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A molecular phylogeny of Staphyleaceae: Implications for generic delimitation and classical biogeographic disjunctions in the family: Phylogegny and Biogeography of Staphyleaceae
Abstract
Staphyleaceae traditionally comprises three genera of temperate and tropical trees and shrubs: Euscaphis Siebold & Zucc., Staphylea L., and Tuprinia Vent. These genera are clearly supported by morphology, but a recent classification based on four chloroplast genes and nuclear ITS treats Staphylea, Euscaphis, and New World Turpinia in Staphylea s.l. and Old World Turpinia in Dalrympelea Roxb. In this study, our objectives were to (1) resolve the phylogenetic relationships within Staphyleaceae using two nuclear and six chloroplast markers, (2) explore morphological synapomorphies that support major clades, and (3) discuss the implications of our results on generic delimitation and biogeography. Our phylogenetic results show five major clades in Staphyleaceae: (1) Old World Turpinia, (2) New World Turpinia, (3) a clade of exclusively Old World Staphylea, (4) an Asian-North American clade of Staphylea comprising all New World species and the rest of the Old World ones, and (5) Euscaphis. Within the two clades each of Staphylea and Turpinia, morphological features traditionally used for delimiting the genera may exhibit convergence. Among morphological features examined in this study, we found that pollen is not taxonomically informative, features of leaf teeth and epicuticular waxes show limited support for the traditional genera of Staphylea and Tuprinia, respectively, and petal length (i.e., flower size) is significantly smaller in Old World Turpinia compared to New World Turpinia. With respect to biogeography, our results support a rare disjunction between eastern North America and the Himalayas.
... , apresenta 40-50 espécies subordinadas a três gêneros: Euscaphis Siebold & Zucc., Staphylea L. e Turpinia Vent. (Li et al. 2008, Harris et al. 2017. A distribuição geográfica da família está restrita a três zonas: (1) leste e sudeste asiático + Himalaia e sul da Índia (Weaver 1980, Li et al. 2008; (2) sul e sudeste da Europa (Li 1952): zona do mar Mediterrâneo, Negro e Cáspio; e (3) América: (3.1) costa oeste e leste dos EUA (Spongberg 1971), (3.2) América Central e Ilhas Caribenhas, e (3.3) oeste e norte da Amazônia , Tiffney 1979. ...
... Um mapa de distribuição geográfica para a família está disponível em Stevens (2017). A combinação das características morfológicas com os padrões biogeográficos dos clados encontrados por Harris et al. (2017) deverá alterar a classificação atual a nível de gênero em Staphyleaceae, que não parece ser consistente, sendo Staphylea e Turpinia parafiléticos. ...
... Turpinia é um gênero parafilético, dividido em dois clados sustentados por características morfológicas e biogeográficas (Harris et al. 2017), provavelmente sendo representado por 40 taxa (Li et al. 2008), com ca. 10-13 taxa na América (veja ...
Este tratamento é composto pelos seguintes táxons: Staphyleaceae, Turpinia.
Disponível em: http://floradobrasil.jbrj.gov.br/reflora/floradobrasil/FB227.
... He recognised two genera: Staphylea s.l., which includes Staphylea s.s., Turpinia (New World species) and Euscaphis, and a second genus, Dalrympelea, consisting of the Old World species of Turpinia (Simmons 2007). More recently, Harris et al. (2017), based on a phylogenetic analysis with chloroplast markers (GBSSI,ITS,ndhF,psbA,rbcL,rps16,trnSGG), recognised five clades in Staphyleaceae: (1) Euscaphis, comprises the traditionally mono-typic genus, Euscaphis; (2) Old World Staphylea is composed exclusively of Old World species of Staphylea; (3) Asian-North American Staphylea, a clade of all other Old World species of Staphylea and all New World species; (4) Old World Turpinia, comprises all species of Turpinia from the Old World; and (5) New World Turpinia, represents all New World species of Turpinia. Nevertheless, the intergeneric circumscription remains controversial. ...
... Cronquist 1981), electronic keys such as Neotropikey-Interactive key (Milliken et al. 2009 onwards), Kevin Nixon's Families of Dicotyledons (http:// www.plantsystematics.org) and information resources for flowering plants (Watson & Dallwitz 1992 onwards;Murguía & Villaseñ or 1993). Subsequently we consulted specialised literature of Staphyleaceae to compare the fossil material with extant members of the family (Dickinson 1986;Carranza-González 2004;González-Villarreal & Jiménez-Reyes 2006;Simmons 2007;Li et al. 2008;Huang et al. 2015;Harris et al. 2017). Owing to the controversial circumscription of Staphylea, comparison of the fossil flower follows the sensu stricto proposal. ...
... The size of the flowers is another character that differentiates flowers within the family (Li et al. 2008). The flowers of Staphylea are larger than those of Turpina and Euscaphis (P5 mm; Harris et al. 2017). The combination of characters found in the new fossil flower would seem to identify it as a Staphylea (Table 2). ...
A new flower preserved in amber in sediments of Simojovel de Allende, México, is identified as an extinct member of Staphyleaceae, a family of angiosperms consisting of only three genera ( Staphylea , Turpinia and Euscaphis ), which has a large and abundant fossil record and is today distributed over the Northern Hemisphere. Staphylea ochoterenae sp. nov. is the first record of a flower for this group, which is small, pedicelled, pentamer, bisexual, with sepals and petals with similar size, dorsifixed anthers and superior ovary. Furthermore, the presence of stamens with pubescent filaments allows close comparison with extant flowers of Staphylea bulmada and S. forresti , species currently growing in Asia. However, their different number of style (one vs. three) and the apparent lack of a floral disc distinguish them from S. ochoterenae. The presence of Staphyleaceae in southern Mexico ca. 23 to 15My ago is evidence of the long history of integration of vegetation in low-latitude North America, in which some lineages, such as Staphylea , could move southwards from high latitudes of the Northern Hemisphere, as part of the Boreotropical Flora. In Mexico it grew in association with tropical elements, as suggested by the fossil record of the area.
... Missing data of unsampled key lineages may lead to violations of the assumptions that underlie algorithms for phylogenetic reconstruction, which may cause inaccuracies in topologies (Heath et al., 2008;Harris et al., 2017). We sampled nearly every genus (except for Serawaia of Wisterieae) within CCH and GAW Clades, although some of the genera have only one representative, e.g., Afgekia, Chesneya, Gueldenstaedtia, Onobrychis and Whitfordiodendron. ...
... Several previous studies (e.g., Hu et al., 2002;Mattapha, 2017) resolved the Callerya group as the first diverged clade in the IRLC, although the undersampling of taxa within Wisterieae or Glycyrrhizinae in these studies may have led to potential topological inaccuracy (Heath et al., 2008;Harris et al., 2017). recently placed the genera of the Callerya group into two separate clades, Adinobotrys and Wisterieae, and together they formed a clade (corresponding to GAW Clade herein) with Glycyrrhizinae, yet the relationships among the three groups (Adinobotrys, Glycyrrhizinae and Wisterieae) were only weakly supported. ...
The inverted repeat-lacking clade (IRLC) is one of the most derived clades within the subfamily Papilionoideae of the legume family, and includes various economically important plants, e.g., chickpeas, peas, liquorice, and the largest genus of angiosperms, Astragalus. Tribe Wisterieae is one of the earliest diverged groups of the IRLC, and its generic delimitation and spatiotemporal diversification need further clarifications. Based on genome skimming data, we herein reconstruct the phylogenomic framework of the IRLC, and infer the inter-generic relationships and historical biogeography of Wisterieae. We redefine tribe Caraganeae to contain Caragana only, and tribe Astragaleae is reduced to the Erophaca-Astragalean clade. The chloroplast capture scenario was hypothesized as the most plausible explanation of the topological incongruences between the chloroplast CDSs and nuclear ribosomal DNA trees in both the Glycyrrhizinae-Adinobotrys-Wisterieae clade and the Chesneyeae-Caraganeae-Hedysareae clade. A new name, Caragana lidou L.Duan & Z.Y.Chang, is proposed within Caraganeae. Thirteen genera are herein supported within Wisterieae, including a new genus, Villosocallerya L.Duan, J.Compton & Schrire, segregated from Callerya. Our biogeographic analyses suggest that Wisterieae originated in the late Eocene and its most recent common ancestor (MRCA) was distributed in continental southeastern Asia. Lineages of Wisterieae remained in the ancestral area from the early Oligocene to the early Miocene. By the middle Miocene, Whitfordiodendron and the MRCA of Callerya-Kanburia-Villosocallerya Clade became disjunct between the Sunda area and continental southeastern Asia, respectively; the MRCA of Wisteria migrated to North America via the Bering land bridge. The ancestor of Austrocallerya and Padbruggea migrated to the Wallacea-Oceania area, which split in the early Pliocene. In the Pleistocene, Wisteria brachybotrys, W. floribunda and Wisteriopsis japonica reached Japan, and Callerya cinerea dispersed to South Asia. This study provides a solid tribal-level phylogenetic framework for further evolutionary/biogeographic/systematic investigations on the ecologically diverse and economically important IRLC legumes.
... On the other hand, Vitis subgenus Vitis exhibits a familiar pattern of intercontinental disjunction in the Northern Hemisphere (Li, 1952;Raven, 1972;Thorne, 1972;Wang, 1989;Wen, 1998Wen, , 1999Wen, , 2001Wen et al., 2010) with species occurring in Asia, Europe, eastern and western North America, and Central America Moore & Wen, 2016). However, many such disjunct groups that are species-rich overall have relatively species-poor, phylogenetically isolated lineages in North America (Wen, 1999(Wen, , 2011Qian & Ricklefs, 2000;Xiang et al., 2004;Ickert-Bond & Wen, 2006;Harris et al., 2013Harris et al., , 2017aHarris et al., , 2017bXiang et al., 2015;Wen et al., 2016). Examples include Acer L., Staphylea L., Picea Mill., and Tsuga Carri ere (Grimm et al., 2006;Ran et al., 2006;Havill et al., 2008;Renner et al., 2008;Harris et al., 2009Harris et al., , 2013Harris et al., , 2016Harris et al., , 2017aHarris et al., , 2017bWen et al., 2016). ...
... However, many such disjunct groups that are species-rich overall have relatively species-poor, phylogenetically isolated lineages in North America (Wen, 1999(Wen, , 2011Qian & Ricklefs, 2000;Xiang et al., 2004;Ickert-Bond & Wen, 2006;Harris et al., 2013Harris et al., , 2017aHarris et al., , 2017bXiang et al., 2015;Wen et al., 2016). Examples include Acer L., Staphylea L., Picea Mill., and Tsuga Carri ere (Grimm et al., 2006;Ran et al., 2006;Havill et al., 2008;Renner et al., 2008;Harris et al., 2009Harris et al., , 2013Harris et al., , 2016Harris et al., , 2017aHarris et al., , 2017bWen et al., 2016). This is not the case for Vitis subgenus Vitis, for which over 20 species occur in the North American flora (see Moore & Wen, 2016;J. ...
Vitis L. (the grape genus) is the economically most important fruit crop, as the source of grapes and wine. Phylogenetic relationships within the genus have been highly controversial. Herein, we employ sequence data from whole plastomes to attempt to enhance Vitis phylogenetic resolution. The results support the New World Vitis subgenus Vitis as monophyletic. Within the clade, V. californica is sister to the remaining New World Vitis subgenus Vitis. Furthermore, within subgenus Vitis, a Eurasian clade is robustly supported and is sister to the New World clade. The clade of Vitis vinifera ssp. vinifera and V. vinifera ssp. sylvestris is sister to the core Asian Vitis clade. Several widespread species in North America are found to be non‐monophyletic in the plastome tree, for example, the broadly defined Vitis cinerea and V. aestivalis each needs to be split into several species. The non‐monophyly of some species may also be due to common occurrences of hybridizations in North American Vitis. The classification of North American Vitis by Munson into nine series is discussed based on the phylogenetic results. Analyses of divergence times and lineage diversification support a rapid radiation of Vitis in North America beginning in the Neogene.
... In this line of thought, based on several reports of environmental effects on the composition of epicuticular waxes, (Hull et al., 1979;Shepherd et al., 1995;Medina et al., 2004;Domínguez et al., 2011;Ortúñez and Cano-Ruiz, 2013;Rajčević et al., 2014;Menzel et al., 2017;Xue et al., 2017;Sharma et al., 2018) as well as on the close link established between the characteristics of epicuticular waxes of many taxa and taxonomic, ecological or evolutive issues, (Li and Christophel, Frontiers in Plant Science | www.frontiersin.org 2000; Versieux et al., 2012;Li et al., 2016;Mitić et al., 2016;Harris et al., 2017;Klimko et al., 2018;Lindelof et al., 2020;Weber and Schwark, 2020;Faria et al., 2021) we propose in this work an unprecedented strategy to contribute to the study of vicariant phenomena in plant science. This new strategy involves a comprehensive physical-chemical analysis of the surface of plant leaves that strengthens the more usual phylogenetic, biogeographic and ecological approaches. ...
Classically, vicariant phenomena have been essentially identified on the basis of biogeographical and ecological data. Here we report unequivocal evidences that demonstrate that a physical-chemical characterization of the epicuticular waxes of the surface of plant leaves represents a very powerful strategy to get rich insight into vicariant events. We found the vicariant similarity between Cercis siliquastrum L. (family Fabaceae, subfamily Cercidoideae) and Ceratonia siliqua L. (family Fabaceae, subfamily Caesalpinoideae). Both taxa converge in the Mediterranean basin (C. siliquastrum on the north and C. siliqua across the south), in similar habitats (sclerophyll communities of maquis) and climatic profiles. These species are the current representation of their subfamilies in the Mediterranean basin, where they overlap. Because of this biogeographic and ecological similarity, the environmental pattern of both taxa was found to be very significant. The physical-chemical analysis performed on the epicuticular waxes of C. siliquastrum and C. siliqua leaves provided relevant data that confirm the functional proximity between them. A striking resemblance was found in the epicuticular waxes of the abaxial surfaces of C. siliquastrum and C. siliqua leaves in terms of the dominant chemical compounds (1-triacontanol (C30) and 1-octacosanol (C28), respectively), morphology (intricate network of randomly organized nanometer-thick and micrometer-long plates), wettability (superhydrophobic character, with water contact angle values of 167.5 ± 0.5˚ and 162 ± 3º, respectively), and optical properties (in both species the light reflectance/absorbance of the abaxial surface is significantly higher/lower than that of the adaxial surface, but the overall trend in reflectance is qualitatively similar). These results enable us to include for the first time C. siliqua in the vicariant process exhibited by C. canadensis L., C. griffithii L., and C. siliquastrum.
... The modern distribution pattern and fossil records of Stachyuraceae and Crossosomataceae indicate that their common ancestor was widely distributed in the Northern Hemisphere before the Tertiary period . Zhu et al. (2006) suggested that orogenies and the gradual climatic cooling might have caused the early extinction of Stachyuraceae in Europe and the discontinuous distribution of Crossosomatales in the Northern Hemisphere (see also Harris et al., 2017). ...
Species concept and delimitation are fundamental to taxonomic and evolutionary studies. Both inadequate informative sites in the molecular data and limited taxon sampling have often led to poor phylogenetic resolution and incorrect species delineation. Recently, the whole chloroplast genome sequences from extensive herbarium specimen samples have shown to be effective to amend the problem. Stachyuraceae are a small family consisting of only one genus Stachyurus of six to 16 species. However, species delimitation in Stachyurus has been highly controversial because of few and generally unstable morphological characters used for classification. In this study, we sampled 69 individuals of seven species (each with at least three individuals) covering the entire taxonomic diversity, geographic range, and morphological variation of Stachyurus from herbarium specimens for genome‐wide plastid gene sequencing to address species delineation in the genus. We obtained high‐quality DNAs from specimens using a recently developed DNA reconstruction technique. We first assembled four whole chloroplast genome sequences. Based on the chloroplast genome and one nuclear ribosomal DNA (nrDNA) sequences of Stachyurus, we designed primers for multiplex PCR and high throughput sequencing of 44 plastid loci for species of Stachyurus. Data of these chloroplast DNA and nrDNA ITS sequences were used for phylogenetic analyses. The phylogenetic results showed that the Japanese species Stachyurus praecox was sister to the rest in mainland China which indicated a typical Sino‐Japanese distribution pattern. Based on diagnostic morphological characters, distinct distributional range, and monophyly of each clade, we redefined seven species for Stachyurus following an integrative species concept, and revised the taxonomy of the family based on literature and specimens, in particular the type specimens. Furthermore, our divergence time estimation results suggested that Stachyuraceae split from its sister group Crossosomataceae from the New World at ca. 54.29 Mya, but extant species of Stachyuraceae started their diversification only recently at ca. 6.85 Mya. Diversification time of Stachyurus in mainland China was estimated to be ca. 4.45 Mya. This research has provided an example of using the herbarium specimen‐based phylogenomic approach in resolving species boundaries in a taxonomically difficult genus. This article is protected by copyright. All rights reserved.
... Taken together, this suggests repeated biogeographic events, such as multiple dispersals out of or back into area A or multiple vicariance events owing to different earth history processes such as orogeny, sea level rise, or glaciation. Many other species, such as Acer L. (Renner et al., 2008) and Staphylea L. (Harris et al., 2017), also show similarly complex biogeographic patterns. Wen et al. (2014) summarized six patterns of evolutionary diversifications of plants on the QTPss and adjacent areas, and we found that at least three of these patterns occurred in Saussurea: (1) The QTPss and adjacent areas serve as a biogeographic source for species distributed elsewhere in Eurasia (Jia et al., 2012;, also called the out-of-QTP hypothesis (Fan et al., 2015;. ...
... Taken together, this suggests repeated biogeographic events, such as multiple dispersals out of or back into area A or multiple vicariance events owing to different earth history processes such as orogeny, sea level rise, or glaciation. Many other species, such as Acer L. (Renner et al., 2008) and Staphylea L. (Harris et al., 2017), also show similarly complex biogeographic patterns. Wen et al. (2014) summarized six patterns of evolutionary diversifications of plants on the QTPss and adjacent areas, and we found that at least three of these patterns occurred in Saussurea: (1) The QTPss and adjacent areas serve as a biogeographic source for species distributed elsewhere in Eurasia (Jia et al., 2012;, also called the out-of-QTP hypothesis (Fan et al., 2015;. ...
... We follow the generic taxonomy for Staphyleaceae adopted by Harris et al. (2017). Although many of the staphyleaceous Trinity seeds are more inflated than those of the modern T. pomifera we have illustrated for comparison ( fig. ...
... However, during long-term field observations, we found that E. japonica are a deciduous or evergreen tree with significant phenotypic differences at varying altitudes, especially with respect to leaves and fruit. In addition, it has been previously discovered that E. japonica has existed on Earth for 33.9 million years [17], which inspired our curiosity as to why Euscaphis has one species only despite its wide range of distribution and long survival time. Therefore, some causes of phenotypic diversity in E. japonica could be explained by exploring phenotypic variation. ...
Fruit traits affect population genetic diversity by affecting seed protection and dispersal strategies, thereby comprising important components of phenotypic variation. Understanding of the phenotypic variation is an indispensable first step for developing breeding strategies. However, little information is known about the genetic variation in E. japonica-a monotypic species with abundant phenotypes that is mainly distributed in southern China. In this study, we evaluated the phenotypic diversity of 67 E. japonica using 23 phenotypic traits. Our results showed that the Shannon-Wiener (I) index of qualitative traits ranged from 0.55 to 1.26, and the color traits had a relatively high I. The average coefficient of variation of compound leaf traits (14.74%) was higher than that of fruit and seed traits (12.77% and 11.47%, respectively). Principal component analysis also showed that compound leaf and fruit traits were important components of total variation. Furthermore, correlation analysis revealed a significant difference in elevation and fruit color, irregular ribs, leaf margin and texture. The F value within populations was smaller than among populations, indicating the variation in phenotypic traits among populations was much greater than within populations. Dehua and Zunyi populations had the highest coefficients of variation, whereas Wenzhou population had the smallest-which may be attributed to habitat destruction. According to Q-type clustering, 67 samples clustered into four groups, with those having similar phenotypes clustering into the same group. In general, leaf and fruit traits had abundant phenotypic diversity, representing the main sources of phenotypic variation. Combined with clustering results and field surveys, this study suggests that the phenotypes of E. japonica are classified into two main categories: The deciduous E. japonica present at high altitudes; and the evergreen E. japonica present at low altitudes. Excavating E. japonica variations provides a theoretical reference for its classification and diversity, and is of great significance for planning genetic resources and establishing conservation strategies.
... Investigators for 2017: Harris et al. 2017. A molecular phylogeny of Staphyleaceae: Implications for generic delimitation and classical biogeographic disjunctions in the family. ...
... Staphylea L. is a Tertiary relict genus in the bladdernut family Staphyleaceae and includes 10 species of large shrubs to small trees (Li et al., 2008). It is native mainly to subtropical areas of the Northern Hemisphere, but a few species also extend into temperate zones, with disjunctive ranges in East Asia, South Asia, eastern and western North America, and the Mediterranean (Spongberg, 1971;Weaver, 1980;Sosa, 1988;Li et al., 2008;Harris et al., 2017). In Japan of East Asia, S. bumalda represents the only living species of this genus (Ohashi et al., 2016). ...
The Pleistocene floristic change in the Northern Hemisphere is marked by extensive extinctions of Tertiary relicts in middle to high latitudes, which are thought to have been moderate in East Asia. However, species losses from geographically isolated areas in East Asia were comparatively heavy. In this study, we report a selective extinction event within the relict genus Staphylea (Staphyleaceae) from the Japanese Pleistocene. We described two species, Staphylea bumalda DC. and S. spinosa Y. Huang et A. Momohara sp. nov. (Staphyleaceae), based on seed remains from the middle early Pleistocene (ca. 1.7–1.2 Ma) Shobudani Formation in the northern Kii Peninsula of southwestern Honshu. According to the fossil records and modern distributions of Staphylea, we presumed that S. bumalda emerged in Japan at least by the early Pliocene and has persisted until today, whereas S. spinosa was exterminated after the middle early Pleistocene. To explain the different fates of the two species, we estimated their climate tolerance by observing the climate requirements of their nearest living relatives. Our results indicate that S. bumalda could tolerate colder climates, particularly in winter, than S. spinosa. Floristic compositional changes at the study area reveal a cooling trend followed by a glacial stage after the last occurrence of S. spinosa. The cold winter temperature in the glacial stage was probably beyond the cold tolerance of S. spinosa, which ultimately led to its demise. Surrounding geomorphological changes, such as the uplift of the Kii Mountains, might also have played a role in the way of preventing plant migration when climate deteriorated. This selective extinction event adds a new episode into our knowledge of the Pleistocene plant extinctions along with their possible underlying mechanisms in the Northern Hemisphere.
... The adaptation to temperate climates might have been a prerequisite for the migration along this northerly route in the colder climate of the Oligocene (Liu et al., 2009). Zanthoxylum is one of many examples of a plant genus with a Eurasian-American disjunct distribution (Donoghue et al., 2001;Qian and Ricklefs, 2004;Wen et al., 2010Wen et al., , 2016Harris et al., 2017), (Wagner et al., 1999) as well as the fact that Asian and Australian lineages account for the largest number of colonizers of the Hawaiian flora. The age estimate for the Hawaiian group is surprisingly high. ...
Zanthoxylum L. (prickly ash) is the only genus in the Citrus L. family (Rutaceae) with a pantropical distribution. We present the first detailed phylogenetic and biogeographic study of the genus and its close relatives in the proto-Rutaceae group. Our phylogenetic analyses based on two plastid and two nuclear markers show that the genus Toddalia Juss. is nested within Zanthoxylum, that earlier generic and intrageneric classifications need revision, and that the homochlamydeous flowers of the temperate species of Zanthoxylum are the result of a reduction from heterochlamydeous flowers. The biogeographic analyses reveal a Eurasian origin of Zanthoxylum in the Paleocene or Eocene with successive intercontinental or long-range migrations. Zanthoxylum likely crossed the North Atlantic Land Bridges to colonize the Americas in the Eocene, and migrated back to the Old World probably via the Bering Land Bridge in the Oligocene or Miocene. Zanthoxylum also colonized several Pacific Islands and the Hawaiian clade shows phylogenetic incongruence between the plastid and nuclear datasets, suggesting hybridization. The Hawaiian species are one of the rare examples of endemic Hawaiian lineages that are older than the current main islands.
... Melaphidina aphids show an eastern Asian-eastern North American disjunct distribution, which is a common biogeographic pattern in plants ( Donoghue and Smith, 2004;Harris et al., 2017;Li, 1952;Tiffney, 1985aTiffney, , 1985bWen, 1999;Wen et al., 2010Wen et al., , 2016Xiang et al., 2004Xiang et al., , 2015 and has been reported in insects (Nordlander et al., 1996;Peña et al., 2010;von Dohlen et al., 2002), fishes ( Sun et al., 2007), and reptiles ( Macey et al., 2006). The Rhus gall aphids are primarily distributed in Asia with only one species, Melaphis rhois, in North America. ...
The Rhus gall aphids are sometimes referred to as subtribe Melaphidina (Aphididae: Eriosomatinae: Fordini) and comprise a unique group that forms galls on the primary host plants, Rhus. We examined the evolutionary relationships within the Melaphidina aphids using sequences of the complete mitochondrial genome and with samples of 11 of the 12 recognized species representing all six genera. Bayesian, maximum likelihood and parsimony analyses of the mitochondrial genome data support five well-supported clades within Melaphidina: (1) Nurudea (except N. ibofushi), (2) Schlechtendalia-Nurudea ibofushi, (3) Meitanaphis-Kaburagia, (4) Floraphis, and (5) Melaphis. Nurudea shiraii and N. yanoniella are sister to each other, but N. ibofushi is nested within Schlechtendalia. The Nurudea shiraii-N. yanoniella clade is sister to the large clade of the remaining taxa of Melaphidina aphids. The Bayesian and maximum likelihood analyses support the North American Melaphis rhois as sister to the clade of Floraphis-Kaburagia-Meitanaphis-Schlechtendalia from eastern Asia, whereas the parsimony analysis suggests Melaphis sister to Floraphis with low support (bootstrap support 38%), and the amino acid data weakly place it sister to Schlechtendalia-Nurudea ibofushi. The Melaphis position needs to be further tested with nuclear data. Meitanaphis flavogallis is sister to Kaburagia species instead of grouping with Meitanaphis elongallis. Using the Bayesian method, the North American Melaphis was estimated to have diverged from its closest Asian relatives around 64.6 (95% HPD 59.4-69.8) Ma, which is in the early Paleocene near the Cretaceous and Paleogene boundary (K/Pg boundary). At the K/Pg boundary, mass extinctions caused many types of insect-plant associations to disappear, and these extinctions may explain some of the difficulties in the phylogenetic placement of Melaphis within the analyses.
Staphylea has abundant isolated seeds in the fossil record, but no fossil fruits of this genus have been confirmed before. In this paper, we report a capsular fruit of Staphylea from the Oligocene Renova Formation of Woodworth, western-central Montana, USA. Detailed investigation of this fruit gives new insights on the phylogenetic and biogeographic history of the genus. Morphological comparison with modern Staphylea fruits shows its closest resemblance to the extant Asian species, S. bumalda DC., which is similar in fruit shape, size, and pericarp venation, but differs by the angle of interlobal sinus and the stipe development. We establish a new fossil species, S. woodworthensis Zhu & Manchester sp. nov. for this fossil fruit. This discovery indicates that Staphylea was already established in western North America at least by the Oligocene, which is inconsistent with the recent interpretation of a late Oligocene origin of the genus in Europe. The distribution of fossils indicates an earlier diversification of Staphylea, along with other staphyleaceous genera, back to early Paleogene in North America. The genus subsequently retracted its range to the east and south in North America as evidenced by younger fossils and its modern geographic range.
We sought to test the utility of two single-copy nuclear genes for resolving phylogenetic relationships within the woody plant tribe, Acereae (Sapindaceae). Acereae comprises Acer (125+ spp.) and Dipteronia (2 spp.), two genera that possess schizocarpic fruits, which split into two winged mericarps. In Acer, the mericarps are elongated with a basally arranged locule and a dorsal or distal wing. In Dipteronia, the mericarp is obovate, and the locule is located centrally and surrounded by the wing. We analyzed 35 species of Acer representing 12 of 16 taxonomic sections plus Dipteronia sinensis to elucidate the phylogeny of Acereae using the single-copy nuclear genes AT103 and SQD1. Both genes exhibited limited variation in Acereae and, therefore, provided limited support for phylogenetic relationships. The phylogeny of concatenated AT103 and SQD1 showed Dipteronia sinensis within Acer with negligible support (0.14 posterior probability, < 50% maximum parsimony bootstrap, MP-BS), a position that is congruent with results from prior studies using chloroplast DNA and internal transcribed spacer (ITS). Based on our results and results from prior studies, we discuss implications for leaf and fruit evolution in Acereae.
In this study, we expanded Acer sect. Rubra Pax to include A. sect. Hyptiocarpa Fang. Traditionally, section Rubra comprises two iconic species, Acer rubrum Linnaeus (red maple) and A. saccharinum Linnaeus (sil-ver maple), of eastern North American forests as well as the rare Japanese montane species, A. pycnanthum K. Koch. Section Hyptiocarpa consists of A. laurinum Hasskarl and A. pinnatinervium Merrill, which occur in subtropical and tropical regions of southwestern China to southeast Asia. Here, we confirm prior phylogenetic results showing the close relationship between sects. Rubra and Hyptiocarpa, and we use scanning electron microscopy to demonstrate that leaves of species within these sections have similar arrangements of cuticular waxes, which account for the silvery color of their abaxial surfaces. We describe that the sections also share labile sex expression; inflorescences that range from compound racemose thyrses, to racemes or umbels and that may have undergone evolutionary reduction; and several features of their fruits, such as seed locules without keels, basal portion of wings straight, acute attachment angle between mericarps, and production of some mericarps that are seedless and partially developed at maturity. Our expansion of sect. Rubra to include sect. Hyptiocarpa better elucidates the biogeographic and evolutionary history of these species. Additionally, we show that A. laurinum and A. pinnatinervium have intergrading morphology and are probably synonymous, but we note that further studies are required to conclude their taxonomic status.
This review shows a close biogeographic connection between eastern Asia and western North America from the late Cretaceous to the late Neogene in major lineages of vascular plants (flowering plants, gymnosperms, ferns and lycophytes). Of the eastern Asian–North American disjuncts, conifers exhibit a high proportion of disjuncts between eastern Asia and western North America. Several lineages of ferns also show a recent disjunct pattern in the two areas. In flowering plants, the pattern is commonly shown in temperate elements between northeastern Asia and northwestern North America, as well as elements of the relict boreotropical and Neogene mesophytic and coniferous floras. The many cases of intercontinental biogeographic disjunctions between eastern Asia and western North America in plants supported by recent phylogenetic analyses highlight the importance of the Bering land bridge and/or the plant migrations across the Beringian region from the late Cretaceous to the late Neogene, especially during the Miocene. The Beringian region has permitted the filtering and migration of certain plant taxa since the Pliocene after the opening of the Bering Strait, as many conspecific taxa or closely related species occur on both sides of Beringia.
Prunus is an economically important genus well-known for cherries, plums, almonds, and peaches. The genus can be divided into three major groups based on inflorescence structure and ploidy levels: (1) the diploid solitary-flower group (subg. Prunus, Amygdalus and Emplectocladus); (2) the diploid corymbose group (subg. Cerasus); and (3) the polyploid racemose group (subg. Padus, subg. Laurocerasus, and the Maddenia group). The plastid phylogeny suggests three major clades within Prunus: Prunus-Amygdalus-Emplectocladus, Cerasus, and Laurocerasus-Padus-Maddenia, while nuclear ITS trees resolve Laurocerasus-Padus-Maddenia as a paraphyletic group. In this study, we employed sequences of the nuclear loci At103, ITS and s6pdh to explore the origins and evolution of the racemose group. Two copies of the At103 gene were identified in Prunus. One copy is found in Prunus species with solitary and corymbose inflorescences as well as those with racemose inflorescences, while the second copy (II) is present only in taxa with racemose inflorescences. The copy I sequences suggest that all racemose species form a paraphyletic group composed of four clades, each of which is definable by morphology and geography. The tree from the combined At103 and ITS sequences and the tree based on the single gene s6pdh had similar general topologies to the tree based on the copy I sequences of At103, with the combined At103-ITS tree showing stronger support in most clades. The nuclear At103, ITS and s6pdh data in conjunction with the plastid data are consistent with the hypothesis that multiple independent allopolyploidy events contributed to the origins of the racemose group. A widespread species or lineage may have served as the maternal parent for multiple hybridizations involving several paternal lineages. This hypothesis of the complex evolutionary history of the racemose group in Prunus reflects a major step forward in our understanding of diversification of the genus and has important implications for the interpretation of its phylogeny, evolution, and classification.
Psilopeganum (Rutaceae) is a rare monotypic genus endemic to the vicinity of the Yangtze River valley in Chongqing, Hubei, Sichuan and Guizhou provinces in China. It differs from most Rutaceae taxa by its herbaceous habit and has been treated as a member of the tribe Ruteae. Our study is the first attempt to place Psilopeganum in a phylogenetic context and our results show that the genus belongs to a clade with Boenninghausenia, Ruta and Thamnosma, which are part of Ruteae. Within this group, the position of Psilopeganum remains unclear because the Boenninghausenia-Thamnosma clade, Psilopeganum and Ruta form a trichotomy in most analyses. The ITS dataset placed Psilopeganum as sister to the Mediterranean and Canarian genus Ruta, which is corroborated by morphological similarities. Our studies support that Ruteae is paraphyletic with respect to Aurantioideae and that Dictamnus does not belong to Ruteae. The Indian, Sri Lankan, and Malagasy genus Chloroxylon is sister to the Boenninghausenia-Psilopeganum-Ruta-Thamnosma clade, despite its traditional placement in the subfamily Flindersioideae. The placement of Chloroxylon is consistent with an origin of the group of Chloroxylon, Boenninghausenia, Psilopeganum, Ruta and Thamnosma in southern Asia. The rapid uplifts of the Himalayas could account for one or two vicariance events splitting the lineages of the Boenninghausenia-Psilopeganum-Ruta-Thamnosma clade, and may explain the short branch length and low support for the relationships among Psilopeganum, Ruta, and the Boenninghausenia-Thamnosma clade.
Evolutionary relationships among 48 genera of Apiaceae (Umbelliferae) were inferred using maximum parsimony, maximum-likelihood, and neighbor-joining analyses of chloroplast DNA rps16 intron and adjacent rps16 3prime exon sequences. Emphasis was placed on woody members of Apiaceae subfamily Apioideae endemic to southern Africa, a region hypothesized to be the place of origin of this largely herbaceous subfamily. The resultant phylogenies were highly concordant and indicate that the apioid genera Polemanniopsis and Steganotaenia form a clade sister to Apiaceae subfamily Saniculoideae. The African genera Anginon, Dracosciadium, Glia, Heteromorpha, and Polemannia also comprise a clade and likely represent the most basal elements within Apioideae. Heteromorpha, however, is not monophyletic, with Heteromorpha arborescens (Spreng.) Cham. & Schltdl. var. abyssinica (A. Rich.) H. Wolff and Heteromorpha arborescens (Spreng.) Cham. & Schltdl. var. arborescens arising in separate subclades. Progressing up the trees, Annesorhiza then Bupleurum fall as successive sister taxa to all remaining Apioideae. The major clades recognized within subfamily Apioideae are largely congruent with those inferred using other types of molecular evidence. Sequence divergence is similar to that of other chloroplast introns, including being generally low among congeners and woody taxa. While the rps16 intron has seen very little use in molecular systematic studies to date, this study demonstrates its ability to discern high-level relationships within Apiaceae.
The Flora of North America north of Mexico treats all native and naturalized vascular plants and bryophytes in Canada, Greenland, St. Pierre et Miquelon, and the continental United States including the Florida Keys and Aleutian Islands (approximately 18 million square kilometers). It provides accepted names, literature citations, basionyms, synonyms, morphological descriptions, habitat, geographical distribution, conservation or weed status, and a discussion of taxonomic issues for approximately 20,000 species. Of the total 30 volumes anticipated, 18 have been published and one is in press, treating 2021 genera and 12,393 species. For the remaining volumes, 763 genera and 5,008 species have been submitted, and 82 of the 144 families have been submitted in full. Completion is anticipated by the end of 2017. The project is managed by the Flora of North America Association. Content from published volumes is available through eFloras and JSTOR and has been provided to the World Flora informatics team.
Single and low copy nuclear genes offer a larger number of, and more rapidly evolving, characters than the chloroplast and nuclear ribosomal gene sequences that have dominated plant phylogenetic studies to date. Until recently, only one or a few low copy nuclear gene markers were included in such studies. Now, the rapid adoption of “next generation sequencing” (NGS) techniques offers simpler and cheaper access to hundreds of, and not just tens of, coding and noncoding DNA regions. In this review, we describe the most commonly-used NGS methods available for accessing nuclear genes and discuss many NGS case studies that have been published in the last two to three years. These approaches include whole genome sequencing to target microsatellites, transcriptome sequencing, Exon-Primed Intron-Crossing sequencing (EPIC), targeted enrichment (or sequence capture), RAD sequencing (RAD-Seq, including genotyping-by-sequencing or GBS), and genome skimming. We also discuss some of the challenges to, and posed by,the NGS approaches.
Otitis media (OM) starts within weeks of birth in almost all Indigenous infants living in remote areas of the Northern Territory (NT). OM and associated hearing loss persist from infancy throughout childhood and often into adulthood. Educational and social opportunities are greatly compromised. Pneumococcus and non-typeable Haemophilus influenzae (NTHi) are major OM pathogens that densely colonise the nasopharynx and infect the middle ear from very early in life. Our hypothesis is that compared to current single vaccine schedules, a combination of vaccines starting at 1 month of age, may provide earlier, broadened protection.
This randomised outcome assessor, blinded controlled trial will recruit 425 infants between 28 and 38 days of age and randomly allocate them (1:1:1) to one of three pneumococcal conjugate vaccine (PCV) schedules: Synflorix at 2, 4, 6 months of age, Prevenar13 at 2, 4 and 6 months of age, or an investigational schedule of Synflorix at 1, 2 and 4 months plus Prevenar13 at 6 months of age. The blinded primary outcomes at 7 months of age are immunogenicity of specific vaccine antigens (geometric mean concentration (GMC) and proportion of participants with above threshold GMC of 0.35 µg/L). Secondary outcomes at all timepoints are additional immunogenicity measures and proportion of participants with nasopharyngeal carriage of vaccine-type pneumococci and NTHi, and any OM, including any tympanic membrane perforation. Parental interviews will provide data on common risk factors for OM.
Ethical approval has been obtained from NT Department of Health and Menzies HREC (EC00153), Central Australian HREC (EC00155) and West Australian Aboriginal Health Ethics Committee (WAAHEC- 377-12/2011). Final trial results, data analyses, interpretation and conclusions will be presented in appropriate written and oral formats to parents and guardians, participating communities, local, national and international conferences, and published in peer-reviewed open access journals.
ACTRN12610000544077 and NCT01174849.
Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.
A revised and updated classification for the families of flowering plants is provided. Many recent studies have yielded increasingly detailed evidence for the positions of formerly unplaced families, resulting in a number of newly adopted orders, including Amborellales, Berberidopsidales, Bruniales, Buxales, Chloranthales, Escalloniales, Huerteales, Nymphaeales, Paracryphiales, Petrosaviales, Picramniales, Trochodendrales, Vitales and Zygophyllales. A number of previously unplaced genera and families are included here in orders, greatly reducing the number of unplaced taxa; these include Hydatellaceae (Nymphaeales), Haptanthaceae (Buxales), Peridiscaceae (Saxifragales), Huaceae (Oxalidales), Centroplacaceae and Rafflesiaceae (both Malpighiales), Aphloiaceae, Geissolomataceae and Strasburgeriaceae (all Crossosomatales), Picramniaceae (Picramniales), Dipentodontaceae and Gerrardinaceae (both Huerteales), Cytinaceae (Malvales), Balanophoraceae (Santalales), Mitrastemonaceae (Ericales) and Boraginaceae (now at least known to be a member of lamiid clade). Newly segregated families for genera previously understood to be in other APG-recognized families include Petermanniaceae (Liliales), Calophyllaceae (Malpighiales), Capparaceae and Cleomaceae (both Brassicales), Schoepfiaceae (Santalales), Anacampserotaceae, Limeaceae, Lophiocarpaceae, Montiaceae and Talinaceae (all Caryophyllales) and Linderniaceae and Thomandersiaceae (both Lamiales). Use of bracketed families is abandoned because of its unpopularity, and in most cases the broader circumscriptions are retained; these include Amaryllidaceae, Asparagaceace and Xanthorrheaceae (all Asparagales), Passifloraceae (Malpighiales), Primulaceae (Ericales) and several other smaller families. Separate papers in this same volume deal with a new linear order for APG, subfamilial names that can be used for more accurate communication in Amaryllidaceae s.l., Asparagaceace s.l. and Xanthorrheaceae s.l. (all Asparagales) and a formal supraordinal classification for the flowering plants.
An interdisciplinary approach combining archaeological, historical, and ethnological data is used in the attempt to draw a general image of the role of bladdernut (Staphylea pinnata) in past societies. The purposes encountered in this literature study extend from nutritional and medicinal uses to particular ritual/religious aspects, incorporating apotropaic and sympathetic magic, the use in grave goods, and the role of bladdernut in rosaries. In the two latter purposes, the ‘cut nose’ aspect of the seeds is suggested to be an important symbolic factor.
A parsimony analysis of 57 angiosperm rbcL sequences was conducted to test the monophyly of the Asteridae and to identify major lineages within the Asteridae. Three major clades, the Caryophyllidae, the Rosidae plus Dilleniidae, and the Asteridae sensu lato, emerge from an unresolved radiation in the "higher" dicots. The Asteridae sens. lat. include the Ericales, Cornales, and Apiales in addition to the Asteridae sens. str. Two major lineages within the Asteridae sens. lat. are identified: the Dipsacales, Apiales, Asterales, and Campanulales in one, and the Gentianales, Scrophulariales, Lamiales, Boraginales, and Solanales in the other. This analysis demonstrates the utility of molecular phylogenies to help place problematic taxa, such as the Menyanthaceae, Oleaceae, and Callitrichaceae, within the Asteridae. Implications from this phylogenetic analysis and evidence from the fossil record lead to the suggestion that the origin and diversification of the major higher-dicot lineages occurred during a relatively short period of time about 80-95 million years ago.
The Qinghai-Tibetan Plateau (QTP) is the highest and one of the most extensive plateaus in the world. Phylogenetic, phylogeographic, and ecological studies support plant diversifications on the QTP through multiple mechanisms such as allopatric speciation via geographic isolation, climatic oscillations and divergences, pollinator-mediated isolation, diploid hybridization and introgression, and allopolyploidy. These mechanisms have driven spectacular radiations and/or species diversifications in various groups of plants such as Pedicularis L., Saussurea DC., Rhododendron L., Primula L., Meconopsis Vig., Rhodiola L., and many lineages of gymnosperms. Nevertheless, much work is needed toward understanding the evolutionary mechanisms of plant diversifications on the QTP. Well-sampled biogeographic analyses of the QTP plants in the broad framework of the Northern Hemisphere as well as the Southern Hemisphere are still relatively few and should be encouraged in the next decade. This paper reviews recent evidence from phylogenetic and biogeographic studies in plants, in the context of rapid radiations, mechanisms of species diversifications on the QTP, and the biogeographic significance of the QTP in the broader context of both the Northern and Southern Hemisphere biogeography. Integrative multidimensional analyses of phylogeny, morphological innovations, geography, ecology, development, species interactions and diversifications, and geology are needed and should shed insights into the patterns of evolutionary assembly and radiations in this fascinating region.
This may be the most straightforward book review imaginable to write.
Just buy this book and use it! You will not regret it.Verlyn
Klinkenborg's 23 August 2005 editorial in the New York Times
(“Grasping the depth of time as a first step in understanding
evolution”) serves as a most timely way begin a review of A
Geologic Time Scale 2004 (GTS2004). Klinkenborg writes, “One of
the most powerful limits to the human imagination is our inability to
grasp, in a truly intuitive way the depths of terrestrial and
cosmological time.”
Tertiary relict floras contain survivors from plant communities that were distributed throughout a large part of the Northern Hemisphere during much of the Tertiary (i.e. 65 – 15 million years ago (Ma)). They are now mainly restricted to warm humid areas (refugia) in southeastern and western North America, East Asia and southwest Eurasia. Recent molecular phylogenetic studies show that within East Asia the Tertiary relict flora is best divided into two distinct refugial groups, with geographical distributions centred on the Japan/Korea/northeast China and southeast China/Himalayas regions respectively. Recognition of this division leads to a significant improvement in our understanding of the origins and evolution of Tertiary relict floras in East Asia and elsewhere. Molecular studies also indicate two putative clusters of divergence times for East Asian-North American Tertiary relict disjuncts occurring at 5 and 10 Ma. These clusters might reflect a break in the continuity of the Tertiary flora between East Asia and North America across Beringia during a cold period 6–8 Ma, i.e. before the Bering Land Bridge was severed approximately 5 Ma. In addition, there is some evidence that evergreen disjuncts diverged earlier than their deciduous counterparts, possibly due to the high latitude of Beringia. Molecular studies further suggest that divergence times for transatlantic Tertiary relict disjuncts generally fall between 10 and 40 Ma, even though most geological evidence shows that the North Atlantic Land Bridge (NALB), which connected the floras of Europe and North America, was severed around 50 Ma. This raises the issue of whether a partial NALB allowed migration of floras between Eurasia and North America throughout much of the Tertiary. Tertiary relict floras are notable for exhibiting slow morphological evolution (stasis). This might result from large-scale allopatric speciation, together with stabilising selection.
Evolutionary relationships among 48 genera of Apiaceae (Umbelliferae) were inferred using maximum parsimony, maximum-likelihood, and neighbor-joining analyses of chloroplast DNA rps16 intron and adjacent rps16 3' exon sequences. Emphasis was placed on woody members of Apiaceae subfamily Apioideae endemic to southern Africa, a region hypothesized to be the place of origin of this largely herbaceous subfamily. The resultant phylogenies were highly concordant and indicate that the apioid genera Polemanniopsis and Steganotaenia form a clade sister to Apiaceae subfamily Saniculoideae. The African genera Anginon, Dracosciadium, Glia, Heteromorpha, and Polemannia also comprise a clade and likely represent the most basal elements within Apioideae. Heteromorpha, however, is not monophyletic, with Heteromorpha arborescens (Spreng.) Cham. and Schltdl. var. abyssinica (A. Rich.) H. Wolff and Heteromorpha arborescens (Spreng.) Cham. and Schltdl. var. arborescens arising in separate subclades. Progressing UP the trees, Annesorhiza then Bupleurum fall as successive sister taxa to all remaining Apioideae. The major clades recognized within subfamily Apioideae are largely congruent with those inferred using other types of molecular evidence. Sequence divergence is similar to that of other chloroplast introns, including being generally low among congeners and woody taxa. While the rps16 intron has seen very little use in molecular systematic studies to date, this study demonstrates its ability to discern high-level relationships within Apiaceae.
Chinese Araliaceae consist of 20 genera and ca. 175 species. To assess the evolutionary relationships of Araliaceae and their biogeographic diversification in China, the phylogeny of Chinese Araliaceae was constructed by sampling 96 accessions representing 20 genera and 50 species of Chinese Araliaceae and 45 closely related taxa using sequences of the nuclear ribosomal internal transcribed spacer (ITS) region and six plastid regions (the ndhF gene, the trnL-trnF region, the rps16 intron, the atpB-rbcL intergenic spacer, the rpl16 intron, and the psbA-trnH intergenic spacer). Phylogenetic analyses of the combined plastid and ITS data supported the results of the previously studies that the Chinese members of Araliaceae were scattered within the Asian Palmate group and the Aralia-Panax group with Osmoxylon at the base of core Araliaceae. The generic status of Pentapanax and Tupidanthus is not supported. Our analysis clearly places them in Aralia and Asian Schefflera, respectively. In a broader phylogenetic framework of Araliaceae, based on the fossil-calibrated Bayesian dating, Chinese Araliaceae was inferred to have originated in Asia and underwent a rapid radiation in its evolutionary history. Its diversification is hypothesized to have been driven largely by the orogenies in Asia during the Cenozoic. In China, the distribution pattern of the phylogenetic diversity of Araliaceae corresponds with its taxonomic diversity across the entire region.
Using rbcL plastid DNA sequences, we evaluated monophyly and relationships of the genera of Crossosomataceae, which are a small group of shrubs from North America and Mexico: Crossosoma, Apacheria, Glossopetalon (Forsellesia), and Velascoa. Morphological characters that correspond to the phylogenetic patterns were examined. The analysis consisted of two steps. In the first, we analyzed the sequences of representatives of the four genera with those of over 500 species of eudicots. Based on these results, a second, restricted analysis with 25 taxa was conducted. Crossosomataceae are monophyletic and the four genera fell into a well-supported clade with representatives of Stachyuraceae and Staphyleaceae. Characters that mark Crossosomataceae are: microphyllous leaves (less than 5 cm long), solitary flowers with an apocarpous ovary and hypanthium, ventrally dehiscent follicles, and seeds with a fimbriate or irregular aril. A brief description of the family and an identification key for the genera are presented.
Reticulate evolution, whether due to lateral gene transfer, introgression, incomplete lineage sorting, or hybrid speciation, is a ubiquitous phenomenon, yet systematists have few tools for analyzing and summarizing the resulting genealogical discordance. Here I argue that a primary concordance tree, a tree built from clades that are true of a plurality of the genome, provides a useful summary of the dominant phylogenetic history for a group of organisms. Residual historical signals can also be extracted in the form of secondary, tertiary, etc. concordance trees, which are built from clades that are present in the genome but contradict clades on the primary concordance tree. Clades on concordance trees can be annotated with their concordance factor (CF), the proportion of the genome for which the clade is true. Concordance trees can potentially be estimated either from population histories or from multilocus molecular datasets. In the latter case one can use the recently developed Bayesian concordance analysis to obtain point estimates and credibility intervals on CF's. I argue that the concepts of concordance trees and concordance factors inform the debate on how to integrate information from multiple independent datasets and help clarify the nature of the boundary between reticulate and divergent genealogy.
Choosing and designing primers based on available DNA sequence data and statistical contrasting of domains or structural features is a common routine among molecular biologists. Currently available, free software tools were found to lack desirable features related to these tasks. This was the motivation for developing a new program, SeqState. SeqState locates regions that remain to be sequenced in phylogenetic DNA datasets, evaluates user-provided primers and selects primers best suited to fill gaps in the sequences. If the primers provided by the user are unsuitable, new primers are designed. Primers can be loaded from a primer database, be supplied as part of the alignment or be entered manually. The position of internal primers is automatically localised in the loaded data file. Primers can be edited, and changes and new primers can be saved to the database. Primer sheets allow the user to view internal dimers, complements to a second primer, mismatches to all loaded sequences, and other primer characteristics. Calculation of various sequence statistics can be requested for the whole dataset or parts thereof (character sets), with standard errors estimated by bootstrapping. Insertion-deletion events can be evaluated statistically and encoded for subsequent phylogenetic analysis according to several published coding principles. Availability: SeqState runs on all major computer platforms and is downloadable for free from http:// www. nees. uni-bonn. de/ downloads/ SeqState, together with documentation and sample data files, or can be requested from the author.
The occurrences of Staphylea L. (Staphyleaceae) fossils have been abundantly documented from the Cenozoic of Eurasia, but none has been confirmed from North America to date. In this study, we describe Staphylea levisemia sp. nov. on the basis of seed remains from the latest Miocene to earliest Pliocene of northeastern Tennessee, southeastern USA. The seeds are characterized by a smoothly inflated body, a large hilar scar perforated by several vascular traces and bordered by a distinctive lip-like rim, a cuticle coating the seed coat interior, and seed coat section containing weakly developed tiny lumina. According to the paleogeographic distribution of the genus, it is hypothesized that Staphylea originated from western Eurasia no later than the late Oligocene, and arrived in eastern North America no later than the late Neogene, most possibly through the North Atlantic land bridges like many other seed plants.
The arcto-Tertiary relictual flora is comprised of many genera that occur non-contiguously in the temperate zones of eastern Asia, Europe, eastern North America, and western North America. Within each distributional area, species are typically endemic and may thus be widely separated from closely related species within the other areas. It is widely accepted that this common pattern of distribution resulted from of the fragmentation of a once more-continuous arcto-Tertiary forest. The historical biogeographic events leading to the present-day disjunction have often been investigated using a phylogenetic approach. Limitations to these previous studies have included phylogenetic uncertainty and uncertainty in ancestral range reconstructions. However, the recently described Bayes-DIVA method handles both types of uncertainty. Thus, we used Bayes-DIVA analysis to reconstruct the stem lineage distributions for 185 endemic lineages from 23 disjunct genera representing 17 vascular plant families. In particular, we asked whether endemic lineages within each of the four distributional areas more often evolved from (1) widespread ancestors, (2) ancestors dispersed from other areas, or (3) endemic ancestors. We also considered which of these three biogeographic mechanisms may best explain the origins of arcto-Tertiary disjunct endemics in the neotropics. Our results show that eastern Asian endemics more often evolved from endemic ancestors compared to endemics in Europe and eastern and western North America. Present-day endemic lineages in the latter areas more often arose from widespread ancestors. Our results also provide anecdotal evidence for the importance of dispersal in the biogeographic origins of arcto-Tertiary species endemic in the neotropics.
The Mojave and Colorado Deserts of the American Southwest are geologically recent in origin, resulting primarily from the rain-shadow caused by the Late Pliocene-Pleistocene elevation of the Sierra Nevada, Transverse, and Peninsular ranges. Their age thus is perhaps two to three million years. The present vegetation is even more recent, largely Holocene in origin, and still evolving. During the last, Wisconsin, glacial episode the California deserts were well supplied with huge, deep lakes and large streams and an open woodland, possibly grassy, supporting numerous large mammals, now mostly extinct. The desert flora, however, is in large part more ancient, having been assembled since early Paleogene time from many sources. Most of the perennials are probably former members of the Madro-Tertiary Geoflora that dominated southern California and adjacent areas during the Tertiary. They are species of dry habitats preadapted to long periods of drought, hot, dry summers, and cool, wet winters and thus able to populate and adapt to the varied desert habitats when they became available. They survived cool, pluvial, glacial periods by migration southward or to lower elevations. Some elements of the American southwestern desert flora are derived from Mexico, South America, central Asia, and a few possibly from North Africa and the Mediterranean region by overland immigration or long distance dispersal. In some instances this was aided by changing ocean size due to continental movement, glacial sea-level lowering, and to changes in oceanic-current patterns. Some desert plants, at least some of the ephemerals, may well be of very recent, even Holocene, origin in our arid Southwest.
Abstract—
Dendropanax (Araliaceae) is a genus of about 80 species disjunctly distributed in tropical to subtropical Asia and the Neotropics, showing an amphi-Pacific tropical disjunction. The phylogeny of the genus was constructed by sampling 95 accessions representing
33 species of Dendropanax and 43 closely related taxa using sequences of the nuclear ribosomal internal transcribed spacer (ITS) region and six plastid regions (the ndhF gene, the trnL-trnF region, the rps16 intron, the atpB-rbcL intergenic spacer, the rpl16
intron, and the psbA-trnH intergenic spacer). Phylogenetic analyses of the combined plastid and ITS data suggested that the monophyly of Dendropanax was not supported because the Asian D. lancifolius - D. hainanensis clade did not group with the main Dendropanax
clade. Nevertheless, the maximally parsimonious trees (MPTs) from the analysis constraining Dendropanax as a monophyletic group were only one step longer than the unconstrained MPTs. The New and Old World Dendropanax species except D. lancifolius and D. hainanensis
each formed a robustly supported clade, and the two clades were sister to each other. Based on the biogeographic analyses and fossil-calibrated Bayesian dating, Dendropanax was hypothesized to have originated in the Old World and migrated into the New World via the North Atlantic land
bridges in the early Tertiary. The amphi-Pacific intercontinental disjunction of Dendropanax was dated to be 41.83 mya with a 95% high posterior density [HPD] interval of 28.46‐56.15 mya.
— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
In this study, we examined the utility of pollen morphology for resolving questions about the evolutionary history of Billia, which is a poorly known genus of Neotropical trees. Billia has been traditionally circumscribed with two species and treated as sister to Aesculus L. However, the number of species in Billia is uncertain, because the genus exhibits abundant morphological diversity but little discontinuous variation. Therefore, Billia may be monotypic and highly polymorphic, or it may have two species with blurred boundaries due to incipient speciation and/or hybridization. Moreover, one recent molecular phylogenetic study shows Billia nested within Aesculus. Our work sought to address the following questions: (1) Are there discontinuities in the pollen of Billia that may suggest species boundaries? (2) Does the pollen of Billia show evidence for inter-specific hybridization? and (3) Do the exine morphology and size of pollen in Billia differ from those in Aesculus? Our results from scanning electron microscopy showed that pollen exine morphology is not taxonomically informative in Billia but that there are significant differences in pollen size between red- and white-flowered individuals. Thus, our pollen data support the utility of flower color in Billia for species delimitation. Our assessments of pollen viability do not support hybridization in the genus, but cannot be used to rule it out. Finally, pollen exine morphology may lend some support to an evolutionary origin of Billia within eastern North American Aesculus. In contrast, data on pollen size suggest that Billia may belong in a topological position outside of Aesculus.
Trichome characters are often considered to be taxonomically important in oak species. In this article, we investigate a group of Mediterranean oaks, Quercus subsection Galliferae and Q. pubescens, using a large dataset and covering the entire distribution range of the group. As a result of the different interpretations of terms in previous studies, trichome terminology was re‐assessed aiming to obtain a practicable nomenclature. In contrast with previous studies, we found that acicular, bifurcate, fasciculate, stellate, uniseriate and capitate trichomes are represented in all taxa. One exception is the lack of bifurcate trichomes in Q. canariensis. This suggests that seemingly taxonomically informative presence/absence data for trichome types, as reported previously, may be the result of too small a sample size, and this may be unrepresentative. In combination with other morphological characters (leaf shape, size and texture), features of the indumentum, such as the floccose, easily removable trichomes in Q. canariensis, can be important in species delimitation. The use of trichome characteristics in Quercus subsection Galliferae requires exhaustive sampling of all taxa in order to extract a reproducible taxonomic signal from quantitative characters. This is the prerequisite for building datasets that can be used for phylogenetic analyses, investigations of character evolution and comparative morphological studies. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169, 611–644.
Despite the absence of major Quaternary glaciations in arid Northwest China, significant climatic oscillations definitely impacted the evolution of the biota in situ. Phylogeography has grown as a discipline because it has provided explicitly tools for the study of geographical subdivision among populations. But phylogeographical application for arid Northwest China has begun to blossom, which provided evidence that aridification played a significant role in the increase of genetic diversity and species diversification. The time frame corresponds with Pleistocene climatic oscillations, which caused extreme aridity and the expansion of sandy deserts. In Asian desert flora subkingdom and Eurasian forest subkingdom of Northwest China, the recurrent phylogeographical scenarios, identified by different case studies broadly agree with longstanding biogeographic, floristic and topographic concepts: 1) aridification promoted diversification and speciation of desert plants; 2) deserts expansion caused habitat fragmentation; 3) altay-Tianshan Mts. have glacial refugia for plants; 4) population expansion and re-colonization from glacial refugia during postglacial period; 5) desert plants persistence and alpine plants retreat during climate oscillations. We discuss the main phylogeographical findings in light of molecular and palaeo-environmental evidence, emphasizing notable gaps in our knowledge and outlining future research perspectives for disentangling the evolutionary history of arid region's flora.
The phylogeny of Asian Schefflera was inferred from sequences of the nuclear ribosomal internal transcribed spacer region, and six plastid regions (the ndhF gene, the trnL-trnF region, the rps16 intron, the atpB-rbcL intergenic spacer, the rpl16 intron, and the psbA-trnH intergenic spacer). Phylogenetic analyses of the combined plastid and internal transcribed spacer data with parsimony and Bayesian methods strongly support the monophyly of Asian Schefflera. The genus is supported to be closely related to Heteropanax and Tetrapanax with the small tropical continental Asian genus Heteropanax as its sister. Within Asian Schefflera, four distinct subclades were identified: (i) the widely distributed Asian Heptapleurum group with no styles in the gynoecium; (ii) the main Agalma group with racemose or spicate inflorescence units with a few umbellate taxa; (iii) the Schefflera hypoleuca group; and (iv) the Schefflera heptaphylla group. In a broader phylogenetic framework of Araliaceae, Asian Schefflera is hypothesized to have originated in continental Asia at 57.41 Mya (95% high posterior density interval of 40.33–76.06 Mya) in the early Tertiary and radiated into the now SE Asia, eastern Himalaya, and E Asia at 46.11 Mya (95% high posterior density interval of 33.02–60.69 Mya). Its subsequent diversification in Asia may have been driven largely by the collision of the Indian plate with the Asian plate in the middle Eocene and the collision of the Australian margin with the Eurasian margin in the early Miocene.
With increases in both the size and scope of phylogenetic trees, we are afforded a renewed opportunity to address long-standing comparative questions, such as whether particular fruit characters account for much of the variation in diversity among flowering plant clades. Studies to date have reported conflicting results, largely as a consequence of taxonomic scale and a reliance on potentially conservative statistical measures. Here we examine a larger and older angiosperm clade, the Campanulidae, and infer the rates of character transitions among the major fruit types, emphasizing the evolution of the achene fruits that are most frequently observed within the group. Our analyses imply that campanulids likely originated bearing capsules, and that all subsequent fruit diversity was derived from various modifications of this dry fruit type. We also found that the preponderance of lineages bearing achenes is a consequence of not only being a fruit type that is somewhat irreversible once it evolves, but one that also seems to have a positive association with diversification rates. Although these results imply the achene fruit type is a significant correlate of diversity patterns observed across campanulids, we conclude that it remains difficult to confidently and directly view this character state as the actual cause of increased diversification rates.
An analysis of rbcL sequence data for representatives of families of putative sapindalean/rutalean affinity identified a robust clade of core "sapindalean" taxa that is sister to representatives of Malvales. The constitution of this clade approximates the broad concept of Sapindales (sensu Cronquist). Five lineages within the order are recognized: a "rutaceae" clade (Rutaceae, Cneoraceae, Ptaeroxylaceae, Simaroubaceae sensu stricto, and Meliaceae); a "sapindaceae" clade (Sapindaceae, Aceraceae, and Hippocastenaceae); Anacardiaceae plus Burseraceae; Kirkiaceae; and Zygophyllaceae pro parte. Relationships among these groups were only weakly resolved, but there was no support for the recognition of the two more narrowly defined orders, Rutales and Sapindales sensu stricto. Several families that have previously been allied to Sapindales or Rutales show no affinity to the core sapindalean taxa identified with the molecular data, and are excluded from the order: viz. Akaniaceae, Bretschneideraceae, Connaraceae, Coriariaceae, Melianthaceae, Meliosmaceae, Physenaceae, Rhabdodrendraceae, Sabiaceae, Staphyleaceae, Stylobasiaceae, Surianaceae, and Zygophyllaceae sensu stricto.
Molecular divergence in the eastern Asia-eastern North American disjunct section Rytidospermum of Magnolia was investigated by allozyme electrophoresis, chloroplast DNA (cpDNA) restriction site analysis, and gene sequencing. We calculated Nei's genetic identities between two Asian species, M. officinalis var. biloba and M. hypoleuca, and three American species, M. tripetala, M. fraseri var. fraseri, and M. macrophylla var. macrophylla, by using gene frequency data from 17 nuclear-encoded allozyme loci in 67 populations. We then estimated cpDNA sequence divergence between the five species by examining restriction site variation for ten endonucleases over the entire genome. Finally, nucleotide sequences of the chloroplast gene rbcL were compared between M. hypoleuca, M. tripetala, and M. macrophylla var. macrophylla. All three methods consistently yielded low divergence values between the American species M. tripetala and its Asian sister taxa, M. officinalis var. biloba and M. hypoleuca (Nei's I = 0.712 and 0.809, respectively; D-cpDNA = 0.083% for both pairs; D-rbcL = 0.000% between M. tripetala and M. hypoleuca). The other two American species, M. fraseri var. fraseri and M. macrophylla var. macrophylla, neither of which is sister to the Asian taxa, exhibited much higher divergence form the Asian taxa. We interpreted the low divergence between M. tripetala adn its Asian sister taxa as a result of recent separation (the late Miocene to the early Pliocene), based on time estimates from molecular data as well as geological and paleoclimatic evidence. A comparison of our results with those of the earlier studies revealed a diverse array of levels of divergence between several eastern Asian and eastern North American species pairs. Though different extinction patterns and variation in molecular evolutionary rates may be partly responsible, this heterogeneous pattern of divergence is best explained by different times of disjunction in different taxa, which in turn suggests that the floristic similarity between the two continents was most likely attained by multiple migrations via both Bering and North Atlantic land bridges, or possibly even with involvement of dispersal.
Hemisphere. There is less agreement on the timing of this process, with suggestions ranging from the Paleocene to the Neogene. In this study, molecular markers from two different plant genomes were used to assess the degree of genetic divergence between the two interfertile, morphologically similar species of the genus Liriodendron, i.e., L. tulipifera and L. chinense. Resulting molecular divergence estimates were translated into approximate dates of separation, independent of evidence from the fossil record. Allozyme data (Nei's genetic identity = 0.434) suggested a divergence time of 10-16 million years before present, whereas sequence divergence in the plastid genomes (1.24%) led to an estimate of approximately 1 1-14 million years before present. A review of the paleobotanical literature indicated that the fossil floras that included, or might have included Liriodendron could not have survived in Beringia after the late Miocene and the onset of southward-migrating Arctic air masses on the North American continent. This interpretation suggests a minimum time of separation of approximately 13 million years before present. Thus, both molecular data sets and the paleobotanical evidence concur in suggesting a divergence time of 10-16 million years before present. Interspecific compatibility and relative morphological stasis must have, therefore, persisted from at least the late Miocene. We emphasize the need for similar studies in other genera, especially those that have both a reasonable Tertiary fossil history and extant species in mesic temperate refugia in Asia, Europe, and westem as well as eastem North America.