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Phylogenetic relationships in the Didiereaceae with special reference to subfamily Portulacarioideae

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The Didiereaceae of the Caryophyllales contains 20 species in three subfamilies: Calyptrothecoideae (2 species from the dry parts of tropical north-east Africa), Didiereoideae (11 species from semi-arid areas in Madagascar) and Portulacarioideae (7 species, mainly from the arid south-western Africa). We performed Bayesian inference and maximum likelihood analyses on data from six plastid DNA regions, trnL-trnF, trnT-trnL, trnS-trnG, trnQ UUGrps16, rps16 and rpl16, for 19 species of the Didiereaceae. Our analyses corroborated the monophyly of the Didiereaceae and of its three subfamilies with high statistical support and also elucidated the relationships within the Portulacarioideae. The family has a very disjunct distribution in Madagascar, East Africa and southern Africa. After the divergence of Portulacaria afra, the Portulacarioideae mainly diversified around the margins of the hyper-arid Namib Desert and its greatest diversity of four species is found on the southern edge of the Namib. We show that the two genera of the Portulacarioideae, Ceraria and Portulacaria, are not monophyletic and we transfer the five accepted species of Ceraria to Portulacaria.
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
Bruyns & al.
• Phylogenetic relationships in the Didiereaceae
TAX O N

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


INTRODUCTION

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

Alluaudia  Alluaudiopsis
Decarya Didierea

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  




 
   
  





Didierea
Pereskia

  

Calyptrotheca
Ceraria Portulacaria 


Cera-
ria Portulacaria  
Calyptrotheca 
 

CalyptrothecaCeraria Portulacaria


Ceraria Portulacaria   
  

  
Calyptrotheca   



Ta linum
Calyptrotheca
Phylogenetic relationships in the Didiereaceae with special reference
to subfamily Portulacarioideae
Peter V. Bruyns,1 Mario Oliveira-Neto,2 Gladys Flavia Melo-de-Pinna2 & Cornelia Klak1
 Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Rondebosch 7701, South Africa
 Departamento de Botânica, Universidade de São Paulo, Caixa Postal 11461, CEP 05422-970, São Paulo, Brasil
 Peter V. Bruyns, peter.bruyns@uct.ac.za
DOI

Abstract

         

trnL-trnF trnT-trnL trnS-trnG trnQ

rp s16 rps16 r pl16

         
Portulacaria afra

Ceraria Portulacaria 
Ceraria Portulacaria.
Keywords

Supplementary Material



TAX O N

Bruyns & al.
• Phylogenetic relationships in the Didiereaceae
Version of Record (identical to print version).

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       
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 

Calyptrotheca
 
Cera riaPortulacaria

Calyp-
trotheca




 


    


Decarya 

 

Decarya
Alluaudia Didierea


Ceraria Portulacaria Cera-
riaP. nama-
quensis C. namaquensis

   Portulacaria
pygmaeaCeraria

Portulacaria

  
   




 Ceraria Portulacaria 

P. armiana
Ceraria



  
        
 





MATERIALS AND METHODS
Sampling of ingroup and outgroups. —


   Alluaudia comosa 
Didierea madagascariensis
Calyptrotheca 
Calyptrotheca somalen-
sis  trnL-trnFtrnT-trnL  rpl16 


        
AnacampserosPortulacaTal i n u m 




 

 
trnL-trnFtrnT-trnLrpl16 

trnQr ps16 trnS-trnG r ps16 

       


DNA extraction, amplification, sequencing and align-
ment. —


  



 

 trnS-trnG
 
trnQr ps16


   trnT-trnL
trnL-
trnFtrnL trnL-F
  
rps16
rpl16



Bruyns & al.
• Phylogenetic relationships in the Didiereaceae
TAX O N

Version of Record (identical to print version).



 






 





Phylogenetic analyses. —
    

 

Calyptrotheca somalensis.
  


 
  



 

  

 





   


   




Geographical, morphological and ecological data. —

   


 

RESULTS
trnS-trnGtrnQr ps16rpl16




trnQrps16 trnS-
trnG r p s16 
  

 
trnQr ps16 trnS-trnGrps16




  


  




Didierea Alluaudia
Alluaudiopsis Alluaudia
A. proceraA. mon-
tagnaciiA. comosa A. dumosa
A. ascendens  A humbertii

Portulacaria armiana 
Ceraria namaquensis
C. long i-
pedunculata 
C. fruticulosa
C. pygmaea 
Ceraria carrissoana 
Table 1.

trnL-trnF trnS-trnG trnT-trnL rps16 rpl16 trnQ-rps16 
 32 24 27 31 25 26 32
 1265 1065 1212 1008 1252 979 6781
       
 166 87 169 53 152 55 682
 11 11 11 15 9 11 68

TAX O N

Bruyns & al.
• Phylogenetic relationships in the Didiereaceae
Version of Record (identical to print version).
Portulacaria afra 




DISCUSSION
Phylogeny. —




 











CerariaAlluau-
dia ascendensAlluaudia ascendens
A. comosa A. dumosa

A. montagnacii
A. montagnacii.
 Alluaudiopsis
Decarya
Didierea
   
AAlluaudiaA
Androyella   Alluaudia    
A. ascendensAAlluaudia 
AAndroyella.
   
  

Portulacaria afra
Ceraria longipeduncu-
lata

Ceraria



Fig. 1.




Bruyns & al.
• Phylogenetic relationships in the Didiereaceae
TAX O N

Version of Record (identical to print version).


 




 

Morphology. —
      
 Alluaudiopsis
 Decarya
Didierea
 Alluaudia Didierea

      Calyptrotheca

Calyptrotheca
AlluaudiaDidierea.
 
      

C. pygmaea



   
   

Ceraria longi-
pedunculata C. namaquensis—


 

C. carrissoana
  
 

P. a fra

 P. armianaC. pygmaea



Biogeography. —



 



Fig. 2.







TAX O N

Bruyns & al.
• Phylogenetic relationships in the Didiereaceae
Version of Record (identical to print version).
  
EuphorbiaAthymalus
ChamaesyceEsulaEuphorbia


    
Calyptrotheca
 






    
EuphorbiaTirucalli
EuphorbiaTirucalli




  


  

Duvalia   

Fig. 3.


A,
Ceraria carrissoana
B,
C. fruti-
culosa
C,
C. longipedunculata
D,
C. namaquensis.

Bruyns & al.
• Phylogenetic relationships in the Didiereaceae
TAX O N

Version of Record (identical to print version).
Portulacaria afra
     spekboom   
    
 




Spekboomveld

  


P. a fra

     P. afra    
 
    
Fig. 4.


Fig. 5.
Portulacaria afraP. armianaP. pygmae a.

TAX O N

Bruyns & al.
• Phylogenetic relationships in the Didiereaceae
Version of Record (identical to print version).

 

   

  
  

 

 
 Ceraria carrisso-
anaC. longi pedunculata
C. carrissoanaPortulacaria afra
C. longi pedunculata 
   
 




C. longipedunculata

Ceraria
namaquensisPortulacaria armiana 
  Ceraria fruticulosaC. pygmaea
 
Portulacaria armianaCeraria fruticulosa
C. namaquensis
TAXONOMIC CONCLUSIONS
Ceraria
Portulacaria Ceraria
PortulacariaCeraria
    Portulacaria 
Ceraria 
 
  
Portulacaria afra 

CerariaC. fruticulosa

CerariaC. car-
rissoanaC. longipedunculata

Por-
tulacaria afra  
P. pygmaeaCeraria
Bruyns 8273 
Ceraria fruticulosaC. namaquensis

C. namaquensis
C. namaquensisC. carrissoana
C. longipedunculata
Ceraria carrissoana
CerariaPortulacaria
 C. fruticulosa 
Portulacaria


 
Ceraria 
Portulacaria


Portu-
lacaria pygmaea




P. pygmaea.
  Ceraria kuneneana  

C. carrissoana
C. kuneneanaC. carrisso-
ana

C. kaokoensis C. longipedunculata 


C. fruticulosaC. longipedunculata.
Portulacarioideae
Portulacaria
    



Leaves

Flowers

P. armiana
ual. SepaloidsCorolla 

Stamens
Ovary
 
Fruit

     

Portulacaria
P. afraCrassula portulacaria Claytonia
portulacaria 
= Ceraria

 C. namaquensis 
& .

Bruyns & al.
• Phylogenetic relationships in the Didiereaceae
TAX O N

Version of Record (identical to print version).
Key to the species of Portulacaria
 
 ......
...................................................... P. pygmaea
     
   
 ..........................................................
  ........
  ..................................
 
 .................................P. armiana
 
 .............
 
 ...................... P. afra
 
 .......................................
  
 .............................. P. fruticulosa
   
 ....... P. carrissoana
 

 ...................... P. namaquensis
   
  
 ............
........................................... P. longipedunculata
Portulacaria afra
Crassula portulacaria
Claytonia portulacaria
  


= Portulaca fruticosa


Portulacaria armiana
 
Van
Jaarsveld & Kritzinger 7893


Portulacaria carrissoana  
 comb. nov. Ceraria carrissoana 

      
Exell & Mendonça 2171

= Ceraria kuneneana

Swanepoel
234

Portulacaria fruticulosa
 comb. nov. Ceraria fruticulosa 
Lecto-
type (designated here): 
Pears on 6142

= Ceraria schaeferi



Portulacaria longipedunculata  
comb. nov. Ceraria longipedunculata

 
 De Winter
& Leistner 5853
Fig. 6.
Portulacaria carrissoana P.namaquensis
    P. carrissoana 


TAX O N

Bruyns & al.
• Phylogenetic relationships in the Didiereaceae
Version of Record (identical to print version).
Acocks, J.P.H. Mem. Bot. Su r v. So uth
Africa 
Applequist , W.L. & Wallace, R. S. 
Pl. Syst. Evol
  
Applequist, W.L. & Wallace, R.S. 
ndhF Syst. Bot  
 
Applequist, W.L. & Wallace, R.S. 
Adansonia
 
Applequist, W.L., Wagner, W.L., Zimmer, E.A. & Nepokroeff, M.
Hec-
torellaSyst. Bot
 
Arakak i, M., Cristin, P.A., Nyffeler, R., Lendel, A., Eggli, U.,
Ogburn, R.M., Spriggs, E., Moore, M.J. & Edwards, E.J. 

Proc. Natl. Acad. Sci. U.S.A
  
Brenan, J.P.M. 
Kew Bull. 
Bruyns, P.V., Mapaya, R.J. & Hedderson, T. 
Euphorbia  
psbA-trnH Ta x o n
 
Bruyns, P.V., Klak, C. & Hanáček, P. 
EuphorbiaTaxon 

Bruyns, P.V., Klak, C. & Hanáček, P.    

Molec. Phylogen. Evol. 
 
Carolin, R. Austral. J. Bot.
  
Doyle, J.J. & Doyle J.S.    
  Phytochem. Bull. Bot. Soc.
Amer.
Dyer, R.A. Portulacaria afra. Fl. Pl. Africa
= Ceraria kaokoensis
 
Swanepoel 224


Portulacaria namaquensis 
Ceraria namaquensis 
Lecto-
type (designated here): 
Wylie s.n.
= Ceraria gariepina 
Lectotype (designated here): 
    
 Pearson 3789

.
Portulacaria pygmaea Cera-
ria pygmaea 

Pillans 5849

ACKNOWLEDGEMENTS

 

     
   
 
  


 

LITERATURE CITED
Fig. 7.
Portulacaria fruticulosa P.longipeduncu-
lata       P. longipedunculata


Bruyns & al.
• Phylogenetic relationships in the Didiereaceae
TAX O N

Version of Record (identical to print version).
Dyer, R.A. Ceraria namaquensis. Fl. Pl. Africa
Exell, A.W. & Mendonça, F.A.  
 Bol. Soc. Brot 
Flores, G. Tra n s.
Geol. Soc. South Africa
Gilg, E.  Bot.
Jahrb. Syst
Hamilton, M.B. 
Molec. Ecol.

Hershkovitz, M.A.  
Calandrinia Montiopsis 
Ann. Missouri
Bot. Gard 
Hershkovitz, M.A . & Zimmer, E.A.   
Ta x o n
Hoare, D.B., Mucina, L., Rutherford, M.C., Vlok, J.H. J., Euston-
Brown, D.I.W., Palmer, A.R., Powrie, L.W., Lechmere-Oertel,
R.G., Procheş, Ş.M., Dold, A.P. & Ward, R.A.  

 T he vegetation of South Africa, Lesotho and Swaziland

Huelsenbeck, J.P. & Rannala, B.    
         
Syst. Biol
  
Jacobsen, H. CerariaA hand-
book of succulent plants
Jensen, U.   
  Bot. Jahrb. Syst  

Jordan, W.C., Courtney, M.W. & Neigel, J.E . 
    
Amer. J.
Bot
Jürgens, N. 
The vegetation of South Africa, Lesotho and
Swaziland. 

Kelchner, S.A. & Clark, L.G. 
rpl16 Chusquea 
Molec. Phylogen. Evol
  
Klak, C., Bruyns, P.V. & Hanáček, P. 

Molec. Phylogen. Evol
 
McCarthy, C. 

Mendelsohn, J., Jarvis, A., Roberts, C. & Robertson, T. Atlas
of Namibia
Mucina, L., Jürgens, N., Le Roux, A., Rutherford, M.C., Schmiedel,
U., Esler, K., Powrie, L.W., Desmet, P.G. & Milton, S.J. 

The vegetation of South Africa, Lesotho and Swazi-
land. 

Nicholas, K.B. & Nicholas, H.B., Jr. 

    

Nyffeler, R. 


Amer. J. Bot  
Nyffeler, R. & Eggli, U.    
      
    
Taxo n  
Ocampo, G. & Columbus, J.T. 

Amer. J. Bot 

Oxelman, B., Lidén, M. & Berglund, D. rp s16
SileneaePl. Syst. Evol.

Pearson, H.H.W. & Stephens, E.L. 
      
Ann. S. African Mus 
Peirson, J.A., Bruyns, P.V., Riina, R., Morawetz, J. J. & Berry, P.E.

EuphorbiaAthymalu s
Taxo n 
Phillips, S.M. Flora
of tropical East Africa
Pickford, M. & Senut, B.  
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Me m. Geo l. Su r v. Nami bia 
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Science
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
Sitzungsber. Heidelberger Akad. Wiss.,
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TAX O N

Bruyns & al.
• Phylogenetic relationships in the Didiereaceae
Version of Record (identical to print version).
Simmons, M.P. & Ochoterena, H.     
Syst. Biol
 
Snijman, D.A.    
Plants of the Greater Cape Floristic RegionTh e Ext ra Ca p e
Flora.   

Stamatak is, A. 

Bioinformatics
 
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
Sitzungsber. Heidelberger Akad. Wiss.,
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Namib ecology: 25 years of Namib research.

Appendix 1.

rpl16r ps16trnL-trnFtrnQr ps16trnS-trnGtrnT-trnL 

OUTGROUPS: Anacampseros albissimaBr uyns 106 99    Bougainvillea spectabilis
Kl ak 987Delosperma esterhuyseniaeBruyns 7141 
    Limeum africanum Trinder-Smith 279 
Mesembryanthemum cordifoliumKl ak 1019         
Mirabilis jalapaKlak 986 Pereskia grandifolia
Phytolacca dioicaKlak 988
Portulaca sp.,BruynsRhipsalis baccifera   
Bruyns 9740aTalinum portulacifolium
Bruyns 10714
INGROUP: Alluaudia ascendens             
Alluaudia comosaOliveira-Neto 4    Alluaudia
comosa,Oliveira-Neto 5Alluaudia dumosa
Oliveira-Neto 11Alluaudia humbertii
Oliveira-Neto 10Alluaudia montagnaciiOliveira-Neto 9
Alluaudia procera    Oliveira-Neto 13  
Alluaudiopsis fiherenensisOliveira-Neto 12 
Alluaudiopsis marnierianaOliveira-Neto 6
Decarya madagascariensis      
Didierea madagascariensisOliveira-Neto 7    
Didierea madagascariensis,Oliveira-Neto 14
 Didierea trolliiOliveira-Neto 8
Calyptrotheca somalensis HN T 57830 Ceraria carrissoana
Bruyns 8026Ceraria fruticulosa
Bruyns 10059Ceraria longipedunculata
Br uyns 10372      Ceraria namaquensis   
Br uyn s 10 073  Ceraria pygmaea
Bruyns 8273         Portulacaria afraBruyns 11348a
Portulacaria armianaBruyns 7245

... Portulacaria afra is one of the dominant medicinally important plants widely grown in the east of South Africa belonging to the family Didiereaceae (Nakamura et al., 2021).In this moist climate, it is relatively rare, and tends to favor dryer rocky outcrops and slopes (Bruyns et al., 2014) .P. afra is an annual succulent herb thick eshy leaves for water storage (Iranshahy et al., 2017). This plant can grow up to 2 meters tall. ...
... Portulacaria afra (P.afra) also known as "elephant bush," is a succulent plant in the Didereaceae family (Sajid-Ur-Rehman et al., 2021a). In a moist climate, it is comparatively infrequent and tends to favor dryer stony outliers and hills (Bruyns et al., 2014).P.afra leaves is used to treat a wide range of human pathologies, including skin diseases, respiratory problems, vomiting and diarrhea, in ammation, metabolic syndrome, and leukemia (De Wet et al., 2013) .The plant extracts seem to have antibacterial and anti-diabetic effects (Olaokun et al., 2017, Nciki, 2015. As previously mentioned, genus Portulaca produces important phytochemicals with high Possibility as drug candidates for a wide range of targets. ...
... The HMPA extract (Figure 6). Acetic acid-induced writhing method HMPA extract at (100,200,400mg/kg) showed dose-dependent reduction in acetic acid-induced writhes.The effect of HMPA extract was compared with standard control ( g.7) Molecular docking analysis Molecular docking was performed to explore the synergistic effect of the GC-MS-identi ed compounds on COX-1, COX-2 inhibition. A high binding a nity was observed for 1-Coprosten-3-one semicarbazone, Phenol, 2,2'-methylenebis, 7,9-ditertbutyl-1-oxaspiro [4.5] deca-6,9-diene-2,8-dione as shown in table (2 and g.8) ...
... Bruyns et al., 2014). Sepals have been described as persistent in all of these taxa (Rauh, 1963;Carolin, 1993;Kubitzki, 1993;Nyffeler and Eggli, 2010;Bruyns et al., 2014). Rauh (1963) described persistent sepals in some but not all species of Didiereoideae as membranous. ...
... According to Bruyns et al. (2014), Rowley (1996 [not accessible to me]) gave no reason for the transfer of the last species to Ceraria. Bruyns et al. (2014) noted that the "original" distinction between Portulacaria and Ceraria based on hermaphroditic flowers in the former versus unisexual in the latter. ...
... According to Bruyns et al. (2014), Rowley (1996 [not accessible to me]) gave no reason for the transfer of the last species to Ceraria. Bruyns et al. (2014) noted that the "original" distinction between Portulacaria and Ceraria based on hermaphroditic flowers in the former versus unisexual in the latter. Possibly this is why the hermaphroditic P. armiana and P. pygmaea were classified in Portulacaria. ...
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This work pretends to demonstrate how the phylogenetic distribution of an ecologically innocuous character – perianth fate – challenges mainstream Darwinian reductionist notions of evolution and its statistical “predictability.” Historically, perianth fate, especially sepal persistence, was a central pillar in the taxonomy of the classically conceived but aphyletic Portulacaceae s. lato (Caryophyllales). In particular, up until the late 20th Century, this trait was supposed to distinguish the two largest classical but aphyletic genera, Talinum Adans. s. l. and Calandrinia Kunth s. lato. Yet, already in the 19th Century, the trait was known to be polymorphic within each of these generic concepts. Reevaluation of the distribution of perianth fate traits in the framework of a phylogenetic reconstruction of Portulacineae reveals that the traits are conserved at various divergence levels, from family to species. And they apparently are polymorphic within some species. The distribution is qualitatively similar to that of traits whose distribution is statistically analyzed and explained in terms of the Darwinist notions of natural selection and adaptation. Since “natural selection” cannot be afforded the prescience to know which traits are adaptive and which are not, the explanation for both must be “natural drift,” in turn a consequence of the determinism of organisms inherent in their fundamental property, autopoiesis. And consequent to autopoiesis, evolution must be idiosyncratic, hence never predictable.
... Historically, P. afra was placed within the Portulacaceae. However, recent work by Applequist & Wallace (2003) and Bruyns et al. (2014) has clearly shown that it is nested within the Didiereaceae (Portulacarioideae). The Didiereaceae (Caryophyllales) is a small succulent family of twentytwo species organised into three subfamilies. ...
... Portulacaria afra used to be monotypic. However, Ceraria species from the western parts of South Africa and Namibia have now been included within the genus Portulacaria (Bruyns et al. 2014). All the other species in the genus Portulacaria (historically placed in the genus Ceraria) occur from the lower Orange River in the Northern Cape and Namibia, to south-western Angola in the north. ...
... The map of Portulacaria afra provided by Bruyns et al. (2014) shows a clear gap in distribution between the Kei and Msikaba Rivers within the Eastern Cape. This isolation is largely due to the difficult access to the steep river valleys of this part of the Eastern Cape. ...
... Portulacaria afra is one of the dominant medicinally important plants, widely grown in the east of South Africa, belonging to the family Didiereaceae [16]. In this moist climate, it is relatively rare, and it tends to favor dryer rocky outcrops and slopes [17]. P. afra is an annual succulent herb with thick fleshy leaves for water storage [18]. ...
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The use of complementary herbal medicines has recently increased in an attempt to find effective alternative therapies that reduce the adverse effects of chemical drugs. Portulacaria afra is a rich source of phytochemicals with high antioxidant activity, and thus may possess health benefits. This study used the latest developments in GC-MS coupling with molecular docking techniques to identify and quantify the hytoconstituents in P. afra tissue extracts. The results revealed that n-butanol P. afra (BUT-PA) dry extracts contained total phenolic and flavonoids contents of 21.69 � 0.28 mgGAE/g and 196.58 � 6.29 mgGAE/g, respectively. The significant potential of antioxidants was observed through CUPRIC, FRAP, and ABTS methods while the DPPH method showed a moderate antioxidants potential for P. afra. Enzymatic antioxidants, superoxide dismutase, peroxidase and catalase also showed a better response in the BUT-PA dry extracts. The thrombolytic activity of the BUT-PA extracts ranged from 0.4 � 0.32 to 11.2 � 0.05%. Similarly, hemolytic activity ranged from 5.76 � 0.15 to 9.26 � 0.15% using the standard (triton x) method. The BUTPA and CHPA showed moderate acetylcholinesterase and butrylcholinesterase inhibition, ranging from 40.78 � 0.52 to 58.97 � 0.33, compared to galantamine. The carrageenan induced hind-paw edema assay, while BUT-PA extracts showed anti-inflammatory properties in a dose-dependent manner. Furthermore, 20 compounds were identified in the BUTPA extracts by GC-MS. Molecular docking was performed to explore the synergistic effect of the GC-MS-identified compounds on COX-1 and COX-2 inhibition. A high binding affinity was observed for Stigmastan-3, 5-diene, Phthalic acid, 3. Alpha-Hydroxy-5, 16-androstenol. The computed binding energies of the compounds revealed that all the compounds have a synergistic effect, preventing inflammation. It was concluded that active phytochemicals were present in P. afra, with the potential for multiple pharmacological applications as a latent source of pharmaceutically important compounds. This should be further explored to isolate secondary metabolites that can be employed in the treatment of different diseases.
... Here, we recovered strong support (100%) in gene tree analyses for a clade including only Alluaudia and Alluaudiopsis ( fig. 1). This result differs from Bruyns et al. (2014) that found Alluaudiopsis to be sister to the remaining Didiereoideae. ...
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Several plant lineages have evolved adaptations that allow survival in extreme and harsh environments including many families within the plant clade Portulacineae (Caryophyllales) such as the Cactaceae, Didiereaceae, and Montiaceae. Here, using newly generated transcriptomic data, we reconstructed the phylogeny of Portulacineae and examined potential correlates between molecular evolution and adaptation to harsh environments. Our phylogenetic results were largely congruent with previous analyses, but we identified several early diverging nodes characterized by extensive gene tree conflict. For particularly contentious nodes, we present detailed information about the phylogenetic signal for alternative relationships. We also analyzed the frequency of gene duplications, confirmed previously identified whole genome duplications (WGD), and proposed a previously unidentified WGD event within the Didiereaceae. We found that the WGD events were typically associated with shifts in climatic niche but did not find a direct association with WGDs and diversification rate shifts. Diversification shifts occurred within the Portulacaceae, Cactaceae, and Anacampserotaceae, and while these did not experience WGDs, the Cactaceae experienced extensive gene duplications. We examined gene family expansion and molecular evolutionary patterns with a focus on genes associated with environmental stress responses and found evidence for significant gene family expansion in genes with stress adaptation and clades found in extreme environments. These results provide important directions for further and deeper examination of the potential links between molecular evolutionary patterns and adaptation to harsh environments.
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Several plant lineages have evolved adaptations that allow survival in extreme and harsh environments including many within the plant clade Portulacineae (Caryophyllales) such as the Cactaceae, Didiereaceae of Madagascar, and high altitude Montiaceae. Here, using newly generated transcriptomic data, we reconstructed the phylogeny of Portulacineae and examine potential correlates between molecular evolution within this clade and adaptation to harsh environments. Our phylogenetic results were largely congruent with previous analyses, but we identified several early diverging nodes characterized by extensive gene tree conflict. For particularly contentious nodes, we presented detailed information about the phylogenetic signal for alternative relationships. We also analyzed the frequency of gene duplications, confirmed previously identified whole genome duplications (WGD), and identified a previously unidentified WGD event within the Didiereaceae. We found that the WGD events were typically associated with shifts in climatic niche and did not find a direct association with WGDs and diversification rate shifts. Diversification shifts occurred within the Portulacaceae, Cactaceae, and Anacampserotaceae, and while these did not experience WGDs, the Cactaceae experienced extensive gene duplications. We examined gene family expansion and molecular evolutionary patterns with a focus on genes associated with environmental stress responses and found evidence for significant gene family expansion in genes with stress adaptation and clades found in extreme environments. These results provide important directions for further and deeper examination of the potential links between molecular evolutionary patterns and adaptation to harsh environments.
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Hybrid enrichment is an increasingly popular approach for obtaining hundreds of loci for phylogenetic analysis across many taxa quickly and cheaply. The genes targeted for sequencing are typically single-copy loci, which facilitate a more straightforward sequence assembly and homology assignment process. However, single copy loci are relatively uncommon elements of most genomes, and as such may provide a biased evolutionary history. Furthermore, this approach limits the inclusion of most genes of functional interest, which often belong to multi-gene families. Here we demonstrate the feasibility of including large gene families in hybrid enrichment protocols for phylogeny reconstruction and subsequent analyses of molecular evolution, using a new set of bait sequences designed for the “portullugo” (Caryophyllales), a moderately sized lineage of flowering plants (~2200 species) that includes the cacti and harbors many evolutionary transitions to C 4 and CAM photosynthesis. Including multi-gene families allowed us to simultaneously infer a robust phylogeny and construct a dense sampling of sequences for a major enzyme of C 4 and CAM photosynthesis, which revealed the accumulation of adaptive amino acid substitutions associated with C 4 and CAM origins in particular paralogs. Our final set of matrices for phylogenetic analyses included 75–218 loci across 74 taxa, with ~50% matrix completeness across datasets. Phylogenetic resolution was greatly improved across the tree, at both shallow and deep levels. Concatenation and coalescent-based approaches both resolve with strong support the sister lineage of the cacti: Anacampserotaceae + Portulacaceae, two lineages of mostly diminutive succulent herbs of warm, arid regions. In spite of this congruence, BUCKy concordance analyses demonstrated strong and conflicting signals across gene trees for the resolution of the sister group of the cacti. Our results add to the growing number of examples illustrating the complexity of phylogenetic signals in genomic-scale data.
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Hybrid enrichment is an increasingly popular approach for obtaining hundreds of loci for phylogenetic analysis across many taxa quickly and cheaply. The genes targeted for sequencing are typically single-copy loci, which facilitate a more straightforward sequence assembly and homology assignment process. However, this approach limits the inclusion of most genes of functional interest, which often belong to multi-gene families. Here we demonstrate the feasibility of including large gene families in hybrid enrichment protocols for phylogeny reconstruction and subsequent analyses of molecular evolution, using a new set of bait sequences designed for the "portullugo" (Caryophyllales), a moderately sized lineage of flowering plants (∼2200 species) that includes the cacti and harbors many evolutionary transitions to C4 and CAM photosynthesis. Including multi-gene families allowed us to simultaneously infer a robust phylogeny and construct a dense sampling of sequences for a major enzyme of C4 and CAM photosynthesis, which revealed the accumulation of adaptive amino acid substitutions associated with C4 and CAM origins in particular paralogs. Our final set of matrices for phylogenetic analyses included 75-218 loci across 74 taxa, with ∼50% matrix completeness across datasets. Phylogenetic resolution was greatly improved across the tree, at both shallow and deep levels. Concatenation and coalescent-based approaches both resolve the sister lineage of the cacti with strong support: Anacampserotaceae + Portulacaceae, two lineages of mostly diminutive succulent herbs of warm, arid regions. In spite of this congruence, BUCKy concordance analyses demonstrated strong and conflicting signals across gene trees. Our results add to the growing number of examples illustrating the complexity of phylogenetic signals in genomic-scale data.
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Traditional classifications of the suborder Portulacineae recognize six families: Basellaceae, Cactaceae, Didiereaceae, Halophytaceae, Hectorellaceae, and Portulacaceae. However, phylogenetic analyses based on molecular sequence data indicate that the traditional family Portulacaceae is paraphyletic and consists of three distinct lineages that also include Cactaceae, Didiereaceae, and Hectorellaceae. We use sequence data from the chloroplast genes matK and ndhF representing 64 species of Portulacineae and outgroups to reconstruct their phylogenetic relationships with Bayesian and maximum parsimony inference methods. Evidence from these molecular phylogenetic analyses as well as from comparative morphological investigations allow us to propose a revised familial classification of the suborder Portulacineae. We recognize eight monophyletic families: Anacampserotaceae (Anacampseros, Grahamia, Talinopsis), Basellaceae, Cactaceae, Didiereaceae (incl. Calyptrotheca, Ceraria, Portulacaria), Halophytaceae, Montiaceae (incl. Hectorellaceae, Calandrinia, Cistanthe, Claytonia, Lewisia, Montia, Phemeranthus), Portulacaceae (Portulaca only), and Talinaceae (Amphipetalum, Talinella, Talinum). We provide a synopsis for this revised family classification with an identification key mainly based on habit and fruit characters, and family diagnoses with information on distribution, taxonomic diversity, and a brief discussion on phylogenetics and classification.
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Although most previous studies on chloroplast (cp) DNA variation in plants have concentrated on systematics and evolution above the species level, intraspecific variation in cpDNA is common and has provided useful insights into population-level evolutionary processes. Polymerase chain reaction methods were used to examine restriction site and sequence variation in the chloroplast rpLI6 gene within and among populations of duckweed species (Spirodela and Lemna) from the southern and eastern United States. To our knowledge, the rpL16 region has not previously been used to investigate cpDNA variation in nature. While considerable restriction site and sequence variation were detected among species, no variation was found within populations of either of the two species (S. punctata and L. minor) selected for sequence analysis, and S. punctata showed no interpopulational variation. Two cpDNA haplotypes were identified in L. minor, with one haplotype restricted to three sites in Louisiana and the other found in all other populations sampled. This paucity of variation cannot be readily explained as the result of a low mutation rate. In general, group II introns appear to be subject to very little functional constraint, and extensive sequence differences have been found between species in the chloroplast rpL16 intron in particular. However, factors such as historical range expansions and contractions, founding effects, fluctuations in local population size, and natural selection may play a role in reducing cpDNA sequence variability in these species.
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The Portulacaceae, Basellaceae, Cactaceae, and Didiereaceae form a monophyletic group within the Caryophyllales, and evidence exists that the first may be paraphyletic if the latter three are recognized at the familial level. Several taxonomic treatments of the Portulacaceae based on morphological features have failed to produce consensus regarding infrafamilial relationships. The present paper employs sequences of the chloroplast gene ndhF to produce a molecular phylogeny of the portulacaceous cohort, focusing on the relationship among major lineages of the Portulacaceae and the three families potentially derived from within them. Results of this analysis supported two major clades within the monophyletic cohort. The first included Portulaca, Anacampseros and its relatives, much of Talinum, Talinella, and Cactaceae; the second, weakly supported, included the remaining genera of Portulacaceae, Basellaceae, and Didiereaceae. This phylogeny also showed that several generic circumscriptions remain inadequate, particularly that of Talinum sensu lato, which was polyphyletic in this analysis, and that all present classifications of the Portulacaceae include demonstrably non-monophyletic tribes.