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| 1 | A tale of worldwide success:Behind the scenes of Carex(Cyperaceae)biogeography and diversification显示文摘The megadiverse genus Carex(c.2000 species,Cyperaceae)has a nearly cosmopolitan distribution,displaying an inverted latitudinal richness gradient with higher species diversity in cold-temperate areas of the Northern Hemisphere.Despite great expansion in our knowledge of the phylogenetic history of the genus and many molecular studies focusing on the biogeography of particular groups during the last few decades,a global analysis of Carex biogeography and diversification is still lacking.For this purpose,we built the hitherto most comprehensive Carex-dated phylogeny based on three markers(ETS-ITS-matK),using a previous phylogenomic Hyb-Seq framework,and a sampling of two-thirds of its species and all recognized sections.Ancestral area reconstaiction,biogeographic stochastic mapping,and diversification rate analyses were conducted to elucidate macroevolutionary biogeographic and diversification patterns.Our results reveal that Carex originated in the late Eocene in E Asia,where it probably remained until the synchronous diversification of its main subgeneric lineages during the late Oligocene.E Asia is supported as the cradle of Carex diversification,as well as a< | Santiago Martin-Bravo Pedro Jimenez-Mejias Tamara Villaverde Marcial Escudero Marlene Hahn Daniel Spalink Eric H.Roalson Andrew L.Hipp the Global Carex Group Carmen Benitez-Benitez Leo P.Bruederle Elisabeth Fitzek Bruce A.Ford Kerry A.Ford Mira Gamer Sebastian Gebauer Matthias H.Hoffmann Xiao-Feng Jin Isabel Larridon Etienne Ldveilld-Bourret Yi-Fei Lu Modesto Luceno Enrique Maguilla Jose Ignacio Marquez-Corro Monica Miguez Robert Naczi Anton A.Reznicek Julian R.Starr | 2019 | Journal of Systematics and Evolution2019，57，6： | 6 |
| 2 | Monograph of Carex section Schiedeanae (Cyperaceae): Unexpected taxonomic and ecological diversity in a Mexican sedge clade显示文摘Carex section Schiedeanae(subg.Euthyceras)has long been thought to comprise at most five species of Mexican sedges.Our morphological studies in the field and herbarium,however,supported by more recent DNA sequencing work,demonstrate that the section is,in fact,three times as species-rich,making it one of the largest sections in Mexico.Its 15 species range from Chihuahua to Tamaulipas south to Veracruz and Oaxaca;a single species,Carex muriculata,extends into the United States.The section has unusual inflorescences with simple(except in Carex complexa),uniformly androgynous,sessile spikes,utriculiform dadoprophylls,and perigynia with a unique combination of pubescence types composed of papillae;unicellular,simple hairs;and(in many species)multicellular tubercles.We recognize five previously described species(C.muriculata,Carex perstricta,Carex schiedeana,Carex stellata,and Carex vizarronensis)and describe 10 additional species(Carex angustilepis,Carex cabralii,Carex complexa,Carex dentata,Carex gypsophila,Carex mesophila,Carex paneroi,Carex planilamina,Carex revoluta,and Carex tehuacana).We have expanded the morphological features used in the section to include particularly anther,staminate scale,and style features,and more detailed micromorphology of the perigynia,especially indumentum.In total,13 of the 15 species recognized herein,with a total of 32 individuals,were examined for ETS and ITS for phylogenetic reconstruction.Phylogenetically,the xeric species(plus C.paneroi)form a grade leading to a clade of the more mesophytic species adapted to forest understories,plus the unique cliff dwelling C.complexa. | Anton A.Reznicek Maria del Socorro Gonzalez-Elizondo Marlene Hahn Mira Gamer Andrew L.Hipp | 2021 | Journal of Systematics and Evolution2021，59，4： | 4 |
| 3 | Assessing the sensitivity of divergence time estimates to locus sampling, calibration points, and model priors in a RAD-seq phylogeny of Carex section Schoenoxiphium显示文摘Restriction site-associated DNA sequencing(RAD-seq)and related methods have become relatively common approaches to resolve species-level phylogeny.It is not clear,however,whether RAD-seq data matrices are well suited to relaxed clock inference of divergence times,given the size of the matrices and the abundance of missing data.We investigated the sensitivity of Bayesian relaxed clock estimates of divergence times to alternative analytical decisions on an empirical RAD-seq phylogenetic matrix.We explored the relative contribution of secondary calibration strategies,amount of missing data,and the data partition analyzed to overall variance in divergence times inferred using BEAST MCMC analyses of Carex section Schoenoxiphium(Cyperaceae)-a recent radiation for which we have nearly complete species sampling of RAD-seq data.The crown node for Schoenoxiphium was estimated to be 15.22(9.56-21.18)Ma using a single calibration point and low missing data,11.93(8.07-16.03)Ma using multiple calibration points and low missing data,and 8.34(5.41-11.22)using multiple calibrations but high missing data.We found that using matrices with more than half of the individuals with missing data inferred younger mean ages for all nodes.Moreover,we have found that our molecular clock estimates are sensitive to the positions of the calibration(s)in our phylogenetic tree(using matrices with low missing data),especially when only a single calibration was applied to estimate divergence times.These results argue for sensitivity analyses and caution in interpreting divergence time estimates from RAD-seq data. | Tamara Villaverde Enrique Maguilla Modesto Luceno Andrew L.Hipp | 2021 | Journal of Systematics and Evolution2021，59，4： | 3 |
| 4 | A framework infrageneric classification of Carex (Cyperaceae) and its organizing principles显示文摘Phylogenetic studies of Carex L.(Cyperaceae)have consistently demonstrated that most subgenera and sections are para-or polyphyletic.Yet,taxonomists continue to use subgenera and sections in Carex classification.Why?The Global Carex Group(GCG)here takes the position that the historical and continued use of subgenera and sections serves to(i)organize our understanding of lineages in Carex,(ii)create an identification mechanism to break the~2000 species of Carex into manageable groups and stimulate its study,and(iii)provide a framework to recognize morphologically diagnosable lineages within Carex.Unfortunately,the current understanding of phylogenetic relationships in Carex is not yet sufficient for a global reclassification of the genus within a Linnean infrageneric(sectional)framework.Rather than leaving Carex classification in its current state,which is misleading and confusing,we here take the intermediate steps of implementing the recently revised subgeneric classification and using a combination of informally named clades and formally named sections to reflect the current state of our knowledge.This hybrid classification framework is presented in an order corresponding to a linear arrangement of the clades on a ladderized phylogeny,largely based on the recent phylogenies published by the GCG.It organizes Carex into six subgenera,which are,in turn,subdivided into 62 formally named Linnean sections plus 49 informal groups.This framework will serve as a roadmap for research on Carex phylogeny,enabling further development of a complete reclassification by presenting relevant morphological and geographical information on clades where possible and standardizing the use of formal sectional names. | Eric H.Roalson Pedro Jiménez-Mejías Andrew L.Hipp Carmen Benítez-Benítez Leo P.Bruederle Kyong-Sook Chung Marcial Escudero Bruce A.Ford Kerry Ford Sebastian Gebauer Berit Gehrke Marlene Hahn Muhammad Qasim Hayat Mathias H.Hoffmann Xiao-Feng Jin Sangtae Kim Isabel Larridon Étienne Léveillé-Bourret Yi-Fei Lu Modesto Luceño Enrique Maguilla Jose IgnacioMárquez-Corro Santiago Martín-Bravo Tomomi Masaki Mónica Míguez Robert F.C.Naczi Anton A.Reznicek Daniel Spalink Julian R.Starr Uzma Tamara Villaverde Marcia J.Waterway Karen L.Wilson and Shu-Ren Zhang | 2021 | Journal of Systematics and Evolution2021，59，4： | 3 |
| 5 | Trait evolution rates shape continental patterns of species richness in North America's most diverse angiosperm genus (Carex, Cyperaceae)显示文摘Ecological opportunity has been associated with increases in diversification rates across the tree of life.Under an ecological diversification model,the emergence of novel environments is hypothesized to promote morpho-and ecospace evolution.Whether this model holds at the clade level within the most species-rich angiosperm genus found in North America(Carex,Cyperaceae)is yet to be tested.Recent works demonstrate a temporal coupling of climate cooling and widespread colonization of Carex in North America,implicating ecological diversification.In addition,research has consistently found asymmetric patterns of lineage-level diversification in the genus.Why does variation in clade sizes exist in the genus?Is ecological diversification involved?In this study,we tested whether rates of morphological and ecological trait evolution are correlated with clade-level species richness in Carex of North America north of Mexico.We constructed a phylogeny of 477 species-an almost complete regional sample.We estimated rates of evolution of morphological traits,habitat,and climatic niche and assessed whether differences in rates of evolution correlate with species richness differences in replicate non-nested sister clades.Our work demonstrates significant positive correlations between climatic niche rates,habitat and reproductive morphological evolution,and species richness.This coupling of trait and niche evolution and species richness in a diverse,continental clade sample strongly suggests that the ability of clades to explore niche and functional space has shaped disparities in richness and functional diversity across the North American flora region.Our findings highlight the importance of the evolutionary history of trait and niche evolution in shaping continental and regional floras. | Jocelyn E.Pender Andrew L.Hipp Marlene Hahn Julian R.Starr | 2021 | Journal of Systematics and Evolution2021，59，4： | 3 |
| 6 | Macroevolutionary insights into sedges (Carex: Cyperaceae): The effects of rapid chromosome number evolution on lineage diversification显示文摘Changes in holocentric chromosome number due to fission and fusion have direct and immediate effects on genome structure and recombination rates.These,in turn,may influence ecology and evolutionary trajectories profoundly.Sedges of the genus Carex(Cyperaceae)comprise ca.2000 species with holocentric chromosomes.The genus exhibits a phenomenal range in the chromosome number(2n=10−132)with almost not polyploidy.In this study,we integrated the most comprehensive cytogenetic and phylogenetic data for sedges with associated climatic and morphological data to investigate the hypothesis that high recombination rates are selected when evolutionary innovation is required,using chromosome number evolution as a proxy for recombination rate.We evaluated Ornstein-Uhlenbeck models to infer shifts in chromosome number equilibrium and selective regime.We also tested the relationship between chromosome number and diversification rates.Our analyses demonstrate significant correlations between morphology and climatic niche and chromosome number in Carex.Nevertheless,the amount of chromosomal variation that we are able to explain is very small.We recognized a large number of shifts in mean chromosome number,but a significantly lower number in climatic niche and morphology.We also detected a peak in diversification rates near intermediate recombination rates.In combination,these analyses point toward the importance of chromosome evolution to the evolutionary history of Carex.Our work suggests that the effect of chromosome evolution on recombination rates,not just on reproductive isolation,may be central to the evolutionary history of sedges. | José I.Márquez-Corro Santiago Martín-Bravo Pedro Jiménez-Mejías Andrew L.Hipp Daniel Spalink Robert F.C.Naczi Eric H.Roalson Modesto Luceño Marcial Escudero | 2021 | Journal of Systematics and Evolution2021，59，4： | 1 |
| 7 | Even more oak species in Mexico? Genetic structure and morphological differentiation support the presence of at least two specific entities within Quercus laeta显示文摘Diferentiation among populations,sometimes despite ongoing gene exchange,is a key step in speciation.Therefore,comparison of intra-and interspecific differentiation patterns is of great significance to understanding speciation.The genus Quercus is an interesting system to test speciation models in the presence of gene flow,due to its weak interspecific reproductive barriers.The aim of the present study was to characterize the degree and pattern of morphological and genetic diferentiation among diferent morphotypes in the white oak Quercus laeta,some corresponding to the previously described species Quercus centralis,Q.laeta,Quercus prinopsis,and Quercus transmontana,as well as geographically structured variation within Q.transmontana not described previously.Our goal was to evaluate if some of these can be considered distinct specific entities or are rather part of a continuum of variation.Nine microsatellite loci and two intergenic regions of chloroplast DNA were analyzed.Morphological diferences were evaluated using geometric morphometrics.Chloroplast DNA showed low differentiation,suggesting introgression or sharing of ancestral haplotypes among the Q.laeta morphotypes.Nuclear microsatellites indicated diferentiation into two distinct main genetic groups,which were congruent with morphological differentiation.In conclusion,nuclear markers and morphological variations suggest the existence of at least two different entities within Q.laeta. | Saddan Morales-Saldana Susana Valencia-Avalos Ken Oyama Efrain Tovar-Sanchez Andrew L.Hipp Antonio Gonzalez-Rodriguez | 2022 | Journal of Systematics and Evolution2022，60，5： | 0 |
| 8 | Geographical vs. ecological diversification in Carex section Phacocystis (Cyperaceae): Patterns hidden behind a twisted taxonomy显示文摘Carex section Phacocystis(Cyperaceae)is one of the most diverse and taxonomically complex groups of sedges(between 116 and 147 species),with a worldwide distribution in a wide array of biomes.It has a very complicated taxonomic history,with numerous disagreements among different treatments.We studied the biogeography and niche evolution in a phylogenetic framework to unveil the relative contribution of geographical and ecological drivers to diversification of the group.We used a large species sampling of the section(82%of extant species)to build a phylogeny based on four DNA regions,constrained with a phylogenomic HybSeq tree and dated with six fossil calibrations.Our phylogenetic results recovered section Phacocystis s.s.(core Phacocystis)as sister to section Praelongae.Ancestral area reconstruction points toward the N Pacific as the cradle for the crown diversification of section Phacocystis during the Middle Miocene.Wide distributions were recurrently inferred across deep nodes.Large Northern Hemisphere lineages with geographical congruence were retrieved,pointing toward the importance of allopatric divergence at deep phylogenetic levels,whereas within-area speciation emerges as the predominant pattern at shallow phylogenetic level.The Southern Hemisphere(Neotropics,SW Pacific)was colonized several times from the Northern Hemisphere.The global expansion of Carex section Phacocystis did not entail major ecological changes along the inner branches of the phylogeny.Nevertheless,ecological differentiation seems to gain importance toward recent times. | Carmen Benitez-Benitez Santiago Martin-Bravo Charlotte S.Bjora Sebastian Gebauer Andrew L.Hipp Matthias H.Hoffmann Modesto Lucefio Tyril M.Pedersen Anton Reznicek Eric Roalson Polina Volkova Okihito Yano Daniel Spalink Pedro Jimenez-Mejias | 2021 | Journal of Systematics and Evolution2021，59，4： | 0 |
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