Main conclusion
Cytogenomic characterization of
Erythrostemon hughesii
reveals a heterogeneity of repeats in its subtelomeric heterochromatin. Comparative analyses with other Caesalpinia group ...species reveal a significant reduction in the abundance of
Ty3-gypsy
/Chromovirus Tekay retrotransposons during its evolution.
In numerically stable karyotypes, repetitive DNA variability is one of the main causes of genome and chromosome variation and evolution. Species from the Caesalpinia group (Leguminosae) are karyotypically characterized by 2
n
= 24, with small chromosomes and highly variable CMA
+
heterochromatin banding patterns that correlate with environmental variables.
Erythrostemon hughesii
differs from other species of the group examined to date for having subtelomeric CMA
+
bands; this contrasts with most species in the group which have proximal bands. Here we analyse the repeatome of
E. hughesii
using genome skimming and chromosomal mapping approaches to characterize the identity of the most abundant repetitive elements and their physical location. The repetitive fraction of
E. hughesii
comprises 28.73% of the genome. The most abundant elements were retrotransposons (RT) with long terminal repeats (LTR-RT; 9.76%) and satellite DNAs (7.83%). Within the LTR-RTs, the most abundant lineages were:
Ty1
/c
opia
-Ale (1%),
Ty3
/g
ypsy
CRM (0.88%) and
Ty3
/g
ypsy
Athila (0.75%). Using fluorescent in situ hybridization four satellite DNAs and several LTR-RT elements were shown to be present in most subtelomeric CMA
+
bands. These results highlight how the repeatome in
E. hughesii
, a species from Oaxaca state in Mexico, is clearly distinct from Northeast Brazilian species of the Caesalpinia group, mainly due to its high diversity of repeats in its subtelomeric heterochromatic bands and low amount of LTR-RT
Ty3
/gypsy
-Tekay elements. Comparative sequence analysis of Tekay elements from different species is congruent with a clade-specific origin of this LTR-RT after the divergence of the Caesalpinia group. We hypothesize that repeat-rich heterochromatin may play a role in leading to faster genomic divergence between individuals, increasing speciation and diversification.
Main conclusion
The chloroplast genomes of Caesalpinia group species are structurally conserved, but sequence level variation is useful for both phylogenomic and population genetic analyses.
...Variation in chloroplast genomes (plastomes) has been an important source of information in plant biology. The Caesalpinia group has been used as a model in studies correlating ecological and genomic variables, yet its intergeneric and infrageneric relationships are not fully solved, despite densely sampled phylogenies including nuclear and plastid loci by Sanger sequencing. Here, we present the de novo assembly and characterization of plastomes from 13 species from the Caesalpinia group belonging to eight genera. A comparative analysis was carried out with 13 other plastomes previously available, totalizing 26 plastomes and representing 15 of the 26 known Caesalpinia group genera. All plastomes showed a conserved quadripartite structure and gene repertoire, except for the loss of four
ndh
genes in
Erythrostemon gilliesii
. Thirty polymorphic regions were identified for inter- or intrageneric analyses. The 26 aligned plastomes were used for phylogenetic reconstruction, revealing a well-resolved topology, and dividing the Caesalpinia group into two fully supported clades. Sixteen microsatellite (cpSSR) loci were selected from
Cenostigma microphyllum
for primer development and at least two were cross-amplified in different Leguminosae subfamilies by in vitro or in silico approaches. Four loci were used to assess the genetic diversity of
C. microphyllum
in the Brazilian Caatinga. Our results demonstrate the structural conservation of plastomes in the Caesalpinia group, offering insights into its systematics and evolution, and provides new genomic tools for future phylogenetic, population genetics, and phylogeographic studies.
The pantropical Caesalpinia group includes 225 species in 27 monophyletic genera, and the group has undergone recent phylogenetic, taxonomic and biogeographic revisions. Previous works have reported ...a diverse pattern of heterochromatin distribution related to ecological niche/geographic distribution, and variation in genome size also correlated with environmental variables. In order to investigate the relationship between cytogenetic and ecological traits using the Caesalpinia group as a model, new cytomolecular data (chromosome number and morphology, CMA/DAPI staining and number and position of 5S and 35S rDNA sites) for 14 species in six genera were generated. These data were analysed by phylogenetic comparative methods. All species studied have 2
n
= 24 (16 M/SM + 8A), and most of them just have one pair of 5S rDNA sites and two to five pairs of 35S rDNA sites. Three heterochromatic patterns were observed on the chromosomes: (i) proximal CMA
+
/DAPI
−
bands, (ii) proximal CMA
0
/DAPI
−
bands and (iii) proximal CMA
0
/DAPI
0
bands. The “
Coulteria
+
Tara”
and “
Arquita
+
Balsamocarpon
+
Erythrostemon
+
Pomaria”
clades (except for
E. gilliesii
,
E. hughesii
and
E. mexicanus
) independently showed CMA
0
/DAPI
−
bands associated with larger genomes and geographic distributions at higher latitudes. We statistically demonstrate that heterochromatin (CMA/DAPI intensity along the chromosome), genome size and latitude are autocorrelated in the Caesalpinia group. On the other hand, we found a non-significant correlation between genome size and amount of heterochromatin. We argue that environmental factors associated with different latitude may have played a role in contributing to the diversification of the heterochromatin in Caesalpinia group.
The Caesalpinia group is a large pantropical clade of ca. 205 species in subfamily Caesalpinioideae (Leguminosae) in which generic delimitation has been in a state of considerable flux. Here we ...present new phylogenetic analyses based on five plastid and one nuclear ribosomal marker, with dense taxon sampling including 172 (84%) of the species and representatives of all previously described genera in the Caesalpinia group. These analyses show that the current classification of the Caesalpinia group into 21 genera needs to be revised. Several genera (
,
,
and
sensu Lewis, 2005) are non-monophyletic and several previously unclassified Asian species segregate into clades that merit recognition at generic rank. In addition, the near-completeness of our taxon sampling identifies three species that do not belong in any of the main clades and these are recognised as new monospecific genera. A new generic classification of the Caesalpinia group is presented including a key for the identification of genera, full generic descriptions, illustrations (drawings and photo plates of all genera), and (for most genera) the nomenclatural transfer of species to their correct genus. We recognise 26 genera, with reinstatement of two previously described genera (
Tod.,
R. Vig.), re-delimitation and expansion of several others (
,
,
and
), contraction of
s.s. and description of four new ones (
,
,
and
), and make 75 new nomenclatural combinations in this new generic system.
The evolution of geophytes in response to different environmental stressors is poorly understood largely due to the great morphological variation in underground plant organs, which includes species ...with rhizomatous structures or underground storage organs (USOs). Here we compare the evolution and ecological niche patterns of different geophytic organs in
Solanum
L., classified based on a functional definition and using a clade-based approach with an expert-verified specimen occurrence dataset. Results from PERMANOVA and Phylogenetic ANOVAs indicate that geophytic species occupy drier areas, with rhizomatous species found in the hottest areas whereas species with USOs are restricted to cooler areas in the montane tropics. In addition, rhizomatous species appear to be adapted to fire-driven disturbance, in contrast to species with USOs that appear to be adapted to prolonged climatic disturbance such as unfavorable growing conditions due to drought and cold. We also show that the evolution of rhizome-like structures leads to changes in the relationship between range size and niche breadth. Ancestral state reconstruction shows that in
Solanum
rhizomatous species are evolutionarily more labile compared to species with USOs. Our results suggest that underground organs enable plants to shift their niches towards distinct extreme environmental conditions and have different evolutionary constraints.
A recent molecular phylogenetic analysis of the Caesalpinia group demonstrated that it comprises 26 genera, but the recognition of a putative 27
genus,
, remained in doubt. This study presents a ...phylogenetic analysis of ITS and five plastid loci revealing a robustly supported monophyletic group representing the Ticanto clade, sister to the morphologically distinct genus
. Based upon this evidence, along with a morphological evaluation, the genus
is here reinstated. Descriptions are provided for all nine species of
, together with a key to the species, maps, and colour photographs. Nine new combinations are made:
(Hand.-Mazz.) R. Clark & Gagnon,
(L.) R. Clark & Gagnon,
(S. J. Li, Z. Y. Chen & D. X. Zhang) R. Clark & Gagnon,
(Metcalf) R. Clark & Gagnon,
R. Clark & Gagnon,
(Hemsl.) R. Clark & Gagnon,
(Craib) R. Clark & Gagnon,
(Champion ex Benth.) R. Clark & Gagnon and
(S. J. Li, D. X. Zhang & Z.Y. Chen) R. Clark & Gagnon. The final major question in the delimitation of segregate genera from within
and the Caesalpinia group is thus resolved.
Numerous studies have identified low copy nuclear genes (LCNG) with phylogenetic potential throughout angiosperms, several specifically focused on Leguminosae. However, phylogenetic resolution at the ...species- to subspecies-level is often inferred based only on a small subset of taxa scattered throughout the higher level study group. This study aims to reassess the phylogenetic resolution of 19 previously published nuclear regions in Leguminosae using 18 species from two clades of the Caesalpinieae representing both distantly related genera and closely related species. Nuclear regions were amplified and aligned throughout the sampled taxa. Sequences were cloned when polymorphism was noted. The plastid loci matK, rps16, trnL, trnD–trnT and the nuclear ribosomal ITS regions were also analyzed for comparison. Phylogenetic analyses using parsimony were performed on individual matrices. Three nuclear regions were eliminated due to the non-specificity of the primers (RNAH, PTSB, GI). Four regions showed lower resolution than predicted from previous studies (MMK1, CYB6, RBPCO, EFGC), while three revealed greater resolution than anticipated (SQD1, AT103, EIF3E). Three other markers indicated previously unidentified duplication events for the genus Caesalpinia s.l. (ATCP and AROB) and at the base of the Caesalpinia and Peltophorum clades (CALTL). Phylogenies reconstructed from the intron-spanning regions AIGP, SHMT, AT103 and EIF3E are congruent with ITS and plastid data and show the best phylogenetic potential for studies of closely related species of caesalpinioid legumes. We present a screening strategy for the evaluation of LCNG for phylogenetic studies.
•Four regions showed lower resolution than predicted from previous studies.•Three revealed greater resolution than anticipated.•Three markers indicated previously unidentified duplication events.•Four intron-spanning regions show the best phylogenetic potential in closely related species.•We propose a screening protocol for low-copy nuclear genes in phylogenetic studies.
While we have largely improved our understanding on what biomes are and their utility in global change ecology, conservation planning, and evolutionary biology is clear, there is no consensus on how ...biomes should be delimited or mapped. Existing methods emphasize different aspects of biomes, with different strengths and limitations. We introduce a novel approach to biome delimitation and mapping, based upon combining individual regionalizations derived from floristic, functional, and phylogenetic data linked to environmentally trained species distribution models. We define “core Biomes” as areas where independent regionalizations agree and “transition zones” as those whose biome identity is not corroborated by all analyses. We apply this approach to delimiting the neglected Caatinga seasonally dry tropical forest biome in northeast Brazil. We delimit the “core Caatinga” as a smaller and more climatically limited area than previous definitions, and argue it represents a floristically, functionally, and phylogenetically coherent unit within the driest parts of northeast Brazil. “Caatinga transition zones” represent a large and biologically important area, highlighting that ecological and evolutionary processes work across environmental gradients and that biomes are not categorical variables. We discuss the differences among individual regionalizations in an ecological and evolutionary context and the potential limitations and utility of individual and combined biome delimitations. Our integrated ecological and evolutionary definition of the Caatinga and associated transition zones are argued to best describe and map biologically meaningful biomes.
Societal Impact Statement
Herbaria can be considered plant libraries, each holding collections of dried specimens documenting plant diversity in space and time. For many plant species, these are our ...only evidence of their existence and the only means of assessing their conservation status. Specimens in all herbaria, especially those in small and often under‐resourced herbaria in megadiverse countries, are key to achieving accurate estimates of the conservation status of the world's plant species. They are also part of a country's shared heritage and critical contributions to knowledge of the world's diversity.
Summary
Internationally agreed targets to assess the conservation status of all plant species rely largely on digitised distribution data from specimens held in herbaria.
Using taxonomically curated databases of herbarium specimen data for the mega‐diverse genera Begonia (Begoniaceae) and Solanum (Solanaceae) occurring in Peru, we test the value added from including data from local herbaria and herbaria of different sizes on estimations of threat status using International Union for Conservation of Nature (IUCN) Red List criteria.
We find that the Global Biodiversity Information Facility (GBIF) has little data from Peruvian herbaria and adding these data influences the estimated threat status of these species, reducing the numbers of Critically Endangered and Vulnerable species in both genera. Similarly, adding data from small‐ and medium‐sized herbaria, whether in‐country or not, also improves the accuracy of threat assessments. Correction added on 08 September 2023, after first online publication: In the preceding sentence, “litter” has been corrected to “little” in this version.
A renewed focus on resourcing and recognising the contribution of small and in‐country herbaria is required if we are to meet internationally agreed targets for plant conservation. We discuss our case study in the broader context of democratising and increasing participation in global botanical science.
Los herbarios pueden considerarse bibliotecas de plantas, cada uno de los cuales contiene colecciones de ejemplares secos que documentan la diversidad de plantas en el espacio y el tiempo. Para muchas especies de plantas, estas son nuestra única evidencia de su existencia y el único medio para evaluar su estado de conservación. Ejemplares en todos los herbarios, especialmente aquellos en herbarios pequeños y con frecuencia de escasos recursos en países megadiversos, son clave para lograr estimaciones precisas del estado de conservación de las especies de plantas del mundo, tambien son parte del patrimonio compartido de un país y una contribución crítica al conocimiento de la diversidad del mundo.
Herbaria can be considered plant libraries, each holding collections of dried specimens documenting plant diversity in space and time. For many plant species, these are our only evidence of their existence and the only means of assessing their conservation status. Specimens in all herbaria, especially those in small and often under‐resourced herbaria in megadiverse countries, are key to achieving accurate estimates of the conservation status of the world's plant species. They are also part of a country's shared heritage and critical contributions to knowledge of the world's diversity.
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