| 1. |
- Alström, Per, Professor, et al.
(författare)
-
Multiple species delimitation approaches applied to the avian lark genus Alaudala
- 2021
-
Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 154
-
Tidskriftsartikel (refereegranskat)abstract
- Species delimitation has advanced from a purely phenotypic exercise to a branch of science that integrates multiple sources of data to identify independently evolving lineages that can be treated as species. We here test species limits in the avian Lesser Short-toed Lark Alaudala rufesens-Sand Lark A. raytal complex, which has an intricate taxonomic history, ranging from a single to three recognised species, with different inclusiveness in different treatments. Our integrative taxonomic approach is based on a combination of DNA sequences, plumage, biometrics, songs, song-flights, geographical distributions, habitat, and bioclimatic data, and using various methods including a species delimitation program (STACEY) based on the multispecies coalescent model. We propose that four species should be recognised: Lesser Short-toed Lark A. rufescens (sensu stricto), Heine's Short-toed Lark A. heinei, Asian Short-toed Lark A. cheleensis and Sand Lark A. raytal. There is also some evidence suggesting lineage separation within A. cheleensis and A. raytal, but additional data are required to evaluate this. The species delimitation based on STACEY agrees well with the non-genetic data. Although computer-based species delimitation programs can be useful in identifying independently evolving lineages, we stress that whenever possible, species hypotheses proposed by these programs should be tested by independent, non-genetic data. Our results highlight the difficulty and subjectivity of delimiting lineages and species, especially at early stages in the speciation process.
|
|
| 2. |
- Andermann, Tobias, et al.
(författare)
-
A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project
- 2020
-
Ingår i: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 10
-
Tidskriftsartikel (refereegranskat)abstract
- High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth. Moreover, it has proven to produce powerful, large multi-locus DNA sequence datasets suitable for phylogenetic analyses. However, target capture requires careful considerations, which may greatly affect the success of experiments. Here we provide a simple flowchart for designing phylogenomic target capture experiments. We discuss necessary decisions from the identification of target loci to the final bioinformatic processing of sequence data. We outline challenges and solutions related to the taxonomic scope, sample quality, and available genomic resources of target capture projects. We hope this review will serve as a useful roadmap for designing and carrying out successful phylogenetic target capture studies.
|
|
| 3. |
|
|
| 4. |
- Eggens, Frida, et al.
(författare)
-
Phylogeny and species delimitation in Silene sect. Arenosae (Caryophyllaceae): a new section
- 2020
-
Ingår i: Phytokeys. - : Pensoft Publishers. - 1314-2011 .- 1314-2003. ; :159, s. 1-34
-
Tidskriftsartikel (refereegranskat)abstract
- A putatively monophyletic group of annual Silene species is revised taxonomically and described as the new section S. sect. Arenosae. The species of this section were previously treated as a part of a widely circumscribed and polyphyletic S. sect. Rigidulae. Silene sect. Arenosae as circumscribed here consists of nine species. Members of the section show a predominantly E Mediterranean to SW Asian distribution pattern from Turkey southward to Egypt and eastward to Iran and Pakistan, although most of the species have a limited distribution range. The species of S. sect. Arenosae are characterized by narrowly lanceolate calyx teeth, which are often highly polymorphic, and lanceolate to oblanceolate (non-spathulate) basal leaves. The provided taxonomic revision is based on morphological characters and supported by phylogenetic analyses of two nuclear loci (nrITS and an intron of the RPB2 gene) and one chloroplast locus (the intron of the rps16 gene). The species descriptions are formalized using a novel implementation of the Prometheus Description Model.
|
|
| 5. |
- Eriksson, J. S., et al.
(författare)
-
Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae)
- 2021
-
Ingår i: BMC Ecology and Evolution. - : Springer Science and Business Media LLC. - 1472-6785 .- 2730-7182. ; 21:1
-
Tidskriftsartikel (refereegranskat)abstract
- Background: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole-genome duplication events in Hibiscus, we tested three alternative scenarios describing different polyploidization events. Results: Using target sequence capture, we designed a new probe set for Hibiscus and generated 87 orthologous genes from four diploid species. We detected paralogues in > 54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of Hibiscus sampled shared one genome duplication with H. syriacus, and one whole genome duplication occurred along the branch leading to H. syriacus. Conclusions: Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult. © 2021, The Author(s).
|
|
| 6. |
- Jafari, Farzaneh, et al.
(författare)
-
A new taxonomic backbone for the infrageneric classification of the species-rich genus Silene(Caryophyllaceae)
- 2020
-
Ingår i: Taxon. - : Wiley. - 0040-0262 .- 1996-8175. ; 69:2, s. 337-368
-
Tidskriftsartikel (refereegranskat)abstract
- The systematization of species in plant taxonomy based on the phylogenetic relationships among them are of utmost importance and also very challenging in large genera. In those, phylogenetic results often may suggest substantially different relationships than previous classifications, and call for large-scale taxonomic revisions. Delimitation of the genusSilenehas been and is still somewhat controversial, and recent molecular phylogenetic studies have settled several monophyletic groups that differ substantially from previous taxonomies. The infrageneric taxonomy ofSilenes.str. has not been updated as a whole taking the phylogenetic information into account. In this study, we review previous phylogenetic results based on multiple loci, and conducted comprehensive gene tree analyses based on the nrDNA ITS and cpDNArps16regions for 1586 and 944 samples representing 415 and 397 species, respectively, includingSileneand its allies, as well as a species tree analysis including 262 samples representing 243 species. We sampled representatives from all 44 sections recognized in the most recent global revision of the genus. The results support the recognition of three subgenera, i.e.,S.subg.Behenantha,S.subg.LychnisandS. subg.Silene, which is partly in agreement with previous molecular phylogenetic findings and contradicts all previous traditional classifications.Silenesect.Atocion, with a few annual species showing a narrow distribution range in the eastern Mediterranean, is treated as incertae sedis because of its uncertain phylogenetic position, possibly due to exceptionally high substitution rates.Silenesubg.Lychnis, weakly supported as sister to the other subgenera, splits into three main clades and includes four sections.Silenesubg.Behenantha, which forms a possible sister group in relation toS.subg.Silene, is poorly resolved basally and includes a large number of mostly small clades recognized as 18 sections. InS.subg.Silene, 11 sections are recognized, among which four are broadly circumscribed:S.sect.Auriculatae,S.sect.Sclerocalycinae,S.sect.SileneandS.sect.Siphonomorpha.Silenesect.AcutifoliaeandS.sect.Portensesare described here as new taxa, whereas new status or new combinations are proposed forS.sect.Anotites,S.sect.Muscipula,S.sect.Petrocoma,S.sect.Pulvinatae,S.sect.SclerophyllaeandS.sect.Uebelinia. Five new combinations and two new names are proposed for taxa inSileneformerly assigned toLychnisandUebelinia. The correct infrageneric nomenclature compatible with the new infrageneric system is provided along with synonymy and type citations. Shortcomings of this study, such as the lack of a morphological diagnostic key and sparse sampling of some large sections, are listed and discussed.
|
|
| 7. |
|
|
| 8. |
- Moiloa, Ntwai A., et al.
(författare)
-
Biogeographic origins of southern African Silene (Caryophyllaceae)
- 2021
-
Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903. ; 162
-
Tidskriftsartikel (refereegranskat)abstract
- Silene (Caryophyllaceae) is distributed predominantly in the northern Hemisphere, where it is most diverse around the Mediterranean Basin. The genus is also well represented in North Africa, extending into tropical, subSaharan and southern Africa. Eight native species are recognized in southern Africa, taxonomically placed in two sections: Elisanthe and Silene s.l. Although the taxonomy of the southern African taxa has recently been revised, their phylogenetic relationships and biogeographic history remain unclear. This study aims to infer the phylogenetic position and geographic origins of the southern African taxa. We generated DNA sequences of nuclear and plastid loci from several individuals belonging to all eight species of Silene recognized from southern Africa, and combined our DNA sequences with existing data representing species from major clades (i.e. sections) based on the recently revised Silene infrageneric taxonomy. We used a Bayesian coalescent species tree continuous diffusion approach to co-estimate the species tree and the ancestral areas of representative members of the genus. Our results show that the perennial southern African members of section Elisanthe form a strongly-supported clade with the Eurasian annual S. noctiflora and the Central Asian perennial S. turkestanica. The rest of the perennial species form a strongly-supported clade together with the annual S. aethiopica, which is nested in a larger Mediterranean clade comprising mostly annual species classified in section Silene s.l. Estimates of ancestral areas indicate a late Pleistocene dispersal to southern Africa from central and East Africa for the sub-Saharan members of section Silene s.l. The Elisanthe clade is inferred to have colonized southern Africa through longdistance dispersal from Eurasia during the late Pleistocene. Our findings support the hypothesis of a relatively recent colonization into southern Africa resulting from two independent dispersal events during the Pleistocene.
|
|
| 9. |
- Moiloa, Ntwai A., et al.
(författare)
-
Chapter 19 Systematics and evolution
- 2022
-
Ingår i: In: de Boer H, Rydmark MO, Verstraete B, Gravendeel B (2022) Molecular identification of plants: from sequence to species. Advanced Books.. - : Pensoft Publishers.
-
Bokkapitel (refereegranskat)
|
|
| 10. |
- Pirani, A., et al.
(författare)
-
Phylogeny ofAcanthophyllums.l. revisited: An update on generic concept and sectional classification
- 2020
-
Ingår i: Taxon. - : Wiley. - 0040-0262 .- 1996-8175. ; 69:3, s. 500-514
-
Tidskriftsartikel (refereegranskat)abstract
- The generic boundary of the broadly definedAcanthophyllums.l., the third-largest genus of the tribe Caryophylleae (Caryophyllaceae), has been a subject of taxonomic confusion.Acanthophyllums.l. now includes five minor genera previously recognized as independent. Among these small genera, the inclusion ofAllochrusa,Ochotonophila, andScleranthopsiswithinAcanthophyllums.l. was confirmed by previous molecular studies, while the positions ofDiaphanopteraandKuhitangiaremained uncertain. We have performed an updated molecular study ofAcanthophyllums.l. including an increased sampling of the genera and sections assigned to this group, using intron sequences of the chloroplast generps16and nuclear ribosomal internal transcribed spacer (ITS) sequences.Cyathophylla,Heterochroa, andSaponariawere chosen as outgroups for performing phylogenetic analyses using maximum likelihood and Bayesian methods. The present results suggest that, in addition to the genera mentioned above, bothDiaphanopteraandKuhitangiashould also be synonymized withinAcanthophyllum. SectionsDiaphanoptera,KuhitangiaandPseudomacrostegiaare introduced as new infrageneric taxa withinAcanthophyllum.Our results also indicate that some annual species ofSaponariaare closely related toAcanthophyllum.
|
|
