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Article ; Online: REFMAKER: Make your own reference to target nuclear loci in low coverage genome skimming libraries. Phylogenomic application in Sapotaceae.

Pouchon, Charles / Boluda, Carlos G

2023 Volume 186, Page(s) 107826

Abstract: Genome skimming approach is widely used in plant systematics to infer phylogenies mostly from organelle genomes. However, organelles represent only 10 % of the produced libraries, and the low coverage associated with these libraries (<3X) prevents the ... ...

Abstract	Genome skimming approach is widely used in plant systematics to infer phylogenies mostly from organelle genomes. However, organelles represent only 10 % of the produced libraries, and the low coverage associated with these libraries (<3X) prevents the capture of nuclear sequences, which are not always available in non-model organisms or limited to the ribosomal regions. We developed REFMAKER, a user-friendly pipeline, to create specific sets of nuclear loci that can be extracted directly from the genome skimming libraries. For this, a catalogue is built from the meta-assembly of each library contigs, and cleaned by selecting the nuclear regions and removing duplicates from clustering steps. Libraries are next mapped onto this catalogue and consensus sequences are generated to produce a ready-to-use phylogenetic matrix following different filtering parameters aiming at removing putative errors and paralogous sequences. REFMAKER allowed us to infer a well resolved phylogeny in Capurodendron (Sapotaceae) on 67 nuclear loci from low-coverage libraries (<1X). The resulting phylogeny is concomitant with one previously inferred on 638 nuclear genes from target enrichment libraries. While it remains preliminary because of this low sequencing depth, REFMAKER therefore opens perspectives in phylogenomics by allowing nuclear phylogeny reconstructions with genome skimming datasets.
MeSH term(s)	Phylogeny ; Sapotaceae ; Cell Nucleus/genetics
Language	English
Publishing date	2023-05-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	33610-5
ISSN	1095-9513 ; 1055-7903
ISSN (online)	1095-9513
ISSN	1055-7903
DOI	10.1016/j.ympev.2023.107826
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Article ; Online: REFMAKER: Make your own reference to target nuclear loci in low coverage genome skimming libraries. Phylogenomic application in Sapotaceae

Pouchon, Charles / Boluda, Carlos G.

Molecular Phylogenetics and Evolution. 2023 Sept., v. 186 p.107826-

2023

Abstract	Genome skimming approach is widely used in plant systematics to infer phylogenies mostly from organelle genomes. However, organelles represent only 10 % of the produced libraries, and the low coverage associated with these libraries (<3X) prevents the capture of nuclear sequences, which are not always available in non-model organisms or limited to the ribosomal regions. We developed REFMAKER, a user-friendly pipeline, to create specific sets of nuclear loci that can be extracted directly from the genome skimming libraries. For this, a catalogue is built from the meta-assembly of each library contigs, and cleaned by selecting the nuclear regions and removing duplicates from clustering steps. Libraries are next mapped onto this catalogue and consensus sequences are generated to produce a ready-to-use phylogenetic matrix following different filtering parameters aiming at removing putative errors and paralogous sequences. REFMAKER allowed us to infer a well resolved phylogeny in Capurodendron (Sapotaceae) on 67 nuclear loci from low-coverage libraries (<1X). The resulting phylogeny is concomitant with one previously inferred on 638 nuclear genes from target enrichment libraries. While it remains preliminary because of this low sequencing depth, REFMAKER therefore opens perspectives in phylogenomics by allowing nuclear phylogeny reconstructions with genome skimming datasets.
Keywords	Sapotaceae ; data collection ; genome ; organelles ; phylogeny ; plant taxonomy ; Bioinformatics ; Nuclear phylogeny ; Shotgun sequencing ; Systematics
Language	English
Dates of publication	2023-09
Publishing place	Elsevier Inc.
Document type	Article ; Online
Note	Pre-press version
ZDB-ID	33610-5
ISSN	1095-9513 ; 1055-7903
ISSN (online)	1095-9513
ISSN	1055-7903
DOI	10.1016/j.ympev.2023.107826
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Article: Two further new species in the highly-diverse Malagasy endemic genus Capurodendron (Sapotaceae)

Gautier, Laurent / Boluda, Carlos G. / Randrianaivo, Richard / Naciri, Yamama

Candollea. 2022 June 1, v. 77, no. 1

2022

Abstract: Gautier, L., C.G. Boluda, R. Randrianaivo & Y. Naciri (2022). Two further new species in the highly-diverse Malagasy endemic genus Capurodendron (Sapotaceae). Candollea 77: 119–126. In English, English and French abstracts. During the course of a ... ...

Abstract	Gautier, L., C.G. Boluda, R. Randrianaivo & Y. Naciri (2022). Two further new species in the highly-diverse Malagasy endemic genus Capurodendron (Sapotaceae). Candollea 77: 119–126. In English, English and French abstracts. During the course of a revision of the Malagasy species of the family Sapotaceae, two new species from the dry forest belonging to the highly-diverse endemic genus Capurodendron Aubrév. were discovered. The first one, C. mikearum L. Gaut. & Boluda, earlier hypothesised to be a hybrid, emerged as a valid species without any hybrid signal, based on a combination of genetic and morphological analyses of a species complex from the southwestern region. The second species, C. namorokense L. Gaut. & Boluda, occupies a basal position in the same species clade. It is clearly morphologically distinct and geographically distant, so far only being known from northwestern Madagascar. Both species are described and illustrated by line drawings and field photographs. Preliminary conservation assessments using the IUCN Red List criteria indicate that both species are threatened (EN and CR, respectively). Received on January 6, 2022. Accepted on April 27, 2022. First published online on June 1, 2022.
Keywords	Agrostis ; Sapotaceae ; dry forests ; hybrids ; new species ; Madagascar
Language	English
Dates of publication	2022-0601
Size	p. 119-126.
Publishing place	Les conservatoire et jardin botaniques de la Ville de Genève (The Conservatory and Botanical Gardens of the City of Geneva)
Document type	Article
ZDB-ID	2648858-9
ISSN	0373-2967
ISSN	0373-2967
DOI	10.15553/c2022v771a9
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Article: A 638‐gene phylogeny supports the recognition of twice as many species in the Malagasy endemic genus Capurodendron (Sapotaceae)

Boluda, Carlos G. / Christe, Camille / Naciri, Yamama / Gautier, Laurent

Taxon. 2022 Apr., v. 71, no. 2

2022

Abstract: The Malagasy genus Capurodendron currently accommodates 26 described species and is the largest genus of the family Sapotaceae in Madagascar. These species are frequently logged because of their valued hardwood, which potentially puts them at risk of ... ...

Abstract	The Malagasy genus Capurodendron currently accommodates 26 described species and is the largest genus of the family Sapotaceae in Madagascar. These species are frequently logged because of their valued hardwood, which potentially puts them at risk of extinction. Species‐level identifications are often problematic, and this hinders both an accurate assessment of their conservation status and the development of effective protection measures. We sorted all the material (ca. 860 collections) available in the herbaria with significant collections for Madagascar into 47 putative species based on morphology. On 41 of these, for which we were able to retrieve suitable DNA, we conducted a phylogenetic reconstruction based on molecular sequences of 638 loci from 108 Capurodendron specimens, performing a target capture approach combined with next‐generation sequencing. Maximum likelihood (RAxML), pseudocoalescence (ASTRAL), and coalescence (STACEY) analyses showed that Capurodendron comprises two deeply divergent lineages. One, which includes a single species, is here newly described as C. subg. Reflexisepala based on its distinctive morphology. The second lineage contains all remaining species, which seem to have resulted from a rapid radiation event. The phylogenetic tree provides good support for most of the species hypothesized based on morphology, with the exception of two species‐groups that we have named the Arid Complex and the Eastern Complex. As many as 20 species‐level lineages genetically distinct from any of the currently recognized species were identified, 17 of which were morphologically well‐characterized, representing strong candidates for new species. This would suggest that Capurodendron is the most species‐rich endemic genus of plants in Madagascar. While 14 of these 20 clades are still under study, we here describe six species new to science: Capurodendron andrafiamenae (provisionally assessed as CR), C. aubrevillei (VU), C. birkinshawii (CR), C. naciriae (EN), C. randrianaivoi (CR), and C. sakarivorum (EN). Capurodendron oblongifolium comb. nov. (EN), previously regarded as a variety of C. perrieri, represents a distinct lineage that is here recognized at the species level. The newly described species are illustrated by line drawings and photographs from the field, and a preliminary threat assessment is provided. We discuss the evolutionary history of Capurodendron and also explore the question of node age estimates and their methodological limitations.
Keywords	DNA ; Sapotaceae ; conservation status ; extinction ; hardwood ; new species ; phylogeny ; risk ; statistical analysis ; Madagascar
Language	English
Dates of publication	2022-04
Size	p. 360-395.
Publishing place	John Wiley & Sons, Inc.
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	204216-2
ISSN	0040-0262
ISSN	0040-0262
DOI	10.1002/tax.12676
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Article: Species Delimitation and Conservation in Taxonomically Challenging Lineages: The Case of Two Clades of Capurodendron (Sapotaceae) in Madagascar

Boluda, Carlos G. / Christe, Camille / Randriarisoa, Aina / Gautier, Laurent / Naciri, Yamama

Plants. 2021 Aug. 18, v. 10, no. 8

2021

Abstract: Capurodendron is the largest endemic genus of plants from Madagascar, with around 76% of its species threatened by deforestation and illegal logging. However, some species are not well circumscribed and many of them remain undescribed, impeding a ... ...

Abstract	Capurodendron is the largest endemic genus of plants from Madagascar, with around 76% of its species threatened by deforestation and illegal logging. However, some species are not well circumscribed and many of them remain undescribed, impeding a confident evaluation of their conservation status. Here we focus on taxa delimitation and conservation of two species complexes within Capurodendron: the Arid and Western complexes, each containing undescribed morphologies as well as intermediate specimens alongside well-delimited taxa. To solve these taxonomic issues, we studied 381 specimens morphologically and selected 85 of them to obtain intergenic, intronic, and exonic protein-coding sequences of 794 nuclear genes and 227 microsatellite loci. These data were used to test species limits and putative hybrid patterns using different approaches such as phylogenies, PCA, structure analyses, heterozygosity level, FST, and ABBA-BABA tests. The potential distributions were furthermore estimated for each inferred species. The results show that the Capurodendron Western Complex contains three well-delimited species, C. oblongifolium, C. perrieri, and C. pervillei, the first two hybridizing sporadically with the last and producing morphologies similar to, but genetically distinct from C. pervillei. The Arid Complex shows a more intricate situation, as it contains three species morphologically well-delimited but genetically intermixed. Capurodendron mikeorum nom. prov. is shown to be an undescribed species with a restricted distribution, while C. androyense and C. mandrarense have wider and mostly sympatric distributions. Each of the latter two species contains two major genetic pools, one showing interspecific admixture in areas where both taxa coexist, and the other being less admixed and comprising allopatric populations having fewer contacts with the other species. Only two specimens out of 172 showed clear genetic and morphological signals of recent hybridization, while all the others were morphologically well-delimited, independent of their degree of genetic admixture. Hybridization between Capurodendron androyense and C. microphyllum, the sister species of the Arid Complex, was additionally detected in areas where both species coexist, producing intermediate morphologies. Among the two complexes, species are well-defined morphologically with the exception of seven specimens (1.8%) displaying intermediate patterns and genetic signals compatible with a F1 hybridization. A provisional conservation assessment for each species is provided.
Keywords	Sapotaceae ; allopatry ; conservation status ; deforestation ; heterozygosity ; hybridization ; hybrids ; microsatellite repeats ; phylogeny ; sympatry ; Madagascar
Language	English
Dates of publication	2021-0818
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants10081702
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Article: Phylogeographic reconstructions can be biased by ancestral shared alleles: The case of the polymorphic lichen Bryoria fuscescens in Europe and North Africa

Boluda, Carlos G. / Rico, Víctor J. / Naciri, Yamama / Hawksworth, David L. / Scheidegger, Christoph

Molecular ecology. 2021 Oct., v. 30, no. 19

2021

Abstract: Large phylogeographic studies on lichens are scarce, and none involves a single species within which different lineages show fixed alternative dispersal strategies. We investigated Bryoria fuscescens (including B. capillaris) in Europe and western North ... ...

Abstract	Large phylogeographic studies on lichens are scarce, and none involves a single species within which different lineages show fixed alternative dispersal strategies. We investigated Bryoria fuscescens (including B. capillaris) in Europe and western North Africa by phenotypically characterizing 1400 specimens from 64 populations and genotyping them with 14 microsatellites. We studied population structure and genetic diversity at the local and continental scales, discussed the post‐glacial phylogeography, and compared dispersal capacities of phenotypes with and without soralia. Our main hypothesis is that the estimated phylogeography, migration routes, and dispersal capacities may be strongly biased by ancestral shared alleles. Scandinavia is genetically the richest area, followed by the Iberian Peninsula, the Carpathians, and the Alps. Three gene pools were detected: two partially linked to phenotypic characteristics, and the third one genetically related to the American sister species B. pseudofuscescens. The comparison of one gene pool producing soredia and one not, suggested both as panmictic, with similar levels of isolation by distance (IBD). The migration routes were estimated to span from north to south, in disagreement with the assessed glacial refugia. The presence of ancestral shared alleles in distant populations can explain the similar IBD levels found in both gene pools while producing a false signal of panmixia, and also biasing the phylogeographic reconstruction. The incomplete lineage sorting recorded for DNA sequence loci also supports this hypothesis. Consequently, the high diversity in Scandinavia may rather come from recent immigration into northern populations than from an in situ diversification. Similar patterns of ancestral shared polymorphism may bias the phylogeographical reconstruction of other lichen species.
Keywords	Bryoria ; gene pool ; genetic variation ; genotyping ; immigration ; lichens ; microsatellite repeats ; phenotype ; phylogeography ; population structure ; refuge habitats ; Iberian Peninsula ; Northern Africa ; Scandinavia
Language	English
Dates of publication	2021-10
Size	p. 4845-4865.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.16078
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Article: Species Delimitation and Conservation in Taxonomically Challenging Lineages: The Case of Two Clades of

Boluda, Carlos G / Christe, Camille / Randriarisoa, Aina / Gautier, Laurent / Naciri, Yamama

Plants (Basel, Switzerland)

2021 Volume 10, Issue 8

Abstract: ... ...

Abstract	Capurodendron
Language	English
Publishing date	2021-08-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants10081702
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Article ; Online: Phylogeographic reconstructions can be biased by ancestral shared alleles: The case of the polymorphic lichen Bryoria fuscescens in Europe and North Africa.

Boluda, Carlos G / Rico, Víctor J / Naciri, Yamama / Hawksworth, David L / Scheidegger, Christoph

Molecular ecology

2021 Volume 30, Issue 19, Page(s) 4845–4865

Abstract	Large phylogeographic studies on lichens are scarce, and none involves a single species within which different lineages show fixed alternative dispersal strategies. We investigated Bryoria fuscescens (including B. capillaris) in Europe and western North Africa by phenotypically characterizing 1400 specimens from 64 populations and genotyping them with 14 microsatellites. We studied population structure and genetic diversity at the local and continental scales, discussed the post-glacial phylogeography, and compared dispersal capacities of phenotypes with and without soralia. Our main hypothesis is that the estimated phylogeography, migration routes, and dispersal capacities may be strongly biased by ancestral shared alleles. Scandinavia is genetically the richest area, followed by the Iberian Peninsula, the Carpathians, and the Alps. Three gene pools were detected: two partially linked to phenotypic characteristics, and the third one genetically related to the American sister species B. pseudofuscescens. The comparison of one gene pool producing soredia and one not, suggested both as panmictic, with similar levels of isolation by distance (IBD). The migration routes were estimated to span from north to south, in disagreement with the assessed glacial refugia. The presence of ancestral shared alleles in distant populations can explain the similar IBD levels found in both gene pools while producing a false signal of panmixia, and also biasing the phylogeographic reconstruction. The incomplete lineage sorting recorded for DNA sequence loci also supports this hypothesis. Consequently, the high diversity in Scandinavia may rather come from recent immigration into northern populations than from an in situ diversification. Similar patterns of ancestral shared polymorphism may bias the phylogeographical reconstruction of other lichen species.
MeSH term(s)	Alleles ; Europe ; Genetic Variation ; Lichens/genetics ; Microsatellite Repeats ; Parmeliaceae ; Phylogeny ; Phylogeography
Language	English
Publishing date	2021-07-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.16078
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Article ; Online: New genetic markers for Sapotaceae phylogenomics: More than 600 nuclear genes applicable from family to population levels.

Christe, Camille / Boluda, Carlos G / Koubínová, Darina / Gautier, Laurent / Naciri, Yamama

Molecular phylogenetics and evolution

2021 Volume 160, Page(s) 107123

Abstract: Some tropical plant families, such as the Sapotaceae, have a complex taxonomy, which can be resolved using Next Generation Sequencing (NGS). For most groups however, methodological protocols are still missing. Here we identified 531 monocopy genes and ... ...

Abstract	Some tropical plant families, such as the Sapotaceae, have a complex taxonomy, which can be resolved using Next Generation Sequencing (NGS). For most groups however, methodological protocols are still missing. Here we identified 531 monocopy genes and 227 Short Tandem Repeats (STR) markers and tested them on Sapotaceae using target capture and NGS. The probes were designed using two genome skimming samples from Capurodendron delphinense and Bemangidia lowryi, both from the Tseboneae tribe, as well as the published Manilkara zapota transcriptome from the Sapotoideae tribe. We combined our probes with 261 additional ones previously published and designed for the entire angiosperm group. On a total of 792 low-copy genes, 638 showed no signs of paralogy and were used to build a phylogeny of the family with 231 individuals from all main lineages. A highly supported topology was obtained at high taxonomic ranks but also at the species level. This phylogeny revealed the existence of more than 20 putative new species. Single nucleotide polymorphisms (SNPs) extracted from the 638 genes were able to distinguish lineages within a species complex and to highlight geographical structuration. STR were recovered efficiently for the species used as reference (C. delphinense) but the recovery rate decreased dramatically with the phylogenetic distance to the focal species. Altogether, the new loci will help reaching a sound taxonomic understanding of the family Sapotaceae for which many circumscriptions and relationships are still debated, at the species, genus and tribe levels.
MeSH term(s)	Cell Nucleus/genetics ; Genetic Markers ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Sapotaceae/genetics
Chemical Substances	Genetic Markers
Language	English
Publishing date	2021-02-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	33610-5
ISSN	1095-9513 ; 1055-7903
ISSN (online)	1095-9513
ISSN	1055-7903
DOI	10.1016/j.ympev.2021.107123
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Article: Evolutionary Trends in the Mitochondrial Genome of Archaeplastida: How Does the GC Bias Affect the Transition from Water to Land?

Pedrola-Monfort, Joan / Lázaro-Gimeno, David / Boluda, Carlos G / Pedrola, Laia / Garmendia, Alfonso / Soler, Carla / Soriano, Jose M

Plants (Basel, Switzerland)

2020 Volume 9, Issue 3

Abstract: Among the most intriguing mysteries in the evolutionary biology of photosynthetic organisms are the genesis and consequences of the dramatic increase in the mitochondrial and nuclear genome sizes, together with the concomitant evolution of the three ... ...

Abstract	Among the most intriguing mysteries in the evolutionary biology of photosynthetic organisms are the genesis and consequences of the dramatic increase in the mitochondrial and nuclear genome sizes, together with the concomitant evolution of the three genetic compartments, particularly during the transition from water to land. To clarify the evolutionary trends in the mitochondrial genome of Archaeplastida, we analyzed the sequences from 37 complete genomes. Therefore, we utilized mitochondrial, plastidial and nuclear ribosomal DNA molecular markers on 100 species of Streptophyta for each subunit. Hierarchical models of sequence evolution were fitted to test the heterogeneity in the base composition. The best resulting phylogenies were used for reconstructing the ancestral Guanine-Cytosine (GC) content and equilibrium GC frequency (GC*) using non-homogeneous and non-stationary models fitted with a maximum likelihood approach. The mitochondrial genome length was strongly related to repetitive sequences across Archaeplastida evolution; however, the length seemed not to be linked to the other studied variables, as different lineages showed diverse evolutionary patterns. In contrast, Streptophyta exhibited a powerful positive relationship between the GC content, non-coding DNA, and repetitive sequences, while the evolution of Chlorophyta reflected a strong positive linear relationship between the genome length and the number of genes.
Language	English
Publishing date	2020-03-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants9030358
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