was achieved for ten D. sagitta forms. The structure revealed for the species mainly confirmed the topology and relationships of the mtDNA lineages. Yet the mitochondrial and nuclear phylogenies were not completely consistent. Some of the D. sagitta genetic lineages were therefore assumed to be a product of reticular evolutionary processes. The taxon was concluded to be the diverse species complex D. sagitta sensu lato, in which long-diverged lineages are not always reproductively isolated.

Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, Otocolobus manul.

Pallas's cat, or the manul cat (Otocolobus manul), is a small felid native to the grasslands and steppes of central Asia. Population strongholds in Mongolia and China face growing challenges from climate change, habitat fragmentation, poaching, and other sources. These threats, combined with O. manul's zoo collection popularity and value in evolutionary biology, necessitate improvement of species genomic resources. We used standalone nanopore sequencing to assemble a 2.5 Gb, 61-contig nuclear assembly and 17097 bp mitogenome for O. manul. The primary nuclear assembly had 56× sequencing coverage, a contig N50 of 118 Mb, and a 94.7% BUSCO completeness score for Carnivora-specific genes. High genome collinearity within Felidae permitted alignment-based scaffolding onto the fishing cat (Prionailurus viverrinus) reference genome. Manul contigs spanned all 19 felid chromosomes with an inferred total gap length of less than 400 kilobases. Modified basecalling and variant phasing produced an alternate pseudohaplotype assembly and allele-specific DNA methylation calls; 61 differentially methylated regions were identified between haplotypes. Nearest features included classical imprinted genes, non-coding RNAs, and putative novel imprinted loci. The assembled mitogenome successfully resolved existing discordance between Felinae nuclear and mtDNA phylogenies. All assembly drafts were generated from 158 Gb of sequence using seven minION flow cells.

Nuclear phylogeny and insights into whole-genome duplications and reproductive development of Solanaceae plants

Solanaceae, the nightshade family, have ∼2700 species, including the important crops potato and tomato, ornamentals, and medicinal plants. Several sequenced Solanaceae genomes show evidence for whole-genome duplication (WGD), providing an excellent opportunity to investigate WGD and its impacts. Here, we generated 93 transcriptomes/genomes and combined them with 87 public datasets, for a total of 180 Solanaceae species representing all four subfamilies and 14 of 15 tribes. Nearly 1700 nuclear genes from these transcriptomic/genomic datasets were used to reconstruct a highly resolved Solanaceae phylogenetic tree with six major clades. The Solanaceae tree supports four previously recognized subfamilies (Goetzeioideae, Cestroideae, Nicotianoideae, and Solanoideae) and the designation of three other subfamilies (Schizanthoideae, Schwenckioideae, and Petunioideae), with the placement of several previously unassigned genera. We placed a Solanaceae-specific whole-genome triplication (WGT1) at ∼81 million years ago (mya), before the divergence of Schizanthoideae from other Solanaceae subfamilies at ∼73 mya. In addition, we detected two gene duplication bursts (GDBs) supporting proposed WGD events and four other GDBs. An investigation of the evolutionary histories of homologs of carpel and fruit developmental genes in 14 gene (sub)families revealed that 21 gene clades have retained gene duplicates. These were likely generated by the Solanaceae WGT1 and may have promoted fleshy fruit development. This study presents a well-resolved Solanaceae phylogeny and a new perspective on retained gene duplicates and carpel/fruit development, providing an improved understanding of Solanaceae evolution.

Plastome-based backbone phylogeny of East Asian Phedimus (Subgenus Aizoon: Crassulaceae), with special emphasis on Korean endemics.

Although the monophyly of Phedimus has been strongly demonstrated, the species relationships among approximately 20 species of Phedimus have been difficult to determine because of the uniformity of their floral characteristics and extreme variation of their vegetative characters, often accompanied by high polyploid and aneuploid series and diverse habitats. In this study, we assembled 15 complete chloroplast genomes of Phedimus species from East Asia and generated a plastome-based backbone phylogeny of the subgenus Aizoon. As a proxy for nuclear phylogeny, we reconstructed the nuclear ribosomal DNA internal transcribed spacer (nrDNA ITS) phylogeny independently. The 15 plastomes of subg. Aizoon were highly conserved in structure and organization; hence, the complete plastome phylogeny fully resolved the species relationships with strong support. We found that P. aizoon and P. kamtschaticus were polyphyletic and morphologically distinct or ambiguous species, and they most likely evolved from the two species complex. The crown age of subg. Aizoon was estimated to be 27 Ma, suggesting its origin to be in the late Oligocene; however, the major lineages were diversified during the Miocene. The two Korean endemics, P. takesimensis and P. zokuriensis, were inferred to have originated recently during the Pleistocene, whereas the other endemic, P. latiovalifolium, originated in the late Miocene. Several mutation hotspots and seven positively selected chloroplast genes were identified in the subg. Aizoon.

PHYLOGENY OF THE <i>DIPUS SAGITTA</i> SPECIES COMPLEX BASED ON THE SEQUENCING OF NUCLEAR GENES

The northern three-toed jerboa Dipus sagitta was long considered to be a single polytypic species. Earlier, a high genetic diversity of D. sagitta was revealed on the basis of several mitochondrial and nuclear genes, and the existence of several separate species within it was hypothesized. However, a small number of available nuclear genes prevented the establishment of relationships between identified phylogenetic lineages. Here, we significantly expand the set of utilized nuclear DNA loci, which resulted in a sufficiently higher resolution of the phylogenetic tree for 10 forms of D. sagitta. The identified species structure mainly confirms the topology and relationship of the mtDNA lineages. At the same time, the mitochondrial and nuclear phylogenies are not completely consistent. Hence, a part of the genetic lineages of D. sagitta is apparently a product of reticular evolutionary processes. This taxon is thus the diverse species complex D. sagitta sensu lato, in which long-diverged lineages are not always reproductively isolated.

Phylogenomic analyses of Camellia support reticulate evolution among major clades

Camellia (Theaceae) is a morphologically highly diverse genus of flowering plants and includes many famous species with high economic value, and the phylogeny of this genus is not fully resolved. We used 95 transcriptomes from 87 Camellia species and identified 1481 low-copy genes to conduct a detailed analysis of the phylogeny of this genus according to various data-screening criteria. The results show that, very different from the two existing classification systems of Camellia, 87 species are grouped into 8 main clades and two independent species, and that all 8 clades except Clade 8 were strongly supported by almost all the coalescent or concatenated trees using different gene subsets. However, the relationships among these clades were weakly supported and different from analyses using different gene subsets; furthermore, they do not agree with the phylogeny from chloroplast genomes of Camellia. Additional analyses support reticulate evolution (probably resulting from introgression or hybridization) among some major Camellia lineages, providing explanation for extensive gene tree conflicts. Furthermore, we inferred that together with the formation of East Asian subtropical evergreen broad-leaved forests, Camellia underwent a radiative divergence of major clades at 23 ∼ 19 Ma in the late Miocene then had a subsequent species burst at 10 ∼ 5 Ma. Principal component and cluster analyses provides new insights into morphological changes underlying the evolution of Camellia and a reference to further clarify subgenus and sections of this genus. The comprehensive study here including a nuclear phylogeny and other analyses reveal the rapid evolutionary history of Camellia.

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.

Museomics reveals the phylogenetic position of the extinct Moroccan trout Salmo pallaryi.

The authors used museomics to reconstruct the mitochondrial genome from two individuals of the Moroccan, endemic and extinct trout, Salmo pallaryi. They further obtained partial data from 21 nuclear genes previously used for trout phylogenetic analyses. Phylogenetic analyses, including publicly available data from the mitochondrial control region and the cytochrome b gene, and the 21 nuclear genes, place S. pallaryi among other North African trouts. mtDNA places S. pallaryi close to Salmo macrostigma within a single North African clade. Although the nuclear coverage of the genome was low, both specimens were independently positioned as sisters to one of two distantly related North African clades, viz. the Atlas clade with the Dades trout, Salmo multipunctatus. Phylogenetic discordance between mtDNA and nuclear DNA phylogenies is briefly discussed. As several specimens that were extracted failed to produce DNA of sufficient quality, the authors discuss potential reasons for the failure. They suggest that museum specimens in poor physical condition may be better for DNA extraction compared to better-preserved ones, possibly related to the innovation of formalin as a fixative before ethanol storage in the early 20th century.

Spatiotemporal process of long-distance seed dispersal in a pantropically distributed sea hibiscus group.

Long-distance dispersal (LDD) of seeds plays an essential role in the migration of plants to a new habitat and maintaining gene flow among geographically isolated populations. Pantropical plants with sea-drifted seeds, which have one of the largest distributions in all flowering plants, have achieved their global distribution by LDD. However, the spatiotemporal processes to achieve the wide distribution and the role of LDD in it have not yet been elucidated. In this study, we conducted phylogenomic analyses on the plastome, genome-wide nuclear SNP, and low-copy gene data of Hibiscus tiliaceus and its relatives. The dated phylogeny suggested that global expansion started approximately 4 million years ago (Ma), and species diversification occurred 1Ma. Plastome phylogeny confirmed the nonmonophyly of the haplotypes in the two widely distributed coastal species, H. tiliaceus and H. pernambucensis. In contrast, genome-wide nuclear SNP phylogenies demonstrated clear genetic segregation among species and/or geographical regions. Ancestral polymorphisms in chloroplast genomes shared among widely distributed species have remained below the range of rapid expansion and speciation of marginal populations. This study demonstrated that the LDD of sea-drifted seeds contributed to the rapid expansion and pantropical distribution of sea hibiscus in the last few million years, and adaptation to local environment or isolation by regional effect after LDD promoted speciation, suppressing gene flow.

Phylogenomics of Anguis and Pseudopus (Squamata, Anguidae) indicates Balkan-Apennine mitochondrial capture associated with the Messinian event

A dated phylogenetic hypothesis on the evolutionary history of the extant taxa of the Western Palearctic lizards Anguis and Pseudopus is revised using genome-wide nuclear DNA and mitogenomes. We found overall concordance between nuclear and mitochondrial DNA phylogenies, with one significant exception – the Apennine A. veronensis. In mitochondrial DNA, this species forms a common clade with the earliest diverging lineage, the southern Balkan endemic A. cephallonica, while it clusters together with A. fragilis in nuclear DNA. The nuclear phylogeny conforms to the morphology, which is relatively similar between A. veronensis and A. fragilis. The most plausible explanation for the mitonuclear discordance is ancient mitochondrial capture from the Balkan ancestor of A. cephallonica to the Apennine population of the A. fragilis-veronensis ancestor. We hypothesize that this capture occurred only in a geographically restricted population. The dating of this presumed mitochondrial introgression and capture coincides with the Messinian event, when the Balkan and Apennine Peninsulas were presumably largely connected. The dated nuclear phylogenomic reconstruction estimated the divergence of A. cephallonica around 12 Mya, while the sister clade representing the A. fragilis species complex consisting of the sister species A. fragilis–A. veronensis and A. colchica–A. graeca further diversified around 7 Mya. The depth of nuclear divergence among the evolutionary lineages of Pseudopus (0.5–1.2 Mya) supports their subspecies status.

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.

Phylogenomics and genome size evolution in Amomum s. s. (Zingiberaceae): Comparison of traditional and modern sequencing methods

Background and AimsA targeted enrichment NGS approach was used to construct the phylogeny of Amomum Roxb. (Zingiberaceae). Phylogenies based on hundreds of nuclear genes, the whole plastome and the rDNA cistron were compared with an ITS-based phylogeny. Trends in genome size (GS) evolution were examined, chromosomes were counted and the geographical distribution of phylogenetic lineages was evaluated. MethodsIn total, 92 accessions of 54 species were analysed. ITS was obtained for 79 accessions, 37 accessions were processed with Hyb-Seq and sequences from 449 nuclear genes, the whole cpDNA, and the rDNA cistron were analysed using concatenation, coalescence and supertree approaches. The evolution of absolute GS was analysed in a phylogenetic and geographical context. The chromosome numbers of 12 accessions were counted. Key ResultsFour groups were recognised in all datasets though their mutual relationships differ among datasets. While group A (A. subulatum and A. petaloideum) is basal to the remaining groups in the nuclear gene phylogeny, in the cpDNA topology it is sister to group B (A. repoeense and related species) and, in the ITS topology, it is sister to group D (the Elettariopsis lineage). The former Elettariopsis makes a monophyletic group. There is an increasing trend in GS during evolution. The largest GS values were found in group D in two tetraploid taxa, A. cinnamomeum and A. aff. biphyllum (both 2n = 96 chromosomes). The rest varied in GS (2C = 3.54–8.78 pg) with a constant chromosome number 2n = 48. There is a weak connection between phylogeny, GS and geography in Amomum. ConclusionsAmomum consists of four groups, and the former Elettariopsis is monophyletic. Species in this group have the largest GS. Two polyploids were found and GS greatly varied in the rest of Amomum.

Taxonomic changes in the Lomentariaceae (Rhodymeniales, Rhodophyta): Yendoa gen. nov. and Ceratodictyon sanctae-crucis sp. nov.

ABSTRACT The Lomentariaceae, previously treated as subfamily Lomentarioideae in the family Champiaceae, is one of the six families currently classified in the Rhodymeniales. Relationships within the family are not well-established, and new genera have been segregated from Lomentaria, a notoriously polyphyletic taxon as currently circumscribed. The lack of access to molecular data of type specimens has limited the taxonomic clarifications within the Lomentariaceae. Using new collections from Brazil, historical collections and data available in GenBank, we generated rbcL and COI-5P phylogenies of the Lomentariaceae, and we used species delimitation methods to assess the species-level diversity among sequences. A nuclear LSU rDNA phylogeny, although less representative in number of taxa, confirmed our findings. Our results recovered Ceratodictyon and Semnocarpa as monophyletic, whereas Lomentaria was polyphyletic. Integrating phylogenetic analyses, analyses of genetic variance, and morphological analyses, we revealed a new species, Ceratodictyon sanctae-crucis sp. nov., collected on the coast of Bahia (northeastern Brazil). Having included a newly generated sequence of the holotype of Lomentaria sinensis, a heterotypic synonym of L. hakodatensis, and a sequence from a sample collected near the type locality of L. hakodatensis, we propose the new genus Yendoa gen. nov. to accommodate this species. Our results support a more phylogenetically coherent taxonomic scheme for the Lomentariaceae, which now includes only monophyletic genera.

Evaluating a species phylogeny using ddRAD SNPs: Cyto-nuclear discordance and introgression in the salmonid genus Thymallus (Salmonidae)

Hybridization and introgression are very common among freshwater fishes due to the dynamic nature of hydrological landscapes. Cyclic patterns of allopatry and secondary contact provide numerous opportunities for interspecific gene flow, which can lead to discordant paths of evolution for mitochondrial and nuclear genomes. Here, we used double digest restriction-site associated DNA sequencing (ddRADseq) to obtain a genome-wide single nucleotide polymorphism (SNP) dataset comprehensive for allThymallus (Salmonidae)species to infer phylogenetic relationships and evaluate potential recent and historical gene flow among species. The newly obtained nuclear phylogeny was largely concordant with a previously published mitogenome-based topology but revealed a few cyto-nuclear discordances. These incongruencies primarily involved the placement of internal nodes rather than the resolution of species, except for one European species where anthropogenic stock transfers are thought to be responsible for the observed pattern. The analysis of four contact zones where multiple species are found revealed a few cases of mitochondrial capture and limited signals of nuclear introgression. Interestingly, the mechanisms restricting interspecific gene flow might be distinct; while in zones of secondary contact, small-scale physical habitat separation appeared as a limiting factor, biologically based reinforcement mechanisms are presumed to be operative in areas where species presumably evolved in sympatry. Signals of historical introgression were largely congruent with the routes of species dispersal previously inferred from mitogenome data. Overall, the ddRADseq dataset provided a robust phylogenetic reconstruction of the genus Thymallus including new insights into historical hybridization and introgression, opening up new questions concerning their evolutionary history.

Phylogenomics as an effective approach to untangle cross-species hybridization event: A case study in the family Nymphaeaceae

Hybridization is common and considered as an important evolutionary force to increase intraspecific genetic diversity. Detecting hybridization events is crucial for understanding the evolutionary history of species and further improving molecular breeding. The studies on identifying hybridization events through the phylogenomic approach are still limited. We proposed the conception and method of identifying allopolyploidy events by phylogenomics. The reconciliation and summary of nuclear multi-labeled gene family trees were adopted to untangle hybridization events from next-generation data in our novel phylogenomic approach. Given horticulturalists' relatively clear cultivated crossbreeding history, the water lily family is a suitable case for examining recent allopolyploidy events. Here, we reconstructed and confirmed the well-resolved nuclear phylogeny for the Nymphaeales family in the context of geological time as a framework for identifying hybridization signals. We successfully identified two possible allopolyploidy events with the parental lineages for the hybrids in the family Nymphaeaceae based on summarization from multi-labeled gene family trees of Nymphaeales. The lineages where species Nymphaea colorata and Nymphaea caerulea are located may be the progenitors of horticultural cultivated species Nymphaea 'midnight' and Nymphaea 'Woods blue goddess'. The proposed hybridization hypothesis is also supported by horticultural breeding records. Our methodology can be widely applied to identify hybridization events and theoretically facilitate the genome breeding design of hybrid plants.

Seventy-eight entire mitochondrial genomes and nuclear rRNA genes provide insight into the phylogeny of the hard ticks, particularly the Haemaphysalis species, Africaniella transversale and Robertsicus elaphensis

Hoogstraal and Kim (1985) proposed from morphology, three groups of Haemaphysalis subgenera: (i) the “structurally advanced”; (ii) the “structurally intermediate”; and (iii) the “structurally primitive” subgenera. Nuclear gene phylogenies, however, did not indicate monophyly of these morphological groups but alas, only two mitochondrial (mt) genomes from the “structurally intermediate” subgenera had been sequenced. The phylogeny of Haemaphysalis has not yet been resolved. We aimed to resolve the phylogeny of the genus Haemaphysalis, with respect to the subgenus Alloceraea. We presented 15 newly sequenced and annotated mt genomes from 15 species of ticks, five species of which have not been sequenced before, and four new 18S rRNA and 28S rRNA nuclear gene sequences. Our datasets were constructed from 10 mt protein-coding genes, cox1, and the 18S and 28S nuclear rRNA genes. We found a 132-bp insertion between tRNA-Glu (E) gene and the nad1 gene in the mt genome of Haemaphysalis (Alloceraea) inermis that resembles insertions in H. (Alloceraea) kitaokai and Rhipicephalus (Boophilus) geigyi. Our mt phylogenies had the three species of Amblyomma (Aponomma) we sequenced embedded in the main clade of Amblyomma: Am. (Aponomma) fimbriatum, Am. (Aponomma) gervaisi and Am. (Aponomma) latum. This is further support for the hypothesis that the evolution of eyes appears to have occurred in the most-recent-common-ancestor of Amblyocephalus (i.e. Amblyomminae plus Rhipicephalinae) and that eyes were subsequently lost in the most-recent-common-ancestor of the subgenus Am. (Aponomma). Either Africaniella transversale or Robertsicus elaphensis, or perhaps Af. transversale plus Ro. elaphensis, appear to be the sister-group to the rest of the metastriate Ixodida. Our cox1 phylogenies did not indicate monophyly of the “structurally primitive”, “structurally intermediate” nor the “structurally advanced” groups of Haemaphysalis subgenera. Indeed, the subgenus Alloceraea may be the only monophyletic subgenus of the genus Haemaphysalis sequenced thus far. All of our mt genome and cox1 phylogenies had the subgenus Alloceraea in a clade that was separate from the rest of the Haemaphysalis ticks. If Alloceraea is indeed the sister to the rest of the Haemaphysalis subgenera this would resonate with the argument of Hoogstraal and Kim (1985), that Alloceraea was a subgenus of “primitive” Haemaphysalis. Alectorobius capensis from Japan had a higher genetic-identity to A. sawaii, which was also from Japan, than to the A. capensis from South Africa. This indicates that A. capensis from Japan may be a cryptic species with respect to the A. capensis from South Africa.

Comparative plastomes of Carya species provide new insights into the plastomes evolution and maternal phylogeny of the genus.

Carya, in the Juglandiodeae subfamily, is to a typical temperate-subtropical forest-tree genus for studying the phylogenetic evolution and intercontinental disjunction between eastern Asia (EA) and North America (NA). Species of the genus have high economic values worldwide for their high-quality wood and the rich healthy factors of their nuts. Although previous efforts based on multiple molecular markers or genome-wide SNPs supported the monophyly of Carya and its two EA and NA major subclades, the maternal phylogeny of Carya still need to be comprehensively evaluated. The variation of Carya plastome has never been thoroughly characterized. Here, we novelly present 19 newly generated plastomes of congeneric Carya species, including the recently rediscovered critically endangered C. poilanei. The overall assessment of plastomes revealed highly conservative in the general structures. Our results indicated that remarkable differences in several plastome features are highly consistent with the EA-NA disjunction and showed the relatively diverse matrilineal sources among EA Carya compared to NA Carya. The maternal phylogenies were conducted with different plastome regions and full-length plastome datasets from 30 plastomes, representing 26 species in six genera of Juglandoideae and Myrica rubra (as root). Six out of seven phylogenetic topologies strongly supported the previously reported relationships among genera of Juglandoideae and the two subclades of EA and NA Carya, but displayed significant incongruencies between species within the EA and NA subclades. The phylogenetic tree generated from full-length plastomes demonstrated the optimal topology and revealed significant geographical maternal relationships among Carya species, especially for EA Carya within overlapping distribution areas. The full-length plastome-based phylogenetic topology also strongly supported the taxonomic status of five controversial species as separate species of Carya. Historical and recent introgressive hybridization and plastid captures might contribute to plastome geographic patterns and inconsistencies between topologies built from different datasets, while incomplete lineage sorting could account for the discordance between maternal topology and the previous nuclear genome data-based phylogeny. Our findings highlight full-length plastomes as an ideal tool for exploring maternal relationships among the subclades of Carya, and potentially in other outcrossing perennial woody plants, for resolving plastome phylogenetic relationships.

Hybridization and genome duplication for early evolutionary success in the Asian Palmate group of Araliaceae

AbstractThe phenomenal advances in sequencing techniques and analytical development during the last decade have provided a unique opportunity to unravel the evolutionary history of lineages under complex patterns of evolution. This is the case of the largest clade of the ginseng family (Araliaceae), the Asian Palmate group (AsPG), where the large internal polytomies and genome incongruences detected in previous studies pointed to a scenario of radiation with hybridization events between genera for the early evolution of the group. In this study, we aim to obtain well‐resolved nuclear and plastid phylogenies of the AsPG using Hyb‐Seq to evaluate the radiation hypothesis and assess the role of hybridization in the early evolution of the group. We performed concatenated‐ and coalescent‐based phylogenetic analyses from the 936 targeted nuclear loci and 261 plastid loci obtained for 72 species representing 20 genera of the AsPG and the main clades of Araliaceae. The impact of hybridization and incomplete lineage sorting (ILS) was assessed with SNaQ, and genome duplications were evaluated with ChromEvol. Our nuclear and plastid phylogenies are compatible with a scenario of early radiation in the AsPG. Also, the identification of extensive signals of hybridization and ILS behind the genome incongruences supports hybridization as a major driving force during the early radiation. We hypothesize a whole‐genome duplication event at the origin of the AsPG, followed by a radiation that led to extensive ILS, which, alongside the early inter‐genera hybridization, is obscuring the phylogenetic signal in the early evolution of this major clade.

Evolution of mitochondrial and nuclear genomes in Pennatulacea

We examine the phylogeny of sea pens using sequences of whole mitochondrial genomes and the nuclear ribosomal cluster generated through low coverage Illumina sequencing. Taxon sampling includes 30 species in 19 genera representing 13 families. Ancestral state reconstruction shows that most sea pen mitochondrial genomes have the ancestral gene order, and that Pennatulacea with diverse gene orders are found in a single clade. The monophyly of Pennatulidae and Protoptilidae are rejected by both the mitochondrial and nuclear dataset, while the mitochondrial dataset further rejects monophyly of Virgulariidae, and the nuclear dataset rejects monophyly of Kophobelemnidae. We show discordance between nuclear ribosomal gene cluster phylogenies and whole mitochondrial genome phylogenies and highlight key Pennatulacea taxa that could be included in cnidarian genome-wide studies to better resolve the sea pen tree of life. We further illustrate how well frequently sequenced markers capture the overall diversity of the mitochondrial genome and the nuclear ribosomal genes in sea pens.

Resolution, conflict and rate shifts: insights from a densely sampled plastome phylogeny for Rhododendron (Ericaceae).

Rhododendron is a species-rich and taxonomically challenging genus due to recent adaptive radiation and frequent hybridization. A well-resolved phylogenetic tree would help to understand the diverse history of Rhododendron in the Himalaya-Hengduan Mountains where the genus is most diverse. We reconstructed the phylogeny based on plastid genomes with broad taxon sampling, covering 161 species representing all eight subgenera and all 12 sections, including ~45 % of the Rhododendron species native to the Himalaya-Hengduan Mountains. We compared this phylogeny with nuclear phylogenies to elucidate reticulate evolutionary events and clarify relationships at all levels within the genus. We also estimated the timing and diversification history of Rhododendron, especially the two species-rich subgenera Rhododendron and Hymenanthes that comprise >90 % of Rhododendron species in the Himalaya-Hengduan Mountains. The full plastid dataset produced a well-resolved and supported phylogeny of Rhododendron. We identified 13 clades that were almost always monophyletic across all published phylogenies. The conflicts between nuclear and plastid phylogenies suggested strongly that reticulation events may have occurred in the deep lineage history of the genus. Within Rhododendron, subgenus Therorhodion diverged first at 56 Mya, then a burst of diversification occurred from 23.8 to 17.6 Mya, generating ten lineages among the component 12 clades of core Rhododendron. Diversification in subgenus Rhododendron accelerated c. 16.6 Mya and then became fairly continuous. Conversely, Hymenanthes diversification was slow at first, then accelerated very rapidly around 5 Mya. In the Himalaya-Hengduan Mountains, subgenus Rhododendron contained one major clade adapted to high altitudes and another to low altitudes, whereas most clades in Hymenanthes contained both low- and high-altitude species, indicating greater ecological plasticity during its diversification. The 13 clades proposed here may help to identify specific ancient hybridization events. This study will help to establish a stable and reliable taxonomic framework for Rhododendron, and provides insight into what drove its diversification and ecological adaption. Denser sampling of taxa, examining both organelle and nuclear genomes, is needed to better understand the divergence and diversification history of Rhododendron.