As part of the Indo-European language family, the Indo-Iranian branch traces its origins back to the Indo-European homeland on the Pontic-Caspian steppe 5000 years ago. But how did it spread from... Show moreAs part of the Indo-European language family, the Indo-Iranian branch traces its origins back to the Indo-European homeland on the Pontic-Caspian steppe 5000 years ago. But how did it spread from there to Asia? The aim of this thesis is to uncover the early prehistory of Indo-Iranian by investigating its relationship to the Balto-Slavic languages of Eastern Europe, which have been hypothesized to form a subgroup with Indo-Iranian: Indo-Slavic. By comparing the linguistic data with evidence from archaeology and genetics, this thesis traces the migration path of prehistoric Indo-Iranian speakers from the Pontic-Caspian steppe, via the rivers and forests of Eastern Europe, across the Ural Mountains, and southwards to the steppes of Central Asia. Show less
The haplolepideous mosses (Dicranidae) comprise about 4000 species distributed over a wide range of habitats, with great gametophytic and sporophytic morphological variation. Their monophyly is... Show moreThe haplolepideous mosses (Dicranidae) comprise about 4000 species distributed over a wide range of habitats, with great gametophytic and sporophytic morphological variation. Their monophyly is well supported by the results of several molecular phylogenetic studies, which shed light on their relationships and circumscriptions, and thus also contributed to identify many remaining problems. Dicranidae ordinal classification is not congruent with current relationship hypotheses and is not supported by morphology. Morphological circumscriptions of some families do not correspond to monophyletic groups. Furthermore, the monophyly of many families and genera with weak morphological circumscriptions remains to be tested. In this thesis, systematics and relationships of the leucobryoid mosses and some families and genera segregated from the former Dicranaceae s.l. were studied using molecular phylogenetic methods. 37 out of the 38 haplolepideous moss families were represented by markers from the three genomes (nrITS, nad5, trnS-trnF, atpB-rbcL). Phylogenetic reconstructions were based on maximum parsimony, maximum likelihood, and Bayesian inference. Ancestral state reconstructions, phylogenetic network analysis (NeighborNet), and relationship hypothesis testing (Shimodaira-Hasegawa test) were performed to contribute to the interpretation of the results of the phylogenetic reconstructions. Morphological circumscriptions were evaluated and improved whenever possible, in line with the results of all analyses performed. Show less
This thesis pioneers diatom molecular identification and quantification through genome-scale methods, with four key aims: (i) reviewing DNA/RNA sequencing methods in aquatic biomonitoring to... Show moreThis thesis pioneers diatom molecular identification and quantification through genome-scale methods, with four key aims: (i) reviewing DNA/RNA sequencing methods in aquatic biomonitoring to highlight their strengths and limitations; (ii) unraveling the evolutionary history of Nitzschia palea and investigating species delimitation within the species complex; (iii) identifying silica genes in N. palea for insights into ecology and evolution; and (iv) assessing a genome-scale quantification method for diatom biomonitoring to improve accuracy and scalability in estimating abundances. The review (Chapter 2) emphasizes disparities between molecular and morphology-based approaches and introduces the challenges in accurately estimating species abundances. Chapter 3 explores N. palea's evolutionary history using transcriptome data and reveals reticulate evolutionary patterns resulting in a putative hybrid between populations with different morphological characteristics. Chapter 4 pinpoints silica genes in N. palea and reveals variations among different populations that may lead to differences in silica metabolism. Chapter 5 introduces a genome-scale quantification approach that provides a promising alternative for molecular diatom biomonitoring due to its improved taxonomic resolution and quantification accuracy. In summary, this thesis underscores that genome-scale methods' have a critical role in diatom identification and quantification, and in advancing our understanding of microalgal taxonomy, ecology, and evolution. Show less
Several groups within tribe Phyllantheae (Phyllanthaceae) formed, independently, an (obligate) pollination mutualism with Epicephala moths, which originally had been parasitic. In this pollination... Show moreSeveral groups within tribe Phyllantheae (Phyllanthaceae) formed, independently, an (obligate) pollination mutualism with Epicephala moths, which originally had been parasitic. In this pollination system, female moths actively collect pollen from staminate flowers and deposit it on the stigma of pistillate flowers, after which they place at least one egg in or against the ovary. The high pollination rate makes the system beneficial for the plants, whereas the larvae are provided with food (part of the developing seeds) and some protection against predation. Qualitative comparisons are made between non-moth-pollinated lineages, used as outgroups and various, independently moth-pollinated Phyllantheae clades, used as ingroups, thereby looking for parallel developments. The flowers of both sexes of various groups display similar, convergent morphological adaptations to the pollination system, likely to secure the obligate relationship and to improve efficiency. Sepals in both sexes, free or partly to highly connate, are commonly upright and form a narrow tube. The staminate flowers often have united, vertical stamens with the anthers along the androphore or on top of the androphore. Pistillate flowers generally reduce the stigmatic surface, either by making the stigmas shorter or by uniting them into a cone with a small opening at the top for pollen deposition. Less obvious is the reduction of the stigmatic papillae; these are often present in non-moth-pollinated taxa, but absent in the moth-pollinated species. The most diverging, parallel adaptations to moth pollination are currently found in the Palaeotropics, whereas in the Neotropics, some groups continue to also be pollinated by other insect groups and are morphologically less changed. Show less
Pramanik, D.; Spaans, M.; Kranenburg, T.; Bogarin Chaves, D.G.; Heijungs, R.; Lens, F.P.; ... ; Gravendeel, B. 2022
Phalaenopsis is an important ornamental pot plant for the global horticultural market. The inflorescences of Phalaenopsis horticultural hybrids require support from a stick during plant... Show morePhalaenopsis is an important ornamental pot plant for the global horticultural market. The inflorescences of Phalaenopsis horticultural hybrids require support from a stick during plant cultivation because of the weight of multiple large flowers. Developing a horticultural hybrid with a sufficiently lignified inflorescence stem that does not require additional support could be a way to reduce the costs of production. This study aimed to (i) determine the orientation and degree of lignification in the inflorescence stem of different species and horticultural hybrids of Phalaenopsis and investigate whether these lignification patterns follow any (ii) topological or (iii) phylogenetic pattern of interest to further explore in genetic precision breeding. Inflorescences of comparable devel- opmental stages of six species and 17 horticultural hybrids of flowering Phalaenopsis orchids were sampled. The orientation of the inflorescence varied from erect, sub-erect, arching, to pendant. The degree of lignification was measured with ImageJ using stained microscopic tissue sections and statistically analyzed. A molecular phylogeny of the species of Phalaenopsis was reconstructed based on plastid and nuclear ribosomal DNA sequences to analyze phylogenetic patterns. Our results show a significant difference in the degree of lignification between the different Phalaenopsis species and hybrids, between peduncle and rachis, and among the six different inflorescence positions analyzed. We found a positive correlation between inflorescence orientation and the proportion of lignified area per total stem area and the proportional thickness of the lignified fiber walls in the peduncle. We conclude that the degree of lignification is heritable, as we observed among our sample size a higher positive correlation between stem lignification variables among closely related taxa compared to more distantly related ones. However, a larger species sampling is needed to further validate our results. Show less
The genus Phyllanthus is paraphyletic as currently circumscribed, with the genera Breynia, Glochidion and Synostemon nested within it. A phylogeny based on nuclear (ITS, PHYC) and chloroplast (matK, .Show moreThe genus Phyllanthus is paraphyletic as currently circumscribed, with the genera Breynia, Glochidion and Synostemon nested within it. A phylogeny based on nuclear (ITS, PHYC) and chloroplast (matK, accD-psaI, trnS-trnG) markers is presented, including 18/18 subgenera and 53/70 sections. Differences in habit, branching type, floral and fruit characters are discussed, and we find indications for shifts in pollination and dispersal strategies possibly underlying the convergent evolution of these characters in multiple clades. Several taxonomic issues were found in the subgeneric classification of Phyllanthus that will require new transfers and rank changes. Phyllanthus subg. Anesonemoides, subg. Conami, subg. Emblica, subg. Gomphidium, subg. Kirganelia and subg. Phyllanthus are polyphyletic, and several sections appear to be paraphyletic (e.g., P. sect. Anisonema, sect. Emblicastrum, sect. Pseudoactephila, sect. Swartziani, and sect. Xylophylla); P. subg. Phyllanthodendron is furthermore paraphyletic with the genus Glochidion nested within. To create a classification of tribe Phyllantheae that comprises exclusively monophyletic taxa, it is necessary to treat several clades at the same taxonomic rank as the genera Breynia, Glochidion and Synostemon. Since combining all genera would lead to one giant heterogeneous genus that is difficult to define, we recommend dividing Phyllanthus into several monophyletic genera, which have previously been recognized and often possess diagnostic (combinations of) morphological characters. This new classification is forthcoming. Show less
During the environmental impact study for a proposed nickel mine near Weda Bay on Halmahera in North Moluccas (Maluku Utara Province), Indonesia, two unknown Euphorbiaceae were discovered.... Show moreDuring the environmental impact study for a proposed nickel mine near Weda Bay on Halmahera in North Moluccas (Maluku Utara Province), Indonesia, two unknown Euphorbiaceae were discovered. Morphological comparisons and molecular phylogenetic analyses using four markers (plastid trnL-F and rbcL, and nuclear ribosomal internal transcribed spacer and external transcribed spacer) indicated that they should be recognized as constituting a new, distinct genus of two species, which are described and illustrated here as Weda fragarioides and Weda lutea. The new taxa are members of the Australasian tribe Ricinocarpeae in subfamily Crotonoideae, and they are most closely related to Alphandia. In contrast with the otherwise mostly sclerophyllous Ricinocarpeae, Weda possesses stellate to dendritic hairs, large, long-petiolate, glandular leaves, and inflorescences with a pair of large, leafy, subopposite bracts. The two narrowly distributed species are distinguished from each other by vegetative and floral features, molecular data, and elevational preferences. Leaf elemental analysis of Weda indicated manganese, but not nickel, accumulation. Newly resolved generic relationships and potential morphological synapomorphies within Crotonoideae are discussed, and the circumscription of Ricinocarpeae is expanded from 7 to 11 genera. Show less
The molecular clock hypothesis is an important concept in biology. Deviations from a constant rate of nucleotide substitution have been found widely among lineages, genomes, genes and individual... Show moreThe molecular clock hypothesis is an important concept in biology. Deviations from a constant rate of nucleotide substitution have been found widely among lineages, genomes, genes and individual sites. Phylogenetic research can accommodate for these differences in applying specific models of evolution. Lineage-specific rate heterogeneity however can generate bi- or multimodal distributions of substitution rates across the branches of a tree and this may mislead phylogenetic inferences with currently available models. The plant family Annonaceae is an excellent case to study lineage-specific rate heterogeneity. The two major sister subfamilies, Annonoideae and Malmeoideae, have shown great discrepancies in branch lengths. We used high-throughput sequencing data of 72 genes, 99 spacers and 16 introns from 24 chloroplast genomes and nuclear ribosomal DNA of 23 species to study the molecular rate of evolution in Annonaceae. In all analyses, longer branch lengths and/or higher substitution rates were found for the Annonoideae compared to the Malmeoideae. The Annonaceae had wide variability in chloroplast length, ranging from minimal 175,684 by to 201,723 for Annonoideae and minimal 152,357 to 170,985 bp in Malmeoideae, mostly reflecting variation in inverted-repeat length. The Annonoideae showed a higher GC-content in the conserved parts of the chloroplast genome and higher omega (dN/c/s)-ratios than the Malmeoideae, which could indicate less stringent purifying selection, a pattern that has been found in groups with small population sizes. This study generates new insights into the processes causing lineage-specific rate heterogeneity, which could lead to improved phylogenetic methods. (C) 2017 Elsevier Inc. All rights reserved. Show less
Using a wide diversity of animal groups, this thesis illustrates how molecular data can provide new insights into taxonomic studies. Traditional taxonomic research within natural history... Show moreUsing a wide diversity of animal groups, this thesis illustrates how molecular data can provide new insights into taxonomic studies. Traditional taxonomic research within natural history collections is based on morphological characters. Most studies show a clear congruence between morphological and genetically distinguished groups. This thesis also shows examples in which the number of genetically distinguished groups is either smaller, or larger, than the number of morphological groups. The first case usually involves undescribed, possibly cryptic, species; in the latter case, morphological differences do not reflect a difference in genealogy (historical origin). Apparent discrepancies between identifications based on morphology and groups that can be distinguished genetically, are sometimes caused by human errors. A number of such errors are demonstrated in GenBank, a public database for DNA sequences. It is shown that genotyping of type-specimens can settle long-standing disputes and facilitate the description of new species. Sequence data can also be used for identification purposes as shown for both taxonomic and forensic studies. In the last chapter a mitogenome of a collection specimen is sequenced without the use of PCR (polymerase chain reaction). This illustrates the potential of NGS (next generation sequencing) for future taxonomic or phylogenetic studies. Show less
In this thesis, different speciation processes were studied that were involved in the origin of V. stagnina and its closest relatives. Phylogenetic analyses of the CHS intron showed that... Show moreIn this thesis, different speciation processes were studied that were involved in the origin of V. stagnina and its closest relatives. Phylogenetic analyses of the CHS intron showed that hybridization and polyploidisation played an important role during speciation and that Viola stagnina is one of the parental species of the alloploid species V. canina, V. lactea and V. pumila and the parental species of the autotetraploid V. elatior. The analyses also confirmed that the closest relatives of V. stagnina were the other arosulate violets V. canina, V. elatior, V. pumila and V. lactea. In an attempt to settle a debate among Dutch botanists about the taxonomic status of V. stagnina var. lacteoides, the morphological and genetic variation within V. stagnina were studied using AFLP, morphometrics analyses, a common garden experiment, and a crossing experiment. The genetic and morphological differences found support for the recognition of the infraspecific taxon V. stagnina var. lacteoides. The nomenclatural studies carried out resulted in a recommendation to formally reject the ambiguous name V. persicifolia for the European Fen Violet and use the name V. stagnina, instead. To bring the common name into line with the usage in Belgium, it is also recommended to change the Dutch common name from Melkviooltje into Vals melkviooltje. Show less
The interspecific relationships in the genus Triturus are incompletely known. InCHAPTER 2, we attempt to resolve them by using allozyme and mtDNA data. Despitethe large number of markers used,... Show moreThe interspecific relationships in the genus Triturus are incompletely known. InCHAPTER 2, we attempt to resolve them by using allozyme and mtDNA data. Despitethe large number of markers used, relationships continue to elude us. The resultssuggest that speciation in the group occurred during a short time period (the end of theMiddle Miocene). Paleogeographic reconstructions of the presumed centre of origin (theBalkans) support this hypothesis. We proposed here that T. macedonicus should beraised to full species given its allopatric distribution and high genetic divergence with T.carnifex.The best way to test the scenario presented in CHAPTER 2 is to look at multipleindependent markers that, unfortunately, were not readily available. CHAPTER 3describes the process through which dozens of markers were designed and tested for thegenus Triturus. Out of more than fifty markers tested, five provided promising resultswith enough variability to study the phylogeny and phylogeography of the genus. Thisopened the door not only for CHAPTER 4, but also for 5 and 6.Taking CHAPTER 2 as the starting point and with the tools developed inCHAPTER 3, CHAPTER 4 attempts to decipher the history of the genus Triturus. Thestudy includes samples from 15 individuals of the seven species of the group. Locationswere selected to cover most of the variability in the group, with the exception of areasclose to other species. Hybridization is known to occur in these areas, and could bias theinferences made. Results show that all the genes, except the two mtDNA ones, haveincongruent phylogenetic signals. We used phylogenetic networks to visualize thealternative phylogenetic signals and have built a phylogenetic tree based on a Bayesianhierarchical method that obtains the species tree based on individual gene trees. Thisapproach successfully resolved the branching order of the newts, although time intervals are very narrow, confirming the near simultaneous speciation scenario of CHAPTER 2.We also found a high genetic differentiation between the two forms of the southerncrested newt (T. karelinii) and proposed that they should be raised to full species (T.karelinii and T. arntzeni).As described in CHAPTER 4, hybridization can have a confounding effect onphylogenetic inferences. Incomplete lineage sorting can also produce similar patterns asgene flow, further complicating matters. CHAPTER 5 takes a new approach indistinguishing between gene flow and incomplete lineage sorting, only possible inspecies with very well defined species borders and limited dispersal capability as thenewts, which limits gene flow to a narrow geographical region.As can be seen in the previous chapters, the crested newts show complex(although interesting) patterns resulting from compound interactions, especially in theBalkans. The marbled newts, on the other hand, are only two species, and therefore wecan cover their evolutionary history in more detail, as it is simpler. CHAPTER 6 studiesthe phylogeography of the two species of marbled newts. Being just a pair and not agroup of species, relationships are not problematic. Their sibling relationship is wellestablished (see CHAPTER 2). This chapter also explores how differences in ecologicalconditions (see CHAPTER 8) along a hybrid zone affect its structure and the amount ofgene flow between species.The morphological distinction of adults of the two marbled species is relativelystraightforward, even though variation is present. Eggs and larvae, on the contrary, areeasy to spot and collect, but impossible to distinguish. CHAPTER 7 describes a cheapand fast molecular technique that allowed the identification of the large number ofsamples used in CHAPTERS 8 and 9.Based on a morphological and genetic identification of individuals of the twospecies of marbled newts and published distributional data, CHAPTER 8 identifiedecological factors associated with the range border of the two species of marbled newt.Ecological models defining the distribution of the two species differed in four mainareas: the northern most region of contact close to Aveiro, the rest of the coastal area(see also CHAPTER 9), the region coinciding with the Tejo river, and the remaindercontact zone going until Madrid. In the coastal area of Portugal, close to Caldas da Rainha, the northern marblednewt was found where only pygmy marbled newts were thought to occur. Thisprompted a detailed study on the distribution of the two species in this area described inCHAPTER 9. This study revealed a small pocket of populations of the northern speciessurrounded by populations of its sister southern species. Given the distance of thispocket to the main distribution, we believe that the enclave was created by T. pygmaeusmoving north, superseding T. marmoratus, rather than the latter species expandingsouthwards. Show less
The snails__ proverbial inertness makes it an ideal subject to study the patterns and processes that lead to speciation. The land snail family Chondrinidae consists of about 70 extant species in... Show moreThe snails__ proverbial inertness makes it an ideal subject to study the patterns and processes that lead to speciation. The land snail family Chondrinidae consists of about 70 extant species in six genera. They occur throughout western and central Europe, northern Africa and as far east as Pakistan. These snails share a long and interesting evolutionary history, to the knowledge of which we contribute here. Show less
The thesis describes the design and evolution of echolocation in the South and Southeast Asian Swiftlets. It starts explaining the molecular phylogenetics of Swiftlets, which is used in subsequent... Show moreThe thesis describes the design and evolution of echolocation in the South and Southeast Asian Swiftlets. It starts explaining the molecular phylogenetics of Swiftlets, which is used in subsequent chapters. Echolocation calls and social vocalisations of Swifts are compared between species and with non-echolocating Swifts and Swiftlets. The following chapters treat potential morphological adaptations in the echolocation system, i.e. in the syrinx, ear, and brain. The final chapters discuss the biogeography of the Swiftlets and integrate the results into an overall hypothesis on the evolution of Swiftlets and their echolocation system. Show less
In vicariance biogeography, the present distribution of species over areas is explained with different historical processes. Vicariance is one of these processes and involves speciation by the... Show moreIn vicariance biogeography, the present distribution of species over areas is explained with different historical processes. Vicariance is one of these processes and involves speciation by the formation of isolating barriers between areas. By assuming this process, a scenario for the history of areas can be obtained from a phylogeny of species and a distribution of these species over areas. This scenario for the history of areas, however, does not explain the distribution of species over areas because species may become extinct or sometimes migrate between areas. To examine extinction and migration in addition to vicariance as causal processes for the distribution of species over areas, different methods have been developed and implemented in software. In this thesis, these different methods and their implementations are assessed for their procedures and results. From the research it is concluded that not all methods obtain a scenario for the history of areas in a valid way. After repair of the computer programs, to enable them to obtain valid scenarios for the history of areas, different methods still do not succeed in obtaining a single scenario for the history of areas when a single dataset is examined. Depending on the formulation and testing of hypotheses of the processes of vicariance, extinction and migration two different categories of methods can be distinguished. Because of better consistence in formulation and testing of hypotheses preference has been given to one of these categories. Show less
