Cyrtandra (Gesneriaceae) is a genus of flowering plants with over 800 species distributed throughout Southeast Asia and the Pacific Islands. On the Hawaiian Islands, 60 named species and over 89 putative hybrids exist, most of which are identified on the basis of morphology. Despite many previous studies on the Hawaiian Cyrtandra lineage, questions regarding the reconciliation of morphology and genetics remain, many of which can be attributed to the relatively young age and evidence of hybridization between species. We utilized targeted enrichment, high‐throughput sequencing, and modern phylogenomics tools to test 31 Hawaiian Cyrtandra samples (22 species, two putative hybrids, four species with two samples each, one species with four samples) and two outgroups for species relationships and hybridization in the presence of incomplete lineage sorting (ILS). Both concatenated and species‐tree methods were used to reconstruct species relationships, and network analyses were conducted to test for hybridization. We expected to see high levels of ILS and putative hybrids intermediate to their parent species. Phylogenies reconstructed from the concatenated and species‐tree methods were highly incongruent, most likely due to high levels of incomplete lineage sorting. Network analyses inferred gene flow within this lineage, but not always between taxa that we expected. Multiple hybridizations were inferred, but many were on deeper branches of the island lineages suggesting a long history of hybridization. We demonstrated the utility of high‐throughput sequencing and a phylogenomic approach using 569 loci to understanding species relationships and gene flow in the presence of ILS.
Acer (the maple genus) is one of the diverse tree genera in the Northern Hemisphere with about 152 species, most of which are in eastern Asia. There are roughly a dozen species in Europe/western Asia and a dozen in North America. Several phylogenetic studies of Acer have been conducted since 1998, but none have provided a satisfactory resolution for basal relationships among sections of Acer. Here we report the first well‐resolved phylogeny of Acer based on DNA sequences of over 500 nuclear loci generated using the anchored hybrid enrichment method and explore the implications of the robust phylogeny for Acer systematics and biogeography. Our phylogenetic results support the most recent taxonomic treatment of Acer by de Jong with some modifications; section Pentaphylla may be expanded to include section Trifoliata, and A. yangbiense may be included in section Lithocarpa. Sections Spicata, Negundo, Arguta, and Palmata form a clade sister to the rest of the genus where sections Glabra and Parviflora comprise the first clade followed by section Macrantha, sections Ginnala, Lithocarpa, Indivisa, sections Platanoidea and Macrophylla, section Rubra, section Acer, and section Pentaphylla. Monotypic sections Glabra and Macrophylla in North America are sister to the Japanese section Parviflora and Eurasian section Platanoidea, respectively. Ancestral area inferences using statistical dispersal and vicariance analysis (S‐DIVA) and dispersal and extinction cladogenesis (DEC) methods suggest that Asia might be the most likely ancestral area of Acer as proposed by Wolfe and Tanai and molecular dating using Bayesian evolutionary analysis by sampling trees (BEAST) indicate that section diversifications of Acer might have completed largely in the late Eocene and the intercontinental disjunctions of Acer between eastern Asia and eastern North America formed mostly in the Miocene.
Torreya Arn., a small genus of Taxaceae, consists of six species occurring in North America and eastern Asia. Several phylogenetic studies have previously been undertaken to reveal relationships within this genus, although only a few DNA segments or species were used. In the present study, we sequenced five Torreya plastomes and combined these with two existing plastomes from the genus to investigate plastome evolution and phylogenetic relationships within Torreya. All sequenced Torreya plastomes shared the same complement of 82 protein‐coding genes, 4 ribosomal RNA genes, and 31 transfer RNA genes. Phylogenetic inference using a maximum likelihood framework consisted of an 82‐gene, 17‐taxon dataset, including all species of Torreya, resolved Torreya as a monophyletic clade. Strongly supported relationships within the genus include the position of the early diverging T. jackii Chun, the two sister pairs T. fargesii Franch.–T. nucifera (L.) Siebold & Zucc. and T. grandis Fortune ex Lindl.–T. californica Torr., and the monophyly of the clade including T. fargesii var. yunnanensis, T. fargesii, and T. nucifera. In addition to the inference of species relationships, divergence time estimation and biogeographical analysis were carried out. The diversification of Torreya was estimated to be approximately 8.9 Ma. Ancestral state reconstruction of the geographical area suggested China/eastern North America as the most likely ancestral region for the six extant Torreya species.
Proto‐Araceae, the earliest diverged lineage within the family Araceae, includes two subfamilies, Gymnostachydoideae (one species) and Orontioideae (eight species). Based on an extensive sampling (a total of 198 accessions) of six chloroplast non‐coding regions (5799 aligned sites), we assessed phylogenetic relationships among the genera and species within subfamily Orontioideae and estimated the timing of intercontinental disjunct events in the Northern Hemisphere. Overall phylogenetic relationships among the genera were consistent with results from previous studies, but several new important findings were discovered, primarily within Symplocarpus Salisb. ex W. P. C. Barton. First, two major lineages within Symplocarpus were identified: one lineage included S. foetidus (L.) Salisb. ex W. Barton, S. nabekuraensis Otsuka & K. Inoue, and S. renifolius Schott ex Tzvelev (Japan), whereas the other included S. nipponicus Makino, S. egorovii N. S. Pavlova & V. A. Nechaev, and S. renifolius (Korea). Symplocarpus renifolius in Japan was tetraploid and closely related to the tetraploid S. foetidus in eastern North America. Populations of S. renifolius in Korea were confirmed to be diploid (2n = 30) and shared the most recent common ancestor with the other diploid species, S. nipponicus. Second, two recently described species, S. nabekuraensis and S. egorovii, were deeply embedded within S. renifolius in Japan and Korea, respectively, and their distinct taxonomic status requires further assessment. Finally, two intercontinental disjunction events in the subfamily, one in Lysichiton Schott between eastern Asia and western North America and the other in Symplocarpus between eastern Asia and eastern North America, were estimated to be between 4.5 and 1.4 million years ago (Pliocene and Pleistocene) and between 1.9 and 0.5 million years ago (Pleistocene), respectively.
“Sky island” species diversification contributes greatly to mountainous biodiversity. However, the underlying genomic divergence and the inferred drivers remain largely unknown. In this study, we examined the diversification history of five diploid species with three exclusively endemic to the sky islands (mountains) of the Himalaya–Hengduan Mountains biodiversity hotspot. All of them together comprise a clade of the genus Eutrema (Brassicaceae). We resequenced genomes of multiple individuals of the found populations for each species. We recovered the inconsistent phylogenetic relationships between plastome and nuclear‐genome trees for one species. Based on nuclear population genomic data, we detected high genetic divergence between five species with limited gene flow. Four species seemed to diverge mainly through geographical isolation, whereas one arose through hybrid origin. The origins of the sampled five species were dated to within the late Miocene when mountains were uplifted and climates oscillated. All species decreased their population sizes since the inferred origin of each species initially, but only two of them expanded after the Last Glacial Maximum. Together, these findings suggest that geographic isolation plays an important role in driving the sky island species diversification of the sampled species in addition to the occasional gene flow that might have led to the hybrid origin of some sky island species, similar to the species diversification of sea islands.
Leandra s.str. clade has around 200 species nearly restricted to eastern Brazil. Most species in this group are narrow endemics, but a few present striking disjunct distributions between eastern Brazil and Andes or Mesoamerica. Given the predominantly “montane” distribution observed in most Leandra s.str., we hypothesized that cyclical range expansions during colder Pleistocene periods, followed by local extinctions during warmer interglacial periods, could have shaped the distribution of the disjunct species in this clade. In order to gather support for this biogeographical scenario in a phylogenetic framework, the species that occur outside eastern Brazil were identified, ages of the dispersal events estimated, climatic niche models for the disjuncts were generated, and the climatic envelope of these species compared. Our results place all dispersal events from eastern Brazil to Andes or Mesoamerica during the Pleistocene. Climatic niche modeling indicates a potential range expansion during the Pleistocene colder times for the disjunct species. Although the surpassing of the “dry diagonal” could have been facilitated during glacial periods, this open corridor is an effective barrier for Leandra, given the reduced number of species that dispersed beyond an eastern Brazilian origin. Additionally, the disjunct species do not present significant differences in their climatic envelopes to the non‐disjunct species. Our results provide support to a short‐dispersion/stepping‐stone migration scenario to account for the observed disjunctions in this clade. Range expansions during Pleistocene colder periods followed by local extinctions during interglacial periods could have shaped the distribution of Leandra s.str.
Quaternary climatic fluctuations have shaped the geographic distribution of lineages, potentially affecting the demography, genetic structure, and patterns of genetic diversity of extant species. Different phylogeographic scenarios have been proposed for plants in neotropical cloud forests during the Last Glacial Maximum based on paleoecological data: the dry refugia hypothesis (DRH) and the moist forest hypothesis. We specifically focus on the Brazilian Atlantic Forest (BAF) range of Cedrela fissilis (Meliaceae), sampling 410 specimens from 50 localities. Our study combines analyses of the genetic diversity, phylogeographic patterns, and past geographic distributions with a particular focus on highland populations. We identified 283 alleles across the 11 microsatellite loci, ranging from 18 to 33 alleles per locus, distributed across five genetic groups. Most populations of C. fissilis from the BAF exhibited a diffuse genetic structure, reflected in low pairwise FST values, which could be the consequence of high gene flow. In addition, the plastid data showed a connection between the western, southern, and eastern populations in the North‐East of Brazil, but no association between genetic data and elevation was observed. Habitat suitability projections over the past 140 000 years showed less fragmentation relative to the present, indicating a higher connectivity and gene flow. Our results provide support for both the moist forest as well as the DRH, suggesting that most likely, a mixture of these processes has acted through space and time.
The biodiversity history on the Qinghai–Tibetan Plateau (QTP) has remained unclear for a long time. Recent paleobotanical investigations provide opportunities for revealing the phytogeographic history on the QTP in deep time and for testing phylogeographic hypotheses. Lagokarpos is an extinct genus with unknown modern affinities. It is easily distinguished by its fruits, which have two long wings and an elliptical fruit body. Previously, Lagokarpos fossils have only been found from North America and Germany, ranging from the latest Paleogene to early middle Eocene. Recently, we found fossil fruits of this genus from the Niubao Formation, near Bangoin County in the central QTP. A new species, namely Lagokarpos tibetensis H. Tang, T. Su & Z. K. Zhou sp. nov., is described. This is the first fossil record of the genus in Asia. The occurrence of L. tibetensis indicates a close floristic linkage between the QTP and other floras in the Northern Hemisphere during the Paleogene. According to the floristic assemblages, we suggest the central QTP experienced a tropical or subtropical humid climate during that period.
Photinia and its morphologically similar allies in Maleae (Rosaceae) consist of five currently recognized genera: Aronia, Heteromeles, Photinia, Pourthiaea, and Stranvaesia, and 68 species, distributed in Asia and North and Central America. Despite previous efforts to clarify relationships in this group, the generic delimitations have remained uncertain. Our goals were to reconstruct a robust phylogeny of Photinia and its close allies to test the monophyly of the currently recognized genera, especially Photinia and Stranvaesia, and the hybrid origin hypothesis of Photinia bodinieri. This study employs complete plastomes and the entire nuclear ribosomal DNA (nrDNA) repeats assembled from the genome skimming approach with a broad taxon sampling of 81 species in 30 genera of Rosaceae, especially Maleae. Based on three datasets, including the whole plastome, coding sequence, and nrDNA repeats, the results of maximum likelihood and Bayesian inference analyses showed that the previously circumscribed Stranvaesia and Photinia were each non‐monophyletic. Six clades have been recovered herein within Photinia and its allied genera: Aronia, Heteromeles, Photinia s.s., Pourthiaea, Stranvaesia, and a new genus Phippsiomeles consisting of the Central American species formerly placed in Photinia. The strong conflicts between the plastome and nrDNA phylogenies of Phippsiomeles and Stranvaesia tomentosa suggest the possibility that they may have each originated involving hybridization events, while no incongruence among datasets was detected to support the hybrid origin of Photinia bodinieri. We provide 12 new combinations, to transfer eight taxa of the New World Photinia into Phippsiomeles and clarify the generic placements of several species of Photinia and Stranvaesia.
The megadiverse genus Carex (c. 2000 species, Cyperaceae) has a nearly cosmopolitan distribution, displaying an inverted latitudinal richness gradient with higher species diversity in cold‐temperate areas of the Northern Hemisphere. Despite great expansion in our knowledge of the phylogenetic history of the genus and many molecular studies focusing on the biogeography of particular groups during the last few decades, a global analysis of Carex biogeography and diversification is still lacking. For this purpose, we built the hitherto most comprehensive Carex‐dated phylogeny based on three markers (ETS–ITS–matK), using a previous phylogenomic Hyb‐Seq framework, and a sampling of two‐thirds of its species and all recognized sections. Ancestral area reconstruction, biogeographic stochastic mapping, and diversification rate analyses were conducted to elucidate macroevolutionary biogeographic and diversification patterns. Our results reveal that Carex originated in the late Eocene in E Asia, where it probably remained until the synchronous diversification of its main subgeneric lineages during the late Oligocene. E Asia is supported as the cradle of Carex diversification, as well as a “museum” of extant species diversity. Subsequent “out‐of‐Asia” colonization patterns feature multiple asymmetric dispersals clustered toward present times among the Northern Hemisphere regions, with major regions acting both as source and sink (especially Asia and North America), as well as several independent colonization events of the Southern Hemisphere. We detected 13 notable diversification rate shifts during the last 10 My, including remarkable radiations in North America and New Zealand, which occurred concurrently with the late Neogene global cooling, which suggests that diversification involved the colonization of new areas and expansion into novel areas of niche space.
