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South American Plant Chromosome Numbers Databases: The Information We Have and the Information We Lack on the Most Plant-Diverse Continent
Abstract
Chromosome numbers have been used in plant taxonomy, and they are still fundamental for taxon delimitation and genome evolution studies. South America is one of the most diverse continents in terms of plant species and there is a considerable number of species not yet analyzed. Accumulated knowledge about plant chromosome numbers has been compiled from online databases, and here we present an overview. The CCDB is one of the largest plant cytological databases and includes data for around 18% of known vascular plants in the world. In this work, we review the information contained in CCDB and in three databases with exclusive information for South America. At present, the three existing databases comprise information on around 1800 plant taxa related to specific regions, countries, or biomes. Efforts are necessary to expand cytological knowledge and to collect all the available information in a plant chromosome database for this continent.
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The exceptional levels of biodiversity found today in the American tropics are the outcome of tens of millions of years of evolution, shaped by the tumultuous geological history of the region, its heterogeneous habitats, climate change, ecological interactions and, in recent millennia, human influence. Although our understanding of diversity patterns and their underlying processes grows steadily in breadth and depth, Neotropical biodiversity is rapidly breaking down. Here, I contrast the long-term evolution of Neotropical biodiversity with its recent and rapid deterioration due to anthropogenic factors. I consider the impacts of the early arrival of humans to the region and the modern intensification of land-use change (primarily driven by agriculture) and other drivers of biodiversity loss, such as direct exploitation, invasive species and climate change. Together, these threats have led to 33% of all Neotropical species for which sufficient data are available being currently threatened with extinction. I outline emerging opportunities for conservation and restoration under the post-2020 Global Biodiversity Framework and call for urgent action from the biodiversity community, for the benefit of people and nature.
Global warming, coupled with habitat destruction and human activity, are accelerating the rates of species extinction worldwide. Species-extinction risk assessment, using the IUCN Red List categories, together with the study of the spatial patterns of biodiversity, are fundamental approaches to identify conservation priorities and targeting government decisions to mitigate impacts on biodiversity. Here, we analyzed threat levels of endemic species for the entire Argentinean vascular flora. Accordingly, we classified species following the IUCN threat categories and analyzed threat levels within different families, plant life-forms, and biogeographic regions of the country. We also analyzed spatial patterns of threat by means of macroecological modeling techniques and explored the effectiveness of current protected areas in relation to the threatened endemics they actually included. The results showed that of the 1683 Argentinean endemic vascular plant taxa, 800 species were categorized under threat (VU, EN, or CR) (~47%). Families with the highest number of threatened species were also those with the highest number of endemics; herbs and climbing plants presented significantly higher threat levels, and among biogeographic provinces, the most affected in terms of threat proportion were the Altoandina, Yungas, and Paranaense. In addition, different hotspots of threatened endemism were detected, mainly associated with mountainous areas with high altitudinal heterogeneity; of these, only nearly half of the hotspots are included, at least partially, within a protected area. An up-to-date species list of Argentinean endemic plants, including their proposed conservation status, is also provided. This work seeks to contribute to the knowledge on geographical patterns of the Argentinean flora and its conservation, complementing the information published in the Flora of Argentina.
Chromosome numbers have been widely used to describe the most fundamental genomic attribute of an organism or a lineage. While providing strong phylogenetic signal, chromosome numbers vary remarkably among eukaryotes at all levels of taxonomic resolution. Changes in chromosome numbers regularly serve as indication of major genomic events, most notably polyploidy and dysploidy. Here, we review recent advancements in our ability to make inferences regarding historical events that led to alterations in the number of chromosomes of a lineage. We first describe the mechanistic processes underlying changes in chromosome numbers, focusing on structural chromosomal rearrangements. Then, we focus on experimental procedures, encompassing comparative cytogenomics and genomics approaches, and on computational methodologies that are based on explicit models of chromosome-number evolution. Together, these tools offer valuable predictions regarding historical events that have changed chromosome numbers and genome structures, as well as their phylogenetic and temporal placements.
Karyotype evolution in cycads has been described in 113 species covering all the 10 genera. Cycads are a conservative group in this regard as the genera with low basic numbers i.e. Dioon, Macrozamia, Lepidozamia, Encephalartos, Bowenia (2n = 18) and Ceratozamia and Stangeria (2n = 16) have relatively symmetrical karyotypes while those with higher numbers i.e. Cycas (2n = 22) and Microcycas (2n = 26) have more asymmetric karyotypes. The situation in Zamia is more complicated with different species showing a range of chromosome numbers of 2n = 16–28 while some species even show intraspecific variation. The increase or decrease in number as seen in some Zamia species has occurred mainly by chromosomal fission/fusion. Some variability is however, seen in chromosome banding as well as the position of rDNA loci. The phylogenetic relationships between the genera have been discussed on the basis of karyotype evolution.
Premise of the study:
Chromosome count data are available for hundreds of plant species and can be explored in text-only format at the Chromosome Counts Database (http://ccdb.tau.ac.il). CCDBcurator and EyeChrom are an R package and a web application, respectively, that first curate and then visualize these data graphically, so that intra- and interspecific variation of chromosome numbers can be easily summarized and displayed for a given genus.
Methods and results:
We developed R code to clean, summarize, and display in several formats the chromosome count data for a selected genus or set of species present in the Chromosome Counts Database. These data and figures can be exported for use in analyses, publications, or teaching.
Conclusions:
Chromosome count data are critical for a number of evolutionary studies in plant biology, and their importance is underscored by the increasing appreciation of the prevalence of polyploidy in land plants. CCDBcurator and EyeChrom provide a fast, easy, and reproducible means of cleaning, curating, and then visualizing the chromosome count data currently available for plants.
We present a list of endemic plants of Paraguay, which includes 374 taxa from 52 families and 162 genera based on the revision of primary data (herbarium collections). Synonyms, habit, distribution in Paraguay and all the voucher specimens seen or cited in recent bibliographies or in the consulted databases are provided for each taxon. A brief analysis of the diversity and importance of this endemic flora is presented. A list of excluded species, which were considered as endemics in previous publications, is also included.
Chilean Plants Cytogenetic Database (CPCD) is a resource available on line in electronic format, which provides a cytogenetics catalogue for continental and insular Chilean vascular plants. In this report, we made reference to the CPCD, discussing aspects on its coverage, features and usages. Currently, the database stores cytogenetic information for 247 species, 107 genera, and 55 families belonging to Pteridophyta, Pinophyta, and Magnoliophyta. RESUMEN La Base de Datos Citogenéticos de Plantas Chilenas (CPCD) es un recurso disponible en formato electrónico en línea, que provee de un catálogo citogenético para plantas vasculares de Chile continental e insular. En esta comunicación hacemos referencia a la CPCD, discutiendo aspectos sobre su cobertura, rasgos y usos. Actualmente, la base de datos contiene información citogenética para 247 especies, 107 géneros y 55 familias pertenecientes a Pteridophyta, Pinophyta y Magnoliophyta. Palabras clave: número cromosómico, cariotipo, plantas chilenas
The vascular plants of the Americas
Botanical exploration in the Americas has a history that stretches back for half a millennium, with knowledge assembled in diverse regional floras and lists. Ulloa Ulloa et al. present a comprehensive and integrated compilation of all known native New World vascular plant species (see the Perspective by Givnish). This compilation, in a publicly available, searchable database, includes 124,993 species—about one-third of the worldwide total. They further present details of the distribution of species across families and genera, the geographical foci of diversity, and the floristic relationships between regions. The rate of plant species discovery in the Americas averages almost 750 annually, so this valuable resource will continue to grow.
Science , this issue p. 1614 ; see also p. 1535
Cerrado is a biodiversity hotspot that has lost ca. 50% of its original vegetation cover and hosts ca. 11,000 species belonging to 1,423 genera of phanerogams. For a fraction of those species some cytogenetic characteristics like chromosome numbers and C-value were available in databases, while other valuable information such as karyotype formula and banding patterns are missing. In order to integrate and share all cytogenetic information published for Cerrado species, including frequency of cytogenetic attributes and scientometrics aspects, Cerrado plant species were searched in bibliographic sources, including the 50 richest genera (with more than 45 taxa) and 273 genera with only one species in Cerrado. Determination of frequencies and the database website (http://cyto.shinyapps.io/cerrado) were developed in R. Studies were pooled by employed technique and decade, showing a rise in non-conventional cytogenetics since 2000. However, C-value estimation, heterochromatin staining and molecular cytogenetics are still not common for any family. For the richest and best sampled families, the following modal 2n counts were observed: Oxalidaceae 2n = 12, Lythraceae 2n = 30, Sapindaceae 2n = 24, Solanaceae 2n = 24, Cyperaceae 2n = 10, Poaceae 2n = 20, Asteraceae 2n = 18 and Fabaceae 2n = 26. Chromosome number information is available for only 16.1% of species, while there are genome size data for only 1.25%, being lower than the global percentages. In general, genome sizes were small, ranging from 2C = ca. 1.5 to ca. 3.5 pg. Intra-specific 2n number variation and higher 2n counts were mainly related to polyploidy, which relates to the prevalence of even haploid numbers above the mode of 2n in most major plant clades. Several orphan genera with almost no cytogenetic studies for Cerrado were identified. This effort represents a complete diagnosis for cytogenetic attributes of plants of Cerrado.
La protección del patrimonio natural del Ecuador representa un reto
para todos, especialmente si se considera que la desaparición de las
especies endémicas o restringidas exclusivamente al Ecuador implica
su extinción global. La información básica acerca de las especies,
los ecosistemas y su estado de conservación sigue siendo insuficiente
para cuantificar con precisión la magnitud de las amenazas a la
conservación de las especies. A nivel mundial, apenas se ha evaluado
el estado de conservación de 4% de las especies vegetales (Baillie et
al. 2004) un porcentaje bajo si se considera que las predicciones de
uso y abuso de las plantas en el futuro inmediato crecerán proporcionalmente
con la población humana. Según Schatz (2009) a fines
de siglo la población humana llegará a los nueve o diez billones de
habitantes y necesitará duplicar la producción de alimentos e incrementar
espacios para vivienda y usar más plantas silvestres para
alimento, combustible, construcción y medicina. Por eso, resulta urgente
disponer de información científica sistematizada para tomar
decisiones responsables sobre el manejo y protección de los ambientes
naturales. El Libro Rojo de las Plantas Endémicas del Ecuador
busca contribuir a este propósito.
Según la Unión Internacional para la Conservación de la Naturaleza
(UICN) hasta el año 2000 solamente se habían asignado categorías
de amenaza a 461 especies de plantas endémicas del
Ecuador. En el año 2000 se publicó la primera edición del “Libro
Rojo de las Plantas Endémicas del Ecuador” (Valencia et al. 2000),
en el cual se analizó el estado de conservación de 4011 especies
endémicas del país. En esta segunda edición, en base a información
actualizada sobre la distribución y la taxonomía de las especies,
se evalúa el estado de conservación de 4500 especies de
plantas endémicas y se asigna una categoría de amenaza a cada
una de ellas según los mismos parámetros usados en Valencia
et al. (2000) (UICN Categorías y criterios utilizados para la Lista Roja
versión 3.1 disponible en: http://www.iucnredlist.org/technicaldocuments/
categories-and-criteria/2001-categories-criteria.)
La presente edición de este libro es un trabajo de colaboración entre
botánicos e instituciones donde se guardan colecciones de plantas
ecuatorianas. El Herbario QCA de la Pontificia Universidad Católica
del Ecuador, lideró este proyecto en el cual participaron las siguientes
instituciones: Herbario de Loja (LOJA), Herbario Nacional
del Museo Ecuatoriano de Ciencias Naturales (QCNE), Herbario del
Padre Luis Sodiro S.J. (QPLS), así como los herbarios del Missouri
Botanical Garden (MO), Aarhus University (AAU), Universidad de
Göttingen (GOET) y muchas otras donde residen nuestros más de
80 colaboradores. En la presente edición, al inicio de cada familia, se
describen los cambios observados en estos últimos diez años. En los
capítulos introductorios también se incluyen perspectivas generales
de conservación de los sistemas terrestres del Ecuador y de cada
región natural del país.
We present revised estimates of the numbers of accepted species of flowering plants (369,434), seed plants (370,492), vascular plants (383,671) and land plants (403,911) based on a recently de-duplicated version of the International Plant Names Index and rates of synonymy calculated from the seed plant families published in the World checklist of selected plant families. Alternative approaches to estimating or calculating the number of accepted plant species are discussed and differences between results are highlighted and interpreted.
El endemismo es uno de los principales aspectos que trata la biogeografía histórica y es uno de los criterios más importantes
para establecer las prioridades de conservación de las especies. En el mundo, más del 90% de las plantas que se encuentra
en alguna categoría de amenaza son endémicas de un sólo país. En Chile, un 45% de las especies de plantas vasculares
son endémicas. Actualmente este número incluye 83 géneros y 4 familias endémicas del país; éstos son valores elevados
en comparación con el resto de Latinoamérica. Sin embargo, la alta tasa de cambios producidos por los estudios de
sistemática molecular en la taxonomía ha generado modificaciones en estos números. Este trabajo pretende discutir
dichas modificaciones y así contribuir a la correcta delimitación de estos géneros endémicos. Utilizando bases de datos y
bibliografía actualizadas, se llevó a cabo una revisión exhaustiva sobre estos géneros. Se sustrajeron de la lista aquellos
géneros con registros fuera del país y aquellos que cuentan con evidencia suficiente para cambiar su estatus taxonómico. Se
entrega una revisión crítica de la bibliografía sistemática respecto de los géneros en cuestión, discutiendo principalmente
aquellos que a la luz de la literatura presentaron ambigüedades en su clasificación.
Assuming that the landscape physiographic characteristics strongly determine the occurrence of land use and land cover types, this study assessed the distribution patterns of natural and converted classes in relation to the major geomorphological units and slope ranges in the central area of continuous savanna formations in Brazil (Cerrado biome), the country’s most important region for cattle ranching and intensive commodity crops. Our results showed that 93% of the agriculture activities are concentrated at slopes of less than 5°, mostly associated to old regional planation surfaces (RPSs). Considering the amount of remnant vegetation and the occupation and land use deterministic trends, we estimated that between 58,041 km2 and 79,677 km2 of conversions may occur in the near future. If the priority areas for biodiversity conservation are properly enforced and effectively incorporated into the system of fully protected areas and areas of sustainable use, a decrease of approximately 24% in the expected potential deforestation could be achieved.
A large portion of the Occidental Region of Paraguay consists of a semi-arid territory with vegetation adapted to the features of this region. For just over a decade, a process of intense deforestation has resulted from the expansion of mechanized farming, carried out without any form of land management or planning; this has led to the fragmentation of the forests in this region. This study has taken satellite imagery from 1975, 1990, 2000 and 2007 with the purpose of determining the average size of the fragments and the rate of forest discontinuity; the results of this multi-temporal imagery analysis show that (a) in some areas of the Central Chaco, the forest matrix was transformed principally into cropped areas; (b) the majority of the fragments are isolated from one other; and (c) the areas mostly covered by forests are in the north-northeastern and northwestern areas and this is mainly as a result of a greater concentration of protected areas. In conclusion, the vulnerability of the vegetation formations increases with the fragmentation process, to which we should add an increased frequency of fires, a reduced resilience and homeostasis of the vegetation formations; thus these are highly exposed to climate change factors. It is imperative that the forest landscapes be restored, through the implementation biological corridors, to ensure the continuity of the remaining forests.
Acevedo-Rodríguez,
Pedro and Strong, Mark T. Catalogue of Seed Plants of the West Indies. Smithsonian
Contributions to Botany, number 98, xxv + 1192 pages, 3 maps, 4 tables, 2012.—The catalogue enumerates
all taxa of Gymnosperms, Dicotyledons, and Monocotyledons occurring in the West Indies archipelago
excluding the islands off the coast of Venezuela (Netherlands Antilles, Venezuelan Antilles, Tobago, and
Trinidad). For each accepted taxon, nomenclature (including synonyms described from the West Indies and
their references to publication), distribution in the West Indies (including endemic, native, or exotic status),
common names, and a numerical listing of literature records are given. Type specimen citations are provided
for accepted names and synonyms of Cyperaceae, Sapindaceae, and some selected genera in several families
including the Apocynaceae (Plumeria), Aquifoliaceae (Ilex), and Santalaceae (Dendrophthora). More than
30,000 names were treated comprising 208 families, 2,033 genera, and 12,279 taxa, which includes exotic
and commonly cultivated plants. The total number of indigenous taxa was approximately 10,470 of which
71% (7,446 taxa) are endemic to the archipelago or part of it. Fifteen new names, 37 combinations, and 7
lectotypifications are validated. A searchable website of this catalogue, maintained and continuously updated
at the Smithsonian Institution, is available at http://botany.si.edu/antilles/WestIndies/.
Chromosome evolution has been demonstrated to have profound effects on diversification rates and speciation in angiosperms. While polyploidy has predated some major radiations in plants, it has also been related to decreased diversification rates. There has been comparatively little attention to the evolutionary role of gains and losses of single chromosomes, which may or not entail changes in the DNA content (then called aneuploidy or dysploidy, respectively). In this study we investigate the role of chromosome number transitions and of possible associated genome size changes in angiosperm evolution. We model the tempo and mode of chromosome number evolution and its possible correlation with patterns of cladogenesis in 15 angiosperm clades. Inferred polyploid transitions are distributed more frequently towards recent times than single chromosome gains and losses. This is likely because the latter events do not entail changes in DNA content and are probably due to fission or fusion events (dysploidy), as revealed by an analysis of the relationship between genome size and chromosome number. Our results support the general pattern that recently originated polyploids fail to persist, and suggest that dysploidy may have comparatively longer-term persistence than polyploidy. Changes in chromosome number associated with dysploidy were typically observed across the phylogenies based on a chi-square analysis, consistent with these changes being neutral with respect to diversification.
The Cyperaceae are well known for having a large amount of variation in chromosome numbers both within and among genera. Most
of this variation has been previously attributed to agmatoploid or qualitative aneuploid chromosome number change. To date
there have been 4,231 reported chromosome number counts in the family. Despite the large number of counts made, they only
represent approximately 16% of the species currently recognized. These counts are here presented in an indexed list with standardized
nomenclature following a draft copy of the World Checklist of Cyperaceae. Additionally, I explore variation within genera
where a significant number of counts have been made. Given the distributions of counts within genera there is evidence for
both agmatoploid and polyploid chromosome number changes.
In Myrtaceae, reports regarding the nuclear DNA content are scarce. The aim of this study is to present genome size data for
fleshy-fruited Myrteae, and to test their relation with chromosome number and ploidy, the available data for cytoevolutionary
studies in Myrtaceae. Thirty species out of ten genera were investigated for chromosome number and genome size using flow
cytometry. Twenty-eight species were diploid with 2n=2x=22 and two species were tetraploid with 2n=4x=44. All genome sizes measured are new. Among the diploid species, a gradual and small variation in 2C-values (0.486pg in Gomidesia schaueriana to 0.636pg in Eugenia multicostata) was observed, whereas the tetraploid genomes of Psidium acutangulum and P. cattleianum had about twice as much DNA (1.053 and 1.167pg, respectively). The total interspecific variation of C-values was 2.45-fold. The fleshy-fruited Myrteae have smaller holoploid genomes than the capsular-fruited Eucalypteae and
Melaleuceae.
Chromosome numbers have been obtained for 39 populations of vascular plants from Paraguay belonging to 33 species grouped in 23 families. Chromosome studies for 13 species is reported for the first time. The data obtained about five other species differ from previous chromosome counts. Some of the numbers are of interest because they relate to endemic or rare species or because they provide data of special evolutionary significance. Noteworthy findings include Angelonia gardneri (n = 10), Angelonia integerrima (2n = 20), Asclepias mellodora (2n = 22), Aspilia montevidensis var. setosa (n = 34), Calea uniflora (n = 16), Dolichopsis paraguariensis (2n = 22, n = 11), Heteropteris glabra (2n = 31), Hibiscus striatus (In = 52), Lupinus paraguariensis (2n = 18), Microlobius foetidus (2n = 26), Myrsine guianensis (2n = 48), Thevetia bicornuta (n = 10), Tibouchina gracilis (n = 12) and Vitex cymosa (n = 16).
The relative importance of local ecological and larger-scale historical processes in causing differences in species richness across the globe remains keenly debated. To gain insight into these questions, we investigated the assembly of plant diversity in the Cerrado in South America, the world's most species-rich tropical savanna. Time-calibrated phylogenies suggest that Cerrado lineages started to diversify less than 10 Mya, with most lineages diversifying at 4 Mya or less, coinciding with the rise to dominance of flammable C4 grasses and expansion of the savanna biome worldwide. These plant phylogenies show that Cerrado lineages are strongly associated with adaptations to fire and have sister groups in largely fire-free nearby wet forest, seasonally dry forest, subtropical grassland, or wetland vegetation. These findings imply that the Cerrado formed in situ via recent and frequent adaptive shifts to resist fire, rather than via dispersal of lineages already adapted to fire. The location of the Cerrado surrounded by a diverse array of species-rich biomes, and the apparently modest adaptive barrier posed by fire, are likely to have contributed to its striking species richness. These findings add to growing evidence that the origins and historical assembly of species-rich biomes have been idiosyncratic, driven in large part by unique features of regional- and continental-scale geohistory and that different historical processes can lead to similar levels of modern species richness.
Since its discovery in 1907, polyploidy has been recognized as an important phenomenon in vascular plants, and several lines of evidence indicate that most, if not all, plant species ultimately have a polyploid ancestry. However, previous estimates of the frequency of polyploid speciation suggest that the formation and establishment of neopolyploid species is rare. By combining information from the botanical community's vast cytogenetic and phylogenetic databases, we establish that 15% of angiosperm and 31% of fern speciation events are accompanied by ploidy increase. These frequency estimates are higher by a factor of four than earlier estimates and lead to a standing incidence of polyploid species within genera of 35% (n = 1,506). Despite this high incidence, we find no direct evidence that polyploid lines, once established, enjoy greater net species diversification. Thus, the widespread occurrence of polyploid taxa appears to result from the substantial contribution of polyploidy to cladogenesis, but not from subsequent increases in diversification rates of polyploid lines.
Chilean Plants Cytogenetic Database (CPCD) is a resource available online in electronic format, providing a cytogenetics catalog for continental and insular Chilean plants that are representative of the floras of the Southern Cone. In the last update carried out in 2021, we increased the cytogenetic data for 499 Chilean native species, and from here on we will include a new section with chromosome number data for 683 exotic species classified as invaders in Chile. Aspects on the coverage, features, and uses of the CPCD are presented here, including background information accumulated since its inception in 2010 to the present. With the new update, the database currently stores cytogenetic information for species belonging to the divisions Bryophyta, Pteridophyta, Pinophyta, and Magnoliophyta, thus contributing to the largest community resource on plant cytogenetics in the world.
The energetic requirements of the Brazilian gypsum industry are mainly provided by firewood transported by road. The cost of transporting firewood is greatly affected by the stacking factor. In this study, we determined how the stacking factor for trailer trucks varied for the firewood harvested from forest species in the Caatinga biome, Brazil. For this purpose, the following steps were carried out: i) the logs were stacked in a frame (volume, 1 stere) and weighed; ii) the solid over bark volume of each log was obtained by scanning and by xylometry (immersion in water); iii) the stacked volume of logs on the truck was measured; and iv) the stacking factor, the stacking density and the apparent density of the unpeeled wood were computed for each of 60 truck trips. The stacking factor was, on average, 1.12. This value is lower than reported for other species; the greater compaction of the timber represents an advantage in terms of transport costs. However, the maximum variation in the load weight was 20%, which is not negligible from an economic point of view because of the associated loss of energy efficiency in the supply chain for the lowest volume loads.
The cotton‐melon aphid Aphis gossypii Glover is a sap‐sucking insect that is considered a serious global pest. The species is distributed over a large geographical range and uses a wide variety of hosts, with some populations having specialized to attack different plant species. Here, we provide de novo chromosome level genome assemblies of a cotton specialist population (Hap1) and a cucurbit specialist population (Hap3). We achieved this by using a combination of third‐generation sequencing platforms, namely Illumina and Hi‐C sequencing technologies. We were able to anchor a total of 334.89 Mb (scaffold N50 of 89.13 Mb) and 359.95 Mb (scaffold N50 of 68.88 Mb) to 4 chromosomes for Hap1 and Hap3, respectively. Moreover, our results showed that the X‐chromosome of Hap3 (113.01 Mb) was significantly longer than that of Hap1 (100.26 Mb), with a high level of sequence conservation between the aphid species. We also report variation in the number of protein‐coding genes and repeat sequences between Hap1 and Hap3. In particular, olfactory and gustatory receptor genes underwent a high level of gene duplication and expansion events in A. gossypii, including between Hap1 and Hap3. Moreover, we identified two glutathione S‐transferase genes which underwent single gene duplications in Hap3, and tandem duplication and inversion events affecting the cytochrome P450 monooxygenase between Hap1 and Hap3, all of which including the CYP3 family. Our results illustrate the variance in the genomic composition of two specialized A. gossypii species and provide a helpful resource for the study of aphid population evolution, host adaption and insecticide resistance.
Changes in chromosome number as a result of fission and fusion in holocentric chromosomes 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 that evolve almost exclusively by fission and fusion. The genus exhibits a phenomenal range in chromosome number (2n =10–132). 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 for 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 to 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.
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Chromosome number and genome variation in flowering plants has stimulated a blossoming number of speculations about the ancestral chromosome number of angiosperms, but estimates so far remain equivocal.
We used a probabilistic approach to model haploid chromosome number (n) changes along a phylogeny embracing more than 10 thousands taxa, to reconstruct the ancestral chromosome number of the common ancestor of extant angiosperms and the most recent common ancestor for single angiosperm families. Independently, we carried out an analysis of 1C genome size evolution, including over 5 thousands taxa.
Our inferences revealed an ancestral haploid chromosome number for angiosperms n = 7, a diploid status, and an ancestral 1C = 1.73 pg. For 160 families, inferred ancestral n are provided for the first time.
Both descending dysploidy and polyploidy played crucial roles in chromosome number evolution. While descending dysploidy is equally distributed early and late across the phylogeny, polyploidy is detected mainly towards the tips. Similarly, also 1C genome size significantly increases (or decreases) in late‐branching lineages. Therefore, no evidence exists for a clear link between ancestral chromosome numbers and ancient polyploidization events, suggesting that further insights are needed to elucidate the organization of genome packaging into chromosomes.
The Species Plantarum Programme: Flora of the World (SPPFW) has been in existence for slightly more than two decades and during this time published basic taxonomic information for just over 1000 species, in 11 families. While an admirable initiative, at this pace it will take about 350 years to reach completion. At the 10th Conference of the Parties of the Convention on Biological Diversity (CBD), which was held in Nagoya, Japan, in October 2010, the Global Strategy for Plant Conservation (GSPC) was updated for the period up to 2020 (the first phase of the GSPC had been adopted in 2002). The first target of the Strategy aims to produce an online flora for all known plants of the world by 2020, in about three years therefore. Governments that are parties to the CBD are due to report over the next few years on progress with achieving all of the 16 GSPC targets, including this challenging first target. While many individual countries have initiatives to prepare online digital floras of their own territory, it is recognized that the achievement of the World Flora target relies on the achievement of an international initiative, rather than having e-floras for each country. For that reason, in 2012 an international project was launched, which was welcomed by the CBD, to take forward this initiative. A World Flora Online (WFO) Consortium was subsequently established, now including 38 organizations and institutions worldwide, to take forward the achievement of this target. Although the SPPFW and WFO may be deemed to have similar objectives, the timeframe available to produce e-floras for countries that are parties to the CBD, and by implication for the world, will mean that conducting original monographic work toward refining and improving existing classifications will in many instances have to be either curtailed or brought to a swift conclusion. Without the necessary global support and funding, the slow progress of the SPPFW has clearly illustrated that producing a WFO is a very ambitious target to reach in less than a decade. Governments, plant taxonomists, botanical institutions, funding agencies, global initiatives, and stakeholders have not pooled resources to make a revision-driven World Flora—the SPPFW—a reality. Target 1 of the 2020 GSPC will, of necessity not be met through exclusively original work, but instead will need to rely on the synthesis of existing information, while identifying and attempting to fill significant taxonomic and geographical gaps. The implications for the SPPFW, as countries work toward achieving Target 1 of the GSPC, are discussed.
Part I: Geobotanical scenario.- The extravagant physical geography of Chile.- Getting geobotanical knowledge.- Part II: Chorology of Chilean Plants.- Geographical relations of the Chilean flora.- Biogeographic regionalization.- Part III: Islands biogeography.- Pacific offshore islands.- Islands on the continent.- Part IV: Case studies on selected families.- Cactaceae, a weird family and postmodern evolution.- The richest family: Chilean Asteraceae.- Nothofagus, key genus in plant geography.- Part V: Where to from here? Projections of Chilean plant geography.- All the possible worlds of biogeography.- Epilogue.- Index.
The Upper Parana Atlantic Forest (BAAPA) in Paraguay is one of the most threatened tropical forests in the
world. Relentless agricultural encroachment has left less than 10% of its original cover intact. Many
strategies and programs have been initiated, such as Payment for Ecosystem Services (PES) schemes,
to halt forest cover loss. While the approach of ecosystem services (ES) has been continuously applied
by policy makers, it has not been perceived strongly by the direct users of the forest. This study provides
a comprehensive understanding on how landowners in the BAAPA perceive and benefits from ES derived
from the forest and examines the influence of farmers on forest conservation. The results were obtained
from an extensive household survey performed in the BAAPA region. An understanding of the high ecological
value of the forest is common to all farmers. A strong dependency on forest-related products was
observed for small and medium landowners whereas large-scale farmers considered the forest’s main
value to be mostly recreational and cultural. PES appears to be well accepted by forest owners, but it must
receive stronger promotion. Understanding the importance of ecosystem services is a valuable contribution
toward to conserving natural resources.
Available online resources for animal and plant chromosome number databases are surveyed and briefly discussed
Nuclear DNA content (2C-value), estimated through flow cytometry using propidium iodide (PI), was shown to vary from 36.5 pg to 78.9 pg among 29 accessions of 12 Alstroemeria species (2 n =2 x =16). The extremes were found in A. magnifica ssp. magnifica and in A. ligtu ssp. simsii , both belonging to the Chilean species group. The four Brazilian species exhibited less variation in nuclear DNA content (49.8–56.4 pg), than the eight Chilean species (36.5–78.9 pg). Nuclear DNA content was positively correlated ( r =0.92, n =7, P <0.01) with the total chromosome length. It was also positively correlated ( r =0.85, n =5, P <0.01) with the length of C-bands, when only the Chilean species were considered. When both karyotype parameters, length of non-C-banded chromosome regions (x) and length of C-bands (y) were determined, it was possible to predict the nuclear DNA content (z) with the formula z=0.65 x +1.31y-0.45 ( R² =0.97, P =0.004).
The DAPI fluorescence of most accessions was proportional to the PI fluorescence ( r =0.98, P <0.001), except for one accession of A. ligtu , that had a relatively high PI/DAPI ratio (1.88). The PI/DAPI ratios of the Brazilian species were lower (1.59–1.67) than those of the Chilean species (1.68–1.88), which might reflect a difference in base pair composition. Four groups of species could be distinguished on the basis of fluorescence values. Diploid interspecific hybrids were shown to have a DNA content intermediate to the values of the parents involved. Both the PI and the DAPI fluorescence values of these hybrids approximated the mid parent values. Tetraploids, derived from selfing of diploids, had PI and DAPI fluorescence values that were twice that of the diploid hybrids. It was possible to distinguish aneuploids from euploids based on fluorescence values.
Detailed comparative karyotype analyses have proved to be an important tool for taxonomy and for understanding chromosome evolution. The basic principle of cytotaxonomy is that closely related species share a more similar karyotype than less related ones. However, phylogenetic studies have demonstrated that some karyotype features are more often recurrent than previously thought, meaning that similarity is not all. Two other criticisms to the cytotaxonomical interpretation are intraspecific variation, traditionally neglected, and the interpretation of chromosomal alterations based only on classical structural changes, without any investigative support. Chromosome numbers and nuclear DNA content are among the most reliable and practical characters for cytotaxonomical analyses involving a large number of species, whereas chromosome mapping with molecular probes is more recommended for a restricted number of species. In both cases, a robust phylogenetic tree is necessary to understand the relationships between species and their karyotype evolution. Evolutionary inferences based only on putative karyological trends are no longer sustainable.
Current Chilean vascular flora and its biogeographical patterns are strongly related to the geographical features of the territory,
past and present. Main characteristics of the physical geography of Chile are described, with emphasis on the geologic and
climatic changes that affected the biome configuration since the Devonian onwards. Approaching the present time, the effects
of the Pleistocene glaciations in the distribution of several communities are discussed.
The amount of DNA varies widely in 20 shrubby Oxalis species analyzed, ranging from 1.76 pg in O. alstonii to 33.00 pg in O. dispar. This wide variation in DNA content coincided with a wide variation in chromosome size and shape. Numerical taxonomy methods showed that this variation in chromosome size and shape in shrubby Oxalis is mainly due to extra DNA. It was also possible to arrange the 20 species examined in six different groups on the basis of karyotypic similarities.Key words: Oxalis, DNA content, chromosome evolution, multivariate analysis.
Cytological observations on eleven species of Ophioglossum revealed low gametic (n) chromosome numbers of 30, 34 and 60 in populations of O.eliminatum, contrasting with an earlier report of n= 90 in the same species. The rest of the species is based on n=120.Cytologically studied species of Ophioglossum exhibit a range of chromosome numbers from n = 30 in O.eliminatum to n=720 in O.reticulatum. The weighted highest common factor (HGF) from all the reported chromosome numbers in twelve species was found to be 30. This number is proposed as the palaeobasic chromosome number for the genuS. Reported chromosome numbers which are not multiples of 30 were subjected to sequential analysis, yielding three distinct ultimate base numbers, 4, 5 and 6, which can produce n= 30 in seven different ways. The neobasic number, n= 120, appears to have arisen through various combinations and permutations of these, theoretically 2401 routes; only a relatively few of these routes exist today, suggesting that extreme selection has been exerted against the majority, and further suggesting that Ophioglossum represents an evolutionary dead end through repeated cycles of polyploidy and is possibly at the verge of extinction. The stoichiometric model of evolution, which derives the various chromosome numbers possessed by the twelve species from the basic and ultimate basic chromosome numbers, is used to explain chromosomal evolution in the genus.
The Cerrado is one of the world's biodiversity hotspots. In the last 35 years, more than 50% of its approximately 2 million km² has been transformed into pasture and agricultural lands planted in cash crops. The Cerrado has the richest flora among the world's savannas (>7000 species) and high levels of endemism. Species richness of birds, fishes, reptiles, amphibians, and insects is equally high, whereas mammal diversity is relatively low. Deforestation rates have been higher in the Cerrado than in the Amazon rainforest, and conservation efforts have been modest: only 2.2% of its area is under legal protection. Numerous animal and plant species are threatened with extinction, and an estimated 20% of threatened and endemic species do not occur in protected areas. Soil erosion, the degradation of the diverse Cerrado vegetation formations, and the spread of exotic grasses are widespread and major threats. The use of fire for clearing land and to encourage new growth for pasture has also caused damage, even though the Cerrado is a fire-adapted ecosystem. Ecosystem experiments and modeling show that change in land cover is altering the hydrology and affecting carbon stocks and fluxes. Cerrado agriculture is lucrative, and agricultural expansion is expected to continue, requiring improvements in and extension of the transportation infrastructure, which will affect not only the Cerrado but also the Amazon forest. Large-scale landscape modification and threats to numerous species have led to renewed interest from various sectors in promoting the conservation of the Cerrado, particularly through strengthening and enlarging the system of protected areas and improving farming practices and thus the livelihoods of local communities.
The sedge family (Cyperaceae: Poales; ca. 5600 spp.) is a hyperdiverse cosmopolitan group with centres of species diversity in Africa, Australia, eastern Asia, North America, and the Neotropics. Carex, with ca. 40% of the species in the family, is one of the most species-rich angiosperm genera and the most diverse in temperate regions of the Northern Hemisphere, making it atypical among plants in that it inverts the latitudinal gradient of species richness. Moreover, Carex exhibits high rates of chromosome rearrangement via fission, fusion, and translocation, which distinguishes it from the rest of the Cyperaceae. Here, we use a phylogenetic framework to examine how the onset of contemporary temperate climates and the processes of chromosome evolution have influenced the diversification dynamics of Carex. We provide estimates of diversification rates and map chromosome transitions across the evolutionary history of the main four clades of Carex. We demonstrate that Carex underwent a shift in diversification rates sometime between the Late Eocene and the Oligocene, during a global cooling period, which fits with a transition in diploid chromosome number. We suggest that adaptive radiation to novel temperate climates, aided by a shift in the mode of chromosome evolution, may explain the large-scale radiation of Carex and its latitudinal pattern of species richness.