Insights into the spatial distribution of genetic diversity is key for understanding the evolutionary history and for effective species conservation. For the lion, all African populations are... Show moreInsights into the spatial distribution of genetic diversity is key for understanding the evolutionary history and for effective species conservation. For the lion, all African populations are considered to belong to one subspecies, while the Asiatic subspecies is confined to a single population in India. However, it is suggested that the genetic diversity is greater than the taxonomy implies. Notably the West and Central African lion represents a unique clade, which is relevant because the populations in this region are generally small and isolated. Phylogenetic analyses of mtDNA data, microsatellites and autosomal SNPs from lion populations throughout their complete geographic range show congruent patterns in which the Asiatic subspecies has a nested position within the West/Central African lion. Recognizing a northern subspecies, including the Asiatic lion, and a southern subspecies, is more in line with the evolutionary history of the lion. A revision of the taxonomy is therefore warranted. Show less
The objective of this thesis was to obtain insight into the processes that play a role in biodiversity patterns of tropical marine species by using marine lakes as a model. Marine lakes are... Show moreThe objective of this thesis was to obtain insight into the processes that play a role in biodiversity patterns of tropical marine species by using marine lakes as a model. Marine lakes are landlocked water bodies that maintain a marine character through narrow submarine connections to the sea. Two regions in Indonesia were studied: Berau (East Kalimantan) and Raja Ampat (West Papua). The following questions were addressed: 1. What are the different types of marine lakes in Indonesia? 2. Are the species assemblages in marine lakes distinct from those in the adjacent coastal environments? 3. To what extent are the populations in the lakes isolated? 4. Can marine lakes in Indonesia be considered natural laboratories of evolution? There is a large diversity in types of marine lakes and many more remain to be documented in Indonesia. The spatial variation in sponge species composition in marine lakes, coastal mangroves and coral reefs show that marine lakes contain three groups of sponge species: (a) widespread species known from various locations in Indo-Pacific reefs, (b) lake species that only occur in lake systems, (c) endemic species restricted to a single lake. The patterns of genetic variation found in the marine lake populations are generally consistent with populations in isolated environments. The lakes appear to be both cradles and refuges of diversity Show less
This thesis investigates mechanisms of adaptation to climate, and in particular temperature, in the African butterfly Bicyclus anynana. The work takes an integrated approach and brings together... Show moreThis thesis investigates mechanisms of adaptation to climate, and in particular temperature, in the African butterfly Bicyclus anynana. The work takes an integrated approach and brings together studies at the phenotypic, physiological and genetic level. By examining geographical variation among wild populations, the thesis investigates how B. anynana is adapted to geographically varying thermal conditions. The first half of the thesis is focused on phenotypic plasticity, which is a major component of adaptation to climate in B. anynana. Chapter 2 compares the plasticity response to temperature of two populations, and reveals a population-specific response for wing pattern but very small to no differences in the response of life history traits. Chapter 3 shows that a discontinuous regulatory hormone signal during development underlies the seasonal plasticity in B. anynana. In the second half of the thesis, I take a molecular genetic approach by studying geographic patterns of neutral and adaptive evolution in wild populations. Chapter 4 indicates that the B. anynana species area expanded southwards after the last ice age from glacial equatorial habitat refugia. Chapter 5 identifies clinal variation in genes coding for metabolic enzymes, indicating a putative role of these genes in thermal adaptation. 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
