Beringia Research Articles

Mitochondrial genomes of Late Pleistocene caballine horses from China belong to a separate clade

There were several species of Equus in northern China during the Late Pleistocene, including Equus przewalskii and Equus dalianensis. A number of morphological studies have been carried out on E. przewalskii and E. dalianensis, but their evolutionary history is still unresolved. In this study, we retrieved near-complete mitochondrial genomes from E. dalianensis and E. przewalskii specimens excavated from Late Pleistocene strata in northeastern China. Phylogenetic analyses revealed that caballoid horses were divided into two subclades: the New World and the Old World caballine horse subclades. The Old World caballine horses comprise of two deep phylogenetic lineages, with modern and ancient Equus caballus and modern E. przewalskii forming lineage Ⅰ, and the individuals in this study together with one Yakut specimen forming lineage Ⅱ. Our results indicate that Chinese Late Pleistocene caballoid horses showed a closer relationship to other Eurasian caballine horses than that to Pleistocene horses from North America. In addition, phylogenetic analyses suggested a close relationship between E. dalianensis and the Chinese fossil E. przewalskii, in agreement with previous researches based on morphological analyses. Interestingly, E. dalianensis and the fossil E. przewalskii were intermixed rather than split into distinct lineages, suggesting either that gene flow existed between these two species or that morphology-based species assignment of palaeontological specimens is not always correct. Moreover, Bayesian analysis showed that the divergence time between the New World and the Old World caballoid horses was at 1.02 Ma (95% CI: 0.86–1.24 Ma), and the two Old World lineages (Ⅰ & Ⅱ) split at 0.88 Ma (95% CI: 0.69–1.13 Ma), which indicates that caballoid horses seem to have evolved into different populations in the Old World soon after they migrated from North America via the Bering Land Bridge. Finally, the TMRCA of E. dalianensis was estimated at 0.20 Ma (95% CI: 0.15–0.28 Ma), and it showed a relative low genetic diversity compared with other Equus species.

Biogeographical divides delineated by the three‐step landforms of China and the East China Sea: Insights from the phylogeography of Kerria japonica

AbstractAimEast Asia exhibits complex geomorphological and climatic characteristics. The aim of this study was to test whether the so‐called three‐step landforms of China, together with the East China Sea (ECS), have acted to shape specific phylogeographical patterns and affected the biogeographical history of the species belonging to the East Asian Flora.LocationChina and Japan.TaxonKerria japonica (L.) DC.MethodsThree chloroplast DNA regions and 15 nuclear microsatellite (nSSR) loci were sequenced and genotyped in 576/450 individuals of K. japonica. Phylogeographical analyses were performed to assess the genetic structure, historical gene flow and demographical history of these individuals, and climatic factors were examined to determine their effects on phylogeographical breaks. Furthermore, time‐calibrated phylogenetic trees and ancestral range reconstruction were used to infer the biogeographical history of K. japonica. Potential habitats at present and during the last glacial maximum (LGM) were identified using ecological niche modelling.ResultsDistinct phylogeographical breaks were found across the ECS and along the boundary of the three‐step landforms of China. Low historical gene flow and significant climatic differences were detected in each pair of adjacent regions. The results of molecular dating and ancestral range reconstruction indicated that K. japonica originated in North America during the mid‐Miocene (14.76 Ma), and intra‐specific diversification began in the late Miocene (7.78 Ma). Compared to the relatively stable distribution range of Chinese populations, Japanese populations experienced range expansion after the LGM in response to Quaternary climate change.Main conclusionsKerria japonica has a complex biogeographical history, with a mid‐Miocene origin in North America and subsequent migration into East Asia via the Bering land bridge. The onset of intra‐specific diversification was probably associated with Asian monsoon intensifications, while exposure to the ECS floor facilitated the formation of the Japanese lineage in the late Miocene. The spatiotemporal population differentiation on the Chinese mainland demonstrates the significant role of biogeographical divides delineated by the three‐step landforms of China and provides clues to understand the floristic regionalization and evolutionary history of plant diversity in East Asia, especially with respect to the Hengduan Mountains, Central China and East China.

Collections‐based systematics and biogeography in the 21st century: A tribute to Dr. Vicki Funk

Collections‐based systematics and biogeography in the 21st century: A tribute to Dr. Vicki Funk

A Cretaceous Gondwana origin of the wax palm subfamily (Ceroxyloideae: Arecaceae) and its paleobiogeographic context

Here we study a well-preserved petrified palm stem from the latest Maastrichtian (Late Cretaceous) to earliest Danian (early Paleocene) sediments (c. 66–65 Ma old) of the Deccan Intertrappean Beds of Madhya Pradesh, Central India. We infer its systematic relationships and relevance to palm evolution. The significant anatomical attributes of the fossil include the presence of fibrovascular bundles (fvbs) with reniform dorsal fibrous sclerenchyma (dcap), 2 to >4 metaxylem vessel elements in each fvb, lacunar ground parenchyma tissue, and centrifugal differentiation of the fibrous dcap parts of the fvbs. These features reveal a close resemblance to extant taxa of the wax palm subfamily Ceroxyloideae, now with a disjunct distribution in America, Australia, Madagascar and the Comoros. The Cretaceous stem is described here as Palmoxylon ceroxyloides Khan, Hazra et Bera, sp. nov. This is the oldest reliable occurrence of Ceroxyloideae in the fossil record. Present fossil evidence indicates that the sub-family was already present in India in the Late Cretaceous (Maastrichtian), about 10–15 million years before the collision of India with Eurasia. Post-collision the subfamily may have been dispersed to East Asia and then to North America via the Bering land bridge (BLB), finally reaching South America via the Isthmus of Panama link during the Miocene. However, the present-day distribution of Ceroxyloideae in Australia, Madagascar and Comoros may be explained by a historical long-distance dispersal (LDD) hypothesis.

Phylogenomics, biogeography, and evolution of the blue‐ or white‐fruited dogwoods (Cornus)—Insights into morphological and ecological niche divergence following intercontinental geographic isolation

AbstractThe eastern Asian (EA)–eastern North American (ENA) floristic disjunction represents a major pattern of phytogeography of the Northern Hemisphere. Despite 20 years of studies dedicated to identification of taxa that display this disjunct pattern, its origin and evolution remain an open question, especially regarding post‐isolation evolution. The blue‐ or white‐fruited dogwoods (BW) are the most species‐rich among the four major clades of Cornus L., consisting of ~35 species divided into three subgenera (subg. Yinquania, subg. Mesomora, and subg. Kraniopsis). The BW group provides an excellent example of the EA–ENA floristic disjunction for biogeographic study due to its diversity distribution centered in eastern Asia and eastern North America, yet its species relationships and delineation have remained poorly understood. In this study, we combined genome‐wide markers from RAD‐seq, morphology, fossils, and climate data to understand species relationships, biogeographic history, and ecological niche and morphological evolution. Our phylogenomic analyses with RAxML and MrBayes recovered a strongly supported and well‐resolved phylogeny of the BW group with three intercontinental disjunct clades in EA and ENA or Eurasia and North America, of which two are newly identified within subg. Kraniopsis. These analyses also recovered a potential new species but failed to resolve relationships within the C. hemsleyi–C. schindleri complex. In an effort to develop an approach to reduce computation time, analysis of different nodal age settings in treePL suggests setting a node's minimum age constraint to the lower bound of a fossil's age range to obtain similar ages to that of BEAST. Divergence time analyses with BEAST and treePL dated the BW stem back to the very Late Cretaceous and the divergence of the three subgenera in the Paleogene. By integrating fossil ages and morphology, a total evidence‐based dating approach was used in conjunction with time‐slice probabilities of dispersal under a DEC model to resolve ancestral ranges of each disjunct in the Miocene: Eurasia and ENA (disjunct 1), EA and western North America (disjunct 2), and EA (disjunct 3). The dated biogeographic history supports dispersal via the North Atlantic Land Bridge in the late Paleogene in disjunct 1 and dispersal via the Bering Land Bridge in the Miocene for disjuncts 2 and 3. Character mapping with a stochastic model in phytools and comparison of ecological niche, morphospace, and rate of evolution indicated differential divergence patterns in morphology, ecological niche, and molecules between disjunct sisters. Although morphological stasis was observed in most of the characters, evolutionary changes in growth habit and some features of leaf, flower, and fruit morphology occurred in one or both sister clades. A significant differentiation of ecological habitats in temperature, precipitation, and elevation between disjunct sisters was observed, suggesting a role of niche divergence in morphological evolution post‐isolation. The patterns of evolutionary rate between morphology and molecules varied among disjunct clades and were not always congruent between morphology and molecules, suggesting cases of non‐neutral morphological evolution driven by ecological selection. Our phylogenetic evidence and comparisons of evolutionary rate among disjunct lineages lend new insights into the formation of the diversity anomaly between EA and ENA, with particular support of an early diversification in EA. These findings, in conjunction with previous studies, again suggest that the EA–ENA disjunct floras are an assembly of lineages descended from the Mesophytic Forests that evolved from the early Paleogene “boreotropical flora” through varied evolutionary pathways across lineages.

Pennaraptoran Theropod Dinosaurs Past Progress and New Frontiers

ABSTRACT The Coelurosauria are a group of mostly feathered theropods that gave rise to birds, the only dinosaurs that survived the Cretaceous-Paleogene extinction event and are still found today. Between their first appearance in the Middle Jurassic up to the end Cretaceous, coelurosaurs were party to dramatic geographic changes on the Earth’s surface, including the breakup of the supercontinent Pangaea, and the formation of the Atlantic Ocean. These plate tectonic events are thought to have caused vicariance or dispersal of coelurosaurian faunas, influencing their evolution. Unfortunately, few coelurosaurian biogeographic hypotheses are supported by quantitative evidence. Here, we report the first, broadly-sampled quantitative analysis of coelurosaurian biogeography using the likelihood-based package BioGeoBEARS. Mesozoic geographic configurations and changes are reconstructed and employed as constraints in this analysis, including their associated uncertainties. We use a comprehensive time-calibrated coelurosaurian evolutionary tree produced from the Theropod Working Group phylogenetic data matrix. Six biogeographic models in the BioGeoBEARS package with different assumptions about the evolution of spatial distribution are tested against the geographic constraints. Our results statistically favour the DIVALIKE+J and DEC+J models, which allow vicariance and founder events, supporting continental vicariance as an important factor in coelurosaurian evolution. Ancestral range estimation indicates frequent dispersal events via the Apulian Route (connecting Europe and Africa during the Early Cretaceous) and the Bering Land Bridge (connecting North America and Asia during the Late Cretaceous). These quantitative results are consistent with commonly inferred Mesozoic dinosaurian dispersals and continental-fragmentation-induced vicariance events. In addition, we recognise the importance of Europe as a dispersal centre and gateway in the Early Cretaceous, as well as other vicariance events like those triggered by the disappearance of land-bridges.

Plastome Phylogenomic and Biogeographical Study on Thuja (Cupressaceae).

Investigating the biogeographical disjunction of East Asian and North American flora is key to understanding the formation and dynamics of biodiversity in the Northern Hemisphere. The small Cupressaceae genus Thuja, comprising five species, exhibits a typical disjunct distribution in East Asia and North America. Owing to obscure relationships, the biogeographical history of the genus remains controversial. Here, complete plastomes were employed to investigate the plastome evolution, phylogenetic relationships, and biogeographic history of Thuja. All plastomes of Thuja share the same gene content arranged in the same order. The loss of an IR was evident in all Thuja plastomes, and the B-arrangement as previously recognized was detected. Phylogenomic analyses resolved two sister pairs, T. standishii-T. koraiensis and T. occidentalis-T. sutchuenensis, with T. plicata sister to T. occidentalis-T. sutchuenensis. Molecular dating and biogeographic results suggest the diversification of Thuja occurred in the Middle Miocene, and the ancestral area of extant species was located in northern East Asia. Incorporating the fossil record, we inferred that Thuja likely originated from the high-latitude areas of North America in the Paleocene with a second diversification center in northern East Asia. The current geographical distribution of Thuja was likely shaped by dispersal events attributed to the Bering Land Bridge in the Miocene and subsequent vicariance events accompanying climate cooling. The potential effect of extinction may have profound influence on the biogeographical history of Thuja.

Phylogenomics, biogeography, and evolution of morphology and ecological niche of the eastern Asian–eastern North AmericanNyssa(Nyssaceae)

AbstractNyssa(Nyssaceae, Cornales) represents a classical example of the well‐known eastern Asian–eastern North American floristic disjunction. The genus consists of three species in eastern Asia, four species in eastern North America, and one species in Central America. Species of the genus are ecologically important trees in eastern North American and eastern Asian forests. The distribution of living species and a rich fossil record of the genus make it an excellent model for understanding the origin and evolution of the eastern Asian–eastern North American floristic disjunction. However, despite the small number of species, relationships within the genus have remained unclear and have not been elucidated using a molecular approach. Here, we integrate data from 48 nuclear genes, fossils, morphology, and ecological niche to resolve species relationships, elucidate its biogeographical history, and investigate the evolution of morphology and ecological niches, aiming at a better understanding of the well‐known EA–ENA floristic disjunction. Results showed that the Central American (CAM)Nyssa talamancanawas sister to the remaining species, which were divided among three, rapidly diversified subclades. Estimated divergence times and biogeographical history suggested thatNyssahad an ancestral range in Eurasia and western North America in the late Paleocene. The rapid diversification occurred in the early Eocene, followed by multiple dispersals between and within the Erasian and North American continents. The genus experienced two major episodes of extinction in the early Oligocene and end of Neogene, respectively. The Central AmericanN. talamancanarepresents a relic lineage of the boreotropical flora in the Paleocene/Eocene boundary that once diversified in western North America. The results supported the importance of both the North Atlantic land bridge and the Bering land bridge (BLB) for the Paleogene dispersals ofNyssaand the Neogene dispersals, respectively, as well as the role of Central America as refugia of the Paleogene flora. The total‐evidence‐based dated phylogeny suggested that the pattern of macroevolution ofNyssacoincided with paleoclimatic changes. We found a number of evolutionary changes in morphology (including wood anatomy and leaf traits) and ecological niches (precipitation and temperature) between the EA–ENA disjunct, supporting the ecological selection driving trait evolutions after geographic isolation. We also demonstrated challenges in phylogenomic studies of lineages with rapid diversification histories. The concatenation of gene data can lead to inference of strongly supported relationships incongruent with the species tree. However, conflicts in gene genealogies did not seem to impose a strong effect on divergence time dating in our case. Furthermore, we demonstrated that rapid diversification events may not be recovered in the divergence time dating analysis using BEAST if critical fossil constraints of the relevant nodes are not available. Our study provides an example of complex bidirectional exchanges of plants between Eurasia and North America in the Paleogene, but “out of Asia” migrations in the Neogene, to explain the present disjunct distribution ofNyssain EA and ENA.

Chloroplast Phylogenomics Reveals the Intercontinental Biogeographic History of the Liquorice Genus (Leguminosae: Glycyrrhiza).

The liquorice genus, Glycyrrhiza L. (Leguminosae), is a medicinal herb with great economic importance and an intriguing intercontinental disjunct distribution in Eurasia, North Africa, the Americas, and Australia. Glycyrrhiza, along with Glycyrrhizopsis Boiss. and Meristotropis Fisch. & C.A.Mey., comprise Glycyrrhiza s.l. Here we reconstructed the phylogenetic relationships and biogeographic history in Glycyrrhiza s.l. using sequence data of whole chloroplast genomes. We found that Glycyrrhiza s.l. is sister to the tribe Wisterieae and is divided into four main clades. Clade I, corresponds to Glycyrrhizopsis and is sister to Glycyrrhiza sensu Meng. Meristotropis is embedded within Glycyrrhiza sensu Meng, and these two genera together form Clades II–IV. Based on biogeographic analyses and divergence time dating, Glycyrrhiza s.l. originated during the late Eocene and its most recent common ancestor (MRCA) was distributed in the interior of Eurasia and the circum-Mediterranean region. A vicariance event, which was possibly a response to the uplifting of the Turkish-Iranian Plateau, may have driven the divergence between Glycyrrhiza sensu Meng and Glycyrrhizopsis in the Middle Miocene. The third and fourth main uplift events of the Qinghai-Tibetan Plateau may have led to rapid evolutionary diversification within Glycyrrhiza sensu Meng. Subsequently, the MRCA of Clade II might have migrated to North America (G. lepidota) via the Bering land bridge during the early Pliocene, and reached temperate South America (G. astragalina) by long-distance dispersal (LDD). Within Clade III, the ancestor of G. acanthocarpa arrived at southern Australia through LDD after the late Pliocene, whereas all other species (the SPEY clade) migrated to the interior of Eurasia and the Mediterranean region in the early Pleistocene. The MRCA of Clade IV was restricted in the interior of Eurasia, but its descendants have become widespread in temperate regions of the Old World Northern Hemisphere during the last million years.

Transoceanic dispersal of terrestrial species by debris rafting

Rare, long‐distance dispersal events are a key process in generating and maintaining patterns in biological diversity and species distributions across space and time. The 9.0 magnitude earthquake that struck the eastern coast of Japan in 2011, and the subsequent 38 m high tsunami washed large amounts of shoreline debris into the Pacific Ocean that led to a large‐scale biological rafting event carrying nearly 300 marine species to the western shores of North America. Whether oceanic, trans‐Pacific dispersal via rafting generates long distance dispersal events for small, flightless, terrestrial species is unknown. By sampling beach debris associated with known hot‐spots of tsunami debris along the north and east shores of Graham Island, Haida Gwaii, Canada, I document significantly dissimilar invertebrate communities associated with tide‐line beach debris and the occurrence of several putative Japanese species of soil‐dwelling mites (Acari: Oribatida). Previous explanations of Haida Gwaii's unique flora and fauna have been attributed to a proximity to the Beringian land bridge and the accumulated evidence of near‐offshore glacial refugia during the last glacial period. However, my research also suggests that stochastic, trans‐Pacific rafting events contribute to the biodiversity and biogeography of soil communities on the west coast of North America.

The saprotrophic Pleurotus ostreatus species complex: late Eocene origin in East Asia, multiple dispersal, and complex speciation

The Pleurotus ostreatus species complex is saprotrophic and of significant economic and ecological importance. However, species delimitation has long been problematic because of phenotypic plasticity and morphological stasis. In addition, the evolutionary history is poorly understood due to limited sampling and insufficient gene fragments employed for phylogenetic analyses. Comprehensive sampling from Asia, Europe, North and South America and Africa was used to run phylogenetic analyses of the P. ostreatus species complex based on 40 nuclear single-copy orthologous genes using maximum likelihood and Bayesian inference analyses. Here, we present a robust phylogeny of the P. ostreatus species complex, fully resolved from the deepest nodes to species level. The P. ostreatus species complex was strongly supported as monophyletic, and 20 phylogenetic species were recognized, with seven putatively new species. Data from our molecular clock analyses suggested that divergence of the genus Pleurotus probably occurred in the late Jurassic, while the most recent common ancestor of the P. ostreatus species complex diversified about 39 Ma in East Asia. Species of the P. ostreatus complex might migrate from the East Asia into North America across the North Atlantic Land Bridge or the Bering Land Bridge at different times during the late Oligocene, late Miocene and late Pliocene, and then diversified in the Old and New Worlds simultaneously through multiple dispersal and vicariance events. The dispersal from East Asia to South America in the middle Oligocene was probably achieved by a long-distance dispersal event. Intensification of aridity and climate cooling events in the late Miocene and Quaternary glacial cycling probably had a significant influence on diversification patterns of the complex. The disjunctions among East Asia, Europe, North America and Africa within Clade IIc are hypothesized to be a result of allopatric speciation. Substrate transitions to Apiaceae probably occurred no earlier than 6 Ma. Biogeographic analyses suggested that the global cooling of the late Eocene, intensification of aridity caused by rapid uplift of the QTP and retreat of the Tethys Sea in the late Miocene, climate cooling events in Quaternary glacial cycling, and substrate transitions have contributed jointly to diversification of the species complex.

Karyotype evolution and new chromosomal data in Erodium: chromosome alteration, polyploidy, dysploidy, and symmetrical karyotypes

Chromosomal data are valuable and very useful for revealing evolution and speciation processes. Due to its wide distribution throughout the world, morphological differences, and chromosomal alterations, Erodium L?Hér. is an important genus for investigating the relationship between chromosomal alterations and karyotype evolution. In the present study, the chromosome records of 15 taxa are provided; three are reported here for the first time (E.birandianum, E. gaillardotii, and E.hendrikii), seven present new chromosome numbers, and five are in agreement with previous reports. Karyotype evolution is summarized in the light of this data, and four different genomes are presented in the genus. Millions of years ago the ancestral karyotype was x = 9 in Asia (Genome I). Then, karyotypes x = 8 (Genome II) and x = 10 (Genome III) were shaped through dysploidy in Anatolia and Asia. They were distributed in the Mediterranean Basin through the Anatolian land bridge and in North and South America via the Bering land bridge and the North Atlantic land bridge. Finally, a high proportion of polyploidization was observed in secondary centers, especially the Mediterranean Basin and Australia (Genome IV).

Phylogenetic biogeography of Hamamelidaceae s. l. based on molecular data

«Вестник Санкт-Петербургского университета. Науки о Земле» — научно-теоретический рецензируемый журнал, обобщающий результаты исследований в области геологии, гидрогеологии и геохимии, петрологии и экологии, ландшафтного планирования и геоморфологии, экономической и социальной географии.

Phylogenomics, co-evolution of ecological niche and morphology, and historical biogeography of buckeyes, horsechestnuts, and their relatives (Hippocastaneae, Sapindaceae) and the value of RAD-Seq for deep evolutionary inferences back to the Late Cretaceous

In this study, we used RAD-seq data to resolve the phylogeny of the tribe Hippocastaneae (Sapindaceae) and conducted comparative analyses to gain insights into the evolution and biogeography of the group that had fossils dating back to the late Cretaceous. Hippocastaneae, including the horsechestnuts and buckeyes, is a well-supported clade in Sapindaceae that comprises 12–14 species in Aesculus, two in Billia, and one in Handeliodendron. Most species in the tribe are distributed in Eurasia and North America and exhibit a classic pattern of intercontinental disjunction in the Northern Hemisphere, while Billia occurs from southern Mexico to northern South America. The earliest fossils of Aesculus date back to at least the earliest Paleocene of eastern Asia and western North America, where there are also putative occurrences from the latest Cretaceous. The group provides an excellent system for understanding floristic disjunction in the Northern Hemisphere extending to the Neotropics. However, a strongly supported and well resolved phylogeny is presently lacking for the tribe. Previous phylogenetic studies using several gene regions revealed five well-supported clades in Aesculus, largely corresponding to five recognized taxonomic sections, but relationships among these clades and among Aesculus, Billia, and Handeliodendron were not well supported. In this study, we used RAD-seq data from 68 samples representing all clades and species of Hippocastaneae except Billia, for which we used one of two species, to further resolve relationships within the tribe. Our phylogenomic analyses showed strong support for a sister relationship between Aesculus and Handeliodendron, in contrast to previous findings which supported Billia as sister to Aesculus. Within Aesculus, relationships among sections were strongly supported as (sect. Calothyrsus, (sect. Aesculus, (sect. Macrothyrsus, (sect. Parryana, sect. Pavia)))). We found that the traditionally recognized section Calothyrsus was monophyletic, with all eastern Asian species sister to the western North American species, A. californica. Analyses of divergence times combined with biogeographic analyses suggested a Late Cretaceous origin of Hippocastaneae, in eastern Asia, western North America, and Central America (including southern Mexico), followed by isolation of Billia in Central America, extinction of the tribe ancestor in western North America, and divergence of Aesculus from Handeliodendron in eastern Asia. A Late Cretaceous origin of the common ancestor of Aesculus in eastern Asia was followed by dispersals into western North America, Europe, and eastern North America during the Late Cretaceous and the Paleogene. Our results support Aesculus as a relic of the boreotropical flora and subsequent intercontinental spread of the genus through the Bering and North Atlantic land bridges. We performed character mapping analyses, which revealed that biogeographic isolation and niche divergence may have played important roles in driving morphological evolution and lineage divergence in Aesculus. Our study demonstrates the value of RAD-seq data for reconstructing phylogeny back to the Late Cretaceous.

Target Capture Sequencing Unravels Rubus Evolution.

Rubus (Rosaceae) comprises more than 500 species with additional commercially cultivated raspberries and blackberries. The most recent (> 100 years old) global taxonomic treatment of the genus defined 12 subgenera; two subgenera were subsequently described and some species were rearranged. Intra- and interspecific ploidy levels and hybridization make phylogenetic estimation of Rubus challenging. Our objectives were to estimate the phylogeny of 94 taxonomically and geographically diverse species and three cultivars using chloroplast DNA sequences and target capture of approximately 1,000 low copy nuclear genes; estimate divergence times between major Rubus clades; and examine the historical biogeography of species diversification. Target capture sequencing identified eight major groups within Rubus. Subgenus Orobatus and Subg. Anoplobatus were monophyletic, while other recognized subgenera were para- or polyphyletic. Multiple hybridization events likely occurred across the phylogeny at subgeneric levels, e.g., Subg. Rubus (blackberries) × Subg. Idaeobatus (raspberries) and Subg. Idaeobatus × Subg. Cylactis (Arctic berries) hybrids. The raspberry heritage within known cultivated blackberry hybrids was confirmed. The most recent common ancestor of the genus was most likely distributed in North America. Multiple distribution events occurred during the Miocene (about 20 Ma) from North America into Asia and Europe across the Bering land bridge and southward crossing the Panamanian Isthmus. Rubus species diversified greatly in Asia during the Miocene. Rubus taxonomy does not reflect phylogenetic relationships and subgeneric revision is warranted. The most recent common ancestor migrated from North America towards Asia, Europe, and Central and South America early in the Miocene then diversified. Ancestors of the genus Rubus may have migrated to Oceania by long distance bird dispersal. This phylogeny presents a roadmap for further Rubus systematics research. In conclusion, the target capture dataset provides high resolution between species though it also gave evidence of gene tree/species tree and cytonuclear discordance. Discordance may be due to hybridization or incomplete lineage sorting, rather than a lack of phylogenetic signal. This study illustrates the importance of using multiple phylogenetic methods when examining complex groups and the utility of software programs that estimate signal conflict within datasets.

Classic Rock Tours 3. Grand Canyon Geology, One Hundred and Fifty Years after John Wesley Powell: A Geology Guide for Visiting the South Rim of Grand Canyon National Park

Classic Rock Tours 3. Grand Canyon Geology, One Hundred and Fifty Years after John Wesley Powell: A Geology Guide for Visiting the South Rim of Grand Canyon National Park

Are subcortical rove beetles truly Holarctic? An integrative taxonomic revision of north temperate Quedionuchus (Coleoptera: Staphylinidae: Staphylininae)

The recognition of Holarctic species, those shared between Nearctic and Palaearctic regions, often implies continuous or recent events of gene flow across the 85-km-wide Bering Strait between Alaska and Russia. During the Pleistocene (2.8–0.012 Mya), the Bering land bridge has provided frequent episodes of continuous, tundra habitat across this barrier, while the taiga forests of the northern hemisphere has been separated for much longer, at least 5.4 Mya. This more ancient divergence has led to allopatric speciation in nearly all forest-specialized organisms, including all tree species, and casts doubt on the taxonomic validity of the few subcortical beetle species that are considered to be Holarctic. Here we test the apparent Holarctic distribution of one such species, the morphologically variable rove beetle Quedionuchus plagiatus. Drawing upon morphological and molecular evidence, including morphometric analysis of male genitalia and phylogenetic and cluster analyses of DNA barcodes, we demonstrate that species-level diversity has been greatly underestimated in this lineage and conclude that none of its members are Holarctic. We propose complete allopatric divergence across Beringia in obligate forest beetles and discuss the role of biological constraints as barriers to Holarctic geneflow. We describe Quedionuchus caucasicus Brunke, sp. nov., Q. deceptor Brunke sp. nov., Quedionuchus gilaensis Brunke sp. nov., and Quedionuchus yunnanensis Brunke sp. nov.; revalidate Quedionuchus glaber (O. Muller) and Quedionuchus longipennis (Mannerheim); and propose the following: Quedius longipennis Mannerheim, 1846 = Quedius rufipennis Maklin, 1853 syn. nov. (previous synonym of Q. plagiatus Mannerheim); Staphylinus glaber O. Muller, 1776 = Quedius planatus Sharp, 1884 syn. nov.

Phylogenetic relationships and biogeographic history of the unique Saxifraga sect. Irregulares (Saxifragaceae) from eastern Asia

AbstractSaxifraga L. is the largest genus in Saxifragaceae and a characteristic component of the herbaceous flora of the temperate and alpine mountains in the Northern Hemisphere. Section Irregulares is a small group of 15–20 species, representing one of the early‐diverged lineages in the genus characterized with unique zygomorphic flowers. We used both nuclear internal transcribed spacer and chloroplast DNA regions (psbA‐trnH, trnL‐F, and matK) to reconstruct its species relationships, estimate divergence times, and infer its historical biogeography. Our phylogenetic results corroborate the monophyly of sect. Irregulares and its sister relationship to sect. Heterisia from North America. The section was well resolved into two lineages corresponding to their morphological features and biogeographic distributions. One represents ser. Stoloniferae including S. stolonifera Curtis and S. nipponica Makino with long‐creeping stolons/rhizomes and small petals with spots and the other comprises the remaining taxa (ser. Rufescentes) which lack long‐creeping rhizomes. Spots on leaves (abaxially spotted vs. abaxially without spots) and spots on petals (without spots vs. with spots) are inferred to be phylogenetically informative within ser. Rufescentes. Divergence time estimates and ancestral area analysis suggested a western North American origin of sect. Irregulares with migration into East Asia by way of the Bering land bridge in the Middle Oligocene. The development of drying and desertification belt in the late Miocene could have played an important role in the subsequent restriction and separation of the north and south lineages within eastern Asia.

A monograph of Caprifoliaceae: Linnaeeae

Tribe Linnaeeae is a diverse group disjunctly distributed in the northern hemisphere between China and Japan and Mexico. The tribe consists of shrubs with showy flowers that are important in the horticultural industry. We present a detailed monograph of tribe Linnaeeae that includes descriptions, identification keys, botanical plates with line drawings and photographs, distribution maps, morphometric analysis of key characters, and discussion on evolution, cultivation and conservation. Twenty species, as well as five new varieties and four new forms, are recognised in six genera. Forty heterotypic names (not including the 218 names for Linnaea borealis) are listed as synonyms. 1,973 specimens were studied and databased from 13 herbaria (A, BM, CAS, E, GZAC, IBSC, KUN, KYO, MAK, PE, TNS, TOFO and TI). The Kolkwitzia–Dipelta–Diabelia clade radiated from the Qinling Mountain Range of China and is disjunctly distributed in Japan. The Linnaea–Vesalea clade may have migrated through the Bering Land Bridge and radiated along the Sierra Madre Oriental in Mexico. Abelia, which is most diverse in China, evolved in relation to the formation of the Qinghai Tibetan Plateau.

Fossil leaves of Berhamniphyllum (Rhamnaceae) from Markam, Tibet and their biogeographic implications

A new occurrence of buckthorn fossil leaves is reported from the upper Eocene strata of Markam Basin, southeastern Tibet, China. The leaf margin is either entire or slightly sinuous. Secondary veins are regularly spaced, forming eucamptodromous venation. These secondaries exist as straight lines from midvein to near margin and then arch abruptly upward and enter into a margin vein. The tertiary veins are densely spaced and parallel, and are percurrent to secondary veins. This leaf architecture conforms with Berhamniphyllum Jones and Dilcher, an extinct fossil genus reported from America. Our fossils are characterized by their dense secondaries, with secondary veins on the upper half portion of the blade accounting for over 40% of all secondaries. A new species, Berhamniphyllum junrongii Z. K. Zhou, T. X. Wang et J. Huang sp. nov., is proposed. Further analysis shows that confident assignment among Rhamnidium, Berchemia, and Karwinskia cannot be made based on leaf characters alone. Berhamniphyllum might represent an extinct common ancestor of these genera. In this study, several fossil Berchemia from Yunnan and Shandong are emended and reassigned to Berhamniphyllum. A new complex, namely the Berchemia Complex, is proposed based on morphology, molecular evidence, and the fossil record. This complex contains the fossil leaves of Rhamnidium, Karwinskia, Berchemia, and Berhamniphyllum. The historical biogeography of the Berchemia Complex is also discussed in this paper. This complex might have originated in the late Cretaceous in Colombia, South America, and dispersed to North America via Central America during the Eocene. Subsequently, the complex moved from North America to East Asia via the Bering Land Bridge no later than the late Eocene. Besides, the complex migrated from North America to Europe via the North Atlantic Land Bridge and then migrated further to Africa. In East Asia, it first appeared in Markam on the Qinghai-Tibetan Plateau, and then dispersed to other regions of Asia.